Haridha Shivram
YOU?
Author Swipe
View article: Identification of robust mortality-associated neutrophil gene programs and cytokine responses using large-scale ARDS endotracheal aspirate scRNA-seq data
Identification of robust mortality-associated neutrophil gene programs and cytokine responses using large-scale ARDS endotracheal aspirate scRNA-seq data Open
Myeloid dysregulation is involved in severe Acute Respiratory Distress Syndrome (ARDS), but the mechanistic understanding is still incomplete. We analyzed endotracheal aspirate (ETA) scRNA-seq data from 40 intubated patients (both COVID-19…
View article: Systemic cytokines drive conserved severity-associated myeloid responses across bacterial and viral infections
Systemic cytokines drive conserved severity-associated myeloid responses across bacterial and viral infections Open
Both bacterial and viral infections can trigger an overwhelming host response, leading to immunopathology and organ dysfunction. Multiple studies have reported dysregulated myeloid cell states in patients with bacterial sepsis or severe SA…
View article: A myeloid program associated with COVID-19 severity is decreased by therapeutic blockade of IL-6 signaling
A myeloid program associated with COVID-19 severity is decreased by therapeutic blockade of IL-6 signaling Open
Altered myeloid inflammation and lymphopenia are hallmarks of severe infections. We identified the upregulated EN-RAGE gene program in airway and blood myeloid cells from patients with acute lung injury from SARS-CoV-2 or other causes acro…
View article: Transcriptomic and proteomic assessment of tocilizumab response in a randomized controlled trial of patients hospitalized with COVID-19
Transcriptomic and proteomic assessment of tocilizumab response in a randomized controlled trial of patients hospitalized with COVID-19 Open
View article: Supplementary Table 4 from <i>ELF4</i> Is a Target of miR-124 and Promotes Neuroblastoma Proliferation and Undifferentiated State
Supplementary Table 4 from <i>ELF4</i> Is a Target of miR-124 and Promotes Neuroblastoma Proliferation and Undifferentiated State Open
Table S4. PANTHER and mSigDB analysis of siELF4 down- and up-regulated genes.
View article: Supplementary Table 1 from <i>ELF4</i> Is a Target of miR-124 and Promotes Neuroblastoma Proliferation and Undifferentiated State
Supplementary Table 1 from <i>ELF4</i> Is a Target of miR-124 and Promotes Neuroblastoma Proliferation and Undifferentiated State Open
Table S1. Cherry picker siRNA list and Primer pairs utilized for qRT-PCR.
View article: Supplementary Table 7 from <i>ELF4</i> Is a Target of miR-124 and Promotes Neuroblastoma Proliferation and Undifferentiated State
Supplementary Table 7 from <i>ELF4</i> Is a Target of miR-124 and Promotes Neuroblastoma Proliferation and Undifferentiated State Open
Table S7. mSigDB analysis of overlap between miR-124 targets and siELF4 downregulated genes.
View article: Supplementary Table 1 from <i>ELF4</i> Is a Target of miR-124 and Promotes Neuroblastoma Proliferation and Undifferentiated State
Supplementary Table 1 from <i>ELF4</i> Is a Target of miR-124 and Promotes Neuroblastoma Proliferation and Undifferentiated State Open
Table S1. Cherry picker siRNA list and Primer pairs utilized for qRT-PCR.
View article: Supplementary Figure Legends from <i>ELF4</i> Is a Target of miR-124 and Promotes Neuroblastoma Proliferation and Undifferentiated State
Supplementary Figure Legends from <i>ELF4</i> Is a Target of miR-124 and Promotes Neuroblastoma Proliferation and Undifferentiated State Open
Figure S1. Knockdown efficiency 48 h after reverse transfection. Figure S2. miR-124 directly binds ELF4 and regulates ELF4 expression. Figure S3. ELF4 ectopic expression antagonizes the effect of miR-124 on differentiation of KELLY cells. …
View article: Supplementary Table 2 from <i>ELF4</i> Is a Target of miR-124 and Promotes Neuroblastoma Proliferation and Undifferentiated State
Supplementary Table 2 from <i>ELF4</i> Is a Target of miR-124 and Promotes Neuroblastoma Proliferation and Undifferentiated State Open
Table S2. siELF4 differentially expressed genes.
View article: Supplementary Table 5 from <i>ELF4</i> Is a Target of miR-124 and Promotes Neuroblastoma Proliferation and Undifferentiated State
Supplementary Table 5 from <i>ELF4</i> Is a Target of miR-124 and Promotes Neuroblastoma Proliferation and Undifferentiated State Open
Table S5. miR-124 target list (mNSC Study and miRTarBase).
View article: Supplementary Table 4 from <i>ELF4</i> Is a Target of miR-124 and Promotes Neuroblastoma Proliferation and Undifferentiated State
Supplementary Table 4 from <i>ELF4</i> Is a Target of miR-124 and Promotes Neuroblastoma Proliferation and Undifferentiated State Open
Table S4. PANTHER and mSigDB analysis of siELF4 down- and up-regulated genes.
View article: Supplementary Table 7 from <i>ELF4</i> Is a Target of miR-124 and Promotes Neuroblastoma Proliferation and Undifferentiated State
Supplementary Table 7 from <i>ELF4</i> Is a Target of miR-124 and Promotes Neuroblastoma Proliferation and Undifferentiated State Open
Table S7. mSigDB analysis of overlap between miR-124 targets and siELF4 downregulated genes.
View article: Supplementary Table 2 from <i>ELF4</i> Is a Target of miR-124 and Promotes Neuroblastoma Proliferation and Undifferentiated State
Supplementary Table 2 from <i>ELF4</i> Is a Target of miR-124 and Promotes Neuroblastoma Proliferation and Undifferentiated State Open
Table S2. siELF4 differentially expressed genes.
View article: Supplementary Figure Legends from <i>ELF4</i> Is a Target of miR-124 and Promotes Neuroblastoma Proliferation and Undifferentiated State
Supplementary Figure Legends from <i>ELF4</i> Is a Target of miR-124 and Promotes Neuroblastoma Proliferation and Undifferentiated State Open
Figure S1. Knockdown efficiency 48 h after reverse transfection. Figure S2. miR-124 directly binds ELF4 and regulates ELF4 expression. Figure S3. ELF4 ectopic expression antagonizes the effect of miR-124 on differentiation of KELLY cells. …
View article: Supplementary Table 3 from <i>ELF4</i> Is a Target of miR-124 and Promotes Neuroblastoma Proliferation and Undifferentiated State
Supplementary Table 3 from <i>ELF4</i> Is a Target of miR-124 and Promotes Neuroblastoma Proliferation and Undifferentiated State Open
Table S3. Survival analysis of Versteeg and Seeger cohorts.
View article: Supplementary Table 3 from <i>ELF4</i> Is a Target of miR-124 and Promotes Neuroblastoma Proliferation and Undifferentiated State
Supplementary Table 3 from <i>ELF4</i> Is a Target of miR-124 and Promotes Neuroblastoma Proliferation and Undifferentiated State Open
Table S3. Survival analysis of Versteeg and Seeger cohorts.
View article: Data from <i>ELF4</i> Is a Target of miR-124 and Promotes Neuroblastoma Proliferation and Undifferentiated State
Data from <i>ELF4</i> Is a Target of miR-124 and Promotes Neuroblastoma Proliferation and Undifferentiated State Open
13-Cis-retinoic acid (RA) is typically used in postremission maintenance therapy in patients with neuroblastoma. However, side effects and recurrence are often observed. We investigated the use of miRNAs as a strategy to replace RA …
View article: Supplementary Table 6 from <i>ELF4</i> Is a Target of miR-124 and Promotes Neuroblastoma Proliferation and Undifferentiated State
Supplementary Table 6 from <i>ELF4</i> Is a Target of miR-124 and Promotes Neuroblastoma Proliferation and Undifferentiated State Open
Table S6. Overlap between miR-124 targets and siELF4 down-regulated genes.
View article: Supplementary Table 6 from <i>ELF4</i> Is a Target of miR-124 and Promotes Neuroblastoma Proliferation and Undifferentiated State
Supplementary Table 6 from <i>ELF4</i> Is a Target of miR-124 and Promotes Neuroblastoma Proliferation and Undifferentiated State Open
Table S6. Overlap between miR-124 targets and siELF4 down-regulated genes.
View article: Supplementary Table 5 from <i>ELF4</i> Is a Target of miR-124 and Promotes Neuroblastoma Proliferation and Undifferentiated State
Supplementary Table 5 from <i>ELF4</i> Is a Target of miR-124 and Promotes Neuroblastoma Proliferation and Undifferentiated State Open
Table S5. miR-124 target list (mNSC Study and miRTarBase).
View article: Data from <i>ELF4</i> Is a Target of miR-124 and Promotes Neuroblastoma Proliferation and Undifferentiated State
Data from <i>ELF4</i> Is a Target of miR-124 and Promotes Neuroblastoma Proliferation and Undifferentiated State Open
13-Cis-retinoic acid (RA) is typically used in postremission maintenance therapy in patients with neuroblastoma. However, side effects and recurrence are often observed. We investigated the use of miRNAs as a strategy to replace RA …
View article: File S4 from Bivalent Chromatin Domains in Glioblastoma Reveal a Subtype-Specific Signature of Glioma Stem Cells
File S4 from Bivalent Chromatin Domains in Glioblastoma Reveal a Subtype-Specific Signature of Glioma Stem Cells Open
Bivalent normalized expression in FPKM of the 840 genes identified by DAVID in Fig. 6A.
View article: File S1 from Bivalent Chromatin Domains in Glioblastoma Reveal a Subtype-Specific Signature of Glioma Stem Cells
File S1 from Bivalent Chromatin Domains in Glioblastoma Reveal a Subtype-Specific Signature of Glioma Stem Cells Open
sequencing statistics for all datasets in this study.
View article: File S3 from Bivalent Chromatin Domains in Glioblastoma Reveal a Subtype-Specific Signature of Glioma Stem Cells
File S3 from Bivalent Chromatin Domains in Glioblastoma Reveal a Subtype-Specific Signature of Glioma Stem Cells Open
Enhancer normalized expression in FPKM of the 307 genes identified by DAVID in Fig. 5A.
View article: File S5 from Bivalent Chromatin Domains in Glioblastoma Reveal a Subtype-Specific Signature of Glioma Stem Cells
File S5 from Bivalent Chromatin Domains in Glioblastoma Reveal a Subtype-Specific Signature of Glioma Stem Cells Open
Bivalent regions that are present in at least 8 tumors, and the gene they are located within or proximal to
View article: File S2 from Bivalent Chromatin Domains in Glioblastoma Reveal a Subtype-Specific Signature of Glioma Stem Cells
File S2 from Bivalent Chromatin Domains in Glioblastoma Reveal a Subtype-Specific Signature of Glioma Stem Cells Open
Merged Tuxedo Suite output for tumor data, combining the cuffdiff and cuffnorm tables by unique ENSEMBL identifier
View article: Table S1, S2, S3, S4 from Bivalent Chromatin Domains in Glioblastoma Reveal a Subtype-Specific Signature of Glioma Stem Cells
Table S1, S2, S3, S4 from Bivalent Chromatin Domains in Glioblastoma Reveal a Subtype-Specific Signature of Glioma Stem Cells Open
Table S1: Output of ChromHMM and color key. Table S2: Enhancer counts. Table S3: Enhancer distribution. Table S4: Bivalent region counts.
View article: File S1 from Bivalent Chromatin Domains in Glioblastoma Reveal a Subtype-Specific Signature of Glioma Stem Cells
File S1 from Bivalent Chromatin Domains in Glioblastoma Reveal a Subtype-Specific Signature of Glioma Stem Cells Open
sequencing statistics for all datasets in this study.
View article: File S5 from Bivalent Chromatin Domains in Glioblastoma Reveal a Subtype-Specific Signature of Glioma Stem Cells
File S5 from Bivalent Chromatin Domains in Glioblastoma Reveal a Subtype-Specific Signature of Glioma Stem Cells Open
Bivalent regions that are present in at least 8 tumors, and the gene they are located within or proximal to