title: Dmrt3;Dmrt5 KO rep4

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

data_processing:
Base-calling: bcl2fastq CASAVA_v1.8.2
Sequencing quality control: FastQC 0.10.1
Alignment to reference genome: STAR 2.3.0e_r291
Count reads for each gene: featureCounts v1.4.6-p1
Differential expression analysis: DESeq2 v1.8.2
Genome_build: mm10

source_name: cortical tissue

extract_protocol:
RNA was extracted using the RNeasy mini kit (Qiagen).  The TruSeq RNA Sample Prep Kit v2 kit was used to prepare the libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: Dmrt3;Dmrt5 KO rep5

status: Public on Dec 28 2018

type: SRA

country: Germany

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

tag: developmental stage

tag: genotype


title: TPB11

city: Chicago

first: Tao

last: Pan

state: Illinois

address: 929 E. 57th Street

department: Biochemistry and Molecular Biology

country: USA

institute: University of Chicago

description: Input sample

data_processing:
RNA-seq and m6A-seq reads were aligned to mouse genome mm10 by HISAT2 version 2.1.0
m6A enriched region were detected by exomePeak R package. RNA-Seq data(no IP, input RNA) in the same condition was used as input information
m6A differentially enriched region between GF and SPF sample were detected by MeTDiff R package.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample…

molecule: polyA RNA

source_name: Specific pathogen free

growth_protocol: SPF mice are housed under specific pathogen free conditions and the mice have been tested free of designated pathogens. GF mice are housed in tightly controlled and monitored isolators to prevent contamination. They are microbiologically sterile and no living organisms can be cultured from germ-free mice specimens.

extract_protocol:
MeRIP-seq/m6A-seq. MeRIP experiments were carried out according to previously published protocols (Nature 485, 201-206 (2012).). Briefly, polyA selection and ribodepletion-treated mRNA samples (1 ug of each) from tissues (brain, intestine, kidney, liver) were used for RNA fragmentation followed by immunoprecipitation with EpiMark N6-Methyladenosine Enrichment Kit (NEB, E1610S). 2 ul of N6-Methyladenosine antibody was reacted with 40 ul Protein G Magnetic Beads prewashed by 250 ul Reaction buffer (150 mM NaCl, 10 mM Tris-HCl, pH 7.5, 0.1% NP-40) for 2 h at 4°C. The beads were washed twice with 250 ul Reaction buffer, fragmented RNAs were added to beads and incubated for 3 h at 4°C. Afterwards, the beads were washed twice with 250 ul Low Salt Reaction Buffer (50 mM NaCl, 10 mM Tris-HCl, pH 7.5, 0.1% NP-40) and twice with 250 ul High Salt Reaction Buffer (500 mM NaCl, 10 mM Tris-HCl, pH 7.5, 0.1% NP-40). RNAs were eluted from the protein G magnetic beads in 30 ul of Buffer RLT (Qiagen, 79216) followed by precipitation in 100% ethanol. RNAs were dissolved in 12 ul RNase-free water. 120 ng of input RNA and immunoprecipitated RNAs were used for library preparation using Illumina TruSeq Stranded mRNA Library Preparation Kit (Illumina) according to the manufacture's instructions. The concentration and quality of libraries were checked by the Agilent 2100 bioanalyzer. RNA sequencing was carried out at the University of Chicago Genomics Facility on an Illumina HiSeq2500 platform to generate 100-bp paired reads.
Tissues were homogenized in TRIzol with glass beads using homogenizer. Total RNA was isolated from frozen tissues using TRIzol reagent following the manufacturer's protocol.

treatment_protocol: Mice tissues (brain, intestine, kidney, liver) were dissected from SPF mice (4-week-old male C57BL/6 mice) and GF mice (4-week-old male C57BL/6 mice). All tissues were freshly frozen on dry ice and stored at –80°C.

tag: brain

tag: tissue

value: Brain

tag: age

tag: Sex

value: male


title: Dmrt3;Dmrt5 KO rep3


title: TPB10

description: Input sample


title: Dmrt3;Dmrt5 KO rep2


title: Dmrt3;Dmrt5 KO rep1


title: Dmrt5 KO rep5


title: Dmrt5 KO rep2


title: Dmrt5 KO rep1


title: Dmrt5 KO rep4


title: Dmrt3 KO rep5


title: Dmrt3 KO rep4


title: Dmrt3 KO rep2


title: WT Rep3

value: wild-type


title: WT Rep1


title: WT Rep2


title: MB231 shPTK2 #1 + Dox

city: Gyeonggi-do

first: Hyonchol

last: Jang

address: 323, Ilsan-ro, Ilsandong-gu, Goyang-si

country: South Korea

institute: National Cancer Center

data_processing:
bcl2fastq v1.8.4 package was used for basecalling.
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence with Trimmomatic0.32.
To estimate expression levels, the RNA-Seq reads were mapped to the genome of Homo sapiens using TopHat 2.0.13, which is capable of reporting split-read alignments across splice junctions and determined using Cufflinks 2.2.1 software in default options.
The reference genome sequence of Homo sapiens (hg19) and annotation data were downloaded from UCSC. The transcript counts in isoform level were calculated, and the relative transcript abundances were measured in FPKM (Fragments Per Kilobase of exon per Million fragments mapped) using Cufflinks.
Raw data (the reads for each transcript) were normalized by FPKM (Fragments Per Kilobase of exon model per Millon mapped fragments).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Homo sapiens

source_name: Breast cancer cell without expressing PTK2

extract_protocol:
RNAs were extracted from the Breast of Homo Sapiens. Poly(A) mRNA using the Illumina  TruSeq RNA Sample Prep Kit v2, according to the manufacturer’s instructions.
Libraries were prepared for multiplex sequencing using Illumina TruSeq RNA Sample Prep Kit , according to the manufacturer’s protocol.

value: Breast cancer

value: without expressing PTK2


title: hda19 (ChIP-seq)

city: Beijing

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

country: China

institute: National Institute of Biological Sciences

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the TAIR10 genome assembly using bowtie2 version 2.3.4 with parameters -k 1 -N 1 -p 40 --local -q
peaks were called using macs2 version 2.1.1.20160309 with the following setting: macs2 callpeak -f BAM -p 1e-3 -g 1.2e8  --bdg --nolambda --nomodel
The macs2 bdgdiff was used to determine differentially expressed peaks between wild-type and mutant plant with default parameters.
Genome_build: TAIR10
Supplementary_files_format_and_content: bw files were generated using bedtools genomecov and were further converted to bigWig using bedGraphToBigWig

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: Arabidopsis seedlings

growth_protocol: Arabidopsis seedlings were grown on MS medium plates with a 8 h light/16 h dark photoperiod at 22ºC.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with anti-acetylated H3 antibody (Millipore, 06-599).
DNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Three gram samples of 18-day-old seedlings were subjected to cross-linking in 1% formaldehyde under vacuum conditions.

value: seedlings

tag: treatment

value: short day

tag: chip antibody


title: hdc1 (ChIP-seq)

value: anti-acetylated H3 antibody (Millipore, 06-599)


title: WT (ChIP-seq)

value: wild type


title: hda6 (ChIP-seq)


title: BT549 shPTK2 #1

source_name: Breast cancer cell with expressing PTK2

value: with expressing PTK2


title: CLB-GA-ctrl_rep3

city: Gent

first: Dries

last: Rombaut

address: Corneel Heymanslaan 10

department: Center for Medical Genetics

country: Belgium

institute: Ghent University

data_processing:
Reads were determined using Kallisto, a pseudo-alignment algorithm.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include read counts per transcript for each Sample

source_name: neuroblastoma

extract_protocol:
Total RNA was extracted from fresh cells using TRIzol® Reagent (Invitrogen) and the miRNeasy Mini kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: CLB-GA-cells were treated with crizotinib for 24h, together with cells treated with a control

tag: cell line

value: CLB-GA

value: control


title: CLB-GA-Crizotinib_rep3

value: crizotinib 500nM


title: CLB-GA-ctrl_rep1


title: CLB-GA-ctrl_rep2


title: control_KD_control_OE_2

city: Birmingham

first: Philip

last: Kitchen

address: IBR Building

country: United Kingdom

institute: University of Birmingham

data_processing:
Trimming of low quality bases (Phred score < 30) and adapter contamination using TrimGalore!
Alignment to hg19 using TopHat
Removal of multi-mapped reads (i.e. reads where primary and secondary alignments have equal mapping scores)
Generation of per-gene count tables using featureCounts and Illumina iGenomes hg19 gene annotation
Calling of differentially expressed genes using DESeq2. FDR q<0.05 was considered differentially expressed.
Genome_build: hg19
Supplementary_files_format_and_content: Excel file - Normalised counts. number of counts per gene, per million reads. Generated using DESeq2

source_name: CCLP1 cholangiocarcinoma cell line

growth_protocol: Grown in DMEM High Glucose (Sigma-Aldrich cat no.5796) + 10% FBS + Non-essential amino acids + penicillin/streptomycin

extract_protocol:
Bioline Isolate II RNA extraction kit
Illumina TruSeq RNA Library Prep kit

tag: shRNA target

value: non-targetting

tag: adenovirus

value: empty


title: CLB-GA-Crizotinib_rep1


title: CLB-GA-Crizotinib_rep2


title: BT549 shPTK2 #1 + Dox


title: Ecad_YFPnegBu_Rep2

city: New York

first: Kenneth

last: Lay

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

data_processing:
Alignment of sequencing reads was performed using STAR version 2.5.2a.
Transcripts were annotated using Gencode release M10 of the mouse genome.
Gene count output from STAR read aligner was used to perform differential gene expression analysis with DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: Processed files are .txt files containing gene count output from STAR read aligner.

source_name: Skin

extract_protocol: HFSCs and their inner bulge niche cells were isolated by fluorescence-activated cell sorting (FACS) and total RNA was extracted. mRNA libarary was prepared using Illumina TruSeq mRNA sample preparation kit and single end sequencing was performed using Illumina HiSeq 4000.

value: post-natal week 12

value: skin


title: MB231 shPTK2 #1


title: Dmrt3 KO rep3


title: Dmrt3 KO rep1


title: Ecad_YFPnegBu_Rep1


title: control_KD_control_OE_1


title: N3_KD_control_OE_1


title: WT Rep4


title: Ecad_cKO_innerBu_Rep2


title: N3_KD_control_OE_2


title: control_KD_PRH_OE_2

value: myc-PRH


title: control_KD_PRH_OE_1


title: Ecad_Het_innerBu_Rep2


title: control_OE_2


title: PRH_OE_2


title: control_OE_1


title: control_KD_2


title: PRH_KD_2

value: HHEX


title: control_KD_1


title: PRH_OE_1


title: Bulk kidney rep2

city: Hangzhou

first: Haide

last: Chen

address: 866 Yuhangtang road

institute: Zhejiang University

data_processing:
Bulk sequencing reads containing multiplexed data were filtered using the bbduk function of the bbmap tool to select reads containing the appropriate sample index.
STAR 2.5.3a with default parameters was used to map filtered reads to the  Ensembl release 75 mouse reference genome.
Aligned reads were normalized by library size to fragments per kilobase of transcript per million mapped reads (FPKM) using the  “fpkm” function in the “DESeq2” package in R.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for all samples

source_name: Bulk kidney

extract_protocol:
The excised tissues were immediately washed in PBS. After washing, each tissue was ground into powder with liquid N2. RNA extraction was performed using Trizol. We used mRNA Capture Beads (VAHTS mRNA-seq v2 Library Prep Kit for Illumina, Vazyme) to extract mRNA from total RNA. A PrimeScript Double Strand cDNA Synthesis Kit (TaKaRa) was used to synthesize double-stranded cDNA from purified polyadenylated mRNA templates according to the manufacturer’s protocol.
We used TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme) to prepare cDNA libraries for Illumina sequencing

value: kidney

value: 6-10 week


title: Ecad_Het_innerBu_Rep1


title: PRH_KD_1


title: Bulk kidney rep1


title: Bulk small intestine rep2

source_name: Bulk small intestine

value: small intestine


title: Bulk lung rep1

source_name: Bulk lung

value: lung


title: Bulk lung rep2


title: Ecad_cKO_innerBu_Rep1


title: N3_KD_PRH_OE_2


title: Mouse Dendritic cells in WT mice on day 4 following IAV infection, replicate2

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

description: Mouse Dendritic cells derived from lung-draining mediastinal lymph nodes in wild type mice on day 4 following influenza a virus (IAV) infection, replicate2

data_processing:
Constructed libraries were sequenced on an NextSeq 500 Illumina platform, producing 2x75nt stranded paired end reads (52 Gb). Image analysis, base calling, and error estimation were performed using Illumina Analysis Pipeline (version 2.8).
Quality control of the primary sequencing data was performed using FastQC (version 0.11.3) and included adapter trimming using cutadapt (version 1.8.3).
Reads were aligned using STAR (version 2.4.0)
Genome_build: Mouse genome (ENSEMBL, MM10/GRCm38)
Supplementary_files_format_and_content: We mapped reads to the mouse reference genome (GRCm38) from Illumina's igenomes using STAR. After mapping, we assigned aligned read counts from BAM files to exons and genes using the python package HT-Seq.  HT-Seq provided the most accurate way of aligning read counts to overlapping exons. Reads that mapped to multiple positions were removed. Raw counts were normalized using the voom function in limma.

growth_protocol: On day 4 following infection, lung-draining mediastinal lymph nodes (dLN)  were isolated from WT and Ifnlr-/- mice. Single cell suspensions were prepared and DCs were enriched using a StemCell DC enrichment kit separation (StemCell), and cDC were sorted into RLT buffer using a FACS Aria. RNA was isolated (Qiagen RNeasy Micro Kit), and mRNA was prepared to perform mRNA sequencing according to manufacturers instructions (Takara SMART-Seq v4 Ultra Low Input RNA Kit).

extract_protocol:
RNA was extracted using RNeasy mini kit (QIAGEN) with on-column DNase treatment.
KAPA Total RNA-seq kit with Ribo Erase
Library quality was evaluated using the Qubit® 3.0 Fluorometer and the Agilent 2100 Bioanalyzer instrument. Constructed libraries were sequenced on an NextSeq 500 Illumina platform, producing 2x75nt stranded paired end reads (52 Gb). Image analysis, base calling, and error estimation were performed using Illumina Analysis Pipeline (version 2.8).

tag: time

value: Day 4

value: IAV

value: WT

tag: replicate


title: Mouse Dendritic cells in WT mice on day 4 following Mock infection, replicate1

description: Mouse Dendritic cells derived from lung-draining mediastinal lymph nodes in wild type mice on day 4 following influenza a virus (IAV) infection, replicate1

value: Mock


title: Mouse Dendritic cells in WT mice on day 4 following Mock infection, replicate2


title: Mouse Dendritic cells in WT mice on day 4 following Mock infection, replicate3

description: Mouse Dendritic cells derived from lung-draining mediastinal lymph nodes in wild type mice on day 4 following influenza a virus (IAV) infection, replicate3


title: Mouse Dendritic cells in WT mice on day 4 following IAV infection, replicate1


title: Bulk small intestine rep1


title: Bulk liver rep2

source_name: Bulk liver

value: liver


title: Bulk liver rep1


title: N3_KD_PRH_OE_1


title: Pooled RNA

city: Piscataway

first: Premal

last: Shah

state: NJ

address: 145 Bevier Road, Rm 326

department: Genetics

institute: Rutgers University

data_processing:
RNA-seq and footprinting reads were mapped to the yeast transcriptome using the riboviz pipeline (Carja et al., BMC Bioinformatics 2017). Sequencing adapters were trimmed from reads using Cutadapt 1.14 (--trim-n -O 1 –minimum-length 24).
The reads from different samples were separated based on the barcodes in their 3’ linkers using fastx_barcode_splitter (FASTX toolkit, Hannon lab) with utmost one mismatch allowed. UMI and barcodes were removed from reads in each sample using Cutadapt (--trim-n -m 10 -u 4 -u -10)
Trimmed reads that aligned to yeast rRNAs and tRNAs were removed using HISAT2 v2.1.0 . Remaining reads were mapped to a set of 5812 genes using HISAT2 v2.1.0. Only reads that mapped uniquely were used for all downstream analyses.
All analyses of ribosome profiling datasets were performed in R.
Genome_build: SGD version R64-2-1_20150113
Supplementary_files_format_and_content: Tab-delimited text files include count values for each sample

organism: Saccharomyces cerevisiae

source_name: CEN.PK, ∆uba4 and ∆ncs2 strains.

extract_protocol:
Cells were grown overnight in rich media and subsequently shifted to minimal media till the OD600 reaches 0.5-0.8. Cells were rapidly harvested by filtration and lysed, as described in detail (Weinberg et al., 2016; McGlincy and Ingolia, 2017). For both transcriptome and ribosome profiling analyses, three biological replicates each for WT and tRNA thiolation mutant cells (∆uba4 and ∆ncs2) were included.
Separate 5’ and 3’ linkers were ligated to the RNA-fragment instead of 3’ linker followed by circularization (Subtelny et al, Nature 2014). 5’ linkers contained 4 random nt unique molecular identifier (UMI) similar to a 5 nt UMI in 3’ linkers. During size-selection, we restricted the footprint lengths to 18-34 nts. Matched RNA-seq libraries were prepared using RNA that was randomly fragmentation by incubating for 14 min at 95C with in 1 mM EDTA, 6 mM Na2CO3, 44 mM NaHCO3, pH 9.3. RNA-seq fragments were restricted to 18-50 nts. Ribosomal rRNA were removed from pooled RNA-seq and footprinting samples using RiboZero (Epicenter MRZY1324). cDNA for the pooled library were PCR amplified for 16 cycles.

tag: genotype/variation

value: CEN.PK,deltauba4 and deltancs2

value: mixed sample (non-demultiplexed)


title: Pooled RPF

description: Ribosome-protected fragments

data_processing:
Library strategy: Ribo-Seq
RNA-seq and footprinting reads were mapped to the yeast transcriptome using the riboviz pipeline (Carja et al., BMC Bioinformatics 2017). Sequencing adapters were trimmed from reads using Cutadapt 1.14 (--trim-n -O 1 –minimum-length 24).
The reads from different samples were separated based on the barcodes in their 3’ linkers using fastx_barcode_splitter (FASTX toolkit, Hannon lab) with utmost one mismatch allowed. UMI and barcodes were removed from reads in each sample using Cutadapt (--trim-n -m 10 -u 4 -u -10)
Trimmed reads that aligned to yeast rRNAs and tRNAs were removed using HISAT2 v2.1.0 . Remaining reads were mapped to a set of 5812 genes using HISAT2 v2.1.0. Only reads that mapped uniquely were used for all downstream analyses.
All analyses of ribosome profiling datasets were performed in R.
Genome_build: SGD version R64-2-1_20150113
Supplementary_files_format_and_content: Tab-delimited text files include count values for each sample


title: Mouse Dendritic cells in IFNLR mice on day 4 following Mock infection, replicate2

description: Mouse Dendritic cells derived from lung-draining mediastinal lymph nodes in interferon lambda receptor knock out mice on day 4 following influenza a virus (IAV) infection, replicate2

value: IFNLR


title: Mouse Dendritic cells in IFNLR mice on day 4 following Mock infection, replicate1

description: Mouse Dendritic cells derived from lung-draining mediastinal lymph nodes in interferon lambda receptor knock out mice on day 4 following influenza a virus (IAV) infection, replicate1


title: Mouse Dendritic cells in IFNLR mice on day 4 following IAV infection, replicate2_S19


title: hda19_long_day (RNA-seq)

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 whole genome using STAR-2.5.2b with parameters  --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 10 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --chimSegmentMin 20  --alignSoftClipAtReferenceEnds No --readFilesCommand zcat-m 10 --best --strata
Fragments  Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cuflink2.0.0 cuffdiff with parameters -p 16 -N
Genome_build: TAIR10
Supplementary_files_format_and_content: bw files were generated using deeptools bamCoverage with parameters --binSize 10 -p 30 --normalizeUsing RPKM --outFileFormat bigwig

growth_protocol: Arabidopsis seedlings were grown on MS medium plates with a 16 h light/8 h dark photoperiod at 22ºC

extract_protocol:
Total RNA was extracted from 1 g samples of two-week-old Arabidopsis seedlings with TRIzol reagent (Invitrogen)
libraries were prepared for mRNA-seq

value: seedlings

value: long day


title: hda6_long_day (RNA-seq)


title: Mouse Dendritic cells in IFNLR mice on day 4 following IAV infection, replicate1_S18


title: Mouse Dendritic cells in IFNLR mice on day 4 following Mock infection, replicate3

description: Mouse Dendritic cells derived from lung-draining mediastinal lymph nodes in interferon lambda receptor knock out mice on day 4 following influenza a virus (IAV) infection, replicate3


title: Mouse Dendritic cells in IFNAR mice on day 4 following Mock infection, replicate3

description: Mouse Dendritic cells derived from lung-draining mediastinal lymph nodes in interferon alpha receptor knock out mice on day 4 following influenza a virus (IAV) infection, replicate3

value: IFNAR


title: hdc1_long_day (RNA-seq)


title: WT_long_day (RNA-seq)

value: wild type


title: Caf905-2 (rep2)

type: RNA

city: Istanbul

first: Halil

middle: ibrahim

last: KISAKESEN

state: Istanbul

address: ITU MOBGAM, SARIYER

department: Molecular Biology, Genetics and Biotechnology

country: Turkey

institute: Istanbul Technical University

description:
Caf905-2 (2)
Gene expression at log-phase in Yeast Minimal Medium.

hyb_protocol: 0.6 ug Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes, according to the manufacturer's instructions. Subsequently, the samples were immediately hybridized onto Agilent Yeast Oligo Microarray (V2) 8x15K G4813 in a rotating Agilent hybridization oven at 65 °C for 17 h.

scan_protocol: Immediately after washing, slides were scanned on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed using Feature Extraction Software 9.1 (Agilent) with default parameters (protocol GE1-v1_91 and Grid: 016322_D_F_20070321). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Log-phase rep2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by purification using Absolutely RNA Nanoprep Kit (Agilent). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Growth in Yeast Minimal Medium at 30 ºC and 150 rpm until early exponential phase (OD600 ~1.0).

extract_protocol: RNeasy Mini Kit (Qiagen) was used, according to the manufacturer’s instructions. RNA quality based on Integrity Numbers (RIN) was checked with Agilent 2100 Bioanalyzer. RNA samples with RIN values > 8 were utilized in the microarray analysis.

treatment_protocol: No treatment.

value: Caf905-2 mutant


title: Mouse Dendritic cells in IFNAR mice on day 4 following Mock infection, replicate2

description: Mouse Dendritic cells derived from lung-draining mediastinal lymph nodes in interferon alpha receptor knock out mice on day 4 following influenza a virus (IAV) infection, replicate2


title: Caf905-2 (rep1)

description:
Caf905-2 (1)
Gene expression at log-phase in Yeast Minimal Medium.

source_name: Log-phase rep1


title: Caf905-2 (rep3)

description:
Caf905-2 (3)
Gene expression at log-phase in Yeast Minimal Medium.

source_name: Log-phase rep3


title: REF (rep3)

description:
REF-3
Gene expression at log-phase in Yeast Minimal Medium.

value: Reference strain


title: REF (rep2)

description:
REF-2
Gene expression at log-phase in Yeast Minimal Medium.


title: REF (rep1)

description:
REF-1
Gene expression at log-phase in Yeast Minimal Medium.


title: C3ABR

city: Copenhagen

first: Jin

last: Zheng

address: 3b Blegdamsvej

country: Denmark

institute: University of Copenhagen

description: APTX proficienct

data_processing:
Base calling software: ZebraCall, V2
SOAPnuke for filter reads: version:v1.5.2 parameters: -l 15 -q 0.5 -n 0.1 website: https://github.com/BGI-flexlab/SOAPnuke
HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts) for mapping step. HISAT2:  Figure3 HISATmappingdemoshow. Version: v2.0.4 Parameters: --phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000 Website: http://www.ccb.jhu.edu/software/hisat
StringTie to reconstruct transcripts, and use Cuffcompare(Cufflinks tools) to compare reconstructed transcripts to reference annotation. CPC to predict coding potential of novel transcripts StringTie: Version: v1.0.4 Parameters: -f 0.3 -j 3 -c 5 -g 100 -s 10000 -p 8 Website: http://ccb.jhu.edu/software/stringtie Cufflinks: Version: v2.2.1 Parameters: -p 12 Website: http://cole-trapnell-lab.github.io/cufflinks CPC: Version: v0.9-r2 Parameters: Default Website: http://cpc.cbi.pku.edu.cn
rMATS to detect differentially splicing gene. rMATS: Version: v3.2.5 Parameters: -analysis U -t paired -a 8 Website: http://rnaseq-mats.sourceforge.net
Bowtie2 for mapping reads to reference, RSEM for calculating gene expression level. Bowtie2 : Version: v2.2.5  Parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no- mixed--no-discordant -p1-k200  Website: http://bowtie-bio.sourceforge.net/ Bowtie2 /index.shtml RSEM : Version: v1.2.12 Parameters: default Website: http://deweylab.biostat.wisc.edu/ RSEM
Genome_build: hg19
Supplementary_files_format_and_content: excel files include RPKM values for each Sample

source_name: lyphoblast cell ine

growth_protocol: The cells were in culture for two-three weeks before RNA extraction. U2OS cells were grown at a density of  2–3 × 106 cells into a T75 flask,  in DMEM medium  (Life Technologies) supplemented with 10% FBS (Sigma) and 1% penicillin-streptomycin. AOA1 patients cells were cultured in RPMI 1640 medium (Life Technologies) supplmented with 10% FBS and 1% penicillin-streptomycin. The cells were cultured at a density of 5-10 x 106 in a T75 flask.

extract_protocol:
total RNA was extracted with RNeasy Mini Kit (Qiagen).
For library construction, polyA-containing mRNA molecules were isolated with magnetic beads. Following purification, the mRNA was fragmented into small pieces. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification. We then quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library.

treatment_protocol: no treatment


title: L939

description: APTX deficient

value: APTX mutant


title: L938

description: APTX deficient


title: C2ABR

description: APTX proficienct


title: Mouse Dendritic cells in IFNAR mice on day 4 following IAV infection, replicate1

description: Mouse Dendritic cells derived from lung-draining mediastinal lymph nodes in interferon alpha receptor knock out mice on day 4 following influenza a virus (IAV) infection, replicate1


title: IRF1 KO BMDM_ M1 R848-U0126

city: Singapore

first: LEI

last: YANG

state: Singapore

address: Science Drive 4, S1A, #05-03, National University of Singapore

department: Biological Sciences

country: Singapore

institute: National University of Singapore

description:
IRF1 KO BMDM_ R848-U0126 vs NT-DMSO
Whole transcriptome data from BMDM stimulated with indicated TLR agonist and MEK1/2 inhibitors

hyb_protocol: The samples were then hybridized to GeneChip® Mouse Transcriptome Array 1.0  at 45°C for 16 h overnight, following manufacturer procedures. GeneChips post-processed were done on the AFX Fluidics 450 Station, according to all AFX protocols and procedures defined for the Mouse Transcriptome Array 1.0 (FS450_0001), as outlined in the kit manual.

scan_protocol: GeneChips were scanned on the GC3000 G7 Scanner.

data_processing: Raw microarray files were then extracted, annotated and normalized using RMA algorithm of Partek Genomic Suite (Partek Incorporated). Probe set information was then log2 transformed and consolidated at gene levels. Analysis of variance (ANOVA) was performed with contrasts set against corresponding non-treated controls.

label: biotin

source_name: IRF1 KO BMDM_ M1 R848-U0126

label_protocol: Double stranded cDNA was generated from the RNA sample using the GeneChip® WT PLUS Reagent Kit according to the manufacturer protocol. Fragmentation and end-terminus labeling of cDNAs were done using the same kit according to the manufacturer protocol.

growth_protocol: All cells were cultured cultured in Dulbecco’s modified Eagle’s medium (Gibco, Thermo Fisher Scientific) supplemented with 10% (v/v) fetal bovine serum (HyClone, Thermo Fisher Scientific) and Pen-Strep (1:100 dilution; Gibco, Thermo Fisher Scientific) at 37°C with 5% CO2.

extract_protocol: RNA isolation was performed using TRIzolTM reagent (Invitrogen, Thermo Fisher Scientific) and RNeasy® Plus Mini Kit (Qiagen) according to the manufacturer’s instructions. Genomic DNA was removed using Ambion™ DNase I (RNasefree)  (Thermo Fisher Scientific) before elution.

treatment_protocol: U026 (10 uM, Cell Signaling Technology) and DMSO control were added into fresh culture medium 1-hour before stimulation with R848 (25 ng/ml, Invivogene) for another six hours.

value: bone-marrow derived macrophages

value: 7-8 weeks


title: APTX-POS-2

description: APTX-KO U2OS cells expressing GFP-APTX

source_name: sarcoma cell line

value: APTX over expression


title: APTX-POS-1

description: APTX-KO U2OS cells expressing GFP-APTX


title: IRF1 KO BMDM_ M2 NT

description: Whole transcriptome data from BMDM stimulated with indicated TLR agonist and MEK1/2 inhibitors

source_name: IRF1 KO BMDM_ M2 NT


title: IRF1 KO BMDM_ M2 R848-U0126

source_name: IRF1 KO BMDM_ M2 R848-U0126


title: WT BMDM_ M1 R848-U0126

description:
WT BMDM_ R848-U0126 vs NT-DMSO
Whole transcriptome data from BMDM stimulated with indicated TLR agonist and MEK1/2 inhibitors


title: IRF1 KO BMDM_ M1 NT

source_name: IRF1 KO BMDM_ M1 NT


title: Mouse Dendritic cells in IFNAR mice on day 4 following  infection, replicate2

value: Day 4

value: IAV


title: Mouse Dendritic cells in WT mice on day 4 following IAV infection, replicate3

value: WT


title: WT BMDM_ M2 R848-U0126


title: APTX-KO-1

description: APTX knockout U2OS cells

value: APTX knockout


title: APTX-KO-2

description: APTX knockout U2OS cells


title: Mouse Dendritic cells in IFNAR mice on day 4 following Mock infection, replicate1

value: Mock


title: Mouse Dendritic cells in IFNLR mice on day 4 following IAV infection, replicate1_S3


title: Control-1

description: wild-type U2OS cells


title: Control-2

description: wild type U2OS cells


title: Mouse Dendritic cells in IFNAR mice on day 4 following IAV infection, replicate2


title: WT BMDM_ M2 R848

description:
WT BMDM_ R848-DMSO vs NT-DMSO
Whole transcriptome data from BMDM stimulated with indicated TLR agonist and MEK1/2 inhibitors

source_name: WT BMDM_ M2 R848


title: Mouse Dendritic cells in IFNLR mice on day 4 following IAV infection, replicate2_S4


title: WT BMDM_ M1 R848

source_name: WT BMDM_ M1 R848


title: N2_Young_Adult [miRNA-seq]

status: Public on Dec 27 2018

city: Hefei

first: Ge

last: Shan

state: Anhui

address: 443 Huangshan Road

department: School of Life Sciences

institute: University of Science and Technology of China

data_processing:
Sequencing reads were mapped to reference transcriptome by Bowtie2 (version 2.1.0)
Dupilcated reads were deplited by samtools rmdup
Genome_build: ce11

organism: Caenorhabditis elegans

source_name: whole worms

growth_protocol: Worms were grown on NGM (Nematode Growth Medium) plates seeded with OP50 at 20 ℃

extract_protocol:
RNAs from either whole worms were isolated with Trizol reagent (Invitrogen, 15596026) according to manufacturer’s instructions, then treated with RNase-free DNase I (Promega, M6101) and extracted with ethanol precipitation
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Young Adult


title: N2_L4 [miRNA-seq]


title: N2_L3 [miRNA-seq]


title: N2_L1 [miRNA-seq]


title: WT rep1 (ChIP-seq)

data_processing:
ChIP-seq reads were aligned to the TAIR10 genome assembly using bowtie2 version 2.3.4 with parameters -k 1 -N 1 -p 40 --local -q
peaks were called using macs2 version 2.1.1.20160309 with the following setting: macs2 callpeak -f BAM -p 1e-3 -g 1.2e8 --bdg --nolambda --nomodel
The macs2 bdgdiff was used to determine differentially expressed peaks between wild-type and mutant plant with default parameters.
Genome_build: TAIR10
Supplementary_files_format_and_content: bg files were generated using bedtools genomecov and were further converted to bigWig using bedGraphToBigWig

source_name: Arabidopsis seedlings

extract_protocol:
Lysates were clarified from sonicated nuclei and SUVH1-DNA complexes were isolated with anti-GFP antibody.
DNA libraries were prepared for sequencing using standard Illumina protocols

value: anti-GFP antibody


title: WT (Bisulfite-seq)

data_processing:
Illumina Casava1.7 software used for basecalling.
Bisulfite treated sequenced reads were map to TAIR10 genome assembly using Bismark v 0.19.0 bismark with parameters -N 1 -q --bowtie2 --sam -p 20
Context-dependent (CpG/CHG/CHH) methylation were extracted using bismark_methylation_extractor with parameters --paired-end --no_overlap --report --bedGraph --buffer_size 20G --cytosine_report --CX --comprehensive
bg files were generated using a python script (countc.py) and were further converted to bigWig using bedGraphToBigWig
Genome_build: TAIR10
Supplementary_files_format_and_content: Bw format files for each chromosome for each cytosine context (CG, CHG, CHH ) with following tab-separated information: Chromosome, start coordinate, stop coordinate,and methylation level (methylated cytosines sequenced/total cytosines sequenced).

extract_protocol:
Genomic DNA was extracted from 10-day-old Arabidopsis seedlings with a DNeasy Plant Mini Kit (QIAGEN, 69104)
DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Bisulfite treatment

value: seedlings


title: N2_L2 [miRNA-seq]


title: suvh1/3 (Bisulfite-seq)


title: sdj1/2/3 (Bisulfite-seq)


title: SUVH1-GFP rep2 (ChIP-seq)

value: SUVH1-GFP in wild type


title: SUVH1-GFP rep1 (ChIP-seq)


title: N2_Young_Adult [lncRNA-seq]

description:
lncRNA
lncRNA_RPKM.txt

data_processing:
Sequencing reads were mapped to reference transcriptome by Bowtie2 (version 2.1.0)
Dupilcated reads were deplited by samtools
Genome_build: ce11


title: N2_L4 [lncRNA-seq]

description:
lncRNA
lncRNA_RPKM.txt


title: N2_L3 [lncRNA-seq]

description:
lncRNA
lncRNA_RPKM.txt


title: N2_L2 [lncRNA-seq]

description:
lncRNA
lncRNA_RPKM.txt


title: N2_L1 [lncRNA-seq]

description:
lncRNA
lncRNA_RPKM.txt


title: WT BMDM_ M2 NT

source_name: WT BMDM_ M2 NT


title: undifferentiated ATDC5 cells, rep2

city: Kunming

first: Wei

last: Wang

state: Yunnan

address: NO.1088, Haiyuan Middle Road,

department: Orthodontics

institute: Kunming Medical University

description: Gene expression data from undifferentiated ATDC5 cells

hyb_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 3 out of 6 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering.

source_name: undifferentiated ATDC5 cells

growth_protocol: The murine chondrogenic cell line ATDC5 was maintained in DMEM/Ham's F-12 medium (Gibco, Grand Island, USA) with 5% FBS (Gibco, Grand Island, USA), 1% penicillin/streptomycin (Gibco, Grand Island, USA) in a humidified atmosphere at 37℃with 5% CO2.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: ATDC5 cells were treated by 1% ITS (0μg/ml recombinant human insulin, 5.5μg/ml human transferrin and 5ng/ml sodium selenite) for chondrogenic differentiation induction for 14 days.

tag: cell type

value: chondrogenic cell line

value: undifferentiated


title: undifferentiated ATDC5 cells, rep3

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.


title: undifferentiated ATDC5 cells, rep1


title: differentiated ATDC5 cells, rep2

description: Gene expression data from differentiated ATDC5 cells

source_name: differentiated ATDC5 cells

value: differentiated


title: 4GY-2

city: chengdu

first: Ting

last: Zhang

address: Chengdu Medical College, The First Affiliated Hospital, No. 278, Baoguang Road, Chengdu, Sichuan 610500, China.

department: The First Affiliated Hospital of Chengdu Medical College

institute: Clinical Laboratory

data_processing:
circRNA: The high quality reads were aligned to the reference genome/transcriptome with STAR software (v2.5.1b) and circRNAs were detected and identified with DCC software (v0.4.4). edgeR software (v3.16.5) was used to normalized the data and perform differentially expressed circRNA analysis. GO and KEGG analysis were performed for the differentially expressed circRNA-associated genes.
LncRNA & mRNA: The high quality reads were aligned to the human reference genome (UCSC hg19) with hisat2 software (v2.0.4). Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (v2.2.1, part of cufflinks) was used to get the FPKM as the expression profiles of LncRNA and mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed LncRNA and mRNA were identified.
Genome_build: hg19
Supplementary_files_format_and_content: Number of raw junction read

extract_protocol:
total RNA was used for removing the rRNAs using Ribo-Zero rRNA Removal Kits (Illumina, USA)
RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, USA)

value: A549 cell


title: 4GY-1


title: 2GY-1


title: 2GY-3


title: 2GY-2


title: 0GY-3


title: differentiated ATDC5 cells, rep3


title: differentiated ATDC5 cells, rep1


title: WT BMDM_ M1 NT

source_name: WT BMDM_ M1 NT


title: 0GY-1


title: 4GY-3


title: 0GY-2


title: Group3, before treatment, rep2

city: Guangzhou

first: Yuchen

last: Jiang

state: Guangdong

address: 600 Tianhe Road

institute: Third Affiliated Hospital of Sun Yat-sen University

data_processing:
Solexa pipeline version 1.8（Off-Line Base Caller software, version 1.8） used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh37 whole genome using Hisat2 v2.1.0
FPKM (ơFragments Per Kilobase of gene/transcript model per Million mapped fragments) were calculated using Ballgown v2.8.4.
Genome_build: GRCh37
Supplementary_files_format_and_content: Differentially expressed genes between groups.

source_name: Group3_before treatment

extract_protocol:
The RNA extraction from PBCs were using PAXgene blood RNA kit.
KAPA Stranded RNA-Seq Library Prep Kit(Illumina)

tag: subject status

value: acne patients

tag: subject group

value: group3:3 without obvious changes

tag: time point

value: before treatment

value: peripheral blood


title: Group2, after treatment, rep1

source_name: Group2_after treatment

value: group2:4 with improvement

value: after treatment


title: Group4, rep2

value: healthy control

value: group4:healthy control


title: Group3, before treatment, rep1


title: Group2, before treatment, rep1

source_name: Group2_before treatment


title: Group3, after treatment, rep3

source_name: Group3_after treatment


title: Group2, before treatment, rep3


title: Group3, after treatment, rep1


title: Group4, rep3


title: Group2, after treatment, rep2


title: Group3, after treatment, rep2


title: Group2, before treatment, rep2


title: Group2, before treatment, rep4


title: Group4, rep1


title: Group3, before treatment, rep3


title: Group2, after treatment, rep4


title: Group1, after treatment, rep4

source_name: Group1_after treatment

value: group1:4 with flare-up


title: Group2, after treatment, rep3


title: Group1, after treatment, rep2


title: Group1, before treatment, rep4

source_name: Group1_before treatment


title: Group1, after treatment, rep3


title: Group1, before treatment, rep3


title: Group1, before treatment, rep2


title: Group1, after treatment, rep1


title: PDS DRIP-seq 1

city: Bologna

first: Giovanni

last: Capranico

state: BO

address: Via Selmi 3

department: FABIT

country: Italy

institute: University of Bologna

data_processing:
Adapters trimming performed with Trimmomatic version 0.35
Reads mapping on human genome (hg19) performed with BWA version 0.7.12 with parameters -n 2 -t 8
Reads filtering by Merged Consensus blacklist fron ENCODE (ftp://encodeftp.cse.ucsc.edu/users/akundaje/rawdata/blacklists/hg19/wgEncodeHg19ConsensusSignalArtifactRegions.bed.gz) and duplicates removal with Samtools version 1.3.1
Peak calling performed with MACS2 version 2.1.1.20160309 with parameters -q 0.05 -m 5 50 -g hs -f BAMPE
Genome_build: hg19
Supplementary_files_format_and_content: Bed files produced by macs2

source_name: U2OS cells

growth_protocol: U2OS cells were grown in Dulbecco's modified Eagle's medium (DMEM, Carlo Erba Reagents) supplemented with 10% fetal bovine serum (FBS, Carlo Erba Reagents) and 2 mM L-glutamine (Carlo Erba Reagents). Cell lines were maintained by trypsinization and splitting 2-3 times a week, and incubated at 37°C in 5% CO2.

extract_protocol:
gDNA was extracted from lysated cells, digested using a restriction enzyme cocktail , incubated with S9.6 antibody and immunoprecipitated
genomic DNA were sonicated. Ligation of Illumina Truseq adapters was performed according to manufacturer’s instructions.

value: bone

tag: disease

value: osteosarcoma

tag: antibody


title: PDS DRIP-seq 2

tag: tissue


title: Group1, before treatment, rep1


title: FG DRIP-seq 1


title: Control DRIP-seq 2


title: FG DRIP-seq 2


title: Control DRIP-seq 1


title: Rptor KO rep1 (scRNA-seq)

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

data_processing:
The Cell Ranger 1.3 Single-Cell Software Suite (10x Genomics) was implemented to process the raw sequencing data from the Illumina HiSeq run.
This pipeline performed de-multiplexing,  alignment (mm10), and barcode processing to generate gene-cell matrices used for downstream  analysis.
Genome_build: mm10
Supplementary_files_format_and_content: cell ranger count matrix for single cells in each sample

source_name: Rptor KO, spleen

extract_protocol:
Mice were immunized with MOG. TCRb+YFP+ cells from spleen at day 9 post-immunization sorted on an iCyt Reflection cell sorter. The cells were counted and examined for viability using a Luna Dual Florescence Cell Counter (Logos Biosystems). All samples were spun down at 2,000 rpm for 5 min. The supernatant was removed, and cells were re-suspended in 100 ul of 1× PBS (Thermo Fisher Scientific) + 0.04% BSA (Amresco)
Single-cell suspensions were loaded onto the Chromium Controller according to their respective cell counts to generate 6000 single cell  GEMs (gel beads in emulsion) per sample. Libraries were prepared using the Chromium Single Cell 3’ v2 Library and Gel Bead Kit (10x  Genomics)

value: Spleen

value: TCRb+YFP+ cells

tag: age

value: 6-10 weeks

tag: genotype


title: Het rep2 (scRNA-seq)

source_name: Het, spleen

value: Het


title: Het rep3 (scRNA-seq)


title: Spl-Het-rep2

data_processing:
reads trimmed using cutadapt (version 1.9) and aligned using BWA32 (version 0.5.9-r26-dev, default parameter), duplicated reads were then marked with Picard (version 1.65 (1160))
only non-duplicated reads kept by samtools (parameter “-q 1 -F 1024” version 0.1.18)
peak calling for nucleosome-free reads by MACS234 (version 2.1.0.20150603)
Genome_build: mm9 (NCBIM37)
Supplementary_files_format_and_content: Consensus peaks and fragment counts for all samples

source_name: Spl-Het

extract_protocol:
Mice were immunized with MOG as described above. TCRb+YFP+ cells were sorted from dLN or spleen at day 9 post-immunization
Cells were lysed in 50 ml ATAC-Seq lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) on ice for 10 min. Resulting nuclei were pelleted at 500 g for 10 min at 4°C. Supernatant was carefully removed with a pipette and discarded. The pellet was resuspended in 50 ml transposase reaction mix (25 ml 2× TD buffer, 22.5 ml nuclease-free water, 2.5 ml Transposase) and incubated for 30 min at 37°C

value: WT


title: Spl-KO-rep3

source_name: Spl-KO


title: dLN-KO-rep4

source_name: dLN-KO

value: dLN


title: Spl-KO-rep5


title: Rptor KO rep3 (scRNA-seq)


title: dLN-Het-rep4

source_name: dLN-Het


title: Spl-Het-rep4


title: Spl-KO-rep4


title: Rptor KO rep2 (scRNA-seq)


title: dLN-KO-rep5


title: Spl-KO-rep2


title: dLN-Het-rep2


title: dLN-KO-rep2


title: Het rep1 (scRNA-seq)


title: dLN-KO-rep1


title: Spl-Het-rep1


title: dLN-KO-rep3


title: dLN-Het-rep1


title: Spl-Het-rep3


title: Spl-KO-rep1


title: dLN-Het-rep3


title: A375 DMSO 24 hr Replicate 2

city: North Chicago

first: Xin

last: Lu

state: IL

address: 1 North Waukegan Rd

department: Oncology Discovery

institute: Abbvie

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Genechip Scanner 3000

data_processing: Background subtraction, normalization and gene expression index calculation were performed using Rosetta Resolver software

source_name: A375 cells treated with vehicle for 24 hours

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA (using Affymetrix 3' IVT Plus amplification kit).

growth_protocol: Melanoma cell lines were grown in RPMI with 10% FBS.

extract_protocol: Qiazol extraction of total RNA followed by Qiagen Rneasy purification was performed according to the manufacturer's instructions.

treatment_protocol: Cells were treated with or without A-485 for the indicated time.

tag: treatment

value: A375 DMSO 24 hr


title: WM2664 DMSO 24 hr Replicate 1

source_name: WM2664 cells treated with vehicle for 24 hours

value: DMSO 24 hr


title: A375 A-485 3.0 mM 24 hr Replicate 1

source_name: A375 cells treated with A-485 for 24 hours


title: WM2664 DMSO 6 hr Replicate 1

source_name: WM2664 cells treated with vehicle for 6 hours

value: DMSO 6 hr


title: A375 DMSO 6 hr Replicate 1

source_name: A375 cells treated with vehicle for 6 hours

value: A375 DMSO 6 hr


title: SKMEL5 DMSO 24 hr Replicate 2

source_name: SKMEL5 cells treated with vehicle for 24 hours


title: SKMEL5 DMSO 6 hr Replicate 1

source_name: SKMEL5 cells treated with vehicle for 6 hours


title: SKMEL5 DMSO 6 hr Replicate 2


title: WM2664 DMSO 24 hr Replicate 2


title: A375 DMSO 24 hr Replicate 1


title: A375 DMSO 6 hr Replicate 2


title: WM2664 DMSO 6 hr Replicate 2


title: SKMEL5 A-485 3.0 mM 24 hr Replicate 1

source_name: SKMEL5 cells treated with A-485 for 24 hours


title: SKMEL5 A-485 3.0 mM 6 hr Replicate 1

source_name: SKMEL5 cells treated with A-485 for 6 hours

value: 3.0 mM 6 hr


title: WM2664 A-485 3.0 mM 6 hr Replicate 1

source_name: WM2664 cells treated with A-485 for 6 hours


title: A375 A-485 3.0 mM 6 hr Replicate 1

source_name: A375 cells treated with A-485 for 6 hours


title: WM2664 A-485 3.0 mM 24 hr Replicate 1

source_name: WM2664 cells treated with A-485 for 24 hours


title: genomic_changes_due_to_re-replication_at_ChrIV 567 kb_10

type: genomic

city: San Francisco

first: duyen

last: Bui

state: CALIFORNIA

address: 600 16th street

institute: UCSF

description: Supp. Figure 1

hyb_protocol: 90% of the re-replicating DNA preparation and 1 µg of the reference DNA were labeled, respectively, with Cy3 and Cy5 fluorescent dye (Fisher Scientific 45-001-270).  The Cy3 and Cy5 labeled DNA were isolated, combined and applied to an in-house printed microarray. Hybridization was performed in 3X SSC, 25mM HEPES pH7.0, 0.25% SDS at 63oC for 18 to 24 hours.

scan_protocol: Arrays were then scanned using an Axon Scanner 4B.  GenePix Pro6.0 and BatchReplicationAnalyzer4.2 were then used to generate copy number information across the genome.

data_processing: Data were filtered in GenePix to flag as bad features that had (1) obvious defects, (2) saturated pixels, (3) regression r^2 values less than 0.5 or (4) fewer than 55% of their pixels with flourescence intensity greater than 2 standard deviations above background. BLAST analysis was used to generate a filter that would flag as bad elements whose PCR product were excessively repetitive. Raw Cy5/Cy3 median of ratios values were normalized such that the average ratio was equal to 1.

source_name: negative control M ARS317+ 1089 strain in G2/M

label_protocol: amino-allyl-dUTP incorporation with Klenow. Chemical coupling of dye to aa-dUTP labelled DNA.

extract_protocol: DNA was purified by organic extraction and ethanol precipitation. This re-replicating genomic DNA was prepared by Method 1 as described in a previous publication from Joachim Li's lab: Finn and Li JJ PloS Genetics 2013.

tag: yjl number

tag: gal induction

source_name: YJL11124_a MC2A strain with ars317-567 kb lys2InsEA14-CAN1- 1081 kb  in G2/M induced in galactose for 3 h

tag: galactose induction

value: re-replication at ChrIV 567 kb


title: genomic_changes_due_to_re-replication_at_ChrIV 567 kb_5

description: Supp. Figure 1

source_name: YJL11112_a MC2A strain with ars317-567 kb lys2InsEA14-CAN1- 637 kb  in G2/M induced in galactose for 3 h


title: genomic_changes_due_to_re-replication_at_ChrIV 567 kb_9

description: Supp. Figure 1

source_name: negative control MC2A strain in G2/M

source_name: YJL11123_a MC2A strain with ars317-567 kb lys2InsEA14-CAN1- 1081 kb  in G2/M induced in galactose for 3 h


title: Positive_control_genomic_changes_due_to_re-replication_at_ChrIV 567 kb_1

description: Supp. Figure 1

source_name: Positive control YJL8363_a MC2A ars317-567kb strain in G2/M induced in galactose for 3 h


title: genomic_changes_due_to_re-replication_at_ChrIV 567 kb_3

description: Supp. Figure 1

source_name: YJL11111_a MC2A strain with ars317-567 kb lys2InsEA14-CAN1- 637 kb  in G2/M induced in galactose for 3 h


title: genomic_changes_due_to_re-replication_at_ChrIV 567 kb_6

description: Supp. Figure 1

source_name: YJL11117_a MC2A strain with ars317-567 kb lys2InsEA14-CAN1- 795 kb  in G2/M induced in galactose for 3 h


title: genomic_changes_due_to_re-replication_at_ChrIV 567 kb_7

description: Supp. Figure 1


title: Positive_control_genomic_changes_due_to_re-replication_at_ChrIV 567 kb_2

description: Supp. Figure 1


title: genomic_changes_due_to_re-replication_at_ChrIV 567 kb_1

description: Supp. Figure 1

source_name: YJL11108_a MC2A strain with ars317-567 kb lys2InsEA14-CAN1- 570 kb  in G2/M induced in galactose for 3 h


title: genomic_changes_due_to_re-replication_at_ChrIV 567 kb_4

description: Supp. Figure 1


title: genomic_changes_due_to_re-replication_at_ChrIV 567 kb_2

description: Supp. Figure 1


title: genomic_changes_due_to_re-replication_at_ChrIV 567 kb_8

description: Supp. Figure 1

source_name: YJL11118_a MC2A strain with ars317-567 kb lys2InsEA14-CAN1- 795 kb  in G2/M induced in galactose for 3 h


title: SKMEL5 DMSO 24 hr Replicate 1

source_name: SKMEL5 cells treated with vehicle for 24 hours

tag: cell line


title: Gcm1_Con-1_ChIPSeq

city: taiyuan

first: Li

middle: jian

last: ting

state: shanxi province taiyuan city

institute: Shanxi Medical University

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using EasyAlign version 3.2 with the following configurations…
Data were filtered using the following specifications…
peaks were called using PeaksFind version 2.2 with the following setting: ChIP threshold (0.2), Enrichment Fold (2), Rescue Fold
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using MACS

source_name: C57BL/6C embryonic stem cells with foalte deficiency

growth_protocol: Folate (Sigma-Aldrich, MO, USA) was prepared in Dulbecco’s Modified Eagle’s Medium low-glucose medium (Sigma-Aldrich), 3.7% filtered sodium hydrogen carbonate (Beijing Chemical Reagent Company, China), and UltraPure™ Distilled Water (Invitrogen, Carlsbad, USA) at a final concentration of 4 mg/ml as our normal control, as described in previous papers(a). After seeding onto culture dishes coated with 0.2% gelatin (Sigma-Aldrich),MEF were cultured in Dulbecco’s modified Eagle’s medium (Sigma-Aldrich) supplemented with 0.1 mM non-essential amino acids, 0.1 mM glutamate, and 10% fetal bovine serum (Invitrogen, Carlsbad, USA) overnight. C57BL/6C mESC were cultured in the following complete medium: Dulbecco’s Modified Eagle’s Medium low-glucose medium (Sigma-Aldrich), UltraPure™ Distilled Water (Invitrogen, Carlsbad, USA), 1 mM high glucose, 0.1 mM non-essential amino acids, 0.1 mM glutamate, 15% fetal bovine serum (Invitrogen, Carlsbad, USA), 0.1 mM β-mercaptoethanol (Life Technology), 1000 U/ml leukemia inhibitory factor (Millipore, USA), and 4 mg/ml folate on the MEF cells.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: With no folate supplyment in in Dulbecco’s Modified Eagle’s Medium low-glucose medium

value: SCRC-1002 embryonic stem cells

tag: passages

tag: strain

tag: chip antibody

value: GCM1 (Santa Cruz,sc-101173)


title: Con-1_InputDNA

source_name: C57BL/6C embryonic stem cells with normal folate

tag: cell type


title: IgG_Con_ChIPSeq

value: normal mouse IgG(Santa Cruz,sc-2025)


title: Con-2_Input DNA


title: Gcm1_Case-2_ChIPSeq


title: Case-2_InputDNA


title: Case-1_InputDNA


title: Gcm1_Con-2_ChIPSeq


title: Gcm1_Case-1_ChIPSeq


title: IgG_Case_ChIPSeq


title: ACCLAIM_312337_0_PD1

city: Bethesda

first: Tielin

last: Qin

state: MD

address: 7500 Old Georgetown Road, Suite 800

institute: Immune Tolerance Network

description:
RNAseq_PD1_raw_counts.csv
RNAseq_PD1_norm_counts.csv

data_processing:
Base-calling was performed automatically by Illumina real time analysis software and demultiplexing was performed on Illumina BaseSpace.
Hard trimming was performed in Galaxy; 1 3'-end base was removed from all reads using the FASTQ Trimmer tool (v1.0.0)
Quality-based trimming was performed in Galaxy; reads were trimmed from both ends using the FASTQ Quality Trimmer tool (v1.0.0) until minimum base quality for each read was >= 30.
Reads were aligned in Galaxy using bowtie and TopHat (Tophat for Illumina tool, v.1.4.1)
Read counts per Ensembl gene ID were computed in Galaxy using htseq-count (htseq-count tool, v.0.4.1).
Sequencing, alignment, and quantitation metrics were obtained for FASTQ, BAM/SAM, and count files in Galaxy using FastQC, Picard, TopHat, Samtools, and htseq-count.
Genome_build: GRCh38
Supplementary_files_format_and_content: raw_counts: Read counts mapped to Ensembl IDs as quantified by htseq-count.
Supplementary_files_format_and_content: norm_counts: Lowly expressed genes and non-protein coding genes were filtered out and the Ensembl gene IDs mapped to MGI gene symbols. Count data was normalized using TMM (Robinson & Oshlack, 2010).

source_name: PBMC

extract_protocol:
500 cells were sorted directly into lysis buffer on a BD FACSAria Fusion flow cytometer. cDNA was constructed per instructions with the Takara SMART-Seq v4 Ultra Low Input RNA Kit.
Libraries were constructed for RNA-seq using standard Illumina protocols.

tag: participantid

tag: visitnumber

tag: barcode

tag: randomized treatment

value: Placebo

tag: Sex

value: Female

tag: race

value: White


title: ACCLAIM_496198_0_PD1

value: Abatacept

tag: age


title: ACCLAIM_536297_0_PD1


title: ACCLAIM_312337_7_PD1


title: ACCLAIM_496198_7_PD1


title: ACCLAIM_931903_7_PD1

value: Black or African American


title: ACCLAIM_536297_7_PD1


title: ACCLAIM_496198_15_PD1


title: ACCLAIM_931903_0_PD1


title: ACCLAIM_815412_0_PD1


title: SC_KM06 [Single Cell RNA-seq]

city: New York

last: Rendl

address: 1428 Madison Avenue

institute: Mount Sinai School of Medicine

description:
processed data file : E15.0_Mesenchymal cells_scRNAseq_Final.csv
KM06_AHN5JMBGX3_S3

data_processing:
(Bulk RNA-seq) All raw RNA sequencing reads were mapped to the mouse genome (mm10) with TopHat v2.0.3 coupled with the Bowtie2 aligner with default parameters. Transcriptomes were assembled and fragments per kilo-base per million reads (FPKM) for each gene were computed with Cufflinks v2.1.1 with default parameters.
(Single Cell RNA-seq) Paired end reads obtained by automated CEL-seq2 were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mm10 mouse genome release downloaded from the UCSC genome browser. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to a sample specific barcode followed by a 4bp unique molecular identifier (UMI). The remainder of the left read contains a polyT stretch followed by a number (<40) of transcript derived bases.
Genome_build: mm10
Supplementary_files_format_and_content:
(Bulk RNA-seq) E15.0_bulkRNAseq.xlsx: Tab separated file for all sequencing libraries combined, listing all genes (rows) and the number of sequenced unique transcripts for all samples. Column name indicates the sorted cell type (each sorted cell type has two biological replicates). The first column lists the official gene symbol.
(Single Cell RNA-seq) E15.0_Mesenchymal cells_scRNAseq.csv: Tab separated data file for all sequencing libraries combined, listing all genes (rows) and the number of sequenced unique transcripts for all samples (including 16 blank wells/plate, called ERCC). Column name indicates the cell type determined from index sorting,  sample number,followed by the cell number of the library, all separated by underscores (i.e. Cell Type_Sample_Cell Number). The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore.

source_name: Single Cell RNA-seq

extract_protocol:
Cells were sorted into 5µl Vapor-Lock (Qiagen) containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius for 5 minutes. mRNA was then reverse transcribed by adding RT mix.
RNA was processed by SORT-Seq, an automated version of the previously described Cel-Seq2 technique. Libraries were sequenced on a Illumina NextSeq500 using 75bp paired end sequencing.

tag: developemental stage

tag: tissue

value: backskin

value: single cell


title: SC_KM05 [Single Cell RNA-seq]

description:
processed data file : E15.0_Mesenchymal cells_scRNAseq_Final.csv
KM05_AHN5JMBGX3_S2


title: SC_KM09 [Single Cell RNA-seq]

description:
processed data file : E15.0_Mesenchymal cells_scRNAseq_Final.csv
allKM9_S1


title: SC_KM07 [Single Cell RNA-seq]

description:
processed data file : E15.0_Mesenchymal cells_scRNAseq_Final.csv
KM12_AHN5JMBGX3_S5


title: SC_KM08 [Single Cell RNA-seq]

description:
processed data file : E15.0_Mesenchymal cells_scRNAseq_Final.csv
allKM8_S1


title: SC_KM04 [Single Cell RNA-seq]

description:
processed data file : E15.0_Mesenchymal cells_scRNAseq_Final.csv
allKM4_S4


title: ACCLAIM_931903_15_PD1


title: ACCLAIM_815412_7_PD1


title: ACCLAIM_673379_7_PD1


title: ACCLAIM_673379_15_PD1


title: SC_KM03 [Single Cell RNA-seq]

description:
processed data file : E15.0_Mesenchymal cells_scRNAseq_Final.csv
KM03_AHN5JMBGX3_S1


title: ACCLAIM_139519_7_PD1


title: ACCLAIM_673379_0_PD1


title: SC_KM02 [Single Cell RNA-seq]

description:
processed data file : E15.0_Mesenchymal cells_scRNAseq_Final.csv
KM2_AH7CM3BGX3_S3


title: ACCLAIM_139519_0_PD1


title: vBM_MSC.r3_S3_R1_001.170913_NB501621_0172_AHHL7JBGX3

city: Suita

first: Takashi

last: Shimbo

state: Osaka

address: 2-2 Yamadaoka

country: Japan

institute: Osaka university

description: vBM_MSC_R12_001_sorted.dedup.posshift_sorted.rm_blacklist.no_gcnorm.atacseq.bedgraph, vBM_MSC.no_gcnorm_peaks.atacseq.narrowPeak

data_processing:
RNA-seq data are aligned using RSEM, the params: rsem-calculate-expression --paired-end --star --star-gzipped-read-file --output-genome-bam --append-names -p 8
ATAC-seq reads are trimmed using TrimGalore, the params: trim_galore --stringency 5 --gzip --paired --trim1 --length 30 -q 0
ATAC-seq reads are aligned using Bowtie, the params: --threads 3 -m 1 -v 2 -S -I 0 -X 2000
ATAC-seq deduplication is done using Picard MarkDuplicates, the params: REMOVE_DUPLICATES=TRUE
ATAC-seq  data to account for Tn5 transposon cleavage position in the mapped reads, we shifted the mapped reads by +4/-5bp depending on the strand, using our own code
ATAC-seq data we remove the black list region using: bedtools intersect
ATAC-seq peak calling  was performed using MACS2 with parameters: macs2 callpeak --nomodel --nolambda --keep-dup all --call-summits
ATAC-seq bedgraph was performed using MACS2 pileup using default parameters
Genome_build: mm10
Supplementary_files_format_and_content: genes.results' file are generated using RSEM mapper, column include read count in Exp.count, TPM, and FPKM normalization. The narrowPeak file are generated using MACS2 callpeaks, the values include peak abundance. The bedgraph file are created using MACS2 pileup, the values include genomic position and peak abundance.

source_name: Vertebral MSC

growth_protocol: Mouse bone marrow-derived MSCs were isolated from femur and vertebrae bone marrow and cultured with MesenCult medium (STEM CELL technologies). For lung and adipose-derived MSCs,, tissues were minced and treated with collagenase (Wako) at 37°C for 30 min. After removing red blood cells, cells were cultured with MesenCult medium.

extract_protocol: RNA-seq library was constructed using smart-seq2. ATAC-seq library was constructed by the FAST-ATAC protocol.

value: mesenchymal stem cell


title: SC_KM01 [Single Cell RNA-seq]

description:
processed data file : E15.0_Mesenchymal cells_scRNAseq_Final.csv
KM1_AH3K7MBGX3_S3


title: ACCLAIM_911284_15_PD1


title: vBM_MSC.r3_S3_R1_001.170908_NB501621_0169_AHHLJ3BGX3


title: ACCLAIM_911284_7_PD1


title: vBM_MSC.r2_S2_R1_001.170913_NB501621_0172_AHHL7JBGX3


title: ACCLAIM_911284_0_PD1


title: ACCLAIM_159059_0_PD1


title: ACCLAIM_795063_15_PD1


title: ACCLAIM_856452_7_PD1


title: ACCLAIM_159059_7_PD1


title: ACCLAIM_795063_7_PD1


title: vBM_MSC.r1_S1_R1_001.170908_NB501621_0169_AHHLJ3BGX3


title: vBM_MSC.r1_S1_R1_001.170913_NB501621_0172_AHHL7JBGX3


title: ACCLAIM_856452_0_PD1


title: fBM_MSC.r3_S6_R1_001.170913_NB501621_0172_AHHL7JBGX3

description: fBM_MSC_R12_001_sorted.dedup.posshift_sorted.rm_blacklist.no_gcnorm.atacseq.bedgraph, fBM_MSC.no_gcnorm_peaks.atacseq.narrowPeak

source_name: Femur MSC


title: fBM_MSC.r3_S6_R1_001.170908_NB501621_0169_AHHLJ3BGX3


title: fBM_MSC.r1_S4_R1_001.170913_NB501621_0172_AHHL7JBGX3


title: fBM_MSC.r2_S5_R1_001.170908_NB501621_0169_AHHLJ3BGX3


title: ACCLAIM_903842_7_PD1


title: fBM_MSC.r2_S5_R1_001.170913_NB501621_0172_AHHL7JBGX3


title: ACCLAIM_795063_0_PD1


title: fBM_MSC.r1_S4_R1_001.170908_NB501621_0169_AHHLJ3BGX3


title: vBM_MSC.r2_S2_R1_001.170908_NB501621_0169_AHHLJ3BGX3


title: P_MSC.r3_S9_R1_001.170913_NB501621_0172_AHHL7JBGX3

description: P_MSC_R12_001_sorted.dedup.posshift_sorted.rm_blacklist.no_gcnorm.atacseq.bedgraph,  P_MSC.no_gcnorm_peaks.atacseq.narrowPeak

source_name: Pulmonary MSC


title: ACCLAIM_903842_0_PD1


title: ACCLAIM_626637_7_PD1


title: ACCLAIM_626637_0_PD1


title: P_MSC.r2_S8_R1_001.170913_NB501621_0172_AHHL7JBGX3


title: P_MSC.r3_S9_R1_001.170908_NB501621_0169_AHHLJ3BGX3


title: P_MSC.r2_S8_R1_001.170908_NB501621_0169_AHHLJ3BGX3


title: ACCLAIM_864448_15_PD1

value: Male


title: P_MSC.r1_S7_R1_001.170913_NB501621_0172_AHHL7JBGX3


title: ACCLAIM_903842_15_PD1


title: ACCLAIM_864448_7_PD1


title: P_MSC.r1_S7_R1_001.170908_NB501621_0169_AHHLJ3BGX3


title: ACCLAIM_768526_7_PD1


title: A_MSC.r3_S12_R1_001.170913_NB501621_0172_AHHL7JBGX3

description: A_MSC_R12_001_sorted.dedup.posshift_sorted.rm_blacklist.no_gcnorm.atacseq.bedgraph, A_MSC.no_gcnorm_peaks.atacseq.narrowPeak

source_name: Adipose MSC


title: A_MSC.r2_S11_R1_001.170913_NB501621_0172_AHHL7JBGX3


title: ACCLAIM_119004_7_PD1


title: A_MSC.r2_S11_R1_001.170908_NB501621_0169_AHHLJ3BGX3


title: A_MSC.r3_S12_R1_001.170908_NB501621_0169_AHHLJ3BGX3


title: ACCLAIM_119004_0_PD1


title: ACCLAIM_349885_7_PD1


title: ACCLAIM_937612_15_PD1


title: vBM_MSC.r3_S3_R1_001.170911_NB501621_0170_AHHJF7BGX3


title: vBM_MSC.r2_S2_R1_001.170911_NB501621_0170_AHHJF7BGX3


title: A_MSC.r1_S10_R1_001.170913_NB501621_0172_AHHL7JBGX3


title: ACCLAIM_119004_15_PD1


title: ACCLAIM_349885_0_PD1


title: A_MSC.r1_S10_R1_001.170908_NB501621_0169_AHHLJ3BGX3


title: vBM_MSC.r1_S1_R1_001.170911_NB501621_0170_AHHJF7BGX3


title: fBM_MSC.r3_S6_R1_001.170911_NB501621_0170_AHHJF7BGX3


title: ACCLAIM_937612_7_PD1


title: fBM_MSC.r2_S5_R1_001.170911_NB501621_0170_AHHJF7BGX3


title: ACCLAIM_937612_0_PD1


title: ACCLAIM_864448_0_PD1


title: P_MSC.r3_S9_R1_001.170911_NB501621_0170_AHHJF7BGX3


title: P_MSC.r2_S8_R1_001.170911_NB501621_0170_AHHJF7BGX3


title: ACCLAIM_750328_7_PD1


title: ACCLAIM_415432_15_PD1


title: ACCLAIM_750328_0_PD1


title: ACCLAIM_415432_7_PD1


title: P_MSC.r1_S7_R1_001.170911_NB501621_0170_AHHJF7BGX3


title: ACCLAIM_768526_0_PD1


title: ACCLAIM_527582_7_PD1


title: ACCLAIM_527582_0_PD1


title: A_MSC.r2_S11_R1_001.170911_NB501621_0170_AHHJF7BGX3


title: ACCLAIM_763271_7_PD1


title: ACCLAIM_360231_0_PD1


title: ACCLAIM_360231_7_PD1


title: A_MSC.r1_S10_R1_001.170911_NB501621_0170_AHHJF7BGX3


title: alveolar macrophage-LPS-4hr-2

city: Seongnam-si

first: Daun

last: Jung

state: Gyeonggi-do

address: Bundang-gu, 삼평동 689

institute: CHA Bundang Medical Center

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: alveolar macrophage-LPS-4hr-2

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: mice of 7~12 wks of age were injected intraperitoneally (i.p) with LPS (20 mg/kg) for 1hr or 4hr

value: Lung

tag: agent

value: LPS

tag: time point

tag: marker


title: alveolar macrophage-LPS-4hr-1

source_name: alveolar macrophage-LPS-4hr-1


title: ACCLAIM_763271_0_PD1


title: alveolar macrophage-LPS-4hr-3

source_name: alveolar macrophage-LPS-4hr-3


title: ACCLAIM_987582_15_PD1


title: alveolar macrophage-LPS-1hr-3

source_name: alveolar macrophage-LPS-1hr-3


title: alveolar macrophage-LPS-1hr-2

source_name: alveolar macrophage-LPS-1hr-2


title: ACCLAIM_987582_7_PD1


title: alveolar macrophage-LPS-1hr-1

source_name: alveolar macrophage-LPS-1hr-1


title: fBM_MSC.r1_S4_R1_001.170911_NB501621_0170_AHHJF7BGX3


title: alveolar macrophage naïve-2

source_name: alveolar macrophage naïve-2


title: alveolar macrophage naïve-1

source_name: alveolar macrophage naïve-1


title: A_MSC.r3_S12_R1_001.170911_NB501621_0170_AHHJF7BGX3


title: ACCLAIM_519740_0_PD1


title: alveolar macrophage naïve-3

source_name: alveolar macrophage naïve-3


title: ACCLAIM_987582_0_PD1


title: Kupffer cell-LPS-4hr-2

source_name: Kupffer cell-LPS-4hr-2

value: Liver


title: ACCLAIM_519740_7_PD1


title: ACCLAIM_509364_7_PD1


title: Kupffer cell-LPS-4hr-1

source_name: Kupffer cell-LPS-4hr-1


title: Kupffer cell-LPS-4hr-3

source_name: Kupffer cell-LPS-4hr-3


title: ACCLAIM_509364_0_PD1

source_name: PBMC


title: ACCLAIM_360231_15_PD1


title: ACCLAIM_578949_7_PD1


title: ACCLAIM_526007_15_PD1


title: ACCLAIM_578949_0_PD1


title: Kupffer cell-LPS-1hr-2

source_name: Kupffer cell-LPS-1hr-2


title: Kupffer cell-LPS-1hr-1

source_name: Kupffer cell-LPS-1hr-1


title: ACCLAIM_526007_7_PD1


title: ACCLAIM_526007_0_PD1


title: ACCLAIM_509364_15_PD1


title: Kupffer cell naïve-2

source_name: Kupffer cell naïve-2


title: Kupffer cell-LPS-1hr-3

source_name: Kupffer cell-LPS-1hr-3


title: ACCLAIM_264812_7_PD1


title: Kupffer cell naïve-1

source_name: Kupffer cell naïve-1


title: ACCLAIM_264812_0_PD1


title: ACCLAIM_323548_15_PD1


title: AB5493

city: Rehovot

first: Yaniv

last: Lubling

address: POB 26

country: Israel

institute: Weizmann Institute of Science

description: Amp batch AB5493

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Note: Second read contained only cell and molecule barcodes. This information was appended to the fastq entry header
UMI counting was performed using the pipeline described in Jaitin et al. 2014 (10.1126/science.1247651)
Note: UMI counts are supplied here, raw sequences are availiable at Europena Genome-phenome Archive (EGA).
Genome_build: hg19
Supplementary_files_format_and_content: T_cells_tcrb.txt: tab-delimited table with the TCRb clonal membership data of the T cells in this study.

source_name: Immune cells sorted from melanoma tumors

extract_protocol:
Cells were digested to form a single cell suspension and FACS sorted into capture plates
3' end mRNA libraries were prepared for sequencing using MARS-seq2.0 - improvements to MARS-seq (Jaitin et al, Science 2014)
single cell RNA-seq for gene expression quantification

treatment_protocol: All samples were dissected from patients and digested into single cell suspension

tag: plate id

tag: amplification batch

tag: sample source

value: PBMC

tag: patient id

tag: facs gate


title: AB5494

description: Amp batch AB5494


title: ACCLAIM_323548_7_PD1

tag: participantid

tag: cell type


title: AB5492

description: Amp batch AB5492

value: CCR7+ CD45RA+


title: AB5491

description: Amp batch AB5491

value: CD3 & CD45


title: ACCLAIM_323548_0_PD1

tag: visitnumber

tag: barcode


title: AB5429

description: Amp batch AB5429


title: AB5490

description: Amp batch AB5490


title: Kupffer cell naïve-3

source_name: Kupffer cell naïve-3

tag: strain


title: AB5427

description: Amp batch AB5427


title: CD56dimCD57plus_D5

city: Columbus

first: Patrick

middle: Leonard

last: Collins

state: OH

address: 770 BRT,  460 W 12th Ave

department: Microbial Infection and Immunity

institute: Ohio State University

data_processing:
ChIP-seq reads were aligned ot the hg19 genome assemply using NovaAlign with the following options:-r None -l 30 -e 100 -i 230 140
duplicates were removed using Picard markDuplicates
peaks were called using MACS2 findpeaks --broad
Bigwigs for visulazation were created using bedGraphToBigWig
RNA seq counts were determined using STAR
Genome_build: hg19

source_name: CD56dim CD57plus NK cells

extract_protocol:
Lysates were clarified from MNase treated nuclei and histone-DNA complexes were isolated with antibody. ATAC-seq were processed as per manufacturers instructions (Illumina FC-121-1030). RNA was purified using Rneasy Plus Microkit, and prepared using SMARTer Universal Low Input RNA kit (Clontech)
Nextera DNA Library Preparation Kit, Illuminia

value: CD56dimCD57plus NK

tag: individual

value: Donor 5


title: CD56dimCD57plus_D8

value: Donor 8


title: CD56dimCD57plus_D6

value: Donor 6


title: CD56dimCD57minus_D7

source_name: CD56dim CD57minus NK cells

value: CD56dimCD57minus NK

value: Donor 7


title: CD56dimCD57minus_D5


title: AB5426

description: Amp batch AB5426


title: AB5425

description: Amp batch AB5425


title: CD56bright_D7

source_name: CD56Bright NK cells

value: CD56Bright NK


title: CD56bright_D6


title: AB5197

description: Amp batch AB5197

value: Tumor


title: AB5198

description: Amp batch AB5198


title: AB5199

description: Amp batch AB5199


title: CD56bright_D8


title: ILC3_D1

source_name: tonsillular ILC3

value: Donor 1


title: AB5195

description: Amp batch AB5195


title: AB5428

description: Amp batch AB5428


title: ILC3_D3

value: Donor 3


title: AB5194

description: Amp batch AB5194


title: AB5196

description: Amp batch AB5196


title: ieILC1_D3

source_name: tonsillular ieILC1


title: AB5193

description: Amp batch AB5193


title: ieILC1_D2

value: Donor 2


title: CD56dimCD57minus_D8


title: AB5424

description: Amp batch AB5424


title: AB5192

description: Amp batch AB5192


title: AB5191

description: Amp batch AB5191


title: ieILC1_D1


title: CD56bright_D5


title: CD56dimCD57plus Donor 7 ATAC

description: DNA - accessability. Illumina FC-121-1030


title: AB5190

description: Amp batch AB5190


title: ILC3_D2


title: CD56dimCD57plus Donor 6 ATAC


title: AB5019

description: Amp batch AB5019


title: CD56dimCD57plus Donor 5 ATAC


title: AB5018

description: Amp batch AB5018


title: CD56dimCD57minus Donor 7 ATAC


title: CD56dimCD57minus Donor 6 ATAC


title: AB5016

description: Amp batch AB5016


title: Liver tissue_surgery_rep4-2

city: Urumqi

first: Chuanshan

state: Xinjiang

address: No. 137 Liyushan Road

department: Clinical Medicine Institute

institute: The First Affiliated Hospital of Xinjiang Medical University

description: LncRNA and mRNA expresssion data from matched distal-liver tissues in case 4 (AE patient)

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%)

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 6 out of 12 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs were identified through Fold Change filtering or Volcano Plot filtering. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 11.5.1). GO analysis and Pathway analysis were performed in the standard enrichment computation method.

source_name: Matched distal-liver tissues, rep4-2

label_protocol: Sample labeling was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: Periparasitic liver tissues and matched distal-liver tissues from six AE patients

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.

treatment_protocol: Liver tissues from AE patients surgery were instantly immersed in liquid nitrogen and preserved at -80 ℃.

tag: gender

value: female

tag: age

tag: diagnosis

value: alveolar echinococcosis (AE)


title: CD56dimCD57minus Donor 5 ATAC


title: Liver tissue_surgery_rep6-1

description: LncRNA and mRNA expresssion data from periparasitic liver tissues in case 6 (AE patient)

source_name: Periparasitic liver tissues, rep6-1

tag: tissue

value: Liver

value: male


title: Liver tissue_surgery_rep4-1

description: LncRNA and mRNA expresssion data from periparasitic liver tissues in case 4 (AE patient)

source_name: Periparasitic liver tissues, rep4-1


title: AB5015

description: Amp batch AB5015


title: Liver tissue_surgery_rep5-2

description: LncRNA and mRNA expresssion data from matched distal-liver tissues in case 5 (AE patient)

source_name: Matched distal-liver tissues, rep5-2


title: CD56Bright Donor 7 ATAC


title: AB5014

description: Amp batch AB5014


title: Liver tissue_surgery_rep3-2

description: LncRNA and mRNA expresssion data from matched distal-liver tissues in case 3 (AE patient)

source_name: Matched distal-liver tissues, rep3-2


title: Liver tissue_surgery_rep3-1

description: LncRNA and mRNA expresssion data from periparasitic liver tissues in case 3 (AE patient)

source_name: Periparasitic liver tissues, rep3-1


title: Liver tissue_surgery_rep6-2

description: LncRNA and mRNA expresssion data from matched distal-liver tissues in case 6 (AE patient)

source_name: Matched distal-liver tissues, rep6-2


title: CD56Bright Donor 6 ATAC


title: AB5017

description: Amp batch AB5017


title: AB5013

description: Amp batch AB5013


title: CD56Bright Donor 5 ATAC


title: Liver tissue_surgery_rep5-1

description: LncRNA and mRNA expresssion data from periparasitic liver tissues in case 5 (AE patient)

source_name: Periparasitic liver tissues, rep5-1


title: Liver tissue_surgery_rep2-2

description: LncRNA and mRNA expresssion data from matched distal-liver tissues in case 2 (AE patient)

source_name: Matched distal-liver tissues, rep2-2


title: Liver tissue_surgery_rep1-1

description: LncRNA and mRNA expresssion data from periparasitic liver tissue in case 1 (AE patient)

source_name: Periparasitic liver tissues, rep1-1


title: AB5012

description: Amp batch AB5012

source_name: Immune cells sorted from melanoma tumors


title: Liver tissue_surgery_rep1-2

description: LncRNA and mRNA expresssion data from matched distal-liver tissues in case 1 (AE patient)

source_name: Matched distal-liver tissues, rep1-2


title: Liver tissue_surgery_rep2-1

description: LncRNA and mRNA expresssion data from periparasitic liver tissues in case 2 (AE patient)

source_name: Periparasitic liver tissues, rep2-1


title: PSC27-BLEO-Oxozeaenol-treated-rep 1 [E1]

city: Shanghai

first: Yu

last: Sun

address: 320 Yueyang Rd, Life Sciences Building A #1508

department: Shanghai Institute of Nutrition and Health

institute: Chinese Academy of Sciences

description: PSC27 expression 7 days after treatment by 5 uM docetaxel for 12 hrs

hyb_protocol: One μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization,Combat between the groups of error correction and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies).

source_name: PSC27 bleomycin (50ug/ml) and Oxozeaenol (200nM)-treated, replicate 1

label_protocol: Sample labeling was performed according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a mixture of oligo(dT) and random primers (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: PSC27 cells were grown in prostate stromal cell complete (PSCC) media supplemented with 10% FBS and 1% antibiotics.

extract_protocol: Total RNAs were prepared with a RNeasy Miniprep kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: For experimental groups, cells were either treated by 50 ug/ml bleomycin for 6 hours, or co-treated by 50 ug/ml bleomycin for 6 hours with 10uM SB203580, 25nM Rapamycin or 200nM Oxozeaenol added to the media 12 hours prior to treatment and lasting for 7 consecutive days in culture vessels.

value: Normal human prostate

value: Primary stromal cells


title: ACCLAIM_536297_0_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19360

data_processing:
Base-calling was performed automatically by Illumina real time analysis software and demultiplexing was performed on Illumina BaseSpace.
Hard trimming was performed in Galaxy; 1 3'-end base was removed from all reads using the FASTQ Trimmer tool (v1.0.0)
Quality-based trimming was performed in Galaxy; reads were trimmed from both ends using the FASTQ Quality Trimmer tool (v1.0.0) until minimum base quality for each read was >= 30.
Reads were aligned in Galaxy using bowtie and TopHat (Tophat for Illumina tool, v.1.4.1)
Read counts per Ensembl gene ID were computed in Galaxy using htseq-count (htseq-count tool, v.0.4.1).
Sequencing, alignment, and quantitation metrics were obtained for FASTQ, BAM/SAM, and count files in Galaxy using FastQC, Picard, TopHat, Samtools, and htseq-count.
Genome_build: GRCh38

source_name: PBMC

value: Treg

value: PBMC

tag: randomized treatment

value: Placebo

tag: Sex

value: Female

tag: race

value: White


title: ACCLAIM_496198_15_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19354

value: Abatacept


title: PSC27-BLEO-Rapamycin-treated-rep 2 [D2]

description: PSC27 expression 7 days after treatment by 1 uM mitoxantrone for 24 hrs

source_name: PSC27 bleomycin (50ug/ml) and Rapamycin (25nM)-treated, replicate 2


title: PSC27-BLEO-Oxozeaenol-treated-rep 3 [E3]

source_name: PSC27 bleomycin (50ug/ml) and Oxozeaenol (200nM)-treated, replicate 3


title: PSC27-BLEO-Oxozeaenol-treated-rep 2 [E2]

source_name: PSC27 bleomycin (50ug/ml) and Oxozeaenol (200nM)-treated, replicate 2


title: PSC27-BLEO-Rapamycin-treated-rep 1 [D1]

source_name: PSC27 bleomycin (50ug/ml) and Rapamycin (25nM)-treated, replicate 1


title: AB5009

description: Amp batch AB5009

tag: plate id

tag: amplification batch


title: ACCLAIM_536297_7_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19363


title: AB5008

description: Amp batch AB5008

tag: sample source

tag: patient id


title: ACCLAIM_496198_7_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19351

tag: participantid


title: ACCLAIM_496198_0_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19348

tag: cell type


title: AB4367

description: Amp batch AB4367

tag: facs gate


title: AB5011

description: Amp batch AB5011


title: AB5010

description: Amp batch AB5010


title: AB4366

description: Amp batch AB4366


title: ACCLAIM_312337_7_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19345

tag: visitnumber

tag: barcode


title: PSC27-BLEO-SB203580-treated-rep 3 [C3]

description: PSC27 expression 7 days after treatment by 50 ug/ml bleomycin for 6 hrs

source_name: PSC27 bleomycin (50ug/ml) and SB203580 (10uM)-treated, replicate 3


title: AB4365

description: Amp batch AB4365


title: PSC27-BLEO-SB203580-treated-rep 2 [C2]

source_name: PSC27 bleomycin (50ug/ml) and SB203580 (10uM)-treated, replicate 2


title: ACCLAIM_312337_0_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19342


title: AB4364

description: Amp batch AB4364


title: ACCLAIM_931903_15_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19336

value: Black or African American


title: PSC27-BLEO-Rapamycin-treated-rep 3 [D3]

source_name: PSC27 bleomycin (50ug/ml) and Rapamycin (25nM)-treated, replicate 3


title: AB4363

description: Amp batch AB4363


title: PSC27-BLEO-SB203580-treated-rep 1 [C1]

source_name: PSC27 bleomycin (50ug/ml) and SB203580 (10uM)-treated, replicate 1


title: PSC27-Control-rep 2 [A2]

description: PSC27 control expression (untreated)

source_name: PSC27 control, replicate 2


title: PSC27-BLEO-treated-rep 1 [B1]

description: PSC27 expression 7 days after treatment by ionizing radiation (Cs137) for 10Gy

source_name: PSC27 bleomycin-treated at 50ug/ml, replicate 1


title: PSC27-BLEO-treated-rep 3 [B3]

source_name: PSC27 bleomycin-treated at 50ug/ml, replicate 3


title: PSC27-Control-rep 3 [A3]

description: PSC27 control expression (untreated)

source_name: PSC27 control, replicate 3


title: PSC27-BLEO-treated-rep 2 [B2]

source_name: PSC27 bleomycin-treated at 50ug/ml, replicate 2


title: ACCLAIM_931903_0_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19330


title: AB4362

description: Amp batch AB4362

source_name: Immune cells sorted from melanoma tumors


title: AB4360

description: Amp batch AB4360

value: CCR7+ CD45RA+


title: PSC27-Control-rep 1 [A1]

description: PSC27 control expression (untreated)

source_name: PSC27 control, replicate 1


title: ACCLAIM_673379_15_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19318


title: AB4359

description: Amp batch AB4359


title: ACCLAIM_673379_7_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19315


title: ACCLAIM_673379_0_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19312


title: AB4239

description: Amp batch AB4239

value: Tumor


title: Ser2-phos in Q Replicates Merged Input

city: Seattle

first: Sarah

middle: G.

last: Swygert

state: WA

address: 1100 Fairview Avenue North MS A1-162

department: Basic Sciences Division

institute: Fred Hutchinson Cancer Research Center

data_processing:
Reads were aligned to the sacCer3 reference genome using Bowtie2 in very sensitive mode.
Aligned reads were filtered and indexed using SAMtools.
Indexed reads were normalized to genome average and the genome average was set to 1 fold enrichment.
Genome_build: sacCer3 reference genome (release R64-2-1)
Supplementary_files_format_and_content: Files are .sgr (can be converted to txt) which describe read count normalized to genome average at each basepair in the genome.  Processed data files for IP samples must be divided by the processed data file for the corresponding input sample in order to be normalized to input.

source_name: Quiescent cells

growth_protocol: All strains were generated in prototrophic W303 backgrounds.  Log cells were grown to ~0.6-0.8 OD.  Q cells were purified from 7-day cultures via Percoll density gradient.

extract_protocol:
Approximately 300 OD units of cells were bead-beat until cell walls were disrupted.  Lysates were sonicated to shear chromatin to ~200-400 bp fragments and clarified.  Protein was immuniprecipitated using the indicated antibody.
Nugen Ovation Ultra-Low v2

treatment_protocol: Cells were fixed in formaldehyde for 20 minutes

tag: genotype

value: WT

tag: strain

tag: chip antibody

value: anti-RNA Pol II CTD phosphor Ser2 (Active Motif, catalog #61083)


title: ACCLAIM_931903_7_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19333

source_name: PBMC

tag: age


title: ACCLAIM_139519_7_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19309

tag: tissue


title: AB4238

description: Amp batch AB4238


title: AB4237

description: Amp batch AB4237


title: Ser2-phos in SMC4-off Replicates Merged Input

source_name: Quiescent cells + doxycycline


title: Ser2-phos in SMC4-off Replicates Merged IP


title: ACCLAIM_139519_0_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19306

tag: randomized treatment


title: Msn2 in Q Replicates Merged Input

value: MSN2::FLAG BRN1::myc

value: M2 anti-FLAG (Sigma, catalog #F1804)


title: ACCLAIM_815412_0_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19324

tag: Sex


title: AB4361

description: Amp batch AB4361


title: AB4236

description: Amp batch AB4236


title: Msn2 in Q Replicates Merged IP


title: Brn1 in msn2 Replicates Merged IP

value: BRN1::myc msn2

value: 9E10 purified anti-Myc (Covance, catalog #139049002)


title: AB4235

description: Amp batch AB4235


title: ACCLAIM_815412_7_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19327

tag: race


title: ACCLAIM_911284_15_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19300


title: Ser2-phos in Q Replicates Merged IP


title: Brn1 in msn2 Replicates Merged Input


title: Brn1 in SMC4-off Replicates Merged Input

value: SMC4-off BRN1::myc


title: Brn1 in SMC4-off Replicates Merged IP


title: ACCLAIM_911284_7_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19297


title: AB4233

description: Amp batch AB4233

tag: plate id


title: AB4234

description: Amp batch AB4234

tag: amplification batch


title: ACCLAIM_911284_0_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19294


title: AB4232

description: Amp batch AB4232

tag: sample source


title: ACCLAIM_159059_7_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19291


title: SMC4-on cells

description:
sacCer3.5000.bins.annot.bed.gz
sacCer3.1000.bins.annot.bed.gz
sacCer3.200.bins.annot.bed.gz

data_processing:
Library strategy: Micro-C XL
Reads were aligned to the sacCer3 reference genome using Bowtie2 in very sensitive mode.
Except for rDNA interaction analyses, all read pairs where both  reads mapped with MAPQ >= 6 were deduplicated, and filtered to exclude in-facing  read pairs with ends < 400 bp apart, which likely represent unligated fragments.
Read pairs were ICE normalized using the Cooler suite balance function with settings --ignore-diags 1 -- mad-max 9.
Genome_build: sacCer3 reference genome (release R64-2-1)
Supplementary_files_format_and_content: The files are txt files with 4 tab-delimited columns which are (only for nonzero values): bin 1, bin 2, raw, normalized.  In order to map bin numbers to genomic coordinates, bin annotation files included in bed format should be used.

source_name: SMC4-on cells

growth_protocol: All strains were generated in prototrophic W303 backgrounds.  200 mL cultures of log cells were grown to 0.55 OD.  Q cells were purified from 25 mL 7-day cultures via Percoll density gradient.

extract_protocol:
Spheroplasts were incubated with a concentration of micrococcal nuclease titrated to each experiment designed to retain ~90% mononucleosome sized fragments in the insoluble chromatin fraction for 20 min at 37 degrees. DNA ends were repaired and biotin labeled, fragments were proximity ligated, crosslinking was reversed, and DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Purified DNA ends were readied for ligation, A-tailed, and Illumina Truseq adapters were ligated.  Proximity ligated DNA was pulled down with streptavidin beads, and library was amplified with Illumina Truseq primers.

treatment_protocol: Cells were fixed in 3% formaldehyde at 30 degrees for 10 minutes, cell walls were permeabilized at 30 degrees in 250 ug/mL zymolyase for 30 min (log) or 1 mg/mL zymolyase for 1.5 hours (quiescent), then spheroplasts were crosslinked in 3mM disuccinimidyl glutarate for 40 min at 30 degrees.

tag: culture condition

value: grown to quiescence and purified


title: Rpb3 in Q Replicate 2 Input

value: none, input


title: Rpb3 in Q Replicate 1 Input


title: Rpb3 in Q All Replicates Merged Input


title: AB4231

description: Amp batch AB4231

tag: patient id


title: Rpb3 in Q All Replicates Merged IP

value: anti-Rpb3 antibody (Biolegend, catalog #665003)


title: ACCLAIM_795063_15_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19282

tag: cell type

value: Treg

value: PBMC

tag: participantid


title: AB4229

description: Amp batch AB4229

tag: facs gate


title: AB4230

description: Amp batch AB4230


title: Log cells

source_name: Log cells

value: log growth


title: ACCLAIM_795063_7_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19279

tag: visitnumber

tag: barcode

value: Abatacept

value: Female

value: White


title: ACCLAIM_795063_0_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19276


title: AB4143

description: Amp batch AB4143

value: Tumor


title: ACCLAIM_856452_7_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19273

value: Placebo


title: SMC4-off cells

source_name: SMC4-off cells

tag: genotype

tag: strain

value: grown to quiescence in the presence of doxycycline and purified


title: ACCLAIM_159059_0_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19288

tag: age


title: Rpb3 in Log All Replicates Merged IP

value: WT

tag: chip antibody


title: Rpb3 in Q Replicate 2 IP


title: AB4142

description: Amp batch AB4142