title: BMMC.RNA

city: New York

first: Sai

address: 1425 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

data_processing:
The data is processed using share-seq alignment v2 pipeline (https://github.com/masai1116/SHARE-seq-alignmentV2)
Assembly: hg19 or mm10
Supplementary files format and content: Counts.csv file contains sumamried information for each cell barcode. Column 1-4 are cell barcodes, column 5 is filtered read count, column 6 is sequencing depth, column 7 is duplciation rate, column 8 is estimated library size
Supplementary files format and content: fragments file contains Tn5 corrected cut sites per cell. Column 1-3 are genomic coordinates, column 4 is cell barcode, column 5 is frequency of the fragment.
Supplementary files format and content: count.matrix file is a sparse matrix file of the filtered ATAC count matrix.
Supplementary files format and content: peak file contain peak range of ATAC count matrix
Supplementary files format and content: metadata table contains cell type annotation, barcode translation table and umap coordiantes
Supplementary files format and content: h5 is the unfiltered RNA count matrix

source_name: bone marrow

extract_protocol:
For colonic epithelial cell collection, ten C57BL/6J male mice at 9 weeks of age were sacrificed and cardiac perfusion was performed using normal saline to deplete circulating immune cells and colonic tissue between the rectum and cecum was isolated. Colonic waste content was flushed and the lumen was exposed. Tissue was then placed in EDTA Dissociation Buffer (4 mM EDTA, 10 mM HEPES pH 7.2, 10% FBS) and rotated at RT for 30 minutes. The epithelial surface was then scraped four to five times with a glass coverslip to collect the mucosa and the remaining tissue was minced finely with scissors. The mucosal and muscle wall tissue were each transferred to Advanced DMEM/F12 (Fisher, 12-634-028 ) containing collagenase 0.4 mg/mL (Sigma, C9263-25MG), dispase II 1.25 U/mL (Sigma, D4693-1G), DNase 1 U/mL (Worthington, LS002004), 10 mM HEPES pH 7.2 and 5 µM Y-27632 (MedChem Express, HY-10071). Following an initial 30 minute incubation, both sets of tissue were triturated every 10 to 15 minutes until dissociated fully to single cells. Both sets of tissue were pooled, washed once with PBS and stained with Calcein Red-AM (BioLegend, 425205) for 15 minutes at room temperature. Cells were then stained with anti-Epcam  PE/Cy7 (Thermo, 14-5791-81), anti-CD45 APC-Cy7 (BioLegend, 103116), anti-Ly6G APC (BioLegend, 127613), anti-SiglecF APC (BioLegend, 155507) and DAPI. Live cells were identified as Calcein+DAPI- events. Both epithelial cells (Epcam+CD45-) and non-granulocytic immune cells (CD45+Ly6G-SiglecF-) were isolated using a BD FACSAria by sorting into Advanced DMEM/F12 with 0.2% RNase-free BSA (AmericanBio, AB01243-00050), RNase inhibitor 0.1 U/µL (Enzymatics, Y9240L) and 15 µM Y-27632.   Human bone marrow samples were purchased from AllCells (BM, CR,MNC, 10M). CD34+ selection was performed using CD34 microbead kit (Miltenyi Biotech, 130-046-703) and FACS- purified for long term HSCs (CD45+Lin-CD34+CD38-CD45RA-CD90+). The following antibodies were used for long term HSC sorting: CD45 PE Dazzle 594 (Biolegend, 304050), Lin FITC (Biolegend, 348801), CD34 APC-Cy7 (Biolegend, 343514), CD38 PE-Cy7 (Biolegend, 303516), CD45RA APC (BD, 564442) and CD90 BV421 (Biolegend cat# 328122). About 5,000 FACS sorted long term HSCs were cultured in expansion medium consisting of StemSpan SFEM II (STEMCELL Technologies) supplemented with StemSpan CD34+ expansion supplement (STEMCELL Technologies, 02691), UM171 (STEMCELL Technologies, 72912) and Stemregenin 1 (STEMCELL Technologies, 72342) in 96 well plates coated with fibronectin (Corning, 354409). After two weeks of culture in the expansion media, about 300,000 cells were harvested and profiled using SHARE-seq V2 protocol.  Frozen human Bone Marrow Mononuclear Cells (BMMCs, Allcells) are thawed in a 37 °C water bath for 1 min and transferred to a 15 ml centrifuge tube. 10 ml of pre-warmed DMEM with 10% FBS was added to cells drop-wisely. The cells were spun at 400g for 3 minutes at room temperature. After removing supernatant, the cells are washed twice in 0.5 ml PBS with 0.04% BSA. To deplete neutrophils, the cells were resuspended in 100 μl chilled DPBS with 0.2% BSA and 10 μl of human TrueStain FcX (BioLegend, 422302) and incubated on ice for 10 min to reduce non-specific labeling. The cells were then incubated on ice for another 30 min after adding 0.5 μl of biotin anti-human CD15 antibody (BioLegend, 301913). After immunostaining, 25 μl of MyOne T1 beads were added to the sample to capture the neutrophils for 5 min at room temperature. We then added 900 μl of DPBS with 0.2% BSA to dilute the sample. The sample was placed on a magnet for 3 minutes and 1 ml of the sample was transferred to a new tube while the sample was on the magnet. The cells were ready for fixation and SHARE-seqV2 experiment.
The libraries are contructed using SHARE-seqV2 procotol.
SHARE-seqV2

value: bone marrow


title: SCC07_AAV_control_A_L1

status: Public on Oct 06 2022

type: SRA

city: Boston

first: Arpiar

last: Saunders

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

country: USA

institute: Harvard Medical School

description:
SCC07
single-cell RNA profiling using 3' counting

library_source: transcriptomic single cell

data_processing:
Sequencing was performed on either an Illumina MiSeq, NextSeq 500 or NovaSeq6000
Sequencing Reads were aligned against a custom genome containing the GRCm38.81 mouse build; the rabies virus genome (SAD-B19-dG-EGFP) and AAV elements using STAR
Aligned Reads within a gene were collapsed to UMI(XM)-Gene Pairs and associated with single-cells through a cell barcode (XC) shared on Read 1
A count matrix - called the digital gene expression (DGE) matrix - was output. Columns belong to STAMPs (cells) and transcript counts (rows)
Viral barcodes (VBCs) were amplified from sequenced EGFP mRNAs. Raw VBC sequences ascertained from viral genomes or scRNA-seq data (RM) were collapsed (RB) using custom algorithms. UMIs were used count/collapse VBC sequences within the context of a cell (XC)
Assembly: GRCm38.81 + custom genomes for SAD-B19-dG-EGFP and AAV elements
Supplementary files format and content: digital gene expression

molecule: total RNA

organism: Mus musculus

source_name: Striatal-Cortex Co-Culture Experiment 7, Well A, Library 1. Control Cells (Infected by AAVs only)

extract_protocol:
Saunders and Macosko et al. 2018 Cell
10x Genomics 3' RNA (v2 or v3 chemistry) & this study (for viral barcode processing/sequencing)
10x Genomics 3' RNA & this study (for viral barcode processing/sequencing)

treatment_protocol: Cells were dissociated from in vitro synaptic cultures, FACS to enrich for those cells infected by rabies virus and scRNA-seq libraries were generated using 10x Genomic v2 or v3 platforms

tag: strain


title: C57BL/6J mouse, IH, muscle, replicate 3, time point 16:30 h [Muscle_IH_16:30_rep3]

status: Public on Sep 30 2022

city: Cincinnati

first: Bala S. C.

last: Koritala

state: Ohio

address: 3333 Burnet Avenue

department: Division of Pediatric Otolaryngology

institute: Cincinnati Children's Hospital Medical Center

library_source: transcriptomic

data_processing:
The Illumina Bcl2fastq2 Conversion Software v2.17 was used to demultiplex the data.
The quality of sequences in FASTQ format was assessed using FASTQC (v0.11.3)
Raw FASTQ reads of each sample were aligned and quantified using an ENSEMBL mouse reference genome, release-102, by Kallisto
The normalized quantification, in transcripts per million (TPM), was used for circadian analysis.
The estimated count from Kallisto was used to test differences between normoxia and IH with the DESeq2 R package.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Muscle

extract_protocol:
The RNA from all tissues was extracted using a Trizol method
In accordance with the manufacturer's protocol, 1 µg of total RNA was used to construct the library using NEBNext® UltraTM II Directional RNA Library Prep Kit for Illumina® (New England Biolabs, #E7765L, Ipswich, MA, USA).

tag: genotype

value: Wild type

tag: treatment

value: Intermittent hypoxia

tag: time

tag: tissue

value: Muscle


title: C57BL/6J mouse, normoxia, muscle, replicate 1, time point 22:30 h [Muscle_Norm_22:30_rep1]

value: Normoxia


title: C57BL/6J mouse, normoxia, muscle, replicate 3, time point 22:30 h [Muscle_Norm_22:30_rep3]


title: C57BL/6J mouse, IH, muscle, replicate 3, time point 19:30 h [Muscle_IH_19:30_rep3]


title: C57BL/6J mouse, IH, muscle, replicate 1, time point 19:30 h [Muscle_IH_19:30_rep1]


title: C57BL/6J mouse, normoxia, muscle, replicate 3, time point 16:30 h [Muscle_Norm_16:30_rep3]


title: C57BL/6J mouse, normoxia, muscle, replicate 3, time point 19:30 h [Muscle_Norm_19:30_rep3]


title: C57BL/6J mouse, IH, muscle, replicate 2, time point 16:30 h [Muscle_IH_16:30_rep2]


title: C57BL/6J mouse, IH, muscle, replicate 2, time point 19:30 h [Muscle_IH_19:30_rep2]


title: C57BL/6J mouse, normoxia, muscle, replicate 1, time point 16:30 h [Muscle_Norm_16:30_rep1]


title: C57BL/6J mouse, normoxia, muscle, replicate 2, time point 16:30 h [Muscle_Norm_16:30_rep2]


title: C57BL/6J mouse, normoxia, muscle, replicate 2, time point 22:30 h [Muscle_Norm_22:30_rep2]


title: C57BL/6J mouse, normoxia, muscle, replicate 1, time point 19:30 h [Muscle_Norm_19:30_rep1]


title: C57BL/6J mouse, normoxia, muscle, replicate 2, time point 19:30 h [Muscle_Norm_19:30_rep2]


title: C57BL/6J mouse, IH, muscle, replicate 3, time point 22:30 h [Muscle_IH_22:30_rep3]


title: C57BL/6J mouse, IH, muscle, replicate 2, time point 22:30 h [Muscle_IH_22:30_rep2]


title: C57BL/6J mouse, normoxia, muscle, replicate 3, time point 13:30 h [Muscle_Norm_13:30_rep3]


title: C57BL/6J mouse, IH, muscle, replicate 1, time point 22:30 h [Muscle_IH_22:30_rep1]


title: C57BL/6J mouse, IH, muscle, replicate 1, time point 16:30 h [Muscle_IH_16:30_rep1]


title: SCC06_control_A_L2

description:
SCC06
single-cell RNA profiling using 3' counting

source_name: Striatal-Cortex Co-Culture Experiment 6, Well A, Library 2. Control Cells (Uninfected by neither AAVs nor EnvA-RVdG-EGFP-VBC)


title: C57BL/6J mouse, normoxia, muscle, replicate 2, time point 13:30 h [Muscle_Norm_13:30_rep2]


title: C57BL/6J mouse, IH, muscle, replicate 2, time point 13:30 h [Muscle_IH_13:30_rep2]


title: C57BL/6J mouse, normoxia, muscle, replicate 1, time point 13:30 h [Muscle_Norm_13:30_rep1]


title: C57BL/6J mouse, IH, muscle, replicate 1, time point 13:30 h [Muscle_IH_13:30_rep1]


title: C57BL/6J mouse, normoxia, muscle, replicate 2, time point 10:30 h [Muscle_Norm_10:30_rep2]


title: C57BL/6J mouse, IH, muscle, replicate 2, time point 10:30 h [Muscle_IH_10:30_rep2]


title: C57BL/6J mouse, normoxia, muscle, replicate 1, time point 10:30 h [Muscle_Norm_10:30_rep1]


title: C57BL/6J mouse, IH, muscle, replicate 3, time point 13:30 h [Muscle_IH_13:30_rep3]


title: C57BL/6J mouse, IH, muscle, replicate 3, time point 10:30 h [Muscle_IH_10:30_rep3]


title: C57BL/6J mouse, normoxia, muscle, replicate 3, time point 10:30 h [Muscle_Norm_10:30_rep3]


title: C57BL/6J mouse, normoxia, muscle, replicate 1, time point 4:30 h [Muscle_Norm_4:30_rep1]


title: C57BL/6J mouse, normoxia, muscle, replicate 2, time point 4:30 h [Muscle_Norm_4:30_rep2]


title: C57BL/6J mouse, IH, muscle, replicate 1, time point 7:30 h [Muscle_IH_7:30_rep1]


title: C57BL/6J mouse, IH, muscle, replicate 1, time point 4:30 h [Muscle_IH_4:30_rep1]


title: C57BL/6J mouse, IH, muscle, replicate 3, time point 4:30 h [Muscle_IH_4:30_rep3]


title: C57BL/6J mouse, normoxia, muscle, replicate 2, time point 7:30 h [Muscle_Norm_7:30_rep2]


title: C57BL/6J mouse, IH, muscle, replicate 3, time point 7:30 h [Muscle_IH_7:30_rep3]


title: C57BL/6J mouse, normoxia, muscle, replicate 2, time point 1:30 h [Muscle_Norm_1:30_rep2]


title: C57BL/6J mouse, IH, muscle, replicate 2, time point 1:30 h [Muscle_IH_1:30_rep2]


title: C57BL/6J mouse, normoxia, muscle, replicate 1, time point 7:30 h [Muscle_Norm_7:30_rep1]


title: C57BL/6J mouse, normoxia, lung, replicate 2, time point 22:30 h [Lung_Norm_22:30_rep2]

source_name: Lung

value: Lung


title: C57BL/6J mouse, normoxia, lung, replicate 3, time point 22:30 h [Lung_Norm_22:30_rep3]


title: C57BL/6J mouse, normoxia, lung, replicate 1, time point 22:30 h [Lung_Norm_22:30_rep1]


title: C57BL/6J mouse, IH, lung, replicate 2, time point 22:30 h [Lung_IH_22:30_rep2]


title: C57BL/6J mouse, normoxia, muscle, replicate 3, time point 7:30 h [Muscle_Norm_7:30_rep3]


title: C57BL/6J mouse, normoxia, muscle, replicate 3, time point 4:30 h [Muscle_Norm_4:30_rep3]


title: C57BL/6J mouse, normoxia, muscle, replicate 3, time point 1:30 h [Muscle_Norm_1:30_rep3]


title: C57BL/6J mouse, IH, lung, replicate 3, time point 22:30 h [Lung_IH_22:30_rep3]


title: C57BL/6J mouse, IH, muscle, replicate 2, time point 4:30 h [Muscle_IH_4:30_rep2]


title: C57BL/6J mouse, IH, muscle, replicate 3, time point 1:30 h [Muscle_IH_1:30_rep3]


title: C57BL/6J mouse, IH, muscle, replicate 2, time point 7:30 h [Muscle_IH_7:30_rep2]


title: C57BL/6J mouse, IH, lung, replicate 3, time point 19:30 h [Lung_IH_19:30_rep3]


title: C57BL/6J mouse, normoxia, lung, replicate 3, time point 19:30 h [Lung_Norm_19:30_rep3]


title: C57BL/6J mouse, IH, muscle, replicate 1, time point 10:30 h [Muscle_IH_10:30_rep1]


title: C57BL/6J mouse, IH, muscle, replicate 1, time point 1:30 h [Muscle_IH_1:30_rep1]


title: C57BL/6J mouse, normoxia, muscle, replicate 1, time point 1:30 h [Muscle_Norm_1:30_rep1]


title: C57BL/6J mouse, normoxia, lung, replicate 2, time point 19:30 h [Lung_Norm_19:30_rep2]


title: C57BL/6J mouse, IH, lung, replicate 1, time point 22:30 h [Lung_IH_22:30_rep1]


title: C57BL/6J mouse, IH, lung, replicate 2, time point 19:30 h [Lung_IH_19:30_rep2]


title: C57BL/6J mouse, normoxia, lung, replicate 1, time point 19:30 h [Lung_Norm_19:30_rep1]


title: C57BL/6J mouse, IH, lung, replicate 2, time point 16:30 h [Lung_IH_16:30_rep2]


title: C57BL/6J mouse, normoxia, lung, replicate 2, time point 16:30 h [Lung_Norm_16:30_rep2]


title: C57BL/6J mouse, normoxia, lung, replicate 1, time point 16:30 h [Lung_Norm_16:30_rep1]


title: C57BL/6J mouse, normoxia, lung, replicate 3, time point 16:30 h [Lung_Norm_16:30_rep3]


title: C57BL/6J mouse, IH, lung, replicate 1, time point 19:30 h [Lung_IH_19:30_rep1]


title: C57BL/6J mouse, IH, lung, replicate 3, time point 10:30 h [Lung_IH_10:30_rep3]


title: C57BL/6J mouse, IH, lung, replicate 3, time point 13:30 h [Lung_IH_13:30_rep3]


title: C57BL/6J mouse, normoxia, lung, replicate 1, time point 13:30 h [Lung_Norm_13:30_rep1]


title: C57BL/6J mouse, IH, lung, replicate 1, time point 13:30 h [Lung_IH_13:30_rep1]


title: C57BL/6J mouse, normoxia, lung, replicate 3, time point 13:30 h [Lung_Norm_13:30_rep3]


title: C57BL/6J mouse, normoxia, lung, replicate 2, time point 10:30 h [Lung_Norm_10:30_rep2]


title: C57BL/6J mouse, normoxia, lung, replicate 3, time point 7:30 h [Lung_Norm_7:30_rep3]


title: C57BL/6J mouse, IH, lung, replicate 3, time point 7:30 h [Lung_IH_7:30_rep3]


title: C57BL/6J mouse, IH, lung, replicate 1, time point 16:30 h [Lung_IH_16:30_rep1]


title: C57BL/6J mouse, IH, lung, replicate 2, time point 13:30 h [Lung_IH_13:30_rep2]


title: C57BL/6J mouse, IH, lung, replicate 2, time point 7:30 h [Lung_IH_7:30_rep2]


title: C57BL/6J mouse, normoxia, lung, replicate 1, time point 10:30 h [Lung_Norm_10:30_rep1]


title: C57BL/6J mouse, normoxia, lung, replicate 2, time point 7:30 h [Lung_Norm_7:30_rep2]


title: C57BL/6J mouse, IH, lung, replicate 2, time point 10:30 h [Lung_IH_10:30_rep2]


title: C57BL/6J mouse, IH, lung, replicate 1, time point 10:30 h [Lung_IH_10:30_rep1]


title: C57BL/6J mouse, normoxia, lung, replicate 3, time point 10:30 h [Lung_Norm_10:30_rep3]


title: C57BL/6J mouse, normoxia, lung, replicate 1, time point 7:30 h [Lung_Norm_7:30_rep1]


title: C57BL/6J mouse, normoxia, lung, replicate 3, time point 4:30 h [Lung_Norm_4:30_rep3]


title: C57BL/6J mouse, IH, lung, replicate 3, time point 4:30 h [Lung_IH_4:30_rep3]


title: C57BL/6J mouse, normoxia, lung, replicate 2, time point 4:30 h [Lung_Norm_4:30_rep2]


title: C57BL/6J mouse, IH, lung, replicate 1, time point 7:30 h [Lung_IH_7:30_rep1]


title: C57BL/6J mouse, IH, lung, replicate 2, time point 4:30 h [Lung_IH_4:30_rep2]


title: C57BL/6J mouse, IH, lung, replicate 3, time point 16:30 h [Lung_IH_16:30_rep3]


title: C57BL/6J mouse, normoxia, lung, replicate 1, time point 4:30 h [Lung_Norm_4:30_rep1]


title: C57BL/6J mouse, normoxia, lung, replicate 2, time point 13:30 h [Lung_Norm_13:30_rep2]


title: C57BL/6J mouse, normoxia, lung, replicate 3, time point 1:30 h [Lung_Norm_1:30_rep3]


title: C57BL/6J mouse, IH, lung, replicate 3, time point 1:30 h [Lung_IH_1:30_rep3]


title: C57BL/6J mouse, IH, lung, replicate 2, time point 1:30 h [Lung_IH_1:30_rep2]


title: C57BL/6J mouse, normoxia, lung, replicate 1, time point 1:30 h [Lung_Norm_1:30_rep1]


title: C57BL/6J mouse, IH, liver, replicate 3, time point 22:30 h [Liver_IH_22:30_rep3]

source_name: Liver

value: Liver


title: C57BL/6J mouse, normoxia, lung, replicate 2, time point 1:30 h [Lung_Norm_1:30_rep2]


title: C57BL/6J mouse, normoxia, liver, replicate 2, time point 22:30 h [Liver_Norm_22:30_rep2]


title: C57BL/6J mouse, normoxia, liver, replicate 1, time point 22:30 h [Liver_Norm_22:30_rep1]


title: C57BL/6J mouse, IH, liver, replicate 2, time point 19:30 h [Liver_IH_19:30_rep2]


title: C57BL/6J mouse, IH, liver, replicate 3, time point 19:30 h [Liver_IH_19:30_rep3]


title: C57BL/6J mouse, IH, lung, replicate 1, time point 1:30 h [Lung_IH_1:30_rep1]


title: C57BL/6J mouse, normoxia, liver, replicate 2, time point 19:30 h [Liver_Norm_19:30_rep2]


title: C57BL/6J mouse, IH, liver, replicate 2, time point 22:30 h [Liver_IH_22:30_rep2]


title: C57BL/6J mouse, IH, liver, replicate 1, time point 22:30 h [Liver_IH_22:30_rep1]


title: C57BL/6J mouse, normoxia, liver, replicate 3, time point 22:30 h [Liver_Norm_22:30_rep3]


title: C57BL/6J mouse, normoxia, liver, replicate 2, time point 16:30 h [Liver_Norm_16:30_rep2]


title: C57BL/6J mouse, normoxia, liver, replicate 3, time point 19:30 h [Liver_Norm_19:30_rep3]


title: C57BL/6J mouse, IH, liver, replicate 2, time point 16:30 h [Liver_IH_16:30_rep2]


title: C57BL/6J mouse, normoxia, liver, replicate 1, time point 19:30 h [Liver_Norm_19:30_rep1]


title: C57BL/6J mouse, IH, liver, replicate 3, time point 16:30 h [Liver_IH_16:30_rep3]


title: C57BL/6J mouse, normoxia, liver, replicate 1, time point 16:30 h [Liver_Norm_16:30_rep1]


title: C57BL/6J mouse, IH, liver, replicate 1, time point 16:30 h [Liver_IH_16:30_rep1]


title: C57BL/6J mouse, normoxia, liver, replicate 3, time point 13:30 h [Liver_Norm_13:30_rep3]


title: C57BL/6J mouse, normoxia, liver, replicate 2, time point 13:30 h [Liver_Norm_13:30_rep2]


title: C57BL/6J mouse, IH, liver, replicate 3, time point 13:30 h [Liver_IH_13:30_rep3]


title: C57BL/6J mouse, IH, lung, replicate 1, time point 4:30 h [Lung_IH_4:30_rep1]


title: C57BL/6J mouse, IH, liver, replicate 2, time point 13:30 h [Liver_IH_13:30_rep2]


title: C57BL/6J mouse, normoxia, liver, replicate 1, time point 13:30 h [Liver_Norm_13:30_rep1]


title: C57BL/6J mouse, IH, liver, replicate 1, time point 13:30 h [Liver_IH_13:30_rep1]


title: C57BL/6J mouse, IH, liver, replicate 3, time point 10:30 h [Liver_IH_10:30_rep3]


title: C57BL/6J mouse, normoxia, liver, replicate 3, time point 10:30 h [Liver_Norm_10:30_rep3]


title: C57BL/6J mouse, normoxia, liver, replicate 2, time point 10:30 h [Liver_Norm_10:30_rep2]


title: C57BL/6J mouse, normoxia, liver, replicate 1, time point 10:30 h [Liver_Norm_10:30_rep1]


title: C57BL/6J mouse, IH, liver, replicate 2, time point 10:30 h [Liver_IH_10:30_rep2]


title: C57BL/6J mouse, IH, liver, replicate 1, time point 19:30 h [Liver_IH_19:30_rep1]


title: C57BL/6J mouse, IH, liver, replicate 1, time point 10:30 h [Liver_IH_10:30_rep1]


title: C57BL/6J mouse, normoxia, liver, replicate 3, time point 7:30 h [Liver_Norm_7:30_rep3]


title: C57BL/6J mouse, IH, liver, replicate 3, time point 7:30 h [Liver_IH_7:30_rep3]


title: C57BL/6J mouse, IH, liver, replicate 1, time point 7:30 h [Liver_IH_7:30_rep1]


title: C57BL/6J mouse, normoxia, liver, replicate 2, time point 7:30 h [Liver_Norm_7:30_rep2]


title: C57BL/6J mouse, normoxia, liver, replicate 3, time point 16:30 h [Liver_Norm_16:30_rep3]


title: C57BL/6J mouse, normoxia, liver, replicate 1, time point 7:30 h [Liver_Norm_7:30_rep1]


title: C57BL/6J mouse, normoxia, liver, replicate 1, time point 4:30 h [Liver_Norm_4:30_rep1]


title: C57BL/6J mouse, IH, liver, replicate 2, time point 7:30 h [Liver_IH_7:30_rep2]


title: C57BL/6J mouse, normoxia, liver, replicate 2, time point 4:30 h [Liver_Norm_4:30_rep2]


title: C57BL/6J mouse, IH, liver, replicate 3, time point 4:30 h [Liver_IH_4:30_rep3]


title: C57BL/6J mouse, normoxia, liver, replicate 3, time point 1:30 h [Liver_Norm_1:30_rep3]


title: C57BL/6J mouse, IH, liver, replicate 1, time point 4:30 h [Liver_IH_4:30_rep1]


title: C57BL/6J mouse, normoxia, liver, replicate 3, time point 4:30 h [Liver_Norm_4:30_rep3]


title: C57BL/6J mouse, IH, liver, replicate 2, time point 4:30 h [Liver_IH_4:30_rep2]


title: C57BL/6J mouse, IH, liver, replicate 3, time point 1:30 h [Liver_IH_1:30_rep3]


title: C57BL/6J mouse, normoxia, liver, replicate 2, time point 1:30 h [Liver_Norm_1:30_rep2]


title: C57BL/6J mouse, IH, liver, replicate 2, time point 1:30 h [Liver_IH_1:30_rep2]


title: C57BL/6J mouse, IH, liver, replicate 1, time point 1:30 h [Liver_IH_1:30_rep1]


title: C57BL/6J mouse, normoxia, liver, replicate 1, time point 1:30 h [Liver_Norm_1:30_rep1]


title: C57BL/6J mouse, IH, kidney, replicate 3, time point 22:30 h [Kidney_IH_22:30_rep3]

source_name: Kidney

value: Kidney


title: C57BL/6J mouse, normoxia, kidney, replicate 3, time point 22:30 h [Kidney_Norm_22:30_rep3]


title: C57BL/6J mouse, normoxia, kidney, replicate 2, time point 22:30 h [Kidney_Norm_22:30_rep2]


title: C57BL/6J mouse, normoxia, kidney, replicate 2, time point 19:30 h [Kidney_Norm_19:30_rep2]


title: C57BL/6J mouse, IH, kidney, replicate 2, time point 19:30 h [Kidney_IH_19:30_rep2]


title: C57BL/6J mouse, IH, kidney, replicate 1, time point 22:30 h [Kidney_IH_22:30_rep1]


title: C57BL/6J mouse, IH, kidney, replicate 3, time point 19:30 h [Kidney_IH_19:30_rep3]


title: C57BL/6J mouse, normoxia, kidney, replicate 1, time point 22:30 h [Kidney_Norm_22:30_rep1]


title: C57BL/6J mouse, normoxia, kidney, replicate 3, time point 19:30 h [Kidney_Norm_19:30_rep3]


title: C57BL/6J mouse, IH, kidney, replicate 2, time point 22:30 h [Kidney_IH_22:30_rep2]


title: C57BL/6J mouse, normoxia, kidney, replicate 1, time point 19:30 h [Kidney_Norm_19:30_rep1]


title: C57BL/6J mouse, IH, kidney, replicate 1, time point 19:30 h [Kidney_IH_19:30_rep1]


title: C57BL/6J mouse, normoxia, kidney, replicate 3, time point 13:30 h [Kidney_Norm_13:30_rep3]


title: C57BL/6J mouse, IH, kidney, replicate 3, time point 13:30 h [Kidney_IH_13:30_rep3]


title: C57BL/6J mouse, IH, kidney, replicate 2, time point 16:30 h [Kidney_IH_16:30_rep2]


title: C57BL/6J mouse, IH, kidney, replicate 1, time point 13:30 h [Kidney_IH_13:30_rep1]


title: C57BL/6J mouse, normoxia, kidney, replicate 3, time point 16:30 h [Kidney_Norm_16:30_rep3]


title: C57BL/6J mouse, normoxia, kidney, replicate 2, time point 16:30 h [Kidney_Norm_16:30_rep2]


title: C57BL/6J mouse, IH, kidney, replicate 3, time point 16:30 h [Kidney_IH_16:30_rep3]


title: C57BL/6J mouse, IH, kidney, replicate 1, time point 16:30 h [Kidney_IH_16:30_rep1]


title: C57BL/6J mouse, normoxia, kidney, replicate 2, time point 10:30 h [Kidney_Norm_10:30_rep2]


title: C57BL/6J mouse, normoxia, kidney, replicate 1, time point 16:30 h [Kidney_Norm_16:30_rep1]


title: C57BL/6J mouse, normoxia, kidney, replicate 1, time point 13:30 h [Kidney_Norm_13:30_rep1]


title: C57BL/6J mouse, IH, kidney, replicate 2, time point 13:30 h [Kidney_IH_13:30_rep2]


title: C57BL/6J mouse, normoxia, kidney, replicate 2, time point 13:30 h [Kidney_Norm_13:30_rep2]


title: C57BL/6J mouse, normoxia, kidney, replicate 3, time point 10:30 h [Kidney_Norm_10:30_rep3]


title: C57BL/6J mouse, IH, kidney, replicate 2, time point 10:30 h [Kidney_IH_10:30_rep2]


title: C57BL/6J mouse, IH, kidney, replicate 3, time point 10:30 h [Kidney_IH_10:30_rep3]


title: C57BL/6J mouse, normoxia, kidney, replicate 1, time point 10:30 h [Kidney_Norm_10:30_rep1]


title: C57BL/6J mouse, normoxia, kidney, replicate 3, time point 7:30 h [Kidney_Norm_7:30_rep3]


title: C57BL/6J mouse, IH, kidney, replicate 3, time point 7:30 h [Kidney_IH_7:30_rep3]


title: C57BL/6J mouse, normoxia, kidney, replicate 2, time point 7:30 h [Kidney_Norm_7:30_rep2]


title: C57BL/6J mouse, IH, kidney, replicate 3, time point 4:30 h [Kidney_IH_4:30_rep3]


title: C57BL/6J mouse, IH, kidney, replicate 2, time point 7:30 h [Kidney_IH_7:30_rep2]


title: C57BL/6J mouse, normoxia, kidney, replicate 2, time point 4:30 h [Kidney_Norm_4:30_rep2]


title: C57BL/6J mouse, IH, kidney, replicate 2, time point 4:30 h [Kidney_IH_4:30_rep2]


title: C57BL/6J mouse, normoxia, kidney, replicate 1, time point 7:30 h [Kidney_Norm_7:30_rep1]


title: C57BL/6J mouse, IH, kidney, replicate 1, time point 7:30 h [Kidney_IH_7:30_rep1]


title: C57BL/6J mouse, IH, kidney, replicate 1, time point 4:30 h [Kidney_IH_4:30_rep1]


title: C57BL/6J mouse, IH, kidney, replicate 1, time point 10:30 h [Kidney_IH_10:30_rep1]


title: C57BL/6J mouse, IH, kidney, replicate 2, time point 1:30 h [Kidney_IH_1:30_rep2]


title: C57BL/6J mouse, normoxia, kidney, replicate 1, time point 1:30 h [Kidney_Norm_1:30_rep1]


title: C57BL/6J mouse, normoxia, heart, replicate 2, time point 22:30 h [Heart_Norm_22:30_rep2]

source_name: Heart

value: Heart


title: C57BL/6J mouse, IH, kidney, replicate 1, time point 1:30 h [Kidney_IH_1:30_rep1]


title: C57BL/6J mouse, normoxia, kidney, replicate 3, time point 1:30 h [Kidney_Norm_1:30_rep3]


title: C57BL/6J mouse, normoxia, heart, replicate 3, time point 19:30 h [Heart_Norm_19:30_rep3]


title: C57BL/6J mouse, IH, heart, replicate 1, time point 22:30 h [Heart_IH_22:30_rep1]


title: C57BL/6J mouse, normoxia, heart, replicate 1, time point 22:30 h [Heart_Norm_22:30_rep1]


title: C57BL/6J mouse, normoxia, kidney, replicate 2, time point 1:30 h [Kidney_Norm_1:30_rep2]


title: C57BL/6J mouse, IH, heart, replicate 2, time point 22:30 h [Heart_IH_22:30_rep2]


title: C57BL/6J mouse, normoxia, heart, replicate 1, time point 19:30 h [Heart_Norm_19:30_rep1]


title: C57BL/6J mouse, normoxia, heart, replicate 2, time point 19:30 h [Heart_Norm_19:30_rep2]


title: C57BL/6J mouse, normoxia, heart, replicate 3, time point 22:30 h [Heart_Norm_22:30_rep3]


title: C57BL/6J mouse, IH, heart, replicate 3, time point 22:30 h [Heart_IH_22:30_rep3]


title: C57BL/6J mouse, IH, heart, replicate 2, time point 19:30 h [Heart_IH_19:30_rep2]


title: C57BL/6J mouse, IH, heart, replicate 1, time point 19:30 h [Heart_IH_19:30_rep1]


title: C57BL/6J mouse, IH, heart, replicate 3, time point 19:30 h [Heart_IH_19:30_rep3]


title: C57BL/6J mouse, normoxia, heart, replicate 3, time point 16:30 h [Heart_Norm_16:30_rep3]


title: C57BL/6J mouse, normoxia, kidney, replicate 3, time point 4:30 h [Kidney_Norm_4:30_rep3]


title: C57BL/6J mouse, normoxia, kidney, replicate 1, time point 4:30 h [Kidney_Norm_4:30_rep1]


title: C57BL/6J mouse, IH, heart, replicate 3, time point 16:30 h [Heart_IH_16:30_rep3]


title: C57BL/6J mouse, IH, heart, replicate 1, time point 16:30 h [Heart_IH_16:30_rep1]


title: C57BL/6J mouse, IH, heart, replicate 3, time point 13:30 h [Heart_IH_13:30_rep3]


title: C57BL/6J mouse, normoxia, heart, replicate 3, time point 13:30 h [Heart_Norm_13:30_rep3]


title: C57BL/6J mouse, normoxia, heart, replicate 1, time point 13:30 h [Heart_Norm_13:30_rep1]


title: C57BL/6J mouse, IH, heart, replicate 2, time point 13:30 h [Heart_IH_13:30_rep2]


title: C57BL/6J mouse, IH, heart, replicate 1, time point 13:30 h [Heart_IH_13:30_rep1]


title: C57BL/6J mouse, normoxia, heart, replicate 2, time point 13:30 h [Heart_Norm_13:30_rep2]


title: C57BL/6J mouse, normoxia, heart, replicate 1, time point 10:30 h [Heart_Norm_10:30_rep1]


title: C57BL/6J mouse, normoxia, heart, replicate 3, time point 10:30 h [Heart_Norm_10:30_rep3]


title: C57BL/6J mouse, IH, heart, replicate 1, time point 10:30 h [Heart_IH_10:30_rep1]


title: C57BL/6J mouse, normoxia, heart, replicate 2, time point 10:30 h [Heart_Norm_10:30_rep2]


title: C57BL/6J mouse, IH, heart, replicate 2, time point 7:30 h [Heart_IH_7:30_rep2]


title: C57BL/6J mouse, IH, heart, replicate 2, time point 10:30 h [Heart_IH_10:30_rep2]


title: C57BL/6J mouse, normoxia, heart, replicate 2, time point 7:30 h [Heart_Norm_7:30_rep2]


title: C57BL/6J mouse, IH, heart, replicate 3, time point 7:30 h [Heart_IH_7:30_rep3]


title: C57BL/6J mouse, IH, heart, replicate 3, time point 4:30 h [Heart_IH_4:30_rep3]


title: C57BL/6J mouse, normoxia, heart, replicate 3, time point 7:30 h [Heart_Norm_7:30_rep3]


title: C57BL/6J mouse, normoxia, heart, replicate 3, time point 4:30 h [Heart_Norm_4:30_rep3]


title: C57BL/6J mouse, IH, heart, replicate 1, time point 7:30 h [Heart_IH_7:30_rep1]


title: C57BL/6J mouse, IH, heart, replicate 3, time point 10:30 h [Heart_IH_10:30_rep3]


title: C57BL/6J mouse, normoxia, heart, replicate 2, time point 4:30 h [Heart_Norm_4:30_rep2]


title: C57BL/6J mouse, IH, heart, replicate 2, time point 16:30 h [Heart_IH_16:30_rep2]


title: C57BL/6J mouse, normoxia, heart, replicate 1, time point 16:30 h [Heart_Norm_16:30_rep1]


title: C57BL/6J mouse, normoxia, heart, replicate 3, time point 1:30 h [Heart_Norm_1:30_rep3]


title: C57BL/6J mouse, normoxia, heart, replicate 2, time point 16:30 h [Heart_Norm_16:30_rep2]


title: C57BL/6J mouse, normoxia, heart, replicate 1, time point 4:30 h [Heart_Norm_4:30_rep1]


title: C57BL/6J mouse, normoxia, heart, replicate 2, time point 1:30 h [Heart_Norm_1:30_rep2]


title: C57BL/6J mouse, IH, heart, replicate 1, time point 4:30 h [Heart_IH_4:30_rep1]


title: C57BL/6J mouse, normoxia, cerebellum, replicate 3, time point 22:30 h [Cerebellum_Norm_22:30_rep3]

source_name: Cerebellum

value: Cerebellum


title: C57BL/6J mouse, IH, heart, replicate 1, time point 1:30 h [Heart_IH_1:30_rep1]


title: C57BL/6J mouse, normoxia, heart, replicate 1, time point 7:30 h [Heart_Norm_7:30_rep1]


title: C57BL/6J mouse, IH, heart, replicate 2, time point 4:30 h [Heart_IH_4:30_rep2]


title: C57BL/6J mouse, IH, cerebellum, replicate 1, time point 22:30 h [Cerebellum_IH_22:30_rep1]


title: C57BL/6J mouse, IH, cerebellum, replicate 2, time point 22:30 h [Cerebellum_IH_22:30_rep2]


title: C57BL/6J mouse, normoxia, cerebellum, replicate 2, time point 22:30 h [Cerebellum_Norm_22:30_rep2]


title: C57BL/6J mouse, IH, cerebellum, replicate 3, time point 22:30 h [Cerebellum_IH_22:30_rep3]


title: C57BL/6J mouse, IH, cerebellum, replicate 1, time point 19:30 h [Cerebellum_IH_19:30_rep1]


title: C57BL/6J mouse, IH, cerebellum, replicate 3, time point 19:30 h [Cerebellum_IH_19:30_rep3]


title: C57BL/6J mouse, IH, cerebellum, replicate 2, time point 19:30 h [Cerebellum_IH_19:30_rep2]


title: C57BL/6J mouse, normoxia, cerebellum, replicate 3, time point 19:30 h [Cerebellum_Norm_19:30_rep3]


title: C57BL/6J mouse, normoxia, cerebellum, replicate 1, time point 19:30 h [Cerebellum_Norm_19:30_rep1]


title: C57BL/6J mouse, normoxia, cerebellum, replicate 3, time point 16:30 h [Cerebellum_Norm_16:30_rep3]


title: C57BL/6J mouse, IH, cerebellum, replicate 2, time point 16:30 h [Cerebellum_IH_16:30_rep2]


title: C57BL/6J mouse, IH, cerebellum, replicate 3, time point 16:30 h [Cerebellum_IH_16:30_rep3]


title: C57BL/6J mouse, IH, kidney, replicate 3, time point 1:30 h [Kidney_IH_1:30_rep3]


title: C57BL/6J mouse, normoxia, cerebellum, replicate 2, time point 19:30 h [Cerebellum_Norm_19:30_rep2]


title: C57BL/6J mouse, IH, cerebellum, replicate 1, time point 16:30 h [Cerebellum_IH_16:30_rep1]


title: C57BL/6J mouse, IH, cerebellum, replicate 3, time point 13:30 h [Cerebellum_IH_13:30_rep3]


title: C57BL/6J mouse, IH, heart, replicate 3, time point 1:30 h [Heart_IH_1:30_rep3]


title: C57BL/6J mouse, normoxia, cerebellum, replicate 2, time point 13:30 h [Cerebellum_Norm_13:30_rep2]


title: C57BL/6J mouse, normoxia, cerebellum, replicate 1, time point 16:30 h [Cerebellum_Norm_16:30_rep1]


title: C57BL/6J mouse, normoxia, cerebellum, replicate 3, time point 13:30 h [Cerebellum_Norm_13:30_rep3]


title: C57BL/6J mouse, normoxia, heart, replicate 1, time point 1:30 h [Heart_Norm_1:30_rep1]


title: C57BL/6J mouse, normoxia, cerebellum, replicate 1, time point 13:30 h [Cerebellum_Norm_13:30_rep1]


title: C57BL/6J mouse, IH, cerebellum, replicate 2, time point 13:30 h [Cerebellum_IH_13:30_rep2]


title: C57BL/6J mouse, normoxia, cerebellum, replicate 3, time point 10:30 h [Cerebellum_Norm_10:30_rep3]


title: C57BL/6J mouse, normoxia, cerebellum, replicate 1, time point 22:30 h [Cerebellum_Norm_22:30_rep1]


title: C57BL/6J mouse, IH, cerebellum, replicate 3, time point 10:30 h [Cerebellum_IH_10:30_rep3]


title: C57BL/6J mouse, normoxia, cerebellum, replicate 1, time point 10:30 h [Cerebellum_Norm_10:30_rep1]


title: C57BL/6J mouse, normoxia, cerebellum, replicate 2, time point 16:30 h [Cerebellum_Norm_16:30_rep2]


title: C57BL/6J mouse, normoxia, cerebellum, replicate 2, time point 7:30 h [Cerebellum_Norm_7:30_rep2]


title: C57BL/6J mouse, normoxia, cerebellum, replicate 1, time point 7:30 h [Cerebellum_Norm_7:30_rep1]


title: C57BL/6J mouse, IH, cerebellum, replicate 3, time point 7:30 h [Cerebellum_IH_7:30_rep3]


title: C57BL/6J mouse, IH, cerebellum, replicate 1, time point 7:30 h [Cerebellum_IH_7:30_rep1]


title: C57BL/6J mouse, IH, cerebellum, replicate 2, time point 4:30 h [Cerebellum_IH_4:30_rep2]


title: C57BL/6J mouse, IH, cerebellum, replicate 3, time point 4:30 h [Cerebellum_IH_4:30_rep3]


title: C57BL/6J mouse, normoxia, cerebellum, replicate 3, time point 1:30 h [Cerebellum_Norm_1:30_rep3]


title: C57BL/6J mouse, normoxia, cerebellum, replicate 2, time point 1:30 h [Cerebellum_Norm_1:30_rep2]


title: C57BL/6J mouse, IH, cerebellum, replicate 3, time point 1:30 h [Cerebellum_IH_1:30_rep3]


title: C57BL/6J mouse, normoxia, cerebellum, replicate 1, time point 1:30 h [Cerebellum_Norm_1:30_rep1]


title: C57BL/6J mouse, IH, cerebellum, replicate 2, time point 10:30 h [Cerebellum_IH_10:30_rep2]


title: C57BL/6J mouse, normoxia, cerebellum, replicate 3, time point 7:30 h [Cerebellum_Norm_7:30_rep3]


title: CTL_2

status: Public on Sep 23 2022

city: Frankfurt am Main

first: Timothy

last: Warwick

state: Hesse

address: Theodor-Stern-Kai 7

department: Institute for Cardiovascular Physiology

country: Germany

institute: Goethe Universität Frankfurt am Main

description: HUVEC treated with control LNA gapmers, replicate 2

data_processing:
FastQC
Read trimming (Reaper 13-100)
Alignment (STAR 2.4.0, “--outFilterMismatchNoverLmax 0.1” )
Quantification (featureCounts, 1.4.5-p1)
Differential analysis (DESeq2 1.62)
Assembly: hg19
Supplementary files format and content: 220318_Oo_PCAT19_RNAseq_NormCounts_GEO.xlsx, normalised counts per gene per sample

organism: Homo sapiens

source_name: HUVEC

growth_protocol: Human umbilical vein endothelial cells (HUVEC) were cultured on gelatine-coated plates in endothelial growth medium (EGM) containing 12% fetal calf serum (FCS, S0113, Biochrom, Germany), penicillin (50 U/mL) and streptomycin (50 µg/mL) (15140-122, Gibco/ Lifetechnologies, USA) in a humidified atmosphere of 5% CO2 at 37°C. HUVEC that had been frozen and stored at passage two, were seeded for passage three and used for experiments without any further passaging. The seeding density was dependent on the experiment to be performed. Standard seeding conditions (50,000 cells/cm2) were used for experiments such as protein or chromatin immunoprecipitation. Experiments involving RNA interference required a cell seeding density of 25,000 cells/cm2 for next day transfection. Cell cycle-related experiments also required a low seed density to ensure continued cycling. For each experiment, at least three different batches of HUVEC from passage 3 were used.

extract_protocol:
Total RNA was isolated and purified from HUVEC using the RNA Mini Kit according to the manufacturer’s protocol (Bio&SELL). Purified RNA was reverse transcribed with SuperScript III Reverse Transcriptase (Thermo Fisher) and oligo(dT)23 together with random hexamer primers (Sigma).
RNA-sequencing was performed as described previously (Leisegang et al., 2019). Briefly, Total RNA and library integrity were verified and 500 ng of total RNA used as input for SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Clontech).
Sequencing was performed on the NextSeq500 instrument (Illumina) using v2 chemistry, resulting in an average of 30M reads per library with 1x75bp single end setup. RNA-IP input samples were sequenced at 150M reads per library

treatment_protocol: Cells were seeded at a density of 25,000 cells/cm2 one day before transfection with LNA GapmeRs (Qiagen). Cells were transfected with LNAs using the RNAiMAX transfection reagent according to the manufacturer’s protocol (Qiagen). A final LNA concentration of 30 nM was used for 48-72h before stopping cells with either RNA lysis buffer or protein lysis buffer. In some cases, cells were re-seeded for further experiments. LNA GapmeRs were designed with the Qiagen/Exiqon LNA probe designer and had the following sequences: PCAT19 5’- AATTCGGCTCTTACAA -3’ and as a negative Control 5’-AACACGTCTATACGC-3’.

tag: cell type

value: HUVEC

tag: knockdown

value: CTL

tag: replicate


title: PCAT19_1

description: HUVEC treated with PCAT19-targeting LNA gapmers, replicate 1


title: mouse-epidermis-frozen-F

city: Copenhagen

first: Olivia

last: Luxford Meyer

address: Frederik V's Vej 11

department: Department of Forensic Medicine

country: Denmark

institute: University of Copenhagen

library_source: genomic

data_processing:
Base-calling was performed by analysing the raw sequencing output, bcl-files, with bcl2fastq2 ver. 2.20 (Illumina). Adapter trimming was performed with AdapterRemoval ver. 2.3.2 (parameters: --qualitybase 33, --minquality 30, --minlength 30, --trimqualities, and --trimns). Since an adaptase tail was added during the library preparation, 15 bases from the end of Read1 (3’ end) and 15 bases from the start of Read2 (5' end) were removed using the --trim3p and --trim5p commands. Reads were aligned to the mm10 (GRCm38.p6) genome, and duplicates were removed using Bismark version 0.22.4 with default parameters (Krueger and Andrews, 2011). Methylation was called using the bismark_methylation_extractor with default parameters. All CpG sites with ≥ 1 read were called.
Assembly: mm10
Supplementary files format and content: coverge output file from bismark_methylation_extractor (default parameters)

molecule: genomic DNA

source_name: epidermis

extract_protocol:
Geonomic DNA extracted with DNeasy Blood and Tissue kit from Qiagen
100 ng genomic DNA was fragmented to 350 bp with the Covaris S220 Focused-ultrasonicator (Covaris). DNA was bisulfite treated using the EZ DNA Methylation-Gold™ Kit (Zymo Research). Whole genome bisulfite sequencing (WGBS) libraries were prepared using the Accel-NGS® Methyl-Seq DNA Library Kit (Swift Biosciences) following the recommended instructions and five PCR cycles for the final library amplification.

treatment_protocol: Mice were euthanized in CO2-atmosphere. The skin of the back of each mice was removed and placed in sodium chloride solution (58.44 g/L) at room temperature for 24 hours. Afterwards, the epidermis was gently removed from dermis using a tweezer.

value: epidermis

value: C3.Cg-HRhr/Tac hairless (Taconic)

tag: Sex

value: Female

tag: group

value: fresh-frozen


title: mouse-epidermis-frozen-D

description:
T2-8_frozen
Mouse was UV treated with three standard erythema doses UVR 3x pr. week for eight weeks

value: UV 8 weeks


title: mouse-epidermis-frozen-E


title: C57BL/6J mouse, normoxia, cerebellum, replicate 2, time point 10:30 h [Cerebellum_Norm_10:30_rep2]


title: PCAT19_3

description: HUVEC treated with PCAT19-targeting LNA gapmers, replicate 3


title: C57BL/6J mouse, IH, cerebellum, replicate 1, time point 10:30 h [Cerebellum_IH_10:30_rep1]


title: CTL_3

description: HUVEC treated with control LNA gapmers, replicate 3


title: mouse-epidermis-fresh-E

value: fresh


title: C57BL/6J mouse, IH, cerebellum, replicate 2, time point 7:30 h [Cerebellum_IH_7:30_rep2]

value: Wild type


title: mouse-epidermis-fresh-D

description:
T2-8_fresh
Mouse was UV treated with three standard erythema doses UVR 3x pr. week for eight weeks


title: C57BL/6J mouse, normoxia, cerebellum, replicate 3, time point 4:30 h [Cerebellum_Norm_4:30_rep3]


title: C57BL/6J mouse, IH, cerebellum, replicate 1, time point 13:30 h [Cerebellum_IH_13:30_rep1]

value: Intermittent hypoxia


title: C57BL/6J mouse, IH, cerebellum, replicate 1, time point 4:30 h [Cerebellum_IH_4:30_rep1]


title: mouse-epidermis-frozen-A

description:
T1_frozen
Mouse was UV treated with three standard erythema doses UVR 3x pr. week for four weeks

value: UV 4 weeks


title: CTL_1

description: HUVEC treated with control LNA gapmers, replicate 1


title: mouse-epidermis-frozen-B

description:
T2_frozen
Mouse was UV treated with three standard erythema doses UVR 3x pr. week for four weeks


title: C57BL/6J mouse, IH, cerebellum, replicate 1, time point 1:30 h [Cerebellum_IH_1:30_rep1]


title: mouse-epidermis-fresh-C

description:
T1-8_fresh
Mouse was UV treated with three standard erythema doses UVR 3x pr. week for eight weeks


title: mouse-epidermis-frozen-C

description:
T1-8_frozen
Mouse was UV treated with three standard erythema doses UVR 3x pr. week for eight weeks


title: C57BL/6J mouse, IH, cerebellum, replicate 2, time point 1:30 h [Cerebellum_IH_1:30_rep2]


title: C57BL/6J mouse, normoxia, cerebellum, replicate 1, time point 4:30 h [Cerebellum_Norm_4:30_rep1]

value: Normoxia


title: C57BL/6J mouse, normoxia, cerebellum, replicate 2, time point 4:30 h [Cerebellum_Norm_4:30_rep2]


title: mouse-epidermis-fresh-F


title: mouse-epidermis-fresh-B

description:
T2_fresh
Mouse was UV treated with three standard erythema doses UVR 3x pr. week for four weeks


title: PCAT19_2

description: HUVEC treated with PCAT19-targeting LNA gapmers, replicate 2


title: mouse-epidermis-fresh-A

description:
T1_fresh
Mouse was UV treated with three standard erythema doses UVR 3x pr. week for four weeks


title: MM150405

status: Public on Sep 19 2022

city: Geneva

first: Phil

middle: Fang

last: Cheng

address: Rue Gabrielle-Perret-Gentil 4

department: Oncology

country: Switzerland

institute: Hopitaux universitaires de Geneve

data_processing:
bcl2Fastq v2.19 software for demultiplexing + basecalling
reads trimmed with skewer v0.2.1
reads mapped with STAR v2.6.0a with default options
counts with STAR --quantmode GeneCounts
differential expression with limma/voom
Assembly: GRCh38, gencode v22
Supplementary files format and content: tab-delimited files include stranded alignment for each sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and sample

growth_protocol: Melanoma cells were grown in RPMI 1640 with 10% FCS, 5 mM glutamine, and 1 mM sodium pyruvate.

extract_protocol:
RNA was extracted with QIAGEN RNeasy mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: melanoma cell culture

value: Before


title: MEFs Casp8 and Mlkl knock-out with ectopic-reexpression of Casp8 rep 2

city: Memphis

first: Douglas

middle: R

last: Green

state: United States

address: 262 Danny Thomas Pl

department: Immunology

institute: St Jude Children's Research Hospital

data_processing:
The reads were trimmed with Trim Galore (version 0.5.0) with default parameters.
Then reads were aligned to the reference mouse mm10 assembly plus ERCC spike-in sequences using STAR (version 2.7.5a).
The resulting alignments, recorded in BAM file, were sorted, indexed, and marked for duplicates with Picard MarkDuplicates function (version 2.19.0).
Transcript quantification was calculated using RSEM.
Murine endogenous retrovirus (mERV) expression was assessed using HOMER (v4.11) by defining mERVs using the annotation provided by the Genome-based Endogenous Viral Element Database (gEVE) for GRCm38 (downloaded in July 2022). The gEVE database identifies specific chromosomal regions as expressing a specific ORF; these chromosomal coordinates were directly used in HOMER analyzeRepeats.pl to count the reads mapped to the regions that encode endogenous retroviruses. Reads were aligned to mouse genome as described above. Reads were filtered out if they failed platform quality checks, or they were duplicates or unmapped or not primary alignment, or their mates were unmapped (samtools view -F 1804). HOMER analyzeRepeats.pl was run with parameters mm10, -noadj, and differential expression was calculated with DESeq2. The mERV regions were pre-filtered if they had no read in any sample. Differentially expressed mERV were defined as loci that had a False Discovery Rate (FDR) < 0.05 and absolute fold change of 2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count values for each sample.
Supplementary files format and content: mERV_count.tab: Tab-delimited text file of read count for murine endogenous retroviruses (mERVs). The columns are gEVE ID of mERV, location of mERV on the genome (mm10) (including chromosome, start and end position and strand), length, and samples from 1 to 12.

source_name: Mouse Embryonic Fibroblasts

growth_protocol: All experiments presented here were performed on Immortalized  Fadd-/-Mlkl-/- or Casp8-/-Mlkl-/- MEFs. Briefly, immortalization of primary MEF were performed by infection with SV40 large T antigen. Cells were maintained in complete DMEM mediain complete DMEM media containing 10% FBS, L-glutamine, pen/strep, 55 uM β-mercaptoethanol, 1 mM sodium pyruvate and non-essential amino acids (GIBCO).

extract_protocol:
Total RNA was isolated from three independent cell cultures of Fadd-/-Mlkl-/- or Casp8-/-Mlkl-/- MEF reconstituted with empty vector (CTRL), FADD or Caspase-8 (Casp8), respectively. Briefly, RNA purification was performed by using RNeasy Kit (QIAGEN) according manufacturer instructions. RNA was quantified using the Quant-iT RiboGreen RNA assay (ThermoFisher) and quality checked by the 2100 Bioanalyzer RNA 6000 Nano assay (Agilent) or 4200 TapeStation High Sensitivity RNA ScreenTape assay (Agilent) prior to library generation.
Libraries were prepared from total RNA with the TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer’s instructions (Illumina, PN 20020599). Libraries were analyzed for insert size distribution using the 2100 BioAnalyzer High Sensitivity kit (Agilent), 4200 TapeStation D1000 ScreenTape assay (Agilent), or 5300 Fragment Analyzer NGS fragment kit (Agilent). Libraries were quantified using the Quant-iT PicoGreen ds DNA assay (ThermoFisher) or by low pass sequencing with a MiSeq nano kit (Illumina). Paired-end 100 cycle sequencing was performed on a NovaSeq 6000 (Illumina). RNAseq data were processed using an automated pipeline maintained by St. Jude Children's Research Hospital. Briefly, reads were trimmed using Cutadapt within the Trim Galore wrapper and aligned to the mm10 genome with the M22 annotation (GENCODE) using STAR, and gene counts were subsequently calculated using RSEM. Gene counts were subsequently compared across conditions using the edgeR and limma and data were visualized using Glimma.

treatment_protocol: Cells under untreated conditions were harvested 24h after plating

value: Mouse Embryonic Fibroblasts

value: Ectopic re-expression of Casp8

value: Casp8 -/-, Mlkl -/-


title: MEFs Casp8 and Mlkl knock-out rep 3


title: MEFs Casp8 and Mlkl knock-out with ectopic-reexpression of Casp8 rep 1


title: MEFs Casp8 and Mlkl knock-out with ectopic-reexpression of Casp8 rep 3


title: MEFs Casp8 and Mlkl knock-out rep 1


title: MEFs Fadd and Mlkl knock-out with ectopic-reexpression of Fadd rep 3

value: Ectopic re-expression of Fadd

value: Fadd -/-, Mlkl -/-


title: MEFs Fadd and Mlkl knock-out with ectopic-reexpression of Fadd rep 2


title: BPH, scRNAseq

status: Public on Sep 09 2022

city: Shanghai

first: Sun

last: Jianming

address: PuDong

country: China

institute: Shanghai Seventh People's Hospital

description: BD-Rhapsody

data_processing:
We applied BD Rhapsody Analysis pipeline (Version:1.8 https://hub.docker.com/r/bdgenomics/rhapsody) with default parameter to align reads and generate feature-barcode matrices. The reads were mapped to mouse genome (GENCODE version M19) utilizing STAR mapping with customized parameter from BD Rhapsody standard pipeline.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Prostate tissue

extract_protocol:
Briefly, samples were first washed with phosphate-buffered saline (PBS), minced into small pieces (approximately 1mm3) on ice and enzymatically digested with 1 mg/mL collagenase I (Gibco)，1 mg/mL collagenase II，60U/mL Hyaluronidase (Sigma), 10U/mL Liberase (Roche) and 0.02mg/mL DNase I (Roche) for 90 min at 37°C, with agitation. After digestion, samples were sieved through a 100µm cell strainer, and centrifuged at 300g for 5 min. After the supernatant was removed, the pelleted cells were suspended in red blood cell lysis buffer (Gibco) to lyse red blood cells. After washing with PBS containing 0.04% BSA, the cell pellets were re-suspended in PBS containing 0.04% BSA and re-filtered through a 40μm cell strainer. Dissociated single cells were then stained for viability assessment using Calcein-AM (BD Biosciences) and Draq7 (BD Biosciences).
BD Rhapsody system was used to capture the transcriptomic information of the single cells. Single-cell capture was achieved by random distribution of a single-cell suspension across >200,000 microwells through a limited dilution approach. Beads with oligonucleotide barcodes were added to saturation so that a bead was paired with a cell in a microwell. The cells were lysed in the microwell to hybridize mRNA molecules to barcoded capture oligos on the beads. Beads were collected into a single tube for reverse transcription and ExoI digestion. Upon cDNA synthesis, each cDNA molecule was tagged on the 5′ end (that is, the 3′ end of a mRNA transcript) with a unique molecular identifier (UMI) and cell barcode indicating its cell of origin. Whole transcriptome libraries were prepared using the BD Rhapsody single-cell whole-transcriptome amplification (WTA) workflow including random priming and extension (RPE), RPE amplification PCR and WTA index PCR. The libraries were quantified using a High Sensitivity D1000 ScreenTape (Agilent）and High Sensitivity D1000 Reagents (Agilent）on a 4150 TapeStation System (Agilent) and the Qubit High Sensitivity DNA assay (Thermo Fisher Scientific). Sequencing was performed by illumina sequencer (Illumina, San Diego, CA) on a 150 bp paired-end run.

value: Suspension cell

value: Prostate tissue

value: ICR

tag: age

value: 5 weeks old


title: Patient 13

status: Public on Sep 01 2022

city: Houston

first: Daniel

middle: Bernard

last: Zamler

state: TX

department: Genomic Medicine

institute: M.D. Anderson Cancer Center

data_processing:
FastQ preparation:
mkfastq (cellranger)
https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/mkfastq
Count Matrix Generation:
count (cellranger)
https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/count
Aggregation of samples:
aggr (cellranger)
https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/aggregate
Visualization and comparisons:
Adapted Seurat Pipeline (Zamler)
Aggregate All.R
Data Normalization:
scTransform (Satija)
https://satijalab.org/seurat/v3.1/sctransform_vignette.html
Assembly: mm10-3.0.0 (mouse); GRCh38-3.0.0 (human)
Supplementary files format and content: Zipped Matrices - Single Cell Gene Counts

source_name: Mixed Immune Cells

extract_protocol:
tissue collection: Tumor samples were mechanically minced before enzymatic digestion, cells were then spun down at 800g with the brake off in a 0.9N sucrose solution to remove myelin. CD45+ FACs selection was performed before entering the 10x protocol
https://assets.ctfassets.net/an68im79xiti/4tjk4KvXzTWgTs8f3tvUjq/2259891d68c53693e753e1b45e42de2d/CG000183_ChromiumSingleCell3__v3_UG_Rev_C.pdf

tag: term source ref

value: EFO

tag: term accession number

tag: developmental stage

value: adult

value: male

value: brain

tag: individual

value: Patient 13

value: leukocyte

tag: disease

value: astrocytoma

tag: sampling site

value: frontal

tag: tumor grading

value: IDH1 protein status (IHC):POSITIVE for p.R132H expression ATRX protein status (IHC):LOSS of nuclear expression p53 protein status (IHC):POSITIVE for nuclear expression (strong, diffuse; 90% of glioma cell population)


title: Patient 14

value: female

value: Patient 14

tag: genotype

value: IDH1 protein status (IHC):POSITIVE for p.R132H expression in glioma cells ATRX protein status (IHC):LOSS of nuclear expression in glioma cells p53 protein status (IHC): Nuclear staining in a major subset of glioma cells (string, diffuse; 80%)


title: MEFs Fadd and Mlkl knock-out rep 1

value: Mouse Embryonic Fibroblasts

value: Fadd -/-, Mlkl -/-


title: MEFs Fadd and Mlkl knock-out rep 2


title: MEFs Fadd and Mlkl knock-out rep 3


title: Patient 11

value: Patient 11

value: anaplastic oligodendroglioma

value: IDH1 protein status (IHC):POSITIVE for p.R132H expression ATRX protein status (IHC):RETAINED wildtype nuclear expression p53 protein status (IHC): Nuclear staining in a minor subset (30%) 1p/19q status (FISH):POSITIVE for codeletion


title: 54-IT

status: Public on Aug 29 2022

city: Taipei

first: Chih-Hung

last: Chung

address: No.155, Sec.2, Linong Street, Taipei, 112 Taiwan (ROC)

department: Institute of Clinical Medicine

country: Taiwan

institute: National Yang Ming Chiao Tung University

data_processing:
Reads were trimmed and clipped for quality control in AfterQC v0.9.7.
Read quality was checked for each sample using FastQC v0.11.7.
High-quality reads were then imported into STAR v2.6.1a for alignment into BAM files.
BAM files were imported into the RSEM v1.3.1 for expected counts, FPKM and TPM estimation.
Expected counts table was extracted from each RSEM output .gene.results file.
Expected counts table was imported into the DESeq2 v1.26.0 for rlog transformation.
Genome_build: hg38, GRCh38.94
Supplementary_files_format_and_content: Tab-delimited text file for expected counts of each sample.  Tab-delimited text file for FPKM of each sample.  Tab-delimited text file for TPM of each sample.  Tab-delimited text file for rlog of each sample.

source_name: Primary Tumor (Inner site)

extract_protocol:
The samples were frozen in the RNALater buffer and stored at -80oC. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction
Sample Prep. Kit : QIAseq FastSelect RNA Removal Kit_Human Cyto & Mito rRNA + Illumina TruSeq Stranded mRNA Sample Prep Kit + limited cycles of PCR by KAPA HiFi Polymerase

treatment_protocol: We collected matched pairs of primary tumor (invasive front region 0.3-0.5cm and inner-tumor region) , lymph node metastatic tumor region and adjacent normal tissue from head and neck squamous cell carcinoma patients at the Taipei Veterans General Hospital (TVGH), according to the current TVGH-IACUC regulations. IRB approval number : 2017-05-013AC.

tag: disease state

value: HNSCC Patient

value: Primary Tumor (Inner site)

tag: unique patient number (upn)


title: 47-IT

tag: cell type


title: Patient 15

value: EFO

value: adult

tag: tissue

value: Patient 15

value: diffuse astrocytoma

value: frontoparietal

value: IDH1 protein status (IHC):POSITIVE for p.R132H expression in glioma cells ATRX protein status (IHC):RETAINED wildtype  nuclear expression in glioma cells p53 protein status (IHC):Nuclear staining in a minor subset (5%) of glioma cells    1p/19q status (FISH):NEGATIVE for codeletion (positive for loss of 1p and monosomy 19)


title: 44-Neck

source_name: Lymph node metastatic tumor

value: Lymph node metastatic tumor


title: 23-IT


title: 59-IT


title: CON, scRNAseq

description: BD-Rhapsody

value: Suspension cell

value: Prostate tissue

tag: strain

value: ICR

value: 5 weeks old


title: MEFs Casp8 and Mlkl knock-out rep 2

value: Mouse Embryonic Fibroblasts

value: Casp8 -/-, Mlkl -/-


title: 22-IT


title: JM8.N4 mESC, F1 RAD21-mAID IAA 3hr, RCMC, rep1

status: Public on Jul 12 2022

city: Cambridge

first: Viraat

middle: Y

last: Goel

address: Building 56 Room 787B, 32 Vassar Street

department: Biological Engineering

institute: Massachusetts Institute of Technology

data_processing:
Basecalls were performed using bcl2fastq v2.20.0.422 for NovaSeq output.
Paired end reads were aligned to the UCSC mm39 genome using bowtie2 v2.3.5.1 with --local --reorder --very-sensitive-local. Aligned paired end reads were then parsed with pairtools (v0.3.0) parse with --add-columns mapq --walks-policy mask --min-mapq 2.
Parsed reads were filtered for PCR duplicates and unmapped/mutiply mapping reads with pairtools dedup with --max-mismatch 1. Remaining reads were indexed (pairix v0.3.7) and filtered to retain only those reads where both read mates lie in a locus of interest. These filtered reads were subsequently converted to .cool format using cooler (v0.8.11) cload pairs, and then to .mcool format with cooler zoomify, including the --balance option.
Assembly: mm39
Supplementary files format and content: mcool file contains all valid Micro-C pairs stored in HDF5 format with multiple resolutions
Library strategy: Micro-C

growth_protocol: Mouse embryonic stem cells (JM8.N4 mESCs) were cultured on plates coated with 0.1% gelatin solution (Sigma-Aldrich) under feeder-free conditions in medium consisting of KnockOut DMEM (Thermofisher) with 15% FBS (HyClone, SH30396.03, Lot. No. AE28209315) and 1000U/mL LIF (home-made), 1 mM MEM Non-Essential Amino Acid Solution (Thermofisher), 2 mM GlutaMAX (Thermofisher), 100 μg/ml Penicillin-Streptomycin (Thermofisher), and 0.1 mM 2-mercapoethanol (Sigma) supplemented with 2i, 10 μM MEK inhibitor (Tocris) and 3 μM GSK inhibitor (Sigma). mESCs were fed daily by replacing half the medium and passaged every two days with 0.05% Trypsin-EDTA (Thermo Fisher Scientific). 1 day prior to harvesting, cells were swapped to medium as described above without 2i.

extract_protocol:
Cells were fixed with 3 mM DSG for 35 minutes, followed by an additional 10 minutes with 1% formaldehyde. Following quenching, nuclei were prepared from fixed cells. Chromatin was digested in situ using MNase, DNA 3' ends were chewed back and biotinylated, and then free DNA ends were proximity ligated. Unligated ends were digested, and followed by reverse crosslinking of the chromatin and Protease K digestion. DNA was purified by phenol chloroform extraction and DNA Clean and Concentrator kit (Zymo), and then size selected for dinucleosomal fragments on an agarose gel. Following end polishing of DNA fragments, a streptavidin pulldown was used to enrich for ligated dinucleosomal fragments.
Size selected DNA fragments bound to streptavidin coated beads were used to prepare Micro-C libraries using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB), using NEBNext Multiplex Oligos for Illumina for indexing samples. Libraries were amplified with 7-8 PCR cycles on the thermocycler using KAPA HiFi HotStart ReadyMix (Roche) and purified using AMPure XP beads (Beckman Coulter). Purified libraries were quantified using qPCR and pooled in a 1:1 ratio to a total of 2-4 µg of DNA. Following the Twist Standard Hybridization Target Enrichment Protocol (Twist Biosciences) with the inclusion of Mouse Cot-1 DNA (Invitrogen) blocker solution, this library pool was hybridized to custom probe panels for loci of interest and bound to streptavidin coated beads. Bead-bound fragments were pulled down, amplified with 6 PCR cycles on the thermocycler using Equinox Library Amp Mix (Twist), and purified using Twist Binding and Purification Beads (Twist). Following qPCR quantification, the target enriched library pool was submitted for sequencing.

treatment_protocol: RAD21 degradation was induced by addition of IAA at 500 µM to the media of confluent cells for 3 hours.

value: Mouse embryonic stem cell

value: Homozygous RAD21-mAID-BFP-V5

tag: treatment

value: IAA

tag: time

value: 3 hours


title: JM8.N4 mESC, F1 RAD21-mAID DMSO, RCMC, rep1

tag: cell line

value: DMSO


title: JM8.N4 mESC, Triptolide 45min, RCMC, rep1

treatment_protocol: Transcription inhibition was performed by adding triptolide to the media of confluent cells at 1 µM for 45 minutes.

value: WT

value: Triptolide

value: 45 minutes


title: MEFs Fadd and Mlkl knock-out with ectopic-reexpression of Fadd rep 1

value: Ectopic re-expression of Fadd

value: Fadd -/-, Mlkl -/-


title: JM8.N4 mESC, WT, RCMC, rep1


title: Patient 12

value: EFO

value: adult

tag: Sex

value: male

value: brain

value: Patient 12

value: leukocyte

value: oligodendroglioma

value: frontotemporal

value: IDH1 protein status (IHC):POSITIVE for IDH1 p.R132H expression ATRX protein status (IHC):RETAINED nuclear expression p53 protein status (IHC):NEGATIVE 1p/19q status (FISH):POSITIVE for codeletion


title: Polysome mRNA fraction at 30 mins recovery rep 3

status: Public on Jun 19 2022

city: Philadelphia

first: Diep

last: Ganguly

state: PA

address: 433 S University Ave

department: Department of Biology

institute: University of Pennsylvania

data_processing:
mRNA-sequencing: Raw read quality was first diagnosed using FastQC (v0.11.7). Trim Galore! (v0.4.4) was used for adapter and low-quality read trimming with PHRED score < 20 (-q 20). Kallisto index (-k 21) was used to build the an index from transcripts defined in the cDNA reference annotation (Arabidopsis_thaliana.TAIR10.cdna.all.fa). Transcript abundance was quantified as TPM using kallisto quant with flags --rf-stranded --bias --single -b 10 -l 300 -s 100 (Bray et al 2016).
Polysome profiling: Quality control of raw reads was carried out using FastQC, with adapter trimming performed using scythe (-p 0.1) and quality trimming performed using sickle (-q 20 -l 20). Reads were aligned to the TAIR10 Arabidopsis genome using subjunc to report a single unambiguous mapping location per read (Liao et al. 2013). Sorting, indexing, and compression was carried out with samtools (Li et al. 2009) and read counts per loci were calculated using featureCounts [-s 2 for reverse stranded libraries, (Liao et al. 2014)]. Reads mapping to rRNA were removed and both normalised read counts of reads per kilobase per million reads (RPKM) and differential gene expression analysis were calculated using edgeR (Robinson et al. 2010). Relative polysomal loading (RPL) was calculated by dividing the RPKM of polysome-bound RNA by that of total RNA on a per replicate basis.
Assembly: TAIR10
Supplementary files format and content: h5: HDF5 file containing run info, abundance esimates (TPM), bootstrap estimates, and transcript length, .counts: gene-level raw counts.

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana 30 mins recovery

growth_protocol: Arabidopsis seeds were sown onto moist soil (Seed Raising and Cutting Mix, Martins, NSW, Australia) supplemented with 1 g/L dry volume of soil Osmocote Exact Mini slow release fertilizer (Scotts, NSW, Australia) and 1 L of 0.3 % (v/v) AzaMax (OCP, NSW, Australia). Seeds were covered with a plastic hood and stratified at 4 °C in the dark for at least 72 hours to break dormancy and coordinate germination. Stratified seeds were transferred to a temperature controlled Conviron S10H growth chamber (Conviron, Winnipeg, MB, Canada), fitted with a mixture of 250 W metal halide lamps (Venture Lighting, MH 250W/U) and high pressure sodium lamps (Phillips, SON‐T 250 W E E40 SL/12), for cultivation under a 12-hour photoperiod (08:00-20:00) of 80-100 μ mol photons m-2 s -1, 22.5/20.5 °C day/night temperatures, and 57/55 % day/night relative humidity.

extract_protocol:
mRNA-sequencing: Frozen tissue was ground into a fine powder using a ⅛” steel ball bearing with 1 min shaking at 25 Hz in a TissueLyser II (Qiagen). Total RNA was extracted from finely ground tissue using TRI reagent at a ratio of 1 mL solution per 100 mg ground tissue (Sigma-Aldrich, #T9424-200ML). Residual phenol was removed from the crude extract through two chloroform extractions at a ratio of 1:5 v/v, followed by precipitation using isopropanol at 1:1 v/v. Precipitated RNA was washed twice with 70% ethanol and resuspended in a 1 mM sodium citrate buffer (pH 5.4). RNA quantification was performed through spectrophotometric analysis at 260 nm using the Nanodrop ND-1000 Spectrophotometer and RNA quality was assessed using 1% agarose gel electrophoresis or on the LabChip GX Touch (PerkinElmer).
polysome profiling: Polysome-associated mRNA sequencing was performed using an adapted protocol (Lecampion et al. 2016). Briefly, 250 mg of frozen and ground plant tissue was dissolved in 1 mL of polysome extraction buffer [160 mM Tris-Cl (pH 7.6), 80 mM KCl, 5 mM MgCl2, 5.36 mM EGTA (pH 8), 0.5% IGEPAL CA-630, 40 U/mL RNasin Plus RNase inhibitor (Promega), 150 µg/mL cycloheximide, and 150 µg/mL chloramphenicol] and incubated on ice for 10 minutes. Samples were repeatedly centrifuged at 16,000 rcf for 5 minutes at 4°C until the supernatant was clear. Samples were loaded onto sucrose gradients, consisting of layers of 50% (1.68 mL), 35% (3.32 mL), 20% (3.32 mL) and 20% (1.68 mL), with the two 20% layers added separately (Lecampion et al. 2016). The buffer used in the gradients consisted of 400 mM Tris-Cl (pH 8.4), 200 mM KCl, 100 mM MgCl2, 10.12 µg/mL cycloheximide and 10.12 µg/mL chloramphenicol. Gradients were centrifuged at 41,000 rpm with an SW41Ti rotor for 2 hours at 4°C. Each gradient was passed through a spectrophotometer from highest to lowest density and absorbance at 260 nm recorded, with 1 mL fractions collected. Fractions were pooled into monosomal and polysomal sets and extracted using 5:1 acid phenol:chloroform. Briefy, an equal volume of the phenol:chloroform mix was added to each fraction, before centrifugation at 16,000 rcf for 10 minutes. The aqueous layer was extracted a second time using a one-fifth volume of chloroform, before the RNA was precipitated using an equal volume of isopropanol in addition to sodium acetate (pH 5.2) to a final concentration of 300 mM. The precipitated RNA was washed twice with 70% ethanol and resuspended in a 1 mM sodium citrate (pH 5.4) solution. Total RNA was extracted from finely ground tissue (as above) using TRI reagent at a ratio of 1 mL solution per 100 mg ground tissue (Sigma-Aldrich, #T9424-200ML). Residual phenol was removed from the crude extract through two chloroform extractions at a ratio of 1:5 v/v, followed by precipitation using isopropanol at 1:1 v/v. Precipitated RNA was washed twice with 70% ethanol and resuspended in a 1 mM sodium citrate buffer (pH 5.4). RNA quantification was performed through spectrophotometric analysis at 260 nm using the Nanodrop ND-1000 Spectrophotometer and RNA quality was assessed using 1% agarose gel electrophoresis or on the LabChip GX Touch (PerkinElmer).
PolyA-enriched RNA-sequencing libraries were constructed using the Illumina TruSeq Stranded mRNA kit as per the manufacterer's instruction, except reaction volumes were scaled-down by 1/3.

treatment_protocol:
Cordycepin infiltration: The transcriptional inhibitor, cordycepin (3'-deoxyadenosine, Sigma-Aldrich), was syringe-infiltrated on the abaxial side of fully-expanded leaves (true leaves 4-6) of 21-day old plants. Individual leaves were infiltrated with 0.1 mL of incubation buffer [1 mM PIPES (pH 6.25), 1 mM sodium citrate, 1 mM KCl, 15 mM sucrose (Seeley et al. 1992)] with 0.6 mM cordycepin, or without (mock), using a 1 mL needleless syringe (Terumo). Excess liquid was removed from the leaf surface and plants were incubated for a minimum of 10 minutes before further treatment and harvesting.
Light-stress was induced by increasing the light intensity to 10× growth irradiance (i.e. 1000 μmol photons m-2 s -1), resulting in a “hot high-light” treatment that effectively induces oxidative stress (Jung et al. 2013). For recovery, plants were returned to pre-stress light conditions.

tag: ecotype

tag: condition

value: 30 mins recovery

value: Recovery

tag: time (min)

tag: molecule subtype

value: Polysome-bound mRNA


title: Polysome mRNA fraction at 60 mins high-light rep 3

source_name: Arabidopsis thaliana 60 mins high-light

value: 60 mins high-light

value: High-light


title: Polysome mRNA fraction at 7.5 mins recovery rep 3

source_name: Arabidopsis thaliana 7.5 mins recovery

value: 7.5 mins recovery


title: Polysome mRNA fraction at 0 mins high-light rep 3

source_name: Arabidopsis thaliana 0 mins high-light

value: 0 mins high-light

value: Unstressed


title: Polysome mRNA fraction at 30 mins high-light rep 3

source_name: Arabidopsis thaliana 30 mins high-light

value: 30 mins high-light


title: Polysome mRNA fraction at 30 mins high-light rep 2


title: Polysome mRNA fraction at 0 mins high-light rep 2


title: Polysome mRNA fraction at 30 mins recovery rep 1


title: Polysome mRNA fraction at 30 mins recovery rep 2


title: Polysome mRNA fraction at 15 mins recovery rep 1

source_name: Arabidopsis thaliana 15 mins recovery

value: 15 mins recovery


title: Polysome mRNA fraction at 60 mins high-light rep 2


title: Polysome mRNA fraction at 7.5 mins recovery rep 1


title: Monosome mRNA fraction at 30 mins recovery rep 3

value: Monosome-bound mRNA


title: Polysome mRNA fraction at 60 mins high-light rep 1


title: Polysome mRNA fraction at 30 mins high-light rep 1


title: Monosome mRNA fraction at 15 mins recovery rep 3


title: Monosome mRNA fraction at 7.5 mins recovery rep 3


title: Monosome mRNA fraction at 60 mins high-light rep 3


title: Monosome mRNA fraction at 30 mins high-light rep 3


title: Polysome mRNA fraction at 15 mins recovery rep 3


title: Monosome mRNA fraction at 0 mins high-light rep 3


title: Monosome mRNA fraction at 15 mins recovery rep 2


title: Monosome mRNA fraction at 30 mins recovery rep 2


title: Monosome mRNA fraction at 7.5 mins recovery rep 2


title: Monosome mRNA fraction at 60 mins high-light rep 2


title: Monosome mRNA fraction at 30 mins high-light rep 2


title: Polysome mRNA fraction at 7.5 mins recovery rep 2


title: Polysome mRNA fraction at 15 mins recovery rep 2


title: Polysome mRNA fraction at 0 mins high-light rep 1


title: Monosome mRNA fraction at 7.5 mins recovery rep 1


title: Monosome mRNA fraction at 30 mins recovery rep 1


title: Monosome mRNA fraction at 60 mins high-light rep 1


title: Monosome mRNA fraction at 0 mins high-light rep 2


title: Monosome mRNA fraction at 15 mins recovery rep 1


title: Monosome mRNA fraction at 30 mins high-light rep 1


title: Monosome mRNA fraction at 0 mins high-light rep 1


title: C57BL/6J mouse, IH, heart, replicate 2, time point 1:30 h [Heart_IH_1:30_rep2]

value: Wild type

value: Intermittent hypoxia

value: Heart


title: Total mRNA fraction at 30 mins recovery rep 3

value: Total mRNA


title: Total mRNA fraction at 7.5 mins recovery rep 3


title: Total mRNA fraction at 30 mins high-light rep 3


title: Total mRNA fraction at 30 mins recovery rep 2


title: Total mRNA fraction at 15 mins recovery rep 3


title: Total mRNA fraction at 15 mins recovery rep 2


title: Total mRNA fraction at 60 mins high-light rep 3


title: Total mRNA fraction at 30 mins recovery rep 1


title: Total mRNA fraction at 0 mins high-light rep 2


title: Total mRNA fraction at 7.5 mins recovery rep 2


title: Total mRNA fraction at 60 mins high-light rep 2


title: Total mRNA fraction at 30 mins high-light rep 2


title: Total mRNA fraction at 7.5 mins recovery rep 1


title: Total mRNA fraction at 30 mins high-light rep 1


title: Total mRNA fraction at 0 mins high-light rep 1


title: Daoy cell line, EED-knockout, rep 2

status: Public on Jun 18 2022

city: Richardson

first: Zhenyu

last: Xuan

address: 800 West Campbell

institute: UT Dallas

data_processing:
The raw reads were processed by Kallisto (ver 0.43.1) to quantify the gene expression levels in TPM and read counts for differential gene expression analysis.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include target_id, length, eff_length, est_counts, tpm

source_name: Daoy

extract_protocol:
Total RNA were expreact with TRIZOL and cleaned with a Qiagen RNeasy Kit.
RNA-seq libraries were prepared using the Illumina RNA-Seq Preparation Kit.

value: Daoy

value: EED-knockout


title: Daoy cell line, wild type, rep 2

value: wild type


title: Daoy cell line, EED-knockout, rep 1


title: mouse medulloblastoma, mutant EED, rep 3

data_processing:
The raw reads were processed by Kallisto (ver 0.43.1) to quantify the gene expression levels in TPM and read counts for differential gene expression analysis.
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text files include target_id, length, eff_length, est_counts, tpm

source_name: medulloblastoma tumor

value: medulloblastoma tumor

value: Eed mutant


title: mouse medulloblastoma, mutant EED, rep 1


title: Daoy cell line, wild type, rep 1


title: mouse medulloblastoma, wildtype EED, rep 1


title: mouse medulloblastoma, wildtype EED, rep 2


title: mouse medulloblastoma, mutant EED, rep 2


title: Total mRNA fraction at 0 mins high-light rep 3


title: 18553X9 BMDC EV 3

status: Public on Jun 13 2022

city: Salt Lake City

first: Ryan

last: O'Connell

state: UT

address: Emma Eccles Jones, Medical Research Building, 15 North Medical Drive East

department: Pathology, Microbiology & Immunology

institute: University of Utah

data_processing:
The mouse GRCm38 genome and gene annotation files were downloaded from Ensembl release 102.
MicroRNAs were downloaded from miRBase v22.
PCR duplicates were removed using a custom Perl script .
Trimmed reads were aligned to the reference database using STAR 2.7.6a  with options for small RNAs
Mapped reads were assigned to miRBase annotations using featureCounts version 1.6.3 with multi-mappers assigned by fractions
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.30.1
Genome_build: mm10
Supplementary_files_format_and_content: FeatureCount output files combined into a tab-delmited raw count matrix

source_name: BMDC culture day 7

growth_protocol: BMDCs differentiated with GMCSF for 7 days in complete RPMI then EV isolation, colon explants incubated 16 hours before EV isolation by differential centrifugation; for colon samples only iodixanol gradient was used and fraction 2 was sequenced

extract_protocol:
RNA was isolated miRNEasy MicroKit
Qiagen QiaSeq miRNA Library Prep

value: Rab27A fl/fl

value: bone marrow dendritic cell EVs


title: Total mRNA fraction at 60 mins high-light rep 1

value: 60 mins high-light

value: High-light


title: 18553X8 BMDC EV 2


title: Total mRNA fraction at 15 mins recovery rep 1

value: Recovery


title: 18553X3 Colon EV 3

source_name: Colon explant

value: colon explant EVs


title: 18553X1 Colon EV 1


title: 18553X2 Colon EV 2


title: 18553X7 BMDC EV 1


title: Cordycepin-infiltrated 30 mins 1000 to 100 uE rep 4

status: Public on Jun 10 2022

data_processing:
Raw read quality was first diagnosed using FastQC (v0.11.7).
Trim Galore! (v0.4.4) was used for adapter and low-quality read trimming with PHRED score < 20 (-q 20).
Kallisto index (-k 21) was used to build the an index from transcripts defined in the cDNA reference annotation (Arabidopsis_thaliana.TAIR10.cdna.all.fa)
Transcript abundance was quantified as TPM using kallisto quant with flags --rf-stranded --bias --single -b 10 -l 300 -s 100 (Bray et al 2016).
Assembly: TAIR10 Ensembl release 51
Supplementary files format and content: h5: HDF5 file containing run info, abundance esimates (TPM), bootstrap estimates, and transcript length

molecule: polyA RNA

source_name: Cordycepin-infiltrated Arabidopsis leaf 30 mins 1000 to 100 uE

extract_protocol:
Frozen tissue was ground into a fine powder using a ⅛” steel ball bearing with 1 min shaking at 25 Hz in a TissueLyser II (Qiagen). Total RNA was extracted from finely ground tissue using TRI reagent at a ratio of 1 mL solution per 100 mg ground tissue (Sigma-Aldrich, #T9424-200ML). Residual phenol was removed from the crude extract through two chloroform extractions at a ratio of 1:5 v/v, followed by precipitation using isopropanol at 1:1 v/v. Precipitated RNA was washed twice with 70% ethanol and resuspended  in a 1 mM sodium citrate buffer (pH 5.4). RNA quantification was performed through spectrophotometric analysis at 260 nm using the Nanodrop ND-1000 Spectrophotometer and RNA quality was assessed using 1% agarose gel electrophoresis or on the LabChip GX Touch (PerkinElmer).
PolyA-enriched RNA-sequencing libraries were constructed using the Illumina TruSeq Stranded mRNA kit as per the manufacterer's instruction, except reaction volumes were scaled-down by 1/3.

treatment_protocol: The transcriptional inhibitor, cordycepin (3'-deoxyadenosine, Sigma-Aldrich), was syringe-infiltrated on the abaxial side of fully-expanded leaves (true leaves 4-6) of 21-day old plants. Individual leaves were infiltrated with 0.1 mL of incubation buffer [1 mM PIPES (pH 6.25), 1 mM sodium citrate, 1 mM KCl, 15 mM sucrose (Seeley et al. 1992)] with 0.6 mM cordycepin, or without (mock), using a 1 mL needleless syringe (Terumo). Excess liquid was removed from the leaf surface and plants were incubated for a minimum of 10 minutes before further treatment and harvesting. Light-stress was induced by increasing the light intensity to 10× growth irradiance (i.e. 1000 μmol photons m-2 s -1), resulting in a “hot high-light” treatment that effectively induces oxidative stress (Jung et al. 2013). For recovery, plants were returned to pre-stress light conditions.

value: Cordycepin


title: Mock-infiltrated 30 mins 1000 to 100 uE rep 4

source_name: Mock-infiltrated Arabidopsis leaf 30 mins 1000 to 100 uE

value: Mock


title: Mock-infiltrated 20 mins 1000 to 100 uE rep 4

source_name: Mock-infiltrated Arabidopsis leaf 20 mins 1000 to 100 uE


title: Cordycepin-infiltrated 10 mins 1000 to 100 uE rep 4

source_name: Cordycepin-infiltrated Arabidopsis leaf 10 mins 1000 to 100 uE


title: mouse medulloblastoma, wildtype EED, rep 3


title: Mock-infiltrated 20 mins 1000 uE rep 4

source_name: Mock-infiltrated Arabidopsis leaf 20 mins 1000 uE

value: High-light (1000 uE)


title: Cordycepin-infiltrated 20 mins 1000 uE rep 4

source_name: Cordycepin-infiltrated Arabidopsis leaf 20 mins 1000 uE


title: Mock-infiltrated 30 mins 1000 uE rep 4

source_name: Mock-infiltrated Arabidopsis leaf 30 mins 1000 uE


title: Cordycepin-infiltrated 30 mins 1000 uE rep 4

source_name: Cordycepin-infiltrated Arabidopsis leaf 30 mins 1000 uE


title: Mock-infiltrated 10 mins 1000 to 100 uE rep 4

source_name: Mock-infiltrated Arabidopsis leaf 10 mins 1000 to 100 uE


title: Cordycepin-infiltrated 10 mins 1000 uE rep 3

source_name: Cordycepin-infiltrated Arabidopsis leaf 10 mins 1000 uE


title: Cordycepin-infiltrated 0 mins 1000 uE rep 3

source_name: Cordycepin-infiltrated Arabidopsis leaf 0 mins 1000 uE


title: Mock-infiltrated 10 mins 1000 uE rep 3

source_name: Mock-infiltrated Arabidopsis leaf 10 mins 1000 uE


title: Cordycepin-infiltrated 30 mins 1000 to 100 uE rep 3


title: Mock-infiltrated 30 mins 1000 to 100 uE rep 3


title: Mock-infiltrated 0 mins 1000 uE rep 3

source_name: Mock-infiltrated Arabidopsis leaf 0 mins 1000 uE


title: Mock-infiltrated 20 mins 1000 to 100 uE rep 3


title: Cordycepin-infiltrated 20 mins 1000 to 100 uE rep 3

source_name: Cordycepin-infiltrated Arabidopsis leaf 20 mins 1000 to 100 uE


title: Mock-infiltrated 10 mins 1000 to 100 uE rep 3


title: Cordycepin-infiltrated 30 mins 1000 to 100 uE rep 2


title: Mock-infiltrated 30 mins 1000 to 100 uE rep 2


title: Cordycepin-infiltrated 20 mins 1000 to 100 uE rep 2


title: Cordycepin-infiltrated 10 mins 1000 to 100 uE rep 3


title: Cordycepin-infiltrated 20 mins 1000 to 100 uE rep 4


title: Cordycepin-infiltrated 10 mins 1000 to 100 uE rep 2


title: Cordycepin-infiltrated 20 mins 1000 uE rep 3


title: Mock-infiltrated 20 mins 1000 to 100 uE rep 2


title: Mock-infiltrated 20 mins 1000 uE rep 3


title: Cordycepin-infiltrated 30 mins 1000 uE rep 3


title: Mock-infiltrated 10 mins 1000 to 100 uE rep 2


title: Cordycepin-infiltrated 0 mins 1000 uE rep 2


title: Mock-infiltrated 30 mins 1000 uE rep 2


title: Cordycepin-infiltrated 20 mins 1000 uE rep 2


title: Mock-infiltrated 20 mins 1000 uE rep 2


title: Cordycepin-infiltrated 10 mins 1000 uE rep 2


title: Cordycepin-infiltrated 10 mins 1000 to 100 uE rep 1


title: Cordycepin-infiltrated 30 mins 1000 to 100 uE rep 1


title: Mock-infiltrated 20 mins 1000 to 100 uE rep 1


title: Cordycepin-infiltrated 30 mins 1000 uE rep 2


title: Mock-infiltrated 30 mins 1000 to 100 uE rep 1


title: Mock-infiltrated 10 mins 1000 to 100 uE rep 1


title: Cordycepin-infiltrated 20 mins 1000 to 100 uE rep 1


title: Cordycepin-infiltrated 30 mins 1000 uE rep 1


title: Mock-infiltrated 0 mins 1000 uE rep 2


title: Cordycepin-infiltrated 20 mins 1000 uE rep 1


title: Mock-infiltrated 30 mins 1000 uE rep 1


title: Cordycepin-infiltrated 0 mins 1000 uE rep 1


title: Mock-infiltrated 30 mins 1000 uE rep 3


title: Mock-infiltrated 10 mins 1000 uE rep 2


title: Cordycepin-infiltrated 10 mins 1000 uE rep 1


title: Mock-infiltrated 20 mins 100 uE rep 3

source_name: Mock-infiltrated Arabidopsis leaf 20 mins 100 uE

value: Unstressed (100 uE)


title: Cordycepin-infiltrated 10 mins 100uE rep 3

source_name: Cordycepin-infiltrated Arabidopsis leaf 10 mins 100uE


title: Mock-infiltrated 0 mins 1000 uE rep 1


title: Cordycepin-infiltrated 20 mins 100uE rep 3

source_name: Cordycepin-infiltrated Arabidopsis leaf 20 mins 100uE


title: Mock-infiltrated 10 mins 1000 uE rep 1


title: Mock-infiltrated 10 mins 100 uE rep 3

source_name: Mock-infiltrated Arabidopsis leaf 10 mins 100 uE


title: Mock-infiltrated 20 mins 1000 uE rep 1


title: Cordycepin-infiltrated 20 mins 100uE rep 2


title: Cordycepin-infiltrated 0 mins 100uE rep 3

source_name: Cordycepin-infiltrated Arabidopsis leaf 0 mins 100uE


title: Mock-infiltrated 0 mins 100 uE rep 3

source_name: Mock-infiltrated Arabidopsis leaf 0 mins 100 uE


title: Mock-infiltrated 20 mins 100 uE rep 2


title: Mock-infiltrated 10 mins 100 uE rep 2

source_name: Mock-infiltrated Arabidopsis 10 mins 100 uE


title: Cordycepin-infiltrated 10 mins 100uE rep 2


title: Mock-infiltrated 0 mins 100 uE rep 2


title: Cordycepin-infiltrated 10 mins 100uE rep 1


title: Mock-infiltrated 20 mins 100 uE rep 1


title: Cordycepin-infiltrated 20 mins 100uE rep 1


title: Cordycepin-infiltrated 0 mins 100uE rep 2


title: Mock-infiltrated 0 mins 100 uE rep 1


title: Mock-infiltrated 10 mins 100 uE rep 1


title: Cordycepin-infiltrated 0 mins 100uE rep 1


title: SU-DIPG25 K27M high 3

status: Public on Jun 08 2022

city: Rehovot

first: Efrat

last: Shema

address: Herzl St 234

department: Biological Information

country: Israel

institute: Weizmann Institute of Science

data_processing:
Bcl files were converted into fastq by bcl2fastq.
Demultiplexing is done using the sample barcode found on R2, the UMI found on R2 is inserted in the read name (in R1 fastq). R1 Fastq data submitted.
MARS-seq analysis was done using the UTAP transcriptome analysis pipeline (Kohen et al., 2019). Reads were trimmed using Cutadapt (parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a “A{10}” –times 2 -u 3 -u -3 -q 20 -m 25) and mapped to hg38 genome using STAR v2.4.2a (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic, –alignSoftClipAtReferenceEnds No).
The pipeline quantifies the 3’ of Gencode annotated genes (The 3’ region contains 1,000 bases upstream of the 3’ end and 100 bases downstream). Counting was done using htseq-count (union mode). Genes having minimum 5 UMI-corrected reads in at least one sample, were considered. Normalization of the counts and differential expression analysis was performed using DESeq2 package.
Differentially expressed genes were defined as genes that had a significant adjusted p value of less than 0.05 and at least 1.5-fold change.
Assembly: hg38
Supplementary files format and content: Excel for processed data. Fastq for raw data.

growth_protocol: Grow in TSM1X at 37C and 5% CO2

extract_protocol:
Qiagen RNA Micro
MARS-Seq

value: brain

tag: k27m expression

value: high

value: glioma cell


title: SU-DIPG25 K27M low 3

value: low


title: SU-DIPG25 K27M low 2


title: SU-DIPG25 K27M high 1


title: day8 RFP-GFP- iTSp6 rep1

status: Public on May 24 2022

first: Tu

middle: zhi

last: fen

address: Tongji University Siping Road Campus

department: life science and technology

institute: Tongji University

description:
TSinduction_counts
TSinduction_FPKM

data_processing:
All sequenced reads were checked for quality control by using FastQC (v0.11.9) with default parameters.
Sequenced reads was removed adapters and low-quality sequence by using trim_galore (v0.6.6 )with the default parameters.
The processed RNA-Seq reads were mapped to hg38 genome using STAR (v2.5.2b). Refseq genes were quantified to FPKM using Stringtie.
Assembly: hg38
Supplementary files format and content: text files of count and FPKM values

source_name: pluripotent stem cells

extract_protocol:
total RNAs were isolated from cells using TRizol (Invitrogen). To generate RNA sequencing libraries, KAPA Stranded mRNA-Seq Kit (KAPA) was used following the manufacturer’s instructions.
mRNA-seq libraries were prepared for sequencing using standard Illumina protocols

value: pluripotent stem cells

value: Trophoblast stem cell

tag: passage

tag: protocol

value: TS induction process


title: day8 RFP-GFP- iTSp6 rep2

description:
TSinduction_counts
TSinduction_FPKM


title: day8 RFP-GFP- iTSp4 rep2

description:
TSinduction_counts
TSinduction_FPKM


title: SU-DIPG25 K27M low 1


title: day8 RFP-GFP- iTSp2 rep1

description:
TSinduction_counts
TSinduction_FPKM


title: day8 RFP-GFP- iTSp4 rep1

description:
TSinduction_counts
TSinduction_FPKM


title: day8 RFP-GFP- iTSp2 rep2

description:
TSinduction_counts
TSinduction_FPKM


title: day6 SSEA4- END rep2

value: Endoderm

value: Endoderm differentiation


title: day6 SSEA4- END rep1


title: day6 SSEA4+ END rep2


title: day6 SSEA4+ END rep3


title: day8 RFP- END rep2


title: day6 SSEA4+ END rep1


title: day8 RFP- END rep1


title: day8 RFP+ END rep2


title: day8 RFP+ END rep1


title: nESC END rep2


title: nESC END rep1


title: SU-DIPG25 K27M high 2


title: pESC END rep2


title: pESC END rep1


title: G401_shNR7_DMSO_input

status: Public on May 09 2022

first: Jacquelyn

middle: A

last: Myers

state: TN

institute: St. Jude Children’s Research Hospital

description: G401 loss NSD1 DMSO treated

data_processing:
trim_galore v0.6.3 remove adapter sequences
align quality reads using bwa mem v0.7.17 to a hybrid reference genome
bamsormadup v2.0.87
samtools used to split bam file for hg19 and dm6 reads base on chromosome names
samtools -F 1024 -q 1 to define quality reads
estimate fragment size using spp R package
slopBed -r fragment size estimation determined by spp
Normalize to 15M reads (for canonical normalization) or 100k dm6 reads using bedtools genomecov and conert to bigwig using UCSC bedGraphToBigWig or spikeinfree normalization (https://github.com/stjude/ChIPseqSpikeInFree)
Genome_build: hg19+dm6 (Gencode GRCh37 and Ensembl r97)
Supplementary_files_format_and_content: normalized coverage in the bigwig file format.
Supplementary_files_format_and_content: peak files in bed and narrowPeak format.

growth_protocol: G401 cells were grown in McCoy's 5A media supplemented with 10% fetal bovine serum and 1% Glutamax (Gibco) at 37°C and 5% CO2.

extract_protocol:
In brief, cells were cross-linked directly on the plate using 1% paraformaldehyde for 10 min at room temperature and quenched with glycine. Nuclei were isolated using the Covaris TruCHIP kit and Chromatin extracts were sonicated for 8 min using a Covaris E220 focused ultrasonicator at a peak power of 140, a duty factor of 5 and 200 cycles per burst. Chromatin immunoprecipitation was carried overnight with antibodies bound to dynabeads. Chromatin was de-crosslinked, digested with RNase and Proteinase K and DNA was ourified using a Zymo ChIP DNA kit.
KAPA HyperPrep Kit (Kapa Biosystems)

treatment_protocol: G401 cells were engineered to express either GFP or SMARCB1 (B1) under doxycycline treatment and further transfected with either control (sgC) or NSD1 (sgN) targeting sgRNAs. Cells were then treated with 1ug/mL dox for 24h and collected for RNA extraction. For EZH2 inhibition studies, G401 cells stably expressing shCTRL or shNSD1 RNAs were treated for 72h with 1uM GSK126 and collected for RNA extraction.

tag: genotype

value: G401 loss NSD1

tag: agent

value: DMSO


title: G401_shNR6_GSK126_H3K27ac

description: G401 loss NSD1 EZH2i treated


title: G401_shNR6_GSK126_H3K27me3

description: G401 loss NSD1 EZH2i treated


title: G401_shNR7_GSK126_H3K36me2

description: G401 loss NSD1 EZH2i treated


title: G401_shNR6_GSK126_H3K36me2

description: G401 loss NSD1 EZH2i treated


title: G401_shCR7_GSK126_H3K27me3

description: G401 control EZH2i treated

value: G401 control


title: G401_shNR7_DMSO_H3K36me2

description: G401 loss NSD1 DMSO treated


title: G401_shNR7_DMSO_H3K27me3

description: G401 loss NSD1 DMSO treated


title: G401_shNR6_DMSO_INPUT

description: G401 loss NSD1 DMSO treated


title: G401_shNR7_DMSO_H3K27ac

description: G401 loss NSD1 DMSO treated


title: G401_shCR7_GSK126_H3K36me2

description: G401 control EZH2i treated


title: G401_shCR7_GSK126_input

description: G401 control EZH2i treated


title: G401_shNR7_GSK126_H3K27me3

description: G401 loss NSD1 EZH2i treated


title: G401_shNR6_GSK126_INPUT

description: G401 loss NSD1 EZH2i treated


title: G401_shNR7_GSK126_H3K27ac

description: G401 loss NSD1 EZH2i treated


title: G401_shNR6_DMSO_H3K36me2

description: G401 loss NSD1 DMSO treated


title: G401_shCR7_DMSO_input

description: G401 control DMSO treated


title: G401_shCR7_DMSO_H3K27me3

description: G401 control DMSO treated


title: G401_shNR6_DMSO_H3K27me3

description: G401 loss NSD1 DMSO treated


title: G401_shCR7_DMSO_H3K27ac

description: control G401 DMSO treated

value: control G401


title: G401_shCR7_DMSO_H3K36me2

description: G401 control DMSO treated


title: G401_shCR6_GSK126_H3K36me2

description: G401 control EZH2i treated


title: G401_shCR6_GSK126_INPUT

description: G401 control EZH2i treated


title: G401_shCR6_GSK126_H3K27me3

description: G401 control EZH2i treated


title: G401_shCR7_GSK126_H3K27ac

description: G401 control DMSO treated


title: G401_shNR7_GSK126_input

description: G401 loss NSD1 EZH2i treated


title: G401_shCR6_GSK126_H3K27ac

description: G401 control EZH2i treated


title: G401_shCR6_DMSO_INPUT

description: G401 control DMSO treated


title: G401_shCR6_DMSO_H3K36me2

description: G401 control DMSO treated


title: G401_shNR6_DMSO_H3K27ac

description: G401 loss NSD1 DMSO treated


title: B1_sgN1_H3K27me3

description: SMARCB1 expressing loss of NSD1

value: SMARCB1 expressing loss of NSD1


title: B1_sgN2_Input

description: SMARCB1 expressing loss of NSD1


title: B1_sgN1_H3K36me2

description: SMARCB1 expressing loss of NSD1


title: G401_shCR6_DMSO_H3K27ac

description: G401 control DMSO treated


title: B1_sgN2_H3K27me3

description: SMARCB1 expressing loss of NSD1


title: G401_shCR6_DMSO_H3K27me3

description: G401 control DMSO treated


title: B1_sgN1_Input

description: SMARCB1 expressing loss of NSD1


title: B1_sgC1_H3K36me2

description: SMARCB1 expressing; control

value: SMARCB1 expressing; control


title: B1_sgC2_H3K27me3

description: SMARCB1 expressing; control


title: B1_sgC2_Input

description: SMARCB1 expressing; control


title: B1_sgC1A_Input

description: SMARCB1 expressing; control


title: B1_sgN2_H3K27ac

description: SMARCB1 expressing loss of NSD1


title: B1_sgN1_H3K27ac

description: SMARCB1 expressing loss of NSD1


title: B1_sgC1A_H3K27ac

description: SMARCB1 expressing; control


title: B1_sgC1_Input

description: SMARCB1 expressing; control


title: GFP_sgN2_H3K27me3

description: GFP expressing; loss NSD1

value: GFP expressing; loss NSD1


title: GFP_sgN2_Input

description: GFP expressing; loss NSD1


title: B1_sgC2_H3K27ac

description: SMARCB1 expressing; control


title: B1_sgC2_H3K36me2

description: SMARCB1 expressing; control


title: GFP_sgN1_H3K27ac

description: GFP expressing; loss NSD1


title: GFP_sgN2_H3K36me2

description: GFP expressing; loss NSD1


title: GFP_sgN1_H3K27me3

description: GFP expressing; loss NSD1


title: GFP_sgN1_H3K36me2

description: GFP expressing; loss NSD1


title: GFP_sgN1_Input

description: GFP expressing; loss NSD1


title: GFP_sgC2_H3K27me3

description: GFP expressing; control

value: GFP expressing; control


title: GFP_sgC2_H3K27ac

description: GFP expressing; control


title: B1_sgN2_H3K36me2

description: SMARCB1 expressing loss of NSD1


title: B1_sgC1_H3K27me3

description: SMARCB1 expressing; control


title: GFP_sgN2_H3K27ac

description: GFP expressing; loss NSD1


title: IGF106044

status: Public on May 08 2022

city: London

first: Rahel

last: Feleke

address: Ducane Road

country: United Kingdom

institute: Imperial College

data_processing:
Quality control (QC) of RNA-seq reads was conducted using FastQC. Low quality reads and ribosome RNA reads were removed. Trimmed reads were then mapped to the Rattus norvegicus reference genome (rno6) using STAR (version 2.5).
Assembly: Rattus norvegicus genome assembly Rnor_6.0 (rn6)  (Ensembl release 104)
Supplementary files format and content: Raw count matrix

organism: Rattus norvegicus

extract_protocol:
The mRNA Isolation Kit was used to extract total RNA from brain tissue samples following the manufacturer’s instructions.
Total RNA was examined for quantity and quality using the TruSeq Stranded Total RNA Library Prep Gold.

value: Brain

value: GAERS

value: non Exposed


title: GFP_sgC1_H3K27me3

description: GFP expressing; control


title: IGF106049


title: GFP_sgC1_Input

description: GFP expressing; control


title: IGF106047

value: VPA Exposed


title: IGF106020


title: GFP_sgC1_H3K27ac

description: GFP expressing; control


title: IGF106030


title: IGF106046


title: GFP_sgC1_H3K36me2

description: GFP expressing; control


title: IGF106041


title: IGF106038


title: IGF106024


title: IGF106026


title: GFP_sgC2_Input

description: GFP expressing; control


title: IGF106039

value: NEC


title: IGF106051


title: IGF106036


title: GFP_sgC2_H3K36me2

description: GFP expressing; control


title: IGF106035


title: IGF106027


title: IGF106022


title: IGF106023


title: IGF106048


title: IGF106045


title: IGF106028


title: IGF106043


title: IGF106033


title: IGF106032


title: IGF106031


title: IGF106042


title: IGF106021


title: IGF106050


title: Peripheral T cells of patinet #28 before TTF treatment

status: Public on Apr 20 2022

city: SOUTH PASADENA

first: SON

middle: B

last: LE

state: CA

address: 1645 Amberwood Drive, Unit 11

institute: University of Southern California

data_processing:
Paired-end reads were trimmed with trimmomatic v/0.36.
Alignment and gene counts were generated against the GRCh38.p12 genome assembly using the annotation GeneCode release 28 by STAR v2.6.0b with default options and quantmode=GeneCounts. Gene expressions in  transcripts per million (tpm)  were calculated as described in  Wagner et all, Theory Biosci. (2012) 131:281–285
the pair end reads from bulk non-targeted RNA-seq were supplied to MiXCR v.3.0.13, using the command analyze shotgun with the option of starting-material rna, only-productive.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample in count or tpm unit and in Ensemble ID and Official gene name
Supplementary_files_format_and_content: Tab delimited format MixCR clonotype fraction file for  each of (ALL, IGH, IGK, IGL, TRA, TRB, TRD, TRG) and each sample

source_name: Peripheral T lymphocytes isolated from PBMC

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were obtained from blood by density gradient centrifugation (Ficoll-Hypaque) and cryopreserved at liquid nitrogen until processed.

extract_protocol:
Frozen PBMC samples were quickly taken from liquid nitrogen and thaw at 37 degree. T lymphcytes were isolated using Pan T Cell Isolation Kit, human (Miltenyi Cat#130-096-535), and the total RNA was extracted using Qiagen RNA extraction kit.
RNA-seq library performed at ICBR Gene Expression & Genotyping (RRID:SCR_019145) using 25 ng of protein-free, DNase-treated total RNA (each sample processed individually) as input. Briefly, 25ng of total RNA was used for mRNA isolation using NEBNext Ploy(A) mRNA Magnetic Isolation module (New England Biolabs, catalog # E7490 ). Then followed by RNA library construction with NEBNext Ultra II Directional Lib Prep (New England Biolabs, catalog #E7760) according to the manufacturer's user guide. Briefly, RNA is fragmented in NEBNext First Strand Synthesis Buffer by heating at 94 °C for desired time. This step is followed by first strand cDNA synthesis using reverse transcriptase and oligo dT primers.  Synthesis of ds cDNA is performed using the 2nd strand master mix provided in the kit, followed by end-repair and adaptor ligation. Finally, library is enriched (each library has an unique barcode) by 12 cycles of amplification, and purified by Agencourt AMPure beads (Beckman Coulter, catalog # A63881).

treatment_protocol: Blood was draw before and one month after TTField treatment started

tag: sample id

value: untreated

tag: disease

value: Glioblastoma