title: HCT116: Human colorectal carcinoma cells-input DNA

city: Nanjing

first: chen

last: Wang

address: xianlin street num 163

institute: Nanjing University

data_processing:
Sequenced reads were aligned to the human genome, and reads with more than two aligned positions were removed. The remaining tags were further filtered by quality score and redundancy. Only nonredundant reads that passed the quality score were retained for downstream analysis. ChIP-seq tags and whole genome sequencing tags were then analyzed using MACS to identify the peaks based on p < 0.005
The remaining tags were further filtered by quality score and redundancy.
Only nonredundant reads that passed the quality score were retained for downstream analysis.
ChIP-seq tags and whole genome sequencing tags were then analyzed using MACS to identify the peaks based on p < 0.005
Genome_build: mm9

source_name: Human colorectal carcinoma cells

extract_protocol:
Chromatin immunoprecipitation (ChIP) assays were performed using a ChIP assay kit (Millipore, Temecula, USA) according to the manufacturer’s instructions. Briefly, cells were fixed with formaldehyde and homogenized. Nuclei were pelleted, and DNA was sheared by sonication and immunoprecipitated with anti-RUNX2 antibody or negative control immunoglobulin G using protein A/G beads. DNA was released from immunoprecipitate complexes using proteinase K and purified. Chromatin was sheered by 8 sonication cycles to generate DNA fragments with an average size of 200 bp for ChIP-seq analysis and 4 sonication cycles to generate DNA fragments with an average size of 600 bp for ChIP-qPCR.
For high-throughput sequencing, 10-20 ng DNA was used to make the ChIP-seq library according to the instructions from Illumina’s ChIP-seq Sample Prep kit. The ChIP-seq library was loaded on Illumina’s cluster station and sequenced with Illumina Genome Analyzer IIx.

value: Human colorectal carcinoma cells

tag: chip antibody


title: follicular granulosa cell layers-F1 Hi-C replicate_2

status: Public on Nov 10 2021

type: SRA

city: chengdu

first: hua

last: kui

address: No 211 Huimin Road

country: China

institute: Sichuan Agricultural University

library_source: genomic

data_processing:
Reads were mapped to the chicken reference genome (GRCg6a) by BWA (v 0.7.15).
Juicer were used HiC data processing to filter duplication, low-quality alignment read pairs (MAPQ < 30) as well as intra-fragment read pairs.
High-quality reads  normalized with Knight-Ruiz [KR] algorithm and quantile  algorithm to structure contact matrixes at 20 or 100 kb resolution.
Compartments A/B were identified with principal component analysis (PCA) as described by Lieberman-Aiden E, et al. science 2009 (PMID: 19815776).
Locations of topologically associated domains (TADs) were computed by combining  directionality index (Dixon et al. Nature. 2012 [PMID: 22495300]) and insulation index (Emily Crane et al. Nature. 2017)
Genome_build: GRCg6a
Supplementary_files_format_and_content: 20 and 100 kb matrixes, hic file
location of paired reads, gz file
A-B index, xls file
locations of TAD for each sample, bed file

molecule: genomic DNA

organism: Gallus gallus

source_name: follicular granulosa cell layers

extract_protocol:
Hi-C experiment were conducted using DpnII, according to the protocol published by Suhas S P Rao. et al. Cell 2014 (PMID: 25497547) .
DNA libraries were prepared during Hi-C protocol according to experimental procedures described in Suhas S P Rao. et al. Cell 2014 (PMID: 25497547).

tag: breed

value: Luhua hens

tag: developmental stage

value: preovulatory follicles

tag: age

value: 31 weeks

tag: tissue

value: follicular granulosa cell layers


title: d0 2 16.7 TST WT

city: Boston

first: Attila

last: Szanto

state: MA

address: 185 Cambridge St.

department: Molecular Biology

country: USA

institute: Massachusetts General Hospital

description:
processed data file: d0_d10_tst_ko_cond_as_analyze.txt
processed data file: d0_d10_tst_ko_comp_diff_expr.txt

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for adaptor sequence, and aligned Mus musculus musculus (mus) and Mus musculus casteneus (cas) or mm9 genomes using Tophat with parameters -p 2 --no-coverage-search --read-edit-dist 3 --read-mismatches 2 --read-gap-length 2 --b2-very-sensitive --mate-inner-dist 20 --mate-std-dev 20 --library-type fr-firststrand
After alignment coverages from mm9 mapping were calculated to get composite (comp) tracks. Allele-specific analysis was performed using in-house scripts for liftover to mm9 genome.
For differential gene expression analysis HOMER was used with parameters: rna mm9 -noadj -count genes -strand + -condenseGenes
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Allelic read counts are summarized in d0_d10_tst_ko_cond_as_analyze.txt.
Supplementary_files_format_and_content: Normalized composite read counts are summarized in d0_d10_tst_ko_comp_diff_expr.txt, and d0-d10, parental-ko comparisons are shown.
Supplementary_files_format_and_content: bw files of comp, cas and mus coverages are separated by strands and normalized by sequencing depth.

molecule: total RNA

organism: Mus musculus

source_name: embryonic stem cells

growth_protocol: Mouse embryonic stem cells from 16.7 Tsix +/TST female cell lines were used as parental line for deleting G9a. Cells were grown without differentiation, day 0 (d0) or differentiated with LIF withdrawal for 4 days in suspension and the placed on gelatinized plates for another 6 days and harvested on day 10 (d10).

extract_protocol:
Total RNA was extracted using Qiagen RNeasy kit and rRNA was removed using Epicentre Ribo-Zero kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were not treated. Day 0 indicated undifferentiated, while day 10 the differentiated states.

tag: cell line

value: 16.7 Tsix +/TST

tag: cell type

value: Embryonic stem cells

tag: genotype/variation

value: WT

tag: gender

value: Female

tag: time of differentiation

value: day 0

tag: donor


title: follicular granulosa cell layers-SWF Hi-C replicate_1

value: prehierarchical follicles


title: T9

city: Bethesda

first: Sunita

middle: K

last: Agarwal

state: MD

address: Bldg. 10, Room 8C101

department: NIDDK

institute: National Institutes of Health

description:
RNA (ribosomal RNA depleted)
Adaptor sequence:
CTGCTGTA

data_processing:
Data processing was outsourced to QUICK BIOLOGY INC., Pasadena, CA.
Supplementary_files_format_and_content: File format: comma separated value (csv). Content: Normalized reads count per million for every gene/transcript in each sample. This file can be viewed in Microsoct Excel.

organism: Homo sapiens

source_name: normal thymus

extract_protocol:
RNA from FFPE tissue samples was isolated with the RNAstorm FFPE RNA extraction kit (Cell Data Sciences). From this total RNA, the Ribosomal RNA was depleted by QUICK BIOLOGY INC., Pasadena, CA.
Library construction, sequencing and data processing was outsourced to QUICK BIOLOGY INC., Pasadena, CA

value: thymus

value: Male

tag: sample preparation

value: FFPE tissue section


title: HCT116: Human colorectal carcinoma cells-RUNX2

value: RUNX2(Cell Signaling Technology, #12556)


title: T10

description:
RNA (ribosomal RNA depleted)
Adaptor sequence:
CCTTAGGT


title: pdgfrb-positive scRNAseq lib2

city: Worcester

first: Nathan

middle: D.

last: Lawson

address: 364 Plantation Street

department: Molecular, Cell, and Cancer Biology

institute: University of Massachusetts Medical School

description: mRNA

data_processing:
Bulk RNA-seq:
Raw HiSeq2000 data files were processed with CASAVA 1.8.2 (Illumina) to generate fastq files for inserts and index sequences. Demultiplexing of index sequences was done with CASAVA. For both samples, if index sequences were non-redundant, we allowed for 1 mismatch or N in the index.
Paired end reads were mapped to the zebrafish genome (GRCz11) using STAR.
Mapped reads were quantified using a custom annotation (V4.3.gtf) using RSEM.
Differentially expressed genes were identified using DEseq2.
Single-cell RNA-seq (scRNA-seq):
Sequencing was performed on a HiSeq4000.
Reads were mapped and quantified using cellranger, v3.1.0 (10x Genomics).
RNAseq pipelines were run in the DolphinNext environment.
Genome_build: GRz11
Supplementary_files_format_and_content: alldetectedWtvUm148.csv: Comma-separated formatted output from DEseq2 for differential gene expression.
Supplementary_files_format_and_content: MEX formatted files (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz) from scRNA-seq cellranger output.

organism: Danio rerio

source_name: pdgfrb:egfp-positive cells

extract_protocol: scRNA-seq libraries generated using 10x Genomics 3' v3 kit.

treatment_protocol: Embryos were dissociated into single cell suspensions and transgene expressing cells were isolated by fluorescence activated cell sorting.

tag: Stage

value: 5 days post fertilization

tag: strain

tag: source

value: FACS-isolated cells

value: pdgfrb:egfp-positive cells


title: VDJ-seq_EXP20000768_Sample_02

first: Natalie

middle: Y. R.

last: Agar

state: Massachusetts

address: Harvard Medical School

department: Neurosurgery

institute: Brigham and Women's Hospital

description: VDJ-seq

data_processing:
Base Calling TCR BCL to TCR FASTQ via Cell Ranger 3.1.0 with the flag "--delete-undetermined" in addition to the standard settings.
Base Calling GEX BCL to GEX FASTQ via Cell Ranger 3.1.0 with the flag "--delete-undetermined" in addition to the standard settings.
Base Calling ADT BCL to ADT FASTQ via Cell Ranger 3.1.0 with the flag "--delete-undetermined" in addition to the standard settings.
Base Calling tetramer BCL to tetramer FASTQ file via bcl2fastq2 version v2.20.0 with the flags "--minimum-trimmed-read-length 0 --mask-short-adapter-reads 0" in addition to the standard settings.
TCR Read Counts: FASTQ to vdj counts via Cell Ranger 3.1.0 using the standard settings.
GEX Read Counts: FASTQ to gene expression counts via Cell Ranger 3.1.0 using the standard settings.
Tetramer FASTQ to Tetramer counts via extracting tetramer barcode from uniquely observed tetramer UMI reads using python script
ADT FASTQ to ADT counts via extracting tetramer barcode from uniquely observed tetramer UMI reads using python script
TCR VDJ counts paired with tetramer and ADT counts via common hydrogel barcode using python script
VDJ and tetramer counts separated via hashtags using Seurat 4.0.3
Dehashed VDJs selected for functional assays.
Genome_build: GRCh38 (hg19)
Supplementary_files_format_and_content: The processed data files conform to the hfad AnnData format: https://anndata.readthedocs.io/en/latest/anndata.AnnData.html
Supplementary_files_format_and_content: Metadta for hashed samples including HTO oligo sequence is available in the file "GEO_upload_seq_CIPHER_2021_11_04_Supplemental_Sample_to_HTO.xlsx"

source_name: CD8+ T cells

extract_protocol:
PBMCs were thawed, and CD8+ T cells were enriched by magnetic-activated cell sorting (MACS) using a CD8+ T Cell Isolation Kit (Miltenyi) following the manufacturers protocol. The CD8+ T cells were then stained with 1 nM final concentration tetramer library in the presence of 2 mg/mL salmon sperm DNA in PBS with 0.5% BSA solution for 20 minutes. Cells were then labeled with anti-TCR antibody-derived tag (ADT, IP26, Biolegend) for 15 minutes followed by washing. Tetramer bound cells were then labeled with phycoerythrin (PE) conjugated anti-DKDDDDK-Flag antibody (BioLegend) followed by dead cell discrimination using 7-amino-actinomycin D (7-AAD). The live, tetramer positive cells were sorted using a Sony MA900 Sorter (Sony). Tetramer positive cells were counted by Nexcelom Cellometer (Lawrence, MA, USA) using AOPI stain following manufacturer’s recommended conditions. Single-cell encapsulations were generated utilizing 5’ v1 Gem beads from 10x Genomics (Pleasanton, CA, USA) on a 10x Chromium controller and downstream TCR, and Surface marker libraries were made following manufacturer recommended conditions. All libraries were quantified on a BioRad CFX 384 (Hercules, CA, USA) using Kapa Biosystems (Wilmington, MA, USA) library quantified kits and pooled at an equimolar ratio. TCRs, surface markers, and tetramer generated libraries were sequenced on Illumina (San Diego, CA, USA) NextSeq550 instruments. Sequencing data were processed using the Cell Ranger Software Suite (Version 3). Samples were demultiplexed and unique molecular identifier (UMI) counts were quantified for TCRs, tetramers, and gene expression.
10X Chromium 5' single-cell

value: PBMC

tag: subject

tag: cohort

value: convalescent


title: VDJ-seq_EXP20000768_Sample_01

description: VDJ-seq


title: TM2

description:
Patient ID 2
RNA (ribosomal RNA depleted)
Adaptor sequence:
AGCGCTTA

source_name: thymoma

value: thymoma


title: X4To

city: Santiago

first: Juan

last: Larraín

address: Portugal 49

department: Cellular and Molecular Biology

country: Chile

institute: Pontificia Universidad Catolica de Chile

data_processing:
Illumina Casava 1.7 software was used for basecalling.
Paired-end reads were mapped to Xenopus laevis model transcriptome v9.1 (Xenbase) using Bowtie. Gene expression level was quantified by RSEM.

organism: Xenopus laevis

source_name: 96h - transection - TORIN1

extract_protocol:
Spinal cords from animals at R-stage were dissected in time-series after surgery and immediately stored in RNAlater. Posterioly the purification of total RNA was performed using the RNeasy Mini Kit.
RNA libraries were prepared by TruSeq RNA Library Prep Kit v2. Posterioly these were sequenced on the Illumina HiSeq 2000 and HiSeq 4000.

value: Caudal section of spinal cord

value: NF stage 50

tag: surgery

value: transection

tag: time of isolation after surgery (hours)

tag: treatment

value: Incubated in TORIN1 during first 24 hours after transection


title: TM5

description:
Patient ID 5
RNA (ribosomal RNA depleted)
Adaptor sequence:
CGGAATCG

source_name: thymoma (NE diffn)

value: thymoma (NE diffn)

value: Female


title: pdgfrb-positive scRNAseq lib1

description: mRNA


title: VDJ-seq_EXP20000722_Sample_07

description: VDJ-seq


title: TC25

description:
Patient ID 14
RNA (ribosomal RNA depleted)
Adaptor sequence:
GCAAGGGT

source_name: thymic carcinoid

value: thymic carcinoid


title: X4D

source_name: 96h - transection - DMSO

value: Incubated in DMSO during first 24 hours after transection


title: X2To

source_name: 48h - transection - TORIN1


title: TC17

description:
Patient ID 12
RNA (ribosomal RNA depleted)
Adaptor sequence:
CGGAATCG

value: Male


title: VDJ-seq_EXP20000722_Sample_06

description: VDJ-seq


title: VDJ-seq_EXP20000768_Sample_03

description: VDJ-seq


title: VDJ-seq_EXP20000722_Sample_04

description: VDJ-seq


title: TC10

description:
Patient ID 10
RNA (ribosomal RNA depleted)
Adaptor sequence:
ACCCAGCA

value: FFPE tissue section


title: X2D

source_name: 48h - transection - DMSO


title: TC11

description:
Patient ID 11
RNA (ribosomal RNA depleted)
Adaptor sequence:
CCGTCCCG


title: X1To

source_name: 24h - transection - TORIN1


title: VDJ-seq_EXP20000722_Sample_05

description: VDJ-seq


title: TC9

description:
Patient ID 9
RNA (ribosomal RNA depleted)
Adaptor sequence:
AGCGCTTA


title: VDJ-seq_EXP20000722_Sample_03

description: VDJ-seq


title: VDJ-seq_EXP20000722_Sample_01

description: VDJ-seq


title: X1D

source_name: 24h - transection - DMSO


title: TC8

description:
Patient ID 8
RNA (ribosomal RNA depleted)
Adaptor sequence:
CTCAGAAT


title: TC7

description:
Patient ID 7
RNA (ribosomal RNA depleted)
Adaptor sequence:
CTATACTT


title: VDJ-seq_EXP20000683_Sample_07

description: VDJ-seq


title: TC6

description:
Patient ID 6
RNA (ribosomal RNA depleted)
Adaptor sequence:
CTAGCTAC


title: VDJ-seq_EXP20000683_Sample_01

description: VDJ-seq


title: SCD13_CMo

city: New York

first: Yunfeng

last: Liu

state: NY

address: 310 East 67th Street

department: Lindsley F. Kimball Research Institute (LFKRI)

institute: New York Blood Center

data_processing:
paired-end analysis on BGISEQ-500 platform
For each sample, at least 60 million pair-end reads were produced, and the raw data was filtered by SOAPnuke to get clean reads and stored in FASTQ format.
After these FASTQ data were mapped to UCSC hg19 transcriptome by HISAT and Bowtie2, gene expression levels were calculated with RSEM.
To identify the differentially expressed genes (DEGs), NOIseq was used and adjusted P < 0.05 were considered significant.
Genome_build: hg19
Supplementary_files_format_and_content: FPKMs

source_name: blood classical monocyte

extract_protocol:
Total monocytes from patients with SCD and HD were enriched from prepared PBMC using a pan monocyte isolation kit (Miltenyi Biotec, Auburn, CA) following manufacturer’s instructions. After that enriched cells were further purified with flow cytometer sorter. Cells were stained with fluorescently labeled anti-human CD14, CD16, HLA-DR and CD45 antibodies, and DAPI. Single DAPI-CD45+HLA-DR+CD14+CD16- classical monocytes were sorted using FACSAria Cell Sorter (BD Biosciences). Sorted cells were lysed and subjected to mRNA isolation with the Dynabeads mRNA Direct Purification kit (Thermo Scientific). We use Agilent 2100 Bio analyzer (Agilent RNA 6000 Nano Kit) to do the total RNA sample QC: RNA concentration, RIN value,28S/18S and the fragment length distribution.
1)mRNA enrichment: Oligo dT Selection or rRNA depletion; 2) RNA fragment and reverse transcription: Fragment the RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer; 3) End repair, add A tailing and adaptor ligation: The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated cDNA fragments; 4) PCR amplification: The ligation products were purified, and many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer;5) Denature and cyclization: Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase.

tag: disease state

value: patient with sickle cell disease

value: Peripheral blood

value: CMo


title: TC4

description:
Patient ID 4
RNA (ribosomal RNA depleted)
Adaptor sequence:
CCGTCCCG

tag: tissue


title: SCD10_CMo


title: SCD9_CMo


title: TC3

description:
Patient ID 3
RNA (ribosomal RNA depleted)
Adaptor sequence:
GACGGAGA


title: VDJ-seq_EXP20000654_Sample_05

description: VDJ-seq


title: VDJ-seq_EXP20000654_Sample_06

description: VDJ-seq


title: SCD8_CMo


title: VDJ-seq_EXP20000683_Sample_08

description: VDJ-seq


title: TC1

description:
Patient ID 1
RNA (ribosomal RNA depleted)
Adaptor sequence:
CACCGGCA


title: SCD12_CMo


title: VDJ-seq_EXP20000654_Sample_04

description: VDJ-seq


title: RNA from MyoD-induced USCs of DMD patient transfected with AON44

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

description:
IG-m 44
total RNA from DMD patient and treated with MyoD and AON

data_processing:
Read quality was verified using fastQC
Raw reads were trimmed for adapters and for length at 100 bp with Trimmomatic
Reads were subsequently aligned to the human reference genome (GRCh38) using STAR
Raw gene counts were obtained in R-3.4.4 using the featureCounts function of the Rsubread R package and the Gencode gene annotation.
Raw counts were normalized to counts per million mapped reads (CPM) using the edgeR package; only genes with a CPM greater than 1 in at least 1 sample were further retained for differential analysis, for a total of 20,716 genes.
Differential gene expression analysis was performed using the exactTest function of the edgeR package. Genes were considered significantly differentially expressed at FDR≤0.05.
Genome_build: hg38
Supplementary_files_format_and_content: Tab delimited file containing raw counts

source_name: Urine derived stem cells MyoD-transformed

growth_protocol: Isolation and proliferation of USCs were obtained from two urine specimens derived from 3 controls and 1 DMD patient carryng the deletion of exon 4. For the isolation and culturing we used Primary and Proliferation media as described in our previous paper, Falzarano et al, 2016 Human Gene Therapy 27, 772-783.

extract_protocol:
Total RNA was extracted using RNAeasy kit (Quiagen) according to the manufacturer’s instructions
Libraries were prepared using TruSeq Kit (Illumina) according to manufacturer’s instructions. Quality and quantity of the RNA library was assessed using the Agilent 2100 Bioanalyzer and the ABI StepOnePlus Real-Time-PCR System.

treatment_protocol: Myogenesis was induced on USCs obtained from DMD patient IG and control individuals through the infection with adenovirus serotype 5 (Ad5)-derived, EA1-deleted adenoviral vector carrying the MyoD gene, as previously described [14]. MyoD transformed USCs were differentiated into myotubes by serum deprivation. Myotubes obtained from the MyoD-transformed USCs of the DMD patient IG were transfected using 2’O-methyl phosphorothioate (2’OMePS) antisense oligoribonucleotide (AON) to induce DMD exon 44 skipping

value: Primary cultures of USCs induced in myogenic cells

value: MyoD + AON

value: DMD patient


title: SCD11_CMo


title: SCD5_CMo


title: RNA from native USCs of DMD patient

description:
IG-n
total RNA from DMD patient

source_name: Urine derived stem cells

value: Primary cultures of USCs


title: GEX_EXP20001394_Sample_05_hashed sample

description: GEX

value: PBMC

value: multiplexed sample


title: RNA pool from native USCs of pool control

description:
C-n
pool of total RNA from 3 healthy donors

value: healthy


title: SCD4_CMo


title: VDJ-seq_EXP20000654_Sample_03

description: VDJ-seq

value: convalescent


title: SCD7_CMo


title: VDJ-seq_EXP20000654_Sample_02

description: VDJ-seq


title: SCD6_CMo


title: GEX_EXP20001394_Sample_06_hashed sample

description: GEX


title: NSC_RNA_rep1

city: Manchester

first: Angela

last: Simeone

address: 200 Hathersage Rd

country: United Kingdom

institute: Genomic Services QIAGEN

data_processing:
Fastq files were trimmed from adapters using cutadapt (-m 10 -q 20 -O 3 -a CTGTCTCTTATACACATCT) and aligned to a the human genome hg38 with bwa-mem. Bam files were generated from the alignment with samtools view. Duplicated reads were marked and removed using picard MarkDuplicates (ver: 2.20.3).Peak calling was performed with macs2 over input (ver. 2.1.2) with fdr 0.05 (default) and --broad option. Regions confirmed across 2 out of 3 tecnical replicates have been assigned to each biological replicate. Regions shared by 2 out of 3 biological replicates have been elected as consensus of the cell type and multiIntersectBed was used for this. Bigwig files have been generated using deeptools bamCoverage --scaleFactor using the 1000000/total_library_size as a  scaling factor.
ATAC-seq: fastq files were trimmed from adapters with cutadapt ( -a AGATCGGAAGAGC -A AGATCGGAAGAG) and aligned to hg38 with bwa-mem for paired-end (-M -t 12 $read1 $read2). Mapped reads have been filtered using samtools view (-Sb -F780 -q 10 -L )  to keep only mapped and properly paired reds. Those reads have been then used to identify accessible reagions using macs2 wih default options. Regions identified in 2 out 3 biolofical replicates have used as consensus each cell type.
RNA-seq fastq have been trimmed from adaptors using cutadapt (cutadapt -q 20 -m 20 -a AGATCGGAAGAGC) and alined to hg38 using RSEM (RSEM-1.3.1, rsem-calculate-expression --phred33-quals -p 40 --bowtie2). We used the gene results to further quantify gene expression level in each individual library. Technical replicates quantification have been summed up before subsequent analysis. TPM have been generated after quantifying the signal per transcript and scaled by transcript length.
Genome_build: hg38
Supplementary_files_format_and_content: broadPeak: broad peak regions obtained with macs2 ( fdr 0.05 and --broad options)
Supplementary_files_format_and_content: narrowPeak: narrowPeak regions obtained with macs2 default options
Supplementary_files_format_and_content: genes.results.txt: count table for gene models based on genecode v.28
Supplementary_files_format_and_content: *ATAC.multi2.sorted.bed: ATAC consensus regions obtained as those observed in 2 out of 3 biologicial replicates
Supplementary_files_format_and_content: bio2out3.bed: G4 consensus regions obtained as regions observed in 2 out of 3 biological replicates
Supplementary_files_format_and_content: TPM_hg38_all_bio_rep_*.csv: Matrix table with expression levels expressed as TPM (transcript per million) for every gene and every sample. In case of multiple technical replicates TPM have been generated from the data obtained after summing up technical replicates.

source_name: neural stem cells (NSC)

growth_protocol: H9-derived neural stem cells (NSC; WiCell) were cultured in StemPro NSC SFM complete media (ThermoFisher) on Geltrex (Thermofisher) pre-coated plates. Media was replenished every two days and NSC were passaged every four to five days using StemPro Accutase (ThermoFisher).

extract_protocol: Total RNA was extracted from 1 x 10^6 cells using the RNeasy Plus Mini Kit (Qiagen) as per manufacturer’s instructions. RNA quality (RIN >9) was checked via Bioanalyzer (Agilent) and RNA concentration determined using a Qubit fluorometer (ThermoFisher). Libraries were prepared from 500ng RNA using the Truseq Stranded mRNA kit (Illumina), as per manufacturer’s instructions and sequenced on a HiSeq 4000 (Illumina) platform (50bp, single-end).

value: H9 embryonic stem cell-derived neural stem cell

tag: cell line of origin

value: H9 ESCs (WA09)


title: Normal_m5_1129

type: genomic

city: Minneapolis

first: Laura

middle: S

last: Stone

state: MN

address: 420 Delaware Street SE, MMC 294

department: Anesthesiology

institute: University of Minnesota

description: Control T cells sample

hyb_protocol: Bisulfite conversion was performed (EZ-DNA methylation Gold Kit - Zymo Research, Irvine, CA, USA) and DNA methylation profiles were generated by Genome Quebec according to standard protocols using Illumina® 850 K bead arrays (Infinium MethylationEPIC Kit).

scan_protocol: Standard Illumina protocols

data_processing:
ChAMP Bioconductor package in R
BMIQ normalization and batch correction with ComBat

label: Cy5 and Cy3

source_name: Control Male 1129

label_protocol: Standard Illumina Protocol

extract_protocol: T cells were positively isolated using Dynabeads CD3 isolation kit (Invitrogen). DNA was isolated using AllPrep DNA/RNA mini kit (Qiagen, Canada).

tag: Sex

value: Control

tag: cell type

value: CD3+ T cells


title: GEX_EXP20001394_Sample_03_hashed sample

description: GEX


title: SCD2_CMo


title: RNA pool from MyoD-induced USCs of pool control

description:
C-m
pool of total RNA from 3 healthy donors and treated with MyoD

value: MyoD


title: SCD1_CMo


title: ESC_RNA_rep4_tech4

source_name: human embryonic stem cells (ESC)

growth_protocol: H9 human embryonic stem cells (ESC, WiCell) were cultured in mTESR1 media (StemCell Technologies) and grown on Matrigel matrix (Corning).  ESCs were fed daily and routinely passaged every 4-6 days using ReLeSR (StemCell Technologies).

value: H9 embryonic stem cells


title: GEX_EXP20001394_Sample_02_hashed sample

description: GEX


title: Normal_m2_1002

description: Control T cells sample

source_name: Control Male 1002

value: Male


title: Normal_m6_1113

description: Control T cells sample

source_name: Control Male 1113


title: SCD3_CMo

value: patient with sickle cell disease

value: Peripheral blood


title: RNA from MyoD-induced USCs of DMD patient

description:
IG-m
total RNA from DMD patient and treated with MyoD

value: Primary cultures of USCs induced in myogenic cells


title: ESC_RNA_rep4_tech3


title: GEX_EXP20001394_Sample_04_hashed sample

description: GEX

source_name: CD8+ T cells


title: Normal_m8_1155

description: Control T cells sample

source_name: Control Male 1155


title: HD6_CMo

value: healthy donor

value: CMo


title: Normal_f7_1143

description: Control T cells sample

source_name: Control Female 1143

value: Female


title: GEX_EXP20001394_Sample_01_hashed sample

description: GEX

value: PBMC


title: HD5_CMo


title: ESC_RNA_rep5_tech2


title: Normal_m7_1154

description: Control T cells sample

source_name: Control Male 1154


title: Normal_f8_1145

description: Control T cells sample

source_name: Control Female 1145


title: ESC_RNA_rep5_tech1


title: GEX_EXP20001265_Sample_03_hashed sample

description: GEX

value: multiplexed sample


title: HD4_CMo


title: Normal_f6_1116

description: Control T cells sample

source_name: Control Female 1116


title: Normal_f5_1061

description: Control T cells sample

source_name: Control Female 1061


title: Normal_f3_1043

description: Control T cells sample

source_name: Control Female 1043


title: HD3_CMo


title: Normal_m3_1005

description: Control T cells sample

source_name: Control Male 1005


title: Normal_m1_1001

description: Control T cells sample

source_name: Control Male 1001


title: Normal_f4_1050

description: Control T cells sample

source_name: Control Female 1050


title: ESC_RNA_rep4_tech2


title: GEX_EXP20001265_Sample_01_hashed sample

description: GEX


title: GEX_EXP20001265_Sample_02_hashed sample

description: GEX


title: ESC_RNA_rep4_tech1


title: GEX_EXP20001260_Sample_05_hashed sample

description: GEX


title: Normal_m4_1053

description: Control T cells sample

source_name: Control Male 1053


title: HD2_CMo

source_name: blood classical monocyte


title: CNCC_RNA_rep3

source_name: cranial neural crest cells (CNCC)

growth_protocol: Cranial neural crest cells (CNCC) were generated from hESCs as previously described (Prescott et al  2015). In brief, hESC colonies were detached and dissociated using collagenase IV and gentle pipetting. After washing with DPBS, colonies with ~100-200 cells were resuspended in neural crest induction media (1:1 ratio of Neurobasal medium and D-MEM F-12 medium, 0.5 x B27, 0.5 x N2 supplement, 20 ng/ml bFGF, 20 ng/ml EGF, 5 mg/ml bovine insulin and 1 x Glutamax-I supplement and transferred to a 10 cm petri dish (Day 0). By day ~7, neural crest cells started to emerge from the attached neuroectoderm spheres. After an additional 4-5 days, neural crest cells were dissociated with StemPro Accutase and cultured on fibronectin coated 6-well plates in Early Maintenance Media (1:1 Neurobasal medium/D-MEM F-12 medium, 0.5 x B27 supplement, 0.5 x N2 supplement, 20 ng/ml bFGF, 20 ng/ml EGF, 1 x Glutamax-I supplement and 1 mg/ml bovine serum albumin, serum replacement grade. After two passages, Early Maintenance Media was then supplemented with 50 pg/ml BMP2 and 3 mM ChIRON 99021. Cranial neural crest cells were harvested after an additional two to three passages for all downstream experiments.

value: H9 embryonic stem cell-derived cranial neural crest cell


title: HD1_CMo


title: CNCC_RNA_rep2


title: H_shD_input

city: Jinan

first: Yan

last: Zheng

state: Shandong

address: No.440 Jiyan road

department: Shandong Provincial Key Laboratory of Radiation Oncology

institute: Shandong Cancer Hospital Affiliated to Shandong University

data_processing:
SOAPnuke version 1.4.0 software used for basecalling.
ChIP-seq reads were aligned to the hg19 genome assembly using SOAPaligner/SOAP2 with the following setting -p 4 -v 2 -s 35.
peaks were called using MACS14 with the following setting: -s 50 -g hs -p 1e-5 -w --space 50 -m 10,30.
Genome_build: hg19
Supplementary_files_format_and_content: wig files were generated using MACS2.

source_name: HGC-27 lentivirus transduced

growth_protocol: Human HGC-27 cells were cultured in RPMI-1640 media supplied with 10% fetal bovine serum (Hyclone) at 37°C with 5% CO2.

extract_protocol:
Lysates were clarified from sonicated nuclei and RNA polII-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

treatment_protocol: HGC-27 cells were transduced with lentivirus harboring DDX5 shRNA or non-targeting shRNA. 48 hours later, puromycin was added to the media to select transducted cells. one week later, cells were collected and DDX5 gene silencing efficiency was detected.

value: gastric adenocarcinoma

tag: cell line

tag: chip antibody

tag: knockdown

value: DDX5 shRNA


title: GEX_EXP20001260_Sample_03_hashed sample

description: GEX


title: H_shD_PolII

value: A-RNA POLY II(Millipore,05-623)


title: GEX_EXP20001260_Sample_04_hashed sample

description: GEX


title: GEX_EXP20001260_Sample_02_hashed sample

description: GEX


title: GEX_EXP20001260_Sample_01_hashed sample

description: GEX


title: CNCC_RNA_rep1

value: H9 ESCs (WA09)


title: H_NC_input

value: non-targeting shRNA


title: Normal_f1_1012

description: Control T cells sample

source_name: Control Female 1012

value: Control

value: CD3+ T cells


title: ESC_RNA_rep2

source_name: human embryonic stem cells (ESC)

value: H9 embryonic stem cells


title: H_NC_PolII


title: ESC_RNA_rep3


title: NSC_RNA_rep4

source_name: neural stem cells (NSC)

value: H9 embryonic stem cell-derived neural stem cell


title: H_LV_NC

data_processing:
SOAPnuke version 1.4.0 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole transcriptome using Bowtie2 with default parameters.
FPKM of each gene was calculated by RSEM version 1.2.8.
Genome_build: hg19
Supplementary_files_format_and_content: bam files were generated using HISAT.

source_name: HGC-27 lentivirus transducted

extract_protocol:
RNA was harvested using Trizol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: transduced with


title: ESC_RNA_rep1


title: H_ShD


title: Affected_m6_1084

description: LBP T cells sample

source_name: LBP Male 1084

value: Male

value: Low Back Pain


title: Affected_m8_1160

description: LBP T cells sample

source_name: LBP Male 1160


title: Normal_f2_1036

description: Control T cells sample

source_name: Control Female 1036


title: GEX_EXP20001249_Sample_05_hashed sample

description: GEX

source_name: CD8+ T cells


title: GEX_EXP20001249_Sample_04_hashed sample

description: GEX


title: NSC_RNA_rep3


title: Affected_m5_1098

description: LBP T cells sample

source_name: LBP Male 1098


title: fatbody_ovary_isoseq

city: Philadelphia

first: Emily

last: Shields

state: Pennsylvania

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

data_processing:
Library strategy: Iso-Seq
Full-length Iso-Seq reads were classified from circular consensus sequences using Lima and refined with Iso-seq3 using --require-polya. Full-length reads were clustered using isoseq3 cluster and poslished using isoseq3 polish.
Supplementary_files_format_and_content: none

molecule: polyA RNA

organism: Harpegnathos saltator

source_name: Harpegnathos fat body and ovary

extract_protocol:
RNA was extracted and purified in TRIzol.
PolyA+ selection was performed and SMRTbell libraries were prepared for sequencing on PacBio Sequel II.

value: Harpegnathos fat body and ovary


title: GEX_EXP20001249_Sample_03_hashed sample

description: GEX


title: Affected_m4_1058

description: LBP T cells sample

source_name: LBP Male 1058


title: brain_isoseq

source_name: Harpegnathos brain

value: Harpegnathos brain


title: d84_worker_rep2

description:
HSAL50.counts.txt
HSAL51.counts.txt
HCWTMBGXF.bulk_45

data_processing:
Reads were aligned using STAR with default parameters except --alignIntronMax=50000 to the Harpegnathos genome (GCF_003227715.1).
Aligned reads were mapped to either the Harpegnathos annotation in NCBI (NCBI Release 102, 6/22/18, "HSAL50") or the annotation constructed for Shields et al. ("HSAL51") using GenomicRanges summarizeOverlaps
Genome_build: GCF_00322715.1
Supplementary_files_format_and_content: Count tables for mapping to HSAL50 or HSAL51

source_name: Day 84 worker brain

extract_protocol:
Brains from transitioning Harpegnathos ants were dissected out in phosphate-buffered saline, placed in TRIzol (Invitrogen #15596026) and stored at -70 C until RNA extraction. Each brain was processed separately. To extract RNA, thawed brains were homogenized in TRIzol by pestle, and frozen and thawed again. Chloroform was added, followed by vigorous vortexing and centrifugation at 21,000 g for 10–15 minutes at 4 C. The aqueous phase was purified using RNA Clean and Concentrator kit (Zymo Research #R1013) following manufacturer’s instructions. Extracted RNA was quantified using NanoDrop 2000 (Thermo Scientific) and RNA integrity was checked using High Sensitivity RNA ScreenTape (Agilent #5067-5579, 5067-5580, 5067-5581) on a TapeStation 2200 or 4200 (Aglient).
250–500 ng extracted RNA was used to prepare libraries with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs #E7760S) following manufacturer’s instructions. Libraries were quantified using Qubit dsDNA High Sensitivity Assay Kit (Invitrogen #Q32854) on a Qubit 2.0 fluorometer (Invitrogen) and fragment size distribution was checked using High Sensitivity D1000 ScreenTape (Agilent #5067-5584, 5067-5585, 5067-5587) on a TapeStation 2200 or 4200 (Aglient). Libraries were combined in two pools and sequenced in two runs of a NextSeq 500 machine (Illumina) in HighOutput mode with a 2x 150 bp configuration.

tag: caste

value: worker

tag: age


title: d27_worker_rep2

description:
HSAL50.counts.txt
HSAL51.counts.txt
HCWTMBGXF.bulk_43

source_name: Day 27 worker brain


title: Affected_m7_1137

description: LBP T cells sample

source_name: LBP Male 1137


title: NSC_RNA_rep2


title: GEX_EXP20001249_Sample_01_hashed sample

description: GEX

value: PBMC


title: Microglia_Sample_3419_R1

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

data_processing:
base calling and de-multipexing using CASAVA version 1.8
Alignment withTopHat2 version v2.0.11 and Bowtie2 version 2.2.1 using the default parameters
Quantification with Partek Genomics Suite V6.6
reads mapped to each transcript against the RefSeq mm10 annotation download on May 2015
Normalization using DeSeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include DeSeq2 normalized counts for each Sample.

source_name: Brain

growth_protocol: Primary isolated macrophage without further culture.

extract_protocol:
The testis, epididymis and brian were cut in small pieces and enzymatically digested by a solution containing RPMI1640 (ThermoFisher) + 1 mg/mL Collagenase II (Sigma) + 50μg/mL DNase I (Sigma) for 40 min at 37oC. Then they were passed through 70 μm cell strainers and the generated single cell suspensions undergone erythrocyte lysis on ice. Single cell suspensions from  testes and epididymides were pooled in a separate tube. Cells from brains, epididiymides, and testes were resuspended into 40% isotonic Percoll (GE Healthcare, Uppsala, Sweden) at a density of 1.072 g/ml in PBS containing 3% FCS. Cells were collected from 1.06 and 1.072 g/ml layers after centrifugation and resuspended. RBCs were lysed in RBC lysis buffer (Qiagen). The cells were blocked with FC-block and stained with antibodies against CD45, Ly6c, CD11b, CD11c, CD11b and F4/80. Macrophage populations were identified and sorted as live (DAPI-), CD45+ Ly6c- CD11c-, CD11b+ F4/80+. The sorted cells were collected in RPMI medium containing 10% FCS.
According to the manufacturer´s instructions in the Tru-Seq RNA library preparation kit v2, 10 ng of RNA was converted into cDNA libraries

treatment_protocol: No treatment.

tag: genetic background

tag: mouseid

value: Brain


title: Microglia_Sample_3418_R1

source_name: Barin

value: Barin


title: GEX_EXP20001234_Sample_04_hashed sample

description: GEX

tag: subject

value: multiplexed sample

tag: cohort


title: GEX_EXP20001249_Sample_02_hashed sample

description: GEX


title: GEX_EXP20001249_Sample_06_hashed sample

description: GEX


title: Iron deficient diet, dam 3

type: RNA

city: London

first: Stephen

middle: J

last: Renaud

state: Ontario

address: 1151 Richmond St, MSB428

country: Canada

institute: University of Western Ontario

description: Gene expression data from placentas isolated from dams fed an iron-deficient diet

hyb_protocol: Samples were hybridized to the Clariom S GeneChip microarray (ThermoFisher) as per directions from the GeneChip WT Plus Reagent kit (ThermoFisher). Overnight hybridization to the Clariom S GeneChip took place at 45C for ~16 h.

scan_protocol: After washing and staining as per directions for the GeneChip WT Plus Reagent kit (ThermoFisher), images were captured using the GeneChip Scanner 3000 and raw data converted to .CEL files using the Affymetrx GCOS software (ThermoFisher).

data_processing:
The CEL file was uploaded to Transcriptome Analysis Console Sotware 4.0 (ThermoFisher) to analyze expression patterns of genes, pathways, and network interactions.
Affymetrix Gene Expression Console (ThermoFisher) using Robust Multi-Chip analysis algorithm.

label: biotin

organism: Rattus norvegicus

source_name: Gestational day 18.5 placenta from iron-deficient diet

label_protocol: Sense strand cDNA was generated, fragmented, and labelled using the GeneChip WT Plus Reagent kit (ThermoFisher) as per directions.

growth_protocol: Dams were fed control or iron-deficient diets starting 2 weeks prior to mating. Placentas were isolated on gestaional day 18.5.

extract_protocol: Frozen placental tissue was homogenized in TRIzol, the aqueous phase removed following mixing in chloroform, mixed with 70% ethanol, and then placed onto an Rneasy column (Qiagen). Following on-column Dnase I digestion, RNA was purified. RNA from two placentas per dam was pooled.

treatment_protocol: Placentas were isolated on gestational day 18.5, cut into cubes, frozen in liquid nitrogen, and maintained at -80C until RNA extraction.

tag: strain

value: Sprague-Dawley

value: Placenta

value: Gestational day 18.5

value: iron-deficient diet


title: Iron deficient diet, dam 2

tag: treatment


title: Iron deficient diet, dam 4


title: GEX_EXP20001234_Sample_03_hashed sample

description: GEX


title: Epididymal_Sample_3416_R1

source_name: Epididymis

value: Epididymis


title: GEX_EXP20001234_Sample_02_hashed sample

description: GEX


title: d5_worker_rep2

description:
HSAL50.counts.txt
HSAL51.counts.txt
HCWTMBGXF.bulk_37

source_name: Day 5 worker brain


title: Microglia_Sample_3417_R1


title: GEX_EXP20001234_Sample_01_hashed sample

description: GEX


title: d0_worker_rep4

description:
HSAL50.counts.txt
HSAL51.counts.txt
HCWTMBGXF.bulk_36

source_name: Day 0 worker brain


title: Epididymal_Sample_3414_R1


title: d9_worker_rep2

description:
HSAL50.counts.txt
HSAL51.counts.txt
HCWTMBGXF.bulk_39

source_name: Day 9 worker brain


title: Iron deficient diet, dam 1


title: GEX_EXP20001148_Sample_04_hashed sample

description: GEX


title: H3K27me3 TIPseq 1cell C

city: Tallahassee

first: Daniel

middle: A

last: Bartlett

state: Florida

address: 319 Stadium Drive

department: Biological Sciences

institute: Florida State University

data_processing:
Library strategy: TIP-seq
Basecalls perfomed using RTA3
For sciTIP-seq only, fastq files were demultiplexed to single cell fastq files based on unique combinations of r5, i5, and i7 barcodes using a custom script.
Reads were aligned to the mm10 or hg38 genome assembly using bowtie2 version 2.3.4.1 with the following configurations "--very-sensitive-local -p 28 --no-mixed --no-discordant --reorder -I 10 -X 700 -q --passthrough"
Mapped reads were filtered by mapping quality (MAPK>10) and PCR duplicates were removed using SAMtools version 1.9.
Reads were binned into 100 bp (bulk) or 5kb (sciTIP) genomic windows using Bedtools coverage version 2.26.0 with setting "-counts"
Genome_build: mm10/hg38
Supplementary_files_format_and_content: bigWig files contain read counts binned into 100 bp genomic windows.  sciTIP-seq Tab-delimited text file includes cell embeddings for each cell. Each column refers to a single cell and each row refers to a genomic bin.

growth_protocol: HCT116 cells were cultured in McCoy’s 5A medium supplemented with 10% FBS according to ATCC’s instruction. F121-9 mouse embryonic stem cell were cultured in 2i media on gelatin-coated dish as described in (PMID:29735606).

extract_protocol:
Cell cultures were harvested and rinsed once with an equal volume of room temperature PBS. Cells were moved to a 2 mL tube and washed twice with room temperature Wash buffer (20mM HEPES, pH 7.5; 150mM NaCl; 0.5mM Spermidine, 1x Protease inhibitor cocktail) before counting with a hemocytometer and aliquoting cells into fresh 1.5 mL LoBind Eppendorf tubes containing 1mL room temperature wash buffer. 10 µL of pre-washed Concanavalin A-coated magnetic beads slurry was added to aliquots of washed cells and rotated for 10 minutes at room temperature to allow beads to bind to cells. Bead-bound cells were incubated with primary antibody [1:100] in 100 µL Antibody buffer (Wash Buffer + 0.01% digitonin, 2mM EDTA, and 1%BSA) overnight at 4°C with rotation. Antibody buffer was removed and replaced with 100 µL Dig-Wash buffer (Wash buffer + 0.01% digitonin) containing Guinea pig anti-Rabbit IgG secondary antibody [1:100] and rotated for 1 hr at room temperature. Cells were washed twice in 1 mL Dig-Wash buffer and then resuspended in 100 µL Dig-300 buffer (0.01% Digitonin, 20 mM HEPES, pH 7.5, 300 mM NaCl, 0.5 mM Spermidine, 1X Protease inhibitor cocktail) containing pA-Tn5 [1:100] loaded with ME-A/B adapters (CUT&Tag) or ME-T7 adapters (TIP-seq) and incubated at room temperature with rotation for 1 hr to allow pA-Tn5 to bind to antibody-bound sites. Cells were washed 3 times with 1 mL Dig-300 buffer to remove unbound pA-Tn5. Tagmentation was activated by resuspension in 100 µL Tag buffer (Dig-300 Buffer + 10 mM MgCl2) for 1h at 37°C and was terminated by adding 3.3 µL of 0.5M EDTA. Cells were mixed with 2 µL 10% SDS (0.2% final) and 0.84 µL 20 mg/mL proteinase K and incubated at 50°C for 30 min or overnight at 37°C before being purified using 2.0x volume SPRI beads (Beckman; A63881).
CUT&Tag: CUT&Tag libraries were prepared by mixing tagmented DNA with 2 µL of uniquely barcoded i5 and i7 primers and 25 µL of NEBNext HiFi 2× PCR Master mix (NEB; M0541L) and PCR amplified using the following thermocycler program: 72 °C for 5 min (gap filling); 98 °C for 30 s; 14 cycles of 98 °C for 10 s and 63 °C for 30 s; final extension at 72 °C for 1 min and hold at 8 °C (12-15 cycles). Amplified libraries were cleaned-up and size selected using 1.1× volume SPRI beads, washed 2x with 80% EtOH, and eluted into 30 µL 10 mM Tris pH 8.0.       TIP-seq: TIP-seq libraries were prepared by mixing tagmented DNA with 2 ml of NEB 5x Taq master mix (NEB; M0285) and incubating at 72 °C for 3 mins for gap-filling. In vitro transcription was performed using the NEB HiScribe T7 high yield synthesis kit (NEB; E2040S) by adding 2mL of each 100mM NTP, 2 mL 10x T7 reaction buffer, 2 mL T7 polymerase mix and 0.3 mL RNase Inhibitor and incubating at 37*C for 16-19 hrs. RNA was purified by adding 2.0x volume SPRI binding buffer (20% PEG 8000, 2.5 M NaCl, 10 mM Tris-HCl, 1 mM EDTA) to reactivate the bead’s binding capacity. After washing twice with 80% EtOH and removing all liquid, residual EtOH was dried from RNA and SPRI beads for 3 minutes before being resuspended in 9 mL RNase-free water. First-strand synthesis was primed by adding 2.5 mL of 20 µM random hexamer to sample and incubating at 70*C for 3 mins, then immediately placing on ice. First strand synthesis was performed using SMART MMLV RTase kit (Takara; 639524) by adding 4 mL of 5x first-strand synthesis buffer, 2 mL of 10mM dNTP mix, 2 mL of 100 mM DTT, and 0.5 mL SMART MMLV RTase. Samples were mixed well and incubated at 22*C for 10 mins, 42*C for 60 min, then terminated at 70*C for 10 min. 1mL of a 1:10 dilution of 5U/µL RNase H was added and incubated at 37*C for 20 mins to degrade RNA in cDNA-RNA hybrids. Second strand synthesis was primed by adding 2.5 µL of 20 µM sss_scnXTv2 oligo (anneals to transposon directly downstream of T7 promoter TSS) and heating sample to 65*C for 2 minutes and placing immediately on ice. Second-strand synthesis was performed by adding 5.9 mL of NEB 5x Taq master mix (NEB;M0285) and incubating at 72*C for 8 mins, then cooling on ice. cDNA was purified by addition of 2.0x SPRI binding buffer, washed twice in 80% EtOH, and resuspended in 7mL water. Fragmentation and 3’-end adapter tagging of cDNA was performed by adding 2 µL TAPS buffer and 2 µL 0.7µM Tn5 (loaded with ME-B adapters only), incubated at 55*C for 6 minutes, and then briefly cooled on ice prior to adding GuHCl (4M final conc.) and vortexing to degrade Tn5. DNA was purified again by adding 2.0x volume SPRI binding buffer, washing twice with 80% EtOH, and Eluting DNA off of beads into 16 µL water. Eluent was moved to a fresh tube, this time leaving behind SPRI beads to discard.  PCR reactions were prepared by adding 20 µL NEBNext 2x master mix (NEB; M0541L), 2 µL of 10 µM standard Nextera index primers, 2 µL of 10 µM standard i7 Nextera indexes, for total vol of 40 µL. The optimal number of PCR cycles were determined as performed in Buenrostro et al. (7-9 cycles). Post PCR libraries were SPRI purified and left-side size selected by 0.85x volume SPRI beads (>200bp).

value: HCT116 colorectal adenocarcinoma

tag: antibody

value: H3K27me3 (Cell Signaling; 9733)


title: d84_worker_rep1

description:
HSAL50.counts.txt
HSAL51.counts.txt
HCWTMBGXF.bulk_34


title: Testicular_Sample_3413_R1

source_name: Testis

tag: tissue

value: Testis


title: Epididymal_Sample_3415_R1


title: Control diet, dam 3

description: Gene expression data from placentas isolated from dams fed a normal diet

source_name: Gestational day 18.5 placenta from control diet

value: control diet


title: Control diet, dam 2


title: Control diet, dam 1


title: d27_worker_rep1

description:
HSAL50.counts.txt
HSAL51.counts.txt
HCWTMBGXF.bulk_32


title: GEX_EXP20001148_Sample_02_hashed sample

description: GEX

source_name: CD8+ T cells


title: Affected_m3_1057

description: LBP T cells sample

source_name: LBP Male 1057

value: Male

tag: disease state

value: Low Back Pain

value: CD3+ T cells


title: Testicular_Sample_3412_R1


title: Control diet, dam 4


title: d28_worker_rep1

description:
HSAL50.counts.txt
HSAL51.counts.txt
HCWTMBGXF.bulk_30

source_name: Day 28 worker brain

value: worker


title: H3K27me3 TIPseq 10 cells


title: GEX_EXP20001148_Sample_03_hashed sample

description: GEX

value: PBMC


title: H3K27me3 TIPseq 1cell B


title: d9_worker_rep1

description:
HSAL50.counts.txt
HSAL51.counts.txt
HCWTMBGXF.bulk_28


title: GEX_EXP20001114_Sample_08

description: GEX

value: unexposed


title: Affected_f8_1156

description: LBP T cells sample

source_name: LBP Female 1156

tag: Sex

value: Female


title: Affected_m1_1027

description: LBP T cells sample

source_name: LBP Male 1027

tag: cell type


title: Affected_f3_1047

description: LBP T cells sample

source_name: LBP Female 1047


title: T23

city: San Diego

first: Wenjing

last: Yanf

state: CA

address: 10770 Science Center Drive

department: Oncology

institute: Pfizer

description:
scRNA-Seq
PF-06821497_16d

data_processing:
Single-cell RNA-sequencing reads were mapped to mouse genome mm10 using the Cell Ranger v2.1.1 (10x Genomics,https://support.10xgenomics.com/). Resulting gene by cell count matrixes per sample were then merged and further analyzed by Seurat package. Low quality cells were filtered out by requiring that the number of expressed genes for each cell was between 500 and  5000. Cells with > 5% of UMI originated from mitochondrial genes were also removed. The gene expression matrix were than log transformed and normalized with default parameters in Seurat. Top 2000 most variable genes were used for downstream analysis such as dimension reduction by PCA and batch effect removal. After aligning samples, clusters were identified using FindClusters() functions implemented in Seurat with default parameter and top expressing genes in each cluster were identified by FindAllMarkers() function in Seurat.
Genome_build: Mouse_mm10

source_name: CD45+ cells isolated from Day 17 post implantation MC38 Tumors

extract_protocol:
CD45+ cells were isolated using CD45 TIL microbeads (Miltenyi, 130-110-618) and libraries were generated using the Single Cell 3’ GEM, Library and Gel Bead Kit v3 (10X Genomics, PN-1000075), Chromium Single Cell B Chip (PN-100073), and Chromium i7 Multiplex Kit (PN-120262).
Libraries were prepared using the standard protocol of the Single Cell 3’ GEM, Library and Gel Bead Kit v3 (10X Genomics, PN-1000075), Chromium Single Cell B Chip (PN-100073), and Chromium i7 Multiplex Kit (PN-120262).

treatment_protocol: For MC38 tumor inoculations, 0.25 x 10^6 MC38 tumor cells were subcutaneously injected into C57BL/6 mice on day 0. One or ten days after implantation mice received 100 mg/kg dosing of PF-06821497 or vehicle control, subcutaneous, daily.


title: Affected_f5_1090

description: LBP T cells sample

source_name: LBP Female 1090


title: d5_worker_rep1

description:
HSAL50.counts.txt
HSAL51.counts.txt
HCWTMBGXF.bulk_26


title: H3K27me3 TIPseq 50 cells

tag: cell line


title: T22

description:
scRNA-Seq
PF-06821497_16d


title: GEX_EXP20001114_Sample_07

description: GEX


title: d0_worker_rep3

description:
HSAL50.counts.txt
HSAL51.counts.txt
HCWTMBGXF.bulk_25


title: H3K27me3 TIPseq 500 cells


title: T21

description:
scRNA-Seq
PF-06821497_16d


title: Affected_f4_1103

description: LBP T cells sample

source_name: LBP Female 1103


title: CTCF TIPseq 50 cells

value: CTCF (Millipore; 07-729)


title: GEX_EXP20001114_Sample_06

description: GEX


title: Affected_m2_1046

description: LBP T cells sample

source_name: LBP Male 1046


title: Affected_f7_1140

description: LBP T cells sample

source_name: LBP Female 1140


title: T18

description:
scRNA-Seq
Vehicle_16d

value: 16 day Vehicle


title: CTCF TIPseq 100 cells


title: GEX_EXP20001114_Sample_05

description: GEX


title: d85_worker_rep2

description:
HSAL50.counts.txt
HSAL51.counts.txt
H5FGTBGXF.bulk.23

source_name: Day 85 worker brain


title: GEX_EXP20001114_Sample_04

description: GEX


title: CTCF TIPseq 1k cells


title: GEX_EXP20001114_Sample_03

description: GEX


title: T17

description:
scRNA-Seq
Vehicle_16d


title: d11_worker_rep2

description:
HSAL50.counts.txt
HSAL51.counts.txt
H5FGTBGXF.bulk.17

source_name: Day 11 worker brain


title: d21_worker_rep2

description:
HSAL50.counts.txt
HSAL51.counts.txt
H5FGTBGXF.bulk.19

source_name: Day 21 worker brain


title: T16

description:
scRNA-Seq
Vehicle_16d


title: d31_worker_rep2

description:
HSAL50.counts.txt
HSAL51.counts.txt
H5FGTBGXF.bulk.21

source_name: Day 31 worker brain


title: T8

description:
scRNA-Seq
PF-06821497_7d


title: H3K27me3 TIPseq 1cell A


title: Affected_f6_1131

description: LBP T cells sample

source_name: LBP Female 1131


title: Affected_f1_1020

description: LBP T cells sample

source_name: LBP Female 1020


title: Affected_f2_1045

description: LBP T cells sample

source_name: LBP Female 1045


title: d28_worker_rep2

description:
HSAL50.counts.txt
HSAL51.counts.txt
HCWTMBGXF.bulk_41


title: d3_worker_rep4

description:
HSAL50.counts.txt
HSAL51.counts.txt
H5FGTBGXF.bulk.15

source_name: Day 3 worker brain


title: GEX_EXP20001114_Sample_02

description: GEX

source_name: CD8+ T cells


title: T7

description:
scRNA-Seq
PF-06821497_7d


title: CTCF CUT&Tag 5k cells rep1

data_processing:
Library strategy: CUT&Tag
Basecalls perfomed using RTA3
For sciTIP-seq only, fastq files were demultiplexed to single cell fastq files based on unique combinations of r5, i5, and i7 barcodes using a custom script.
Reads were aligned to the mm10 or hg38 genome assembly using bowtie2 version 2.3.4.1 with the following configurations "--very-sensitive-local -p 28 --no-mixed --no-discordant --reorder -I 10 -X 700 -q --passthrough"
Mapped reads were filtered by mapping quality (MAPK>10) and PCR duplicates were removed using SAMtools version 1.9.
Reads were binned into 100 bp (bulk) or 5kb (sciTIP) genomic windows using Bedtools coverage version 2.26.0 with setting "-counts"
Genome_build: mm10/hg38
Supplementary_files_format_and_content: bigWig files contain read counts binned into 100 bp genomic windows.  sciTIP-seq Tab-delimited text file includes cell embeddings for each cell. Each column refers to a single cell and each row refers to a genomic bin.


title: GEX_EXP20001095_Sample_08

description: GEX

value: convalescent


title: d31_worker_rep1

description:
HSAL50.counts.txt
HSAL51.counts.txt
H5FGTBGXF.bulk.11


title: IgG TIPseq 1k cells

value: Guinea pig anti-Rabbit IgG (Antibodies-Online; ABIN101961)


title: T3

description:
scRNA-Seq
Vehicle_7d

value: 7 day Vehicle


title: GEX_EXP20001095_Sample_07

description: GEX


title: d11_worker_rep1

description:
HSAL50.counts.txt
HSAL51.counts.txt
H5FGTBGXF.bulk.7


title: CTCF CUT&Tag 5k cells rep2


title: d21_worker_rep1

description:
HSAL50.counts.txt
HSAL51.counts.txt
H5FGTBGXF.bulk.9


title: T2

description:
scRNA-Seq
Vehicle_7d


title: GEX_EXP20001095_Sample_05

description: GEX


title: T1

description:
scRNA-Seq
Vehicle_7d


title: d3_worker_rep3

description:
HSAL50.counts.txt
HSAL51.counts.txt
H5FGTBGXF.bulk.5


title: GEX_EXP20001095_Sample_06

description: GEX


title: GEX_EXP20001114_Sample_01

description: GEX


title: GEX_EXP20001095_Sample_04

description: GEX


title: H3K27me3 TIP-seq 100 cells


title: H3K27me3 TIP-seq 1k cells


title: d85_worker_rep1

description:
HSAL50.counts.txt
HSAL51.counts.txt
H5FGTBGXF.bulk.13


title: d3_worker_rep2

description:
HSAL50.counts.txt
HSAL51.counts.txt
H5FGTBGXF.bulk.4


title: T6

description:
scRNA-Seq
PF-06821497_7d


title: GEX_EXP20001095_Sample_03

description: GEX


title: day4tg3

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

data_processing:
RTA 3.4.4, bcl2fastq 2.20.0.422 (Illumina)
Before alignment to reference genome each sequence in the raw FASTQ files were trimmed on base call quality and sequencing adapter contamination using Trim Galore! wrapper tool. Reads shorter than 20 bp were removed from FASTQ file. Trimmed reads were aligned to the reference genome using open source short read aligner STAR (https://code.google.com/p/rna-star/) with settings according to log file. Feature counts were determined using R package “Rsubread”. Only genes showing counts greater 5 at least two times across all samples were considered for further analysis (data cleansing). Gene annotation was done by R package “bioMaRt. Before starting the statistical analysis steps,  expression data was log2 transformed and TMM normalized (edgeR).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw countsfor each Sample ...
Supplementary_files_format_and_content: Matrix table with TMM-normalizedl log2CPM for every gene and every sample

source_name: small intestinal crypt organoids

growth_protocol: Mouse small intestinal crypts were isolated ex vivo and cultured in 3D Matrigel following the manufacturer’s protocol (Mouse IntestiCult™ Organoid Growth Medium, Stemcell Technologies)

extract_protocol:
For RNA isolation from organoids, the organoid medium was replaced with ice–cold PBS and pipetted up- and down 20 times. RLT buffer (Qiagen) was added directly to the organoid pellets
Libraries were prepared using NEBNext Single Cell/Low Input RNA Library Prep (New England BioLabs)

treatment_protocol: To delete ACC1 in organoids derived from villin-creERT2 x ACC1lox/lox mice, 300nM 4-hydroxytamoxifen (4-OHT, Sigma) was added to the culture for 24h

value: intestinal epithelial cells

tag: genotype

tag: time point


title: d3_worker_rep1

description:
HSAL50.counts.txt
HSAL51.counts.txt
H5FGTBGXF.bulk.3


title: day4tg2


title: H3K27me3 TIP-seq 10k cells

value: HCT116 colorectal adenocarcinoma


title: H3K27me3 CUT&Tag 10k cells

value: H3K27me3 (Cell Signaling; 9733)


title: day4tg1


title: GEX_EXP20001095_Sample_02

description: GEX


title: H3K27me3 TIP-seq 50 cells


title: CTLA4_post

city: Cambridge

first: Michelle

last: Ramseier

address: 400 Main St

department: Harvard-MIT Health Sciences and Technology

institute: Massachusetts Institute of Technology

data_processing:
Reads aligned and pre-processed according to the DropSeq Computational Protocol v2.0 (https://github.com/broadinstitute/Drop-seq)
Genome_build: hg19
Supplementary_files_format_and_content: Processed data is a tab delimited text file containing a digital gene expression matrix with the number of UMIs for each gene (rows) and cell barcode (columns)

source_name: IgD+CD27- B cells sorted from PBMC

extract_protocol:
Transitional B cells from all donors were flow sorted from thawed PBMCs. Sorted cells were processed according to the Seq-Well protocol with second strand synthesis (Hughes*, Wadsworth*, Gierahn*, et al., Immunity, doi.org/10.1016/j.immuni.2020.09.015).
Library construction followed from the protocol above (Hughes et al.)

value: IgD+CD27- B cells sorted from PBMC

value: treated (abatacept)

tag: donor


title: day4wt3

value: WT


title: CTLA4_pre

value: untreated


title: GEX_EXP20001095_Sample_01

description: GEX

data_processing:
Base Calling TCR BCL to TCR FASTQ via Cell Ranger 3.1.0 with the flag "--delete-undetermined" in addition to the standard settings.
Base Calling GEX BCL to GEX FASTQ via Cell Ranger 3.1.0 with the flag "--delete-undetermined" in addition to the standard settings.
Base Calling ADT BCL to ADT FASTQ via Cell Ranger 3.1.0 with the flag "--delete-undetermined" in addition to the standard settings.
Base Calling tetramer BCL to tetramer FASTQ file via bcl2fastq2 version v2.20.0 with the flags "--minimum-trimmed-read-length 0 --mask-short-adapter-reads 0" in addition to the standard settings.
TCR Read Counts: FASTQ to vdj counts via Cell Ranger 3.1.0 using the standard settings.
GEX Read Counts: FASTQ to gene expression counts via Cell Ranger 3.1.0 using the standard settings.
Tetramer FASTQ to Tetramer counts via extracting tetramer barcode from uniquely observed tetramer UMI reads using python script
ADT FASTQ to ADT counts via extracting tetramer barcode from uniquely observed tetramer UMI reads using python script
TCR VDJ counts paired with tetramer and ADT counts via common hydrogel barcode using python script
VDJ and tetramer counts separated via hashtags using Seurat 4.0.3
Dehashed VDJs selected for functional assays.
Genome_build: GRCh38 (hg19)
Supplementary_files_format_and_content: The processed data files conform to the hfad AnnData format: https://anndata.readthedocs.io/en/latest/anndata.AnnData.html
Supplementary_files_format_and_content: Metadta for hashed samples including HTO oligo sequence is available in the file "GEO_upload_seq_CIPHER_2021_11_04_Supplemental_Sample_to_HTO.xlsx"


title: d0_worker_rep1

description:
HSAL50.counts.txt
HSAL51.counts.txt
H5FGTBGXF.bulk.1

source_name: Day 0 worker brain

tag: caste


title: d0_worker_rep2

description:
HSAL50.counts.txt
HSAL51.counts.txt
H5FGTBGXF.bulk.2

tag: age


title: GEX_EXP20001003_Sample_08

description: GEX


title: CTLA4_2


title: day1tg3


title: CTLA4_3


title: day4wt1


title: day1tg2


title: GEX_EXP20001003_Sample_06

description: GEX


title: GEX_EXP20001003_Sample_05

description: GEX


title: GEX_EXP20001003_Sample_04

description: GEX


title: CTLA4_1


title: day1tg1


title: siScb6

city: Angers

first: Charlotte

last: ORRE

address: Rue des Capucins (Institut de Biologie en Santé, CHU d'Angers)

country: France

institute: MitoVasc, Mitolab team

data_processing:
Torrent Suite 5.10.1
BaseCaller module (barcode-filter-minreads 10 --phasing-residual-filter=2.0 --max-phasing-levels 2 --num-unfiltered 1000; barcode-filter-postpone 1  –wells-normalization on)
Torrent Mapping Alignment Program aligner v5.2  software (mapall -q 50000)
AmpliSeq RNA plugin  (Read filters: Alignment length (17+), samtool)
RPM (reads assigned per million mapped reads)
Genome_build: hg19_AmpliSeq_Transcriptome_21K_v1
Supplementary_files_format_and_content: raw counts

source_name: MCF-7dox cells

growth_protocol: Doxorubicin resistant human breast cancer cell line MCF-7dox cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM High Glucose - Lonza) containing 10% fetal bovine serum (Gibco), 50 μg/ml uridine, 100μg/ml sodium pyruvate and 2mM glutamine (Thermofisher).

extract_protocol:
Total RNAs were extracted of 0.5 million of cells with the “RNAqueous ™ -Micro Kit” (Invitrogen ™, Thermofischer) according to the manufacturer instructions and were treated with DNase 1.
cDNA was synthetized from 10 ng of total RNA using the SuperScript™ VILO™ cDNA Synthesis Kit (Thermofisher). Up to 20,000 genes were amplified with multiplexed targeted Ampliseq panels (Ion AmpliSeq™ Human Gene Expression Core Panel, Thermofisher). After ligation of adaptators and barcodes, libraries were loaded on Ion 540™ Chips using an Ion Chef™ apparatus (Thermofisher). Libraries were sequenced on the Ion GeneStudio S5 Next Generation Sequencer and gene count was realized thanks to the ampliSeqRNA pipeline from Ion Torrent Suite (Thermofisher).

treatment_protocol: Silencing of the lncRNA SAMMSON was performed on MCF-7dox cells by using a pre-designed siRNA directed against the target lncRNA (SAMMSON Silencer® Select (n509333), Thermofischer). The siRNA Scramble was used as control (Silencer® Select Negative control # 1, Thermofischer).

value: doxorubicin resistant human breast cancer cell line

tag: sirna transfection

value: transfected with a no-target siRNA (siScb)


title: siScb5


title: siSAMMSON5

value: transfected with a siRNA targeting the lncRNA SAMMSON (siSAMMSON)


title: Control_1B

value: control


title: GEX_EXP20001003_Sample_07

city: Boston

description: GEX

extract_protocol:
PBMCs were thawed, and CD8+ T cells were enriched by magnetic-activated cell sorting (MACS) using a CD8+ T Cell Isolation Kit (Miltenyi) following the manufacturers protocol. The CD8+ T cells were then stained with 1 nM final concentration tetramer library in the presence of 2 mg/mL salmon sperm DNA in PBS with 0.5% BSA solution for 20 minutes. Cells were then labeled with anti-TCR antibody-derived tag (ADT, IP26, Biolegend) for 15 minutes followed by washing. Tetramer bound cells were then labeled with phycoerythrin (PE) conjugated anti-DKDDDDK-Flag antibody (BioLegend) followed by dead cell discrimination using 7-amino-actinomycin D (7-AAD). The live, tetramer positive cells were sorted using a Sony MA900 Sorter (Sony). Tetramer positive cells were counted by Nexcelom Cellometer (Lawrence, MA, USA) using AOPI stain following manufacturer’s recommended conditions. Single-cell encapsulations were generated utilizing 5’ v1 Gem beads from 10x Genomics (Pleasanton, CA, USA) on a 10x Chromium controller and downstream TCR, and Surface marker libraries were made following manufacturer recommended conditions. All libraries were quantified on a BioRad CFX 384 (Hercules, CA, USA) using Kapa Biosystems (Wilmington, MA, USA) library quantified kits and pooled at an equimolar ratio. TCRs, surface markers, and tetramer generated libraries were sequenced on Illumina (San Diego, CA, USA) NextSeq550 instruments. Sequencing data were processed using the Cell Ranger Software Suite (Version 3). Samples were demultiplexed and unique molecular identifier (UMI) counts were quantified for TCRs, tetramers, and gene expression.
10X Chromium 5' single-cell

value: PBMC

value: unexposed


title: GEX_EXP20001148_Sample_01_hashed sample

description: GEX

value: multiplexed sample


title: day1wt3


title: GEX_EXP20001003_Sample_02

description: GEX

value: convalescent


title: siSAMMSON4


title: Control_1A


title: day4wt2


title: siSAMMSON6


title: siScb4


title: day1wt2


title: siSAMMSON3


title: GEX_EXP20000910_Sample_12

description: GEX


title: Control_2


title: B8: KO_infected_rep4

city: San Francisco

first: Eric

last: Verdin

address: 1418D WASHINGTON BLVD

institute: Buck institute

data_processing:
Reads were mapped using STAR v2.7.0 on a composite human - SARS-Cov-2 genome. Reads mapping to exons were counted using Subread featurecount v2.0.3
Differential expression analysis was performed with DESeq2, and the normalized count table uses results from DESeq2.
Genome_build: GRCh38 and SARS-CoV-2, USA/WA-1/2020 isolate (Genbank MT246667.1)
Supplementary_files_format_and_content: DESeq2 resulst table containing normalized counts for ENSEMBL genes, as well as log2 fold change, p-value and q-value between mock infected WT and SIRT5-KO

source_name: A549 cells

growth_protocol:
A549-ACE2 cells were cultured in DMEM supplemented with 10% FBS (GeminiBio, USA), blasticidin (20 μg/ml) (Sigma-Aldrich, USA).
Sirt5 knockout (Sirt5-KO) celks was generated using CRISPR-Cas9 editing in A549-ACE2 cells. sgRNAs were commercially designed by Synthego, and knockout efficiency was validated by Sanger sequencing and Western blot.
SARS-CoV-2 Isolate USA-WA1/2020 (BEI NR-52281) was used for all infection studies. All live virus experiments were performed in a Biosafety Level 3 laboratory. SARS-CoV-2 stocks were propagated in Vero-E6 cells and their sequences verified by next-generation sequencing. Viral stock titer was measured by plaque assays.

extract_protocol:
Total RNA resuspended in RNA STAT-60 buffer was extracted using Direct-zol RNA Miniprep kit (ZymoResearch, USA), with DNAse treatment
Library preparation and sequencing were performed by DNA Technologies and Expression Analysis Core at the UC Davis Genome Center (Davis, CA, USA), supported by NIH Shared Instrumentation Grant 1S10OD010786-01. Strand-specific and barcode indexed RNA-seq libraries were generated from 500 ng total RNA each, after poly-A enrichment, using the Kapa mRNA-seq Hyper kit (Kapa Biosystems-Roche, Basel, Switzerland)  following the instructions of the manufacturer.  The fragment size distribution of the libraries were verified via micro-capillary gel electrophoresis on a LabChip GX system (PerkinElmer, Waltham, MA).   The libraries were quantified by fluorometry on a Qubit instrument (LifeTechnologies, Carlsbad, CA) and pooled in equimolar ratios. The pool was quantified by qPCR with a Kapa Library Quant kit (Kapa Biosystems) and sequenced on an Illumina NovaSeq 6000 (Illumina, San Diego, CA) with paired-end 150 bp reads.

treatment_protocol: A549-ACE2 WT and SIRT5-KO were seeded into 12-well plates and rested for 24 hours prior to infection. At the time of infection, media containing viral inoculum (MOI of 1) was added to the cells for 24 hours. At 24 hours post-infection, fresh media was added to the cells. After 3 days, cells were harvested by adding RNA STAT-60 extraction buffer (AMSbio, UK). Samples were stored at -80°C.

value: SARS-CoV-2 Infected

value: lung adenocarcinoma A549


title: GEX_EXP20000910_Sample_11

description: GEX


title: B7: KO_infected_rep3


title: siScb3


title: AK9136_hom_P3_d5

city: Dresden

first: Francis

last: Stewart

address: Tatzberg 47-49

institute: BIOTEChnology Center TU Dresden

description:
L68508
Mll1FC/FC_Passage 3_ day 5

data_processing:
bcl2fastq: bcl2fastq2 2.20.0
Alignment: Fastq files were aligned with gsnap (2020-12-16) to the mm10 reference which was obtained from Ensembl. Additionally Ensembl annotation version 98 from mm10 was used to support splicesite detection for gsnap (-d mm10 --gunzip -A sam -t 16 -n 1 -m 0.6 -s EnsemblGene-98.ss.mm10.iit -N 0).
Fragment counting: FeatureCounts (2.0.1) was used to count fragments per gene. Ensembl annotation version 98 as gtf file was used to detect genomic coordinates of genes (-s 2 -p -Q 1 -T 8).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bfx1571.mm10.e98.P3only.tsv: Tab-separated text file where the first six columns provide details about the genes (ID, chromosome, start, end, strand, length) which is followed by the fragment counts per gene per sample.

source_name: Intestinal organoids

growth_protocol: Purified crypts were resuspended in 10 ml DMEM/F12 (Life Technologies). 10 µl of the crypt suspension was used to count the number of crypts under the microscope. The pelleted crypts were resuspended in Matrigel® matrix (Corning) at desired crypt density. Approximately, 400 crypts in 25 µl Matrigel® matrix were seeded per well in a pre-warmed 24-well plate and incubated for 15 min at 37°C until the Matrigel® matrix solidified. Then, 400 µl of IntestiCult™ Organoid Growth Medium (STEMCELL Technologies) was added to each well. Organoids were cultured at 37°C in a 5% CO2 incubator and maintained in culture for 5 days before being passaged and split for experimental procedures. The growth medium was replaced every 2-3 days.

extract_protocol:
RNA from organoids was extracted using Trizol (Sigma-Aldrich).
mRNA was enriched from 500 ng total RNA by poly-dT enrichment using the NEBNext Poly(A) mRNA Magnetic Isolation Module according to the manufacturer’s instructions. The polyadenylated RNA fraction was eluted in 15ul 2x first strand cDNA synthesis buffer (NEBnext, NEB). After chemical fragmentation by incubating for 15 min at 94°C the samples were directly subjected to the workflow for strand specific RNA-seq library preparation (Ultra II Directional RNA Library Prep, NEB). In short, the first and second strand synthesis followed an end repair and A-tailing of the fragments that were ligated with the universal NEB hairpin loop adapter. Finishing ligation with incubation at 20°C for 15 minutes, cDNA was subjected to size selection by AMPure XP beads (Beckman Coulter) to remove fragments longer than 800 bp and shorter than 200 bp. Remaining adapters were depleted with an additional XP bead purification with equal amounts of sample and XP bead solution. During the PCR enrichment with 12 cycles, dual unique index primers were incorporated carrying the sequence for i7 and i5 tails (Primer 1: AAT GAT ACG GCG ACC ACC GAG ATC TAC AC XXXXXXXX ACA TCT TTC CCT ACA CGA CGC TCT TCC GAT CT, Primer 2: CAA GCA GAA GAC GGC ATA CGA GAT XXXXXXXX GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATC T; X represents the different barcode sequences). After two more AMPure XP bead purifications (in a ratio of 1:0.9), libraries were quantified using the Fragment Analyzer (Agilent).

treatment_protocol: Intestinal organoids were induced on day 2 after splitting at passage 1 using 800 nM 4-OH tamoxifen (Sigma H7904) for 24 hours.

value: Intestinal organoids

value: Mll1FC/FC; RosaCreERT2/+

tag: passage

tag: day


title: B5: KO_infected_rep1


title: AK8986_het_P3_d5

description:
L68504
Mll1FC/+_Passage 3_ day 5

value: Mll1FC/+; RosaCreERT2/+


title: siScb2


title: GEX_EXP20000910_Sample_10

first: Natalie

last: Agar

address: Harvard Medical School

institute: Brigham and Women's Hospital

description: GEX

tag: subject

tag: cohort


title: B4: WT_infected_rep4

tag: treatment


title: siSAMMSON1


title: AK9134_het_P3_d5

description:
L68507
Mll1FC/+_Passage 3_ day 5


title: B6: KO_infected_rep2


title: AK8985_hom_P3_d5

description:
L68503
Mll1FC/FC_Passage 3_ day 5


title: GEX_EXP20000910_Sample_08

description: GEX


title: CTCF TIPseq 5k cells

value: HCT116 colorectal adenocarcinoma

tag: antibody

value: CTCF (Millipore; 07-729)


title: siScb1


title: GEX_EXP20000910_Sample_09

description: GEX

tag: tissue


title: AK8836_het_P3_d5

description:
L68500
Mll1FC/+_Passage 3_ day 5


title: GEX_EXP20001003_Sample_01

description: GEX


title: day1wt1

value: intestinal epithelial cells

value: WT


title: B2: WT_infected_rep2


title: GEX_EXP20000910_Sample_07

description: GEX


title: B3: WT_infected_rep3


title: follicular_granulosa_cell_layers-POF_RNA-seq_replicate_6

city: chengdu

first: hua

last: kui

address: No 211 Huimin Road

institute: Sichuan Agricultural University

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
POF-6

data_processing:
TPM-submission.xlsx: bulk-RNAseq reads were aligned to the galGal6 using kallisto version 0.44.0 ,then tpm and counts matrixs were generated using R version 3.6.1.
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx: bulk-RNAseq reads were aligned to the galGal6 using kallisto version 0.44.0 ,then tpm and counts matrixs were generated using R version 3.6.1.
SWF.filtered_feature_bc_matrix.h5: single cell reads were aligned to the galGal6 using cellranger version 6.0.1
F1.filtered_feature_bc_matrix.h5: single cell reads were aligned to the galGal6 using cellranger version 6.0.1
POF.filtered_feature_bc_matrix.h5: single cell reads were aligned to the galGal6 using cellranger version 6.0.1
ATAC-SWF_peaks.xls: ATAC-seq reads were algned to the galGal6 using bowtie2 version 2.2.6, mitochondrial alignments and PCR duplicates were filtered using removeChrom and Picard version 1.126 and peaks were called using macs2 version 2.1.1.
ATAC-F1_peaks.xls: ATAC-seq reads were algned to the galGal6 using bowtie2 version 2.2.6, mitochondrial alignments and PCR duplicates were filtered using removeChrom and Picard version 1.126 and peaks were called using macs2 version 2.1.1.
ATAC-POF_peaks.xls: ATAC-seq reads were algned to the galGal6 using bowtie2 version 2.2.6, mitochondrial alignments and PCR duplicates were filtered using removeChrom and Picard version 1.126 and peaks were called using macs2 version 2.1.1.
IP-SWF_AllEnhancers.table.txt: chip-seq reads were aligned to the galGal6 using BWA version 0.7.15, data were filtered using samtools version 1.3.1 and super-enhancers were defined using ROSE algorithms.
IP-F1_AllEnhancers.table.txt: chip-seq reads were aligned to the galGal6 using BWA version 0.7.15, data were filtered using samtools version 1.3.1 and super-enhancers were defined using ROSE algorithms.
IP-POF_AllEnhancers.table.txt: chip-seq reads were aligned to the galGal6 using BWA version 0.7.15, data were filtered using samtools version 1.3.1 and super-enhancers were defined using ROSE algorithms.
F1.POF.silico.bulk.DEG.result.by.DEseq2.txt: single cell reads were aligned to the galGal6 using cellranger version 6.0.1, silico bulk-RNAseq counts matrixs were extracted using Python 2.7 and DEGs were generated using DEseq2 algorithms.
SWF.F1.silico.bulk.DEG.result.by.DEseq2.txt: single cell reads were aligned to the galGal6 using cellranger version 6.0.1, silico bulk-RNAseq counts matrixs were extracted using Python 2.7 and DEGs were generated using DEseq2 algorithms.
SWF.POF.silico.bulk.DEG.result.by.DEseq2.txt: single cell reads were aligned to the galGal6 using cellranger version 6.0.1, silico bulk-RNAseq counts matrixs were extracted using Python 2.7 and DEGs were generated using DEseq2 algorithms.
Genome_build: galGal6
Supplementary_files_format_and_content: bulk-RNAseq (xlsx files)
Supplementary_files_format_and_content: single cell RNAseq (matrix.h5 files)
Supplementary_files_format_and_content: ATAC-seq (peaks.xls files)
Supplementary_files_format_and_content: chip-seq (AllEnhancers.table.txt files)
Supplementary_files_format_and_content: single cell RNAseq (silico.bulk.DEG.result.by.DEseq2.txt files)

source_name: granulosa cells

extract_protocol:
total RNA was extracted from each sample using RNAiso Plus reagent (TaKaRa, Otsu, Shiga, Japan) following the manufacturer’s instructions.
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, NEB Next 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 m in followed by 5min 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.
We estimated the integrity and quality of total RNA using a Bioanalyzer 2100 system (Agilent Technologies, Palo Alto, CA, USA) with an RNA 6000 Nano kit. Subsequently, 30 strand-specific libraries (total of 10 stages with three biological replicates in each stage) were generated after depleting rRNA by the Ribo-Zero™ Gold Kit (Illumina, San Diego, CA, USA) and then sequenced on the Illumina HiSeq X Ten platform (Illumina Inc., San Diego, CA, USA) with a paired-end sequencing length of 150 bp (PE150) at Novogene Corporation (Beijing, China).

value: granulosa cells

tag: breed

value: Luhua hens

tag: developmental stage

value: postovulatory follicles

value: 31 weeks

tag: follicle growth stage

value: POF


title: siSAMMSON2

tag: cell type

value: doxorubicin resistant human breast cancer cell line

value: transfected with a siRNA targeting the lncRNA SAMMSON (siSAMMSON)


title: B1: WT_infected_rep1

tag: genotype

tag: cell line


title: GEX_EXP20000910_Sample_05

description: GEX

value: PBMC

value: unexposed


title: follicular_granulosa_cell_layers-POF_RNA-seq_replicate_4

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
POF-4


title: AK9136_hom_P1_d5

description:
L68506
Mll1FC/FC_Passage 1_ day 5

data_processing:
bcl2fastq: bcl2fastq2 2.20.0
Alignment: Fastq files were aligned with gsnap (2020-12-16) to the mm10 reference which was obtained from Ensembl. Additionally Ensembl annotation version 98 from mm10 was used to support splicesite detection for gsnap (-d mm10 --gunzip -A sam -t 16 -n 1 -m 0.6 -s EnsemblGene-98.ss.mm10.iit -N 0).
Fragment counting: FeatureCounts (2.0.1) was used to count fragments per gene. Ensembl annotation version 98 as gtf file was used to detect genomic coordinates of genes (-s 2 -p -Q 1 -T 8).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bfx1571.mm10.e98.P1only.tsv: Tab-separated text file where the first six columns provide details about the genes (ID, chromosome, start, end, strand, length) which is followed by the fragment counts per gene per sample.


title: GEX_EXP20000910_Sample_06

description: GEX


title: follicular_granulosa_cell_layers-POF_RNA-seq_replicate_5

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
POF-5


title: A7: KO_Mock_rep3

value: Mock

value: lung adenocarcinoma A549


title: AK8985_hom_P1_d5

description:
L68501
Mll1FC/FC_Passage 1_ day 5

value: Intestinal organoids

value: Mll1FC/FC; RosaCreERT2/+


title: AK9134_het_P1_d5

description:
L68505
Mll1FC/+_Passage 1_ day 5

value: Mll1FC/+; RosaCreERT2/+


title: GEX_EXP20000910_Sample_02

description: GEX


title: AK8986_het_P1_d5

description:
L68502
Mll1FC/+_Passage 1_ day 5


title: follicular_granulosa_cell_layers-POF_RNA-seq_replicate_3

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
POF-3


title: A5: KO_Mock_rep1


title: GEX_EXP20000910_Sample_04

description: GEX


title: GEX_EXP20000910_Sample_03

description: GEX


title: AK8836_het_P1_d5

description:
L68498
Mll1FC/+_Passage 1_ day 5


title: A6: KO_Mock_rep2


title: A4: WT_Mock_rep4


title: GEX_EXP20000910_Sample_01

description: GEX


title: follicular_granulosa_cell_layers-POF_RNA-seq_replicate_1

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
POF-1


title: follicular_granulosa_cell_layers-F1_RNA-seq_replicate_6

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
F1-6

value: preovulatory follicles


title: AK8835_hom_P1_d5

description:
L68497
Mll1FC/FC_Passage 1_ day 5


title: AK8835_hom_P3_d5

description:
L68499
Mll1FC/FC_Passage 3_ day 5


title: GEX_EXP20000880_Sample_04_hashed sample

description: GEX

value: multiplexed sample


title: A3: WT_Mock_rep3

value: WT


title: A8: KO_Mock_rep4


title: follicular_granulosa_cell_layers-F1_RNA-seq_replicate_5

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
F1-5

value: granulosa cells


title: GEX_EXP20000880_Sample_03_hashed sample

description: GEX


title: A2: WT_Mock_rep2


title: GEX_EXP20000880_Sample_02_hashed sample

description: GEX


title: A1: WT_Mock_rep1


title: follicular_granulosa_cell_layers-POF_RNA-seq_replicate_2

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
POF-2

value: Luhua hens


title: K-Luc Untreated [29566]

city: Duarte

first: Hsun

middle: Teresa

last: Ku

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

data_processing:
bcl2fastq v2.20 (loaded by cellranger mkfastq (3.0.1)) software used for basecalling.
reads were aligned to refdata-cellranger-mm10-1.2.0 genome assembly using cellranger v3.0.1
Counting data of reference gene expression levels were generated by cellranger v3.0.1 (automatic identification of chemistry properties)
Genome_build: mm10
Supplementary_files_format_and_content: Tab separated values; MatrixMarket

source_name: CD45+ cells isolated from brain tumor microenvironment

growth_protocol: 1e5 K-Luc tumor cells were orthotopically implanted in C57/B6 mice for 7 days

extract_protocol:
le5 K-Luc tumor cells and Le6 mIL 13BBz-CAR+ T cells encapsulated into droplets, and libraries were prepared using Chromium Single Cell 3′ Reagent Kits v3 (1000075) according to manufacturer’s protocol (10x Genomics). The generated scRNA-seq libraries were sequenced on a HiSeq using a read structure of 28 bp for Read 1, 8 bp for Index 1, and 101 bp for Read 2.
Library preparation was performed using 10x Genomics Chromium Single Cell 3’ Solution with v3 chemistry following manufacturer protocols (10x Genomics).

treatment_protocol: 1e6 mIL13BBz-CAR+ T cells were injected or not intratumorally, and mice rested for three days before tissue collection

tag: strain

value: KR158-Luc tumor bearing mouse

value: Untreated

value: brain


title: K-Luc + mIL13BBz-CAR-T treatment [29567]

value: mIL13BBz-CAR-T Treated


title: GEX_EXP20000880_Sample_01_hashed sample

description: GEX


title: 50018209 Tumor RNA_C4D1

city: Houston

first: David

last: Hong

state: TX

address: 1515 Holcombe Boulevard Unit 455

institute: University of Texas M.D. Anderson Cancer Center

description: Tumor RNA_C4D1

data_processing: For RNA Sequencing, tumor samples were analyzed through Personalis somatic RNA pipeline for small variant calling (SNVs, InDels and Fusions) and Expression (gene and variant level) data.

source_name: FFPE Tumor RNA

extract_protocol:
RNA sequencing of formalin-fixed, paraffin-embedded tumor samples was conducted at Personalis Inc. (Menlo Park, CA, USA). Dual DNA and RNA extractions were performed using Qiagen AllPrep DNA/RNA kit as per manufacturer’s protocol.
Exome capture was performed using Agilent SureSelect Clinical Research Exome (SSCR) according to manufacturers’ recommendations. Additional supplementation with Personalis ACE proprietary target probes was performed to enhance coverage in difficult to sequence regions within sets of biomedically and medically relevant genes.

treatment_protocol: Paired tumor biopsy samples were collected from each patient at baseline and after 4 cycles of ivuxolimab treatment

tag: deidentified patient id

tag: de-identified sample accession#

value: Treated

tag: visit/collection

value: Cycle 4 Day 1


title: follicular_granulosa_cell_layers-F1_RNA-seq_replicate_2

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
F1-2

tag: age

value: 31 weeks


title: GEX_EXP20000854_Sample_08

description: GEX

value: PBMC

value: convalescent


title: 50018209 Tumor RNA_SCRN

description: Tumor RNA_SCRN

value: Screening


title: Brain LPS-LPS injection rep3

city: Guangzhou

first: Xinping

last: Yang

state: Guangdong

address: 1838 N. Guangzhou Ave

institute: Southern Medical University

data_processing:
Sequenced reads were mapped to GRCm38 whole genome using STAR_2.5.2b with parameters --runMode alignReads --outSAMstrandField intronMotif --runThreadN 6
Raw counts are calculated by htseq-count version 0.11.2. with parameters -s no -t exon -i gene_id -f bam
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: whole brain

extract_protocol:
Each RNA sample was extracted from the whole brain of one adult mice according to the manufacturer’s protocol (RNAeasy Mini Kit, Qiagen, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: intraperitoneal injection (IPI) of lipopolysaccharide (LPS) (Saline injection as control) into the pregnant mice at G16 (16th day after gestation) and second time during puberty by IPI of LPS (Saline injection as control) into the male offspring at P30 (30th day after birth)

value: whole brain

value: post natal day 32

value: LPS-LPS injection


title: Brain LPS-LPS injection rep4


title: follicular_granulosa_cell_layers-F1_RNA-seq_replicate_1

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
F1-1

value: preovulatory follicles


title: Brain LPS-LPS injection rep2


title: GEX_EXP20000854_Sample_07

description: GEX


title: Brain LPS-LPS injection rep1


title: 50052569 Tumor RNA_C4D1

description: Tumor RNA_C4D1


title: GEX_EXP20000854_Sample_06

description: GEX


title: follicular_granulosa_cell_layers-F2_RNA-seq_replicate_6

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
F2-6


title: 50052569 Tumor RNA_SCRN

description: Tumor RNA_SCRN


title: follicular_granulosa_cell_layers-F2_RNA-seq_replicate_5

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
F2-5


title: GEX_EXP20000854_Sample_05

description: GEX

value: unexposed


title: Brain Saline-LPS injection rep4

value: Saline-LPS injection


title: follicular_granulosa_cell_layers-F2_RNA-seq_replicate_4

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
F2-4

value: granulosa cells

value: Luhua hens


title: follicular_granulosa_cell_layers-F1_RNA-seq_replicate_4

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
F1-4


title: Brain Saline-LPS injection rep3


title: 50063730 Tumor RNA_C4D1

description: Tumor RNA_C4D1


title: GEX_EXP20000854_Sample_04

description: GEX


title: 50063730 Tumor RNA_SCRN

description: Tumor RNA_SCRN

value: Untreated


title: Brain Saline-LPS injection rep2


title: follicular_granulosa_cell_layers-F2_RNA-seq_replicate_3

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
F2-3


title: GEX_EXP20000854_Sample_03

description: GEX


title: follicular_granulosa_cell_layers-F1_RNA-seq_replicate_3

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
F1-3


title: 50078173 Tumor RNA_C4D1

description: Tumor RNA_C4D1


title: follicular_granulosa_cell_layers-F2_RNA-seq_replicate_2

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
F2-2


title: Brain Saline-LPS injection rep1


title: 50078173 Tumor RNA_SCRN

description: Tumor RNA_SCRN


title: GEX_EXP20000854_Sample_02

description: GEX


title: follicular_granulosa_cell_layers-F2_RNA-seq_replicate_1

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
F2-1


title: Brain LPS-Saline injection rep4

value: LPS-Saline injection


title: 50055250 Tumor RNA_C4D1

description: Tumor RNA_C4D1


title: Brain LPS-Saline injection rep3


title: 50055250 Tumor RNA_SCRN

description: Tumor RNA_SCRN


title: GEX_EXP20000780_Sample_03

description: GEX


title: follicular_granulosa_cell_layers-F3_RNA-seq_replicate_5

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
F3-5


title: GEX_EXP20000854_Sample_01

description: GEX


title: follicular_granulosa_cell_layers-F3_RNA-seq_replicate_6

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
F3-6


title: GEX_EXP20000780_Sample_02

description: GEX


title: Brain LPS-Saline injection rep2


title: Brain LPS-Saline injection rep1


title: GEX_EXP20000768_Sample_04

description: GEX


title: 50577942 Tumor RNA_C4D1

description: Tumor RNA_C4D1


title: Brain Saline-Saline injection rep4

value: saline-saline injection


title: follicular_granulosa_cell_layers-F3_RNA-seq_replicate_4

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
F3-4


title: follicular_granulosa_cell_layers-F3_RNA-seq_replicate_3

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
F3-3


title: follicular_granulosa_cell_layers-F3_RNA-seq_replicate_2

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
F3-2


title: Brain Saline-Saline injection rep3


title: GEX_EXP20000768_Sample_02

description: GEX


title: 50085250 Tumor RNA_SCRN

description: Tumor RNA_SCRN


title: follicular_granulosa_cell_layers-F3_RNA-seq_replicate_1

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
F3-1


title: Brain Saline-Saline injection rep2


title: 50053968 Tumor RNA_C4D1

description: Tumor RNA_C4D1

value: Treated


title: Brain Saline-Saline injection rep1


title: GEX_EXP20000722_Sample_07

description: GEX


title: 50053968 Tumor RNA_SCRN

description: Tumor RNA_SCRN


title: follicular_granulosa_cell_layers-F4_RNA-seq_replicate_6

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
F4-6


title: follicular_granulosa_cell_layers-F4_RNA-seq_replicate_5

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
F4-5


title: follicular_granulosa_cell_layers-F4_RNA-seq_replicate_4

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
F4-4


title: 50577942 Tumor RNA_SCRN

description: Tumor RNA_SCRN


title: human-Healthy_3

city: hefei，anhui，china

first: jian-xiong

last: wang

state: anhui

address: No. 218，Ji-xi Road，Hefei 230022, Anhui, China.

institute: Hospital

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2  Qvalue < =0.05
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM values for each Sample

source_name: Whole blood cell

growth_protocol: In this case-control study, 3 healthy humans and 5 patients with AS who met the modified New York 1984 criteria. they were all recruited from the Department of Rheumatology and Immunology, First Affiliated Hospital of Anhui Medical University. Clinical records were collected and questionnaire were interviewed by professional rheumatologists. All patients were first diagnosed and they were excluded from the study if with infectious diseases, serious kidney diseases, serious liver diseases, endocrine disorders. Moreover, significant data missing, treated with steroid or any nonsteroidal anti-inflammatory drugs (NSAIDs) or disease-modifying anti-rheumatic drugs (DMARDs) within the past were also eliminated. In this study, each participant provided the informed consent to participate, and study was performed in accordance with the Declaration of Helsinki

extract_protocol:
Total RNA was extracted by the TRIZOL (Ambion). The RNA was further purified with two phenol-chloroform treatments and then treated with RQ1 DNase (Promega) to remove DNA. The quality and quantity of the purified RNA were redetermined by measuring the absorbance at 260 nm/280 nm (A260/A280) using Smartspec Plus (BioRad). The integrity of RNA was further verified by 1.5% agarose gel electrophoresis.
For each sample, 1μg of total RNA was used for RNA-seq library preparation by VAHTS Stranded mRNA-seq Library Prep Kit (Vazyme). Polyadenylated mRNAs were purified and fragmented, and then converted into double strand cDNA. After the step of end repair and A tailing, the DNAs were ligated to VAHTS RNA Adapters (Vazyme). Purified ligation products corresponding to 200-500 bps were digested with heat-labile UDG, and the single strand cDNA was amplified, purified, quantified and stored at -80℃ before sequencing.
For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to Illumina system for 150 nt paired-end sequencing.

value: Whole blood cell

tag: disease state

value: healthy control


title: GEX_EXP20000722_Sample_06

description: GEX

value: PBMC

tag: subject


title: GEX_EXP20000722_Sample_05

description: GEX

tag: cohort

value: convalescent


title: follicular_granulosa_cell_layers-F4_RNA-seq_replicate_3

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
F4-3

value: 31 weeks


title: GEX_EXP20000768_Sample_03

description: GEX


title: GEX_EXP20000722_Sample_04

description: GEX


title: 50085250 Tumor RNA_EoT

description: Tumor RNA_EoT

tag: treatment

value: End-of-Treament


title: human-Healthy_1


title: GEX_EXP20000722_Sample_03

description: GEX


title: follicular_granulosa_cell_layers-F4_RNA-seq_replicate_2

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
F4-2


title: follicular_granulosa_cell_layers-F4_RNA-seq_replicate_1

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
F4-1


title: GEX_EXP20000768_Sample_01

description: GEX