title: Spleen_RNASeq1

city: La Jolla

first: Nathan

last: Lewis

address: 9500 Gilman Dr

department: Pediatrics

institute: UCSD

description:
eTSS_NCBI_picr.bed.gz
eTSS_NCBI_picr.meta.tsv.gz
eTSS_syn20999279_picr.bed.gz
eTSS_syn20999279_picr.meta.tsv.gz
peaks_location.tsv

data_processing:
5' and control processing: cutadapt (Martin, 2011) was used to trim adapter sequences and low quality bases from the reads. Reads were aligned to the Chinese Hamster genome assembly PICR (Rupp et al., 2018) and annotation GCF_003668045.1, part of the NCBI Annotation Release 103. Sequence alignment was accomplished using the STAR aligner v2.5.3a. Reads mapped to multiple locations were removed from analysis. Tags were then made using Homer v4.11 command "makeTagDirectory {o_dir} -genome {g} -checkGC -single {bam}"
5' and control processing: Peaks for 5'GRO-seq csRNA-seq was done using Homer v4.11 with input GRO-Seq, using "findPeaks {tss_tag_file} -style tss -i {control_tag_file} -norm 1000000"
5' and control processing: Peaks were then merged using homer command "mergePeaks -d 150 -strand {in_files} > {out}"
Ribosome-depleted RNA: Alignment performed using STAR v2.5.3a with default parameters and removing reads mapped to multiple locations. Quantification performed using htseq-count, with the command "htseq-count -f bam -s reverse -t exon -i gene {bam_f} {annotation} > {out)}"
ATAC-seq: ATAC-seq was processed using the pipeline here: https://github.com/kundajelab/atac_dnase_pipelines . Briefly, the reads were trimmed using cutadapt v1.9.1. Reads were aligned using Bowtie v2.2.4. Peaks were called using Macs2 v2.1.3 with a p-value of 0.01, and replicates were merged using irreproducible discovery rate (IDR) (Li et al., 2011) of 0.1. The fold-change value is the number of normalized counts over the local background, taken as 10,000 kb surrounding.
TSS called using custom Python scripts and thresholding based on distance to NCBI annotation.
Bedgraph were generated by constructing single-nucleotide resolution bedGraph files based on 5' read positions using HOMER. TSS peak files contain TSS cluster positions defined using HOMER's findPeaks.pl command (tab-delimited text files). Normalized to 1e7 uniquely aligned reads.
RNA bedgraph files, which was strand agnostic, created first by making the tag directory , with command  "makeTagDirectory {tag_dir} {bam_file} -read2 -single". Then, bedgraph file was made using "makeUCSCfile {tag_dir} -o {bedgraph_file} -style rnaseq". Normalized to 1e7 uniquely aligned reads.
Genome_build: PICR GCF_003668045.1
Genome_build: [genome annotation]  PICR NCBI Annotation 103
Genome_build: [genome annotation]  picr_proteogenomics.gff (https://www.synapse.org/#!Synapse:syn20999279)
[normalized_TSS_counts.tsv]  Counts-per-million (CPM) matrix, n-by-m matrix, where n is the number of TSS, and m is the number of samples. Each column has a header that names after the title column above, and there is an ID column which gives an ID for each peak.
[peaks_location.tsv]  tsv file of locations of the peaks, along with average CPM.
[eTSS_NCBI_picr.bed.gz]  Updated TSS annotation in bed format where the TSS are adjusted based on our analysis and informed by NCBI Refseq.
[eTSS_NCBI_picr.meta.tsv.gz]  Additional info on eTSS bed file. A tab-separated-value file where each row is a TSS corresponding to the TSS in the bed file. In the file the columns are (1) The name of the TSS that corresponds to the bed file IDs (2) Comma-separated list of biosamples that express the TSS (3) Confidence score with three binary values, where the leftmost bit is one if the maximum CPM is greater or equal to 2 CPM, the second bit is if there were more than one biosample with the TSS, and the third bit is 1 if it is considered a stable TSS, meaning there was total-RNA reads present there as well. (4) The location of the the CHO ATAC region, if there is one near the TSS (5) Corresponding gene (6) Corresponding transcript (7) If this TSS was annotated from the current paper or was from the previous annotation, (which is only there if there was no experimental TSS seen for that transcript) 8) Binary value if there was an open-chromatin region near the TSS in any of the samples.
[eTSS_syn20999279_picr.bed.gz]  Updated TSS annotation in bed format where the TSS are adjusted based on our analysis and informed by Synapse.org ID syn20999279.
[eTSS_syn20999279_picr.meta.tsv.gz]  Additional info on eTSS bed file. A tab-separated-value file where each row is a TSS corresponding to the TSS in the bed file. In the file the columns are (1) The name of the TSS that corresponds to the bed file IDs (2) Comma-separated list of biosamples that express the TSS (3) Confidence score with three binary values, where the leftmost bit is one if the maximum CPM is greater or equal to 2 CPM, the second bit is if there were more than one biosample with the TSS, and the third bit is 1 if it is considered a stable TSS, meaning there was total-RNA reads present there as well. (4) The location of the the CHO ATAC region, if there is one near the TSS (5) Corresponding gene (6) Corresponding transcript (7) If this TSS was annotated from the current paper or was from the previous annotation, (which is only there if there was no experimental TSS seen for that transcript) 8) Binary value if there was an open-chromatin region near the TSS in any of the samples.
[ATAC_peaks.bed.gz]  A tsv file outputted from Homer mergePeaks on bed files outputted from macs2 using the aforementioned pipeline. The Stat column is the averaged 10*log10qvalue over the samples that contained the peak. This is a modified bed file with a header and a column that indicates which samples contained the open-chromatin position.

extract_protocol:
[RNA-seq]  RNA was extracted from organs that were homogenized in Trizol LS using an Omni Tissue homogenizer. After incubation at RT for 5 minutes, samples were spun at 21.000g for 3 minutes, supernatant transferred to a new tube and RNA extracted following manufacturerâs instructions. Strand-specific total RNA-seq libraries from ribosomal RNA-depleted RNA were prepared using the TruSeq kit Stranded Total RNA Library kit (Illumina) according to the manufacturer-supplied protocol.
[csRNA-seq]  Capped small RNA-sequencing was performed identically as described by (S. H. Duttke et al., 2019). Briefly, total RNA was size selected on 15% acrylamide, 7M UREA and 1x TBE gel (Invitrogen EC6885BOX), eluted and precipitated over night at -80Â°C. Given that the RIN of the tissue RNA was often as low as 2, essential input libraries were generated to facilitate accurate peak calling. csRNA libraries were twice cap selected prior to decapping, adapter ligation and sequencing. Input libraries were decapped prior to adapter ligation and sequencing to represent the whole repertoire of small RNAs with 3â-OH.
[sRNA-seq]  Similar to csRNA-seq, without the decapping.
[5'GRO-seq and GRO-seq]  Global nuclear run-on sequencing (GRO-seq (Core et al., 2008) and 5âGRO-seq (Core et al., 2008; Lam et al., 2013)) were performed as described below. Nuclei from hamster tissues were isolated as described in (Hetzel et al., 2016). Hamster BMDM nuclei were isolated using hypotonic lysis [10 mM Tris-HCl pH 7.5, 2 mM MgCl2, 3 mM CaCl2; 0.1% IGEPAL] and flash frozen in GRO-freezing buffer [50 mM Tris-HCl pH 7.8, 5 mM MgCl2, 40% Glycerol]. 0,5-1 x 106 BMDM nuclei were run-on with BrUTP-labelled NTPs as described (S. H. C. Duttke et al., 2015) with 3x NRO buffer [15mM Tris-Cl pH 8.0, 7.5 mM MgCl2, 1.5 mM DTT, 450 mM KCl, 0.3 U/Âµl of SUPERase In, 1.5% Sarkosyl, 366 ÂµM ATP, GTP (Roche) and Br-UTP (Sigma Aldrich) and 1.2 ÂµM CTP (Roche, to limit run-on length to ~40 nt)]. Reactions were stopped after five minutes by addition of 750 Âµl Trizol LS reagent (Invitrogen), vortexed for 5 minutes and RNA extracted and precipitated as described by the manufacturer.
[GRO-seq]  RNA pellets were fully resuspended in 18 Âµl ddH2O + 0.05% Tween (dH2O+T). Subsequently, 2 Âµl fragmentation mix [100 mM ZnCl2, 10 mM Tris-HCl pH 7.5] was added and the samples incubated at 70Â°C for 15 minutes. RNA fragmentation was stopped by placing samples on ice and addition of 2.5 Âµl 100 mM EDTA p.H. 8.0 and 500 Î¼l cold GRO binding buffer [GRO-BB; 0.25Ãsaline-sodium-phosphate-EDTA buffer (SSPE), 0.05% (vol/vol) Tween, 37.5 mM NaCl, 1 mM EDTA p.H. 8.0]. BrU enrichment was performed using a BrdU Antibody (Sigma B8434-200 Âµl Mouse monoclonal BU-33) coupled to Protein G (Dynal 1004D) beads. Per run on reaction, 3x 20 Âµl of Protein G beads were washed twice in DPBS+0.05% Tween 20 (DPBS+T) and then the antibody coupled in a total volume of 1 ml DPBS+%T under gentle rotation. 1 Âµl of antibody was used per 8 Âµl of beads. After one hour at RT, the beads were collected using a magnet and the supernatant saved for future coupling reactions. Coupled beads were washed twice with GRO-BB prior to use. It is recommended to pre-chill beads to 4áµC prior to the IP as traces of RNase may be observed. RNase activity can be monitored e.g. using IDTâs RNaseAlertÂ®. No crosslinking is required and worked best in our hands followed by DMP >>> Bs3. To each reaction of fragmented NRO-RNA with added GRO-BB, 20 Î¼l equilibrated Î±BrdU beads were added and the samples slowly rotated at 4 Â°C for 80 minutes. Beads were subsequently collected on a magnet and the IP reaction washed twice with 500 Î¼l GRO binding buffer before RNA was eluted by incubation of the beads in 500 Î¼l Trizol LS (Thermo Fisher) under medium agitation for 5 minutes. 120 Î¼l of TET [10 mM Tris-HCl pH 7.5, 1 mM EDTA p.H. 8.0, 0.05 % Tween20] was added to increase the supernatant and RNA extracted as described by the manufacturer. For end-repair and decapping, RNA pellets were dissolved in 8 Âµl TET by vigorous vortexing, heated to 70Â°C for 2 minutes and placed on ice. After a quick spin, 22 Âµl Repair MM [3 Âµl 10x PNK buffer, 15.5 Âµl dH2O+T, 0.5 Âµl SUPERase-In RNase Inhibitor (10 U, Ambion), 2 Âµl PNK (20U, Enzymatics Y904L), 1 Âµl RppH (5U, NEB)] was added, mixed by flicking and incubated at 37Â°C for 1 hour. To phosphorylate the 5âend, 1 Âµl 10 mM ATP was subsequently added and the reactions were incubated for another 45 minutes at 37Â°C (the high ATP concentration is advised to quench RppH activity). Following end repair, 2.5 Âµl 50 mM EDTA was added, reactions mixed and then heated to 70Â°C for 2 minutes before being placed on ice. A second BrdU enrichment was performed as detailed above. For library preparation, RNA pellets were dissolved in 2.75 Âµl TET + 0.25 Âµl Illumina TruSeq 3âAdapter (10 mM), heated to 70Â°C for 2 minutes and placed on ice. 7 Âµl of 3âMM [4.75 Âµl 50% PEG8000, 1 Âµl 10x T4 RNA ligase buffer (NEB), 0.25 Âµl SUPERase-In, 1 Âµl T4 RNA Ligase 2 truncated (200U; NEB)] was added, mixed well by flicking and reactions incubated at 20Â°C for 1 hour. Reactions were diluted by addition of 10 Âµl TET + 2 Âµl 50 mM EDTA, heated to 70Â°C for 2 minutes, placed on ice and a third round of BdUTP enrichment was performed. RNA was transferred as a pellet to PCR strips during the 75% ethanol wash and dried. Samples were dissolved in 4 Âµl TET [10 mM Tris-HCl pH 7.5, 0.1 mM EDTA, 0.05% Tween 20] + 1 Âµl 10 mM reverse transcription (RT) primer. To anneal the RT-primer, the mixture was incubated at 75Â°C for 5 minutes, 37Â°C for 15 minutes and 25Â°C for ~10 minutes.  To ligate the 5â Illumina TruSeq adapter, 10 Âµl 5âMM [1.5 Âµl ddH2O + 0.2% Tween20, 0.25 Âµl denaturated 5âTruSeq adapter (10 mM), 1.5 Âµl 10x T4 RNA ligase buffer, 0.25 Âµl SUPERase-In, 0.2 Âµl 10 mM ATP, 5.8 Âµl 50% PEG8000, 0.5 Âµl T4 RNA ligase 1 (5U; NEB)] was added and reactions were incubated at 25Â°C for 1 hour. Reverse transcription was performed using Protoscript II (NEB) [4 Âµl 5x NEB FirstStrand buffer (NEB; E7421AA), 0.25 Âµl SUPERase-In, 0.75 Âµl Protoscript II (150U; NEB)] at 50Â°C for 1 hour. After addition of 30 Âµl PCR MM [25 Âµl 2x LongAmp Taq 2X Master Mix (NEB), 0.2 Âµl 100 mM forward primer, 2.8 Âµl 5 M Betaine and 2 Âµl 10 mM individual barcoding primer], mixtures were amplified for 13 cycles. PCR reactions were cleaned up using 1.5 volumes of SpeedBeadsâ¢ (GE Healthcare) in 2.5 M NaCl/20%PEG8000 and the libraries size selected on a PAGE/TBE gels to 150â225 bp. Gel slices were shredded by spinning through a 0.5 ml perforated PCR tube placed on top of a 1.5 ml tube. 150 Âµl Gel EB [0.1% LDS, 1M LiCl, 10 mM Tris-HCl pH 7.8] was added and the slurry incubated under agitation overnight. To purify the eluted DNA, 800 Âµl Zymogen ChIP DNA binding buffer (D5205) was added into the 1.5 ml tube containing the shredded gel slice and the Gel EB, mixed by pipetting and the slurry transferred to a ZymoMiniElute column. Samples were first spun at 1000g for 3 minutes, then 10k g for 30 seconds. Flow through was removed, and samples washed with 200 Âµl Zymo WashBuffer (with EtOH). Gel remainders were removed by flicking and columns washed by addition on another 200 Âµl Zymo WashBuffer. Flow through was removed, columns spun dry by centrifugation at 14k g for 1 minute and DNA eluted by addition of 20 Âµl pre-warmed Sequencing TET [10 mM Tris-HCl pH 8.0, 0.1 mM EDTA, 0.05% Tween 20]. Libraries were sequenced on an Illumina NextSeq 500 at using 75 cycles single end.
[5' GRO-seq]  RNA pellets were resuspendend in 10 Âµl TET, heated to 70Â°C for 2 minutes and placed on ice. 10 Âµl of dephosporylation MM [2 Âµl 10x CutSmart, 6.75 Âµl dH2O+T, 1 Âµl Calf Intestinal alkaline Pho

value: Female

value: Spleen; blood

tag: assay

value: rRNA Depletion RNA (Stranded)

tag: molecule


title: Tax1BP1 knock-out 1 [miRNA]

status: Public on Oct 06 2020

type: RNA

city: Frankfurt

first: Claudia

last: Döring

address: Theodor Stern Kai 7

department: Medical School, Institite of Pathology

country: Germany

institute: Johann Wolfgang-Goethe University Frankfurt a.M.

hyb_protocol: GeneChip® miRNA 3.0 arrays (Affymetrix) were hybridized with 500 ng labelled microRNA, Hybridisation time was 18 hours.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Statistical analysis was done with the statistical computing environment R. Additional software packages (affy, geneplotter, multtest, and vsn) were taken from the Bioconductor project.  Microarray preprocessing: Probe level normalization was conducted using the variance stabilization method (vsn) from Huber et al..
probe group file: UnsupportedGeneChip® miRNA 3.0 Array CDF Files
meta-probeset file: miRNA 3.0 Annotations, Unsupported, CSV format from Affymetrix

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Tax1BP1 knock-out

label_protocol: miRNA was labeled with the Affymetrix FlashTag Biotin HSR RNA Labeling Kit

growth_protocol: Mice were housed under 12 h day/night cycles, were fed standard rodent chow and had access to drinking water ad libitum.

extract_protocol: miRNA was extracted with the miRNeasy Mini Kit from Qiagen

treatment_protocol: no treatment

tag: strain background

tag: genotype/variation

value: Tax1BP1 knock-out

tag: age

value: 12 weeks

tag: Sex

value: male

tag: tissue

value: liver


title: H9-B3GALT5-KO+2iLAF Naïve

type: SRA

city: Taoyuan

first: Ruey-Jen

last: Lin

address: No.5, Fuxing St., Guishan Dist.

department: Institute of Stem Cell & Translational Cancer Research

country: Taiwan

institute: Chang Gung Memorial hospital

description:
KO-2i
FullTable_processed data.txt

library_source: transcriptomic

data_processing:
The bases with low quality and sequences from adapters in raw data were removed using program Trimmomatic (version 0.39).
The filtered reads were aligned to the reference genomes using Bowtie2 (version 2.3.4.1).
A user-friendly software RSEM (version 1.2.28) was applied for the quantification of the transcript abundance.
Genome_build: hg19
Supplementary_files_format_and_content: FullTable_processed data.txt: Tab-delimited text file includes TPM and FPKM values for all Samples.

organism: Homo sapiens

source_name: H9 hESC

extract_protocol:
RNA was extracted using the RNeasy Kit (QIAGEN) and quantified using a Nanodrop ND-2000 (Nanodrop).
mRNA was purified from total RNA (1 μg) by oligo(dT)-coupled magnetic beads and fragmented into small pieces under elevated temperature. The first-strand cDNA was synthesized using reverse transcriptase and random primers. After the generation of double-strand cDNA and adenylation on 3’ ends of DNA fragments, the adaptors were ligated and purified with AMPure XP system (Beckman Coulter, Beverly, USA). The quality of the libraries was assessed on the Agilent Bioanalyzer 2100 system and a Real-Time PCR system.
TruSeq Stranded mRNA Library Prep Kit.

treatment_protocol: WT and B3GALT5-KO cells treated with indicated media (basal, 5iLAF or 2iLAF).

tag: cell line

tag: genotype

tag: treatment

value: 2iLAF medium

tag: pluripotency

value: naive


title: DN_m4

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

country: USA

institute: Emory University

library_source: genomic

data_processing:
RRBS FASTQ files were aligned to the in silico bisulfite converted genome mm9 using Bismark with the Bowtie2 option.  Binary Alignment Map BAM files were parsed to derive DNA methylation calls that were collapsed to the CpG level using custom R scripts that made use of the ‘Rsamtools’ and ‘data.table’ packages available upon request  Data were summarized for CpGs that were covered at 10x in all samples and CpGs that were covered at 10x by all groups
Genome_build: mm10
Supplementary_files_format_and_content: Count matrix of methylaed and unmethylated reads for each CpG covered by a minimum of 10 reads within each group.  For each CpG there is the chromosome location and for each sample there are three columns of data containing the sample name followed by the following extensions: ".meth", % of reads methylated; ".u", number of reads unmethylated; ".m", number of reads methylated.

molecule: genomic DNA

source_name: pooled inguinal, brachial, axillary, cervical, and popliteal lymph nodes

growth_protocol: BM cells were cultured in RPMI supplemented with 10% FBS, 2 mM L-glutamine, 1 mM sodium pyruvate, 100 U penicillin-streptomycin, 0.05 mM 2-ME, and 20% of Flt3L containing supernatant, secreted by an SP2/0 transfected cell line for the indicated number of days.

extract_protocol:
Genomic DNA was isolated by phenol-chloroform extraction followed by ethanol precipitation.
Two aliquots of DNA were separately digested with either TaqI or MspI restriction enzymes over night and subsequently pooled for all downstream processing.  Digested DNA was end-repaired, A-tailed, and adapters containing methylated cytosines ligated on using the KAPA HyperPrep kit according to the manufacturers instructions.  Adapter-ligated DNA was bisulfite converted over using the EpiTech Bisulfite kit Qiagen, Inc.  Bisulfite treated libraries were PCR amplified using indexed primers and the HiFi HotStart Uracil+ polymerase KAPA Biosystems.

tag: strain

tag: cell type

value: CD4-CD8-TCR-ab+ T cells


title: Pancreas_RNASeq1

middle: E

state: California

organism: Cricetulus griseus

source_name: Pancreas

growth_protocol: See paper for complete protocol details. Female Chinese hamsters (Cricetulus griseus) were generously provided by George Yerganian (Cytogen Research and Development, Inc) and housed at the University of California San Diego animal facility on a 12h/12h light/dark cycle with free access to normal chow food and water. All animal procedures were approved by the University of California San Diego Institutional Animal Care and Use Committee in accordance with University of California San Diego research guidelines for the care and use of laboratory animals. None of the used Hamsters were subject to any previous procedures and all of them were used naive without any previous exposure to drugs. Euthanized hamsters were quickly chilled in a wet ice/ethanol mixture (~50/50), organs were isolated, placed into Trizol LS, flash frozen in liquid nitrogen and stored at -80C for later use. CHO-K1 cells were grown on F-K12 media at 37 Â°C with 5 % CO2 (GIBCO-Invitrogen, carlsbad, CA, USA). Hamster bone marrow-derived macrophages (BMDMs) were generated as detailed previously (Link et al., 2018). Hamster bone marrow-derived macrophages (BMDMs) were generated as detailed previously (Link et al., 2018).

value: Pancreas


title: H9-WT+5iLAF Naïve

description:
H9-5i
FullTable_processed data.txt

value: wild type

value: 5iLAF medium


title: DN_m3


title: H9-B3GALT5-KO Primed

description:
KO
FullTable_processed data.txt

value: basal medium

value: primed


title: Muscle_RNASeq1

source_name: Muscle

value: Muscle


title: ATAC-seq - ABa 350 minutes #1

city: Vienna

first: Jingkui

last: Wang

address: Campus-Vienna-Biocenter 1

country: Austria

institute: Research Institute of Molecular Pathology (IMP)

description: ATAC-Seq 14.9k cells, sorted (ABa) 350' (green)

data_processing:
For ChIP-seq, the single-end raw reads of ChIP-seq dataset were mapped to the C. elegans genome (ce11) with bowtie2 (v2.2.4). Uniquely mapped reads were retained and duplicated reads were marked and discarded using SAMtools (v0.1.18). For visualization, the coverage tracks (i.e. bigWig files) were generated from bam files using kent-ucsc (v2.79). Sharp peaks were identified with macs2 (v2.1.0) against the pooled control samples with default parameters.
For ATAC-seq, the paired-end raw reads of ATAC-seq data were trimmed with Cutadapt (v1.18) and mapped to the C. elegans genome (ce11) with bowtie2 (v2.2.4). For all samples, multi-mapped reads were filtered with SAMtools (v0.1.20) and duplicate reads were marked and discarded with Picard-tools (v2.18.27; Broad Institute). For visualization, the normalized coverage tracks (i.e. bigWig files) were generated from bam files using with R packages GenomicRanges (v1.38.0) and rtracklayer (v1.46.0) with paired-end option.
Genome_build: ce11
Supplementary_files_format_and_content: *.bw files: bigWig Track format of read density coverage in reads per million

organism: Caenorhabditis elegans

source_name: Embryo (ABa) - 350 minutes

extract_protocol:
ChIP assays were performed as previously described in (Askjaer et al., 2014) with minor modifications. ATAC-seq libraries were prepared as described in (Corces et al., 2017) with minor modifications.
ChIP-seq: NEBNext® Ultra II DNA Library Prep Kit. ATAC-seq: Nextera DNA Library Prep Kit

value: lucIs39[tbx-37p(1,87kb)::mNeonGreen::2xNLS::tbx-37 3'UTR(20ng); pal-1p::mScarlet-I::2xNLS::tbb-2 3'UTR (100ng); med-2p::mScarlet-I::2xNLS::tbb-2 3'UTR (100ng); pBluescript(30ng)]

tag: developmental stage

value: Embryo - 350 minutes

value: ABa


title: H9-WT+2iLAF

description:
H9-2i
FullTable_processed data.txt

value: primed-naive


title: CD8_m5

value: CD8+ T cells


title: Misc_RNASeq1

source_name: Whole Organism

value: Female

value: Whole Organism

value: rRNA Depletion RNA (Stranded)


title: ATAC-seq - ABp 90 minutes #1

description: ATAC-Seq 25k cells, sorted (ABp) 90' (black)

source_name: Embryo (ABp) - 90 minutes

value: Embryo - 90 minutes

value: ABp


title: H9-WT Primed

description:
H9
FullTable_processed data.txt


title: Lung_RNASeq1

source_name: Lung

value: Lung


title: carotid_3

city: New York

first: Chenyi

last: Xue

state: NY

institute: Columbia University

description: scRNA-Seq

data_processing:
Fastq file generation and read alignment were performed by 10X Cell Ranger v3.1.0. Reads were aligned to human reference genome GRCh38 and transcriptome based on Ensembl 93 annotation.
Unique molecular identifier (UMI) count matrix was generated by Cell Ranger "count" command.
Genome_build: GRCh38
Supplementary_files_format_and_content: Gene-cell UMI count matrix.

molecule: polyA RNA

source_name: Carotid artery

extract_protocol: Libraries were prepared using the 10x Genomics Chromium Single Cell 3’ Reagent Kits v2 (mouse samples) or v3 (human samples) according to manufacturer’s instructions. 5000 cells and 200M reads per sample were targeted. 12 cycles for cDNA amplification and 12 cycles for sample index PCR were used.

value: Carotid artery from endarterectomy

tag: race

value: Caucasian

tag: symptom presence

value: Asymptomatic


title: CD8_m4


title: CD8_m3


title: carotid_2

description: scRNA-Seq

value: Male


title: carotid_1

description: scRNA-Seq

value: Symptomatic


title: Liver_RNASeq1

source_name: Liver

value: Liver


title: ATAC-seq - ABa 90 minutes #1

description: ATAC-Seq 25k cells, sorted (ABa) 90' (green)

source_name: Embryo (ABa) - 90 minutes

value: lucIs39[tbx-37p(1,87kb)::mNeonGreen::2xNLS::tbx-37 3'UTR(20ng); pal-1p::mScarlet-I::2xNLS::tbb-2 3'UTR (100ng); med-2p::mScarlet-I::2xNLS::tbb-2 3'UTR (100ng); pBluescript(30ng)]


title: HCT116 cells, Extract treated N=2

city: Nottingham

first: Nigel

middle: P

last: Mongan

address: University Park

department: Biodiscovery Institute

country: United Kingdom

institute: University of Nottingham

data_processing:
Quality control and base calling was completed using Illumina CASAVA.
Raw fastq reads were adapter trimmed and quality assessed using the Trimgalore wrapper for FastQC and Cutadapt. Reads with phred scores >30 were retained.
Reads were aligned to the GRCh38 reference genome using STAR and genes quantified using FeatureCounts and differential expressed genes between vehicle control and extrated treated cells were identified using edgeR with FDR <0.05 considered significant.
Differential canonical and novel splicing was assessed using rMATS3.2.5 using the Ensembl annotation for the GRCh38.83 genome build to generate the standard rMATs splicing outputs in tab delimtied format which statistically quantifiy alternative 5' splice site (A5SS), alternative 3' splice sites (A3SS), mutually exclusive exons (MX), skipped exons (SE) and retained introns (RI).
Genome_build: GRCh38.83
Supplementary_files_format_and_content: tab delimited text files

growth_protocol: Human HCT116 colorectal carcinoma cells were maintained in RPMI-1640 medium containing 10% FBS and 1% Glutamine in a humidified chamber containing 5% CO2.

extract_protocol:
Total RNA was isolated from treated and untreated cells using TRIreagent (Sigma). RNA quality and quantity were measured using a Spectrophotometer (NanoDrop2000, ThermoFisher Scientific) and samples were stored at -80°C.
Illumina TruSeq stranded library prepartion for paired end sequencing.

treatment_protocol: Cells were treated with crude extract of Cotyledon orbiculata plants. Cotyledon orbiculata plants were purchased from Van den Berg Garden Village (Western Cape Province, Stellenbosch, South Africa). The leaves of the plants were removed, washed with water, cut into small pieces and dried in a ventilated oven at 40°C for 120 hours. The dried leaves were crushed in a blender. Two and half (2.5) liters of boiling water were added to 100g crushed leaf material and the mixture was stirred for 16hrs at room temperature. This water extract was filtered through Whatman filter paper (0.45 µm pore size), frozen in liquid nitrogen and subsequently freeze-dried. The dried extract was kept in a desiccator until further use. Stock solutions of the extract was prepared in DMSO at 10mg/ml, which was stored at -20°C.

value: HCT116 colorectal carcinoma cell line

value: Extract Treatment


title: TBX-38 ChIP - 90 minutes #1

source_name: Embryo - 90 minutes

value: Whole embryo


title: HCT116 cells, Extract treated N=3


title: Heart_RNASeq1

source_name: Heart

value: Heart


title: TBX-37 ChIP - 90 minutes #2


title: 10x_038_BeMe03_Pre_TCR

city: San Diego

first: Pandurangan

last: Vijayanand

address: 9420 Athena Circle

department: Vaccine Discovery

institute: La Jolla Institute for Immunology

description: Single-cell RNA-seq with 10x Genomics v1 V(D)J

data_processing:
mkfastq (Cell Ranger 3.1.0) was used to generate FASTQ files with default parameters
count (Cell Ranger 3.1.0) was used to generate the filtered UMI matrix with default parameters
Seurat (3.1.5) was used to filter, normalize and scale the UMI matrix
Genome_build: GRCh38-alts-ensembl-2.0.0 from Cell Ranger
Genome_build: GRCh37 (hg19-3.0.0 from Cell Ranger)
Supplementary_files_format_and_content: cd4t24_annotation.txt.gz meta data for 31341 cells
Supplementary_files_format_and_content: cd4t24_umi.txt.gz UMI count data matrix for 31341 cells
Supplementary_files_format_and_content: cd4t6_annotation.txt.gz meta data for 91140 cells
Supplementary_files_format_and_content: cd4t6_umi.txt.gz UMI count data matrix for 91140 cells

source_name: PBMC

growth_protocol: Not applicable

extract_protocol:
For combined single-cell RNA-seq and TCR-seq assays (10x Genomics), a maximum of 60,000 virus-reactive memory CD4+ T cells from up to 8 donors were pooled by sorting into low retention 1.5mL collection tubes, containing 500 µL of a1:1 solution of PBS:FBS supplemented with RNAse inhibitor (1:100). Following sorting, ice-cold PBS was added to make up to a volume of 1400 µl. Cells were then centrifuged for 5 minutes (600 g at 4 ˚C) and the supernatant was carefully removed leaving 5 to 10 µl. 25 µl of resuspension buffer (0.22 µm filtered ice-cold PBS supplemented with ultra-pure bovine serum albumin; 0.04 %, Sigma-Aldrich) was added to the tube and the pellet was gently but thoroughly resuspended. Following careful mixing, 33 µl of the cell suspension was transferred to a PCR-tube for processing as per the manufacturer’s instructions (10x Genomics).
Single-cell RNA-seq using 10x genomics platform was performed using Chromium™ Single Cell 5' v1 Reagent Kits following the manufacturer’s protocol
Libraries were constructed using Chromium™ Single Cell 5' v1 Reagent Kits following the manufacturer’s protocol
100 x 100 bp paired-end reads, 3'TAG, Hg19 human reference genome.

treatment_protocol:
PBMCs from each donor, were thawed, washed, plated in 6-well culture plates at a concentration of 5 x 106 cells/ml in 1 ml of serum-free TexMACS medium (Miltenyi Biotec) and left overnight (5 % CO2, 37 ˚C). Cells were stimulated by the addition of individual virus-specific peptide polls (1 µg/ml) for 6 h in the presence of a blocking CD40 antibody (1 µg/ml; Miltenyi Biotec). For subsequent MACS-based enrichment of CD154+, cells were sequentially stained with fluorescence-labeled surface antibodies, Cell-hashtag TotalSeq™-C antibody (0.5 µg/condition), and a biotin-conjugated CD154 antibody (clone 5C8; Miltenyi Biotec) followed by anti-biotin microbeads (Miltenyi Biotec). Labelled cells were added to MS columns (Miltenyi Biotec) and positively selected cells (CD154+) were eluted and used for FACS sorting of CD154+ memory CD4+ T cells. The flow-through from the column was collected and re-plated for harvesting cells responding 24 h after peptide stimulation.
Analogous to enrichment for CD154+, CD137-expressing CD4+ memory T cells cells were positively selected by staining with biotin-conjugated CD137 antibody (clone REA765; Miltenyi Biotec) followed by anti-biotin MicroBeads and applied to a new MS column. Following elution, enriched populations were immediately sorted using a FACSAria Fusion Cell Sorter (Becton Dickinson) based on dual expression of CD154 and CD69 for 6-hour stimulation condition, and CD137 and CD69 for 24-hour stimulation condition.

value: Blood

value: Memory CD4 T cells, helper enriched:CD3+ CD4+ CD45RA- CD154+ CD69+


title: ATAC-seq - ABa 200 minutes #1

description: ATAC-Seq 25k cells, sorted (ABa) 200' (green)

source_name: Embryo (ABa) - 200 minutes

value: Embryo - 200 minutes

value: ABa


title: HCT116 cells, Extract treated N=1


title: HCT116 cells, Vehicle Control N=3

value: Control


title: 10x_038_BeMe03_Post_TCR


title: 10x_038_BeMe03_Pre_CITE

description: Single-cell RNA-seq with 10x Genomics 5' v1


title: ReproductiveTract_RNASeq1

source_name: FemaleReproductive

value: Female

value: FemaleReproductive

value: rRNA Depletion RNA (Stranded)


title: HCT116 cells, Vehicle Control N=2


title: TBX-37 Input - 90 minutes

description: Input-MLC813 - 4mg

value: Embryo - 90 minutes


title: N2 ChIP - 90 minutes #1

description: N2 - 4mg

value: wt


title: 10x_038_BeMe03_Post_CITE


title: Brain_RNASeq2

source_name: Brain

value: Brain


title: CoVi15_4_MS_24_6P_TCR

value: Memory CD4 T cells, helper enriched:CD3+ CD4+ CD45RA- CD137+ CD69+


title: Kidney_RNASeq1

source_name: Kidney

value: Kidney


title: DL1 RNA-Seq IntS8-depleted replicate 3

city: Boston

first: Karen

last: Adelman

state: MA

address: 45 Shattuck St. LHRRB-201a

department: Biological Chemistry and Molecular Pharmacology

institute: Harvard Medical School

description:
Oligo-dT selectred total RNA isolated from Drosophila DL1 cells treated with dsRNA taregting Integrator 8
IntS8_noCopper_DEseq.txt

data_processing:
PRO-seq: Paired-end reads were trimmed to 40nt, for adaptor sequence and low quality 3' ends using cutadapt 1.14, discarding those containing reads shorter than 20nt (-m 20 -q 10); RNA-seq: Reads were filtered to require a mean quality score ≥ 20, trimmed to 100 nt, and mapped to the hg38 human genome assembly using STAR.
PRO-seq: Remaining pairs were paired-end aligned (using Bowtie 1.2.2) to the hg38 spike genome index to determine spike-normalization ratios based on uniquely mapped reads. Mappable pairs were omitted from subsequent analysis; RNA-seq: Default parameters were used, except that multimappers were randomly assigned (outMultimapperOrder Random), spurious junctions were filtered (outFilterType BySJout), minimum overhang for non-annotated junctions was set to 8 nt (alignSJoverhangMin 8), and non-canonical alignments were removed (outFilterIntronMotifs RemoveNoncanonicalUnannotated).
PRO-seq: Remaining unmapped pairs were aligned to the dm3 genome assembly. Identical parameters were used in each alignment described: up to 2 mismatches, and uniquely mappable and unmappable pairs routed to separate output files (-v2, -un, --best).
PRO-seq: Pairs mapping to dm3, representing biotin-labeled RNA 3' ends, were separated, and strand-specific counts of the 3' mapping positions determined at single nucleotide resolution, genome-wide, and expressed in bedGraph format with "plus" and "minus" strand labels swapped for each 3' bedGraph, to correct for the "forward/reverse" nature of Illumina paired-end sequencing.
PRO-seq: Based on similar recovery of spike-in reads, depth normalization was performed and bedGraphs from replicates of each condition were combined by summing counts per nucleotide.
Genome_build: dm3 (PRO-seq, RNA-seq); hg38 (RNA-seq)
Supplementary_files_format_and_content: PRO-seq: bedGraph containing combined count of end 1 3' mapping locations for all replicates for a given treatment; RNA-seq: bigWig containing coverage of all replicates for a given treatment

organism: Drosophila melanogaster

source_name: Drosophila DL1 cells

growth_protocol: Cells were cultured at 27°C in Schneider’s Drosophila medium supplemented with 10% (v/v) fetal bovine serum, 1% (v/v) Antibiotic-Antimycotic.

extract_protocol:
DL1 cells were were harvested and washed with PBS. Cells were counted, and 40 x 10^6 cells were resuspended in 1mL of Trizol and RNA was purified.
1 µg of RNA from each sample was subjected to Click-Seq Total RNA prep (Jaworski et al. MiMB 2018), with Oligo-d(T) bead selection (NEB)

treatment_protocol: IntS8 targeting dsRNA (60 hr)

value: Dissociated embryos, near hatching

tag: rna fraction

value: total RNA

value: IntS8 targeting dsRNA


title: TBX-37 ChIP - 90 minutes #1

description: MLC813 - 4mg

value: Whole embryo


title: BC1_New_ChIP-seq_Input

city: Tampa

first: Mingxiang

last: Teng

state: FL

address: 12902 Magnolia Dr

department: Department of Biostatistics and Bioinformatics

institute: H Lee Moffitt Cancer Center and Research Institute

data_processing:
ChIP-seq reads were aligned to humen genome hg19 using Bowtie v2.2.3. ChIP-seq peaks were called on each replicate samples using MACS v2.1.0 by comparing ChIP to INPUT control. Peaks were merged from replicates in each cell line using IDR v2.0.3
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq peaks

source_name: B lymphoma cells

growth_protocol: BC1 cell line was rountinly cultured in RPMI1640 supplemented with 20% FCS.

extract_protocol:
DNA was purified with Ampure xp Beads
Libraries were prepared for sequencing using standard Illumina protocols

value: Pleura

tag: stages

value: Cell line

value: B cell

tag: antibody

value: Input


title: Brain_RNASeq1

tag: assay

tag: molecule


title: CoVi12_4_MS_24_5P_TCR

value: Blood


title: 293T IntS8 knockdown replicate 3

description:
ribo-depleted Total RNA isolated from 293T cells treated with siiRNA targeting IntS8
Adelman_hg38_293T_IntS8dep_RNAseq_N3_plus.bw
Adelman_hg38_293T_IntS8dep_RNAseq_N3_minus.bw

source_name: embryonic kidney

growth_protocol: 293T cells were grown at 37°C with 5% CO2 in DMEM, supplemented with 10% (v/v) FBS and 1% (v/v) penicillin-streptomycin.

extract_protocol:
293T cells were harvested and washed with PBS. Cells were counted, and 1 x 106 cells were resuspended in 1mL of Trizol and spiked with 1 µL of 1:10 diluted ERCC Spike-in Mix (Invitrogen) and RNA was purified.
1 µg of RNA from each sample was diluted in 10uL of water. The input RNA was subjected to RNA-seq library generation using the TruSeq Stranded Total RNA sequencing kit with RiboZero rRNA depletion (Illumina). The final libraries were amplified to 10 cycles and purified using AMPure XP beads (Beckman Coulter).

treatment_protocol: IntS8-targeting siRNA treatment (48 hr)

value: embryonic kidney

tag: genotype/variation

value: IntS8-targeting siRNA

tag: spike in

value: 1 uL of a 1:10 dilution of ERCC spike RNAs (Invitrogen) was added to 1 million 293T cells resuspended in Trizol


title: BC1_New_ChIP-seq_IRF4SEi_rep2

tag: tissue


title: DL1 RNA-Seq IntS8-depleted replicate 2

tag: cell line


title: 293T IntS8 knockdown replicate 2


title: CoVi06_4_S_24_8P_TCR


title: DL1 RNA-Seq IntS8-depleted replicate 1


title: N2 ChIP - 90 minutes #2

tag: genotype

value: Embryo - 90 minutes


title: BC1_New_ChIP-seq_IRF4SEi_rep1


title: DL1 RNA-Seq Control replicate 3

description:
Oligo-dT selectred total RNA isolated from Drosophila DL1 cells treated with control dsRNA
IntS8_noCopper_DEseq.txt

treatment_protocol: β-galactosidase targeting dsRNA (60 hr)

value: Beta-galactosidase targeting dsRNA


title: CoVi06_4_M_24_8P_TCR


title: 293T Control replicate 3

description:
ribo-depleted Total RNA isolated from 293T cells treated with control siiRNA
Adelman_hg38_293T_Control_RNAseq_N3_plus.bw
Adelman_hg38_293T_Control_RNAseq_N3_minus.bw

treatment_protocol: Nontargeting siRNA treatment (48 hr)

value: Nontargeting siRNA


title: BC1_New_ChIP-seq_ctrl_rep2


title: CoVi03_4_MS_24_5P_TCR

value: Memory CD4 T cells, helper enriched:CD3+ CD4+ CD45RA- CD137+ CD69+


title: 293T Control replicate 2


title: 293T Control replicate 1


title: CoVi15_4_MS_24_6P_Gex

description: Single-cell RNA-seq with 10x Genomics 5' paired-end


title: BC1_New_ChIP-seq_ctrl_rep1


title: DL1 RNA-Seq Control replicate 2


title: B3GALT5-KO+2iLAF Naïve

data_processing:
Sequencing reads were processed to remove the first 6 bases, adapter sequences and poor-quality reads; and the remaining sequences were mapped to human genome build GRCh37/hg19 using CLC genomics workbench v11.0.0 (QIAGEN).
The CpG methylation calls were extracted and analyzed using MATLAB software.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files of methylation over mapped CGs for each Sample

source_name: H9 hESC

extract_protocol:
Genomic DNA was extracted using the Gentra Puregene Cell Kit (QIAGEN) and quantified using a Nanodrop ND-2000 (Nanodrop).
Bisulfite sequencing libraries were prepared using the Truseq methyl capture EPIC library kit (Illumina). Unmethylated Lambda phage DNA was spiked in at input DNA quantity to determine conversion efficiency, which was 99 % for all libraries.

treatment_protocol: WT and B3GALT5-KO cells treated with indicate media (basal, 5iLAF or 2iLAF)

value: ESC

tag: treatment

value: 2iLAF medium

value: naïve


title: CoVi06_4_S_24_8P_Gex


title: CD107aHigh 3

city: Baltimore

first: Aaron

middle: W

last: James

state: MD

address: 600 North Wolfe Street

department: Pathology

institute: Johns Hopkins University School of Medicine

data_processing:
Paired-end 150nt sequencing on Illumina NextSeq 500
Base calling with RTA version 2.4.11
Data filtering to strip adapters with bcl2fastq 2.17.1.14
Read alignment to Homo sapiens sequence GRCh38.p13 Dec-'19, with CLCGenomicsServer 10.0.1 with: Mismatch cost =2, Insertion cost = 3, Deletion cost = 3, Length fraction = 0.8, Similarity fraction = 0.8
FPKM calculation with CLCGenomicsServer 10.0.1 as above
FPKM vaues log2 converted (FPKM = 0 ignored) and quantile normalized with Partek Genomics Suite v7.0
Genome_build: Homo sapiens sequence GRCh38.p13
Supplementary_files_format_and_content: Single tab-delimeted text file of quantile normalized log2 FPKM values for all samples. Raw FPKM values of 0 are represented as Nulls in log space.

source_name: Human CD31-CD45-CD107aHigh adipose stromal cells

growth_protocol: CD107aLow or CD107aHigh adipose stromal cells were isolated from human adipose tissue via fluorescence activated cell sorting (FACS). Human lipoaspirate was obtained from healthy adult donors and was stored no more than 72 h at 4 °C before processing. Equal volume of phosphate buffered saline (PBS) was used to wash lipoaspirate.  The washed lipoaspirate was digested with 1 mg/ml type II collagenase (Washington Biochemical; Lakewood, NJ, USA) in Dulbecco's Modified Eagle's Medium (DMEM) containing 0.5% bovine serum albumin (Sigma-Aldrich, St. Louis, MO) at 37°C for 60 min under agitation, followed by centrifugation to remove adipocytes. The cell pellet was resuspended and incubated in red cell lysis buffer (155 mM NH4Cl, 10 mM KHCO3, and 0.1 mM EDTA) at RT for 10 min. After centrifugation, the Stromal Vascular Fraction (SVF) was resuspended in PBS and filtered at 40 μm.

extract_protocol:
Total RNA was extract from cells by Trizol (Life technologies corporation, Gaitherburg, MD, USA) and subjected to first-strand complementary deoxyribonucleic acid (cDNA) synthesis using the iScript™ cDNA Synthesis Kit (Bio-Rad, Hercules, CA) to a final volume of 20 μL. The reverse transcription reaction was performed at 25°C for 5 min, followed by 46°C for 20 min and 95°C for 1 min.
Library construction used the NuGEN Ovation Ultralow library system V2  with NextSeq reagent Kit and manufacturer's protocol.

treatment_protocol: SVF cells were incubated with anti-CD45-allophycocyanin-cyanin 7 (1:30; BD Pharmingen, San Diego, CA), anti-CD31-allophycocyanin-cyanin 7 (1:100, BD Pharmingen), and anti-CD107a-allophycocyanin (1:20; BD Pharmingen), for 20 min on ice. Propodium Iodide (PI) staining solution (BD Pharmingen, 00-6990-42) was used to gate out non-viable cells. CD31-CD45-CD107aLow and CD31-CD45-CD107aHigh adipose stromal cells were isolated by FACS sorting and resuspended in Trizol (Life technologies corporation, Gaitherburg, MD, USA) for RNA isolation. Total RNA was extract from cells by Trizol (Life technologies corporation, Gaitherburg, MD, USA) and subjected to first-strand complementary deoxyribonucleic acid (cDNA) synthesis using the iScript™ cDNA Synthesis Kit (Bio-Rad, Hercules, CA) to a final volume of 20 μL. In this dataset, we detected the expression data by RNA sequencing.

value: adipose stromal cells

tag: passage

value: Fresh isolated cells

tag: facs sorting


title: CD107aHigh 2

tag: cell type


title: CoVi12_4_MS_24_5P_Gex


title: DL1 RNA-Seq Control replicate 1

value: Dissociated embryos, near hatching

value: total RNA


title: DL1 RNA-Seq IntS8-depleted + IntS8 WFEF/A Mutant rescue replicate 2

description:
Oligo-dT selectred total RNA isolated from Drosophila DL1 cells treated with dsRNA taregting Integrator 8
Adelman_dm3_DL1_IntS8depWFEFArescue_RNAseq_N3_plus.bw
Adelman_dm3_DL1_IntS8depWFEFArescue_RNAseq_N3_minus.bw

treatment_protocol: IntS8 targeting dsRNA (60 hr) + Flag-IntS8 WFEF/A mutant (200 μM CuSO4  for 24 hr)

value: IntS8 targeting dsRNA + Flag-IntS8 WFEF/A mutant


title: DL1 RNA-Seq IntS8-depleted + IntS8 WFEF/A Mutant rescue replicate 3


title: DL1 RNA-Seq IntS8-depleted + IntS8 WFEF/A Mutant rescue replicate 1


title: ATAC-seq - ABp 350 minutes #1

description: ATAC-Seq 15.99k cells, sorted (ABp) 350' (black)

source_name: Embryo (ABp) - 350 minutes

tag: strain

value: lucIs39[tbx-37p(1,87kb)::mNeonGreen::2xNLS::tbx-37 3'UTR(20ng); pal-1p::mScarlet-I::2xNLS::tbb-2 3'UTR (100ng); med-2p::mScarlet-I::2xNLS::tbb-2 3'UTR (100ng); pBluescript(30ng)]

tag: developmental stage

value: Embryo - 350 minutes

value: ABp


title: CD107aHigh 1


title: CD107aLow 3

source_name: Human CD31-CD45-CD107aLow adipose stromal cells


title: HCT116 cells, Vehicle Control N=1

value: HCT116 colorectal carcinoma cell line

value: Control


title: 293T IntS8 knockdown replicate 1

value: embryonic kidney

value: IntS8-targeting siRNA

value: 1 uL of a 1:10 dilution of ERCC spike RNAs (Invitrogen) was added to 1 million 293T cells resuspended in Trizol


title: CoVi03_4_MS_24_5P_Gex

value: Blood

value: Memory CD4 T cells, helper enriched:CD3+ CD4+ CD45RA- CD137+ CD69+


title: CoVi06_4_M_24_8P_Gex


title: B3GALT5-KO Primed

value: ESC

value: basal medium

tag: pluripotency

value: primed


title: DL1 RNA-Seq IntS8-depleted + IntS8 Wildtype rescue replicate 3

description:
Oligo-dT selectred total RNA isolated from Drosophila DL1 cells treated with dsRNA taregting Integrator 8
Adelman_dm3_DL1_IntS8depWTrescue_RNAseq_N3_plus.bw
Adelman_dm3_DL1_IntS8depWTrescue_RNAseq_N3_minus.bw

treatment_protocol: IntS8 targeting dsRNA (60 hr) + Flag-IntS8 wildtype (200 μM CuSO4 for 24 hr)

tag: rna fraction

value: IntS8 targeting dsRNA + Flag-IntS8 wildtype


title: CD107aLow 2

value: adipose stromal cells

value: Fresh isolated cells


title: CoVi15_4_MS_24_6P_CITE


title: DL1 RNA-Seq IntS8-depleted + IntS8 Wildtype rescue replicate 2

value: Dissociated embryos, near hatching

value: total RNA


title: DL1 RNA-Seq IntS8-depleted + IntS8 Wildtype rescue replicate 1


title: CD107aLow 1


title: Young 4

city: Rochester

first: Jie

last: Sun

state: MN

address: 200 1st St SW

department: medicine, immunology

institute: mayo clinic

data_processing:
Paired-end libraries were sequenced on an Illumina HiSeq 4000 following Illumina’s standard protocol using the Illumina cBot and HiSeq 3000/4000 PE Cluster Kit. Base-calling was performed using Illumina’s RTA software (version 2.5.2). Paired-end RNA-seq reads were aligned to the mouse reference genome (GRCm38/mm10) using RNA-seq spliced read mapper Tophat2 (v2.1.1).
Pre- and post-alignment quality controls, gene level raw read count and normalized read count (i.e. FPKM) were performed using RSeQC package (v2.3.6) with NCBI mouse RefSeq gene model. For functional analysis, GSEA was used to identify enriched gene sets, from the hallmark and C5 databases of MSigDB, having up-regulated and down-regulated genes, using a weighted enrichment statistic and a log2 ratio metric for ranking genes.
Genome_build: mm10

source_name: Lung tissue

extract_protocol:
RNA was extracted from Trizol reagent with Chloroform and RNA quality was determined (RIN>7) via Agilent Bioanalyzer
total RNA was used to generate the RNA sequencing library.
cDNA synthesis, end-repair, A-base addition, and ligation of the Illumina indexed adapters were performed according to the TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, CA). The concentration and size distribution of the completed libraries was determined using an Agilent Bioanalyzer DNA 1000 chip (Santa Clara, CA) and Qubit fluorometry (Invitrogen, Carlsbad, CA).

treatment_protocol: mechanically homogenized lung tissue in Trizol

value: Lung

tag: cell markers

value: bulk lung tissue

tag: infection

value: Influenza A/PR8/34 (60 d.p.i.)


title: H9+5iLAF Naïve

value: wild type

value: 5iLAF medium

value: naïve


title: DL1 RNA-Seq IntS8-depleted plus Cu replicate 3

description:
Oligo-dT selectred total RNA isolated from Drosophila DL1 cells treated with dsRNA taregting Integrator 8
Adelman_dm3_DL1_IntS8dep_RNAseq_N3_plus.bw
Adelman_dm3_DL1_IntS8dep_RNAseq_N3_minus.bw

treatment_protocol: IntS8 targeting dsRNA (60 hr) +(200 μM CuSO4 for 24 hr)

value: IntS8 targeting dsRNA


title: CoVi12_4_MS_24_5P_CITE

value: Blood


title: CoVi06_4_S_24_8P_CITE

value: Memory CD4 T cells, helper enriched:CD3+ CD4+ CD45RA- CD137+ CD69+


title: RPE1_IRp53KO_S2

city: PHILADELPHIA

first: Irfan

last: Asangani

state: PA

address: 421 Curie Bld.

department: Cancer Biology

institute: University of Pennsylvania

data_processing:
Illumina Nextseq 500 reads were demultiplexed using bcl2fastq
Read quality was checked for each sample usign FastQC.
Alignment of reads were performed using STAR aligner with the default setting in Illumina Basespace (https:// basespace.illumina.com/home/indexIllumina)
Aligned reads for RNA-seq samples were assembled using CUFFQUANT and normalized  using CUFFNORM
Differential expression analysis for RNA-seq was performed using DESeq2 with DMSO samples for each cellline as the respective control
Genome_build: hg19
Supplementary_files_format_and_content: rawcounts, Cuffnorm FPKM

source_name: hTERT RPE-1 p53 KO_10 Gy+ATRi_3 days

growth_protocol: MCF10A cells were cultured in DMEM/F-12 media with 5% horse serum (Thermo Fisher Scientific), 20 ng/ml human EGF (Peprotech), 0.5 mg/ml hydrocortisone, 100 ng/ml cholera toxin and 10μg/ml recombinant human insulin (Sigma). hTERT RPE-1 cells were cultured in DMEM media with 10% bovine calf serum (Hyclone). All cells were maintained with penicillin and streptomycin (Thermo Fisher Scientific).

extract_protocol:
Total RNA was isolated using miRNeasy Kit (Invitrogen) following the manufacturer’s instructions. Purified RNA was poly-A selected according to Illumina's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
Cells were irradiated with 10 Gy or left untreated. Drug treatments including CDK1i and ATRi were administrated 1 h prior to irradiation and maintained till collection. Media with or without drugs were changed every 2 days after treatment.
knockout protocol: Knockout cells were generated using CRISPR-Cas9. Lentiviruses of LentiCas9-blast and LentiGuide-Puro (gifts from F. Zhang, Addgene #52962, Addgene#52963) were produced and concentrated as previously described (Kutner et al., 2009). Cells were infected with lentiviruses overnight in the presence of 8 ug/ml polybrene. Cells infected with LentiCas9 were subjected to 10μg/ml blasticidin (Invivogen) until control cells without infection were all killed. Knockout clones were generated by infecting cells with lentivirus using lentiGuide-Puro followed by selection in 2 μg/ml puromycin (Sigma) for 2 days. Single colonies were achieved by seeding one cell per 96-well.

tag: cell line background

value: hTERT RPE-1

value: p53 KO

tag: tissue source

value: retinal pigment epithelia

value: 10 Gy+ATRi, 3 days


title: RPE1_IRp53KO_S1

tag: genotype/variation


title: CoVi06_4_M_24_8P_CITE


title: Young 3


title: RPE1_IRwtcGAS_S2

source_name: hTERT RPE-1 WT cGAS_10 Gy+ATRi_3 days

value: WT cGAS


title: DL1 RNA-Seq Control plus Cu replicate 3

description:
Oligo-dT selectred total RNA isolated from Drosophila DL1 cells treated with control dsRNA
Adelman_dm3_DL1_Control_RNAseq_N3_plus.bw
Adelman_dm3_DL1_Control_RNAseq_N3_minus.bw

treatment_protocol: β-galactosidase targeting dsRNA (60 hr) +(200 μM CuSO4 for 24 hr)

value: Beta-galactosidase targeting dsRNA


title: CoVi03_4_MS_24_5P_CITE


title: Young 2


title: DL1 RNA-Seq IntS8-depleted plus Cu replicate 1

value: Dissociated embryos, near hatching


title: GTAGAGGAGTACAC_Lane1_Ctrl_nonTfh2

city: Bonn

first: Dirk

last: Baumjohann

state: NRW

address: Venusberg-Campus 1

department: Medical Clinic III

institute: University Hospital Bonn

data_processing:
Fastq reads were processed with the zUMIs pipeline (Parekh et al., 2017)
cDNA reads were aligned to the Mouse (mm10) Genome with STAR 2.6.0a
Quantification was done with ENSEMBL gene models (GRCm38.75)
Genome_build: Mouse: mm10, Ensembl 75
Supplementary_files_format_and_content: sample (columns) and gene (rows) -wise UMI expression table

source_name: murine popliteal lymph node

extract_protocol:
secondary lymphoid organs were removed, single cell suspensions and antibody stainings for flow cytometry and cell sorting were prepared on ice. Cells were sorted directly into lysis buffer and immediately spun down and frozen on dry ice. RNA was isolated using magnetic beads
Libraries were constructed using a bulk adjusted mcSCRB-seq protocol.

treatment_protocol: mice were treated with tamoxifen to induce the CreERT2-mediated knockout of Bcl6 or CXCR5 in CD4 T cells

tag: celltype

value: CD4 T cell

value: Cd4-CreERT2+ CXCR5+/+


title: RPE1_IRwt_S2

source_name: hTERT RPE-1 WT_10 Gy+ATRi_3 days

value: WT


title: CoVi14_4_S_6_8P_TCR

source_name: PBMC

tag: tissue

value: Memory CD4 T cells, helper enriched:CD3+ CD4+ CD45RA- CD154+ CD69+


title: CoVi14_4_M_6_8P_TCR


title: H9 Primed

tag: cell line

value: ESC

value: wild type

value: basal medium

value: primed


title: DL1 RNA-Seq Control plus Cu replicate 2

value: total RNA


title: Old 4

value: Lung

value: bulk lung tissue

value: Influenza A/PR8/34 (60 d.p.i.)


title: OSC11 trated with DHT

city: Biella

first: Paola

last: Ostano

address: via Malta 3

country: Italy

institute: Fondazione Edo ed Elvo Tempia

hyb_protocol: Equal amounts of differentially labeled specimens from sample and reference were put together, fragmented and hybridized to oligonucleotide glass arrays. All steps were performed using the In Situ Hybridization kit-plus (Agilent Technologies) and following the 60-mer oligo microarray processing protocol (Agilent Technologies). Then, slides were washed following the Agilent wash procedure. For each sample, a dye-swap replicate was performed.

scan_protocol: Slides were scanned with the dual-laser Agilent scanner G2505C

data_processing: The LIMMA (LInear Models for Microarray Analysis) package was used to analyze gene expression profiles of normal prostates and prostate cancer tissues. Raw intensity values were background subtracted (method = normexp, offset = 50) and normalized using the loess method, for the within array normalizaton, and Aquantile, for the between array normalization. Duplicated probes were averaged. Then, Cy3 and Cy5 channels were separated using the separate channel analysis of two-color data, available within the Limma package.

source_name: prostate cancer

label_protocol: RNA was amplified by means of the Amino Allyl MessageAmp aRNA Kit (Life Technologies) to obtain amino allyl antisense RNA (aaRNA) following the method developed by Eberwine and coworkers. Briefly: mRNA was reverse transcribed in cDNA single strand; after the second strand synthesis, cDNA was in vitro transcribed in aaRNA including amino allyl modified nucleotides (aaUTP). Both dsDNA and aaRNA underwent a purification step using columns provided with the kit. Labeling was performed using NHS ester Cy3 or Cy5 dyes (Amersham Biosciences) able to react with the modified RNA. Labeling efficiency and mRNA quantity were checked by means of NanoDrop ND-1000 Spectrophotometer (Thermo Scientific).

growth_protocol: Tissue specimens have been cut into thick slices (350 μm) using McILWAIN TISSUE CHOPPER and cultured at a liquid-air interface using semi-porous tissue culture inserts (PICM03050, Millipore) placed in a six-well culture plate. Slices were cultured at 37 °C in humidified air with 5% CO2 with Iscove’s Modified Dulbecco’s Medium (IMDM) (GIBCO-ThermoFisherScientific Waltham, US-MA) supplemented with 10% hormone depleted serum FBS (HyClone), 2 mM glutamine, 100 µg/ml penicillin and streptomycin (method was optimized with regard to number of slices for tissue culture inserts, 5 slices each).

extract_protocol: TotRNA was isolated following TriReagent (Sigma Aldrich) protocol. TotRNA quality and quantity were checked by means of Agilent 2100 bioanalyzer (Agilent Technologies) and NanoDrop ND-1000 Spectrophotometer (Thermo Scientific) respectively.

treatment_protocol: Medium was replaced daily and after 3 or 4 days, slices were treated with or without 17b-estradiol (E2 ,10-7M) for 6 hours or DHT for 3 hours, then removed from insert and transferred at −80° for final RNA/proteins extraction.

value: GapLacZ + DHT treatment for 3 hours

source_name: OSC11 control

value: GapLacZ


title: RPE1_IRwt_S1

value: hTERT RPE-1

value: retinal pigment epithelia

value: 10 Gy+ATRi, 3 days


title: CoVi11_4_S_6_5P_TCR

value: Blood


title: DL1 RNA-Seq IntS8-depleted plus Cu replicate 2

value: Dissociated embryos, near hatching

value: IntS8 targeting dsRNA


title: DL1 RNA-Seq Control plus Cu replicate 1

value: Beta-galactosidase targeting dsRNA


title: CoVi11_4_MS_6_4P_TCR

value: Memory CD4 T cells, helper enriched:CD3+ CD4+ CD45RA- CD154+ CD69+


title: Old 1


title: MCF10A_XRCC4p53DKOATRi_S2

source_name: MCF10A XRCC4 p53 DKO_10 Gy+ATRi_3 days

value: XRCC4 p53 DKO

value: breast epithelia


title: RPE1_IRwtcGAS_S1

value: WT cGAS


title: MCF10A_XRCC4p53DKOATRi_S1


title: CoVi11_4_M_6_5P_TCR


title: GAA Knock-out-AAV-LSPhGAApA treated- 6month old-3

city: Durham

first: Wei

last: Chen

state: NC

address: 101 Science Drive

department: Center for Genomic and Computational Biology

institute: Duke University

description:
AAV_vs_KO-expression_matrix.csv
AAV-G5-317

data_processing:
HiSeq Control Software (Application Version: HD 3.4.0.38, RTA Version: 2.7.7)
Illumina HiSeq 4000 reads were processed using the TrimGalore toolkit v0.4.1 to trim low quality bases and Illumina sequencing adapters from the 3’ end of the reads.  Only reads that were 20nt or longer after trimming were kept for further analysis. Read quality was checked for each sample using FastQC v0.11.2.
Reads were mapped to the GRCm38v73 version of the mouse genome and transcriptome using the STAR RNA-seq alignment tool v2.5.0c.  Reads were kept for subsequent analysis if they mapped to a single genomic location.
Gene counts were compiled using the HTSeq tool v0.6.1.  Only genes that had at least 10 reads in any given library were used in subsequent analysis.
Normalization and differential expression was carried out using the DESeq2 Bioconductor package v1.16.1 with the R statistical programming environment v3.4.1_3.
Genome_build: GRCm38v73
Supplementary_files_format_and_content: normalized expression matrix in csv format

source_name: quadriceps

extract_protocol:
RNeasy Fibrous Tissue Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: quadriceps muscle

tag: age

value: 6 months

tag: genotype

value: GAA Knock-out

value: AAV2/8-LSPhGAApA53 (2x10e12 vg/kg) via tail vein injection


title: DL1 PRO-seq IntS8-depleted + IntS8 WFEF/A Mutant rescue replicate 2

description:
biotin labeled nascent RNA isolated from Drosophila DL1 permeabilized cells
Adelman_dm3_DL1_IntS8depWFEFArescue_PROseq_N2_plus.bedGraph.gz
Adelman_dm3_DL1_IntS8depWFEFArescue_PROseq_N2_minus.bedGraph.gz

data_processing:
Library strategy: PRO-seq
PRO-seq: Paired-end reads were trimmed to 40nt, for adaptor sequence and low quality 3' ends using cutadapt 1.14, discarding those containing reads shorter than 20nt (-m 20 -q 10); RNA-seq: Reads were filtered to require a mean quality score ≥ 20, trimmed to 100 nt, and mapped to the hg38 human genome assembly using STAR.
PRO-seq: Remaining pairs were paired-end aligned (using Bowtie 1.2.2) to the hg38 spike genome index to determine spike-normalization ratios based on uniquely mapped reads. Mappable pairs were omitted from subsequent analysis; RNA-seq: Default parameters were used, except that multimappers were randomly assigned (outMultimapperOrder Random), spurious junctions were filtered (outFilterType BySJout), minimum overhang for non-annotated junctions was set to 8 nt (alignSJoverhangMin 8), and non-canonical alignments were removed (outFilterIntronMotifs RemoveNoncanonicalUnannotated).
PRO-seq: Remaining unmapped pairs were aligned to the dm3 genome assembly. Identical parameters were used in each alignment described: up to 2 mismatches, and uniquely mappable and unmappable pairs routed to separate output files (-v2, -un, --best).
PRO-seq: Pairs mapping to dm3, representing biotin-labeled RNA 3' ends, were separated, and strand-specific counts of the 3' mapping positions determined at single nucleotide resolution, genome-wide, and expressed in bedGraph format with "plus" and "minus" strand labels swapped for each 3' bedGraph, to correct for the "forward/reverse" nature of Illumina paired-end sequencing.
PRO-seq: Based on similar recovery of spike-in reads, depth normalization was performed and bedGraphs from replicates of each condition were combined by summing counts per nucleotide.
Genome_build: dm3 (PRO-seq, RNA-seq); hg38 (RNA-seq)
Supplementary_files_format_and_content: PRO-seq: bedGraph containing combined count of end 1 3' mapping locations for all replicates for a given treatment; RNA-seq: bigWig containing coverage of all replicates for a given treatment

source_name: Drosophila DL1 cells

extract_protocol:
DL1 cells were washed in PBS and permeabilized and flash frozen. PRO-seq run-on reactions of permeabilized cells were performed in nuclear run-on mix containing biotin-NTPs. Nascent RNA was extracted using a Total RNA Purification Kit following manufacturer instructions (Norgen Biotek Corp.).
Extracted nascent RNA was fragmented by base hydrolysis, bead purified, and trizol extracted. Purified RNA was then subjected to 3' adaptor ligation, bead purification, 5' decapping, and 5' hydroxyl repair, followed by 5' adaptor ligation. Libraries were prepared by on-bead reverse transcription and 11-12 cycle amplification of final PRO-seq libraries.

value: nascent RNA

value: IntS8 targeting dsRNA + Flag-IntS8 WFEF/A mutant

tag: spike in

value: 50,000 permeabilized 293T cells were added to 1 million permeabilized DL1 cells


title: DL1 PRO-seq IntS8-depleted + IntS8 Wildtype rescue replicate 2

description:
biotin labeled nascent RNA isolated from Drosophila DL1 permeabilized cells
Adelman_dm3_DL1_IntS8depWTrescue_PROseq_N2_plus.bedGraph.gz
Adelman_dm3_DL1_IntS8depWTrescue_PROseq_N2_minus.bedGraph.gz

value: IntS8 targeting dsRNA + Flag-IntS8 wildtype


title: DL1 PRO-seq IntS8-depleted + IntS8 WFEF/A Mutant rescue replicate 1


title: MCF10A_XRCC4p53DKO_S1

source_name: MCF10A XRCC4 p53 DKO_10 Gy_3 days

tag: treatment

value: 10 Gy, 3 days


title: CoVi08_4_M_6_7P_TCR

value: Blood

tag: cell type


title: MCF10A_XRCC4p53DKO_S2


title: ATAC-seq - ABp 200 minutes #1

description: ATAC-Seq 25k cells, sorted (ABp) 200' (black)

source_name: Embryo (ABp) - 200 minutes

tag: strain

value: lucIs39[tbx-37p(1,87kb)::mNeonGreen::2xNLS::tbx-37 3'UTR(20ng); pal-1p::mScarlet-I::2xNLS::tbb-2 3'UTR (100ng); med-2p::mScarlet-I::2xNLS::tbb-2 3'UTR (100ng); pBluescript(30ng)]

value: Embryo - 200 minutes

value: ABp


title: CoVi08_4_S_6_7P_TCR

description: Single-cell RNA-seq with 10x Genomics v1 V(D)J

value: Memory CD4 T cells, helper enriched:CD3+ CD4+ CD45RA- CD154+ CD69+


title: CoVi05_4_S_6_8P_TCR


title: MCF10A_XRCC4KOATRi_S2

source_name: MCF10A XRCC4 KO_10 Gy+ATRi_3 days

value: XRCC4 KO

value: 10 Gy+ATRi, 3 days


title: GAA Knock-out-AAV-LSPhGAApA treated- 6month old-1

description:
AAV_vs_KO-expression_matrix.csv
AAV-G5-315


title: DL1 PRO-seq IntS8-depleted replicate 2

description:
biotin labeled nascent RNA isolated from Drosophila DL1 permeabilized cells
Adelman_dm3_DL1_IntS8dep_PROseq_N2_plus.bedGraph.gz
Adelman_dm3_DL1_IntS8dep_PROseq_N2_minus.bedGraph.gz

value: Dissociated embryos, near hatching

value: IntS8 targeting dsRNA


title: OSC11 trated with E2

value: GapLacZ + E2 treatment for 6 hours

value: GapLacZ


title: GAA Knock-out-PBS-treated- 6month old-4

description:
KO_vs_WT-expression_matrix.csv
KO-G6-D

value: quadriceps muscle

value: 6 months

value: GAA Knock-out

value: PBS


title: Old 2

value: Lung

value: bulk lung tissue

value: Influenza A/PR8/34 (60 d.p.i.)


title: DL1 PRO-seq IntS8-depleted replicate 1

value: nascent RNA

value: 50,000 permeabilized 293T cells were added to 1 million permeabilized DL1 cells


title: MCF10A_XRCC4KO_S2

source_name: MCF10A XRCC4 KO_10 Gy_3 days

value: breast epithelia

value: 10 Gy, 3 days


title: GAA Knock-out-AAV-LSPhGAApA treated- 6month old-4

description:
AAV_vs_KO-expression_matrix.csv
AAV-G5-318

value: AAV2/8-LSPhGAApA53 (2x10e12 vg/kg) via tail vein injection


title: GAA Knock-out-PBS-treated- 6month old-3

description:
KO_vs_WT-expression_matrix.csv
KO-G6-C


title: CoVi02_4_S_6_5P_TCR

value: Blood

value: Memory CD4 T cells, helper enriched:CD3+ CD4+ CD45RA- CD154+ CD69+


title: CoVi02_4_M_6_5P_TCR


title: DL1 PRO-seq Control replicate 1

description:
biotin labeled nascent RNA isolated from Drosophila DL1 permeabilized cells
Adelman_dm3_DL1_Control_PROseq_N2_plus.bedGraph.gz
Adelman_dm3_DL1_Control_PROseq_N2_minus.bedGraph.gz

value: Dissociated embryos, near hatching

value: Beta-galactosidase targeting dsRNA


title: GAA Knock-out-AAV-LSPhGAApA treated- 6month old-2

description:
AAV_vs_KO-expression_matrix.csv
AAV-G5-316


title: GAA Knock-out-PBS-treated- 6month old-1

description:
KO_vs_WT-expression_matrix.csv
KO-G6-A


title: GAA Knock-out-PBS-treated- 6month old-2

description:
KO_vs_WT-expression_matrix.csv
KO-G6-B


title: DL1 PRO-seq IntS8-depleted + IntS8 Wildtype rescue replicate 1

value: IntS8 targeting dsRNA + Flag-IntS8 wildtype


title: BeMe04_Respiro_TCR


title: BeMe04_Meta_TCR


title: Wild-type_4-6month old

description:
KO_vs_WT-expression_matrix.csv
WT-G7-68

value: quadriceps muscle

value: WT


title: MCF10A_p53KO_S2

source_name: MCF10A p53 KO_10 Gy_3 days

value: p53 KO


title: DJ-1 KO-4

city: Tübingen

first: Genomics Core Facility

address: Calwerstraße 7

department: Institute of Medical Genetics and Applied Genomics

institute: University Hospital Tübingen

data_processing:
Basecalling of raw sequencing output was performed with Illumina bcl2fast2 version 2.19.1.
For adapter sequence trimming, low quality filtering and UMI extraction in FASTQ files, fastp version 0.20.0 was used.
Cleaned read sequences were aligned with STAR version 2.7.3a.
Read assignment for exonic regions was performed with subread featureCounts version 2.0.0.
UMI counts per gene were generated with UMI-tools version 1.0.0.
Genome_build: GRCm38
Supplementary_files_format_and_content: Gene-UMI counts in tab-separated format.

source_name: Mid Brain including Substantia nigra region

extract_protocol:
RNA isolation was done with QIAGEN RNeasy Mini Kit.
Libraries were prepared from 100ng total RNA input with Lexogen QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina following the manufacturer's manual.
RNA-Seq (3')

value: DJ-1 KO


title: DJ-1 KO-5


title: MCF10A_p53KO_S1


title: CoVi05_4_M_6_8P_TCR


title: MCF10A_XRCC4KOATRi_S1

value: XRCC4 KO

value: 10 Gy+ATRi, 3 days


title: BeMe04_Covid_TCR


title: MCF10A_WT_S1

source_name: MCF10A WT_10 Gy_3 days


title: DJ-1 KO-3


title: Wild-type_3-6month old

description:
KO_vs_WT-expression_matrix.csv
WT-G7-67

value: 6 months


title: Wild-type_2-6month old

description:
KO_vs_WT-expression_matrix.csv
WT-G7-117


title: DJ-1 KO-2


title: MCF10A_10Gy5D_crXRCC4_S2

source_name: MCF10A XRCC4 KO_10 Gy_5 days

value: 10 Gy, 5 days


title: MCF10A_XRCC4KO_S1


title: CoVi14_4_M_6_8P_Gex

description: Single-cell RNA-seq with 10x Genomics 5' paired-end


title: DL1 PRO-seq Control replicate 2

value: nascent RNA

value: 50,000 permeabilized 293T cells were added to 1 million permeabilized DL1 cells


title: Wild-type_1-6month old

description:
KO_vs_WT-expression_matrix.csv
WT-G7-116


title: DJ-1 KO-1


title: MCF10A_10Gy5D_crXRCC4_S1

value: breast epithelia


title: CoVi11_4_S_6_5P_Gex


title: MCF10A_WT_S2

value: 10 Gy, 3 days


title: WT-4


title: Osteoclast-Day1-scRNAseq

city: Tokyo

first: Masayuki

last: Tsukasaki

address: 7-3-1 Hongo Bukyo-ku

department: Department of Immunology  Graduate School of Medicine and Faculty of Medicine

country: Japan

institute: The University of Tokyo

data_processing:
Single-cell RNA-seq was performed on cells on Day 0, Day 1 and Day3 of the osteoclast culture system with a target output of 3,000 cells/ per time point.  Single cells were captured with the 10x Genomics Chromium system.  The sequencing library was generated using the 10x Genomics Single Cell 3′ Solution (version 2) kit and subjected to Illumina sequencing (HiSeq 4000).  Alignment, quantitation and aggregation of sample count matrices were performed using the 10x Genomics Cell Ranger pipeline as the manufacturer’s protocol (GENEWIZ JAPAN Corp.). For bulk-RNA-seq, cDNA and sequencing libraries were processed using FastQC (v0.1.1.8), TrimGalore (v0.6.4) and Kallisto (v0.46.0) with the mouse transcriptome index (mus musculus GRCm38.96), and analyzed by DESeq2 (v1.26) to quantify gene expression with PCA, hierarchical clustering and differential expression analysis (using log fold change shrinkage and adjusted p-value <0.05).
Supplementary_files_format_and_content: Excel files include expression values for each sample

source_name: osteoclasts

extract_protocol:
This osteoclast culture was performed on collagen-coated dishes, which permitted a harvesting of the adherent cells by enzymatic treatment and then a preparation of the single-cell suspensions.  Murine bone marrow cells were cultured with M-CSF for 2 days, and these cells were further cultured for 3 days with RANKL in the presence of M-CSF.  scRNA-seq, bulk RNA-seq and proteome analyses were performed at the following time points: Day 0 (before RANKL stimulation), Day 1 (1 day after RANKL stimulation) and Day 3 (3 days after RANKL stimulation). Bulk-RNA seq analysis was also performed using control and Cited2-KO cells on Day 3 of the osteoclastogenic culture system to investigate the role and point of action of Cited2 in the trajectory of osteoclastogenesis.
RNA libraries were prepared for sequencing using standard Ion Torrent Proton protocols

value: In vitro cultured osteoclasts (24h after RANKL stimulation)

value: 8 weeks old


title: Osteoclast-Day0-scRNAseq

value: In vitro cultured osteoclasts (before RANKL stimulation)


title: CoVi11_4_M_6_5P_Gex

value: Blood

value: Memory CD4 T cells, helper enriched:CD3+ CD4+ CD45RA- CD154+ CD69+


title: MCF10A_10Gy5D_crSTING_S1

source_name: MCF10A STING KO_10 Gy_5 days

value: STING KO


title: CoVi08_4_S_6_7P_Gex


title: CoVi14_4_S_6_8P_Gex


title: CoVi08_4_M_6_7P_Gex


title: WT-1

value: WT


title: CoVi05_4_S_6_8P_Gex


title: MCF10A_10Gy5D_crcGAS_S2

source_name: MCF10A cGAS KO_10 Gy_5 days

value: cGAS KO


title: MCF10A_10Gy5D_CDK1i_S2

source_name: MCF10A WT_10 Gy+CDK1i_5 days

value: 10 Gy+CDK1i, 5 days


title: MCF10A_10Gy5D_CDK1i_S1


title: KO-D8-2

city: Worcester

first: David

middle: A

last: Guertin

address: 373 Plantation St.

institute: University of Massachusetts Medical School

data_processing:
PE reads were mapped to mm10 with star_2.5.3
annotated with ENSEMBL annotation GRCm38.94
Aligned exon fragments with MQ ≥ 20 were counted toward gene expression with featureCounts_1.5.2
Data normalized with TPM method

source_name: Primary preadipocytes (from stromal vascular fraction)

growth_protocol: Preadipocytes were cultured in complete DMEM medium containing pyruvate, glutamine and 10% FBS. Differentiation is achieved by supplementation of IBMX, Insulin, Rosiglitazone and Dexamethasone at D0-D2, and then insulin only from D2-D4. Medium was changed every other day through D8.

extract_protocol:
Cells were harvested by Qiazol and RNA was extracted by Rneasy kit from Qiagen.
Libraries were prepared following the instructions from NEBNext directional RNA Prep Kit (#7760)

treatment_protocol: For KO cells, Tamoxifen (4-OHT) was added to the precursor cells. For WT cells, vehicle (EtOH) was added to the cells.

value: Primary preadipocytes

value: Rictor-KO (Cre-induced)

tag: time


title: ZsGreen1+ ApoE KO 22 weeks WD

description: scRNA-seq

data_processing:
Fastq file generation and read alignment were performed by 10X Cell Ranger v3.0.2. Reads were aligned to mouse reference genome mm10 and transcriptome based on Ensembl 93 annotation.
Unique molecular identifier (UMI) count matrix was generated by Cell Ranger "count" command.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Gene-cell UMI count matrix.

source_name: Aorta

extract_protocol: Libraries were prepared using the 10x Genomics Chromium Single Cell 3’ Reagent Kits v2 (mouse samples) or v3 (human samples) according to manufacturer’s instructions. 5000 cells and 200M reads per sample were targeted. 12 cycles for cDNA amplification and 12 cycles for sample index PCR were used.

value: Ascending aorta, brachiocephalic artery and thoracic aorta

value: Myh11(Cre), ROSA(ZsGreen1), ApoE(-/-)

value: 22-week Western diet

tag: smc lineage

value: SMC lineage


title: KO-D8-1


title: KO-D8-3


title: CoVi05_4_M_6_8P_Gex

source_name: PBMC


title: ZsGreen1- ApoE KO 16 weeks WD

description: scRNA-seq

value: 16-week Western diet

value: non-SMC lineage


title: WT-D8-3

value: Rictor-present (no Cre)

value: EtOH


title: MCF10A_10Gy5D_crSTING_S2

value: breast epithelia

value: 10 Gy, 5 days


title: CoVi02_4_S_6_5P_Gex

value: Blood

value: Memory CD4 T cells, helper enriched:CD3+ CD4+ CD45RA- CD154+ CD69+


title: CoVi11_4_MS_6_4P_Gex


title: WT-3

value: WT


title: Osteoclast-Day3-scRNAseq

value: In vitro cultured osteoclasts (72h after RANKL stimulation)

value: 8 weeks old


title: MCF10A_10Gy5D_DMSO_S1

source_name: MCF10A WT_10 Gy_DMSO_5 days

value: 10 Gy, DMSO, 5 days


title: WT-2


title: MCF10A_10Gy5D_DMSO_S2


title: ZsGreen1+ ApoE KO16 weeks WD

description: scRNA-seq


title: WT-D8-1

value: Primary preadipocytes


title: ZsGreen1- ApoE KO 22 weeks WD

description: scRNA-seq

value: Ascending aorta, brachiocephalic artery and thoracic aorta


title: MCF10A_10Gy5D_crcGAS_S1

value: cGAS KO


title: CoVi02_4_M_6_5P_Gex


title: MCF10A_10Gy3D_DMSO_S2

source_name: MCF10A WT_10 Gy_DMSO_3 days

value: 10 Gy, DMSO, 3 days


title: WT-D8-2


title: BeMe04_Respiro_Gex


title: KO-D2-3

value: Rictor-KO (Cre-induced)


title: ZsGreen1- ApoE KO 8 weeks WD

description: scRNA-seq

value: Myh11(Cre), ROSA(ZsGreen1), ApoE(-/-)

value: 8-week Western diet


title: BeMe04_Meta_Gex


title: ZsGreen1+ ApoE KO 8 weeks WD

description: scRNA-seq

value: SMC lineage


title: MCF10A_10Gy3D_DMSO_S1


title: BeMe04_Covid_Gex


title: MCF10A_NIR_S2

source_name: MCF10A WT_untreated

value: untreated


title: ZsGreen1+ Ldlr KO 26 weeks WD

description: scRNA-seq

value: Myh11(Cre), ROSA(ZsGreen1), Ldlr(-/-)

value: 26-week Western diet


title: MCF10A_NIR_S1

value: breast epithelia


title: ZsGreen1- Ldlr KO 26 weeks WD

description: scRNA-seq

value: non-SMC lineage


title: 10x_038_BeMe03_Pre_Gex

value: Blood

value: Memory CD4 T cells, helper enriched:CD3+ CD4+ CD45RA- CD154+ CD69+


title: KO-D2-1


title: JSC_ChIP_seq_Input

data_processing:
ChIP-seq reads were aligned to humen genome hg19 using Bowtie v2.2.3. ChIP-seq peaks were called on each replicate samples using MACS v2.1.0 by comparing ChIP to INPUT control. Peaks were merged from replicates in each cell line using IDR v2.0.3
HiChIP reads were align to human genome hg19 using HiC-Pro v2.11.1. All valid interaction read pairs were then analyzed with hichipper v0.7.5 for detection of significant long-range interactions. Interaction scores were normalized by the total number of valid read pairs.
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq peaks
Supplementary_files_format_and_content: HiChIP long range interactions

source_name: B lymphoma cells

growth_protocol: The four PEL cell lines were rountinly cultured in RPMI1640 supplemented with 20% FCS.

tag: strategy

value: ChIP-Seq

value: PEL cell line

value: JSC

tag: antibody

value: input


title: ZsGreen1- Ldlr KO 16 weeks WD

description: scRNA-seq

value: Ascending aorta, brachiocephalic artery and thoracic aorta

value: 16-week Western diet


title: 10x_038_BeMe03_Post_Gex


title: WT-D2-3

value: Primary preadipocytes

value: Rictor-present (no Cre)

value: EtOH


title: WT-D2-2


title: ZsGreen1+ Ldlr KO 16 weeks WD

description: scRNA-seq

value: SMC lineage


title: ZsGreen1- Ldlr KO 8 weeks WD

description: scRNA-seq

value: 8-week Western diet


title: CoVi14_4_S_6_8P_CITE

description: Single-cell RNA-seq with 10x Genomics 5' v1


title: CoVi14_4_M_6_8P_CITE


title: KO-D0-3

value: Rictor-KO (Cre-induced)


title: JSC_ChIP_seq (2 replicates)

description: 2 replicates


title: BC1_ChIP_seq (2 replicates)

description: 2 replicates


title: ZsGreen1- Ldlr KO 0 week WD

description: scRNA-seq

value: Myh11(Cre), ROSA(ZsGreen1), Ldlr(-/-)

value: 0-week Western diet


title: BC1_ChIP_seq_Input


title: CoVi11_4_S_6_5P_CITE


title: ZsGreen1+ Ldlr KO 8 weeks WD

description: scRNA-seq


title: KO-D0-2


title: BCBL1_ChIP_seq_Input


title: KO-D2-2


title: KO-D0-1


title: CoVi11_4_M_6_5P_CITE


title: WT-D0-3


title: BCBL1_ChIP_seq (2 replicates)

description: 2 replicates


title: ZsGreen1+ Ldlr KO 0 week WD

description: scRNA-seq


title: RNA-seq CBFB-SMMHC knock-in Runx1 knock-out rep3

city: Bethesda

first: Tao

last: Zhen

state: Maryland

address: 9000 Rockville Pike

institute: NIH

description:
RNA-seq_gene_exp.diff
RNA-seq_gene_exp.txt

data_processing:
For RNA-seq: Raw reads were mapped to mouse genome mm10 by STAR (v2.5.1b). The gene expression levels were quantified and normalized by cuffnorm from cufflinks (v2.2.1) package into an FPKM matrix. Genes were filtered if their expressions < 1 FPKM in all samples. The expression matrix was further log2-transformed. The significant differentially expressed genes (DEGs) were called by cuffdiff (v2.2.1) by requiring q-value <0.01, fold change >=2 and genes in the filtered expression matrix. The enriched GO terms were identified by findGO.pl from HOMER package5 for the DEGs. Gene set enrichment analysis was performed using GenePattern 2.0. Ingenuity Pathway Analysis (Ingenuity Systems) was performed to identify upstream regulator of the DEGs.
For ChIC-seq: Paired-end raw reads were mapped to mouse genome mm10 by Bowtie2 (v2.3.5) with key parameters of --no-mixed --no-discordant --local --very-sensitive. For the mapped paired end reads, only MAPQ>=10, non-redundant and fragment size >=140bp were kept for following analysis. The ChIC IgG data for Mx1-CreCbfb+/56M and Runx1f/fMx1-CreCbfb+/56M samples were pooled as control for calling peaks and normalization, the corresponding samples from two batches were pooled together to call peaks. ChIC-seq peaks were call by cLoops2 (https://github.com/YaqiangCao/cLoops2) with key parameters of -minPts 5 -eps 100,200. Briefly, the new peak-calling algorithm for ChIC-seq was based on the similar idea of cLoops, reads were clustered to find candidate peaks, and the candidate peaks were compare to local permutated background and control data to estimate significance. The target genes of peaks were annotated by annotatePeaks.pl from HOMER, motif analysis for Runx1 knockout changed peaks were carried out by findmotifsgenome.pl from HOMER. The aggregated normalized reads per million (RPM) signals for genes TSS were obtained from cLoops2 agg command.
For single cells RNA-sequencing (scRNA-seq): Reads were processed by 10x Cell Ranger (v3.1.0) command count, to the Cell Ranger mouse reference genome mm10-v3.0.0. The raw counts were further normalized by scaling the median counts through all cells, and two batches of data were separated for clustering analysis of UMAP with key parameters n_neighbors=100, n_components=2, min_dist=0, metric="euclidean" and epoch=1000.
Genome_build: mm10

source_name: abnormal myeloid progenitors cell

extract_protocol: Total RNA from AMP cells was extracted with AllPrep DNA/RNA/Protein Mini Kit (QIAGEN). Poly-A selected stranded mRNA libraries were constructed using the Illumina TruSeq Stranded mRNA Sample Prep Kits according to manufacturer’s instructions. Unique barcode adapters were applied to each library. All libraries were combined in equimolar proportion into one pool for sequencing with a NovaSeq6000 sequencer

treatment_protocol: Mx1-CreCbfb+/56M and Runx1f/fMx1-CreCbfb+/56M mice were injected with pIpC and 2-3 weeks later, the AMP population in the bone marrow cells of these mice were sorted out.

value: CBFB-SMMHC knock-in Runx1 knock-out

value: abnormal myeloid progenitors cell

value: Bone marrow


title: CoVi11_4_MS_6_4P_CITE

data_processing:
mkfastq (Cell Ranger 3.1.0) was used to generate FASTQ files with default parameters
count (Cell Ranger 3.1.0) was used to generate the filtered UMI matrix with default parameters
Seurat (3.1.5) was used to filter, normalize and scale the UMI matrix
Genome_build: GRCh38-alts-ensembl-2.0.0 from Cell Ranger
Genome_build: GRCh37 (hg19-3.0.0 from Cell Ranger)
Supplementary_files_format_and_content: cd4t24_annotation.txt.gz meta data for 31341 cells
Supplementary_files_format_and_content: cd4t24_umi.txt.gz UMI count data matrix for 31341 cells
Supplementary_files_format_and_content: cd4t6_annotation.txt.gz meta data for 91140 cells
Supplementary_files_format_and_content: cd4t6_umi.txt.gz UMI count data matrix for 91140 cells

extract_protocol:
For combined single-cell RNA-seq and TCR-seq assays (10x Genomics), a maximum of 60,000 virus-reactive memory CD4+ T cells from up to 8 donors were pooled by sorting into low retention 1.5mL collection tubes, containing 500 µL of a1:1 solution of PBS:FBS supplemented with RNAse inhibitor (1:100). Following sorting, ice-cold PBS was added to make up to a volume of 1400 µl. Cells were then centrifuged for 5 minutes (600 g at 4 ˚C) and the supernatant was carefully removed leaving 5 to 10 µl. 25 µl of resuspension buffer (0.22 µm filtered ice-cold PBS supplemented with ultra-pure bovine serum albumin; 0.04 %, Sigma-Aldrich) was added to the tube and the pellet was gently but thoroughly resuspended. Following careful mixing, 33 µl of the cell suspension was transferred to a PCR-tube for processing as per the manufacturer’s instructions (10x Genomics).
Single-cell RNA-seq using 10x genomics platform was performed using Chromium™ Single Cell 5' v1 Reagent Kits following the manufacturer’s protocol
Libraries were constructed using Chromium™ Single Cell 5' v1 Reagent Kits following the manufacturer’s protocol
100 x 100 bp paired-end reads, 3'TAG, Hg19 human reference genome.

treatment_protocol:
PBMCs from each donor, were thawed, washed, plated in 6-well culture plates at a concentration of 5 x 106 cells/ml in 1 ml of serum-free TexMACS medium (Miltenyi Biotec) and left overnight (5 % CO2, 37 ˚C). Cells were stimulated by the addition of individual virus-specific peptide polls (1 µg/ml) for 6 h in the presence of a blocking CD40 antibody (1 µg/ml; Miltenyi Biotec). For subsequent MACS-based enrichment of CD154+, cells were sequentially stained with fluorescence-labeled surface antibodies, Cell-hashtag TotalSeq™-C antibody (0.5 µg/condition), and a biotin-conjugated CD154 antibody (clone 5C8; Miltenyi Biotec) followed by anti-biotin microbeads (Miltenyi Biotec). Labelled cells were added to MS columns (Miltenyi Biotec) and positively selected cells (CD154+) were eluted and used for FACS sorting of CD154+ memory CD4+ T cells. The flow-through from the column was collected and re-plated for harvesting cells responding 24 h after peptide stimulation.
Analogous to enrichment for CD154+, CD137-expressing CD4+ memory T cells cells were positively selected by staining with biotin-conjugated CD137 antibody (clone REA765; Miltenyi Biotec) followed by anti-biotin MicroBeads and applied to a new MS column. Following elution, enriched populations were immediately sorted using a FACSAria Fusion Cell Sorter (Becton Dickinson) based on dual expression of CD154 and CD69 for 6-hour stimulation condition, and CD137 and CD69 for 24-hour stimulation condition.

value: Blood

value: Memory CD4 T cells, helper enriched:CD3+ CD4+ CD45RA- CD154+ CD69+


title: RNA-seq CBFB-SMMHC knock-in Runx1 knock-out rep2


title: WT-D0-2


title: WT-D0-1


title: CoVi08_4_S_6_7P_CITE


title: RNA-seq CBFB-SMMHC knock-in Runx1 knock-out rep1


title: BC3_ChIP_seq (2 replicates)

description: 2 replicates

value: ChIP-Seq

value: PEL cell line


title: BC3_ChIP_seq_Input

value: input


title: CoVi08_4_M_6_7P_CITE


title: JSC_HiChIP (2 replicates)

description: 2 replicates

value: HiChIP-Seq

value: JSC


title: WT-D2-1

value: Primary preadipocytes

value: Rictor-present (no Cre)


title: CoVi05_4_S_6_8P_CITE


title: BC1_HiChIP (2 replicates)

description: 2 replicates


title: 10x scRNA-seq CBFB-SMMHC knock-in Runx1 knock-out rep1

extract_protocol: 10X genomics chromium platform was used to capture isolated AMP cells and all steps were performed according to manufacturer’s instructions. The Chromium Single Cell 3’ Library & Gel Bead Kit v2 was used. Libraries were sequenced on an Illumina NextSeq 550 sequencer


title: 10x scRNA-seq CBFB-SMMHC knock-in Runx1 knock-out rep2


title: CoVi05_4_M_6_8P_CITE


title: CoVi02_4_S_6_5P_CITE


title: RNA-seq CBFB-SMMHC knock in rep2

value: CBFB-SMMHC knock in


title: BC3_HiChIP (2 replicates)

description: 2 replicates

extract_protocol:
DNA was purified with Ampure xp Beads
Libraries were prepared for sequencing using standard Illumina protocols


title: BCBL1_HiChIP (2 replicates)

description: 2 replicates


title: RNA-seq CBFB-SMMHC knock in rep3


title: CoVi02_4_M_6_5P_CITE


title: RNA-seq CBFB-SMMHC knock in rep1


title: 10x scRNA-seq CBFB-SMMHC knock-in rep2

value: CBFB-SMMHC knock-in


title: HMGB1sgRNA2-Mock

status: Public on Oct 05 2020

city: New Haven

first: Qin

last: Yan

email: qin.yan@yale.edu, craig.wilen@yale.edu

address: 310 Cedar St.

institute: Yale University

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were aligned using STAR aligner v2.7.3a to chlSab2 with parameters --winAnchorMultimapNmax 200 --outFilterMultimapNmax 100 --quantMode GeneCounts.
Bigwig files were generated using deeptools v3.1.3 (Ramírez et al., 2016) with parameter --normalizeUsing RPKM.
DEseq2 v1.32 was used to determine differential gene expression using counts.
Genome_build: chlSab2
Supplementary_files_format_and_content: bigwig (Merged), txt (DESeq2 results), txt (raw counts)

organism: Chlorocebus sabaeus

source_name: Vero-E6 sgHMGB1 sg2 uninfected with SARS-CoV2

growth_protocol: Vero-E6 cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) with 10% heat-inactivated fetal bovine serum (FBS), and 1% Penicillin/Streptomycin.

extract_protocol:
Cells were infected with SARS-CoV-2 at a MOI of 1 for 24 hours then RNAs were extracted using Direct-zol RNA MiniPrep Kit and submitted to the Yale Center for Genome Analysis for library preparation.
Libraries were prepared using TruSeq stranded mRNA library prep kit (Illumina)

value: african green monkey kidney cells

tag: infection

value: uninfected

tag: condition

value: sgHMGB1 sg2


title: HMGB1sgRNA1-Mock

source_name: Vero-E6 sgHMGB1 sg1 uninfected with SARS-CoV2

value: sgHMGB1 sg1


title: 10x scRNA-seq CBFB-SMMHC knock-in rep1

value: abnormal myeloid progenitors cell


title: HMGB1sgRNA1-SARS-CoV-2

source_name: Vero-E6 sgHMGB1 sg1 infected with SARS-CoV2

value: infected with SARS-CoV2


title: HMGB1sgRNA2-SARS-CoV-2

source_name: Vero-E6 sgHMGB1 sg2 infected with SARS-CoV2


title: A2-Ctrl-Mock

source_name: Vero-E6 sgCtrl uninfected with SARS-CoV2

value: sgCtrl


title: A2-Ctrl-SARS-CoV-2

source_name: Vero-E6 sgCtrl infected with SARS-CoV2


title: A10-Ctrl-2-SARS-CoV-2


title: HMGB1sgRNA2_rep1

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were trimmed of adapters using Trimmomatic v0.39
Trimmed reads were aligned using Bowtie2 v2.2.9 to chlSab2 using standard parameters and a maximum fragment length of 2000
Duplicate reads were determined using Picard tools v2.9.0
Bam files were filtered using samtools -F 1804
Reads were then processed where only the most 5' base pair for each read was kept and forward strand reads were shifted +4bp, and reverse strand reads were shifted -5bp.
For a consensus peak set, all bam files were merged using samtools and used for peak calling
Peak calling was performed using MACS2 v2.2.6 with parameters --nomodel --keep-dup all -s 1 --shift -75 --extsize 150.
featureCounts v1.6.2 was used to count reads from replicates that fall within the consensus peak set using default parameters
DEseq2 v1.32 was used to determine differential accessibility using counts.
Bigwig files were generated using deeptools v3.1.3 with parameter --normalizeUsing RPKM
Genome_build: chlSab2
Supplementary_files_format_and_content: bigwig (Merged rep1, rep2), bed (all ATAC peaks), txt (DESeq2 results), txt (raw counts)

source_name: Vero-E6 sgHMGB1 sg2

extract_protocol:
50,000 cells were treated with Transposase. Protocol as previously described in Corces et al (Nat.Methods 2017).
DNA libraries were prepared as previously described in Corces et al (Nat.Methods 2017).

value: HMGB1 KO sg2


title: HMGB1sgRNA1_rep2

source_name: Vero-E6 sgHMGB1 sg1

value: HMGB1 KO sg1


title: HMGB1sgRNA1_rep1


title: HMGB1sgRNA2_rep2


title: CtrlsgRNA_rep2

source_name: Vero-E6 sgCtrl

value: control sgRNA


title: Input_sg2

city: Orange

first: Matthew

last: Simon

state: CT

address: 100 West Campus Drive, Ste MIC 231

department: Molecular Biophysics and Biochemistry

data_processing:
Reads were trimmed of adaptor sequences using Cutadapt.
Reads were aligned to chlSab2 genome using Bowtie2 v2.2.9.
Peaks were called using MACS2 with default parameters.
Fold enrichment bigwig tracks were created using MACS2 bdgcamp compared to input control.
Genome_build: chlSab2, NCBI annotation release 100
Supplementary_files_format_and_content: bigwig files of fold enrichment tracks over input control
Supplementary_files_format_and_content: narrowPeak peak files from MACS2

source_name: Kidney epithelial cell line

extract_protocol:
20 million cells per IP were crosslinked with formaldehyde for 10 minutes. Nuclei were sonicated, lysates were clarified, and histone-DNA complexes were isolated with antibody.
Libraries were prepared using standard Illumina protocols.

value: Vero-E6 cells

value: Kidney epithelial cell line

value: Input

tag: sgrna


title: H3K27ac_sg2_2

value: Abcam H3K27ac ab4729


title: CtrlsgRNA_rep1


title: H3K27ac_sg2_1


title: Input_sg1


title: H3K27ac_sg1_1


title: H3K27ac_sg1_2


title: Input_WT

value: Empty

value: WT


title: H3K27ac_WT_1


title: H3K27ac_WT_2


title: A10-Ctrl-2-Mock


title: RNA_8_I191 [M8]

city: Cleveland

first: Anna

last: Miller

state: Ohio

address: 2109 Adelbert Rd

institute: Case Western Reserve University

data_processing:
FastQC was used to assess the quality of the reads. Adapter sequences were removed using TrimGalore
Reads were aligned to the Ensembl GRCm38.p5 primary DNA assembly reference sequence using Hisat2
Read counts were calculated using HTSeq v0.11.1
Genes with read counts of 0 or of a low yield were removed and normalized by EdgeR
All QTL analyses were performed using Rqtl v.1.44-9
Genome_build: Ensembl GRCm38.p5
Supplementary_files_format_and_content: Excel file containing differently expressed RNAs

source_name: Mouse liver cells

extract_protocol:
Total RNA was extracted from liver using PureLink RNA mini kit (Thermo Fisher Scientific)
Total RNA (1 ug) from each liver was used to generate next-generation RNA-seq libraries using Illumina TruSeq stranded library preparation kit per manufacturer's protocol

value: F2 mice with A/J-derived substituted chromosomes 4 and 6 on an otherwise C57BL/6J genetic background

tag: Sex

value: male

value: adult

value: Liver


title: RNA_7_I176 [M7]


title: RNA_3_I125 [M3]


title: RNA-seq_Tex11PM/Y SSCs-rep 1

city: Shanghai

first: Jinsong

last: Li

state: Shanghai

address: 320 岳阳路，上海

country: China

institute: 中国科学院上海分子细胞科学卓越创新中心

data_processing:
Raw reads are filtered by fastp program, with parameters -e 20 -l 36
Clean reads are mapping to the mm10 genome using STAR for RNA-seq data
For RNA-seq data, only uniquely mapped reads are counted using featurecount program, and TPM is calculated by Stringtie; Differential Expression is done by DESeq2 in R, and GO is called by clusterprofile.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include counts for each Sample .
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample .
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample .

source_name: Spermatogonial Stem Cells

growth_protocol: SSCs were growthed in standard culture medium and passaged every 5-10 days

extract_protocol:
Cell were collected from FACS AriaII sorter. RNA was harvested using Trizol reagent
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.  Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Spermatogonial Stem Cells derived from a mouse testis

tag: mouse age

value: post natal day 10


title: Tex11PM/Y SSCs

institute: 中国科学院上海分子细胞科学卓越创新中心

data_processing:
Library strategy: DNA-seq
Raw reads are filtered by fastp program, with parameters -e 20 -l 36
Clean reads are mapping to the mm10 genome using BWA for WGS data
For WGS data, mapped reads are subject to GATK best practice using default parameters, SNP is called by Mutect2 and filtered using parameters: (SNP)DP<10, QD < 2.0, QUAL < 30.0, SOR > 3.0, FS > 60.0, Q < 40.0, MQRankSum < -12.5, ReadPosRankSum < -8.0, (INDEL)DP<10, QD < 2.0, QUAL < 30.0, ReadPosRankSum < -20.0, FS > 200.0.
Passed SNPs and Indels were filtered in excel by allele DP >10, minor allele frequency > 0.35 for heterozygous SNPs, allele frequency > 0.85 for homozygous SNPs.
All SNPs and Indels were annotated by ANNOVAR (2019Oct24)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include called SNP and Indels.

extract_protocol:
Cell were collected from FACS AriaII sorter and performed gDNA extraction with TIANamp Genomic DNA Kit (QIAGEN) following the the manufacturer’s instructions
A total amount of 0.2 μg DNA per sample was used as input material for the DNA library preparations. Sequencing library was generated using NEB Next® Ultra™ DNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to each sample. Briefly, genomic DNA sample was fragmented by sonication to a size of 350 bp. Then DNA fragments were endpolished, A-tailed, and ligated with the full-length adapter for Illumina sequencing, followed by further PCR amplification. After PCR products were purified by AMPure XP system (Beckman Coulter, Beverly, USA), DNA concentration was measured by Qubit®3.0 Flurometer (Invitrogen, USA), libraries were analyzed for size distribution by NGS3K/Caliper and quantified by real-time PCR (3 nM).

tag: passage

value: passage 14


title: RNA-seq_Tex11PM/Y SSCs-rep 2

institute: 中国科学院上海分子细胞科学卓越创新中心


title: RNA_4_I126 [M4]

tag: tissue


title: RNA-seq_WT SSCs-rep 2

institute: 中国科学院上海分子细胞科学卓越创新中心


title: RNA_6_I133 [M6]

tag: age


title: RNA_59_I284 [M59]


title: RNA_9_I186 [M9]


title: HDR-1 SSCs

institute: 中国科学院上海分子细胞科学卓越创新中心


title: RNA_56_I261 [M56]


title: RNA_57_I274 [M57]


title: RNA_1_I120 [M1]


title: RNA-seq_WT SSCs-rep 1

institute: 中国科学院上海分子细胞科学卓越创新中心


title: RNA_55_I248 [M55]


title: RNA_51_I245 [M51]


title: RNA_50_I237 [M50]


title: RNA_49_I229 [M49]


title: T-47D cells, FZR1 ko-DDP

city: Tianjin

first: Shuo

last: Liu

address: 94 Weijin Road

institute: Nankai University

data_processing:
A total of 2 samples were measured using the BGISEQ-500 platform in this project.
This project uses SOAPnuke(v1.4.0), a filtering software independently developed by Huada, for statistics and trimmomatic(v0.36) for filtering.
After getting clean reads, we used HISAT(v2.1.0) to align clean reads to the reference genome sequence.
Use Bowtie2(v2.2.5) to compare clean reads to the reference gene sequence, and then use RSEM to calculate the expression levels of genes and transcripts
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample

source_name: Breast Cancer Cells

extract_protocol: Total RNA was extracted using TRIZOL reagent (Invitrogen) following manufacturer’s instructions.

tag: cell line

tag: genotype

value: FZR1 ko

tag: drug

value: cisplatin

tag: treatment dose


title: T-47D cells, WT-DDP


title: RNA_45_I217 [M45]

tag: strain


title: RNA_47_I220 [M47]


title: RNA_46_I219 [M46]


title: RNA_44_I198 [M44]


title: RNA_42_I195 [M42]


title: RNA_40_I192 [M40]


title: RNA_38_I183 [M38]


title: RNA_36_I174 [M36]


title: RNA_37_I175 [M37]


title: RNA_33_I123 [M33]


title: RNA_29_I285 [M29]


title: RNA_28_I283 [M28]


title: RNA_30_I296 [M30]


title: RNA_32_I121 [M32]


title: RNA_23_I254 [M23]


title: RNA_24_I255 [M24]


title: RNA_34_I124 [M34]


title: RNA_31_I114 [M31]


title: RNA_26_I257 [M26]


title: RNA_22_I248 [M22]


title: RNA_25_I256 [M25]


title: RNA_35_I127 [M35]


title: RNA_21_I244 [M21]


title: RNA_27_I276 [M27]


title: RNA_16_I221 [M16]


title: RNA_43_I197 [M43]


title: RNA_17_I227 [M17]


title: RNA_20_I243 [M20]


title: RNA_19_I236 [M19]


title: RNA_12_I196 [M12]


title: RNA_13_I215 [M13]


title: RNA_15_I218 [M15]


title: RNA_18_I230 [M18]


title: RNA_14_I216 [M14]


title: RNA_11_I194 [M11]


title: RNA_10_I191 [M10]