title: Il2ramut/mut_ATACseq_Treg2_LN

city: Bronx

first: Gregoire

middle: S

last: Lauvau

state: NY

address: 1301 Morris park

department: M&I

institute: Albert Einstein College of Medicine

description: naïve/unstimulated

data_processing:
After trimming adapter sequences with trim_galore (ver0.3.7), the sequences mapped using bwa mem (ver0.7.13).
Filtering out non-uniquely mapped reads by samtools (ver0.1.19) view -q 30
ChrM mapped reads and duplicated reads were eliminated by the picard-tools (ver1.92) MarkDuplicates function and samtool (ver0.1.19) rmdup functions.
Peak was called with macs2 (ver2.1.0)
Peaks below the IDR cutoff of 0.05 were selected
Genome_build: mm10
Supplementary_files_format_and_content: BED6+4 format file which contains the peak locations together with peak summit, pvalue and qvalue. (MACS2 narrowPeak file)

source_name: MUT_RFP+ Treg cells_ATACseq

extract_protocol:
Briefly, nuclei were isolated from 50,000 FACS sorted RFP+ Treg cells from reporter mice using a solution of 10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, and 0.1% IGEPAL CA-630.
Immediately following nuclei isolation, the transposition reaction was conducted using Tn5 transposase and TD buffer (Illumina) for 45 min at 37o C. Transposed DNA fragments were purified using Qiagen MinElute Kit and PCR amplified using NEBNext High Fidelity 2x PCR master mix (New England Labs) with dual indexes primers (Illumina Nextera). The size distribution and molarity of the sequencing library were determined by using an Bioanalyzer analysis (High Sensitivity DNA chip, Agilent).

treatment_protocol: Naïve steady state mice of 6- 8 weeks old were bred in our SPF facility and lymph nodes used as a source of donor T cells.

tag: strain background

tag: age

value: 6-8 weeks

value: female

value: Lymph nodes

value: Foxp3+ CD4+ Treg cell


title: WT_ATACseq_Treg1_LN

status: Public on Nov 20 2018

type: SRA

country: USA

description: naïve/unstimulated

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: WT_RFP+ Treg cells_ATACseq

tag: genotype/variation

value: wild type

tag: Sex

tag: tissue

tag: cell type


title: RHM342_12M_100k

city: Macau

first: Edwin

last: Cheung

address: Avenida da Universidade,Taipa

department: faculty of health sciences

country: China

institute: University of Macau

library_source: transcriptomic

data_processing:
Reads were mapped as paired-end sequencing reads with the Tophat package (v.2.0.6) against the UCSC hg19 human gene annotation reference using default parameters
The FPKM (Fragments Per Kilobase of exon model per Million mapped fragments) expression values were calculated from the BAM file generated by Tophat using the Cufflink package (v.2.0.2).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: MCF-7 and T47D ERα-positive human breast cancer cell lines were obtained from ATCC and maintained in DMEM and RPMI 1640 media (Gibco), respectively. Both media were supplemented with 5 % fetal bovine serum (FBS) (Gibco) and grown in a 37°C incubator with 5% CO2.

extract_protocol: Single cell and bulk population samples were barcoded and pooled together for library preparation using the Nextera XT Sample Prep Kit (Illumina). The pooled libraries were quantified through quantitative PCR using the KAPA Library Quantification Kit (KAPA Biosystems)

treatment_protocol: Three days prior to E2 stimulation, MCF-7 and T47D cells were transferred into phenol-red free DMEM/F12 and RPMI media (Gibco), respectively. Both media were supplemented with 5 % charcoal/dextran-stripped FBS (Hyclone). Cells were then stained with CellTracker Green CMFDA or Orange CMTMR (Molecular Probes) 24 h before drug treatment. Stained cells were treated with either ethanol (vehicle) or E2 at 4 time points (0 and 3 h: Green, 6 and 12 h: Orange), before being dissociated and triturated into single-cell suspensions for single-cell and bulk population analyses.

tag: time

tag: cell line

value: ER-positive breast cancer cell line


title: Il2ramut/mut_ATACseq_Treg1_LN

description: naïve/unstimulated


title: MKN45 cell line ADAR knock-down RNA seq

city: Daejeon

first: Jaeeun

last: Jung

address: 125 Gwahak-ro, Youseong-gu

country: South Korea

institute: KRIBB

data_processing:
Basecalls performed using bcl2fastq Conversion Software version 2.19.
Sequenced reads were trimmed for adaptor sequence using cutadapt v1.13, and trimmed low-quality sequence using sickle-maser v1.33, then mapped to hg19 whole genome using STAR v2.5 with parameters -outFilterMultimapNmax 1 -outFilterMismatchNoverReadLmax 0.05.
Variants were called using samtools v1.5.
False positive variants were eliminated using criteria: 1)less than 3 reads including mismatch, 2) less than 10% allele frequency, 3) less than 10 mapping depth, 4) annotated SNPs (using dbSNP build 138 except “cDNA” molecular types, 1000 Genomes Project and the University of Washington Exome Sequencing Project), 5) those in simple repeat region or segmental duplication (RepeatMasker, genomicSuperDups from UCSC genomic browser, respectively), 6) those within splice junction or homopolymeric region of ≥ 5 base pairs, 7) more than 99% strand biased reads, and end position biased mismatches (10% of 5’-end or 20% of 3’-end).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include RNA-editing information for each sample.

molecule: total RNA

source_name: MKN-45 gastric epithelial cancer cell line

growth_protocol: AGS and MKN-45 were grown in RPMI medium with 10% fetal bovine serum. All cells were maintained at 37 °C and 5% CO2.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Gastric epithelial cancer cell line


title: AGS cell line small RNA seq

source_name: AGS gastric epithelial cancer cell line

value: AGS


title: AGS cell line ADAR knock-down small RNA seq


title: WT_ATACseq_Treg2_LN

description: naïve/unstimulated


title: RHV135_3M_100k


title: AGS cell line ADAR knock-down RNA seq


title: AGS cell line RNA seq


title: RHM357_12M_10k


title: SiO2d28_smallRNA-seq

city: Chiba

first: Shigeyuki

last: Shichino

address: 2641, Yamasaki, Noda-shi

department: Department of Molecular regulation of Inflammatory and Immune Diseases

country: Japan

institute: Tokyo University of Science

data_processing:
CLC Genomics Workbench software version 6.0.5 (CLC bio, Aarhus, Denmark) was used to trim the adapters and sequence reads. miRNA expression analysis was performed by counting the resulting tags using miRBase database v19. Total tag counts were normalized to 80,000 tags and the tag counts from two independent sequencing reads were averaged.
Genome_build: miRBase v19
Supplementary_files_format_and_content: tab-delimited text files include tag-count values for each Sample

source_name: primary lung fibroblast

extract_protocol:
Primary lung fibroblasts were isolated from lungs of untreated, bleomycin-treated and silica-treated Col1a2-GFP mice. Lungs were cut into small pieces with a razor blade and digested enzymatically using 0.2% collagenase (Wako, Osaka, Japan), 0.96 mg/mL Dispase II (Roche, Basel, Switzerland), and 20 kU/mL DNase I (Sigma-Aldrich, St Louis, MO) for 60 min at 37°C. Erythrocytes and silica particles were removed by 70% Percoll (GE Healthcare, Buckinghamshire, UK) density separation. The single-cell suspensions were then depleted of lineage+ (CD31+, CD45+, EpCAM+ and Ter119+) cells by negative selection with an AutoMACS cell separator (Miltenyi Biotech, Bergisch Gladbach, Germany). Lineage− GFP+ fibroblasts were further purified by cell sorting using a FACS Aria II (BD).
Small RNAs were isolated from lineage- GFP+ fibroblasts using a mirVana miRNA isolation kit (Thermo Fisher Scientific, Waltham, MA). Small RNA libraries were constructed using Ion Total RNA-Seq Kit v2 (Thermo Fisher Scientific) according to the manufacturer’s instructions. The samples were sequenced twice on an Ion PGM™ System and an Ion PGM™ Sequencing 200 Kit (Thermo Fisher Scientific) according to the manufacturer’s instructions.

treatment_protocol: Col1a2-GFP mice were anesthetized with isoflurane before a single dose of bleomycin sulfate (1.25 mg/kg dissolved in 50 μL of sterile saline solution; Toronto Research Chemical, Toronto, ON, Canada) or crystalline silica particles (400 mg/kg in 50 μL of sterile saline solution; MIN-U-SIL5, US Silica, Frederick, MD; mass-median-diameter [d50] Z 1.4 μm) was instilled by oropharyngeal aspiration.

value: Col1a2-GFP Transgenic

tag: treated with

value: crystalline silica particles

value: lung

value: lineage (CD45, CD31, EpCAM and Ter119) negative, Col1a2-GFP positive fibroblast


title: RHM262_6h


title: BLMd28_smallRNA-seq

value: bleomycin sulfate


title: SiO2d14_smallRNA-seq


title: SiO2d7_smallRNA-seq


title: BLMd14_smallRNA-seq


title: BLMd7_smallRNA-seq


title: miR20a_3_3'SAGE-seq

data_processing:
Adapter trimming and quality filtering of sequencing data were performed by using Trimommatic-v0.36 and PRINSEQ-0.20.4. Filtered reads were mapped to Refseq mm10 by using Bowtie2-2.2.5. Reads that were not mapped to NlaIII sites were removed, and quantified tag numbers of each gene as the expression level of each gene.
Total tag number was adjusted to 1 million tags, and between-sample normalization was performed by using R-3.1.1 and TCC package.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized tag-count values for each sample

extract_protocol:
Transferred lung fibroblasts were isolated from bleomycin-treated lungs of C57BL/6 mice at day 3 post-transfer. Lungs were cut into small pieces with a razor blade and digested enzymatically using 0.2% collagenase (Wako, Osaka, Japan), 0.96 mg/mL Dispase II (Roche, Basel, Switzerland), and 20 kU/mL DNase I (Sigma-Aldrich, St Louis, MO) for 60 min at 37°C. Erythrocytes were removed by 70% Percoll (GE Healthcare, Buckinghamshire, UK) density separation. The single-cell suspensions were then depleted of lineage+ (CD31+, CD45+, EpCAM+, CD146+ and Ter119+) cells by negative selection with an AutoMACS cell separator (Miltenyi Biotech, Bergisch Gladbach, Germany). Lineage− Col1a2GFP+ hLNGFR+ fibroblasts were further purified by cell sorting using a FACS Aria II (BD).
polyA RNAs were isolated and amplified from donor fibroblasts according to the protocol described in (Huang H, Nucleic Actd Res, 2014) with some modifications. 3'SAGE-seq libraries were constructed according to the protocol described in (Matsumura H, Methods Mol Biol, 2012) with some modifications. Sequencing was performed by using Ion Hi-Q Chef Kit, Ion PI v3 Chip Kit and Ion Proton Sequencer (Thermo Fisher Scientific) according to the manufacture’s instructions except the input library concentration (100 pM) and cycle number (200).

treatment_protocol: C57BL/6 mice were anesthetized with isoflurane before a single dose of bleomycin sulfate (2 mg/kg dissolved in 50 μL of sterile saline solution; Toronto Research Chemical, Toronto, ON, Canada) was instilled by oropharyngeal aspiration. Primary fibroblasts were isolated from Col1a2-GFP murine lungs and miR-20a and control vector (marker : hLNGFR) were retrovirally transduced. 5x10^6 of each transduced cell were intratracheally-transferred to B6 mice at day 7 post-administration of 2 mg/kg of bleomycin.

value: lung fibroblast

value: lineage (CD45, CD31, EpCAM, CD146 and Ter119) negative, Col1a2-GFP and LNGFR positive fibroblast


title: miR20a_2_3'SAGE-seq


title: ChIP-seq TFEB

city: Candiolo

first: Davide

last: Cora'

state: TO

department: Dept. of Oncology

country: Italy

institute: Piemonte Orientale University and IRCCS Candiolo Cancer Institute

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie v0.12.7 using the following parameters : -q --max /dev/null -v 1  -S --sam-nohead -m 1
Data were filtered using the following specifications: duplicate reads were filtered out
Genome_build: hg19
Supplementary_files_format_and_content: peaks files were called by using MACS tool by using the following parameters: --nolambda -p 1E-5

source_name: HUVEC

growth_protocol: Human ECs were isolated from veins of umbilical cords and maintained as described(Napione et al., 2012). To minimize cell variability, pools of 5 different donors were used.

extract_protocol:
For ChIP-seq, approximately 2 x 10E7 cells were cross-linked by addition of formaldehyde to 1% for 10 min at RT, quenched with 0.125 M glycine for 5 min at RT, and then washed twice in cold PBS. The cells were resuspended in Lysis Buffer 1 (50 mM Hepes-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP-40, 0.25% Triton X-100 and protease inhibitor) to disrupt the cell membrane and in Lysis Buffer 2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA and protease inhibitor) to isolate nuclei. The isolated nuclei were then resuspended in SDS ChIP Buffer (20 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS and protease inhibitors). Extracts were sonicated using the Bioruptor H Twin (Diagenode) for 2 runs of 10 cycles [30 sec ‘‘ON’’, 30 sec ‘‘OFF’’] at high power setting. Cell lysate was centrifuged at 12,000 g for 10 min at 4°C. The supernatant was diluted with ChIP Dilution Buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton) before immunoprecipitation step. Magnetic beads (Dynabeads®Protein, Life Technologies) were saturated with PBS/1% BSA and the samples were incubated with 2 micrograms of antibody overnight at 4°C on a rotator.  Next day samples were incubated with saturated beads for two hours at 4°C on a rotator. Successively immunoprecipitated complexes were washed five times with RIPA buffer (50 mM Hepes-KOH pH7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0,7% Na-Deoxycholate) at 4°C for 5 minutes each on a rotator. Elution Buffer was added and incubated at 65°C for 15 minutes. The decrosslinking was performed at 65°C overnight. Decrosslinked DNA was purified using QIAQuick PCR Purification Kit (QIAGEN) according to the manufacture’s instruction.
For ChIP-seq, approximately 10 ng of purified ChIP DNA were end-repaired, dA-tailed, and adapter-ligated using the NEBNext ChIP-Seq Library Prep Master Mix Set (NEB), following manufacturer instructions.

tag: strain

value: endothelial cells from umbilical cords newborn healthy humans

tag: antibody


title: ChIP-seq IgG

extract_protocol:
For ChIP-seq, approximately 2 x 10E7 cells were cross-linked by addition of formaldehyde to 1% for 10 min at RT, quenched with 0.125 M glycine for 5 min at RT, and then washed twice in cold PBS. The cells were resuspended in Lysis Buffer 1 (50 mM Hepes-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP-40, 0.25% Triton X-100 and protease inhibitor) to disrupt the cell membrane and in Lysis Buffer 2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA and protease inhibitor) to isolate nuclei. The isolated nuclei were then resuspended in SDS ChIP Buffer (20 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS and protease inhibitors). Extracts were sonicated using the Bioruptor H Twin (Diagenode) for 2 runs of 10 cycles [30 sec ‘‘ON’’, 30 sec ‘‘OFF’’] at high power setting. Cell lysate was centrifuged at 12,000 g for 10 min at 4°C. The supernatant was diluted with ChIP Dilution Buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton) before immunoprecipitation step. Magnetic beads (Dynabeads®Protein G, Life Technologies) were saturated with PBS/1% BSA and the samples were incubated with 2 micrograms of antibody overnight at 4°C on a rotator.  Next day samples were incubated with saturated beads for two hours at 4°C on a rotator. Successively immunoprecipitated complexes were washed five times with RIPA buffer (50 mM Hepes-KOH pH7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0,7% Na-Deoxycholate) at 4°C for 5 minutes each on a rotator. Elution Buffer was added and incubated at 65°C for 15 minutes. The decrosslinking was performed at 65°C overnight. Decrosslinked DNA was purified using QIAQuick PCR Purification Kit (QIAGEN) according to the manufacture’s instruction.
For ChIP-seq, approximately 10 ng of purified ChIP DNA were end-repaired, dA-tailed, and adapter-ligated using the NEBNext ChIP-Seq Library Prep Master Mix Set (NEB), following manufacturer instructions.

value: IgG (12-370, Millipore)


title: miR20a_1_3'SAGE-seq


title: control_3_3'SAGE-seq

value: mock control


title: control_2_3'SAGE-seq


title: F44pH4

city: TianJin

first: Kairen

last: Tian

address: No. 135, YaGuan Road, JinNan District

institute: Tianjin university

data_processing:
CASAVA(v1.8.2) softwares used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using the software Trimmomatic (v0.30), then mapped to F44 whole genome using bowtie (0.12.7).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using the software rsem.
Gene Differentiation Analysis Using the edgeR (V3.4.2) of Bioconductor Package.
Genome_build: F44
Supplementary_files_format_and_content: xls files include RPKM values for each Sample.

organism: Lactococcus lactis

source_name: cell

growth_protocol: Before treatment, the experimental and the control  were cultivated in the seed medium and taken at mid-log phase.

extract_protocol:
Total RNA of the strains was isolated by using Quick-RNA™ MicroPrepkit (ZYMO, Research, USA) and treated with DNAse I (NEB) as per manufacturer’s instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: the strains were cultured at 30°C seed medium with pH 4.0 (treatment) for one hour. One samples were cultured at pH 7.0 as the control group

value: pH 4.0 medium for 1hr


title: G423pH7

data_processing:
RTA2.7.3 and bcl2fastq2-v2.16 softwares used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to G423 whole genome using Bowtie2（v 2.2.5） with the 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 -p 1 -k 200.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using the software RSEM.
Gene Differentiation Analysis Using the possionDis algorithm with the parameters: abs log2(FoldChange) >= 1 &&  FDR  <= 0.005.
Transcript rearrangement was performed on each sample using Rockhopper with the parameters :-TIME -fr -s false and using software CPC (Coding Potential Calculator) to predict each new transcript's protein coding ability.
Genome_build: G423
Supplementary_files_format_and_content: xls files include RPKM values for each Sample.

value: none (pH7)


title: control_1_3'SAGE-seq


title: H3K4me3_FCFC_ChIPSeq_rep1

status: Public on Nov 18 2018

city: Yokohama

first: Shin-ichi

last: Tomizawa

state: Kanagawa

address: 3-9 Fukuura, Kanazawa-ku

department: School of Medicine

institute: Yokohama City University

data_processing:
Basecalls performed using CASAVA version 1.8
Reads were quality- and adaptor-trimmed using Trim Galore! version 0.4.0.
ChIP-seq reads were aligned to mouse genome using Bowtie version 1.1.1 with the parameters -n 2 -l 30 --best --strata -m 1.
RNA-seq reads were aligned to mouse genome using TopHat version 2.0.14 with default parameters except that a gtf reference file was used.
ChIP-seq and RNA-seq read count was done using SeqMonk version 0.30.2, correcting for total count per million reads.
Genome_build: mm10
Supplementary_files_format_and_content: Text files generated using SeqMonk contain corrected RNA-seq read count for all genes and corrected ChIP-seq read count for TSSs ±0.5 kb.

source_name: GSCs

growth_protocol: GSCs were grown on fibroblast feeder cells in GS media for 6 days after 4-OHT treatment prior to harvesting.

extract_protocol:
For ChIP-seq, cells were crosslinked and chromatin was prepared according to a previous report (Nat. Protoc. 3, 1032–1045) with modifications. For RNA-seq, total RNA was purified using Isogen (Nippon Gene), and treated with DNaseI to digest genomic DNA.
ChIP-seq and RNA-seq libraries were prepared using NEBNext Ultra DNA Library Prep Kit for Illumina (NEB) and NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB), respectively, according to manufacturer's instructions.

treatment_protocol: Kmt2b knockout in GSCs was done by adding 4-OHT at a final concentration of 1 μM to the media. For control, Kmt2bF/F; Rosa26-CreERT2 GSCs was mock-treated with 100% ethanol in parallel with the knockout.

value: germline stem cells (GSCs)

tag: genotype

tag: chip antibody

value: H3K4me3 (Abcam, ab8580)


title: RNAseq_FF_rep2


title: input_DNA_FCFC_rep2

value: none (input)


title: F44pH7


title: G423pH4


title: RNAseq_FCFC_rep1


title: RNAseq_FF_rep1


title: input_DNA_FCFC_rep1


title: input_DNA_FF_rep2


title: UT_smallRNA-seq

value: none (untreated)


title: H3K27me3_FCFC_ChIPSeq_rep2

value: H3K27me3 (Millipore, 07-449)


title: H3K27me3_FCFC_ChIPSeq_rep1


title: H3K4me3_FCFC_ChIPSeq_rep2


title: input_DNA_FF_rep1


title: H3K27me3_FF_ChIPSeq_rep2


title: H3K4me3_FF_ChIPSeq_rep2


title: H3K27me3_FF_ChIPSeq_rep1


title: RNAseq_FCFC_rep2


title: mES_GPS_methylation

status: Public on Nov 17 2018

city: Shanghai

first: Jin

last: Li

state: Shanghai

address: 130 Dong-An Road

department: Institutes of Biomedical Sciences (IBS)

institute: Fudan University

data_processing:
Library strategy: Guide Positioning Sequencing (GPS)
Methylation by GPS: We firstly filtered out low quality reads. Read2 were aligned onto reference genome (hg19) using Bowtie2 (v2.2.3) with default parameters except "-k 20". We used the Smith-Waterman algorithm to map the Read1 to the reference target sequence that is located within 1kb of opposite strand of downstream of the Read2. Cytosines which are covered by no less than 5 reads are used for methylation analysis.
Methylation by WGBS: We firstly filtered out low quality reads. Read1 and Read2 were aligned onto reference genome (hg19) using BSMAP with default parameters except -v 3 -g 1. Cytosines which are covered by no less than 5 reads are used for methylation analysis.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include loci, methylation level and covered layers (methylated and unmethylated) for each Sample.

source_name: ESC

growth_protocol: Cell lines were cultured at 37˚C in 5% CO2 in high-glucose DMEM (Hyclone, USA) supplemented with 10% fetal bovine serum (Hyclone, USA), and collected under standard culture protocols.

extract_protocol:
Methylation: Genomic DNA from tissues and cell lines was extracted using QIAamp DNA Mini Kit (Qiagen, 51306, Valencia, CA). 3μg genomic DNA was fragmented into 300-500bp by sonication.
Libraries were prepared for sequencing using standard Illumina protocols

value: embryonic stem cells


title: Technical_replicate_4

city: Cambridge

first: Hugo

last: Brandao

state: MA

address: 77 Massachusetts Ave. E25-526C

institute: Massachusetts Institute of Technology

description: Immortalized Cell Line

data_processing:
Library strategy: Hi-C
The raw reads were processed using the cMapping pipeline publicly available at https://github.com/dekkerlab/cMapping , using the default parameters.
The details of the alignment method of this pipeline can be found in The Hitchhiker’s guide to Hi-C analysis: Practical guidelines, Methods, 2015, Lajoie et. al ( http://www.sciencedirect.com/science/article/pii/S1046202314003582?via%3Dihub ).
The output of the cMapping pipeline, interaction pairs, were converted to cooler file format. See http://cooler.readthedocs.io/en/latest/ and https://github.com/mirnylab/cooler for details.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix of whole-genome locus interaction frequencies binned at 10kb, 250kb resolutions stored in the Cool file format.

source_name: HFF-hTERT

growth_protocol: Human foreskin fibroblasts (HFF) immortalized with hTert were grown in DMEM with 10% FBS, 1% PenStrep  as described in Naumova et al., 2013

extract_protocol:
Cells were incubated in 660ul of cold lysis buffer mixed with 60 ul of protease inhibitors as decribed in Naumova et al., 2013
Dilution Hi-C was performed as described in Naumova et al., 2013 with 20-25 million formaldehyde cross-linked cells. Chromatin was digested with HindIII.

treatment_protocol: No treatments

value: HFF-hTERT

tag: enzyme

value: HindIII

value: skin; foreskin

value: Fibroblast


title: H3K4me3_FF_ChIPSeq_rep1


title: Technical_replicate_3

description: Immortalized Cell Line


title: Technical_replicate_2

description: Immortalized Cell Line


title: mES_WGBS_methylation

data_processing:
Methylation by GPS: We firstly filtered out low quality reads. Read2 were aligned onto reference genome (hg19) using Bowtie2 (v2.2.3) with default parameters except "-k 20". We used the Smith-Waterman algorithm to map the Read1 to the reference target sequence that is located within 1kb of opposite strand of downstream of the Read2. Cytosines which are covered by no less than 5 reads are used for methylation analysis.
Methylation by WGBS: We firstly filtered out low quality reads. Read1 and Read2 were aligned onto reference genome (hg19) using BSMAP with default parameters except -v 3 -g 1. Cytosines which are covered by no less than 5 reads are used for methylation analysis.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include loci, methylation level and covered layers (methylated and unmethylated) for each Sample.


title: Technical_replicate_1

description: Immortalized Cell Line


title: TF-1 miR-200a

city: Beijing

first: yadong

last: yang

address: No.1-104 Beichen West Road, Chaoyang

institute: Beijing Institute of Genomics

data_processing:
TopHat for mapping of Ion Proton RNA-Seq data
Converting the unmapped to fastq from bam, and aligning the unmapped with bowtie2
Cufflinks for assembling transcripts, estimating their abundances, and testing for differential expression and regulation in RNA-Seq samples
Computation and visualization were achieved using the heatmap plus package in R.
IPA and the Gene Ontology for functional analysis of specific genes
Genome_build: hg19

source_name: TF-1 transfected with vector contain primary miR-200a sequence

growth_protocol: RPMI-1640 Medium, fetal bovine serum to a final concentration of 10%, with additional  3 ng/ml recombinant human GM-CSF;   incubated in a  37°C incubator with  5% CO2.

extract_protocol:
total RNA was extracted by using TRIzol according to manufacturer's instruction
Libraries were prepared with poly(A) RNA according to standard proton protocol

value: erythroleukemia


title: TF-1 pcDNA

source_name: TF-1 transfected with empty vector


title: 437WTsRN

status: Public on Nov 16 2018

city: Barcelona

first: Evarist

middle: Planet

last: Letschert

state: Spain

address: C/ Baldiri Reixac 10

department: Biostatistics

country: Spain

institute: IRB Barcelona

description: rRNA-depleted small RNA

data_processing:
Reads were aligned to reads were mapped to the mouse genome (mm9) with TopHat (v2.0.11). Counts of mRNA reads on genes were computed using HTseq-count v0.6.1 with default parameters.
SmRNA-Seq analysis was performed through the RNA-Seq analysis tool of the HTS Station platform http://htsstation.epfl.ch, where reads were mapped to a custom genome, and a custom script was used for mapping options (provided as additional file).
Genome_build: mm9
Supplementary_files_format_and_content: hepa_june2013_smRNAseq.tab: abundance measurements on genes
Supplementary_files_format_and_content: hepa_april2013_smRNAseq.tab: abundance measurements on tRNAs and snoRNAs
Supplementary_files_format_and_content: liver_dec2013_smRNAseq.tab: abundance measurements on tRNAs and snoRNAs

source_name: primary murine hepatocytes WT

growth_protocol: Hepa 1.6 cells were cultured in DMEM supplemented with 10% FCS. Primary hepatocyted were processed directly after purification.

extract_protocol:
Total RNA was extracted and DNase-I treated using a spin column-based RNA purification kit (Macherey-Nagel). For small RNA-seq, RNA was extracted with Trizol (Thermo Fisher Scientific) followed by miRNeasy (QIAGEN) purification and Ribo-zero rRNA removal kit (Illumina, for Hepa 1.6 cells) or GeneRead rRNA depletion kit (QIAGEN, for primary murine hepatocytes).
TruSeq stranded RNA sample preparation kit (Illumina).

treatment_protocol: Hepa 1.6 were transduced 5 days before collection.

value: Primary hepatocytes

value: wild type


title: 40KOsRN

description: rRNA-depleted small RNA

source_name: primary murine hepatocytes Kap1 KO

value: Kap1 Knock-out


title: HpshRNAEmpty

description: rRNA-depleted small RNA

source_name: cells were transfected with a plasmid encoding a control shRNA

value: Hepa 1.6 hepatoma cell line

value: control


title: Hp01mRN2

description: polyA RNA

source_name: cells were transfected with a plasmid encoding an shRNA targeting KAP1

value: Kap1 Knock-down


title: HpshRNA01

description: rRNA-depleted small RNA


title: HpaEmRNA

description: polyA RNA


title: HpEmRNA2

description: polyA RNA


title: Hp01mRNA

description: polyA RNA


title: shKP2TI

data_processing:
Alignement for ChIP-seqs were done with bowtie
Peak calling for ChIP-seqs were done using MACS or ChIP-part module of the ChIP-seq analysis platform (http://ccg.vital-it.ch/chipseq/)
Genome_build: mm9
Supplementary_files_format_and_content: A bed file containing the output of the peak called by MACS or ChIP-Part is provided.

growth_protocol: Hepa 1.6 cells were cultured in DMEM supplemented with 10% FCS.

extract_protocol:
ChIP and library preparation were done according to (Ecco, Cassano et al. 2016), with modifications as described in Supplemental Experimental Procedures.
Libraries were ligated with Illumina adaptors

treatment_protocol: Hepa 1.6 were transduced 5 days before fixation.


title: 0 ng/mL BMP-2 and 0 nM Dexamethasone hMSC Replicate 2

city: Stanford

first: Peter

last: Yang

state: CA

address: 300 Pasteur Drive

department: Orthopaedic Surgery

institute: Stanford University

description:
adapter sequence: GATCGGAAGAGCACACGTCTGAACTCCAGTCACAGTTCCATCTCGTATGCCGTCTTCTGCTTG
161107 Supplementary Information hMSCMinDiffExp.txt

data_processing:
Illumina Casava software used for base calling.
Sequenced reads were trimmed for adaptor sequence  then mapped to human or bovine whole genome using STARS 2.3.0, SAMtools 0.1.19 and Cufflinks 2.1.1.1
Genome_build: Bovine (bosTau7) genome for fallow deer samples and human (pre-indexed hg19) genome for human samples
Supplementary_files_format_and_content: Tab Delimited Text Files Showing Differentially Expressed Genes and Abudance As Computed By Cufflinks

source_name: Human Mesenchymal Stem Cell

growth_protocol: Refer to sample description

extract_protocol:
RNA of in vitro cultured cells were extracted using Qiagen RNeasy Plus Mini kit and reverse- transcribed into cDNA using Nugen Ovation RNA-seq System V2 kit.
cDNA was sheared using Covaris S2 focused-ultrasonicator followed by, end-repair, dA-tailing as well as adapter ligation using custom primers and New England Biolabs NEBNext DNA Library Prep Master Mix Set for Illumina. Library was PCR-amplified for 6 cycles. Human and FD proliferation samples were sequenced to an average depth of 87,276,798 reads per library while human and FD mineralization samples were sequenced to an average depth of 74,904,447 reads per library

treatment_protocol: Refer to sample description

value: Human Mesenchymal Stem Cell (Lonza, Isolate 24268)

value: Bone marrow-derived

tag: time point

value: Cultured for 24 days

tag: condition

value: DMEM, 10% FBS, 1% PS, 50 µg/mL ascorbic acid, 10 mM β-glycerophosphate, 0 ng/mL BMP-2, 0 nM Dexamethasone


title: 100 ng/mL BMP-2 and 100 nM Dexamethasone hMSC Replicate 2

description:
adapter sequence: GATCGGAAGAGCACACGTCTGAACTCCAGTCACCCGTCCATCTCGTATGCCGTCTTCTGCTTG
161107 Supplementary Information hMSCMinDiffExp.txt

value: DMEM, 10% FBS, 1% PS, 50 µg/mL ascorbic acid, 10 mM β-glycerophosphate, 100 ng/mL BMP-2, 100 nM Dexamethasone


title: 10 % Serum hMSC Replicate 2

description:
adapter sequence: GATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAATCTCGTATGCCGTCTTCTGCTTG
161107 Supplementary Information hMSCProDiffExp.txt

value: Cultured for 2.5 days

value: DMEM, 10% FBS, 1% PS


title: 0 % Serum hMSC Replicate 2

description:
adapter sequence: GATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGCCGTCTTCTGCTTG
161107 Supplementary Information hMSCProDiffExp.txt

value: DMEM, 0% FBS, 1% PS


title: 10 % Serum hMSC Replicate 1

description:
adapter sequence: GATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGCCGTCTTCTGCTTG
161107 Supplementary Information hMSCProDiffExp.txt


title: 0 % Serum hMSC Replicate 1

description:
adapter sequence: GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGCCGTCTTCTGCTTG
161107 Supplementary Information hMSCProDiffExp.txt


title: 0 ng/mL BMP-2 and 0 nM Dexamethasone hMSC Replicate 1

description:
adapter sequence: GATCGGAAGAGCACACGTCTGAACTCCAGTCACAGTCAAATCTCGTATGCCGTCTTCTGCTTG
161107 Supplementary Information hMSCMinDiffExp.txt


title: shEP2TI

value: none (input)


title: shEP3TI


title: shKP3ChP

value: PolIII RPC32 (Santa Cruz, sc-21754)


title: shEP3ChP


title: HepH3K27ChIP

source_name: cells were cultured in standard conditions before fixation

value: H3K27ac (Abcam, ab4729)


title: 100 ng/mL BMP-2 and 100 nM Dexamethasone hMSC Replicate 1

description:
adapter sequence: GATCGGAAGAGCACACGTCTGAACTCCAGTCACATGTCAATCTCGTATGCCGTCTTCTGCTTG
161107 Supplementary Information hMSCMinDiffExp.txt


title: shKP2ChP

value: PolII CTD4H8 (Millipore, 05-623)


title: HepaTI2


title: shEP2ChP


title: HepaKap1ChIP

value: KAP1 (Trono laboratory, rabbit polyclonal S23470)


title: HepaH3K9ChIP

value: H3K9me3 (Diagenode, C15410056)


title: shKP3TI

value: Hepa 1.6 hepatoma cell line


title: RHM235_12h

value: ER-positive breast cancer cell line


title: HepaH3K4ChIP

value: H3K4me1 (Diagenode, pAb-037-050)


title: HA4POS

city: Houston

first: Navin

last: Varadarajan

state: Texas

address: 4726 Calhoun Rd

department: Chemical and Biomolecular Engineering

institute: University of Houston

data_processing:
Quality control of the sequencing data was performed by using Cutadapt (1.8.3) to remove the adapter sequences from the 3’ end, followed by trimming of the first 12 bases of all reads at 5’ end to address the non-uniform distribution caused either by biased selection of reads or contamination of other sequences.
Reads shorter than 20bp were then dropped to avoid potential mapping to multiple locations on the reference genome.
Transcripts were aligned to the human reference genome UCSC hg19 using TopHat2 (v2.1.0). The mapped genes were annotated using R package “GenomicAlignments” (1.0.6) and gene annotation information in R package “TxDb.Hsapiens.UCSC.hg19.knownGene” (2.14.0).
Differentially expressed genes (DEGs) were identified using DEseq2 (1.4.5) tool that tests for differential gene expression based on a model using the negative binomial distribution.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file with normalized count of gene transcripts from each sample

source_name: hemagglutinin-specific B cells

extract_protocol:
Antigen-specific B cells were sorted from PBMCs from patients' blood directly into lysis buffer and RNA was isolated using RNA isolation kit (Macherey-Nagel, RNA-XS).
cDNA libraries were synthesized using the commercially available SMART-Seq Ultra Low Input RNA kit (Clontech), cDNA libraries were first tagmented and then barcoded by indexing primers using the Nextra XT kit (Illumina)

tag: sample preparation

value: Ex vivo

value: B cells

value: Blood


title: HA3POS


title: 100 ng/mL BMP-2 and 100 nM Dexamethasone FD RM Cell Replicate 1

description:
adapter sequence: GATCGGAAGAGCACACGTCTGAACTCCAGTCACGGCTACATCTCGTATGCCGTCTTCTGCTTG
161107 Supplementary Information FD2MinDiffExp.txt

organism: Dama dama

source_name: Fallow Deer Reserve Mesenchyme

value: Fallow Deer Reserve Mesenchyme Cells (Isolate 2)

value: Antler-Derived

value: Cultured for 24 days


title: RA4-CCPPOS

source_name: CCP-specific B cells


title: RA1-CCPNEG

source_name: CCP-negative B cells


title: RA3-CCPNEG


title: RHM217_12h


title: HA1POS


title: 100 ng/mL BMP-2 and 100 nM Dexamethasone FD RM Cell Replicate 2

description:
adapter sequence: GATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTAATCTCGTATGCCGTCTTCTGCTTG
161107 Supplementary Information FD2MinDiffExp.txt

value: DMEM, 10% FBS, 1% PS, 50 µg/mL ascorbic acid, 10 mM β-glycerophosphate, 100 ng/mL BMP-2, 100 nM Dexamethasone


title: RA2-CCPPOS


title: RA2-CCPNEG


title: 0 ng/mL BMP-2 and 0 nM Dexamethasone FD RM Cell Replicate 2

description:
adapter sequence: GATCGGAAGAGCACACGTCTGAACTCCAGTCACTAGCTTATCTCGTATGCCGTCTTCTGCTTG
161107 Supplementary Information FD2MinDiffExp.txt

value: DMEM, 10% FBS, 1% PS, 50 µg/mL ascorbic acid, 10 mM β-glycerophosphate, 0 ng/mL BMP-2, 0 nM Dexamethasone


title: 0 ng/mL BMP-2 and 0 nM Dexamethasone FD RM Cell Replicate 1

description:
adapter sequence: GATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGATCTCGTATGCCGTCTTCTGCTTG
161107 Supplementary Information FD2MinDiffExp.txt


title: 10 % Serum FD RM Cell Replicate 2

description:
adapter sequence: GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATGCCGTCTTCTGCTTG
161107 Supplementary Information FD2ProDiffExp.txt

value: Cultured for 2.5 days

value: DMEM, 10% FBS, 1% PS


title: 0 % Serum FD RM Cell Replicate 2

description:
adapter sequence: GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGCTTG
161107 Supplementary Information FD2ProDiffExp.txt

value: DMEM, 0% FBS, 1% PS


title: 10 % Serum FD RM Cell Replicate 1

description:
adapter sequence: GATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGCCGTCTTCTGCTTG
161107 Supplementary Information FD2ProDiffExp.txt


title: AAAC0

status: Public on Nov 15 2018

city: La Jolla

first: Yifeng

last: Xia

address: 10010 North Torrey Pines Road

department: Laboratory of Genetics

institute: Salk Insitute

description: genes.read_group_tracking, gene_exp.diff

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequence reads were mapped to the mm9 mouse genome build using RNA-STAR v2.3.0e.
Raw reads of each individual gene were counted and normalized to fpkm using Cuffdiff v2.1.1.
Differential gene expression was called using Cuffdiff v2.1.1.
Genome_build: mm9
Supplementary_files_format_and_content: genes_read_group_tracking file (abundance measurements) and gene_exp.diff file (differential gene expression) output from Cuffdiff. q1 = normal mouse lung, q2 = luciferase SCLC, q3 = IkBaM SCLC.

source_name: SCLC, induced by lentiviral vector expressing IkBaM-Mycl-shp53-shRb

growth_protocol: Mouse SCLCs were induced by lentiviral vector expressing luciferase-Mycl-shp53-shRb or IkBaM-Mycl-shp53-shRb. Tumor tissues were isolated from mice that reached clinical endpoints. Normal lung tissue was trimmed away from tumor tissue using a dissecting microscope.

extract_protocol:
RNA was isolated using Direct-zol kit according to manufacturer's protocol with the addition of Dnase (Zymo Research).
cDNA libraries were prepared using the TruSeq RNA Sample Prep kit (Illumina).

value: SCLC

value: IkBaM


title: AAAG9


title: KB1


title: WT2


title: 0 % Serum FD RM Cell Replicate 1

description:
adapter sequence: GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG
161107 Supplementary Information FD2ProDiffExp.txt


title: AAAC1


title: HA2POS


title: WT4

source_name: SCLC, induced by lentiviral vector expressing luciferase-Mycl-shp53-shRb

value: control (luciferase)


title: RA4-CCPNEG


title: AAAH0


title: WT3


title: RA1-CCPPOS


title: AAB1


title: RA3-CCPPOS


title: WT1


title: AAB2


title: N4

source_name: normal lung

value: normal lung


title: N3


title: AAA2


title: AAA1


title: N2


title: AAA0


title: AAA3


title: N1


title: exS5 rep3

city: boston

first: ruggero

last: spadafora

address: 55 fruit street

department: newborn medicine

institute: MGH

data_processing:
alignment with STAR to hg19 (version: 2.4.1d)
counting with featureCounts (version: 1.4.4)
Supplementary_files_format_and_content: text files with the output of featureCounts generated using BAM files output by STAR

source_name: preterm lung

growth_protocol: Tracheal aspirates were collected during routine suctioning of intubated newborns enrolled in our aforementioned protocols. Briefly, tracheal aspirates were plated in regular DMEM media, with FBS and antibiotics. When confluent, the cells were purified using fluorescence-activated cell sorting with an MSC phenotyping kit (Milteny Biotec- order no. 130-095-198).

extract_protocol: RNA was extracted from cell lines using a trizol and alcohol-based protocol. Coding and non-coding RNA was enriched by depleting ribosomal RNA (rRNA) using the Ribo-minus kit (ThermoFisher-order no. A15026). RNA quality and efficiency of rRNA depletion were ascertained using an Agilent 2100 Bioanalyzer with RNA 6000 Nano LabChip kit (Agilent Technologies-order no 5067-1511). cDNA libraries were generated using a NEBNext kit (New England Biolabs- order no. E6040s).

value: preterm lung

value: Lung-derived mesenchymal stromal cells (MScs)

tag: passages in-vitro

tag: cga at collection

tag: bronchopulmonary dysplasia severity

value: moderate


title: exS4 rep2

value: mild


title: exS5 rep1


title: exS4 rep3


title: exS5 rep2


title: exS4 rep1


title: exs3 rep2

value: severe


title: exs3 rep3


title: exs2 rep3


title: exS1 rep1


title: exS1 rep2


title: exS1 rep3


title: A4 rep3


title: exs2 rep2


title: exs2 rep1


title: exs3 rep1


title: A3 rep3


title: A4 rep2


title: A3 rep2


title: A4 rep1


title: A3 rep1


title: A2 rep3


title: A2 rep2


title: A1 rep1


title: S6 rep2


title: S6 rep3


title: A1 rep3


title: A2 rep1


title: S6 rep1


title: A1 rep2


title: S5 rep1

value: No BPD


title: S4 rep2


title: S3 rep2


title: S4 rep1


title: S3 rep3


title: S5 rep2


title: S3 rep1


title: S2 rep2


title: C4 rep3


title: C4 rep1


title: S1 rep2


title: S2 rep1


title: C3 rep2


title: S2 rep3


title: C3 rep1


title: C3 rep3


title: C2 rep1


title: C2 rep3


title: AAA4

tag: genotype/variation


title: C1 rep3

tag: tissue


title: C1 rep1

tag: cell type


title: C1 rep2


title: 4EP32

first: Stephen

middle: Mack

last: Christopher

state: TX

address: 1102 Bates Avenue C1030.02

department: Pediatrics

institute: Baylor College of Medicine

data_processing:
Base calling: Performed according to default Illumina HiSeq2000 parameters
Index De-Multiplexing: Performed according to default Illumina HiSeq2000 parameters
Alignment: Using Bowtie2 (v2.1.0) using the parameters: Phred quality scale, end to end alignment, minimum fragment length = 0, maximum fragment length = 500,
PCR duplicate removal: Using Picard Tools according to default parameters
Peak Calls: Using MACS(v2.09) with a p-value cutoff of 1e-5 and with a local lambda value of 100,000 kb
Genome_build: HG19
Supplementary_files_format_and_content: Peak Calls files

source_name: Brain

extract_protocol:
Upon surgical resection, primary tumors were snap frozen and pulvarized in liquid nitrogen, before proceeding with the ChIP experiment (Mack et al., Nature, 2014)
ChIP samples were quantified using Picogreen (Invitrogen) and libraries were constructed using the Rubicon Thruplex DNA-seq kit, according to manufacturers recommendations

tag: tumor type

value: Ependymoma

tag: epigenetic mark

tag: diagnosis

value: Primary

tag: molecular subgroup

value: PFB

value: anti-H3K27ac (Abcam, AB4729, Lot #GR184557)


title: 401750783

value: PFA


title: 42141138


title: 42608321


title: 3955733


title: 4A47


title: BT2009136

value: RELA


title: 7A11

value: NON-RELA


title: 4EP18


title: BT2010129


title: S1 rep1


title: C4 rep2


title: C2 rep2


title: BT2011086


title: BT2012113


title: BT2012116


title: BT2013064


title: BTTB673


title: HSC2237282


title: HSC2326979


title: HSC2068011


title: HSC2366617


title: BTTB792


title: 13B13


title: HSC2429300


title: 69A98


title: POL15474


title: JC0905378


title: SG2137_09


title: SG366_10


title: BRL130

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

description: H3 WT Set2D mutant

data_processing:
2 X100 bp paired end stranded sequencing was performed on an Illumina HiSeq 2500. Basecalling was performed using Illumina Casava 1.7
FASTQ sequences adapter trimmed (cutadapt) and mapped to the S. Pombe  genome by STAR
Bams are sorted by samtools by name and mapped reads were counted with HTSEQ
Genome_build: Schizosaccharomyces_pombe. ASM294v2.29
Supplementary_files_format_and_content: count files are txt format files that contain raw read counts that map  to  transcripts for each defined gene.

organism: Schizosaccharomyces pombe

source_name: S. pombe Set2D cells

growth_protocol: Cultures were grown overnight in YES at 25°C to a density of 2.5 x 106 cells/ml in a 25mL culture.

extract_protocol:
The cells were pelleted by centrifugation and washed in DEPC H2O. The pellet was resuspended in 750ul TES Buffer [50mM Tris-HCl pH 7.5, 10mM EDTA, 100mM NaCl, 0.5% SDS made in DEPC H2O] along with an equal volume of 5:1 phenol:chloroform pH 4.7 and incubated at 65°C for one hour with vortexing for 10 seconds every 10 minutes. The samples were then cooled on ice and centrifuged for five minutes at 13,000 RPM. The aqueous phase was transferred to a 2mL phase lock tube and an additional phenol:chloroform extraction was performed. After centrifugation, the aqueous phase was transferred to a new tube and an equal volume of chloroform was added. To precipitate the RNA, the aqueous phase was transferred to a 2mL microcentrifuge tube and three volumes of ice cold ethanol and 3M NaOAc pH 5.2 were added and the samples were kept at -20°C to precipitate the RNA. The next day, samples were centrifuged at 14,000 RPM and 4°C for 15 minutes to pellet the RNA. The pellet was washed with ice cold 70% ethanol and air dried for 30 minutes. A Turbo DNAse (Ambion) reaction was set up with 100ug of RNA in a 150ul reaction containing 5ul of Turbo DNAse. The reaction was incubated at 37°C for 30 minutes and another 5ul of Turbo DNAse was added and incubated for an additional 30 minutes prior to the removal of the DNAse using 50ul of inactivation beads. An RNeasy Mini kit (Sigma) was used to further clean up and concentrate the RNA which was eluted in a final volume of 30ul of DEPC H2O.
Libraries were prepared from 2ug of RNA. Ribosomal RNA was removed from the samples using Ribo-Zero Gold rRNA Removal Kit (Yeast) following manufacturer instructions (Illumina). Libraries were prepared using the TruSeq Strand Total RNA Library Prep Kit, beginning at Elution 2 – Fragment – Prime step immediately preceding cDNA synthesis according to the manufacturer instructions (Illumina) with the following modifications; the 94 C Elution 2 – Fragment – Prime incubation was reduced to five minutes and the PCR was reduced to 11 cycles.

treatment_protocol: Not applicable

value: H3 WT Set2D mutant


title: BRL129

description: H3 G34V mutation

source_name: S. pombe G34V cells

value: H3 G34V mutation


title: BRL132

description: H3 WT Set2D mutant


title: BRL126

description: H3 G34R mutation

source_name: S. pombe G34R cells

value: H3 G34R mutation


title: BT2010182


title: BRL127

description: H3 G34V mutation


title: BT2011020


title: BRL125

description: H3 G34R mutation


title: BTTB484


title: BRL128

description: H3 G34V mutation


title: BRL122

description: H3 WT

source_name: S. pombe WT cells

value: H3 WT


title: Control rep2

city: Lund

first: Saloe

middle: Bispo

last: Poubel

state: skane

address: Building 404:B3 Scheelevägen 2

country: Sweden

institute: Lund University

description: RBP-bound fraction

data_processing:
sequence were mapped against T. cruzi Sylvio X/10 genome v. 9., using bowtie v1.2.1.1 with parameters -f -Q -n 3 -C --best.
Enrichment analysis was performed in the EdgeR package from R software consisted of genes above 2-fold enrichment and p<0.01

organism: Trypanosoma cruzi

source_name: Epimastigotes

growth_protocol: T. cruzi Dm28c epimastigotes were grown in liver infusion tryptose (LIT) medium supplemented with 10% heat-inactivated fetal bovine serum at 28 ºC. Experiments were carried out at the exponential growth phase when the culture density was approximately 3x107 parasites/mL. Selected transfectants were confirmed for the tagged protein expression.

extract_protocol:
RBPs were co-immunoprecipitated with magnetic beads mobilized with anti-GFP. After proper wash, mRNAs were isolated with RNeasy Extraction Kit from Qiagen.
Sequencing libraries were prepared with the SOLiD Total RNA-Seq Kit (Applied Biosystems), selecting for fragments of 150-250 bp.

tag: strain

value: GFP-tag transfected epimastigotes


title: Control rep3

description: RBP-bound fraction


title: Control rep1

description: RBP-bound fraction

value: GFP-TcRBP40 transfected epimastigotes


title: BRL124

description: H3 G34R mutation

tag: genotype


title: TcRBP40 targets rep3

description: RBP-bound fraction


title: TcRBP40 targets rep1

description: RBP-bound fraction


title: TcRBP7 targets rep2

description: RBP-bound fraction

value: GFP-TcRBP7 transfected epimastigotes


title: TcRBP7 targets rep3

description: RBP-bound fraction


title: TcRBP7 targets rep1

description: RBP-bound fraction


title: BRL121

description: H3 WT


title: BRL131

description: H3 WT Set2D mutant


title: Day8 Ezh2-deficient Tfh rep2

status: Public on Nov 14 2018

city: Washington

first: Weiqun

last: Peng

state: DC

address: 1918 F Street, NW , DC

institute: The George Washington University

data_processing:
The sequencing quality of RNA-Seq libraries was assessed by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
RNA-Seq libraries were mapped to mouse genome using Tophat (v2.1.0, Trapnell et al., Bioinformatics). UCSC genes for mouse mm9 from iGenome (http://support.illumina.com/sequencing/sequencing_software/igenome.html) were used for gene annotation.
Mapped reads were then processed by Cuffdiff (v2.2.1, Trapnell et al., Nature biotechnology) to estimate expression levels of all genes and identify differentially expressed genes (FDR = 0.05). The expression level of a gene is expressed as a gene-level Fragments Per Kilobase of transcripts per Million mapped reads (FPKM) value.
Genome_build: mm9
Supplementary_files_format_and_content: Excel file includes FPKM values for each Sample ...

source_name: Tfh cells

extract_protocol:
Tfh cells were sort-purified and total RNA was extracted using standard Qiagen RNease columns
RNA libraries were prepared for sequencing using stardard Illumina protocol

value: splenic Tfh cells

tag: cell phenotype

value: CD4+, CXCR5+, SLAM-low, CD44-high, and CD62L low


title: Day8 WT Tfh rep2

value: wild type


title: Day8 WT Tfh rep1


title: Tcf1-deficient CD4+, Tcf1 ChIP-Seq

data_processing:
The sequencing quality of ChIP-Seq libraries was assessed by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Bowtie2 (v2.2.5, Langmead et al., Nature Methods) was used to align the sequencing reads to the mouse genome. UCSC genes for mouse mm9 from iGenome (http://support.illumina.com/sequencing/sequencing_software/igenome.html) were used for gene annotation.
SICER (v1.1, Zang et al., Bioinformatics) was used for peak calling. In each library, islands were identified with false discovery rate (FDR) of less than 1E-4 and island-filtered tags were used for downstream analysis.
Genome_build: mm9

source_name: naïve CD4 T cells

extract_protocol:
CD4+ follicular helper T cells were sort-purified on day 8 post-infection. Tcf1- or Ezh2-deficient naive CD4+ T cells were sorted from uninfected naive mice. The cells were then fixed and sonicated to generate chromatin fragments, followed by immunoprecipitation with antibodies against Tcf1 or Ezh2, which were then properly washed and immunoprecipitated DNA extracted.
The DNA segments from ChIP were end-repaired and ligated to indexed Illumina adaptors, followed by amplification by PCR with a low number of cells (18-21 cycles). The resulting libraries were seqeunced with Illumina Hiseq-2000 platform.

value: CD4-Cre, Tcf1 fl/fl

value: Tcf1-deficient naïve CD4+ T cells from the spleen

value: CD4+, CD62L high, CD44 low to medium

tag: chip antibody


title: Day8 Ezh2-deficient Tfh rep1


title: Day8 WT Tfh,  Ezh2 ChIP-Seq

value: WT Tfh cells from the spleen


title: WT_rep4

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

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

data_processing:
Signal intensities were converted to individual base calls during a run using the system's Real Time Analysis (RTA) software
Sequencing reads were retrieved as FASTQ files and then demultiplexed using CASAVA software suite version 1.8.2
Reads were aligned against the murine genome version mm10 using HISAT with all default options
BAM files were imported into Partek® Genomics Suite® software, version 6.6 Copyright©; 2017 (PGS)
Quantification of mRNA was performed against the mm10-RefSeq Transcripts database version 2016-02-02 to obtain read counts for each individual RefSeq gene; 18,939 genes were finally retrieved
The obtained read count table was normalized using the R package DESeq2 (Love et al., 2014) and then imported back into PGS
All normalized count values smaller than 1 were set to 1 to avoid spurious Fold-Changes later on
Genes were reduced to those, which had a mean normalized read count of 10 in at least one of the investigated groups for the corresponding dataset; 14,905 genes remained
Genome_build: mm10
Supplementary_files_format_and_content: TAB-delimited text file containing normalized abundance measurements for a filtered list of genes

source_name: visceral adipose tissue (VAT)

extract_protocol:
RNA extraction and purification was performed using RNeasy kits (Qiagen) according to manufacturer’s instructions.  Total RNA quality is determined by estimating the A260/A280 and A260/A230 ratios by nanodrop.   RNA integrity is determined by running an Agilent Bioanalyzer gel, which measures the ratio of the ribosomal peaks.
mRNA was purified from approximately 500ng of total RNA with oligo-dT beads and sheared by incubation at 94C.  Following first-strand synthesis with random primers, second strand synthesis was performed with dUTP for generating strand-specific sequencing libraries.  The cDNA library is then end-repaired, and A-tailed, adapters are ligated and second-strand digestion is performed by Uricil-DNA-Glycosylase. Indexed libraries that meet appropriate cut-offs for both are quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution determined with the LabChip GX or Agilent Bioanalyzer. Samples with a yield of ≥0.5 ng/ul are used for sequencing.

treatment_protocol: Cells were sorted on a BD FACS Aria into RPMI+20%FBS, stored on ice until they could be pelleted and resuspended in trizol for RNA extraction

value: macrophages

tag: cell markers

value: visceral adipose tissue (VAT)

tag: background strain


title: WT_rep2


title: Ezh2-deficient naïve CD4+, Ezh2 ChIP-Seq

value: CD4-cre, Ezh2 fl/fl

value: Ezh2-deificient naive CD4+ T Cells form the spleen


title: WT_rep3


title: WT_rep1


title: Nucb2_KO_rep3


title: Nucb2_KO_rep1


title: Nucb2_KO_rep2


title: BRL123

description: H3 WT


title: TcRBP40 targets rep2

description: RBP-bound fraction


title: Nucb2_KO_rep4


title: D0_2_MBDseq

city: Daejeon

first: Jong Hwan

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

department: Genome structure research center

institute: Korea Research Institute of Bioscience and Biotechnology

data_processing:
RNA_seq:
Illumina Casava1.7 software used for basecalling.
mapped to rn5 whole genome using STAR v2.5.1.
Gene expression levels were calculated count-per-million (CPM) values normalized with trimmed mean of M-values (TMM) using a edgeR v.3.12.1. The CPM values are on log2 scale.
MeDIP_seq and HMeDIP_seq:
Base calling performed using CASAVA version 1.7
mapped to rn5 whole genome using bowtie2 v.2.1.0
Methylation levels were called using MEDIPS v.1.12.0 (100 bp window). Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated each window. The rpkm values are on log2 scale.
ChIP seq:
Base calling performed using CASAVA version 1.7
mapped to rn5 whole genome using bowtie2 v.2.1.0
Enrichment levels were called using homer v.4.9.1. Histone modification ChIP-seq was prossed with homer histone option, and NFI ChIP-seq was prossed with homer transcription factor option.
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample
Supplementary_files_format_and_content: bedgraph files were generated using deeptools v.2.4.2

organism: Rattus norvegicus

extract_protocol:
MBD2-immunoprecipitated chromatin fragments were extracted for MeDIP-seq and HMeDIP-seq. The RNA sequencing library was prepared using the TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA, USA). and For ChIP-seq, Cells were fixed using 1% formaldehyde, lysed and sonicated using a Bioruptor (Diagenode Inc.).
We collected MBD2-immunoprecipitated chromatin fragments and genomic libraries were constructed using the TruSeq ChIP Sample Prep Kit (Illumina). RNA libraries were prepared for sequencing using standard Illumina protocols. For ChIP-seq, immunoprecipitation was performed with anti-H3K27ac (Abcam, ab4729) or anti-H3K4me1 (Abcam, ab8895). 250-400 bp genomic libraries were generated from the input and immunoprecipitated DNA and sequenced using Illumina HiSeq2000 to generate 75 bp single-end reads.

tag: strain background

value: Sprague-Dawley

value: neural stem cell

tag: cell type abbreviation

tag: tag

value: MBDseq


title: VC+_2_hMeDIPseq

description:
hMeDIPseq
H16_Rat_D5_AA_+__2.R1

value: differentiated neural stem cell with vitamin C

value: VC+

value: hMeDIPseq


title: VC-_1_hMeDIPseq

description:
hMeDIPseq
H8_Rat_D4_AA_-__1.R1

value: differentiated neural stem cell

value: VC-


title: VC-_NFI_ChIPseq

tag: chip antibody vendor

value: Santa Cruz

tag: chip antibody cat. #

tag: chip antibody lot/batch #

value: ChIPseq


title: VC+_NFI_ChIPseq

tag: cell type


title: Day8 WT Tfh, Tcf1 ChIP-Seq

value: wild type

tag: tissue

value: CD4+, CXCR5+, SLAM-low, CD44-high, and CD62L low


title: VC+_1_hMeDIPseq

description:
hMeDIPseq
H9_Rat_D4_AA_+__1.R1


title: VC+_NFI_Input

value: Input


title: VC+_2_MBDseq


title: VC-_2_hMeDIPseq

description:
hMeDIPseq
H15_Rat_D5_AA_-__2.R1


title: D0_1_hMeDIPseq

description:
hMeDIPseq
H7_Rat_D0_1.R1


title: D0_2_Input


title: D0_2_hMeDIPseq

description:
hMeDIPseq
H14_Rat_D0_2.R1


title: VC-_2_MBDseq


title: Nucb2_KO_rep5

value: macrophages


title: VC-_NFI_Input


title: VC-_1_MBDseq


title: VC-_2_RNAseq

description:
processed data file:
cpm_normalized_result.txt
H5_Rat_D5_AA_-__2.R1

value: RNAseq


title: VC+_2_RNAseq

description:
processed data file:
cpm_normalized_result.txt
H6_Rat_D5_AA_+__2.R1


title: VC-_1_RNAseq

description:
processed data file:
cpm_normalized_result.txt
H2_Rat_D4_AA_minus.R1


title: VC+_1_RNAseq

description:
processed data file:
cpm_normalized_result.txt
H3_Rat_D4_AA_plus.R1


title: D0_2_RNAseq

description:
processed data file:
cpm_normalized_result.txt
H4_Rat_D0_2.R1


title: D0_1_RNAseq

description:
processed data file:
cpm_normalized_result.txt
H1_Rat_D0.R1


title: D0_1_MBDseq


title: WT KDM5A 1

first: Lance

middle: E

last: Palmer

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

description: SJNBL043608_C1-HCT116-CRISPR-Ctrl-E1-KDM5A-AB1

data_processing:
Basecalls performed using CASAVA
BWA (version 0.5.9-r26-dev, default parameters) was used to align both input and sample ChIP-seq reads to the hg19 reference genome (GRCh37-lite)(parameter “-q 1 -F 1024” version 0.1.18 (r982:295)). We followed the ENCODE criterion to quality control (QC) the data that non-duplicated version of SPP (version 1.11) have been used to draw cross-correlation and calculated relative strand correlation value (RSC) under support of R (version 2.14.0) with packages caTools(version 1.17) and bitops(version 1.0-6) and estimated the fragment size.
Samtools (version: 0.1.17 (r973:277)) with the -q 1 -F 1024 parameters was used to exclude duplicated reads.
For quality control (QC) purposes and to estimate fragment size, SPP (version 1.11, for samples with duplicates removed) was used to generate cross-correlation plots using R (version 2.14.0) with the caTools(version 1.17) and bitops (version 1.0-6) packages.  All data passed QC following ENCODE criterion.
BAM files were converted to BED files using bamToBed (Bedtools version 2.17.0). The fragment sizes estimated by SPP were used to extend each read in a new BED file
Per base coverage was determined with genomeCoverageBed (Bedtools) and scaled to 15 million reads total.
MACS2 (version 2.0.9 20111102, nomodel with extsize defined as fragment size estimated by SPP) was used to call peaks from the original BED file generated above.  For each each different ChIP-Seq experiment (H3K4me3, KDM5A), peaks were combined using merge from Bedtools.
Genome_build: hg19(GRCh37)
Supplementary_files_format_and_content: bigWig,bed

source_name: HCT116 cells

growth_protocol: Cells were cultured in DMEM media with 10%  FCS, 1% L-glutamine, 1% penicillin–streptomycin, at 37 °C in 5% CO2.

extract_protocol:
DNA was extracted by Qiagen PCR purification kit
Libraries were prepared from the ChIP material using the ChIP-Seq Sample Prep Kit (Illumina) and sequenced on Illumina HiSeq 2000 (50-bp reads).

value: HCT116 cells

value: WT

tag: ip


title: KDM5A KO H3K4me3 1

description: SJNBL043610_C1-HCT116-CRISPR-KDM5A-A12-H3K4me3-AB3

value: KDM5A KO


title: KDM5A KO H3K4me3 2

description: SJNBL043611_C1-HCT116-CRISPR-KDM5A-D12-H3K4me3-AB3


title: WT KDM5A 2

description: SJNBL043609_C1-HCT116-CRISPR-Ctrl-E9-KDM5A-AB1


title: KDM5A KO input 2

description: SJNBL043611_C1-HCT116-CRISPR-KDM5A-D12-INPUT


title: WT H3K4me3 1

description: SJNBL043608_C1-HCT116-CRISPR-Ctrl-E1-H3K4me3-AB3


title: VC+_1_MBDseq

value: Sprague-Dawley


title: D0_1_Input

value: neural stem cell


title: WT input 2

description: SJNBL043609_C1-HCT116-CRISPR-Ctrl-E9-INPUT


title: WT input 1

description: SJNBL043608_C1-HCT116-CRISPR-Ctrl-E1-INPUT


title: DL1

city: Seoul

first: Eun Jung

last: Thak

address: 84, Heukseok-ro, Dongjak-gu

institute: CHUNG-ANG University

data_processing:
The sequence data for the reference genome was retrieved from the NCBI database.
Quality-filtered reads were aligned to the reference-genome sequence using Bowtie2.
The relative transcript abundance was measured in fragments in reads per kilobase of exon sequence per million mapped sequence reads (FPKM).
The eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) database was used to cluster genes into functionally related groups and the KEGG (Kyoto Encyclopedia of Genes and Genomes) database was used to analyze metabolic pathway.
Visualization of mapping results and differentially expressed gene (DEG) analysis were performed using the CLRNASeqTM program (ChunLab, South Korea).
Genome_build: GCF_000187245.1

organism: Ogataea parapolymorpha

source_name: yeast

growth_protocol: H. polymorpha DL1-L strain were grown to an OD600 of 1.0 in YPD medium at 37°C.

extract_protocol:
Total RNA was isolated according to the hot phenol extraction method.
Libraries for Illumina sequencing were made using the TruSeq Stranded mRNA Sample Prep kit (Illumina, USA) using the manufacturer’s protocol. RNA sequencing was performed on the Illumina HiSeq 2500 platform using paired-end 100-bp sequencing.

treatment_protocol: One-half of the cells was harvested, while the second half was treated with 20 mM caffeine for 2 hours.

tag: genotype/variation

value: leu-


title: exome16

status: Public on Nov 13 2018

first: Aikaterini

last: Symeonidi

state: Barcelona

address: Baldiri i Reixac, 10

department: Oncology

institute: Institut for Research in Biomedicine (IRB-Barcelona)

description: Mice were sacrificed when their largest tumour reached 1.5 mm diameter.

data_processing:
Quality trimming and removal of artifacts with Trimmomatic version 0.33 and parameters adapters-all.fa:2:30:10 TRAILING:5 SLIDINGWINDOW:4:15 MINLEN:25
Alignment to the mouse genome using BWA version 0.7.5a-r405
Removal of duplicated reads using samtools rmdup version 1.4.1
Realignment around INDELS, fixing the mates and recalibrating the base quality with GATK version 3.3-0-g37228af
Somatic calling using Strelka version 1.0.14
For the Control samples germline calling with GATK UnifiedGenotyper
Removal of germline mutations (as identified in the Control samples) from all somatic sets, using bedtools version v2.17.0
Genome_build: mm9
Supplementary_files_format_and_content: VCF files generated by Strelka

source_name: DMBA/TPA tumor G9a cKO

extract_protocol:
For whole exome sequencing, 1–2 105 tumour cells were FACS-sorted directly into 10 lysis buffer (200 mM DTT, 100 mM TrisHCl pH 7.4, 5% SDS, 5 µg µl–1 proteinase K) and incubated at 60C for 5 h, followed by isopropanol DNA precipitation. DNA was resuspended in 0.2 mg ml–1 RNase A (Promega) and incubated for 20 min at 37C. DNA was further purified using Agencourt AMPure XP DNA beads (Beckman Coulter), washed twice in 80% ethanol and eluted in TE buffer. DNA concentration was determined using a Qubit Fluorometer (Thermo Fisher). 50 ng of gDNA from each tumour was fragmented using a Bioruptor (Diagenode) to reach an average fragment size of 300–350 bp, and fragmentation was monitored using a 2100 BioAnalyser (Agilent).
Libraries for Exome capture were prepared using Kapa Library Prep Kit (KK8250) following the manufacturer´s instructions. 10 cycles of amplification.
Exome capture was done by hybridization of the amplified library (200 ng/library) to the SeqCap EZ Mouse library Design Name: 110624_MM9_Exome L2R_D02_EZ_HX1 Reference #: 9999042611 (Roche Nimblegen). The purified captured DNA was then amplified by Post-LM PCR for 13 cycles.

treatment_protocol: DMBA and TPA (200 µl of 0.25 mg ml–1 or 0.02 mg ml–1 solution in acetone, respectively) were applied once weekly to the shaved back skin of 8-week-old mice for 6 weeks. For tumour formation studies, TPA treatment was continued twice weekly for up to 20 weeks

tag: age begining of the treatment

value: G9a cKO


title: exome13

tag: strain


title: exome11

tag: genotype


title: exome15

source_name: DMBA/TPA tumor G9a WT

value: G9a WT


title: exome12


title: exome17


title: exome24


title: exome22


title: exome20


title: exome25


title: exome5


title: KDM5A KO input 1

description: SJNBL043610_C1-HCT116-CRISPR-KDM5A-A12-INPUT


title: exome3


title: exome4


title: exome26


title: exome10


title: DL1_Caffeine

tag: treated with

value: 20 mM caffeine for 2 h


title: WT H3K4me3 2

description: SJNBL043609_C1-HCT116-CRISPR-Ctrl-E9-H3K4me3-AB3


title: ControlKO

source_name: Homeostatic skin G9a cKO


title: exome2


title: exome8


title: ATAC12_WT

data_processing:
Quality trimming and removal of artifacts with Trimmomatic version 0.33 and parameters adapters-all.fa:2:30:10 TRAILING:5 SLIDINGWINDOW:4:15 MINLEN:25
Alignment of ATAC-seq reads with BWA version 0.7.5a-r405 and parameters 1) aln -n 2 -l 25 -k 1 2)sampe -a 2000 -o 1 -n 1
Removal of duplicated reads with samtools version 1.3.1
Random sampling of the reads to the lowest number of reads for each respective cell type (Bulge 10298844 paired-reads as in sample ATAC9_KO  and Interfollicular Epidermis  16358470 paired-redas as in sample ATAC10_KO)
Conversion of bam to bedpe format with bedtools version 2.17.0
Peak calling with MACS2 version 2.1.1.20160309 and parameters  –nomodel --shift 37 --extsize 73 --broad --broad-cutoff 0.05
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph files were generated using the genomecov command from the bedtools suite. Peaks falling within blacklisted regions (as defined in  http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm9-mouse/mm9-blacklist.bed.gz) have been removed

source_name: Homeostatic skin interfollicular epidermis cells G9a WT

extract_protocol:
To purify epidermal cells, back skins from mice  were incubated for 1 h in 0.25 % trypsin at 37 C. Trypsin activity was neutralized by the addition of 10% chelated FBS Ca2+-free EMEM, followed by mechanical dissociation and sequential filtration through 100 µm and 40 µm cell strainers (SPL Life Sciences).
Library preparation for ATAC sequencing used 50,000 IFE or bulge stem cells FACS-sorted from three independent mice as previously described in Buenrostro et al., Nat. Methods 2013

tag: age

value: 15-week old


title: ATAC16_WT


title: ATAC4_KO

source_name: Homeostatic skin interfollicular epidermis cells G9a cKO


title: ATAC14_KO


title: ATAC2_WT


title: ATAC10_KO


title: ATAC13_KO

source_name: Homeostatic skin bulge cells G9a cKO


title: K002000059_48027

status: Public on Nov 12 2018

city: Cologne

first: Andreas

last: Beyer

address: Joseph-Stelzmann-Str. 26

department: System Biology

institute: University of Cologne

data_processing:
Paired end total RNA-seq data was mapped to the mouse genome (mm10) using STAR aligner (v.2.5) with the default options and splice junction annotation from Ensembl (GRCm38.83).
Count value for each gene was obtained using featureCount command from subread program (v.1.5) with the following options: paired end (-p) only considering primary alignment (--primary) and strand-specific for reverse forward protocol (-s 2; -S fr).
For normalization, we used the transcript per millions (TPM).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include TPM for each sample.

extract_protocol:
All animals were perfused with phosphate buffered saline and kidneys were extracted immediately afterwards. Then they were divided into to halves and immediately put into liquid nitrogen. Afterwards they were stored at -80°C. until RNA preparation. From 1 µl input of total RNA, ribosomal RNA was removed using biotinylated target-specific oligos combined with Ribo-Zero rRNA removal beads. Samples of cytoplasmic rRNA wer depleted by the Ribo-Zero Human/Mouse/Rat kit. RNA was fragmented into small pieces using divalent cations under elevated temperature. After copying the cleaved RNA fragments into first strand cDNA using random primers and reverse transcriptase, the second strand cDNA synthesis was performed with DNA DNA Polymerase I and RNase H. Then single‘A’ base was added and subsequently adapter ligation took place.
RNA libraries were prepared for sequencing using standard Illumina protocols
RNA-seq total RNA – rRNA depleted by the Ribo-Zero Human/Mouse/Rat kit.

treatment_protocol: treatment: organ harvest 72 h hours after intraperitoneal cisplatin (cis) or vehicle (sodium chloride 0.9%, veh) injection.  HP: preconditioning of the mice by hypoxia (2 h, 4 h, 8 h) on three following days at least 1 h prior to injection  CR: preconditioning of the mice by calorie restriction 4 weeks prior to injection  BL: no preconditioning of the mice prior to injection

value: kidney

value: 20 weeks

tag: preconditioning

value: hypoxia

tag: injection


title: K002000059_48015

source_name: vehicle (sodium chloride 0.9%, veh) injection.

value: baseline


title: ATAC5_WT

source_name: Homeostatic skin bulge cells G9a WT


title: ATAC11_WT


title: ATAC3_KO


title: K002000059_48024

source_name: organ harvest 72 h hours after intraperitoneal cisplatin (cis)


title: ATAC15_WT


title: K002000059_48012

source_name: intraperitoneal cisplatin (cis)

value: caloric restriction

value: intraperitoneal cisplatin (cis)


title: K002000059_48014

value: vehicle (sodium chloride 0.9%, veh) injection.


title: K002000059_48013


title: ControlWT

source_name: Homeostatic skin G9a WT


title: K002000059_48011


title: K002000053_48004


title: K002000053_48003


title: H10m_rice_42oC_10min_riboseq_rep2.fastq.gz

city: University Park

first: Zhao

last: SU

state: PA

address: 354 N. Frear

department: Biology

institute: The Penn State University

description:
polysomal RNA
replicate 2

data_processing:
Approximately 150 million 150 bp single-end sequencing reads were obtained for each library. To calculate the translational efficiency change, firstly the adapter 5′-ACTGTAGGCACCATCAAT-3′ at the 3′ end of the reads were removed using cutadapt. Any reads shorter than 20 nt or longer than 40 nt or with a quality score < 30 (-q flag of cutadapt) were discarded. Reads were then mapped to rice reference genome and cDNA libraries using Bowtie2. As we obtained a high correlation between the 2 biological replicates in each condition, replicates were combined for further analysis. Translation efficiency in each condition are derived using Ribosome profiling library as (+) library and RNA-seq library at 10 min as the control libraries. Read depth of each nucleotide on each RNA is normalized by the total number of reads in each library and then the natural log (ln) is taken on the normalized read depth. Ribo-seq signal of each nucleotide is calculated by subtracting the normalized (and natural-logged) read depth of each nucleotide in the library from that in the (+) library.
Genome_build: ensemblgenomes_Oryza_sativa_release_31
Supplementary_files_format_and_content: txt file with ribo-seq signal data

organism: Oryza sativa

source_name: Shoot

growth_protocol: The wild-type rice were grown in greenhouse and shoot tissue of two-week-old plant was used for library preparation.

extract_protocol:
The RPFs (ribosome protected fragments) isolation and library construction were done as described in the literature45 with some major changes. Rice shoots were grounded into powder with liquid nitrogen. Two mL of tissue powder was used for each sample and then dissolved and homogenized in 10 ml polysome extraction buffer. The buffer contains 200 mM Tris-Cl (pH 8.0), 100 mM KCl, 25 mM MgCl2, 5 mM DTT, 1 mM PMSF, 100 μg/mL cycloheximide, 1% Brj-35, 1% TritonX-100, 1% Igepal CA630, 1% Tween-20, 1% polyoxyethylene 10 tridecyl ether. After centrifugation at 16 000 g for 10 min at 4 °C, the supernatant was collected. The supernatant was then layered on top of an 8 mL sucrose cushion (1.75 M sucrose in 200 mM Tris (pH 8.0), 100 mM KCl, 25 mM MgCl2, 5 mM DTT, 100 μg/mL cycloheximide), and centrifuged at 170 000 g at 4 °C for 3 h. The pellet was resuspended in 400 μL RNase I digestion buffer (50 mM Tris-Cl (pH 8.0), 100 mM KCl, 20 mM MgCl2, 1 mM DTT and 100 μg/mL cycloheximide). After adding 20 μL RNase I (Cat# AM2294, Thermo Fisher), RNase digestion was performed at room temperature with rotation for 2 h.
TRIzol reagent (Cat# 15596026, Thermo Fisher) was used to extract the RPFs followed by fragment size selection using NucleoSpin miRNA kit (Cat# 740971, Macherey Nagel) to collect the fragments smaller than 200 nt. 10% of Urea-PAGE gel was then applied to size select 28-32 nt fragments. After dephosphorylation using PNK (Cat# M0201S, NEB), the RPFs were ligated to AIR adenylated RNA linker (Cat# 510201, BIOO Scientific). The ligation products were then subjected to reverse transcription using SSIII (Cat# 18080093, Thermo Fisher) and circularization using Circligase II (Cat# CL9021K, Illumina). Sequence libraries were ultimately obtained through PCR amplification by Q5 polymerase (Cat# M0491S, NEB). Ribosome profiling libraries were sequenced to generate single-end 100 nt reads done by the Genomics Core Facility at Penn State University.
Ribo-seq

treatment_protocol: The plants in pots were inverted and the shoots were immersed in a water bath at 22 °C or 42 °C for 10 min treatment.

value: two-week-old

tag: treatment

value: Heat

tag: temperature

value: 42 C for 10 min


title: C10m_rice_22oC_10min_riboseq_rep1.fastq.gz

description:
polysomal RNA
replicate 1

value: Control

value: 22 C for 10 min


title: ATAC9_KO


title: Rice_42oC_10min_plusDMS_rep3.fastq.gz

description: replicate 3

data_processing:
Library strategy: Structure-seq
Normalization of RT stop counts. For each transcript, the RT stop counts on each nucleotide is incremented by 1 and then taken natural log (ln), followed by normalization by the transcript’s abudance and length
Calculation of DMS reactivity. The raw DMS reactivity is calculated by subtracting the normalized RT stop counts between  (+) DMS and (-) DMS libraries
Perform normalization on the raw DMS reactivity θ(i) of all the nucleotides on all the transcripts to obtain the derived DMS reactivity of each nucleotide.
Normalization of DMS reactivities between conditions to obtain the final reactivity.
Genome_build: ensemblgenomes_Oryza_sativa_release_31
Supplementary_files_format_and_content: excel file with DMS reactivity change data
Supplementary_files_format_and_content: DMS_reactivity_RT.react.txt: This DMS reactivity file is the analyzed result of rice structure-seq datasets at 22oC with values to show DMS modification rate at single nucleotide resolution. This result can be used directly to fold and convert to RNA secondary structure.
Supplementary_files_format_and_content: DMS_reactivity_heat.react.txt: This DMS reactivity file is the analyzed result of rice structure-seq datasets at 42oC with values to show DMS modification rate at single nucleotide resolution. This result can be used directly to fold and convert to RNA secondary structure.

extract_protocol:
Total RNA for the 12 individual biological samples was obtained in a chemical fume hood using the NucleoSpin RNA Plant kit. For each sample, 300 µg total RNA comprised the starting material for two rounds of poly(A) selection using the Poly(A)Purist MAG Kit, in order to obtain high purity mRNA for library construction.
Reverse transcription was performed using SuperScript III First-Strand Synthesis System kit using the same RT primer as previously used (1): 5'CAGACGTGTGCTCTTCCGATCNNNNNN3' which is a fusion of a random hexamer and an Illumina TruSeq Adapter. The first-strand cDNA was size-selected above 52 nt on 8M urea 10% polyacrylamide gels to remove excess RT primer and increase the ligation efficiency in the next step. After recovering cDNA using the crush-soak method, the cDNA was dissolved in 5 µL RNase-free water. Ligation was performed using T4 DNA ligase which ligated the 3'end of the cDNA to a low bias single-stranded DNA linker /5Phos/TGAAGAGCCTAGTCGCTGTTCANNNNNNCTGCCCATAGAG/3SpC3/ where the underlined sequence can forms a hairpin structure and the random hexamer can then hybridize to any cDNA fragment. Reagents were added into the cDNA solution as follows: 2 µL 10x buffer, 2 µL 5M betaine, 2 µL 100 µM linker DNA, 8 µL 50% PEG8000, 1 µL T4 DNA ligase (400U/µL). The ligation was performed at 16°C for 6 h and then 30°C for 6 h, and the enzyme was then deactivated at 65°C for 15 min. The ligation product was size selected above 90 nts on 8M urea 10% polyacrylamide gels to remove extra single-stranded linker DNA and a 67 nt ligation byproduct, consisting of one copy of the hexamer and one copy of the linker DNA. After recovery using the crush-soak method, the purified ligation product was dissolved in 10 µL RNase-free water. PCR amplification was performed using a primer specific to the single-stranded linker DNA and fused with an Illumina TruSeq Universal Adapters.

treatment_protocol: For the 22°C treatment, non-DMS-treated (−DMS) and DMS-treated (+DMS) samples were prepared. 1 g of shoot tissue was excised from the plant immediately before each treatment. For the +DMS sample, the material was immersed in 20 mL DMS reaction buffer (40 mM HEPES (pH 7.5), 100 mM KCl, and 0.5 mM MgCl2) in a 50 mL conical centrifuge tube. Then 150 µl DMS was immediately added to the solution to a final concentration of 0.75% (~75 mM), followed by 10 min of gentle inversion and mixing for every 30 seconds. Next, to quench DMS in the reaction, dithiothreitol (DTT) at a final concentration of 0.5 M was supplied by adding 1.5 g DTT powder into the solution. After vigorous vortexing to dissolve the DTT, the quench proceeded for 2 min. The −DMS sample was processed through the same procedure without addition of DMS. Three biological replicates were prepared for each −/+ DMS sample for a total of six samples. For the heat shock treatment, −DMS and +DMS samples were similarly prepared but under 42°C.

value: shoot

value: +DMS


title: K002000053_48001


title: Rice_42oC_10min_plusDMS_rep2.fastq.gz

description: replicate 2


title: K002000059_48022


title: K002000059_48023


title: K002000059_48025

value: organ harvest 72 h hours after intraperitoneal cisplatin (cis)


title: Rice_42oC_10min_plusDMS_rep1.fastq.gz

description: replicate 1


title: C10m_rice_22oC_10min_riboseq_rep2.fastq.gz

description:
polysomal RNA
replicate 2


title: Rice_42oC_10min_minusDMS_rep2.fastq.gz

description: replicate 2

value: −DMS


title: exome1

value: G9a WT


title: Rice_42oC_10min_minusDMS_rep3.fastq.gz

description: replicate 3


title: Rice_22oC_10min_plusDMS_rep3.fastq.gz

description: replicate 3


title: HR10h_rice_42oC_10min_30oC_9h50min_rep2.fastq.gz

description:
replicate 2
HR10h_2

data_processing:
Approximately 40-50 million 150 bp single-end sequencing reads were obtained for each library. After sequencing, adapter contamination was computationally removed from the libraries and adapter sequences were trimmed from the 3′ ends of the raw reads using cutadapt. Low-quality bases (Q < 30) were also trimmed from both the 5′ and 3′ ends of the reads. Next, reads from each of the four libraries were mapped independently to the rice genome (IRGSP-1.0) using Tophat2, with a GTF (Gene Transfer File) annotation file supplied as an argument.Transcript abundance and differential gene expression were calculated using Cufflinks. Gene expression levels were normalized using fragments per kilobase of exon per million mapped reads (FPKM).
Genome_build: ensemblgenomes_Oryza_sativa_release_31
Supplementary_files_format_and_content: text file with FPKM data

extract_protocol:
Total RNA was extracted from each sample using the NucleoSpin RNA plant kit (Cat# 740949, Macherey-nagel). Examination of the quantity and quality of these RNA samples was determined by NanoDrop 2000 (Thermo Fisher Scientific, USA) and Bioanalyzer 2100 (Agilent Genomics, USA).
Total RNA samples were sent to the Genomics Core Facility at Penn State University for the standard RNA-seq library preparation and next generation sequencing (Hiseq 2500, Illumina).

treatment_protocol: Two week old rice plants in pots were inverted and the shoots were immersed in a water bath at 22°C or 42°C for 10 min treatment, and the plants were then transferred to a growth chamber set at the same temperature as in the greenhouse (30°C) for ease of sampling during the recovery period. Three rice shoots comprised one biological replicate, and two biological replicates were obtained for each treatment and time-point.

value: 42°C for 10 min, then 30°C for 9h50 min


title: HR10h_rice_42oC_10min_30oC_9h50min_rep1.fastq.gz

description:
replicate 1
HR10h_1


title: Rice_22oC_10min_plusDMS_rep1.fastq.gz

description: replicate 1


title: K002000053_48002

value: kidney

value: 20 weeks


title: Rice_22oC_10min_minusDMS_rep2.fastq.gz

description: replicate 2


title: Rice_22oC_10min_plusDMS_rep2.fastq.gz

description: replicate 2


title: Rice_22oC_10min_minusDMS_rep3.fastq.gz

description: replicate 3


title: HR2h_rice_42oC_10min_30oC_1h50min_rep2.fastq.gz

description:
replicate 2
HR2h_2

value: 42°C for 10 min, then 30°C for 1h50 min


title: H10m_rice_42oC_10min_riboseq_rep1.fastq.gz

description:
polysomal RNA
replicate 1


title: HR2h_rice_42oC_10min_30oC_1h50min_rep1.fastq.gz

description:
replicate 1
HR2h_1


title: HR1h_rice_42oC_10min_30oC_50min_rep2.fastq.gz

description:
replicate 2
HR1h_2

value: 42°C for 10 min, then 30°C for 50 min


title: K002000059_48026

value: hypoxia


title: K002000053_48000

data_processing:
Paired end total RNA-seq data was mapped to the mouse genome (mm10) using STAR aligner (v.2.5) with the default options and splice junction annotation from Ensembl (GRCm38.83).
Count value for each gene was obtained using featureCount command from subread program (v.1.5) with the following options: paired end (-p) only considering primary alignment (--primary) and strand-specific for reverse forward protocol (-s 2; -S fr).
For normalization, we used the transcript per millions (TPM).
Genome_build: mm10
Supplementary_files_format_and_content: CSV file include TPM for each sample.

value: baseline

value: intraperitoneal cisplatin (cis)


title: Rice_42oC_10min_minusDMS_rep1.fastq.gz

description: replicate 1

value: two-week-old


title: Rice_22oC_10min_minusDMS_rep1.fastq.gz

description: replicate 1


title: C20m_rice_22oC_10min_30oC_10min_rep1.fastq.gz

description:
replicate 1
C20m_1

value: 22°C for 10 min, then 30°C for 10 min


title: C10m_rice_22oC_10min_rep1.fastq.gz

description:
replicate 1
C10m_1

value: Control

value: 22°C for 10 min


title: H10m_rice_42oC_10min_rep2.fastq.gz

description:
replicate 2
H10m_2

value: Heat

value: shoot

value: 42°C for 10 min


title: C1h_rice_22oC_10min_30oC_50min_rep1.fastq.gz

description:
replicate 1
C1h_1

value: 22°C for 10 min, then 30°C for 50 min


title: H10m_rice_42oC_10min_rep1.fastq.gz

description:
replicate 1
H10m_1


title: C10h_rice_22oC_10min_30oC_9h50min_rep2.fastq.gz

description:
replicate 2
C10h_2

value: 22°C for 10 min, then 30°C for 9h50 min


title: HR1h_rice_42oC_10min_30oC_50min_rep1.fastq.gz

description:
replicate 1
HR1h_1


title: HR20m_rice_42oC_10min_30oC_10min_rep1.fastq.gz

description:
replicate 1
HR20m_1

value: 42°C for 10 min, then 30°C for 10 min


title: HR20m_rice_42oC_10min_30oC_10min_rep2.fastq.gz

description:
replicate 2
HR20m_2


title: C2h_rice_22oC_10min_30oC_1h50min_rep1.fastq.gz

description:
replicate 1
C2h_1

value: 22°C for 10 min, then 30°C for 1h50 min


title: C2h_rice_22oC_10min_30oC_1h50min_rep2.fastq.gz

description:
replicate 2
C2h_2


title: H_pC

city: Dalian

first: Yang

last: Wang

address: No.9 West section, South Lv Road

institute: Dalian Medical University

data_processing:
Base-calling performed with CASAVA 1.8.2 software
Alignment performed with Tophat software, aligning to Human Genome Consortium Reference Human Genome hg19
Relative abundances calculated using Cufflinks software
The change of splicing isoforms were analyzed using MISO package with the annotation of all known alternative splicing events
Genome_build: hg19

source_name: lung cancer cells

growth_protocol: H1299 cells were cultured in RPMI-1640 medium containing 10% FBS.

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

treatment_protocol: H1299 cells were treated with or without 6 Gy ionizing radiation.

value: human lung cancer cells

tag: knockdown

value: control


title: H_6C

value: knockdown of SRSF1


title: H_6T

value: Ionizing radiation


title: C10h_rice_22oC_10min_30oC_9h50min_rep1.fastq.gz

description:
replicate 1
C10h_1


title: C1h_rice_22oC_10min_30oC_50min_rep2.fastq.gz

description:
replicate 2
C1h_2


title: UCLA1 PGCLC without SCF replicate 2 RNA-seq

status: Public on Nov 10 2018

city: Haining

first: Wanlu

last: Liu

state: Zhejiang

address: 718 East Haizhou Rd.,

department: Zhejiang University - University of Edinburgh Institute

institute: Zhejiang University

data_processing:
Raw reads in qseq format obtained from sequencer were first converted to fastq format with customized perl script. Reads quality were controlled with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). High quality reads were then aligned to hg19 reference genome using Tophat (Trapnell et al., 2009, v 2.0.13) by using ‘-no-coverage-search’ option, allowing up to two mismatches and only keeping reads that mapped to one location. Basically, reads were first mapped to hg19 gene annotation with known splice junction. When reads did not map to the annotated genes, the reads were mapped to hg19 genome. Number of reads mapping to genes were calculated by HTseq49 (v 0.5.4) with default parameters. Expression levels were determined by RPKM (reads per kilobase of exons per million aligned reads) in R using customized scripts.
Genome_build: hg19
Supplementary_files_format_and_content: RNASeq:raw reads count of all samples

source_name: PGCLC without SCF made from UCLA1 hESCs

extract_protocol:
Sorted cells or cell pellets were lysed in 350uL of RLT buffer (QIAGEN) and total RNA was extracted with RNeasy micro kit (QIAGEN, 74004). Total RNA was reverse transcribed and cDNA was amplified using Ovation RNA-Seq System V2 (Nugen, 7102-32) according to manufacturer’s instructions. Amplified cDNA was fragmented into ~200bp by Covaris S220 Focused-ultrasonicators.
RNA-seq libraries were generated using Ovation® Rapid Library Systems (Nugen, 0319-32 for index 1-8 and 0320-32 for index 9-16) and quantified by KAPA library quantification kit (Illumina, KK4824).
Library type = Ovation RNASeq System V2

value: PGCLC without SCF made from UCLA1 hESCs

tag: passage number

value: Passage 15


title: 4i PGCLC replicate 1 RNA-seq

description: 4i PGCLC replicate 1 RNA-seq

source_name: PGCLC made from 4i hESCs

value: PGCLC made from 4i hESCs

value: Not Available


title: 4i PGCLC replicate 2 RNA-seq

description: 4i PGCLC replicate 2 RNA-seq


title: 4i WIS2 hESC replate 2 RNA-seq

description: 4i WIS2 hESC replate 2 RNA-seq

source_name: 4i WIS2 hESCs

value: 4i WIS2 hESCs


title: 4i WIS2 hESC replate 1 RNA-seq

description: 4i WIS2 hESC replate 1 RNA-seq


title: C20m_rice_22oC_10min_30oC_10min_rep2.fastq.gz

description:
replicate 2
C20m_2

value: two-week-old

value: Control

value: 22°C for 10 min, then 30°C for 10 min


title: UCLA17 iMeLC induction replicate 1 RNA-seq

source_name: UCLA17 hESCs

value: UCLA17 hESCs

value: Passage 14


title: UCLA18 iMeLC induction replicate 1 RNA-seq

source_name: UCLA18 hESCs

value: UCLA18 hESCs

value: Passage 23


title: UCLA17 iMeLC induction replicate 2 RNA-seq


title: C10m_rice_22oC_10min_rep2.fastq.gz

description:
replicate 2
C10m_2

value: shoot

value: 22°C for 10 min


title: UCLA18 iMeLC induction replicate 2 RNA-seq


title: H_pT

value: human lung cancer cells

value: control


title: UCLA15 iMeLC induction replicate 1 RNA-seq

source_name: UCLA15 hESCs

value: UCLA15 hESCs


title: UCLA14 iMeLC induction replicate 2 RNA-seq

source_name: UCLA14 hESCs

value: UCLA14 hESCs

value: Passage 17


title: UCLA15 iMeLC induction replicate 2 RNA-seq

value: Passage 15


title: UCLA16 iMeLC induction replicate 1 RNA-seq

source_name: UCLA16 hESCs

value: UCLA16 hESCs

value: Passage 13


title: UCLA13 iMeLC induction replicate 2 RNA-seq

source_name: UCLA13 hESCs

value: UCLA13 hESCs

value: Passage 12


title: UCLA14 iMeLC induction replicate 1 RNA-seq


title: UCLA12 iMeLC induction replicate 2 RNA-seq

source_name: UCLA12 hESCs

value: UCLA12 hESCs


title: UCLA12 iMeLC induction replicate 1 RNA-seq


title: UCLA10 iMeLC induction replicate 2 RNA-seq

source_name: UCLA10 hESCs

value: UCLA10 hESCs


title: UCLA11 iMeLC induction replicate 1 RNA-seq

source_name: UCLA11 hESCs

value: UCLA11 hESCs


title: UCLA16 iMeLC induction replicate 2 RNA-seq


title: UCLA8 iMeLC induction replicate 2 RNA-seq

source_name: UCLA8 hESCs

value: UCLA8 hESCs


title: UCLA10 iMeLC induction replicate 1 RNA-seq


title: UCLA9 iMeLC induction replicate 2 RNA-seq

source_name: UCLA9 hESCs

value: UCLA9 hESCs

value: Passage 11


title: UCLA8 iMeLC induction replicate 1 RNA-seq


title: UCLA11 iMeLC induction replicate 2 RNA-seq


title: UCLA13 iMeLC induction replicate 1 RNA-seq


title: UCLA6 iMeLC induction replicate 2 RNA-seq

source_name: UCLA6 hESCs

value: UCLA6 hESCs


title: UCLA7 iMeLC induction replicate 2 RNA-seq

source_name: UCLA7 hESCs

value: UCLA7 hESCs


title: UCLA6 iMeLC induction replicate 1 RNA-seq


title: UCLA7 iMeLC induction replicate 1 RNA-seq

value: Passage 18


title: UCLA9 iMeLC induction replicate 1 RNA-seq


title: UCLA5 iMeLC induction replicate 2 RNA-seq

source_name: UCLA5 hESCs

value: UCLA5 hESCs

value: Passage 24


title: UCLA4 iMeLC induction replicate 1 RNA-seq

source_name: UCLA4 hESCs

value: UCLA4 hESCs


title: UCLA3 iMeLC induction replicate 2 RNA-seq

source_name: UCLA3 hESCs

value: UCLA3 hESCs


title: UCLA4 iMeLC induction replicate 2 RNA-seq


title: UCLA3 iMeLC induction replicate 1 RNA-seq


title: UCLA2 iMeLC induction replicate 2 RNA-seq

source_name: UCLA2 hESCs

value: UCLA2 hESCs


title: UCLA2 iMeLC induction replicate 1 RNA-seq


title: UCLA1 iMeLC induction replicate 1 RNA-seq

source_name: UCLA1 hESCs

value: UCLA1 hESCs


title: UCLA18 hESC induction replicate 2 RNA-seq

source_name: UCLA18 hESCs

value: UCLA18 hESCs

value: Passage 23


title: UCLA18 hESC induction replicate 1 RNA-seq


title: UCLA16 hESC induction replicate 2 RNA-seq

value: UCLA16 hESCs

value: Passage 13


title: UCLA17 hESC induction replicate 2 RNA-seq

source_name: UCLA17 hESCs

value: UCLA17 hESCs

value: Passage 15


title: UCLA16 hESC induction replicate 1 RNA-seq


title: UCLA14 hESC induction replicate 2 RNA-seq

source_name: UCLA14 hESCs

value: UCLA14 hESCs

value: Passage 17


title: UCLA1 iMeLC induction replicate 2 RNA-seq

value: Passage 12


title: UCLA14 hESC induction replicate 1 RNA-seq


title: UCLA15 hESC induction replicate 2 RNA-seq

source_name: UCLA15 hESCs

value: UCLA15 hESCs


title: UCLA12 hESC induction replicate 2 RNA-seq

value: UCLA12 hESCs


title: UCLA13 hESC induction replicate 2 RNA-seq

source_name: UCLA13 hESCs

value: UCLA13 hESCs


title: UCLA11 hESC induction replicate 1 RNA-seq

value: UCLA11 hESCs


title: UCLA11 hESC induction replicate 2 RNA-seq


title: UCLA10 hESC induction replicate 2 RNA-seq

value: UCLA10 hESCs


title: UCLA10 hESC induction replicate 1 RNA-seq


title: UCLA9 hESC induction replicate 2 RNA-seq

value: UCLA9 hESCs

value: Passage 11


title: UCLA15 hESC induction replicate 1 RNA-seq

value: Passage 14


title: UCLA13 hESC induction replicate 1 RNA-seq


title: UCLA12 hESC induction replicate 1 RNA-seq

source_name: UCLA12 hESCs


title: UCLA8 hESC induction replicate 2 RNA-seq

value: UCLA8 hESCs


title: UCLA7 hESC induction replicate 1 RNA-seq

value: UCLA7 hESCs

value: Passage 18


title: UCLA6 hESC induction replicate 2 RNA-seq

value: UCLA6 hESCs


title: UCLA6 hESC induction replicate 1 RNA-seq


title: UCLA8 hESC induction replicate 1 RNA-seq


title: UCLA5 hESC induction replicate 2 RNA-seq

value: UCLA5 hESCs

value: Passage 24


title: UCLA17 hESC induction replicate 1 RNA-seq

value: UCLA17 hESCs


title: UCLA5 hESC induction replicate 1 RNA-seq


title: UCLA4 hESC induction replicate 2 RNA-seq

value: UCLA4 hESCs

value: Passage 13


title: UCLA4 hESC induction replicate 1 RNA-seq


title: UCLA2 hESC induction replicate 2 RNA-seq

value: UCLA2 hESCs


title: UCLA3 hESC induction replicate 1 RNA-seq

value: UCLA3 hESCs


title: UCLA1 hESC induction replicate 2 RNA-seq

value: UCLA1 hESCs

value: Passage 12


title: UCLA5 iMeLC induction replicate 1 RNA-seq


title: UCLA1 hESC induction replicate 1 RNA-seq


title: UCLA3 hESC induction replicate 2 RNA-seq


title: UCLA9 hESC induction replicate 1 RNA-seq


title: UCLA1 PGCLC without SCF replicate 1 RNA-seq

source_name: PGCLC without SCF made from UCLA1 hESCs

value: PGCLC without SCF made from UCLA1 hESCs


title: UCLA1 PGCLC with SCF replicate 2 RNA-seq

source_name: PGCLC with SCF made from UCLA1 hESCs

value: PGCLC with SCF made from UCLA1 hESCs

value: Passage 15


title: UCLA2 PGCLC with SCF replicate 1 RNA-seq

source_name: PGCLC with SCF made from UCLA2 hESCs

value: PGCLC with SCF made from UCLA2 hESCs


title: UCLA2 PGCLC with SCF replicate 2 RNA-seq

value: Passage 14


title: UCLA2 hESC induction replicate 1 RNA-seq

value: Passage 11


title: UCLA7 hESC induction replicate 2 RNA-seq

value: UCLA7 hESCs

value: Passage 17


title: UCLA2 PGCLC without SCF replicate 1 RNA-seq

source_name: PGCLC without SCF made from UCLA2 hESCs

value: PGCLC without SCF made from UCLA2 hESCs


title: UCLA2 PGCLC without SCF replicate 2 RNA-seq


title: Female 89d gonad sorted with INTa6/EpCAM RNA-seq*

source_name: 89d female fetal gonad

value: 89d female fetal gonad

value: Not Available


title: 26 - ALV-J-resistant chicken

city: Guangzhou

first: Xinheng

last: Zhang

state: Guangdong

address: No.483, Wushan Road, Tianhe District

department: Animal Science

institute: South China Agricultural University

data_processing:
Basecalls performed using CASAVA version 1.8
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).
The high quality reads were aligned to the reference genome/transcriptome with bowtie2 software and circRNAs were detected and identified with find_circ software. Raw junction reads for all samples were normalized by total mapped reads number and log2 transformed.
Differentially expressed circRNAs were identified by ttest between two groups.
Genome_build: galGal4
Supplementary_files_format_and_content: excel format; Number of raw and normalized junction reads.

organism: Gallus gallus

source_name: liver

extract_protocol:
Total RNA from each sample was used to prepare the circRNA sequencing library. 5 μg total RNA were pretreated to enrich circRNA using CircRNA Enrichment Kit (Cloud-seq Inc, China).
RNA libraries were constructed by using pretreated RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.
Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). The libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 150 cycles on Illumina HiSeq Sequencer according to the manufacturer’s instructions.

tag: phenotype

value: ALV-J-resistant chicken

tag: age for circrna-sequencing

value: post infection 10 weeks

tag: infection

value: ALV-J NX0101

tag: the date of infection alv-j nx0101

value: post natal day 1

value: liver


title: 4 - ALV-J-resistant chicken

tag: tissue


title: Female 89d gonad sorted with INTa6/EpCAM RNA-seq

tag: cell type


title: UCLA1 PGCLC with SCF replicate 1 RNA-seq


title: 3 - ALV-J-resistant chicken