title: shRNA5 differentiation Day7-3, RNA-seq

source_name: human HUDEP2 cells

tag: time

value: differentiation Day7


title: Input_HSV_1_5h

status: Public on Mar 21 2022

type: SRA

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

country: USA

institute: UT Health Science Center at San Antonio

library_source: transcriptomic

data_processing:
Library strategy: meRIP-seq
Illumina bcl2fastq software used for base-calling
reads algined to corresponding genomes (hg19 for human and mm9 for mouse) using TopHat (stranded), converted to sorted BAM using SAMTools, and further processed using exomePeak
gene count measurements were obtained using HTSeq-count
Genome_build: hg19 or mm9
Supplementary_files_format_and_content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

molecule: total RNA

organism: Homo sapiens

source_name: cervical carcinoma/epithelial cells

growth_protocol: Cells are maintained in Dulbecco's Modified Eagle's Medium with 10% fetal bovine serum  at 37 °C in a humidified atmosphere with 5% CO2.

extract_protocol:
Total RNA were extraction follows TRI reagent protocol (Thermo-Fisher) and then treated with DNase I to remove DNA contamination. . For m6A MeRIP-seq, the m6A enrichment were performed using m6A antibody (m6A antibody cat#202203, synaptic systems) and m6A-enriched and fragmented RNA was purified using RNeasy Mini Kit as IP.
KAPA Stranded RNA-seq Kit (Illumina) was used for the library preparation of both m6A-IP RNA and input mRNAs. The quality of the completed libraries was performed with Agilent 2100 Bioanalyzer

treatment_protocol: RAW264.7 cells at 4×10^5 cells per mL were treated with LPS at 10 ng/mL and harvested at 6 h post treatment. HeLa cells were infected with HSV1 at 5 MOIs and harvested at 5 or 8 h post-infection

tag: cell line

value: Hela

tag: treatment

value: 5hr after HSV-1 infection

tag: rna harvest

value: Input RNA


title: pooled m2hmscRNAseq

city: New Haven

first: Jack

middle: Anthony

last: Collora

state: CT

address: 295 Congress Ave

department: Microbial Pathogenesis

institute: Yale University

description:
m2hmbarcodes.tsv.gz
m2hmfeatures.tsv.gz
m2hmmatrix.mtx.gz

data_processing:
RTA3 was used for basecalling.
Cellranger count (3.0)
Cellranger vdj (3.1)
Seurat (4.0.3)
VDJ results further processed using Presto(0.6.2) and Changeo (1.1.0)
Genome_build: hg38
Supplementary_files_format_and_content: scRNA-seq counts sparse matricies from cellranger, unfiltered, scTCRs - fasta and csv/tsv annotation files, Bulk TCR - tsv annotation files ( Adaptive Immune Receptor Repertoire (AIRR) fromat)

molecule: polyA RNA

source_name: CD4+ T cells

growth_protocol: Isolated resting CD4+ T cells by negative selection: no growth conditions ; antigen stimulated CD4+ T cells: RPMI with 10% human serum for 9h after antigen stimulation

extract_protocol:
10X was used for all single cell experiements following the 5' v1.1 immune profiling with feature barcoding protocol. For the bulk TCR, CD4+ T cells were isolated by negative selection, and total RNA was extracted using the Zymo Directzol RNA kit.
10X Immune Profiling V1.1. Briefly, after cDNA amplification, cDNA is separated into high molecular weight (HMW) and low molecular weight (LMW) fractions. The LMW fraction is library prepped to generate CITE-seq libraries of surface protein expression. The HMW is sheered enzymatically, end repaired, and adapters are ligated on to generate the transcriptome library. In parallel, targetted amplification of TCR sequences occurs on the HMW fraction.

treatment_protocol: Isolated resting CD4+ T cells by negative selection: no treatment protocol ; antigen stimulated CD4+ T cells: treated with antigen peptide pools for 9h in the presence of T20 fusion inhibitor, sorted using FACS ARIA for AIM+

tag: cell state

value: antigen stimulated CD4+ T cells

tag: hiv-1 infection status


title: shRNA5 differentiation Day7-2, RNA-seq

city: bethesda

first: Xiang

last: Guo

state: MD

address: 50 south drive, blg50

department: NIDDK

institute: NIH

data_processing:
Sequenced reads were trimmed for adaptor sequence,  then mapped to hg38 and mm10  whole genome using hisat2 v2.1.0 with default parameters respectively. Multimappnig reads were filtered using samtoools 1.9, uniquely aligned reads were then mapped to gene features using Subread featureCounts v1.6.4
Differential expression between groups of samples was tested using R version 3.5.1 with DESeq2 1.20.0
Genome_build: hg38 , mm10
Supplementary_files_format_and_content: tab-delimited text files include gene count values for each Sample ...

growth_protocol: Primary CD34+ umbilical cord cells (Lonza, cat. 2C-101) were cultured as described (Wilber et al., 2010). HUDEP2 cells was cultured in SFEM medium and induced in DMEM medium as described (Vinjamur and Bauer, 2018). K562 cells were cultured in RPMI 1640 medium containing 10 % fetal bovine serum.Hemogen WT and KO mice were housed in NIDDK mouse core facility, in accordance with guidelines of the Animal Care and Use Committee of the National Institutes of Health under a Division of Intramural Research, NIDDK approved animal study protocols. Fetal livers isolated from E14.5 control and knockout mice.

extract_protocol:
Total RNA was isolated using RNeasy Plus Micro Kit
RNA sequencing libraries were generating from 100ng-1 ug of RNA using Illumina TruSeq Stranded mRNA Library Preparation kit (20020594) following manufacturer’s protocol.

tag: genotype


title: pooled hdm1scTCR

description:
hdm1_all_contig.fasta
hdm1_all_contig_annotations.csv

data_processing:
Library strategy: TCR-seq
RTA3 was used for basecalling.
Cellranger count (3.0)
Cellranger vdj (3.1)
Seurat (4.0.3)
VDJ results further processed using Presto(0.6.2) and Changeo (1.1.0)
Genome_build: hg38
Supplementary_files_format_and_content: scRNA-seq counts sparse matricies from cellranger, unfiltered, scTCRs - fasta and csv/tsv annotation files, Bulk TCR - tsv annotation files ( Adaptive Immune Receptor Repertoire (AIRR) fromat)

value: Uninfected


title: K562 WT-1, RNA-seq

source_name: human K562 cells

value: WT


title: pooled hdcmvscRNAseq

description:
hdcmvbarcodes.tsv.gz
hdcmvfeatures.tsv.gz
hdcmvmatrix.mtx.gz


title: shRNA5 differentiation Day7-1, RNA-seq


title: 2023scTCR 2

description: M2filtered_contig_igblast_db-pass_parse-select.tab

value: Isolated unstimulated CD4+ T cells by negative selection


title: WT_Hippocampus_RNA_3

city: Houston

first: Tianpeng

last: Gu

address: Cambridge steet

institute: Baylor College of Medicine

data_processing:
STAR v2.5.4a was used to map to the genome. Gencode.mouse.v1.annotation.gtf was used for gene annotation.
2-pass strategy of STAR was used, see https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline/ for more details.
htseq/0.11.0 was used to calculate the raw read counts for each gene. htseq-count -m intersection-nonempty -i gene_id -s reverse -r pos -f bam
Genome_build: mm9

organism: Mus musculus

source_name: Hippocampus

extract_protocol:
The hippocampus were isolated, crushed and homogenized. Total RNA were purified with AllPrep DNA/RNA Mini Kit (Qiagen).
RNA-Seq libraries were prepared with TruSeq® Stranded mRNA Library Prep (illumina).

tag: tissue

value: Hippocampus

tag: strain

value: Wild type

tag: developmental stage

value: postnatal day 21


title: 2023scTCR 1

description: M1filtered_contig_igblast_db-pass_parse-select.tab


title: 2004scTCR

description: M3filtered_contig_igblast_db-pass_parse-select.tab


title: 3a1KO_Hippocampus_RNA_2


title: pooled m1cmscRNAseq

description:
m1cmbarcodes.tsv.gz
m1cmfeatures.tsv.gz
m1cmmatrix.mtx.gz


title: pooled m2cmscRNAseq

description:
m2cmbarcodes.tsv.gz
m2cmfeatures.tsv.gz
m2cmmatrix.mtx.gz


title: RIV829scTCR

description: RIV829filtered_contig_igblast_db-pass_parse-select.tab

value: Viremic


title: 3a1KO_Hippocampus_RNA_1


title: pooled hdm2scRNAseq

description:
hdm2barcodes.tsv.gz
hdm2features.tsv.gz
hdm2matrix.mtx.gz


title: RDS799scTCR

description: RDS799filtered_contig_igblast_db-pass_parse-select.tab

value: Suppressed


title: pooled hdm1scRNAseq

description:
hdm1barcodes.tsv.gz
hdm1features.tsv.gz
hdm1matrix.mtx.gz


title: 3AKO_ES_NP

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using BWA v0.7.17 with configurations: bwa mem -t 8 -c 1
Duplicates were removed using Samtools v1.10
Coverage tracks were generated by deepTools normalizing to 1*depth: bamCoverage --bam $samplename --effectiveGenomeSize 2150570000 --normalizeUsing RPGC --extendReads 200 --binSize 30
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files

molecule: genomic DNA

source_name: Embryonic stem cells

growth_protocol: Mouse embryonic stem cells were culture on 0.1% gelatin-coated dishes in DMEM supplemented with 15% Fetal Bovine Serum, 1×Non-Essential Amino Acids, 1×Sodium pyruvate, 1×GlutaMAX, 1 μM 2-Mercaptoethanol, 1×Penicillin/Streptomycin and 1000 U/ml LIF.

extract_protocol:
Cells were cross-linked in 1% formaldehyde, and chromatin was sheared with a Bioruptor sonicator. Protein-DNA complexes were immunoprecipitated with indicated antibody.
ChIP-Seq Libraries were prepared with ThruPLEX® DNA-seq 48D Kit (Rubicon Genomics)

value: Embryonic stem cells

value: Dnmt3a-/-, NP over-expressed

tag: chip antibody

value: anti-FLAG


title: pooled m1hcascRNAseq

description:
m1hcabarcodes.tsv.gz
m1hcafeatures.tsv.gz
m1hcamatrix.mtx.gz


title: WT_Hippocampus_RNA_2


title: DV910scTCR

description: DV910filtered_contig_igblast_db-pass_parse-select.tab


title: shRNA5 differentiation Day5-2, RNA-seq

value: differentiation Day5


title: control differentiation Day7-3, RNA-seq

value: control

value: differentiation Day7


title: WT_Hippocampus_RNA_1


title: RIV236scTCR

description: RIV236filtered_contig_igblast_db-pass_parse-select.tab


title: IS640scTCR

description: IS640filtered_contig_igblast_db-pass_parse-select.tab


title: control differentiation Day7-2, RNA-seq


title: 3AKO_ES_N

value: Dnmt3a-/-, N over-expressed


title: C96_M3_Trap

city: Columbia

first: Gary

last: Stacey

state: Missouri

address: 271E Christopher S. Bond Life Sciences Center

institute: University of Missouri at Columbia

data_processing:
library strategy: Targeted purification of polysomal mRNA screening (TRAP-Seq)
Quality check with FastQC version 0.11.9
Adapter trimming with TrimGalore-0.6.5
Read alignment with STAR 2.7.6a
Genome_build: Glycine max Wm82.a4.v1
Supplementary_files_format_and_content: Tab-delimited text files including TPM values as raw gene counts for each sample

organism: Glycine max

source_name: Root tissue

growth_protocol: Seeds of cultivar Williams 82 of soybean (Glycine max) were surface sterilized, germinated, and grown in vermiculite: perlite soil mixture (3:1) or germination paper in a growth chamber with a 16-h light and 8-h dark photoperiod, set to 23°C during the dark and 26°C during the light regime at 80 % humidity.

extract_protocol:
TRAP was modified based on the method by (Zanetti et al., 2005) as described previously (Castro‐Guerrero et al., 2016). The optimized protocol required 10 g of root material per sample when using cortex-layer specific HisFLAG-GmRPL18 expressing hairy root. This was sufficient to obtain at least 500 ng of mRNA for library preparation and subsequent RNA sequencing. In this study, three biological replicates were prepared for each time point (72 and 96hr) for each treatment (mock- and B. japonicum-inoculated).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The plants were inoculated with B. japonicum strain USDA110. we used wild-type B. japonicum USDA110 for each experiment. B. japonicum cells were grown at 30°C for 3 days in HM medium (Cole and Elkan, 1973) with the appropriate antibiotics. After three days of culture, bacteria were pelleted, washed twice with sterilized deionized (DI) water, and diluted to an OD600 of 1.0 for inoculation in sterilized DI water. Plants were supplied with B&D (Broughton and Dilworth) (Broughton and Dilworth, 1971) with no nitrogen nutrient solution or with 0.5 mM NH4NO3 as in non-infected experiments.

value: Mock for 96 h

tag: targeted purification of polysomal mrna screening(trap-seq)

value: TRAP

value: root


title: shRNA5 differentiation Day5-3, RNA-seq


title: shRNA5 differentiation Day5-1, RNA-seq


title: control differentiation Day5-3, RNA-seq


title: control differentiation Day7-1, RNA-seq


title: pooled m2hcscRNAseq

description:
m2hcbarcodes.tsv.gz
m2hcfeatures.tsv.gz
m2hcmatrix.mtx.gz

value: antigen stimulated CD4+ T cells


title: RDS739scTCR

description: RDS739filtered_contig_igblast_db-pass_parse-select.tab

value: Isolated unstimulated CD4+ T cells by negative selection


title: 3AKO_ES_DNMT3A1DN

value: Dnmt3a-/-, DNMT3A1DN over-expressed


title: control differentiation Day5-1, RNA-seq


title: DS799scTCR

description: DS799filtered_contig_igblast_db-pass_parse-select.tab


title: 3AKO_ES_NPA

value: Dnmt3a-/-, NPA over-expressed


title: 3AKO_ES_DNMT3A2_R2

value: Dnmt3a-/-, DNMT3A2 over-expressed


title: DS739scTCR

description: DS739filtered_contig_igblast_db-pass_parse-select.tab


title: IV640scTCR

description: IV640filtered_contig_igblast_db-pass_parse-select.tab

value: Viremic


title: 3AKO_ES_DNMT3A2_R1


title: 3AKO_ES_DNMT3A1DPA

value: Dnmt3a-/-, DNMT3A1DPA over-expressed


title: 3AKO_ES_DNMT3A1DA

value: Embryonic stem cells

value: Dnmt3a-/-, DNMT3A1DA over-expressed


title: 3AKO_ES_DNMT3A1DP

value: Dnmt3a-/-, DNMT3A1DP over-expressed

value: anti-FLAG


title: shRNA5 differentiation Day3-2, RNA-seq

value: differentiation Day3


title: DS910scTCR

description: DS910filtered_contig_igblast_db-pass_parse-select.tab

value: Suppressed


title: 3AKO_ES_DNMT3A1_R2

value: Dnmt3a-/-, DNMT3A1 over-expressed


title: C96_Bj1_Trap

value: Treated with Bj for 96 h


title: RIV236Feature Barcoding

data_processing:
Library strategy: scFeature Barcoding
RTA3 was used for basecalling.
Cellranger count (3.0)
Cellranger vdj (3.1)
Seurat (4.0.3)
VDJ results further processed using Presto(0.6.2) and Changeo (1.1.0)
Genome_build: hg38
Supplementary_files_format_and_content: scRNA-seq counts sparse matricies from cellranger, unfiltered, scTCRs - fasta and csv/tsv annotation files, Bulk TCR - tsv annotation files ( Adaptive Immune Receptor Repertoire (AIRR) fromat)

molecule: other


title: control differentiation Day5-2, RNA-seq

value: control

value: differentiation Day5


title: DV799Feature Barcoding


title: C96_M2_Trap

value: Mock for 96 h

value: TRAP

value: root


title: C96_M1_Trap


title: RDS799Feature Barcoding

value: Isolated unstimulated CD4+ T cells by negative selection


title: DS739Feature Barcoding


title: C96_Bj2_Trap


title: RDS739Feature Barcoding


title: 3AKO_ES_input


title: shRNA5 differentiation Day3-3, RNA-seq


title: C96_Bj3_Trap


title: 3AKO_ES_DNMT3A1_R1


title: DS799Feature Barcoding


title: 72Bj2_TRAP

value: Treated with Bj for 72 h


title: control differentiation Day3-2, RNA-seq


title: DV739Feature Barcoding

value: Viremic


title: RIV829Feature Barcoding

value: Virmeic


title: 72Bj3_TRAP


title: control differentiation Day3-3, RNA-seq


title: 72M3_TRAP

value: Mock for 72 h


title: shRNA5 differentiation Day3-1, RNA-seq


title: IV829Feature Barcoding


title: WT_ES_H3K4me3

value: Embryonic stem cells

value: Wild type


title: shRNA5 differentiation Day0-2, RNA-seq

value: differentiation Day0


title: 72M1_TRAP


title: IS236Feature Barcoding


title: IS829Feature Barcoding


title: control differentiation Day3-1, RNA-seq

value: differentiation Day3


title: 72Bj1_TRAP


title: WT_ES_H3K36me3


title: 72M2_TRAP


title: RIV829scRNA-seq

description:
RIV829filtered_contig_igblast_db-pass_parse-select.tab
RIV829matrix.tar


title: WT_ES_H3K27me3


title: IV236Feature Barcoding


title: control differentiation Day0-3, RNA-seq


title: control differentiation Day0-2, RNA-seq


title: 3a1dN_Cortex_RNA_2

data_processing:
STAR v2.5.4a was used to map to the genome. Gencode.mouse.v1.annotation.gtf was used for gene annotation.
2-pass strategy of STAR was used, see https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline/ for more details.
htseq/0.11.0 was used to calculate the raw read counts for each gene. htseq-count -m intersection-nonempty -i gene_id -s reverse -r pos -f bam
Genome_build: mm9
Supplementary_files_format_and_content: Text files with raw read counts for each genes.

source_name: Cerebral cortex

extract_protocol:
Cerebral cortices were isolated, crushed and homogenized. Genomic DNA and total RNA were purified from the same materials with AllPrep DNA/RNA Mini Kit (Qiagen)
RNA-Seq libraries were prepared with TruSeq® Stranded mRNA Library Prep (illumina)

value: Cerebral cortex

value: postnatal day 21


title: RIV236scRNA-seq

description:
RIV236filtered_contig_igblast_db-pass_parse-select.tab
RIV236matrix.tar


title: control differentiation Day0-1, RNA-seq


title: shRNA5 differentiation Day0-1, RNA-seq


title: MUT 3

city: Jerusalem

first: Tikva

last: Shore

address: Ein Karem Campus

country: Israel

institute: Hebrew University of Jerusalem

data_processing:
Fastq files were obtained from the bcl files using bcl2fastq, version 2.17.1.14, allowing one mismatch in barcode sequence.
The first 9 bases of each read were removed, then low quality and adapter sequences were trimmed using cutadapt, version 1.11. Reads that became shorter than 15 bases were discarded. The fastq_quality_filter program of the FASTX package was used to filter out reads with overall low quality, using parameters -q 20 and -p 90.
Alignment was done with Tophat, version 2.0.14, with parameters: -G genes.gtf, -N 5, --read-gap-length 5, --read-edit-dist 10, --segment-length 20, --read-realign-edit-dist 3 and --library-type fr-firststrand.
Quantification was done with htseq-count, version 0.6.0, with parameter -s reverse and using a GTF file without rRNA, tRNA and small non-coding RNA genes (such as miRNA or piRNA).
DESeq2, version 1.12.4, was used for differential expression analysis, after discarding genes with less than 2 reads, using default parameters and a significance threshold of padj<0.1. Additional filtering of significant genes was applied, such that the effect, absolute value of the log2FoldChange, in mutant-rescued flys is higher, at least 0.1, than in wild type-rescued ones.
Genome_build: BDGP6, supplumented with the GFP and the RFP-NUP construct sequences.
Supplementary_files_format_and_content: Excel of expression data. The file includes general gene details, raw counts, normalized counts, the baseMean, differential expression results for all comparisons, and the final choice of significant genes. The first two rows are header rows explaining the meaning of columns. A '?' denotes missing value; genes with less than 2 raw reads were discarded and have '?' in all further columns. A gene with 'NA' in the pvalue and padj columns is an outlier gene (according to DESeq2), a gene with 'NA' value only in the padj column was filtered out due to the independentFiltering step.

organism: Drosophila melanogaster

source_name: larval gonad

growth_protocol: Larvae were collected from the vial wall using biological tweezers, five days following their being laid by mated females on fresh food supplemented with yeast.  They were removed immediately following the wandering stage, prior to the pupal transition. Larvae were sexed and females moved to dissection dish containing room-temperature Ringer's medium. Gonads were dissected from the fat body and immediately placed in liquid nitrogen for preservation until RNA extraction could be performed.

extract_protocol:
Gonads were removed and flash frozen in liquid nitrogen. RNA was harvested using the Rneasy Kit from Qiagen.
RNA libraries were prepared with LEXOGEN's SENSE Total RNA-Seq Library Kit for Illumina-compatible sequencing, after PolyA selection.

value: yw; Nup107E8 ; Nup107mut


title: shRNA5 differentiation Day0-3, RNA-seq


title: MUT 2

value: yw; Nup107E8 ; RFP-Nup107mut


title: RDS799scRNA-seq

description:
RDS799filtered_contig_igblast_db-pass_parse-select.tab
RDS799matrix.tar

value: Suppressed


title: WT_ES_input


title: MUT 1


title: WT_Cortex_RNA_n2


title: WT 3

value: yw; Nup107E8 ; Nup107wt


title: WT_Cortex_RNA_n3


title: CD34+ differentiation Day16-KD2, RNA-seq

source_name: human CD34+ cells

value: KD

value: differentiation Day16

tag: cell type

value: CD34+ cells


title: 3a1dN_Cortex_RNA_3


title: CD34+ differentiation Day16-KD1, RNA-seq


title: WT 2

value: yw hs-flp; Nup107E8 ; RFP-Nup107wt


title: WT 1


title: CD34+ differentiation Day16-WT2, RNA-seq

value: WT


title: DV799scRNA-seq

description:
DV799filtered_contig_igblast_db-pass_parse-select.tab
DV799matrix.tar

value: Isolated unstimulated CD4+ T cells by negative selection

value: Viremic


title: DS799scRNA-seq

description:
DS799filtered_contig_igblast_db-pass_parse-select.tab
DS799matrix.tar


title: 3a2KO_Cortex_RNA_2


title: RDS739scRNA-seq

description:
RDS739filtered_contig_igblast_db-pass_parse-select.tab
RDS739matrix.tar


title: YW

value: yw


title: 3a1dN_Cortex_RNA_1


title: DS739scRNA-seq

description:
DS739filtered_contig_igblast_db-pass_parse-select.tab
DS739matrix.tar


title: CD34+ differentiation Day16-WT1, RNA-seq


title: Fibroblast-like synoviocytes, SOXCGFP3

city: Atlanta

first: Sergio

last: Ramirez-Perez

state: Georgia

address: 615 Michael St NE

department: Orthopaedics

institute: Emory University

data_processing:
NovaSeq 6000 Paired-end sequencing was used, PE150, Q30≥85%.
Sequenced reads were mapped to the mm10 mouse genome assembly using Strand NGS v4.0, normalization was performed using DESeq with a threshold at 1 for all aligned reads. We obtained 53342 genes.
Genome_build: mm10 mouse
Supplementary_files_format_and_content: Matrix table - delimited text files include normalized expression levels for each sample

source_name: Synovium

extract_protocol:
FLS from SoxC mice were cultured and stimulated with 10ng/mL recombinant human TNF for 16h. RNA was harvested using Trizol reagent.
Mouse mRNA Sequencing (WOBI) was used to perform RNA sample QC. Poly A enrichment was implemented for mRNA library preparation. NovaSeq PE150 was used to generate 6 G raw data per sample.

value: Fibroblast-like synoviocytes

value: Synovium

value: control

tag: diagnosis

value: Control


title: WT_Cortex_RNA_r2

value: Cerebral cortex

value: Wild type

value: postnatal day 21


title: DV739scRNA-seq

description:
DV739filtered_contig_igblast_db-pass_parse-select.tab
DV739matrix.tar


title: IS829scRNA-seq

description:
IS829filtered_contig_igblast_db-pass_parse-select.tab
IS829matrix.tar

value: Suppressed


title: 3a2KO_Cortex_RNA_1


title: CD34+ differentiation Day14-WT2, RNA-seq

value: differentiation Day14


title: Fibroblast-like synoviocytes, SOXCGFP2


title: CD34+ differentiation Day14-KD2, RNA-seq

value: KD


title: WT_Cortex_RNA_r1


title: Fibroblast-like synoviocytes, SOXCGFP1


title: CD34+ differentiation Day14-KD1, RNA-seq


title: CD34+ differentiation Day14-WT1, RNA-seq


title: IV829scRNA-seq

description:
IV829filtered_contig_igblast_db-pass_parse-select.tab
IV829matrix.tar


title: 3a1KO_Cortex_RNA_3


title: IS236scRNA-seq

description:
IS236filtered_contig_igblast_db-pass_parse-select.tab
IS236matrix.tar


title: 3a1KO_Cortex_RNA_2


title: Fibroblast-like synoviocytes, SOXCGFPTNF3

value: Ade5CMV-eGFP and TNF

value: inflammation


title: Fibroblast-like synoviocytes, SOXCGFPTNF2


title: CD34+ differentiation Day12-KD1, RNA-seq

value: differentiation Day12

value: CD34+ cells


title: WT_Cortex_RNA_n1


title: 3a1KO_Cortex_RNA_1


title: Fibroblast-like synoviocytes, SOXCGFPTNF1


title: Panc1-GR W7 10xGenomics

city: Chicago

first: Elizaveta

middle: V

last: Benevolenskaya

state: IL

address: 900 S. Ashland Ave.

department: Biochemistry and Molecular Genetics

institute: University of Illinois at Chicago

description: Single cell RNA-seq was performed using 10x Genomics

data_processing:
DropSeq: Illumina Casava1.7 software used for basecalling. 10xGenomics: Fastq files from NovaSeq was processed using the function "count" (Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1) in 10X Genomics Cellranger version 6.0.0 with default paramaters.
Drop-seq: Illumina paired end raw FastQ file were processed for read alignment and gene expression. Drop-seq single-cell data was analyzed using the data anlysis protocol described in Drop-seq cook-book (Macosko et al. 2015)(http://mccarrolllab.com/dropseq/) and used the Drop-seq_tools-1.13 using STAR as aligner. Both Drop-seq and 10x Genomics reads were aligned against genome version GRCh37.p13 hg19 (From Ensembl) and corresponding gene model is extracted from Ensembl version 74.
Quality of read and mapping were checked using the program FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) or CellRanger 6.0.0.
Drop-seq: The aligned libraries were further processed into Digital Gene Expression (DGE) matrix using the Drop-seq program DigitalExpression tool (integrated in Drop- seq_tools-1.13). The number of cells that were extracted from aligned BAM file was based on the knee plot procedure, which extracts the number of reads per cell, then plots the cumulative distribution of reads and selects the knee of the distribution.
Genome_build: GRCh37.p13
Supplementary_files_format_and_content: Drop-seq: Tab-delimited text file; gene expression (as count) of each gene for each extracted cell. 10x Genomics: features, barcodes and matrix as the deafult from CellRanger 6.0.0. Processed Seurat objects.
10x Genomics: features, barcodes and matrix as the deafult from CellRanger 6.0.0. Processed Seurat objects.

source_name: Panc1-GR treated with 10 µM W-7

growth_protocol: Panc1 cells was grown in DMEM + 10% FBS + 1% P/S (HyClone) media containing penicillin and streptomycin in 5% CO2 at 37ºC. Cells obtained from vendor were maintained for no more than 5 passages before collection for scRNA-seq analysis. Panc1-GR cells were grown similarly, though the culture media supplemented with 10uM Gemcitabine prior to the experiment.

extract_protocol:
Drop-seq or 10x Genomics Chromium Controller on the single cell suspension
Drop-seq: Nextera XT tagmentation using Illumina cat# FC-131-1096 (Drop-seq protocol). 10x Genomics: Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1

treatment_protocol: 500,000 Panc1 cells were seeded in 6 well plates in DMEM + 10% FBS + 1% P/S. After two days, the media was aspirated and replaced with 2mL of either a vehicle control (media with 2µL PBS per 2mL, PANC1CTRL) or media supplemented with 2µM Gemcitabine (2uL stock solution per 2mL, PANC1GEM24H). After 24 hours, cells were trypsinized, centrifuged, resuspended in DMEM, counted, and processed for Drop-seq. Experiments using Panc1-GR were performed similarly, though cells were treated with 10µM (2uL stock solution per 2mL) of either W-7, BAPTA-AM, or 5µM  (1uL stock solution per 2mL) Amlodipine, and processed for 10x Genomics.

value: Treated for 24 h


title: WT_Cortex_RNA_3


title: Fibroblast-like synoviocytes, SOXCKO3

value: SoxC knockout


title: WT_Cortex_RNA_2


title: Fibroblast-like synoviocytes, SOXCKO2


title: CD34+ differentiation Day12-WT1, RNA-seq

value: WT


title: Fibroblast-like synoviocytes, SOXCKO1

value: Fibroblast-like synoviocytes


title: CD34+ differentiation Day12-WT2, RNA-seq


title: WT_Cortex_H3K27me3

extract_protocol:
Cerebral cortices were isolated, crushed and homogenized briefly by pipetting. Lysates were clarified from cross-linked and sonicated tissues. Protein-DNA complexes were immunoprecipitated with indicated antibody.
ChIP-Seq libraries were prepared with ThruPLEX® DNA-seq 48D Kit (Rubicon Genomics)

value: Dnmt3a-FLAG knock-in

value: postnatal day 18


title: Panc1-GR Amlodipine 10xGenomics

source_name: Panc1-GR treated with 5 µM Amlodipine


title: Fibroblast-like synoviocytes, SOXCKOTNF3

value: Synovium

value: Ade5CMV-Cre and TNF


title: CD34+ differentiation Day10-KD1, RNA-seq

value: differentiation Day10


title: WT_Cortex_RNA_1

value: Cerebral cortex

value: Wild type

value: postnatal day 21


title: WT_Cortex_DNMT3A-FLAG

value: anti-FLAG


title: CD34+ differentiation Day12-KD2, RNA-seq

value: KD


title: IV236scRNA-seq

description:
IV236filtered_contig_igblast_db-pass_parse-select.tab
IV236matrix.tar

value: Isolated unstimulated CD4+ T cells by negative selection

value: Viremic


title: Panc1-GR BAPTA 10xGenomics

source_name: Panc1-GR treated with 10 µM BAPTA-AM


title: CD34+ differentiation Day10-WT2, RNA-seq

value: CD34+ cells


title: WT_Cortex_H3K4me3


title: Panc1-GR 10xGenomics

source_name: Panc1-GR untreated

value: Treated with Gemcitabine for several passages, until viable in approximately 10x the known IC50 value


title: H3K4me3_T16_rep1

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

data_processing:
ChIP-seq and RNAseq reads were aligned to the hg38 reference genome using bowtie2 version 2.4.1 for ChIP-seq reads and BWA-MEM version 0.7.12  for RNAseq reads
Duplicate reads were removed using picard MarkDuplicates
For RNA-seq,  reads per transcript were counted using featureCounts from Subread package 2.0.1. Differential gene expression was determined using DESeq2 1.30.0.
For histone modification ChIPseq, H3K4me1 peaks were called from both replicated using macs2 2.2.7.1 .
For LMNB1 ChIPseq, Peak calling was done using Enriched Domain Detector (EDD) version 1.1.15, run 10 times on each sample to optimize BinSize and GapPenalty settings.
Genome_build: hg38
Supplementary_files_format_and_content: bedgraph files with 4 columns: chromosome, start position, end position, score
Supplementary_files_format_and_content: featureCounts.txt : tab-delimited text files with 2 columns: transcript ID , read count
Supplementary_files_format_and_content: DESeq2_counts.txt :  tab-delimited text files with 2 columns: transcript ID , DESeq2 normalized count
Supplementary_files_format_and_content: bed files with 4 columns: chromosome, start position, end position, score
Supplementary_files_format_and_content: Bigwig file with log2ratio ChIP/Input were generated using bamCompare from deeptools 3.5.1.

source_name: Human primary adipose stem cells

growth_protocol: Human normal ASCs purifed from adipose tissue were cultured in proliferating state in DMEM/F12 containing 10 % fetal calf serum and 20 ng/ml basic fibroblast growth factor.

extract_protocol:
For ChIP, cells were sonicated to produce chromatin fragments of ~200 base-pairs, lysates were clarified by sedimentation and histone-DNA or Lamin-DNA complexes were isolated from supernatants by ChIP using specific antibodies. RNA was purified from cell lysates using the RNEasy mini kit (Qiagen).
ChIP-seq and RNA-seq sequencing libraries were prepared according to  Illumina protocols for sequencing on a Nextseq500 or Novaseq (ChIP-seq) or on a Nextseq500 (RNA-seq) at the Norwegian Sequencing Center.

treatment_protocol: Proliferating cells were harvested, re-seeded at confluency and cultured confluent for 48 h without fibroblast growth factor. At T00, ASCs were induced to differentiate with 10 µg/ml insulin, 200 µM indomethacin, 1µM dexamethasone and 0.5 µM 3-isobutyl-1-methylxanthine.  Cells were collected at indicated timepoints for protein, RNA and chromatin preparations and analyses.

tag: time point

value: 16 Hours (T16)

value: ASCs on 16 hours after adipogenic induction

value: anti-H3K4me3 antibody (Diagenode c15410003), at 2.5 microgram per 10e6 cells

tag: replicate


title: WT_Cortex_input

value: Dnmt3a-FLAG knock-in


title: CD34+ differentiation Day8-KD4, RNA-seq

value: differentiation Day8


title: CUG200-m-3

city: Wuhu

first: Xiaopeng

last: Shen

address: 1 East Beijing Rd.

country: China

institute: Anhui Normal University

data_processing:
trim_galore
Hisat2
Stringtie
Genome_build: GRCm38
Supplementary_files_format_and_content: matrix table and raw fastq sequencing data

extract_protocol:
Total RNA samples were extracted using the Total RNA Isolation Reagent (Biosharp).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mouse myoblast

tag: Stage

value: myoblast differentiation day 4

value: miR-322/-503 overexpression


title: CD34+ differentiation Day10-KD2, RNA-seq

tag: time

value: differentiation Day10


title: CD34+ differentiation Day8-KD3, RNA-seq


title: CUG200-m-2

tag: cell line


title: H3K4me3_T12_rep1

value: 12 Hours (T12)

value: ASCs on 12 hours after adipogenic induction


title: H3K4me3_T08_rep1

value: 08 Hours (T08)

value: ASCs on 08 hours after adipogenic induction


title: aba2-3 IAA treated shoot replicate 2

city: Saint Louis

first: Ryan

middle: Joseph

last: Emenecker

state: MO

address: 660 S Euclid Ave

department: Biochemistry and Molecular Biophysics

description: run_2808_s_*_withindex_sequence.txt_TTTGGCG

data_processing:
The samples were sequenced across three (1x50bp) lanes using an Illumina HiSeq 3000.
The reads were then demultiplexed and aligned to the TAIR 10 Ensemble Release 23 assembly using STAR.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount.
Gene counts were normalized using the R/Bioconductor package EdgeR, and TMM normalization size factors were calculated to adjust values due to differences in library size. Ribosomal genes and genes not expressed in any sample greater than 2 counts-per-million were not considered for further analysis.
The calculated TMM size factors and the matrix of counts were then imported into the R/Bioconductor Limma package. The weighted likelihoods based on observed mean-variance relationship of every gene for every sample were calculated using the voomWithQualityWeights function.
The residual standard deviation of every gene to the gene’s average log-count was plotted to assess gene performance, and these values were used to fit a trendline of the residuals
A generalized linear model was then created to test for gene level differential expression, and results for genes with a Benjamini-Hochberg flase-discovery rate adjusted p-value of greater than or equal to 0.05 were filtered out.
Genome_build: TAIR 10
Supplementary_files_format_and_content: The processed data is in the form of .txt files for each sample and contain information on gene notation, chromosome location, the strand orientation, the length, the raw coiunt number, the (CPM), and the RPKM

organism: Arabidopsis thaliana

source_name: aba2-3 IAA treated shoot

growth_protocol: Before plating, seeds were surface sterilized  and then resuspended in 0.1% agar. The seeds were then stratified for 2 days at 4°C. After stratification, the seeds were plated on plant nutrient (PN) media containing 0.6% agar and supplemented with 0.5% sucrose (PNS).  The seeds were incubated for 24 hours under continuous light. After the 24 hours of exposure to continious light, the plates were then wrapped in three sheets of aluminum foil and incubated for four days at which time treatment was carried out (either mock, 10um IAA, or 10um ABA).

extract_protocol:
Total RNA was isolated from each tissue for each respective treatment using the RNeasy Plant Mini Kit from Qiagen according to manufacturer’s instructions.
Samples were prepared for sequencing using the SMARTer cDNA synthesis kit (Clontech) according to manufacturer’s instructions. Library construction was carried out by the Genome Technology Access Center (GTAC) at Washington University School of Medicine.

treatment_protocol: The dark-grown plants were transferred to liquid PNS containing either 10uM IAA, 10uM ABA, or the equivalent amount of ethanol for the mock treatment in a dark room with only a green safe-light for illumination. Each treatment was repeated in triplicate for both lines. After incubation for two hours, the seedlings were removed from the liquid PNS, cut and separated at the root shoot junction, and the isolated tissue was then immediately frozen in liquid nitrogen.

tag: treatment

value: 10 uM IAA treated (2 hours)

tag: growth duration

value: five days old (1 day continious light 4 days dark)

value: shoot


title: H3K4me3_T24_rep1

value: 24 Hours (T24)

value: ASCs on 24 hours after adipogenic induction


title: H3K4me3_T04_rep1

value: 04 Hours (T04)

value: ASCs on 04 hours after adipogenic induction


title: CUG200-ctrl-3

value: control


title: aba2-3 IAA treated root replicate 3

institute: Washington University School of Medicine

description: run_2808_s_*_withindex_sequence.txt_AATTCAT

source_name: aba2-3 IAA treated root

value: root


title: H3K4me3_T00_rep1

value: 00 Hours (T00)

value: ASCs on the day of differentiation induction

value: anti-H3K4me3 antibody (Diagenode c15410003), at 2.5 microgram per 10e6 cells


title: aba2-3 IAA treated shoot replicate 1

description: run_2808_s_*_withindex_sequence.txt_AGGCGAA


title: CUG200-ctrl-1

value: mouse myoblast

value: myoblast differentiation day 4


title: CD34+ differentiation Day8-KD2, RNA-seq

value: KD

value: differentiation Day8

value: CD34+ cells


title: CUG200-m-1

value: miR-322/-503 overexpression


title: CD34+ differentiation Day8-WT4, RNA-seq

value: WT


title: CD34+ differentiation Day10-WT1, RNA-seq

value: differentiation Day10


title: CD34+ differentiation Day8-KD1, RNA-seq


title: Fibroblast-like synoviocytes, SOXCKOTNF1

value: Fibroblast-like synoviocytes

value: Synovium

value: Ade5CMV-Cre and TNF

value: SoxC knockout

value: inflammation


title: aba2-3 IAA treated root replicate 1

description: run_2808_s_*_withindex_sequence.txt_GTAAAAA

value: 10 uM IAA treated (2 hours)

value: five days old (1 day continious light 4 days dark)

value: root


title: aba2-3 IAA treated root replicate 2

description: run_2808_s_*_withindex_sequence.txt_CTGCAAT


title: CD34+ differentiation Day8-WT3, RNA-seq


title: Fibroblast-like synoviocytes, SOXCKOTNF2


title: 3a1dN_Neuron nuclei_Me_2

description: 3a1dN_Neuron nuclei_Me_2

data_processing:
Raw reads of EM-Seq data were mapped to mouse genome (mm9) using BSMAP (v2.90) with default parameters
Duplicated reads were removed and only properly paired reads that uniquely mapped to genome were used.
CpG methylation ratios on both strands were combined and CpG loci with sequencing depth less than 5 were excluded.
Genome_build: mm9

source_name: Cortical neuron nuclei

extract_protocol: Cortical neuron nuclei were isolated by douncing the cerebral cortex tissue in a dounce homogenizer and sorted with an anti-NEUN antibody. Genomic DNA and total RNA were purified from the same materials with AllPrep DNA/RNA Mini Kit (Qiagen).

value: Cortical neuron nuclei

value: postnatal day 21


title: H3K4me3_H3K27ac_Input_T24

value: 24 Hours (T24)

value: ASCs on 24 hours after adipogenic induction


title: H3K4me3_T20_rep1

value: 20 Hours (T20)

value: ASCs on 20 hours after adipogenic induction

value: anti-H3K4me3 antibody (Diagenode c15410003), at 2.5 microgram per 10e6 cells


title: CUG200-ctrl-2

value: mouse myoblast

value: myoblast differentiation day 4

value: control


title: H3K4me3_H3K27ac_Input_T20


title: aba2-3 IAA treated shoot replicate 3

description: run_2808_s_*_withindex_sequence.txt_TAACAAG

value: shoot


title: H3K4me3_H3K27ac_Input_T16

value: 16 Hours (T16)

value: ASCs on 16 hours after adipogenic induction


title: 3a1dN_Neuron nuclei_Me_1

description: 3a1dN_Neuron nuclei_Me_1


title: aba2-3 mock treated shoot replicate 3

description: run_2808_s_*_withindex_sequence.txt_TGGCATA

source_name: aba2-3 mock treated shoot

value: mock treated


title: CD34+ differentiation Day8-WT1, RNA-seq

value: WT

value: differentiation Day8

value: CD34+ cells


title: 3a2KO_Neuron nuclei_Me_2

description: 3a2KO_Neuron nuclei_Me_2

value: Cortical neuron nuclei


title: H3K4me3_H3K27ac_Input_T08

value: 08 Hours (T08)

value: ASCs on 08 hours after adipogenic induction


title: Male_H3K79me2_Rep1

city: ROSCOFF

first: Olivier

last: GODFROY

address: Place Georges Teissier CS90074

department: Station Biologique de Roscoff

country: France

institute: CNRS

data_processing:
Illumina base calling
Sequence quality was evaluated with FASTQC and poor quality sequence removed with Cutadapt (Hansen et al., 2016)
ChIP-seq Illumina reads were mapped onto the Ectocarpus genome using Bowtie (Langmead et al., 2009) and duplicates were removed using samtools markdup (v 1.9 - Li et al., 2009).
H3K79me2 was analysed using SICER (v1.1) (minimum FDR of 0.01) (Xu et al., 2014; Zang et al., 2009) with a window size of 200 bp and a gap size of 400 bp. The signal was normalized using the Signal Extraction Scaling (SES) method (Diaz et al., 2012).
Genome_build: Ectocarpus sp. Ec32 genome v2 2018 (https://bioinformatics.psb.ugent.be/orcae/overview/EctsiV2)
Supplementary_files_format_and_content: bigWig files were generated from bam files, which were merges of the two replicates, normalised with SES with the signal subtract from the input using deeptools (v3.2.0; Fidel R, Ryan DP, Grüning B, Bhardwaj V, Kilpert F, Richter AS, Heyne S, Dündar F, Manke T. 2016. deepTools2: A next Generation Web Server for Deep-Sequencing Data Analysis. Nucleic Acids Research 44:W160-W165). Peak calling files, based on the bigWig files, are in either narrowPeak (bed9) or broadPeak (bed12) format.

organism: Ectocarpus sp. Ec457

growth_protocol: Cultures were grown in 140 mm round Petri dishes in natural sea water with 0.01% Provasoli enrichment at 13°C with a 12h/12h day/night cycle and 20 (µmol photons).m-2.s-1 irradiance.

extract_protocol:
For ChIP-seq, Ectocarpus tissue was fixed for five minutes in seawater containing 1% formaldehyde and the formaldehyde eliminated by rapid filtering followed by incubation in PBS containing 400 mM glycine. Nuclei were isolated by grinding in liquid nitrogen and in a Tenbroeck Potter in nuclei isolation buffer (0.1% triton X-100, 125 mM sorbitol, 20 mM potassium citrate, 30 mM MgCl2, 5 mM EDTA, 5 mM β-mercaptoethanol 55 mM HEPES at pH 7.5 with complete ultra protease inhibitors), filtering through Miracloth and then washing the precipitated nuclei in nuclei isolation buffer with and then without 1% triton X-100. Chromatin was fragmented by sonicating the purified nuclei in nuclei lysis buffer (10 mM EDTA, 1% SDS, 50 mM Tris-HCl at pH 8 with complete ultra protease inhibitors) in a Covaris M220 Focused-ultrasonicator (duty 25%, peak power 75, cycles/burst 200, duration 900 sec at 6°C). The chromatin was incubated with an anti-histone PTM antibody overnight at 4°C and the immunoprecipitation carried out using Dynabeads protein A and Dynabeads protein G. Following immunoprecipitation and washing, a reverse cross-linking step was carried out by incubating for at least six hours at 65°C in 200mM NaCl and the samples were then digested with Proteinase K and RNAse A. The purified DNA was then prepared for Illumina sequencing. For RNA-seq, RNA was extracted from the same duplicate male and female gametophytes cultures as were used for the ChIP-seq analysis using the Qiagen RNeasy plant mini kit with an on-column Deoxyribonuclease I treatment. RNA concentration have been assessed using a Qubit 2.0 Fluorometer (Thermofisher). RNA contamination for genomic DNA have been tested by PCR using pairs of primers specific to the non-coding genome.
Illumina librairies corresponding to “NAR_” files were prepared and sequenced in the Genome Center of the Max Planck Institute for Developmental Biology (Tuebingen, Germany)  using the TruSeq ChIP-seq.

treatment_protocol: No treatment

tag: Sex

value: Male

value: whole organism

value: mature, 4 weeks old

tag: phenotype

value: imm

value: Di-Methyl-Histone H3 (Lys79) (D15E8) XP Rabbit mAb, CST, lot 5427


title: 3a2KO_Neuron nuclei_Me_1

description: 3a2KO_Neuron nuclei_Me_1

tag: genotype

value: postnatal day 21


title: aba2-3 mock treated shoot replicate 1

description: run_2808_s_*_withindex_sequence.txt_CCATCAT

value: five days old (1 day continious light 4 days dark)

tag: tissue


title: aba2-3 mock treated shoot replicate 2

description: run_2808_s_*_withindex_sequence.txt_GGAGTCC

value: shoot


title: 3a1KO_Neuron nuclei_Me_1

description: 3a1KO_Neuron nuclei_Me_1

tag: strain


title: aba2-3 mock treated root replicate 1

description: run_2808_s_*_withindex_sequence.txt_CCGGCAG

source_name: aba2-3 mock treated root

value: root


title: Male_H3_Rep1_2

value: Histone H3 (D2B12) XP Rabbit mAb (ChIP Formulated), CST #4620 Lot No 12


title: Male_H3K79me2_Rep2


title: H3K27ac_T24_rep1

value: 24 Hours (T24)

value: ASCs on 24 hours after adipogenic induction

value: anti-H3K27ac antibody (Diagenode c15410174), at 2.5 microgram per 10e6 cells


title: H3K4me3_H3K27ac_Input_T00

value: 00 Hours (T00)

value: ASCs on the day of differentiation induction


title: aba2-3 mock treated root replicate 2

description: run_2808_s_*_withindex_sequence.txt_GATGGCC

value: mock treated


title: Male_H3_Rep2_2


title: Col-O ABA treated shoot replicate 3

description: run_2808_s_*_withindex_sequence.txt_AGTTATG

source_name: Col-O ABA treated shoot

value: Col-O (wild-type)

value: 10 uM ABA treated (2 hours)


title: WT_Neuron nuclei_Me_1

description: WT_Neuron nuclei_Me_1

value: Cortical neuron nuclei

value: Wild type

tag: developmental stage


title: H3K27ac_T20_rep1

value: 20 Hours (T20)

value: ASCs on 20 hours after adipogenic induction

tag: chip antibody


title: WT_Neuron nuclei_Me_2

description: WT_Neuron nuclei_Me_2

value: postnatal day 21


title: aba2-3 mock treated root replicate 3

description: run_2808_s_*_withindex_sequence.txt_TGACTCT

value: five days old (1 day continious light 4 days dark)


title: Male_Input_Rep1_2

value: Male

value: whole organism

value: mature, 4 weeks old

value: imm

value: none (input)


title: H3K4me3_H3K27ac_Input_T12

value: 12 Hours (T12)

value: ASCs on 12 hours after adipogenic induction


title: CD34+ differentiation Day8-WT2, RNA-seq

value: WT

value: differentiation Day8

value: CD34+ cells


title: T8-10X-260321

city: Cambridge

first: Samar

middle: Hayat Khan

last: Tareen

address: Babraham Hall, Babraham

country: United Kingdom

institute: Babraham Institute

data_processing:
Initial QC and counts generated via Cell Ranger v6.0
Data imported into Seurat v4.0 and filtered to retain cell with <10% mitochondrial expression in total expression
Filtered data normalised via SCT and filtered to remove multiplets via scDblFinder
Data projected in UMAP, clusters produced via Louvain algorithm, and cell types identified by known markers
T-cells and microglia separated into subsets and analysed for differential expression using negative binomial tests
Pathway analysis performed using GAGE v2.40.2, Pathview v1.30.1 and clusterProfiler v3.18.1
Genome_build: Mus_musculus.GRCm38.101
Supplementary_files_format_and_content: Processed files are .RData files containing the respective seurat objects for the full data, and the microglia and T cell subsets

source_name: Sorted brain glia

growth_protocol: Traumatic brain injury (TBI) or sham surgery, day 0.

extract_protocol:
Day 14, T cells (TCRβ+CD45+CD11b-) and microglia (CD11b+CD45+) were sorted from the perfused brains for 10x single cell transcriptomics.
Library preparations for the scRNA-seq was performed using 10X Genomics Chromium Single Cell 3’ Kit, v3 (10X Genomics).

treatment_protocol: Intravenous injection of PHP.GFAP-IL2 or PHP.GFAP-GFP, day -14.

tag: t cell group

value: Sham

tag: microglia group


title: Col-O ABA treated shoot replicate 2

description: run_2808_s_*_withindex_sequence.txt_ATGTTCT

value: Col-O (wild-type)

value: 10 uM ABA treated (2 hours)

value: shoot


title: H3K27ac_T12_rep1

tag: cell type

value: anti-H3K27ac antibody (Diagenode c15410174), at 2.5 microgram per 10e6 cells


title: H3K4me3_H3K27ac_Input_T04

tag: time point

value: 04 Hours (T04)

value: ASCs on 04 hours after adipogenic induction


title: Male_H4K20me3_Rep2

description:
Corresponding replicate: ADPH-36
Male_ChIP_H4K20me3_inputH3_subtract.bdg.bw
Male_ChIP_H4K20me3_SICER

data_processing:
Illumina base calling
Sequence quality was evaluated with FASTQC and poor quality sequence removed with Cutadapt (Hansen et al., 2016)
ChIP-seq Illumina reads were mapped onto the Ectocarpus genome using Bowtie (Langmead et al., 2009) and duplicates were removed using samtools markdup (v 1.9 - Li et al., 2009).
Peaks corresponding to regions enriched in H3K4me3, H3K9ac and H3K27ac were identified using the MACS2 (version 2.1.1) callpeak module (minimum FDR of 0.01) and refined with the MACS2 bdgpeakcall and bdgbroadcall modules (Zhang et al., 2008). H3K36me3 and H4K20me3 were analysed using SICER (v1.1) (minimum FDR of 0.01) (Xu et al., 2014; Zang et al., 2009) with a window size of 200 bp and a gap size of 400 bp. The signal was normalized using the Signal Extraction Scaling (SES) method (Diaz et al., 2012).
RNAseq reads were trimmed and filtered using Cutadapt (Martin, 2011) with a quality threshold of 33 (quality-cutoff) and a minimal size of 30 bp. Then filtered reads were mapped to version v2 of the Ectocarpus sp. genome (Cormier et al., 2017a) using TopHat2 with the Bowtie2 aligner (Kim et al., 2013).
Mapped RNA-seq data was processed with featureCounts (Liao et al., 2014) to obtain counts of numbers of reads mapped to exons. Expression values were represented as TPM.
Differential expression was detected using the DESeq2 package (Bioconductor; Love MI, Huber W, Anders S. 2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15: 550) using an adjusted p‐value cut‐off of 0.05 and a minimal fold‐change of 2.
Genome_build: Ectocarpus sp. Ec32 genome v2 2018 (https://bioinformatics.psb.ugent.be/orcae/overview/EctsiV2)
Supplementary_files_format_and_content: bigWig files were generated from bam files, which were merges of the two replicates, normalised with SES with the signal subtract from the input using deeptools (v3.2.0; Fidel R, Ryan DP, Grüning B, Bhardwaj V, Kilpert F, Richter AS, Heyne S, Dündar F, Manke T. 2016. deepTools2: A next Generation Web Server for Deep-Sequencing Data Analysis. Nucleic Acids Research 44:W160-W165). Peak calling files, based on the bigWig files, are in either narrowPeak (bed9) or broadPeak (bed12) format.

extract_protocol:
For ChIP-seq, Ectocarpus tissue was fixed for five minutes in seawater containing 1% formaldehyde and the formaldehyde eliminated by rapid filtering followed by incubation in PBS containing 400 mM glycine. Nuclei were isolated by grinding in liquid nitrogen and in a Tenbroeck Potter in nuclei isolation buffer (0.1% triton X-100, 125 mM sorbitol, 20 mM potassium citrate, 30 mM MgCl2, 5 mM EDTA, 5 mM β-mercaptoethanol 55 mM HEPES at pH 7.5 with complete ultra protease inhibitors), filtering through Miracloth and then washing the precipitated nuclei in nuclei isolation buffer with and then without 1% triton X-100. Chromatin was fragmented by sonicating the purified nuclei in nuclei lysis buffer (10 mM EDTA, 1% SDS, 50 mM Tris-HCl at pH 8 with complete ultra protease inhibitors) in a Covaris M220 Focused-ultrasonicator (duty 25%, peak power 75, cycles/burst 200, duration 900 sec at 6°C). The chromatin was incubated with an anti-histone PTM antibody overnight at 4°C and the immunoprecipitation carried out using Dynabeads protein A and Dynabeads protein G. Following immunoprecipitation and washing, a reverse cross-linking step was carried out by incubating for at least six hours at 65°C in 200mM NaCl and the samples were then digested with Proteinase K and RNAse A. The purified DNA was then prepared for Illumina sequencing. For RNA-seq, RNA was extracted from the same duplicate male and female gametophytes cultures as were used for the ChIP-seq analysis using the Qiagen RNeasy plant mini kit with an on-column Deoxyribonuclease I treatment. RNA concentration have been assessed using a Qubit 2.0 Fluorometer (Thermofisher). RNA contamination for genomic DNA have been tested by PCR using pairs of primers specific to the non-coding genome.
Illumina librairies were prepared by Fasteris using the TruSeq ChIP-seq (for ChIP-seq) or TruSeq RNA stranded protocol (for RNA-seq) before sequencing.

value: Male

value: Tri-Methyl-Histone H4 (Lys20) (D84D2) Rabbit mAb, CST #5737

tag: sample code


title: H3K27ac_T16_rep1

value: 16 Hours (T16)

value: ASCs on 16 hours after adipogenic induction

tag: replicate


title: 3a1KO_Neuron nuclei_Me_2

description: 3a1KO_Neuron nuclei_Me_2

value: Cortical neuron nuclei

value: postnatal day 21


title: T7-10X-260321

value: TBI


title: T6-10X-260321


title: Male_Input_Rep2_2

value: whole organism

tag: Stage

value: mature, 4 weeks old

value: imm

value: none (input)


title: Male_H4K20me3_Rep1

description:
Corresponding replicate: ADPH-37
Male_ChIP_H4K20me3_inputH3_subtract.bdg.bw
Male_ChIP_H4K20me3_SICER


title: Col-O ABA treated shoot replicate 1

description: run_2808_s_*_withindex_sequence.txt_CGCTACA

value: Col-O (wild-type)

value: five days old (1 day continious light 4 days dark)


title: Col-O ABA treated root replicate 2

description: run_2808_s_*_withindex_sequence.txt_GGCAGCG

source_name: Col-O ABA treated root

value: 10 uM ABA treated (2 hours)

value: root


title: H3K27ac_T08_rep1

value: 08 Hours (T08)

value: ASCs on 08 hours after adipogenic induction

value: anti-H3K27ac antibody (Diagenode c15410174), at 2.5 microgram per 10e6 cells


title: Col-O ABA treated root replicate 1

description: run_2808_s_*_withindex_sequence.txt_TCGTGCG


title: Male_H3K9ac_Rep2

description:
Corresponding replicate: ADPH-42
Male_ChIP_H3K9ac_merge_sorted.bam.subtract.bdg.bw
Male_ChIP_H3K9ac_MACS2

value: Male

value: Acetyl-Histone H3 (Lys9) (C5B11) Rabbit mAb, CST #9649 Lot No 0011


title: T4-10X-260321

value: Sham


title: Male_H3K9ac_Rep1

description:
Corresponding replicate: ADPH-46
Male_ChIP_H3K9ac_merge_sorted.bam.subtract.bdg.bw
Male_ChIP_H3K9ac_MACS2


title: H3K27ac_T04_rep1

value: 04 Hours (T04)

value: ASCs on 04 hours after adipogenic induction


title: Male_H3K4me3_Rep2

description:
Corresponding replicate: ADPH-34
Male_ChIP_H3K4me3_merge_sorted.bam.subtract.bdg.bw
Male_ChIP_H3K4me3_MACS2

value: Tri-Methyl-Histone H3 (Lys4) (C42D8) Rabbit mAb, CST #9751Lot No 0009


title: C6

city: Changsha

first: Xi

middle: Yu

last: Zhou

state: Hunan Province

address: No. 72 Xiangya Road, Changsha City, Hunan Province

institute: Xiangya Stomatological Hospital

data_processing:
Basecalls performed using  Solexa pipeline v1.8
The trimmed reads (trimmed 5',3'-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.1.0)software
The transcript abundances for each sample was estimated with StringTie（1.3.3）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.10.0)
Genome_build: GRCh37
Supplementary_files_format_and_content: The xlsx format file contains the FPKM value of gene in every sample

source_name: hip joint capsule of control subjects

extract_protocol:
The joint capsule tissues were washed by phosphate buffer saline, and then synovium tissues were removed from joint capsules. The isolated joint capsule tissues were used in following study，RNA was harvested using Trizol reagent.RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis
Libraries were prepared by using KAPA Stranded RNA-Seq Library Prep Kit(Illumina). Briefly,Total RNA of each sample was used to prepare the RNA sequencing library 1)RNA fragment；2)Random primed first strand cDNA synthesis；3)dUTP based second strand cDNA synthesis;4)Adaptor ligation and PCR amplification.

tag: subject status

value: control

value: hip joint capsule


title: Male_H3K4me3_Rep1

description:
Corresponding replicate: ADPH-38
Male_ChIP_H3K4me3_merge_sorted.bam.subtract.bdg.bw
Male_ChIP_H3K4me3_MACS2

value: whole organism

value: mature, 4 weeks old

value: imm


title: H3K27ac_T00_rep1

value: 00 Hours (T00)

value: ASCs on the day of differentiation induction


title: T3-10X-260321

tag: treatment

value: TBI


title: Col-O IAA treated shoot replicate 3

description: run_2808_s_*_withindex_sequence.txt_GGCAAGA

source_name: Col-O IAA treated shoot

value: Col-O (wild-type)

value: 10 uM IAA treated (2 hours)

tag: growth duration

value: five days old (1 day continious light 4 days dark)

value: shoot


title: C5


title: Col-O IAA treated shoot replicate 2

description: run_2808_s_*_withindex_sequence.txt_GTATCCT


title: T2-10X-260321


title: Male_H3K36me3_Rep2

description:
Corresponding replicate: ADPH-31
Male_ChIP_H3K36me3_inputH3_subtract.bdg.bw
Male_ChIP_H3K36me3_SICER

tag: Sex

value: Male

value: Anti-Histone H3 (tri methyl K36) antibody, Abcam ab9050


title: Col-O ABA treated root replicate 3

description: run_2808_s_*_withindex_sequence.txt_ACGCGGG

value: 10 uM ABA treated (2 hours)

value: root


title: C4


title: T1-10X-260321

value: Sham


title: Male_H3K36me3_Rep1

description:
Corresponding replicate: ADPH-32
Male_ChIP_H3K36me3_inputH3_subtract.bdg.bw
Male_ChIP_H3K36me3_SICER

tag: phenotype


title: Col-O IAA treated Root replicate 3

description: run_2808_s_*_withindex_sequence.txt_GGTGAAT

source_name: Col-O IAA treated Root

tag: genotype


title: Col-O IAA treated shoot replicate 1

description: run_2808_s_*_withindex_sequence.txt_GCCTCCC

tag: tissue


title: T5-10X-260321


title: Col-O IAA treated Root replicate 2

description: run_2808_s_*_withindex_sequence.txt_AATACGC


title: 3a1dN_Cortex_BS_2

data_processing:
Raw reads of EM-Seq data were mapped to mouse genome (mm9) using BSMAP (v2.90) with default parameters
Duplicated reads were removed and only properly paired reads that uniquely mapped to genome were used.
CpG methylation ratios on both strands were combined and CpG loci with sequencing depth less than 5 were excluded.
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph files

source_name: Cerebral cortex

extract_protocol:
Cerebral cortices were isolated, crushed and homogenized. Genomic DNA and total RNA were purified from the same materials with AllPrep DNA/RNA Mini Kit (Qiagen)
Bisulfite-Seq libraries were prepared with NEBNext® Enzymatic Methyl-seq Kit (NEB)

value: Cerebral cortex

tag: strain

value: postnatal day 21


title: Male_H3K27ac_Rep2

description:
Corresponding replicate: ADPH-50
Male_ChIP_H3K27ac_merge_sorted.bam.subtract.bdg.bw
Male_ChIP_H3K27ac_MACS2

value: whole organism

value: Anti-acetyl-Histone H3 (Lys27) Antibody, Millipore 07-360 Lot No 2987402


title: Male_H3K27ac_Rep1

description:
Corresponding replicate: ADPH-53
Male_ChIP_H3K27ac_merge_sorted.bam.subtract.bdg.bw
Male_ChIP_H3K27ac_MACS2

value: mature, 4 weeks old

value: imm


title: C2

value: control

value: hip joint capsule


title: C1


title: Male_H3_Rep1

description: Corresponding replicate: ADPH-48

value: Histone H3 (D2B12) XP Rabbit mAb (ChIP Formulated), CST #4620 Lot No 12


title: Male_H3_Rep2

description: Corresponding replicate: ADPH-47


title: 3a1dN_Cortex_BS_1

tag: developmental stage


title: T5

source_name: hip joint capsule of patients with DDH

value: Developmental dysplasia of the hip (DDH)


title: Male_Input_Rep2

description: Corresponding replicate: ADPH-52

tag: chip antibody


title: 3a2KO_Cortex_BS_2


title: 3a2KO_Cortex_BS_1


title: 3a1KO_Cortex_BS_2


title: Col-O IAA treated Root replicate 1

description: run_2808_s_*_withindex_sequence.txt_AAATGCA

value: Col-O (wild-type)

value: 10 uM IAA treated (2 hours)

value: five days old (1 day continious light 4 days dark)


title: Col-O mock treated shoot replicate 2

description: run_2808_s_*_withindex_sequence.txt_CTCACCC

source_name: Col-O mock treated shoot

value: mock treated

value: shoot


title: T4


title: 3a1KO_Cortex_BS_1


title: Col-O mock treated shoot replicate 1

description: run_2808_s_*_withindex_sequence.txt_ACTGGAT


title: T3


title: Col-O mock treated root replicate 3

description: run_2808_s_*_withindex_sequence.txt_CAGAGTC

source_name: Col-O mock treated root

value: root


title: WT_Cortex_BS_2

value: Wild type


title: C3


title: T2


title: WT_Cortex_BS_1

value: Cerebral cortex


title: Col-O mock treated root replicate 1

description: run_2808_s_*_withindex_sequence.txt_GATAGTT


title: T1


title: HEK293A cells, VT_rep3

status: Public on Mar 20 2022

city: La Jolla

first: Fulong

last: Li

state: CA

address: 2880 Torrey Pines Scenic Dr, SCRM 4805

institute: UC San Diego

data_processing:
HISAT2  program (Galaxy Version 2.2.1+galaxy0) for  alignment
htseq-count program (Galaxy Version 0.9.1) for counting aligned reads in a BAM file that overlap features in a GFF file
Assembly: hg38
Supplementary files format and content: text files include RAW htseq-count for each Sample

extract_protocol:
Total RNAs were extracted by RNeasy Plus Kit (QIAGEN, #74136)
The RNA sequencing library was prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina.

treatment_protocol: treated with vehicle ctrl or 20nM VT01454 for 2 hours

tag: cell line

value: human embryonic kidney cells

value: 20nM VT01454 for 2 hours


title: TECs AireKO

city: Tsurumi-ku, Yokohama

first: Hideyuki

last: Yoshida

state: Kanagawa

address: 1-7-22 Suehiro-cho

country: Japan

institute: RIKEN IMS

data_processing:
Illumina bcl2fastq software was used for generating FASTQ files
Sequenced reads were processed using Cell Ranger v3.0.0 software provided by 10x GENOMICS
Supplementary files format and content are described at http://software.10xgenomics.com/single-cell/overview/welcome
Genome_build: mm10
Supplementary_files_format_and_content: Unfiltered feature-barcode matrices containing all barcodes in MEX format

source_name: thymic epithelial cells

extract_protocol:
Mouse thymus was enzymatically  digested and then CD45-EpCAM+ cells were FACS-sorted. single‑cell emulsions were generated using a Chromium instrument from 10× Genomics.
RNA libraries were prepared for sequencing using Chromium Single Cell 3′ Reagent Kits v3 Chemistry

value: thymus

value: CD45-EpCAM+ thymic epithelial cells

tag: age

value: 8 weeks old

value: Aire-/-


title: HEK293A cells, Ctrl_rep3

tag: cell type

value: control vehicle DMSO


title: T6

value: hip joint capsule


title: HEK293A cells, VT_rep1


title: Hs, U3461MG-2

city: Uppsala

first: Xingqi

address: Husargata

department: Immunology, Genetics and Pathology

country: Sweden

institute: uppsala university

data_processing:
adaptors were trimmed.
ATAC-seq reads were aligned to hg19 using bowtie2 with the following parameters --very-sensitive
duplicate reads were marked and removed with picard tools version 1.119
Reads mapped to repeated regions and chromosomal M were removed.
the rest of reads were shifted +4/-5bp depending on the strand of the read around Tn5 cleavage position and were then extended to 50bp centered by the cleavage position
Peak calling was performed using MACS2 with options  -f BED, -g hs, -q 0.01, --nomodel, --shift 0
Genome_build: hg19 and mm9
Supplementary_files_format_and_content: bigwig

source_name: glioblastoma stem cells

growth_protocol: Mouse GBM cells (mGCs) were explanted and established as cultures in mouse cancer stem cell media without addition of EGF and FGF2 as described previously.  Surgical samples from GBM patients were obtained and human glioblastoma cell cultures (HGCC) were established from these samples as explained previously (Maturi et al., 2019; Xie et al., 2015). A total of 65 HGCC were used in this paper, among which 59 HGCC were established and sustained in serum-free medium. Whereas 4 HGCC were established and sustained in serum containing medium and 2 HGCC were switched and maintained as serum-free culture from serum containing medium (U3096MG and U3112MG).

extract_protocol:
All the libraries are ATAC protocol, DNA was purified with MiniElution kit
The ATAC library construction was done with standard ATAC-seq protocol.

treatment_protocol: no treatment for the cells

value: brain

value: glioblastoma stem cells

tag: growth protocol

value: Established and sustained in serum-free medium


title: Hs, U3461MG-1


title: HEK293A cells, VT_rep2


title: HEK293A cells, Ctrl_rep2


title: Hs, U3440MG-2


title: Hs, U3468MG-2


title: HEK293A cells, Ctrl_rep1


title: Hs, U3440MG-1


title: Col-O mock treated shoot replicate 3

description: run_2808_s_*_withindex_sequence.txt_CCGATTA

value: Col-O (wild-type)

value: five days old (1 day continious light 4 days dark)


title: Hs, U3468MG-1


title: Hs, U3429MG-1


title: Hs, U3340MG-2b

value: Established and sustained in serum containing medium


title: Hs, U3340MG-2a


title: Hs, U3323MG-1


title: Hs, U3340MG-1a


title: Hs, U3308MG-2


title: Male_RNA_Rep2

description: Corresponding replicate: ADPH-63

value: Male

value: whole organism

value: mature, 4 weeks old

value: imm

tag: sample code


title: Hs, U3308MG-1


title: Male_RNA_Rep1

description: Corresponding replicate: ADPH-64


title: Col-O mock treated root replicate 2

description: run_2808_s_*_withindex_sequence.txt_CGAAAGT

value: mock treated

value: root


title: Hs, U3340MG-1b


title: Hs, U3230-2b


title: Hs, U3323MG-2


title: Hs, U3230-1a


title: Hs, U3230-1b


title: Hs, U3201-2


title: Male_Input_Rep1

description: Corresponding replicate: ADPH-54


title: Hs, U3201-1


title: Hs, U3202-1


title: Hs, U3175-2


title: Hs, U3230-2a


title: Hs, U3175-1


title: Hs, U3180MG-2


title: Hs, U3180MG-1


title: Hs, U3263MG-1


title: Hs, U3429MG-2


title: Hs, U3202-2


title: Hs, U3173-2


title: Hs, U3173-1


title: Hs, U3169MG-2


title: Hs, U3172MG-1


title: Hs, U3172MG-2


title: Hs, U3140-2


title: Hs, U3164MG-1


title: Hs, U3167MG-1


title: Hs, U3155-2


title: Hs, U3164MG-2


title: Hs, U3137-1b


title: Hs, U3263MG-2


title: Hs, U3137-2a


title: QM6a_replicate_2

city: Vienna

first: Nadine

middle: Elpida

last: Tatto

address: Muthgasse 18

department: Department of Biotechnology

country: Austria

institute: University of Natural Resources and Life Sciences

data_processing:
Quality Control with FastQC v0.11.5
Read trimming with AfterQC v.0.9.7
Read quantification with kallisto v0.43.1  (kallisto index based on T.reesei QM6a release 38 genomic sequence as reference)
Differential expression analysis with R (DESeq2 v1.14.1)
Genome_build: T.reesei QM6a release 38
Supplementary_files_format_and_content: tsv file with estimated counts and TPM.  CSV file with normalized counts on series record.

organism: Trichoderma reesei QM6a

source_name: T. reesei RNA

growth_protocol: T. reesei QM6a and Δace1 were cultivated in shake flasks (28°C, 250 rpm) containing MA medium + 1% D-glucose for 24 hours. Mycelia was washed and transferred  to MA medium containing 1% D-mannitol for 3h.

extract_protocol:
after biomass harvest, RNA was isolated according to QIAGEN RNeasy® Plant Mini Kit
Illumina stranded TruSeq RNA library incl poly(A) enrichment

value: wildtype


title: Hs, U3155-1

last: Chen


title: QM6a_replicate_3


title: delta_ace1_replicate 3


title: Hs, U3137-2b


title: Hs, U3169MG-1


title: Hs, U3140-1


title: Hs, U3198MG-2


title: Hs, U3198MG-1


title: Hs, U3129MG-1


title: Hs, U3129MG-2


title: Hs, U3137-1a


title: QM6a_replicate_1


title: Hs, U3123-2


title: Hs, U3123-1


title: delta_ace1_replicate 2


title: Hs, U3121MG-2


title: Hs, U3121MG-1


title: Hs, U3118-2


title: delta_ace1_replicate 1


title: Hs, U3118-1


title: BL8_ER2W2

first: Cátia

last: Pacífico

state: Vienna

address: Veterinaerplatz 1

institute: University of Veterinary Medicine Vienna

data_processing:
Demultiplexing of the sequencing reads was performed with Illumina bcl2fastq (2.20).
Adapters were trimmed with Skewer (version 0.2.2) (Jiang et al. 2014).
Demultiplexed reads were analyzed using sRNAbench. Reads with an average PHRED score below 20 were discarded.
Assembly: UMD3_1_mp
Supplementary files format and content: tab-delimited text file include counts of all samples (sRNAbench output)
Supplementary files format and content: tab-delimited text file include DESeq2-normalized counts of all samples

organism: Bos taurus

source_name: Leucocytes

extract_protocol:
Total RNA from blood leucocytes was extracted using NucleoSpin miRNA kit (Macherey-Nagel, Germany), while plasma total RNA was extracted with the NucleoSpin Plasma miRNA kit (Macherey-Nagel, Germany).
Library preparation was prepared using the NETflex Small RNA-Seq Kit (Bioo Scientific).

value: Leucocytes

tag: diet

value: High grain


title: Hs, U3117MG-2


title: BL7_CR2W2


title: BL5_AR2W2


title: Hs, U3112D-2

value: Switched and maintained as serum-free culture from serum containing medium


title: Hs, U3112D-1


title: Hs, U3112C-1


title: Hs, U3110MG-1


title: Hs, U3112C-2


title: Hs, U3096C-2


title: Hs, U3096C-1


title: Hs, U3110MG-2


title: BL1_AR2W1

value: Forage


title: BL3_CR2W1


title: Hs, U3093MG-2

value: brain


title: Hs, U3088-2

value: glioblastoma stem cells


title: Hs, U3093MG-1

value: Established and sustained in serum-free medium


title: Hs, U3086MG-2


title: Plas8_R2W2

source_name: Plasma

value: Plasma


title: Hs, U3088-1


title: Plas7_R2W2


title: Plas6_R2W2


title: Hs, U3085MG-2


title: Hs, U3086MG-1


title: Hs, U3085MG-1


title: Hs, U3084MG-2


title: Plas5_R2W2


title: Hs, U3084MG-1


title: Hs, U3082-2


title: Hs, U3078MG-2


title: Hs, U3073MG-2


title: Plas4_R2W1


title: Hs, U3078MG-1


title: Hs, U3082-1


title: Plas3_R2W1


title: Plas2_R2W1


title: Hs, U3073MG-1


title: Hs, U3071MG-1


title: Plas1_R2W1


title: Hs, U3117MG-1


title: KD patient, whole blood [UCSD-153043-SA]

first: Chisato

last: Shimizu

address: 9500 Gilman Dr.

institute: UCSD

data_processing:
The RNA-Seq analysis pipeline consisted of: quality control using FastQC , MultiQC and alignment and read counting using STAR, Salmon, FeatureCounts and ensembl GCh38 genome and annotation. Normalisation was performed using the DESeq2 method for estimating scale factors with a subsequent log transformation.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Whole blood

growth_protocol: Not applicable

extract_protocol:
Total whole blood RNA from PAXgene tubes was isolated using PAXgene Blood miRNA Kit
polyA capture: Total RNA was assessed for quality using an Agilent Tapestation 4200, and samples with an RNA Integrity Number (RIN) greater than 8.0 were used to generate RNA sequencing libraries using the TruSeq Stranded mRNA Sample Prep Kit with TruSeq Unique Dual Indexes (Illumina, San Diego, CA). Samples were processed following manufacturer’s instructions, modifying RNA shear time to five minutes. Resulting libraries were multiplexed and sequenced with 100 basepair (bp) paired end reads (PE100) to a depth of approximately 50 million reads per sample on an Illumina NovaSeq 6000. Samples were demuxltiplexed using bcl2fastq v2.20 Conversion Software (Illumina, San Diego, CA). ribosomal/globin depletion: Library preparation and sequencing of 30 million 75 or 100 bp paired end reads was conducted using the Illumina’s TruSeq RNA Sample Preparation Kit, ribosomal and globin RNA depletion was performed using the Illumina® Ribo-Zero Gold kit and HiSeq 4000 at The Wellcome Centre for Human Genetics.
Ribosomal depletion, globin depletion or poly-A capture

treatment_protocol: Not applicable

tag: disease

value: Kawasaki Disease

tag: disease stage

value: Subacute

tag: cdna prep

value: polyA capture


title: KD patient, whole blood [UCSD-3806-SA]


title: BL4_ER2W1


title: KD patient, whole blood [UCSD-3709-SA]


title: KD patient, whole blood [UCSD-3534-SA]


title: Hs, U3068-2


title: Hs, U3071MG-2


title: MSC_Pool

city: Ottawa

first: David

last: Cook

state: ON

address: 501 Smyth Rd

department: Cancer Therapeutics Program

country: Canada

institute: Ottawa Hospital Research Institute

description: MULTI-seq

data_processing:
Raw sequencing reads were processed using CellRanger v3.1.0, aligning reads to the mm10 build of the mouse genome. Except for explicitly setting --expect-cells=25000, default parameters were used for all samples. MULTI-seq barcode libraries were trimmed prior to demultiplexing to 28bp using Trimmomatic (v0.36)
Demultiplexing was performed using the deMULTIplex R package (v1.0.2). Only cells positive for a single barcode were kept for further analysis and sample annotations were added to all cells in the data set.
Assembly: mm10
Supplementary files format and content: Cell metadata table: Various metadata (sample ID, cluster, etc) for each cell contained in the UMI count matrix. UMI count matrix: Matrix containing UMI counts for all cells passing quality control filters. MULTI-seq barcode UMI count matrix: Cell-by-barcode matrix of MULTI-seq barcode counts for each cell that was used to demultiplex samples. LMO list: A list containing

source_name: Cultured MSCs

growth_protocol: Following isolation and FACS, CD31-/CD45-/EpCAM-/LY6A- and CD31-/CD45-/EpCAM-/LY6A+ lung cells from each mouse were plated separately in T25 culture flasks (ThermoFisher Scientific, Burlington, ON, Canada). Cells were cultured in 5ml growth media containing alpha-modified Minimum Essential Medium Eagle (αMEME) medium (Sigma-Aldrich, Oakville, ON, Canada), complemented with 20% FBS, 1% antibiotic-antimycotic (ThermoFisher Scientific, Burlington, ON, Canada), and 2mM L-Glutamine (ThermoFisher Scientific, Burlington, ON, Canada). Cell medium was exchanged 24 hours after isolation and in 48 hours intervals after that. After reaching 70% confluency, usually 4-5 days after isolation, cells were passaged to T75 culture flasks (Sarstedt, Nümbrecht, Germany). Cells were kept at 37°C with 5% CO2 and 5% O2.

extract_protocol:
Single-cell suspensions were processed using the 10x Genomics Single Cell 3’ v3 RNA-seq kit by Ottawa Hospital Research Institute Stem Core Laboratories. Gene expression libraries were prepared according to the manufacturer’s protocol. MULTI-seq barcode libraries were retrieved from the samples and libraries were prepared independently. Final libraries were sequenced on the NextSeq500 platform (Illumina) to reach an approximate depth of 20,000-25,000 reads/cell.
3' scRNA-seq

tag: sample type

value: 3' RNA


title: KD patient, whole blood [UCSD-3562-SA]


title: Hs, U3068-1


title: Hs, U3065MG-2


title: KD patient, whole blood [UCSD-153043-A]

value: Acute


title: sham-operation-3W  rat bladder-rep2

type: RNA

city: Chengdu

first: Junyu

last: Lai

address: No. 37 Guo Xue Xiang, Chengdu, Sichuan

institute: Sichuan University

description: Gene expression in sham-operation-3 weeks  rat bladder

hyb_protocol: 1.5 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Rat Genome Microarrays (GPL14746) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with Gene Expression Wash Buffer 1(Agilent) and 1 minute with 37°C Gene Expression Wash Buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2565BA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded

organism: Rattus norvegicus

source_name: sham-operation-3 weeks  rat bladder-replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the One-Color Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy mini kit (Qiagen, Hilden, Germany).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNasey Mini Kit (Qiagen, Hilden, Germany) following the manufacturer's recommendations. The protocol includes Five bladder specimens from each group were examined. RNA quantification and quality assurance by NanoDrop-1000 and RNA integrity and gDNA contamination test by Denaturing Agarose Gel Electrophoresis.

treatment_protocol: S group: A urethral catheter (outer diameter: 1 mm) was placed through the urethra of anesthetized female rats and ligated the proximal urethra with 4-0 wires to simulate pBOO, C group: sham operation group, urethral ligation was not performed. B group: PBOO rat treated with tolterodine.

value: bladder

tag: gender

value: female


title: sham-operation-3W  rat bladder-rep3

source_name: sham-operation-3 weeks  rat bladder-replicate 3


title: Hs, U3065MG-1


title: KD patient, whole blood [UCSD-173019-A]


title: KD patient, whole blood [UCSD-3806-A]


title: KD patient, whole blood [UCSD-173015-A]


title: Hs, U3062-1


title: KD patient, whole blood [UCSD-3709-A]


title: Hs, U3062-2


title: sham-operation-3W  rat bladder-rep1

source_name: sham-operation-3 weeks  rat bladder-replicate 1


title: Hs, U3060MG-2


title: pBOO-3W rat bladder-rep3

description: Gene expression in pBOO-3W rat bladder

source_name: partial bladder outlet obstruction (PBOO) -3 weeks rat bladder-replicate 3


title: Hs, U3056MG-2


title: KD patient, whole blood [UCSD-163098-A]


title: Hs, U3060MG-1


title: Hs, U3056MG-1


title: KD patient, whole blood [UCSD-163071-A]


title: Hs, U3053-2


title: KD patient, whole blood [UCSD-3562-A]


title: Hs, U3053-1


title: Hs, U3047-2


title: KD patient, whole blood [UCSD-163028-A]


title: MIA PaCa-2 Mir-29a OE Replicate4

city: Indianapolis

first: Janaiah

last: Kota

state: Indiana

address: 975 W. Walnut Street, IB 244C

department: Medical & Molecular Genetics

institute: Indiana University School of Medicine

description:
Sample name: PaCa-2 29al R4
Processed data file: Kota_May2018_human_DE_paired_PaCa_v2.xlsx (PaCa.29a.R4)

data_processing:
Base calling and quality scoring were performed by Real-Time Analysis (RTA) v2 in Illumina HiSeq 4000.
The bcl2fastq2 Conversion software were used to convert base call (bcl) files to FASTQ files, and trim adapter sequence at the same time.
The reads were mapped to the human genome using STAR (v2.5) RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned to hg38 genes using featureCounts (from subread v1.5.1) with the following parameters: “-s 2 –p –Q 10”.
The data was filtered using read count per million (CPM) > 0.5 in more than 4 of the samples, normalized using TMM (trimmed mean of M values) method and subjected to differential expression analysis using edgeR (v3.20.8).
Genome_build: hg38
Supplementary_files_format_and_content: Raw counts and analysis (excel) from edgeR

source_name: MIA PaCa-2 Mir-29a OE

growth_protocol: Panc-1 and MIA PaCa-2 cells were grown using DMEM High Glucose Culture Media supplemented with 10% FBS in a humidified 5% CO2 incubator at 37degreesC.

extract_protocol:
RNA was isolated using Trizol reagent following manufacturer's protocol. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequence library.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: MIA PaCa-2

tag: origin

value: pancreatic carcinoma of ductal origin

value: miR-29 overexpressing


title: Hs, U3167MG-2


title: Sample 6 - SA008

city: New York

first: Steven

last: Marx

state: NY

address: 622 W168 Street

institute: Columbia University

data_processing:
Real-time analysis (RTA, Illumina) was used for base calling and bcl2fastq2 (version 2.19) was used for converting BCL to fastq format, coupled with adaptor trimming. We performed a pseudoalignment to a kallisto index created from transcriptomes (GRCm38) using kallisto (0.44.0).
Assembly: GRCm38

source_name: Myocardium

extract_protocol:
Qiagen RNeasy kit was used to isolate RNA following manufacturer's guidelines. DNAse digestion on column was performed.
Sequencing libraries were constructed using the TruSeq Stranded Total RNA Library Prep Gold mRNA (Illumina, San Diego CA) with an input of 1000ng and 11 cycles final amplification.

tag: genotype

value: 4SA-Rad knock-in

value: Myocardium


title: Hs, U3047-1

tag: tissue


title: pBOO + tolterodine-3W  rat bladder-rep3

description: Gene expression in pBOO + tolterodine-3W  rat bladder

source_name: partial bladder outlet obstruction (PBOO) + tolterodine-3 weeks  rat bladder-replicate 3


title: MIA PaCa-2 Mir-29a OE Replicate2

description:
Sample name: PaCa-2 29a R2
Processed data file: Kota_May2018_human_DE_paired_PaCa_v2.xlsx (PaCa.29a.R2)


title: pBOO + tolterodine-3W  rat bladder-rep1

source_name: partial bladder outlet obstruction (PBOO) + tolterodine-3 weeks  rat bladder-replicate 1


title: MIA PaCa-2 Mir-29a OE Replicate1

description:
Sample name: PaCa-2 29a R1
Processed data file: Kota_May2018_human_DE_paired_PaCa_v2.xlsx (PaCa.29a.R1)


title: Hs, U3046MG-2


title: pBOO-3W rat bladder-rep1

description: Gene expression in pBOO-3W rat bladder

source_name: partial bladder outlet obstruction (PBOO) -3 weeks rat bladder-replicate 1


title: Sample 5 - SA007

tag: strain


title: MIA PaCa-2 Control Replicate4

description:
Sample name: PaCa-2 Ctrl R4
Processed data file: Kota_May2018_human_DE_paired_PaCa_v2.xlsx (PaCa.Ctrl.R4)

source_name: MIA PaCa-2 Control

value: Control


title: pBOO-3W rat bladder-rep2

description: Gene expression in pBOO-3W rat bladder

source_name: partial bladder outlet obstruction (PBOO) -3 weeks rat bladder-replicate 2


title: MIA PaCa-2 Control Replicate2

description:
Sample name: PaCa-2 Ctrl R2
Processed data file: Kota_May2018_human_DE_paired_PaCa_v2.xlsx (PaCa.Ctrl.R2)


title: Hs, U3042MG-2

source_name: glioblastoma stem cells

value: brain


title: Hs, U3046MG-1

value: glioblastoma stem cells


title: Hs, U3042MG-1

value: Established and sustained in serum-free medium


title: MIA PaCa-2 Control Replicate1

description:
Sample name: PaCa-2 Ctrl R1
Processed data file: Kota_May2018_human_DE_paired_PaCa_v2.xlsx (PaCa.Ctrl.R1)


title: Panc-1 Mir-29a OE Replicate3

description:
Sample name: Panc-1 29a R3
Processed data file: lrtKota_3322_human_Panc_DE_v3.xlsx (R7_Panc_A)

source_name: Panc-1 Mir-29a OE


title: Panc-1 Mir-29a OE Replicate2

description:
Sample name: Panc-1 29a R2
Processed data file: lrtKota_3322_human_Panc_DE_v3.xlsx (R4_Panc_A)


title: Hs, U3039MG-2


title: Panc-1 Mir-29a OE Replicate1

description:
Sample name: Panc-1 29a R1
Processed data file: lrtKota_3322_human_Panc_DE_v3.xlsx (29A_Panc_R1)


title: Hs, U3039MG-1


title: new_sc84_rep2

data_processing:
adaptors were trimmed.
ATAC-seq reads were aligned to hg19 using bowtie2 with the following parameters --very-sensitive
duplicate reads were marked and removed with picard tools version 1.119
Reads mapped to repeated regions and chromosomal M were removed.
the rest of reads were shifted +4/-5bp depending on the strand of the read around Tn5 cleavage position and were then extended to 50bp centered by the cleavage position
Peak calling was performed using MACS2 with options  -f BED, -g hs, -q 0.01, --nomodel, --shift 0
Genome_build: hg19 and mm9

source_name: mouse xenograft glioblastoma stem cell

growth_protocol: Mouse GBM cells (mGC’s) were explanted and established as cultures in mouse cancer stem cell media without addition of EGF and FGF2 as described previously.  Surgical samples from GBM patients were obtained and human glioblastoma cell cultures (HGCC) were established from these samples as explained previously (Maturi et al., 2019; Xie et al., 2015). A total of 65 HGCC were used in this paper, among which 59 HGCC were established and sustained in serum-free medium. Where as 4 HGCC were established and sustained in serum containing medium and 2 HGCC were switched and maintained as serum -free culture from serum containing medium (U3096MG and U3112MG).

extract_protocol:
All the libraries are ATAC procol, DNA was purified with MiniElution kit
The ATAC library construction was done with standard ATAC-seq procol.

treatment_protocol: there is no treaemnt for the cells

value: mouse xenograft glioblastoma stem cell


title: KD patient, whole blood [UCSD-3534-A]

value: Kawasaki Disease


title: pBOO + tolterodine-3W  rat bladder-rep2

source_name: partial bladder outlet obstruction (PBOO) + tolterodine-3 weeks  rat bladder-replicate 2


title: Panc-1 Control Replicate2

description:
Sample name: Panc-1 Ctrl R2
Processed data file: lrtKota_3322_human_Panc_DE_v3.xlsx (R4_Panc_Ctrl)

source_name: Panc-1 Control


title: new_sc83_rep2


title: new_sc84_rep1


title: new_sc83_rep1


title: Panc-1 Control Replicate3

description:
Sample name: Panc-1 Ctrl R3
Processed data file: lrtKota_3322_human_Panc_DE_v3.xlsx (R7_Panc_Ctrl)


title: Hs, U3037MG-2


title: new_sc81_rep2


title: Hs, U3037MG-1


title: Hs, U3034MG-2


title: Hs, U3034MG-1


title: Hs, U3033MG-2


title: new_sc81_rep1


title: new_sc74_rep2_2


title: Hs, U3033MG-1


title: IRE_1_dpi

city: München

first: Safouane

last: Kadri

address: 1, Ingolstädter Landstraße

department: Institute of Regenerative Biology and Medicine

country: Germany

institute: Helmholtz Zentrum München

data_processing:
STAR (version 2.5.2a) was used for mapping.
Reads were aligned to the hg19 genome reference (provided by Drop-seq group, GSE63269).
For barcode filtering, we excluded barcodes with less than 200 genes detected.
A high proportion (> 10%) of transcript counts derived from mitochondria-encoded genes were removed from downstream analyses.
Assembly: hg19
Supplementary files format and content: Matrix table (tab-delimited) with raw read counts for every gene and every sample.

source_name: Adult livers

extract_protocol:
The electroporated area was punched out with a circular 4 mm biopsy punch, and subsequently minced with fine scissors to small pieces (approximately 1 mm2). The same, but non-injured area was used in control livers. The resulting fragments were further processed by enzymatic digestion in 5 mL enzyme mix consisting of dispase (50 caseinolytic units/ml), collagenase (2 mg/ml), and DNase (30 μg/ml), for 30 min at 37 °C under constant agitation (180 RPM). Enzyme activity was inhibited by adding 5 ml of phosphate-buffered saline (PBS) supplemented with 10% fetal bovine serum (FBS). Dissociated cells in suspension were passed through a 70 μm strainer and centrifuged at 500 × g for 5 min at 4 °C. Red blood cell lysis (Thermo Fisher 00-4333-57) was performed for 2 min and stopped with 10% FBS in PBS.
1 ng of pre-amplified cDNA from an estimated 1000 cells was tagmented by Nextera XT (Illumina) with a custom P5 primer (Integrated DNA Technologies). Single cell libraries were sequenced in a 100 bp paired-end run on the Illumina HiSeq4000 using 0.2 nM denatured sample and 5% PhiX spike-in.

treatment_protocol: A negative electrode was placed on top of the superior surface of the liver, while a positive electrode was placed on the inferior surface of the same liver lobe, approximately 0.5-1.0 cm apart. To induce liver damage, eight 50 ms pulses were delivered at 75V with an ECM 830 Square Wave Electroporation System, with 1 second between pulses.

value: Adult mouse liver cells

tag: treatment

value: Irreversible electroporation, sacrifice at 1 day post-injury


title: IRE_7_dpi

value: Irreversible electroporation, sacrifice at 7 days post-injury


title: Hs, U3031MG-2


title: Sham_control

value: Sham surgery, sacrifice after 1 day


title: LPS_IL10_3 [RNA-seq]

city: Chapel Hill

first: Shehzad

middle: Z

last: Sheikh

state: North Carolina

address: 111 Mason Farm Road

department: Center of Gastrointestinal Biology and Disease

institute: University of North Carolina at Chapel Hill

description: 3_8_RNA-3_8_BMDM_RNA_ATGAGGCC-GTTAATTG_S88_L008

data_processing:
Reads extracted using TagDust v 1.13
Reads aligned using STAR
Reads quantified using RSEM v 1.2.31
Genome_build: mm9
Supplementary_files_format_and_content: RSEM output

source_name: BMDMs_LPS Stimulated_IL-10

growth_protocol: Bone marrow was harvested from Il10-/- mice (C57BL/6J background; n=3) and cultured for 6 days in RPMI 1640 media supplemented with 10% FBS and 10% L929 conditioned media.

extract_protocol:
RNA was isolated from murine BMDMs using the Norgen Biotek Corp. Total RNA Purification Kit (Cat. 17200) according to the manufacturer’s protocols.
RNA-seq libraries were prepared using the Illumina KAPA Stranded RNA-seq Kit with RiboErase (HMR)

treatment_protocol: Mature BMDMs were re-seeded at a density of 5x10^5 cells/well and treated for 12 hours with 500nM (+)-JQ1, 10ng/mL IL-10 or remained untreated, followed by the addition of LPS (50ng/mL) or PBS for an additonal 4 hours. Cells were collected in TRIzol at the end of 16 hours.

tag: strain background

value: Bone Marrow Derived Macrophages (BMDMs)

tag: stimulation

value: LPS Stimulated


title: Hs, U3031MG-1


title: Sample 4 - SA006


title: new_sc74_rep1_1


title: Sample 2 - SA003

value: wild-type


title: new_sc74_rep1_2


title: Hs, U3028MG-2


title: new_sc64_rep2


title: LPS_IL10_1 [RNA-seq]

description: 1_8_RNA-1_8_BMDM_RNA_TGGATCGA-GTGCGATA_S81_L007


title: Hs, U3028MG-1


title: Hs, U3027MG-2


title: LPS_JQ1_3 [RNA-seq]

description: 3_6_RNA-3_6_BMDM_RNA_AACGTTCC-GGAGTACT_S89_L008

source_name: BMDMs_LPS Stimulated_(+)-JQ1


title: new_sc52_rep2


title: LPS_JQ1_1 [RNA-seq]

description: 1_6_RNA-1_6_BMDM_RNA_GCTTGTCA-GAACATAC_S76_L007


title: Hs, U3027MG-1


title: new_sc52_rep1


title: Panc-1 Control Replicate1

description:
Sample name: Panc-1 Ctrl R1
Processed data file: lrtKota_3322_human_Panc_DE_v3.xlsx (Ctrl_Panc_R1)

tag: cell line

value: pancreatic carcinoma of ductal origin


title: LPS_Untreated_3 [RNA-seq]

description: 3_5_RNA-3_5_BMDM_RNA_GGTACCTT-AAGACGTC_S90_L008

source_name: BMDMs_LPS Stimulated_Untreated

tag: cell type

value: Untreated


title: new_sc50_rep2_2


title: LPS_Untreated_2 [RNA-seq]

description: 2_5_RNA-2_5_BMDM_RNA_CCAAGTCT-AAGGATGA_S83_L008


title: Hs, U3024MG-1

tag: growth protocol


title: new_sc50_rep2_1


title: Hs, U3022-2


title: LPS_Untreated_1 [RNA-seq]

description: 1_5_RNA-1_5_BMDM_RNA_ATCCACTG-AGGTGCGT_S71_L007


title: new_sc50_rep1_1


title: Hs, U3022-1


title: Unstimulated_IL10_3 [RNA-seq]

description: 3_4_RNA-3_4_BMDM_RNA_GCACGGAC-GTCTCGCA_S91_L008

value: Unstimulated


title: new_sc74_rep2_1


title: Sample 1 - SA002

value: Myocardium


title: Unstimulated_IL10_2 [RNA-seq]

description: 2_4_RNA-2_4_BMDM_RNA_CTCTCGTC-TATAACCT_S77_L007


title: LPS_IL10_2 [RNA-seq]

description: 2_8_RNA-2_8_BMDM_RNA_AATCCGGA-CTACAGTT_S86_L008


title: new_sc37_rep2


title: Hs, U3020-1


title: Hs, U3017MG-2


title: new_sc37_rep1


title: new_sc112_rep2


title: Unstimulated_JQ1_3 [RNA-seq]

description: 3_2_RNA-3_2_BMDM_RNA_CGGCGTGA-GCGCCTGT_S93_L008


title: Hs, U3017MG-1


title: new_sc112_rep1


title: LPS_JQ1_2 [RNA-seq]

description: 2_6_RNA-2_6_BMDM_RNA_TTGGACTC-GGAAGCAG_S84_L008


title: new_sc64_rep1


title: Unstimulated_JQ1_1 [RNA-seq]

description: 1_2_RNA-1_2_BMDM_RNA_TTATAACC-GATATCGA_S74_L007


title: Hs, U3013MG-1


title: Hs, U3024MG-2


title: Mm, SC84_3

value: mouse xenograft glioblastoma stem cells

value: Explanted and established as cultures  in mouse cancer stem cell media


title: Mm, SC84_2

value: brain


title: Hs, U3009MG-2

value: glioblastoma stem cells

value: Established and sustained in serum-free medium


title: Unstimulated_Untreated_3 [RNA-seq]

description: 3_1_RNA-3_1_BMDM_RNA_TAATACAG-ATATTCAC_S87_L008


title: Unstimulated_Untreated_2 [RNA-seq]

description: 2_1_RNA-2_1_BMDM_RNA_AGTTCAGG-CCAACAGA_S80_L007


title: Mm, SC83_2


title: Mm, SC83_1


title: Hs, U3008-2


title: Hs, U3009MG-1


title: Unstimulated_Untreated_1 [RNA-seq]

description: 1_1_RNA-1_1_BMDM_RNA_CCGCGGTT-AGCGCTAG_S75_L007


title: LPS_IL10_3 [ATAC-seq]

data_processing:
processed PEPATAC v0.9.0
uniquely mapped reads aligned using bowtie2
peaks called using MACS2
post-processing using ChIPSeeker
Genome_build: mm9
Supplementary_files_format_and_content: counts.peaks

extract_protocol:
Prepared according to Buenrostro et. al. Cells were pelleted and washed with cold PBS followed by lysis using cold lysis buffer (10mM Tris-HCl, 10mM NaCl, 3 mM MgCl2, and 0.1% NP-40). Pelleted nuclei underwent transposition using the Nextera DNA Library Prep Kit (Illumina #FC-121-1030). Samples were resuspended in the transposition reaction (12.5µL 2x TD buffer, 2 µL transposase, and 10.5 µL nuclease-free water) and incubated at 37C for 1 hour at 1000 RPM. Transposed DNA samples were purified using the Qiagen MinElute Kit (#28204).
Prepared according to Buenrostro et. al. Amplified using 1x PCR master mix (NEB #M0541S) and 25µM Ad1_noMX and Ad2.* indexing primer for 10-14 cycles. Libraries were purified and size selected by magnetic separation using Agencourt AMPure XP magnetic beads (Beckman Coulter #A63880)


title: new_sc50_rep1_2

value: mouse xenograft glioblastoma stem cell


title: Hs, U3020-2


title: Mm, SC81_2


title: Hs, U3008-1


title: LPS_IL10_2 [ATAC-seq]


title: Mm, SC81_1


title: Hs, U3005MG-2


title: LPS_IL10_1 [ATAC-seq]


title: Mm, SC74_2


title: Hs, U3005MG-1


title: Unstimulated_IL10_1 [RNA-seq]

description: 1_4_RNA-1_4_BMDM_RNA_AAGTCCAA-TATGAGTA_S72_L007


title: Hs, U3002-2


title: Mm, SC74_1


title: LPS_JQ1_3 [ATAC-seq]


title: Mm, SC6L_2


title: LPS_JQ1_1 [ATAC-seq]


title: Hs, U3002-1


title: Mm, SC6L_1


title: Hs, 3096D-2

value: Switched and maintained as serum-free culture from serum containing medium


title: Unstimulated_JQ1_2 [RNA-seq]

description: 2_2_RNA-2_2_BMDM_RNA_GACCTGAA-TTGGTGAG_S79_L007


title: Hs, U3013MG-2


title: LPS_Untreated_3 [ATAC-seq]


title: Mm, SC52_3


title: Sample 3 - SA005


title: Hs, 3096D-1


title: LPS_Untreated_2 [ATAC-seq]


title: Mm, SC52_2


title: Hs, 3035MG-2


title: LPS_Untreated_1 [ATAC-seq]


title: Mm, SC50_2


title: Unstimulated_IL10_3 [ATAC-seq]


title: Hs, 3035MG-1


title: Mm, SC50_1


title: Mm, SC37_2


title: Unstimulated_IL10_2 [ATAC-seq]


title: Unstimulated_IL10_1 [ATAC-seq]


title: Mm, SC37_1


title: Unstimulated_JQ1_3 [ATAC-seq]


title: Unstimulated_JQ1_2 [ATAC-seq]


title: ExVivoBlood_stroke_rep5

city: Guangzhou

first: Wen

last: Jiang

state: Guangdong

address: 111 Dade Road

department: Department of Second Institute of Clinical Medicine

institute: Guangzhou University of Traditional Chinese Medicine

description: Gene expression in stroke human blood

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity > 9.0 pmol Cy3 per μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions.On completion of the fragmentation reaction, 250 ml of 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Hybridization Chamber(Agilent p/n G2534A) for 17 hours at 65 °C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with Gene Expression Wash Buffer 1 (Agilent) and 1 minute with 37 °C Gene Expression Wash Buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately to minimize the impact of environmental oxidants on signal intensities by Agilent Microarray Scanner (Agilent p/n G2565BA)(Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent).Add the images (.tif) to be extracted to the FE Project.Set FE Project Properties.Check the Extraction Set Configuration.Save the FE Project (.fep) by selecting File > Save As and browse for desired location. Select Project > Start Extracting and export data to txt.

source_name: Peripheral Blood

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1ug RNA using the Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442) according to the manufacturer's instructions, followed by RNeasy Mini Kit (Qiagen p/n 74104).   Take 1.5 μl of each sample to determine the yield and specific activity by using the NanoDrop ND-1000.

extract_protocol: RNA isolation was performed by using Trizol (Invitrogen, USA), added into every cryopreserved serum supernatant sample according to the manufacturer’s protocol.The protocol includes homogenization,phase separation,RNA Precipitation and Wash,redissolving the RNA. RNasey Mini Kit(Qiagen p/n 74104) was used to clean up total RNA.Total RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Blood collection was done once from each participant,and then it was snap frozen and stored at -80℃ until use.

value: whole blood

tag: condition

value: stroke


title: U87 ADAR3 replicate 2

city: Bloomington

first: Heather

middle: Ann

last: Hundley

state: IN

address: 1001 E 3rd St

department: Medical Sciences

institute: Indiana University Bloomington

data_processing:
Reads were trimmed using fastp (version 0.20.1)
Reads were aligned to reference genome GRCh38 using STAR (version 2.7.9a)
Read counts for each gene were created using featureCounts from the Subread package (version 2.0.2) and ENSEMBL release 103 as the annotation
Differential expression analysis was performed using the DESeq2 package (version 1.30.1) in R/Bioconductor (R version 4.0.4)
Assembly: GRCh38
Supplementary files format and content: .xlsx files from featurecounts with raw read counts
Supplementary files format and content: .xlsx files from DESeq2 analysis with normalized read counts

source_name: U87 cells

growth_protocol: U87 cells were maintained in  Dulbecco’s modified Eagle’s medium (DMEM)  (Mediatech) supplemented with 10% fetal bovine  serum (FBS) (Sigma), 200ug/ml G418, 100ug/ml penicillin and 100  units/ml streptomycin (MediaTech).

extract_protocol:
RNA was isolated using Trizol (Invitrogen), purified by treatment with TURBO DNAase (Ambion) and isolated using the RNeasy Extraction Kit (Qiagen).
Poly-A selected mRNA library preparation was done using KAPPA stranded library preparation kit

treatment_protocol: All cells were incubated at 37°C in 5% CO2 and grown to 80-90% under optimum conditions

tag: expression plasmid

value: 3X-FLAG ADAR3 (neomycin)

tag: rna source

value: RNA from whole cell lysate


title: Mm, SC112_2


title: U87 ADAR3 replicate 1