title: E1910N

first: Howard

last: Yang

address: 37 CONVENT DR, Room 5120

department: CCR

institute: NCI

description: frozen tissue extracted by AllPrep DNA/RNA/Protein Mini kit from GIAGEN

hyb_protocol: For mRNA array, total RNA was reverse transcripted to cDNA, reverse transcripted to labelled aRNA, purified, fragmented, and hybridized to each array chip according to the manufacturer's instructions.

scan_protocol: The mRNA arrays were washed using Affymetrix fluidics stations, and scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: Microarray data were normalized using the RMA method .

label: Biotin

source_name: adjacent normal tissue

label_protocol: As per manufacturer (Affymetrix).

extract_protocol: Two methods were used to extract total RNA. One is by standard Trizol method and Second is by AllPrep DNA/RNA/Protein Mini Kit from QIAGEN. After extractiong, all are followed with qualification check by Agilent 2100.

value: adjacent normal tissue


title: UTP3-OE-ChIP

status: Public on May 12 2020

type: SRA

city: Beijing

first: Hai

last: Qi

address: Zhongguancun North Street

department: School of Medicine

country: China

institute: Tsinghua University

library_source: genomic

data_processing:
Basecalls performed using CASAVA version
Reads obtained from ChIP-seq/ATAC-seq library sequencing were aligned to the mm9 genome assembly using bowtie2 program with default parameters.
Reads obtained from RNA-seq library sequencing were aligned to the mm9 genome assembly using tophat with uniq mapping parameters.
Peaks were called using the MACS program (p < 10e-3).
Genome_build: mm9
Supplementary_files_format_and_content: bed files containing peaks called from ChIP-seq,  bedgraph files containing the sequencing signals of ChIP-seq or ATAC-seq
Supplementary_files_format_and_content: bedgraph files containing the sequencing signals of TT-seq

molecule: genomic DNA

organism: Mus musculus

source_name: FB(OE)-UTP3 mESC (constructed from BirA J1 mES cells)

growth_protocol:
ESCs  were maintained in strandard ES medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and supplied with 1011 U/ml recombinant leukemia inhibitory factor (LIF, millipore).
ESCs  were maintained in strandard ES medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and supplied with 1000 U/ml recombinant leukemia inhibitory factor (LIF, millipore). 293T cells  were maintained in medium supplemented with 10% heat-inactivated FCS, Penicillin-Streptomycin Solution (100 × stock, Life Technologies).

extract_protocol:
ChIP was done following previously protocol with modifications (Shen, 2008). Briefly, cells were crosslinked on plate with 3% FMA for 10 min, then quenched by 1/20 volume of 2.5 M glycine. after two times of ice cold PBS wash, cell were harvested by trypsin digestion, and lysis by 1 x nuclei lysis buffer. The lysate were further sonicated into average DNA size 200-500 bp. spin at 14000rpm for 15 min, transferred the supernatant into a new tube and diluted by adding 5 × volume of ChIP dilution buffer. Added 5 μg FLAG antibody, end to end rotate overnight at 4℃. The target were further captured by adding 20 ul Protein A/G UltraLink Resin, further rotated for 4 hours at 4℃. After thoroughly washing, the targeted DNA was eluted by elution buffer with protease K at 66℃.
Libraries were prepared by NEBNext Ultra II DNA library preparation kit according to the standard protocols provided by the manufacturer.

tag: cell type

value: embryonic stem cells

tag: treatment

tag: chip antibody

value: FLAG (Sigma-Aldrich, F3169)

tag: affinity purification

tag: strain


title: E1910T

type: RNA

city: Bethesda

state: MD

country: USA

molecule: total RNA

organism: Homo sapiens

source_name: tumor tissue

tag: tissue

value: tumor tissue


title: 12-0160p17Ctrl

city: Durham

first: Landon

middle: J

last: Hansen

state: NC

address: 203 Research Drive, MSRB1 Rm 171

institute: Duke University School of Medicine

description: Control

hyb_protocol: Product generated from the label protocol was hybridized onto the Affymetrix GeneChip Human Genome 2.0 plus array in Affymetrix GeneChip® hybridization oven 645, washed in Affymetrix GeneChip®  Fluidics Station 450 according to standard Affymetrix GeneChip® Hybridization, Wash, and Stain protocols. (Affymetrix, Santa Clara,CA).

scan_protocol: Arrays were scanned with Affymetrix GeneChip® Scanner 7G according to Affymetrix GeneChip protocols

data_processing: Data was initially processed using the Affymetrix Expresson Console and Affymetrix Transcriptome Analysis Console v3.0 software

label: biotin

source_name: Patient-derived GBM cell line_MTAP deleted

label_protocol: Total RNA were assessed for quality with Agilent 2100 Bioanalyzer G2939A (Agilent Technologies,Santa Clara, CA)) and Nanodrop 8000 spectrophotometer (Thermo Scientific/Nanodrop, Wilmington, DE). Hybridization targets were prepared with the affymetrix GeneChip 3' IVT Plus Kit from total RNA.

growth_protocol: Patient derived GBM cell lines were grown in human Neural Stem Cell media following the NeuroCult NS-A Proliferation Protocol

extract_protocol: Total RNA was extracted using the Zymo Quick RNA prep kit

tag: cell line

value: patient-derived primary glioblastoma cell line

tag: genotype/variation

value: MTAP Deleted

tag: treated with

value: vehicle control NaOH (1:1000 dilution)


title: 12-0106p9Ctrl

description: Control


title: E1905N


title: E1905T


title: case4-liver1

city: Boston

first: David

middle: T

last: Ting

state: MA

address: 149 E 13th street

department: Cancer Center

institute: Massachusetts General Hospital

library_source: transcriptomic

data_processing:
Reads aligned to HG38
Deduplicated BAM files used with HTSeq-Count to create count tables
Data was analyzed with DESeq2 for differential expresison analysis
Genome_build: GRCH38
Supplementary_files_format_and_content: Text file with raw counts
Supplementary_files_format_and_content: Text file with DESeq2 Normalized counts

molecule: polyA RNA

source_name: liver

growth_protocol: Rapid autopsy was performed for samples collection.

extract_protocol:
RNA extraction from FFPE slides was done using the FormaPure Total nucleic acid extraction kit (C16675, Beckman Coulter) according to manufacturer instructions. Three 5 um thin tissue sections from areas devoid of acute inflammation were used per sample
The Smarter Stranded Total RNA-Seq kit v2 (634413, Illumina) was used with 10 ng RNA input, according to the manufacturer instructions to generate libraries.
Dual-indexed pooled libraries were sequenced on the Illumina NextSeq 500 platform using a 150 cycles kit with paired end read mode.

treatment_protocol: Samples were formalin fixed for 3 days prior to embedding in paraffin and sectioning.

tag: sample case

tag: tissue type

value: Formalin fixed paraffin embedded tissue

tag: pool no

tag: infection


title: HSD male rat liver tissue S1P1_F06

city: Research Triangle Park

first: Will

last: Gwinn

address: 111 Alexander Dr.

department: National Toxicology Program

institute: National Institute of Health Sciences

description: HSD male rat liver tissue

data_processing:
TempO-Seq data are analyzed using the Tempo-SeqR software package using the statistical computing  language R. The input for TempO-Seq data analysis is a folder of zipped FASTQ files. Each FASTQ file contains  the reads and quality scores for one sample. Each FASTQ file is aligned using the Bowtie algorithm to a pseudotranscriptome  input by the user. The output for TempO-Seq data analysis is a table of counts with each column  representing a sample and each row representing a gene.
Data normalization was not done
Supplementary_files_format_and_content: Raw data matrix all smaples

organism: Rattus norvegicus

extract_protocol: The liver and left and right kidneys were collected, weighed, and the left liver lobe and right kidney were preserved in RNAlater (Qiagen, Valencia, CA) and stored at 4°C for RNA extraction. Total RNA was extracted from liver and kidney within 1 week of harvest using the RNeasy Mini Kit (Qiagen) with a DNA digestion step. RNA was sent frozen to BioSpyder (Carlsbad, CA) for HTT analysis using the rat S1500+ TempO-Seq platform.

treatment_protocol: Eight to ten concentrations plus vehicle control were tested for each of the eighteen selected chemicals with n = 4 rats per exposure concentration. Exposure concentrations for each chemical were selected based on those used in the chronic or sub-chronic toxicity study and included concentrations that were both higher and lower than those previously tested. Whenever possible, the gavage vehicle was matched to that used in the chronic or sub-chronic study; however, multiple chemicals were orally administered in feed (MTE, DEHP, PFOA, EE2, and TCPP) or drinking water (BDCA and ACR) in the chronic or sub-chronic study. On day 5, the rats were weighed and euthanized via exsanguination.

value: Sprague Dawley

tag: gender

value: male

tag: age

value: 8-10 weeks

tag: animal id

value: liver

tag: chemical

value: Triclosan

tag: dose(mg/kg)


title: case4-heart1

source_name: heart


title: case4-lung1

source_name: lung


title: PSPC1-24h-TTseq-2

source_name: AID-FB(KI)-PSPC1 mESC (constructed from CJ9 mES cells)

growth_protocol:
ESCs  were maintained in strandard ES medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and supplied with 1000 U/ml recombinant leukemia inhibitory factor (LIF, millipore).
ESCs  were maintained in strandard ES medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and supplied with 1000 U/ml recombinant leukemia inhibitory factor (LIF, millipore). 293T cells  were maintained in medium supplemented with 10% heat-inactivated FCS, Penicillin-Streptomycin Solution (100 × stock, Life Technologies).

extract_protocol:
TT-seq was performed as described previously with some modifications (Schwalb et al., 2016; Yin et al., 2020). Cells were labeled in media for 10 minutes with 500 µM 4-thiouridine (4sU, Sigma-Aldrich, St. Louis, MO, USA.). RNA extraction was performed with TRIzol (Life Technologies, Carlsbad, CA, USA). Labelled RNAs were further biotinylated and fragmented as previously described. The fragmented RNAs were then subjected to two times of affinity purification. After first time affinity capture by M-280 dynabeads (Invitrogen), beads were washed 2 times (5-10 min each) with 0.5 ml of washing buffer (100 mM Tris pH 7.4, 10 mM EDTA, 1 M NaCl, 0.1% Tween-20) at 45 ℃, followed by another 2 times of wash with 0.5 ml of SDS washing buffer (50 mM Tri-Cl, pH8.1, 10 mM EDTA, 1% SDS) at room temperature. RNA was eluted by 50 μl SDS washing buffer at 95 °C for 5 minutes. Repeat once and combine the eluate. 50 μl pre-washed M280 beads were added to the eluate and incubated for another 20 minutes with rotation at room temperature. Beads were washed as described above. RNA was eluted with 100 µl SDS washing buffer supplemented with 0.1 M dithiotheitol (DTT) and purified as reported.
Libraries were prepared by NEBNext Ultra II directional RNA library prep kits according to the standard protocols provided by the manufacturer.

treatment_protocol: Cells were treated by adding 1 mM IAA, and culture at 37℃ for 24 hours

tag: cell type

tag: treatment

value: IAA, 24 hours

value: M280 Streptavidin Dynabeads (Invitrogen, 11205D)


title: PSPC1-24h-TTseq-1

tag: chip antibody

tag: affinity purification


title: HSD male rat liver tissue S1P1_F05

description: HSD male rat liver tissue

tag: strain

tag: tissue


title: case3-lung2


title: E1902N


title: E1901T


title: HSD male rat liver tissue S1P1_F04

description: HSD male rat liver tissue


title: HSD male rat liver tissue S1P1_F03

description: HSD male rat liver tissue


title: PSPC1-6h-TTseq-2

treatment_protocol: Cells were treated by adding 1 mM IAA, and culture at 37℃ for 6 hours

value: IAA, 6 hours


title: case3-heart1


title: PSPC1-6h-TTseq-1


title: PSPC1-3h-TTseq-2

treatment_protocol: Cells were treated by adding 1 mM IAA, and culture at 37℃ for 3 hours

value: IAA, 3 hours


title: hnRNPU-OE-ChIP

source_name: FB(OE)-hnRNPU mESC (constructed from BirA J1 mES cells)

growth_protocol:
ESCs  were maintained in strandard ES medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and supplied with 1007 U/ml recombinant leukemia inhibitory factor (LIF, millipore).
ESCs  were maintained in strandard ES medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and supplied with 1000 U/ml recombinant leukemia inhibitory factor (LIF, millipore). 293T cells  were maintained in medium supplemented with 10% heat-inactivated FCS, Penicillin-Streptomycin Solution (100 × stock, Life Technologies).

extract_protocol:
ChIP was done following previously protocol with modifications (Shen, 2008). Cells were crosslinked by 2 mM DSP (dithiobis succinimidyl propionate) for 30 minutes, followed by a 10-minute 1% formaldehyde crosslinking. The crosslinked cells were first partially fragmented by 12 U/ml DNase I at 37 °C for 10 minutes, then sonicated at 25% amplitude for 30 seconds. The lysate were further sonicated into average DNA size 200-500 bp. spin at 14000rpm for 15 min, transferred the supernatant into a new tube and diluted by adding 5 × volume of ChIP dilution buffer. Added 5 μg FLAG antibody, end to end rotate overnight at 4℃. The target were further captured by adding 20 ul Protein A/G UltraLink Resin, further rotated for 4 hours at 4℃. After thoroughly washing, these samples were subjected to a second purification step using 30 μl M-280 Streptavidin Dynabeads (Invitrogen 11205D). The rest of the steps were performed as previously described (Shen et al., 2008)
Libraries were prepared by NEBNext Ultra II DNA library preparation kit according to the standard protocols provided by the manufacturer.

value: FLAG (Sigma-Aldrich, F3165)


title: HSD male rat liver tissue S1P1_F02

description: HSD male rat liver tissue


title: case2-heart1


title: case3-lung1


title: PSPC1-0h-TTseq-2

value: embryonic stem cells


title: PSPC1-3h-TTseq-1


title: E1897T


title: HSD male rat liver tissue S1P1_F07

description: HSD male rat liver tissue


title: E1897N

value: adjacent normal tissue


title: HSD male rat liver tissue S1P1_F01

description: HSD male rat liver tissue


title: case2-lung3


title: HSD male rat liver tissue S1P1_E12

description: HSD male rat liver tissue

value: TCAB


title: PSPC1-0h-TTseq-1


title: HSD male rat liver tissue S1P1_E11

description: HSD male rat liver tissue


title: case2-jejunum1

source_name: jejunum


title: E1892N


title: PSPC1-6h-Ser5P-2

extract_protocol:
ChIP was done following previously protocol (Shen, 2008). Briefly, cells were crosslinked on plate with 1% FMA for 10 min, then quenched by 1/20 volume of 2.5 M glycine. after two times of ice cold PBS wash, cell were harvested by trypsin digestion, and lysis by 1 x nuclei lysis buffer. The lysate were further sonicated into average DNA size 200-500 bp. spin at 14000rpm for 15 min, transferred the supernatant into a new tube and diluted by adding 5 × volume of ChIP dilution buffer. Added 2 μg antibody, end to end rotate overnight at 4℃. The target were further captured by adding 20 ul Protein A/G UltraLink Resin, further rotated for 4 hours at 4℃. After thoroughly washing, the targeted DNA was eluted by elution buffer with protease K at 65℃.
Libraries were prepared by NEBNext Ultra II DNA library preparation kit according to the standard protocols provided by the manufacturer.

value: Pol II Ser5P (CST, 13523)


title: E1892T

value: tumor tissue


title: HSD male rat liver tissue S1P1_E10

description: HSD male rat liver tissue


title: E1901N


title: PSPC1-6h-Ser5P-1


title: case2-lung1


title: HSD male rat liver tissue S1P1_E09

description: HSD male rat liver tissue


title: case1-heart1


title: HSD male rat liver tissue S1P1_E08

description: HSD male rat liver tissue


title: PSPC1-0h-Ser5P-2


title: PSPC1-0h-Ser5P-1


title: case1-lung4


title: HSD male rat liver tissue S1P1_E07

description: HSD male rat liver tissue


title: HSD male rat liver tissue S1P1_E06

description: HSD male rat liver tissue


title: PSPC1-6h-Ser2P-1

value: Pol II Ser2P (CST，13499)


title: PSPC1-0h-Ser2P-2


title: HSD male rat liver tissue S1P1_E05

description: HSD male rat liver tissue


title: PSPC1-6h-Ser2P-2


title: E1902T


title: HSD male rat liver tissue S1P1_E04

description: HSD male rat liver tissue


title: case1-lung1

value: Formalin fixed paraffin embedded tissue


title: HRAS-NTC-3

city: Melbourne

first: Keefe

last: Chan

state: VIC

address: 305 Grattan St

department: Division of Cancer Research

country: Australia

institute: Peter MacCallum Cancer Centre

data_processing:
The quality of the 3' end reads was assessed with FastQC 0.11.2.
Adapters were trimmed using Cutadapt v1.7
Reads were mapped to the human reference genome (hg19/GRCh37) using HISAT2 (v2.0.4)
Picard 1.125 was used to generate BAM indices and to calculate insert size.
Samtools 1.1.0 was used to sort and merge.
featureCounts (v1.6.2) was used to count the number of reads per gene with ENSEMBL GTF v87
Genome_build: hg19
Supplementary_files_format_and_content: csv file includes normalized counts for each sample

source_name: BJ-TERT fibroblasts

growth_protocol: BJ-TERT cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) + 20 mM HEPES, 17% Medium 199, 15% fetal bovine serum (FBS), and 1% GlutaMAXTM L-alanyl-L-glutamine dipeptide at 37°C under 5% CO2.

extract_protocol:
Total RNA was extracted using the Qiagen Rneasy Mini Kit as per the manufacturer's instructions.
RNA libraries were prepared for sequencing according to standard protocols (QuantSeq 3’ mRNA-Seq FWD, Lexogen).
3' RNA-seq

treatment_protocol: BJ-TERT cells were transduced with pBabe-puro or pBabe-puro-HRASG12V and RNA-seq was performed using total RNA extracted from triplicate samples on Day 14 post-transduction.

value: replicate 3

tag: timepoint

value: 14 days


title: case1-lung3


title: PSPC1-0h-Ser2P-1


title: case2-lung2


title: case1-lung2


title: HRAS-NTC-2

value: replicate 2


title: HRAS-NTC-1

value: replicate 1


title: HSD male rat liver tissue S1P1_D12

description: HSD male rat liver tissue

value: Sprague Dawley

value: male

value: 8-10 weeks

value: liver


title: PSPC1-0h-input

growth_protocol:
ESCs  were maintained in strandard ES medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and supplied with 1001 U/ml recombinant leukemia inhibitory factor (LIF, millipore).
ESCs  were maintained in strandard ES medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and supplied with 1000 U/ml recombinant leukemia inhibitory factor (LIF, millipore). 293T cells  were maintained in medium supplemented with 10% heat-inactivated FCS, Penicillin-Streptomycin Solution (100 × stock, Life Technologies).

extract_protocol:
ChIP was done following previously protocol with modifications (Shen, 2008). Briefly, cells were crosslinked on plate with 3% FMA for 10 min, then quenched by 1/20 volume of 2.5 M glycine. after two times of ice cold PBS wash, cell were harvested by trypsin digestion, and lysis by 1 x nuclei lysis buffer. The lysate were further sonicated into average DNA size 200-500 bp. spin at 14000rpm for 15 min, transferred the supernatant into a new tube and diluted by adding 5 × volume of ChIP dilution buffer. Added 5 μg FLAG antibody, end to end rotate overnight at 4℃. The target were further captured by adding 20 ul Protein A/G UltraLink Resin, further rotated for 4 hours at 4℃. After thoroughly washing, the targeted DNA was eluted by elution buffer with protease K at 65℃.
Libraries were prepared by NEBNext Ultra II DNA library preparation kit according to the standard protocols provided by the manufacturer.


title: PSPC1-KI-ChIP-2


title: T47D_input

city: Salt Lake City

first: Jason

last: Gertz

state: UT

address: 1950 Cir of Hope Dr

institute: University of Utah

data_processing:
Reads were aligned to hg19 using bowtie (Langmead et al., 2009) with the following parameters: -m 1 -t –best -q -S -l 32 –e 80 -n 2.
MACS2 (Zhang et al., 2008) was used to call peaks with a p-value cutoff of 1e-10 and the mfold parameter bounded between 5 and 50. The broad peak calling feature was used for H3K27ac ChIP-seq.
Bedtools (Quinlan and Hall, 2010) was used to count reads in peaks. A window of 2 kb centered on the summit was used for counting H3K27ac reads within peaks.
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files
Supplementary_files_format_and_content: narrowPeak files (from MACS2)

source_name: T47D  (Ductal carcinoma, mammary gland)

growth_protocol: T47D cells were maintained in RPMI 1640 (Gibco) supplemented with 10% FBS (Gibco) and 1% pencillin/streptomycin (Gibco). Cells were placed in either hormone-depleted RPMI (phenol red-free RPMI-1640 supplemented with 10% Charcoal/Dextran treated fetal bovine serum (HyClone) and 1% penicillin-streptomycin) or kept in full media: (RPMI 1640 (Gibco) supplemented with 10% FBS (Gibco) and 1% pencillin/streptomycin (Gibco)) for at least 6 days.

extract_protocol:
To crosslink chromatin, 37% formaldehyde (Sigma-Aldrich) was added directly to the media and allowed to incubate at room temperature for 10 minutes. Glycine was added at a final concentration of 125 mM to stop crosslinking, and cells were washed with cold 1X PBS. Plates were scraped in Farnham lysis buffer with 1X protease inhibitor (Thermo Fisher). Chromatin was sonicated using an Active Motif EpiShear Probe Sonicator with 6 cycles of 30 s, at 40% amplitude, with 30 s of rest. ChIP was performed as previously described (Reddy et al., 2009) using anti-ER (Santa Cruz HC-20) and anti-H3K27ac (Active Motif 39133) antibodies.
ChIP and library construction was performed as described in Reddy et al, Genome Research, 2009. The following antibodies were used: H3K27ac (Active Motif pAb Cat #39133) and ER (Santa Cruz HC-20) Libraries were sequenced on an Illumina HiSeq 2500 as single-end 50 basepair reads

treatment_protocol: For ER ChIP-seq, a 1 h 10 nM E2 induction was performed prior to harvest. For H3K27ac ChIP-seq, an 8 h 10 nM estradiol or DMSO treatment was performed prior to harvest.

value: input

tag: anibody target


title: T47D H3K27ac ChIP full media

value: Full Media

value: Histone 3 Lysine 27 acetylation (H3K27ac)


title: HSD male rat liver tissue S1P1_E01

description: HSD male rat liver tissue


title: PSPC1-KI-ChIP-1

value: embryonic stem cells

value: FLAG (Sigma-Aldrich, F3165)


title: pBabe-NTC-3

value: pBabe


title: T47D H3K27ac ChIP hormone stripped media

value: Hormone Stripped Media


title: HSD male rat liver tissue S1P1_D11

description: HSD male rat liver tissue

value: TCAB


title: Laryngeal Squamous Cell Carcinoma tissue 2

city: Harbin

first: Lianhao

last: Song

address: Baojian road

institute: Harbin Medical University

data_processing:
The BD RhapsodyTM analysis pipeline v1.0 and was used to process sequencing data
The sequencing reads were quality controled by FastQC v 0.11.7
The sequencing reads were trimming by fastp v 1.0
The transcripts were aligned to GRCh37 using STAR v 2.5.3a.
UMI adjustment was performed with the distribution-based error correction (DBEC) algorithms.
Genome_build: Genome Reference Consortium Human Build 37 (GRCh37)
Supplementary_files_format_and_content: csv files include the distribution-based error correction (DBEC) UMI counts for each sample.

source_name: laryngeal tissue of a 64-year-old male LSCC patient

extract_protocol:
For each tissue, half of the tissue was used for single-cell RNA sequencing and the other for formalin-fixed paraffin-embedded (FFPE) tissue. Each sequencing tissue was cut into about 1 mm3 pieces and digested by SoloTM Tumor Dissociation Kit (JZ-SC-58201) at 37°C for 90 min. After digestion, the cell suspension was filtered using a 70 um diameter filter. Dissociated cells were pelleted and re-suspended in PBS. Then the single-cell suspension was kept on ice until loading to BD Rhapsody cartridge for cDNA library construction.
LSCC01: cDNA Libraries for isolated single cells were generated based on the BD RhapsodyTM system with the following steps: RNA purifying, cDNA synthesising and sequencing. The main supplies were as follows: RNA was purified using Agencourt® AMPure® XP magnetic beads (Beckman Coulter, A63880) prior to reverse transcription with NEBNext® Ultra II Non-Directional RNA Second Strand Synthesis Module (NEB, E6111S), NEBNext® UltraTM II End Repair/dA-Tailing Module (NEB, E7546S) and NEBNext® UltraTM II Ligation Module (NEB, E7595S). Double strand full length cDNA was amplificated by random priming amplification with BD Rhapsody cDNA Kit (BD Biosciences, 633732). Full length cDNA libraries were targeted using the BD RhapsodyTM cDNA Kit (BD Biosciences, 633732). LSCC02: cDNA Libraries were constructed according to Singleron GEXSCOPETM protocol by GEXSCOPETM Single-Cell RNA Library Kit (Singleron Biotechnologies). Individual libraries were diluted to 4nM and pooled for sequencing. Each sample were pooled and sequenced as paired-end 150 base reads on the Illumina Hiseq 2500 instrument.

value: Laryngeal Squamous Cell Carcinoma (LSCC) Tissues

value: untreated

tag: Sex


title: pBabe-NTC-1

value: 14 days


title: Laryngeal Squamous Cell Carcinoma tissue 1

source_name: laryngeal tissue of a 66-year-old male LSCC patient

value: Laryngeal Squamous Cell Carcinoma (LSCC) Tissue


title: HSD male rat liver tissue S1P1_D09

description: HSD male rat liver tissue

value: Triclosan


title: HSD male rat liver tissue S1P1_E03

description: HSD male rat liver tissue

value: Sprague Dawley


title: Infection 24 hpi rep1

city: Chengdu

first: Yun

last: Shi

address: No 37, Guoxuexiang

institute: West China Hospital, Sichuan University

description:
4-1
processed data file: ALL_samples_RPKM.xlsx

data_processing:
Raw data of sequencing were cleaned using Trimmomatic software.
The clean reads after quality control were mapped to the mouse genome GRCm38 with STAR software (version 2.5.3a). The reads counts for each gene were calculated using FeatureCounts (version1.5.1) and expressed as RPKM (reads per kilobase per million reads). EdgeR package were used to identify the differentially expressed genes by statistics with an adjusted P value < 0.05 and log2(fold change) >1. Gene Ontology (GO) and (Kyoto Encyclopedia of Genes and Genomes) KEGG enrichment was done with Kobas (Version 2.1.1). Hierarchical clustering and heatmaps were drawn using pheatmap R package and MA-plot was drawn using EdgeR package.
Genome_build: GRCm38
Supplementary_files_format_and_content: ALL_samples_RPKM.xlsx: Excel file includes RPKM values.

extract_protocol:
Total RNAs were extracted from lung samples using TRIzol (Invitrogen) and DNA was digested by DNaseI after RNA extraction. A260/A280 was examined with NanodropTM One spectrophotometer (Thermo Fisher Scientific Inc) to determine RNA quality. RNA Integrity was confirmed by 1.5% agarose gel electrophoresis. Qualified RNAs were finally quantified by Qubit3.0 with QubitTM RNA Broad Range Assay kit (Life Technologies).
Total RNAs (2 μg) were used to prepare sequencing library using KC-Total RNA-seq Library Prep Kit for Illumina® (Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. PCR products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Hiseq X 10 sequencer (Illumina).

tag: genotype/variation

value: Lung

value: Acinetobacter baumannii

tag: time point

value: 24 hpi


title: PSPC1-6h-input

growth_protocol:
ESCs  were maintained in strandard ES medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and supplied with 1002 U/ml recombinant leukemia inhibitory factor (LIF, millipore).
ESCs  were maintained in strandard ES medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and supplied with 1000 U/ml recombinant leukemia inhibitory factor (LIF, millipore). 293T cells  were maintained in medium supplemented with 10% heat-inactivated FCS, Penicillin-Streptomycin Solution (100 × stock, Life Technologies).

value: IAA, 6 hours


title: Infection 24 hpi rep2

description:
4-2
processed data file: ALL_samples_RPKM.xlsx

tag: infection


title: HSD male rat liver tissue S1P1_D10

description: HSD male rat liver tissue

tag: gender

value: male

value: 8-10 weeks

value: liver


title: DC2_Myc_Rep2

city: Basel

first: Antoine

last: Peters

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research (FMI)

description: processed data file: CBX2.2_ChIPseq_TSS_count_table_v2.csv

data_processing:
Reads were mapped using the 'qAlign' function of the R/Bioconductor package QuasR
Reads corresponding to biological replicates were pooled for analysis
The QuasR::qCount function was used for calculation of promoter levels
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: 1 csv file is provided: a count table containing raw counts per promoter region (TSS +/- 1kb)

growth_protocol: Cells were grown in Dulbecco's modified eagle medium (DMEM) with 10% (v/v) fetal bovine serum.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 15 minutes before lysis and chromatin extraction. ChIP were performed overnight using Dynabeads (ThermoFisher Scientific) coupled with the appropriate antibodies. Beads were washed and crosslinking was reversed by heating samples at 65˚C overnight. Recovered DNA was subsequently purified with MinElute PCR Purification Kit (Qiagen) according to the manufacturer's protocol.
ChIP-Seq_NEB ultraII according to manufacturer’s instructions

treatment_protocol: Cells were transfected twice with the indicated plasmids using Lipofectamine 3000 (ThermoFisher Scientific) according to the manufacturer's protocol.

tag: transfection

value: DAXX-Myc and GAL4DBD-CBX2.2

value: Myc Tag, Abcam #ab9132

tag: transgene

value: Stable and unique insertion of a 5xUAS followed by Luciferase sequence in the first intron of NCOA5 (Stielow et al. EMBO Rep. 2008)


title: HSD male rat liver tissue S1P1_E02

description: HSD male rat liver tissue

tag: age

tag: animal id

tag: chemical


title: Control rep3

description:
1-3
processed data file: ALL_samples_RPKM.xlsx

value: Control


title: DC2_Myc_Rep1


title: pBabe-NTC-2

tag: cell type

value: replicate 2

tag: treatment

value: pBabe


title: HSD male rat liver tissue S1P1_D07

description: HSD male rat liver tissue

tag: dose(mg/kg)


title: Control rep2

description:
1-2
processed data file: ALL_samples_RPKM.xlsx


title: DC2_Input_Rep2

tag: chip antibody


title: Control rep1

description:
1-1
processed data file: ALL_samples_RPKM.xlsx

tag: tissue


title: Infection 24 hpi rep3

description:
4-3
processed data file: ALL_samples_RPKM.xlsx


title: HSD male rat liver tissue S1P1_D06

description: HSD male rat liver tissue

tag: strain


title: B Cell Control 7

first: Jack

last: Bibby

address: 10 Center Drive

institute: National Institutes of Health

data_processing:
Read alignment was conducted on Partek using STAR
The aligned reads were annotated using hg19
Data has not been filtered downstream of annotation
Genome_build: hg19
Supplementary_files_format_and_content: Processed data are provided as raw counts

source_name: Blood

extract_protocol:
RNA was isolated by column centrifugation using RNeasy Plus mini kit (with gDNA removal step) as per manufacturer’s instructions (Qiagen)
Library preparation was completed using NEBNext Ultra Directional RNA Library Prep Kit for Illumina. Depletion of ribosomal RNA was performed using Next rRNA Depletion kit (New England BioLabs). RNA quality was confirmed by bioanalyser (Agilent 2100 Bioanalyzer G2938B), resulting in a mean RIN score of 8.1, ranging from 7.3-8.7

value: B cell

tag: stimulation

value: CpG (1uM) for 12 hours


title: B Cell GGTi 5


title: B Cell Control 6


title: B Cell GGTi 6


title: B Cell GGTi 7


title: HSD male rat liver tissue S1P1_D05

description: HSD male rat liver tissue


title: DC2_Input_Rep1


title: HSD male rat liver tissue S1P1_D04

description: HSD male rat liver tissue


title: titanium estrogen 2

city: Providence

first: Tania

last: Emi

state: RI

address: 593 Eddy St.

department: Rhode Island Hospital

institute: Brown University

data_processing:
FASTQC was used for initial QC of raw reads and trimming by Trim Galore (parameters: quality- 20, adapter- AGATCGGAAGAGC, stringency- 1, length- 50).
Bismark was used to prepare the reference genome (Ensembl Release 89 of GRCm38) and to align trimmed reads using the Bowtie2 parameter. Bismark methylation extractor was used to extract methylation information.
The DSS package was used to find differentially methylated loci and regions. The DMLfit.multiFactor function was used to fit the model using an ~Estrogen*Additive formula. DMLtest.ultiFactor was used to find differentially methylated loci, and callDMR was used to find differentially methylated regions (DMR) with the p value ≤ 0.05 for threshold of statistical significance. The methyAnalysis package was used to annotate DMR with a flank range of 3000.
ClusterProfiler and enrichPlot were used to query and visualize enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways.
Genome_build: Ensembl Release 89 of GRCm38
Supplementary_files_format_and_content: Files are in bismark.cov; they contain chromosome names, start and end of genomic positions, percent methylation, number of methylated and unmethylated cytosines.

source_name: J774 cells

growth_protocol: J774 cells were cultured in phenol red free media, supplemented with FBS, L-glutamine, penicillin and streptomycin, and, HEPES.

extract_protocol:
DNA extraction by Qiagen DNeasy Blood and Tissue protocol
CpG enrichment by RRBS started with Msp1 restriction enzyme digestion, bisulfite conversion and next-generation sequencing library preparation

treatment_protocol: Cells were serum-starved for 24 hrs in macrophage-SFM prior to particle exposure. Then they were treated with 2 µg/mL of 17-β estradiol; 10 ug/well of Talc or TiO2; ethanol served as vehicle control.

tag: additive

value: titanium

tag: estrogen

value: estrogen


title: B Cell Control 5


title: titanium estrogen 3


title: DC2_Myc_Rep3


title: HSD male rat liver tissue S1P1_D03

description: HSD male rat liver tissue

value: Sprague Dawley


title: B Cell GGTi 4


title: DC2_Gal_Rep2

value: Gal4-DBD, Millipore #06-262


title: titanium estrogen 1


title: DC2_Gal_Rep1


title: B Cell Control 4


title: HSD male rat liver tissue S1P1_D02

description: HSD male rat liver tissue


title: titanium 3

value: no estrogen


title: B Cell GGTi 3


title: DC2_Gal_Rep3


title: titanium 2


title: DC1_Myc_Rep2

description: processed data file: CBX2.1_ChIPseq_TSS_count_table.csv

value: DAXX-Myc and GAL4DBD-CBX2.1


title: HSD male rat liver tissue S1P1_C12

description: HSD male rat liver tissue

value: male

value: TCAB


title: HSD male rat liver tissue S1P1_D01

description: HSD male rat liver tissue

value: 8-10 weeks

value: liver


title: B Cell Control 3


title: titanium 1


title: HSD male rat liver tissue S1P1_C11

description: HSD male rat liver tissue


title: DC1_Myc_Rep1

value: Myc Tag, Abcam #ab9132


title: B Cell GGTi 2


title: talc estrogen 2

value: talc


title: DC1_Input_Rep2

value: Stable and unique insertion of a 5xUAS followed by Luciferase sequence in the first intron of NCOA5 (Stielow et al. EMBO Rep. 2008)


title: talc estrogen 3


title: talc estrogen 1


title: DC1_Input_Rep1


title: DC1_Input_Rep3


title: B Cell GGTi 1


title: DC1_Myc_Rep3


title: HSD male rat liver tissue S1P1_C08

description: HSD male rat liver tissue

value: Triclosan


title: DC1_Gal_Rep3


title: B Cell Control 1


title: H4K20me3_4Gy

city: Seoul

first: Tae-Gul

last: Lee

address: 75 Nowon-Ro, Nowon-Gu

country: South Korea

institute: Korea Cancer Center Hospital

data_processing:
Illumina Casava1.8 software used for basecalling.
The reads were trimmed and aligned using Bowtie2 (Langmead and Salzberg, 2012).
We used MACS (Model-based Analysis of ChIP-Seq) to identify peaks from the alignment file.
Genome_build: hg19

extract_protocol:
ChIP assay was conducted using an EpiTect ChIP OneDay Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instruction.
The construction of library was performed using NEBNext®UltraTM DNA Library Prep Kit for Illumina (New England Biolabs, UK) according to the manufacturer’s instructions.

treatment_protocol: Cells were subjected to gamma radiation at the indicated doses in a BIOBEAM 8000 gamma irradiator (Gamma-Service Medical GmbH, Leipzig, Germany).

tag: cell line

value: NSCLC cell line

value: 4 Gy of gamma radiation

value: anti-H4K20me3 (Cell signaling technology, mAb #5737)


title: talc 2


title: talc 3


title: H4K20me3_0Gy

value: 0 Gy of gamma radiation


title: HSD male rat liver tissue S1P1_C07

description: HSD male rat liver tissue


title: B Cell Control 2

value: B cell

value: CpG (1uM) for 12 hours


title: Veh-4Gy

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Tophat
Read count extraction and nomalization were performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using Lexogen SENSE mRNA Library Preparation Kit standard protocols.

treatment_protocol: Cells were subjected to gamma radiation at the indicated doses in a BIOBEAM 8000 gamma irradiator (Gamma-Service Medical GmbH, Leipzig, Germany), and then treated with 2 uM of 3-deazaneplanocin A (DZNep) HCl (Selleck Chemicals, Houston, TX) or DMSO as a control for 48 h.

value: 4 Gy of gamma radiation, DMSO as a control


title: HSD male rat liver tissue S1P1_C09

description: HSD male rat liver tissue

value: Sprague Dawley


title: DC1_Gal_Rep2

value: DAXX-Myc and GAL4DBD-CBX2.1

value: Gal4-DBD, Millipore #06-262


title: DC1_Gal_Rep1


title: estrogen 3

value: estrogen


title: HSD male rat liver tissue S1P1_C04

description: HSD male rat liver tissue

value: male

value: 8-10 weeks


title: HSD male rat liver tissue S1P1_C10

description: HSD male rat liver tissue

value: liver


title: D_Myc_Rep3

value: DAXX-Myc

value: Myc Tag, Abcam #ab9132


title: estrogen 2


title: Veh-0Gy

value: 0 Gy of gamma radiation, DMSO as a control


title: DZNep-4Gy

value: NSCLC cell line

value: 4 Gy of gamma radiation, 2 uM of DZNep


title: D_Myc_Rep2

value: Stable and unique insertion of a 5xUAS followed by Luciferase sequence in the first intron of NCOA5 (Stielow et al. EMBO Rep. 2008)


title: HSD male rat liver tissue S1P1_B12

description: HSD male rat liver tissue

value: TCAB


title: estrogen 1


title: HSD male rat liver tissue S1P1_B11

description: HSD male rat liver tissue


title: DZNep-0Gy

value: 0 Gy of gamma radiation, 2 uM of DZNep


title: D_Input_Rep3


title: D_Myc_Rep1


title: vehicle 2

value: vehicle

value: no estrogen


title: vehicle 3


title: HSD male rat liver tissue S1P1_C05

description: HSD male rat liver tissue

value: Sprague Dawley


title: TAX_siDDX5/17_Replicat_3

city: lyon

first: franck

last: mortreux

address: 46 allee d'Italie

country: France

institute: oncovirology and Biotherapies, UMR5239, LBMC

description: The HTLV-1 TAX oncoprotein induces alternative splicing modifications in a DDX5/17 dependent manner

data_processing:
Trimming with Cutadapt (1.13)
Mapping & QC-mapped with Tophat2 (2.0.13) & Samtools (0.1.19)
Splicing analysis with FARLINE pipeline (doi: 10.1038/s41598-018-21770-7)
Gene expression analysis with HTSeq-count & package DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: excel files containing splicing events differentially observed (events : acceptor, donor, mutually exclusive, multi exon skipping) and genes differentially expressed. Xls & xlsx

source_name: HEK 293T-LTR-GFP

growth_protocol: cells were cultured in DMEM+Glutamax medium supplemented with decomplemented 10% FBS and 1% penicilline/streptomycine.

extract_protocol:
Total RNAs were extracted using TRIzol (Invitrogen)
RNA-seq libraries were generated at the Aros Applied Biotechnology (Aarhus, Denmark) using Stranded mRNA Sample Prep kit (Illumina, Reverse)

treatment_protocol: Transient transfection with siGL2, siDDX5/17, pSG5M-empty, and pSG5M-TAX

value: HEK 293T-LTR-GFP

value: siDDX5/17 + pSG5M-TAX

value: cells contain an integrated GFP reporter gene under the control of the TAX-responsive HTLV-1 LTR


title: TAX_siDDX5/17_Replicat_2


title: HSD male rat liver tissue S1P1_C06

description: HSD male rat liver tissue

value: male


title: talc 1

value: talc


title: D_Input_Rep1


title: HSD male rat liver tissue S1P1_C03

description: HSD male rat liver tissue

value: 8-10 weeks

value: liver


title: D_Input_Rep2

value: DAXX-Myc


title: HSD male rat liver tissue S1P1_B09

description: HSD male rat liver tissue

value: Triclosan


title: D_Gal_Rep3

value: Gal4-DBD, Millipore #06-262


title: vehicle 1


title: HSD male rat liver tissue S1P1_B08

description: HSD male rat liver tissue


title: HSD male rat liver tissue S1P1_B10

description: HSD male rat liver tissue


title: Control_siDDX5/17_Replicat_2

value: siDDX5/17 + pSG5M-empty


title: TAX_siDDX5/17_Replicat_1


title: HSD male rat liver tissue S1P1_D08

description: HSD male rat liver tissue


title: D_Gal_Rep2

value: Stable and unique insertion of a 5xUAS followed by Luciferase sequence in the first intron of NCOA5 (Stielow et al. EMBO Rep. 2008)


title: D_Gal_Rep1


title: HSD male rat liver tissue S1P1_B07

description: HSD male rat liver tissue


title: S_TG92

city: La Jolla

first: Timothy

last: Huang

state: CA

address: 10901 N Torrey Pines Rd.

institute: Sanford Burnham Prebys Medical Discovery Institute

data_processing:
Illumina CASAVA1.8 used for base calling.
Sequenced reads were trimmed for adaptor sequence, reads containing N > 10% (N represents base that cannot be determined) were removed; remove low quality reads: the quality value of over 50% bases of the read is <=20.
groups by using the DESeq2 R package, while the significant criterion is p<0.05
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for each sample

source_name: hippocampus

extract_protocol:
Total RNA was extracted from postnatal day 22 mouse motor cortex tissue using the RNA Extraction from Tissue kit (Kurabo, RT-S2).
NEBNext® UltraTM RNA library construction

tag: genotype

value: SORLA TG

value: c

value: hippocampus


title: S_TG1301


title: TAX_siGL2_Replicat_3

value: siGL2 + pSG5M-TAX


title: WT_87

value: WT


title: Control_siDDX5/17_Replicat_3

value: HEK 293T-LTR-GFP


title: S_TG91


title: HSD male rat liver tissue S1P1_B05

description: HSD male rat liver tissue

value: Sprague Dawley

tag: gender


title: Sample_27_VavPBcl2_SHMT2_repl3_ERRBS

city: New York

first: Matt

last: Teater

state: NY

address: 445 E 69th St

institute: Weill Cornell Medical College

data_processing:
Illumina Casava1.8 software used for basecalling.
ERRBS reads were aligned to a bisulfite-converted mm10 reference genome with Bismark and Bowtie 2 using default settings
Genome_build: mm10
Supplementary_files_format_and_content: Methylcall files were obtained using ERRBS pipeline

source_name: B220+ cells

extract_protocol: Genomic DNA (200 ng) was modified by bisulfite treatment according to the manufacturer's instructions (MethylDetector, Active Motif). DNA fragments were PCR amplified, and direct sequencing reaction was performed using standard conditions (Applied Biosystems)

treatment_protocol: Included as additional column of SAMPLES section

tag: transfection


title: HSD male rat liver tissue S1P1_B04

description: HSD male rat liver tissue

extract_protocol: The liver and left and right kidneys were collected, weighed, and the left liver lobe and right kidney were preserved in RNAlater (Qiagen, Valencia, CA) and stored at 4°C for RNA extraction. Total RNA was extracted from liver and kidney within 1 week of harvest using the RNeasy Mini Kit (Qiagen) with a DNA digestion step. RNA was sent frozen to BioSpyder (Carlsbad, CA) for HTT analysis using the rat S1500+ TempO-Seq platform.


title: PSPC1-OE-ChIP

source_name: FB(OE)-PSPC1 mESC (constructed from BirA J1 mES cells)

extract_protocol:
ChIP was done following previously protocol (Shen, 2008). Briefly, cells were crosslinked on plate with 1% FMA for 10 min, then quenched by 1/20 volume of 2.5 M glycine. after two times of ice cold PBS wash, cell were harvested by trypsin digestion, and lysis by 1 x nuclei lysis buffer. The lysate were further sonicated into average DNA size 200-500 bp. spin at 14000rpm for 15 min, transferred the supernatant into a new tube and diluted by adding 5 × volume of ChIP dilution buffer. Added 5 μg FLAG antibody, end to end rotate overnight at 4℃. The target were further captured by adding 20 ul Protein A/G UltraLink Resin, further rotated for 4 hours at 4℃. After thoroughly washing, the targeted DNA was eluted by elution buffer with protease K at 65℃.
Libraries were prepared by NEBNext Ultra II DNA library preparation kit according to the standard protocols provided by the manufacturer.

value: embryonic stem cells

value: FLAG (Sigma-Aldrich, F3165)

tag: affinity purification


title: WT_82

tag: age


title: HSD male rat liver tissue S1P1_B03

description: HSD male rat liver tissue

value: male

tag: animal id


title: AAV_4days_WT_242552

city: Milan

first: Marco

last: Filipuzzi

address: Via Giuseppe Ripamonti, 435

country: Italy

institute: IEO

description: WT

data_processing:
Read filtering with fastx toolkit 0.0.13.2: fastq_masker -Q33 -q 20 -r N -v -i
alignment with tophat version 2.0.8: tophat -r 170 -p 8 --no-novel-juncs --no-novel-indels --library-type fr-unstranded --transcriptome-index transcriptome_index reffile fastq_file_R1 fastq_file_R2
Removing duplicate reads: samtools rmdup -sS bamfile
Quantifying read counts over features with featureCounts v. 1.4.5-p1: featureCounts -T 2 -p -P -a gtffile
Idendifying Differentially Expressed Genes (DEG) using DESeq2 R Bioconductor package
Genome_build: Genome_build: mm9
Supplementary_files_format_and_content: txt file reporting the eRPKM, log2FC and padj from DESEq2 output

source_name: primary liver

extract_protocol:
Liver tissue was homogenized with GentleMACS M Tubes (Miltenyi Biotech, #130-096-335) and gentleMACS™ Dissociator (Miltenyi Biotech, #130-093-235) in RNA lysis buffer (Zymo, #R1054), and total RNA was purified from these lysates onto Quick-RNA Miniprep columns (Zymo, #R1054) and treated on-column with DNaseI. RNA quality was checked with the Agilent 2100 Bioanalyser (Agilent Technologies).
0.5-1 µg of RNA were used to prepare libraries for RNA-Seq with the TruSeq stranded total RNA Sample Prep Kit (Illumina, #20020596) following manufacturer instruction. RNA-seq libraries were then run on the Agilent 2100 Bioanalyser (Agilent Technologies) for quantification and quality control and then sequenced on Illumina NovaSeq or Illumina 2000 as detailed below.
Strand Specific RNA-Seq

treatment_protocol: For short-term liver-specific activation of the various alleles, 10^11 AAV8-TBG-CRE particles were given to 6- to 8-week-old mice and mice sacrificed after 4 days,

value: Liver

tag: treatment protocol

value: AAV8-TBG-CRE 10^11IV injection 4days


title: TAX_siGL2_Replicat_2

tag: cell type

value: cells contain an integrated GFP reporter gene under the control of the TAX-responsive HTLV-1 LTR


title: HSD male rat liver tissue S1P1_A12

description: HSD male rat liver tissue

value: 8-10 weeks

value: liver

tag: chemical

value: TCAB


title: AAV_4days_WT_243916

description: WT


title: Sample_26_VavPBcl2_SHMT2_repl2_ERRBS


title: HSD male rat liver tissue S1P1_A11

description: HSD male rat liver tissue

value: Triclosan

tag: dose(mg/kg)


title: TAX_siGL2_Replicat_1


title: Control_siDDX5/17_Replicat_1

value: siDDX5/17 + pSG5M-empty


title: Sample_25_VavPBcl2_SHMT2_repl1_ERRBS


title: Control siGL2_Replicat_3

value: siGL2 + pSG5M-empty


title: Sample_23_VavPBcl2_control_repl2_ERRBS

value: control


title: AAV_4days_WT_242173

description: WT


title: Control siGL2_Replicat_2


title: Sample_24_VavPBcl2_control_repl3_ERRBS


title: Sample_22_VavPBcl2_control_repl1_ERRBS


title: AAV_4days_WT_238348

description: WT


title: HSD male rat liver tissue S1P1_A10

description: HSD male rat liver tissue


title: AAV_4days_MYC_EX3_244914

description: R26-lslMYC/b-cat Ex3

value: R26-lslMYC/beta-cat Ex3


title: HSD male rat liver tissue S1P1_A08

description: HSD male rat liver tissue


title: AAV_4days_MYC_EX3_243912

description: R26-lslMYC/b-cat Ex3


title: HSD male rat liver tissue S1P1_A07

description: HSD male rat liver tissue


title: F/FCtr_TAC_1week_5

city: Charlestown

first: Robert

last: Kitchen

institute: MGH / HMS

data_processing:
Samples were run on the Illumina HiSeq 2500 (Illumina) for 50 cycles with a 7 cycle indexing read
Raw sequence image files from the Illumina HiSeq 2500 in the form of .bcl were converted to the fastq format using bcltofastq v1.8.4 and checked for quality to ensure the quality scores do not deteriorate drastically at the read ends.
The adapters from the 3’ end were clipped using cutadapt v.1.10. Reads shorter than 15 nts were discarded and after adapter trimming, the 3’ bases below a quality score of 30 were trimmed as well.
Reads that arise from mouse rRNA and contamination from library preparation protocols were removed before being mapped to the mouse genome. The reads were first mapped to a library of UniVec contaminants, a collection of common vector, adapter, linker and PCR primer sequences collated by the NCBI.
They were then mapped to mouse rRNA sequences obtained from NCBI The reads are mapped to the rRNA and UniVec sequences using Bowtie and those that map were removed from the analysis. The alignment to the mouse genome and transcriptome was carried out in two stages.
First, the rRNA and UniVec free reads were mapped to the mouse genome (GRCm38) using STAR. The reads that mapped to the genome were then mapped to the mouse transcriptome.
Also, the reads that were not mapped to the mouse genome were mapped to the mouse transcriptome, The library for the mouse transcriptome is built by concatenating miRNAs and hairpins from miRBase tRNAs from gtRNAdb piRNAs from piRBase v1.0,25 protein-coding, non-coding and other RNA sequences from ENSEMBL.
The STAR alignment was performed end to end with a single mismatch allowed while mapping and each read is allowed to multimap to at most 40 RNA annotations. Here, there was no mismatch allowed and each read was allowed to multimap to at most 40 RNA annotations.
The raw miRNA reads were normalized, and differential expression analysis was performed using DESeq2

source_name: Heart, post-TAC, 1 week

extract_protocol:
RNA was isolated from frozen heart using Trizol (Qiagen), phase separation followed by column purification was carried out using an RNA isolation kit from Trizol according to manufacturer's instructions.
Reverse transcription was carried out using the Universal cDNA Synthesis kit (Exiqon), and libraries were prepared using the NEXTflex Small RNA Sequencing kit by Bioo-Scientific

treatment_protocol: Mice underwent transverse aortic constriction (TAC), one week post-surgery, mice were anaestethized and hearts were harvested and stored at -80°C.

tag: genotype/variation

value: floxed control


title: C4KO_TAC_1week_4

value: CITED4 knockout


title: HSD male rat liver tissue S1P1_A05

description: HSD male rat liver tissue

value: Sprague Dawley

tag: tissue


title: AAV_4days_MYC_EX3_238335

description: R26-lslMYC/b-cat Ex3

tag: strain


title: Control siGL2_Replicat_1

value: HEK 293T-LTR-GFP


title: AAV_4days_MYC_EX3_238347

description: R26-lslMYC/b-cat Ex3


title: C4KO_TAC_1week_3


title: HSD male rat liver tissue S1P1_A09

description: HSD male rat liver tissue


title: Ecoli_P4_T5_kinetic3

city: Toulouse

first: Laurence

last: Girbal

address: 135 avenue de rangueil

institute: TBI

description: Cells were in P4 phase (starvation) the sampling was performed 5 min after rifampicin addition. It is the third kinetics out of 3 for this phase

hyb_protocol: According to manufacturer instructions, 2 µg of labeled cDNA were hybridized onto E. coli K-12 gene expression arrays (Nimblegen, Roche) during 17 h at 42 °C.

scan_protocol: Arrays were later washed and scanned using MS200 Microarray Scanner (Nimblegen, Roche). Pictures were analyzed with DEVA 1.2.1 software.

data_processing: Raw probe intensities ( .pair files three replicates for each strain before and after transcription arrest by rifampicin addition) were processed and analyzed with R computing environment using the affy and limma package of Bioconductor. Twelve arrays (three reference T0 samples, and nine time points after addition of rifampicin) were used for P2 and P4 and eleven arrays (three reference T0 samples, and eight time points after addition of rifampicin) were used for P3. Only a normalization between arrays according to an invariant probeset intensities was performed. For each growth condition, a set of probes in the background for which the ranks were roughly invariant across all arrays was selected. The median value of the invariant probe set intensities was used as a scaling factor for normalization between the growth conditions. After normalization, the intensity of a transcript was calculated by a RMA-summarization procedure [Irizarry et al, 2003, Biostatistics 4(2): 249-264] within each condition.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: E. coli in P4 phase, Sampling 5 minutes after rifampicin addition in kinetic 3

label_protocol: According to manufacturer instructions, 1 µg of cDNA was labeled using one color DNA labeling kit

growth_protocol: The laboratory strain E. coli K12 MG1655 was grown in bioreactors in M9 glucose (3g/l) at 37 °C. The pH was set to 7. All cultures were inoculated at OD 0.2 from overnight pre-cultures performed in similar conditions. Biomass was estimated from absorbance at 600 nm. Each culture was repeated three times to provide independent biological kinetics.

extract_protocol: After thawing and centrifugation steps, total RNA was extracted with TRIZOL® Reagent (Ambion) according to the manufacturer’s instructions. DNA contamination was eliminated with Turbo DNase kit (Ambion). Total RNA concentration and integrity were measured using a Nanodrop® spectrophotometer and Agilent BioAnalyzer, respectively.

treatment_protocol: At glucose exhaustion, during acetate consumption and during carbon starvation, samples were collected for the reference time point (T0) for the half-life determination procedure. Subsequently, rifampicin (500 µg.mL-1) was added to inhibit transcription initiation, and cells were harvested at different time points after this addition. Cultures were performed in independent biological triplicates. Samples were immediately frozen in liquid nitrogen upon collection.

tag: sampling time, repetition


title: HSD male rat liver tissue S1P1_A04

description: HSD male rat liver tissue


title: Ecoli_P4_T0_kinetic3

description: Cells were in P4 phase (starvation), the sampling was performed just before rifampicin addition. It is the third kinetics out of 3 for this phase

source_name: E. coli in P4 phase, Sampling before rifampicin addition in kinetic 3


title: F/FCtr_TAC_1week_3


title: Ecoli_P4_T3_kinetic3

description: Cells were in P4 phase (starvation) the sampling was performed 3 min after rifampicin addition. It is the third kinetics out of 3 for this phase

source_name: E. coli in P4 phase, Sampling 3 minutes after rifampicin addition in kinetic 3


title: AAV_4days_MYC_245233


title: Ecoli_P4_T0.5_kinetic3

description: Cells were in P4 phase (starvation) the sampling was performed 0.5 min after rifampicin addition. It is the third kinetics out of 3 for this phase

source_name: E. coli in P4 phase, Sampling 0.5 minute after rifampicin addition in kinetic 3


title: AAV_4days_WT_240831

description: WT

value: WT


title: HSD male rat liver tissue S1P1_A03

description: HSD male rat liver tissue

value: male


title: Ecoli_P4_T2_kinetic2

description: Cells were in P4 phase (starvation) the sampling was performed 2 min after rifampicin addition. It is the second kinetics out of 3 for this phase

source_name: E. coli in P4 phase, Sampling 2 minutes after rifampicin addition in kinetic 2


title: C4KO_TAC_1week_5


title: Ecoli_P4_T7_kinetic2

description: Cells were in P4 phase (starvation) the sampling was performed 7 min after rifampicin addition. It is the second kinetics out of 3 for this phase

source_name: E. coli in P4 phase, Sampling 7 minutes after rifampicin addition in kinetic 2


title: HSD male rat liver tissue S1P1_A06

description: HSD male rat liver tissue


title: AAV_4days_MYC_245234

value: Liver


title: HSD male rat liver tissue S1P1_B06

description: HSD male rat liver tissue


title: C4KO_TAC_1week_2


title: F/FCtr_TAC_1week_4


title: AAV_4days_MYC_EX3_242171

description: R26-lslMYC/b-cat Ex3

value: AAV8-TBG-CRE 10^11IV injection 4days


title: AAV_4days_MYC_243902


title: Ecoli_P4_T0_kinetic2

description: Cells were in P4 phase (starvation), the sampling was performed just before rifampicin addition. It is the second kinetics out of 3 for this phase

source_name: E. coli in P4 phase, Sampling before rifampicin addition in kinetic 2


title: AAV_4days_MYC_238334


title: F/FCtr_TAC_1week_1


title: AAV_4days_MYC_242164


title: C4KO_TAC_1week_1


title: F/FCtr_TAC_1week_2


title: Adjacent normal tissues from CRC patient 6

city: Jinan

first: Xin

last: Zhang

state: Shandong

address: 107 Wenhua Xi Road

institute: Qilu Hospital, Shandong University

description: histological diagnosis confirmed

hyb_protocol: One μg of each Cy3-labeled, linearly amplified cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

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

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

source_name: Adjacent normal tissues

label_protocol: mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Cyanine-3 (Cy3) labeled cRNA was prepared from 1ug RNA using the Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop NanoDrop-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated from tissues using Trizol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer(Thermo Fisher Scientific, Waltham, MA) and RNA integrity was assessed by standard denaturing agarose gel electrophoresis and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: Sex

value: Female

value: normal colon

tag: tumor location

value: Colon

tag: regional lymph nodes metastasis

value: Yes

tag: Stage

value: III

tag: recurrence after operation

tag: status after 5 years

value: Dead


title: Adjacent normal tissues from CRC patient 4

description: histological diagnosis confirmed

value: normal rectum

value: Rectum


title: AAV_4days_EX3_245228

description: b-cat Ex3

tag: genotype

value: beta-cat Ex3


title: AAV_4days_EX3_238349

description: b-cat Ex3


title: Ecoli_P4_T4_kinetic1

description: Cells were in P4 phase (starvation), the sampling was performed 4 min after rifampicin addition. It is the first kinetics out of 3 for this phase

source_name: E. coli in P4 phase, Sampling 4 minutes after rifampicin addition in kinetic 1


title: Adjacent normal tissues from CRC patient 5

description: histological diagnosis confirmed

tag: age

value: No

value: II

value: Alive


title: WT_10min_tot

city: Lausanne

first: Ana

last: Marques

address: Rue du Bugnon 27

department: Department of Computational Biology

institute: University of Lausanne

description:
Biological Replicate 1, wild-type mESC 10 minute 4sU labelled RNA sample, preexisting RNA.
processed data file: 4sU_TPM_table.txt

data_processing:
Hundred nucleotides long single-end stranded reads were mapped to mouse ribosomal RNA sequences with STAR V 2.5.0 (Dobin et al., 2013).
Reads not mapping to ribosomal RNA were then aligned to intronic and exonic sequences using STAR and quantified using RSEM (Li and Dewey, 2011).
Rates of synthesis, processing and degradation were independently inferred using biological duplicates at each labelling points using the INSPEcT Bioconductor package Version 1.8.0 (de Pretis et al., 2015) and biotype differences in the average rate across the 3 labeling times.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: The processed 4sU expression table contains the expression levels of transcript exons and introns (Transcripts Per Million, TPM).
Supplementary_files_format_and_content: The processed 4sU rates table contains the inferred RNA metabolic rates of transcript (rate of synthesis, processing and degradation).
Supplementary_files_format_and_content: The processed smallRNAseq table contains the counts of miRNAs levels of transcript exons and introns (Transcripts Per Million, TPM).

growth_protocol: mESC: Feeder depleted Mouse DTCM23/49 XY embryonic stem cells were grown on 0.1% gelatin-coated tissue culture treated plates in a humidified incubator with 5% (v/v) CO2 at 37ºC in 1X DMEM medium supplemented with 1x Non-Essential Amino Acids, 50 uM β-mercaptoethanol, 15% Fetal Bovine Serum, 1% Penicillin/Streptomycin, and 0.01% of Recombinant mouse Leukemia Inhibitory factor. Cultures were maintained by passaging cells every 48 hours (replating density ~ 3.8*10e4 cells/cm2).

extract_protocol:
4sU labelling and extraction protocol: Five million DTCM23/49 XY mESCs (WT and miRNA depleted) were seeded and allowed to grow to 70-80% confluency (approximately 1 day). 4sU was added to the growth medium (final concentration of 200 µM) and the cells were incubated at 37 ºC for 10 minutes and extracted using Trizol, according to manufacturer instructions. RNA was DNase treated using RNeasy on column digestion according to manufacturer’s instructions. 100 µg of RNA was incubated for 2 h at room temperature with rotation in 1/10 volume of 10X biotinylation buffer (Tris-HCl pH 7.4, 10 mM EDTA) and 2/10 volume of biotin-HPDP (1mg/ml in Dimethylformamide (Thermo Fisher, 21341)). Following biotinylation, total RNA was purified through phenol:chloroform:isoamyl alcohol extraction and precipitated with equal volume of Isopropanol and 1/10 volume of 5M NaCl. Precipitated RNA was washed once with 75% Ethanol and resuspended in in DEPC-treated H2O. Equal volume of biotinylated RNA and pre-washed DynabeadsTM MyOneTM Streptavidin T1 beads were mixed and incubated at room temperature for 15 minutes under rotation. The beads were then separated using a DynaMagTM-2 Magnetic stand. The supernatant (that contains unlabeled preexisting RNA) was placed at 4oC until precipitation. Beads were washed and biotinylated RNA dissociated from streptavidin coated beads by treatment with 100 mM 1,4-Dithiothreitol for 1 minute, followed by 5 minutes in RTL buffer. Beads were separated from the solution using DynaMagTM-2 Magnetic stand and the RNA was recovered from the supernatant was extracted using Qiagen RNeasy Mini Kit according to the manufacturer’s instructions. Preexisting RNA was precipitated with equal volume of Isopropanol and 45 minutes centrifugations at 15 000 g (4oC). Preexisting RNA pellet was washed with 75% Ethanol and resuspended in DEPC-treated H2O. Metabolic labelling was carried out twice (2 biological replicates).
Total RNA libraries were prepared from 10 ng of preexisting RNA and newly transcribed RNA using Ovation® RNA-Seq and sequenced on Illumina HiSeq 2500.

value: ESC

tag: labeling time (min)

tag: rna

value: total

tag: biological replicate


title: Ecoli_P4_T11_kinetic1

description: Cells were in P4 phase (starvation), the sampling was performed 11 min after rifampicin addition. It is the first kinetics out of 3 for this phase

source_name: E. coli in P4 phase, Sampling 11 minutes after rifampicin addition in kinetic 1


title: Adjacent normal tissues from CRC patient 1

description: histological diagnosis confirmed

value: Male


title: AAV_4days_EX3_243910

description: b-cat Ex3

tag: cell type

value: Liver

tag: treatment protocol


title: Adjacent normal tissues from CRC patient 2

description: histological diagnosis confirmed


title: WT_10min_lab

description:
Biological Replicate 1, wild-type mESC 10 minute 4sU labelled RNA sample newly transcribed RNA.
processed data file: 4sU_TPM_table.txt

tag: genotype/variation

value: WT

value: label


title: Primary CRC tissues from CRC patient 6

description: histological diagnosis confirmed

source_name: primary colorectal cancer tissues

value: Female

tag: tissue

value: colorectal cancer


title: AAV_4days_EX3_241331

description: b-cat Ex3

tag: strain

value: AAV8-TBG-CRE 10^11IV injection 4days


title: ZCWPW1 CUT&RUN  (B6/CAST)

city: Bethesda

first: Mohamed

last: Mahgoub

address: 6 Center Dr

department: Division of Developmental Biology

institute: NICHD

data_processing:
Mapping: paired-end reads were mapped to mm10 genome assembly by BWA-MEM version 0.7.17  using default parameters.   Peak calling: peaks were called by MACS2 version 2.1.2 using default parameters (with exception of the parameter -p 0.001).   Read coverage: bigwig files were generated by bamCoverage tool of deepTools suite with the options: --MNase –centerReads. Heatmap plotting was done by computeMatrix and plotHeatmap tools. Integrative Genomics Viewer was used for read coverage visualization
Genome_build: mm10

source_name: Testis

extract_protocol:
Testes were dissected, tunica removed, and tubules were gently chopped with a blade. Tissues were then incubated for 30 minutes in dissociation buffer. Dissociation enzymes were inactivated by adding DMEM containing 10% FBS. 300,000 cells were used for each CUT&RUN reaction.
SMARTer ThruPLEX DNA-Seq Kit

value: F1 B6/CAST hybrid from mating male CAST (CAST/EiJ ) and female B6 (C57BL/6J)

value: wild type

value: Adult

value: male

value: whole testis

tag: assay

value: CUT&RUN

tag: anitbody used

value: α-ZCWPW1 (custom)

tag: library layout

value: paired-end


title: Ecoli_P3_T5_kinetic3

description: Cells were in P3 phase (acetate consumtion) the sampling was performed 5 min after rifampicin addition. It is the third kinetics out of 3 for this phase

source_name: E. coli in P3 phase, Sampling 5 minutes after rifampicin addition in kinetic 3

tag: sampling time, repetition


title: Ecoli_P4_T1.5_kinetic2

description: Cells were in P4 phase (starvation) the sampling was performed 1.5 min after rifampicin addition. It is the second kinetics out of 3 for this phase

source_name: E. coli in P4 phase, Sampling 1.5 minute after rifampicin addition in kinetic 2


title: Ecoli_P3_T1_kinetic3

description: Cells were in P3 phase (acetate consumtion) the sampling was performed 1 min after rifampicin addition. It is the  third kinetics out of 3 for this phase

source_name: E. coli in P3 phase, Sampling 1 minute after rifampicin addition in kinetic 3


title: Ecoli_P4_T1_kinetic1

description: Cells were in P4 phase (starvation), the sampling was performed 1 min after rifampicin addition. It is the first kinetics out of 3 for this phase

source_name: E. coli in P4 phase, Sampling 1 minute after rifampicin addition in kinetic 1


title: H3K4me3 CUT&RUN  (B6/CAST)

tag: Sex

value: α-H3K4me3 (Abcam # ab8580)


title: Primary CRC tissues from CRC patient 5

description: histological diagnosis confirmed

tag: tumor location

value: Rectum

tag: regional lymph nodes metastasis

value: No

tag: Stage

value: II

tag: recurrence after operation

value: Alive


title: IgG Control for CUT&RUN  (B6/CAST)

tag: genotype

tag: age

value: α-GFP (Abcam # ab290)


title: Primary CRC tissues from CRC patient 4

description: histological diagnosis confirmed

value: Female

value: Yes

value: III

tag: status after 5 years

value: Dead


title: Ecoli_P4_T0_kinetic1

description: Cells were in P4 phase (starvation), the sampling was performed just before rifampicin addition. It is the first kinetics out of 3 for this phase

source_name: E. coli in P4 phase, Sampling before rifampicin addition in kinetic 1


title: Adjacent normal tissues from CRC patient 3

description: histological diagnosis confirmed

value: Male

value: normal rectum


title: H3K4me3 CUT&RUN  (B6/B6)

value: wild type

value: Adult

value: male


title: AAV_4days_EX3_238332

description: b-cat Ex3

source_name: primary liver

tag: cell type

value: Liver

value: beta-cat Ex3

value: AAV8-TBG-CRE 10^11IV injection 4days


title: IgG Control for CUT&RUN (B6/B6)

value: whole testis

value: CUT&RUN

value: paired-end


title: Ecoli_P3_T11_kinetic2

description: Cells were in P3 phase (acetate consumtion) the sampling was performed 11 min after rifampicin addition. It is the second kinetics out of 3 for this phase

source_name: E. coli in P3 phase, Sampling 11 minutes after rifampicin addition in kinetic 2


title: Ecoli_P3_T0_kinetic3

description: Cells were in P3 phase (acetate consumtion), the sampling was performed just before rifampicin addition. It is the third kinetics out of 3 for this phase

source_name: E. coli in P3 phase, Sampling before rifampicin addition in kinetic 3


title: Daxx_2cell_m-z+.KO.Zp3_rep3

description: processed data file: Daxx_GENES_ReadCounts.txt

data_processing:
Spliced alignment of paired-end RNA-Seq data (R1 and R3 fastq files, 51 bp reads) to a custom genome which contained M. musculus genome assembly (GRCm38/mm10 Dec. 2011) and ERCC92 sequences was done using STAR (version 2.5.0a, Dobin et al. 2013) with parameters "-outFilterMultimapNmax 300 -outMultimapperOrder Random -outSAMmultNmax 1 -alignIntronMin 20 -alignIntronMax 1000000", allowing multimappers with up to 300 matches in the genome and choosing positions for multimappers randomly. BAM files for technical replicates were merged using samtools and potential PCR duplicates were removed using UMIs (R2 fastq file, 8bp reads) and python script nudup.py from NuGEN Technologies (version 2.2). Replicate 1 for condition Daxx f/f; Zp3-cre; m-z+ was discarded due to low quality.
Genome_build: mm10 + ERCC92
Supplementary_files_format_and_content: bigWig files for bins of 100 bp were generated by QuasR package (version 1.22.0) using both mates and only uniquely mapped reads (minimum mapping quality mapqMin=255) and the output values in the bigWig files were linearly scaled such that the total number of aligned reads per sample is 1e+6 (parameter scaling=1e+6).
Supplementary_files_format_and_content: Daxx_GENES_ReadCounts.txt: Read count table (TXT file) for each gene in TxDb.Mmusculus.UCSC.mm10.knownGene (version 3.4.4) was created by qCount function in QuasR package selecting only uniquely mapped reads.

source_name: 2-cell embryo

growth_protocol: Daxxtm2Led F/F mice were maintained with or without the transgene Tg(Zp3-cre)93KnwMGI.

extract_protocol:
50 MII oocytes or late stage 2-cell embryos obtained from 2-3 female mice were pooled and allocated as one biological group. 3 biological groups were used as replicates. Oocytes and 2-cell embryos were placed into Low-bind EP tube directly with 100 µl Cell Lysis Master Mix buffer (NuGEN) supplemented with 1% beta-mercaptoethanol. The EP-tubes with samples were kept in -80 °C for further processing.
RNA isolation, reverse transcription, PCR, quality control and library preparation were conducted as described using SoLo RNA-Seq system protocol (NuGEN).

treatment_protocol: MII oocytes were collected from over 8-week-old Daxx F/F, Zp3-cre or Daxx F/F female mice 20 hours post HCG injection. Hybrid 2-cell embryos were generated by in vitro fertilization (IVF) of above MII oocytes and sperm from 8-week-old JF1 male mice. Fertilized zygotes with 2 pronuclei were selected and cultured in KSOM medium until 33 hours post IVF for RNA extraction. Ovulation was induced by injection 5 IU pregnant mare serum gonadotropin (PMSG) and then 5 IU human chorionic gonadotropin (hCG) (MSD Animal Health) 46–48 h later.

tag: strain/background

value: C57BL/6J and 129/Sv Oocyte x JF1 sperm

value: Daxx f/f; Zp3-cre; m-z+

value: 2-cell embryo


title: wt1

first: Sam

middle: E

last: Tischfield

address: 1275 York Ave

department: Center for Molecular Oncology

institute: Memorial Sloan-Kettering Cancer Center

description: Spo11-associated DNA oligonucleotides

data_processing:
Base calls perfomed using HiSeq Control Software v.2.0.10.0 for samples sequenced on Illumina HiSeq 2500
Adapters (AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) were clipped from reads using fastx_clipper, part of the FASTX Toolkit 0.0.13.2, with parameters -l 15 -n -v -Q33 -i
First five bases (diffusion primer added in library prep) in each sequence were trimmed and trimmed sequence was recorded in the FASTQ ID tag for downstream tracking
Clipped reads were mapped using SHRiMP 2.1.1b with parameters -N 15 -U -g -1000 -q -1000 -m 10 -i -20 -h 100 -r 50% -n 1 -s 1111111111,11110111101111,1111011100100001111,1111000011001101111 -o 1001 -Q -E --sam-unaligned --strata
Sequences clipped from a read during mapping should be polyC on the 3' end or polyG on the 5' end. If clipped bases were not polyC or polyG the alignment score was corrected by deducting the mismatch score for each non-C,G base in the clipped sequence.
Maps of 5' ends of sequence reads were compiled and analyzed in R
Genome_build: Reads were mapped to the SGD assembly released in June 2008, called "sacCer2" by UCSC: http://genome.ucsc.edu/cgi-bin/hgGateway?hgsid=340067645
Supplementary_files_format_and_content: wig files include RPM (reads per million mapped) for each sample at each non-zero base position in the genome

organism: Saccharomyces cerevisiae

source_name: meiotic culture

growth_protocol: Cells were grown in YPA (1% yeast extract, 2% Bacto Peptone, 1% potassium acetate) for 14 hr at 30°C, harvested, resuspended to OD600=6.0 in 2% potassium acetate, 0.2 × supplements (2 μg/mL adenine, 2 μg/mL histidine, 6 μg/mL leucine, 2 μg/mL tryptophan, 2 μg/mL uracil) and sporulated at 30°C.

extract_protocol:
Based on Pan et al. 2011 Cell, and Zhu and Keeney 2015 Genetics, with modifications. Whole cell extracts were prepared by grinding frozen cells in a bead mill and resuspending powder in 10%TCA. Pellets were then extracted with SDS and soluble protein was subjected to affinity purification of Spo11-Flag fusion with Protein-G Dynabeads. Protein was digested with proteinase K and Spo11-associated oligonucleotides were recovered by ethanol precipitation.
Based on Pan et al. 2011 Cell, and Thacker et al. 2014 Nature. Oligonucleotides were tailed with ribo-G using rGTP and terminal transferase, then ligated to duplex DNA adaptors with a dC overhang using T4 RNA ligase 2. Complementary strands were synthesized with Klenow, then purified by denaturing polyacrylamide electrophoresis. Purified complementary strands were subjected to 3' tailing with ribo-G using rGTP and terminal transferase, then another duplex adaptor was ligated using T4 RNA ligase 2. Ligated material was amplified with 16 cycles of PCR to add Illumina HiSeq adaptors

tag: epitope tag

tag: meiotic time point

value: 4 hr in meiosis


title: Daxx_2cell_m-z+.KO.Zp3_rep2

tag: genotype/variation


title: Primary CRC tissues from CRC patient 3

description: histological diagnosis confirmed

tag: tissue

value: colorectal cancer

value: Rectum

value: No

value: II

value: Alive


title: Primary CRC tissues from CRC patient 1

description: histological diagnosis confirmed

value: Male

value: Colon


title: Primary CRC tissues from CRC patient 2

description: histological diagnosis confirmed

value: Yes

value: III

value: Dead


title: F260A2

description: Spo11-associated DNA oligonucleotides


title: Ecoli_P3_T2_kinetic3

description: Cells were in P3 phase (acetate consumtion) the sampling was performed 2 min after rifampicin addition. It is the  third kinetics out of 3 for this phase

source_name: E. coli in P3 phase, Sampling 2 minutes after rifampicin addition in kinetic 3


title: Ecoli_P3_T7_kinetic1

description: Cells were in P3 phase (acetate consumtion) the sampling was performed 7 min after rifampicin addition. It is the first kinetics out of 3 for this phase

source_name: E. coli in P3 phase, Sampling 7 minutes after rifampicin addition in kinetic 1


title: Ecoli_P3_T4_kinetic1

description: Cells were in P3 phase (acetate consumtion) the sampling was performed 4 min after rifampicin addition. It is the first kinetics out of 3 for this phase

source_name: E. coli in P3 phase, Sampling 4 minutes after rifampicin addition in kinetic 1


title: Daxx_2cell_WT_rep3

value: Daxx f/f; m+z+


title: ZCWPW1 CUT&RUN  (B6/B6)

tag: strain

value: wild type

value: Adult

value: male

value: whole testis

tag: assay

value: CUT&RUN

tag: anitbody used

value: α-ZCWPW1 (custom)


title: Ecoli_P3_T0_kinetic2

description: Cells were in P3 phase (acetate consumtion) the sampling was performed just before rifampicin addition. It is the second kinetics out of 3 for this phase

source_name: E. coli in P3 phase, Sampling before rifampicin addition in kinetic 2

tag: sampling time, repetition


title: Ecoli_P3_T0.5_kinetic1

description: Cells were in P3 phase (acetate consumtion) the sampling was performed 0.5 min after rifampicin addition. It is the first kinetics out of 3 for this phase

source_name: E. coli in P3 phase, Sampling 0.5 minute after rifampicin addition in kinetic 1


title: wholeembryo_CLB_CEWAFHi3

city: Quebec

first: Valerie

middle: S

last: Langlois

state: QC

address: 490 rue de la Courrone

department: Centre Eau Terre Environnement

country: Canada

institute: Intitut national de la recherche scientifique (INRS)

description: Gene expression after exposure from fertilization to hatch

hyb_protocol: Agilent One-Color Low-Input Labeling kit

scan_protocol: SureScan Microarray Scanner, 5 uM

data_processing: R package limma

organism: Oryzias latipes

source_name: whole embryo, CLB, CEWAF Hi 3

growth_protocol: Medaka embryos were collected from a colony at Queen’s University and maintained according to a protocol approved by the Queen’s Animal Care Committee (Langlois-2015-1584).

extract_protocol: Qiagen Rneasy Micro Kit

treatment_protocol: Within 24 hours post-fertilization, eggs were assigned randomly to treatment groups. Each treatment included duplicate jars of at least 15 eggs (n = 30/treatment) exposed for up to 16 days by a static daily renewal protocol; fresh WAF and CEWAF solutions were made daily. Jars were constantly gently agitated on a New Brunswick Scientific Innova 2000 platform shaker (Eppendorf, Germany) at 60 rpm to ensure water movement and gas exchange. Newly-hatched fish were sampled < 24 h post-hatch at the same time each day.

value: whole embryo

tag: oil

value: CLB

tag: treatment

value: CEWAF Hi

tag: grouping


title: wholeembryo_CLB_CEWAFHi2

source_name: whole embryo, CLB, CEWAF Hi 2

label_protocol: Agilent One-Color Low-Input Labeling kit


title: wholeembryo_CLB_CEWAFLo1

source_name: whole embryo, CLB, CEWAF Lo 1

value: CEWAF Lo


title: Daxx_2cell_WT_rep2

value: C57BL/6J and 129/Sv Oocyte x JF1 sperm

value: 2-cell embryo


title: F260A1

description: Spo11-associated DNA oligonucleotides

value: 4 hr in meiosis


title: wt2

description: Spo11-associated DNA oligonucleotides


title: Daxx_2cell_WT_rep1


title: SAE2_2

growth_protocol: Cells were grown in YPA (1% yeast extract, 2% Bacto Peptone, 1% potassium acetate) for 14 hr at 30°C, harvested, resuspended to OD600=6.0 in 2% potassium acetate and sporulated at 30°C.

extract_protocol:
Based on Mimitou et al. 2017 Science. Genomic DNA was extracted in low-melting point (LMP) agarose to yield intact high molecular weight DNA. Each cell pellet was resuspended in 150 μl 50 mM EDTA pH 8.0 and allowed to thaw at 40°C. 498 μl LMP agarose (2% in 50 mM EDTA pH 8.0) was mixed with 102 μl Solution 1 (SCE (1 M sorbitol, 0.1 M sodium citrate, 60 mM EDTA pH 7.0) plus 5% β- mercaptoethanol and 1 mg/ml zymolyase 100T) and the mix was prewarmed at 40°C before adding to the cells. The resuspended cells were pipetted into plug molds and chilled at 4°C for 30 min. Once solidified, the agarose plugs (three at a time) were expressed into 3 ml of Solution 2 (0.45 M EDTA pH 8.0, 0.01 M Tris-HCl pH 7.5, 7.5 % β-mercaptoethanol, 10 μg/ml RNase A) and incubated at 37°C for 1 h. Solution 2 was then replaced with Solution 3 (0.25 M EDTA pH 8.0, 0.01 M Tris-HCl pH 7.5, 1% SDS, 1 mg/ml proteinase K) and plugs were incubated at 50°C overnight. Plugs were finally washed three times with 3 ml 50 mM EDTA pH 8 and stored in plug storage solution (0.05 M EDTA pH 8.0, 50% glycerol) at -20°C until all plugs were ready to be processed for library preparation.
Based on Mimitou et al. 2017 Science. Ten plugs of each sample to be analyzed were equilibrated in 500 μl 1× S1 buffer (50 mM sodium acetate pH 4.5, 0.28 M NaCl, 4.5 mM ZnSO4) per plug in 2 ml conical tubes for 30 min and this was repeated three times. Fresh 1× S1 buffer (500 ul) containing 9 U of S1 nuclease (Promega) was added to each tube and the plugs were incubated on ice for 15 min to allow the enzyme diffuse into the plugs, followed by 20 min incubation at 37°C. S1 nuclease was inactivated by addition of EDTA pH 8.0 to a final concentration 10 mM and incubation on ice for 15 min. Plugs were rinsed with 1× TE and further equilibrated in 500 μl T4 polymerase buffer (1× T4 DNA ligase buffer (NEB), 1× BSA, 100 μM dNTPs), four times for 30 min each. Fresh T4 polymerase buffer (500 μl) containing 30 U of T4 DNA polymerase (NEB) was added to each tube and the plugs were incubated on ice for 15 min, followed by 30 min incubation at 12°C. T4 polymerase was inactivated by addition of EDTA pH 8.0 to a final concentration of 10 mM and incubation on ice for 15 min. At this point all buffer was aspirated,the plugs were rinsed with 1× TE and incubated at 75°C for 20 min to fully inactivate T4 polymerase. Plugs were allowed to gradually cool and solidify, before equilibrating in 250 μl 1× T4 ligase buffer (NEB), four times for 15 min each. After the last equilibration step, 200 μl of the buffer were removed leaving each plug immersed in 50 μl 1× T4 DNA ligase buffer, to which 1 μl of 50 μM adaptor and 1 μl of 2000 U/μl T4 DNA ligase were added. Ligation took place at 4°C for ≥18 h. The adaptor was prepared the day of the experiment by mixing oligos P5-top (5BiosG/ACACTCTTTCCCTACACGACGCTCTTCCGATCT, biotin attached to the 5′- end of the oligo) and P5-bottom (5Phos/AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT/3InvdT, 5′- end phosphorylated with inverted dT incorporated at the 3′-end to block ligation) at equimolar concentration, boiling for 5 min and cooling down at room temperature for at least 1 h.  To retrieve the DNA from the agarose plugs, the Epicentre GELase Enzyme Digestion protocol was used, followed by phenol extraction and ethanol precipitation. During this process plugs of DNA from a single culture and time point were pooled. The purified DNA was then subjected to size selection by electrophoresis through a 1% LMP 1× TAE agarose gel at 80 V/cm for 2 h to separate the high-molecular-weight genomic DNA from the excess unligated adaptor. The genomic DNA was excised and extracted from the gel using the Epicentre GELase enzyme protocol, phenol extraction and ethanol precipitation; then the DNA was dissolved in 100 μl 1× TE. To ensure complete removal of unligated adaptor, each sample was further purified by passing three times through Chroma Spin-1000 (Clontech) columns. The eluates were then subjected to shearing according to the Covaris instrument protocol to DNA fragment sizes ranging between 200-500 bp.  Following shearing, fragments containing the biotinylated adaptor were enriched by affinity purification with streptavidin. For each sample, 50 μl of streptavidin M-280 beads (Roche) were used, prewashed twice with 1× TE and twice with 1× B&W (binding and washing buffer, 10 mM Tris-HCl pH 7.5, 1 mM EDTA, 2 M NaCl), according to the manufacturer’s instructions. Binding was carried out at 20°C for 30 min, followed by two washes with 500 μl 1x B&W buffer and two washes with 500 μl 10 mM Tris-HCl pH 7.5. The remaining steps were performed with the DNA fragments still bound to the streptavidin beads. Because sheared ends are not always readily ligatable, an end-repair step was included according to Epicentre’s End-it DNA Repair kit protocol. The beads for each sample were incubated in 100 μl of reaction mix according to manufacturer’s instructions and incubated at 20°C for 45 min. Following washes with 500 μl 1× B&W buffer (twice) and 500 μl 10 mM Tris-HCl pH 7.5 (twice), the beads were incubated in 100 μl of 1× T4 DNA ligase buffer containing 400 U T4 ligase and 1 μM P7 adaptor. The adaptor was prepared by annealing oligos P7 top (5Phos/GATCGGAAGAGCACACGTCTGAACTCCAGTCAC/3InvdT) and P7 bottom (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATC) at equimolar concentration, boiling for 5 min and allowing to cool down at room temperature for at least one hour. Ligation of the P7 adaptor was allowed at 20°C for 4 h and was followed by washes with 500 μl 1× TE and 500 μl 10 mM Tris-HCl pH 7.5 (three times each). Beads of each sample were resuspended in 20 μl 10 mM Tris-HCl pH 7.5.  Each sample of beads was split into two PCR reactions in a total of 50 μl containing 10 μl of the resuspended beads, 1× Phusion HF buffer, 0.2 mM dNTP, 1 U Phusion HF polymerase (Thermo Scientific), 0.4 μM P5 universal primer (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC T) and 0.4 μM P7 indexed primer (CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCAGACGTGTG, shown here with Illumina TruSeq index 1 underlined). PCR was initiated by a denaturation step at 98°C for 30 sec, followed by 16 cycles of amplification (98°C for 10 sec, 65°C for 20 sec, and 72°C for 20 sec). PCR products were pooled, and the DNA was precipitated by adding ammonium acetate to 2.5 M and 2.5 volumes of ice-cold 100% ethanol. Following an overnight incubation at -20°C, the samples were spun at 16000 g for 30 min, washed with ice-cold 70% ethanol, air-dried and dissolved in 20 μl 10 mM Tris, pH 7.5. PCRs from each sample were pooled and separated on a 5% non-denaturing polyacrylamide gel in 1× TBE. The gel piece between 200–600 bp was excised, crushed, and eluted in 300 μl 10 mM Tris pH 8.0 at 37°C overnight. The elution mixture was spun through a SPIN-X column, and DNA was precipitated with ammonium acetate and ethanol as above. The DNA pellet was dissolved in 20 μl 10 mM Tris pH 7.5 and sequenced on the Illumina HiSeq platform (50 bp single-end) in the Integrated Genomics Operation at Memorial Sloan Kettering Cancer Center.


title: wholeembryo_CLB_CEWAFHi1

source_name: whole embryo, CLB, CEWAF Hi 1


title: Daxx_MII_KO.Zp3_rep3

source_name: MII oocyte

value: Mixed genetic background of C57BL/6J and 129/Sv

value: Daxx f/f; Zp3-cre

value: MII oocyte


title: wholeembryo_CLB_CEWAFLo2

source_name: whole embryo, CLB, CEWAF Lo 2


title: wholeembryo_CLB_CEWAFLo3

source_name: whole embryo, CLB, CEWAF Lo 3


title: SAE2_1


title: Ecoli_P3_T0_kinetic1

description: Cells were in P3 phase (acetate consumtion), the sampling was performed just before rifampicin addition. It is the first kinetics out of 3 for this phase

source_name: E. coli in P3 phase, Sampling before rifampicin addition in kinetic 1


title: Daxx_MII_KO.Zp3_rep2


title: Ecoli_P2_T5_kinetic3

description: Cells were in P2 phase (glucose exhaustion) the sampling was performed 5 min after rifampicin addition. It is the third kinetics out of 3 for this phase

source_name: E. coli in P2 phase, Sampling 5 minutes after rifampicin addition in kinetic 3


title: spo11-F260A2

value: spo11-F260A, sae2-delta


title: Ecoli_P2_T2_kinetic3

description: Cells were in P2 phase (glucose exhaustion) the sampling was performed 2 min after rifampicin addition. It is the third kinetics out of 3 for this phase

source_name: E. coli in P2 phase, Sampling 2 minutes after rifampicin addition in kinetic 3


title: Daxx_MII_KO.Zp3_rep1


title: spo11-F260A1


title: Daxx_MII_WT_rep3

value: Daxx f/f


title: Daxx_MII_WT_rep2


title: NAA100-E-L38-B_FPKM

city: Beijing

first: Lei

last: He

address: No. 17 Tsinghua east road

institute: China Agricultural University

data_processing:
The original image data was transfered into sequence data by base calling, which is defined as raw data or raw reads and saved as fastq files.
The dirty raw reads including reads with adaptors, reads in which unknown bases are more than 10% and low quality reads (the percentage of the low quality bases of quality value ≤ 5 is more than 50% in a read) were removed to get the clean reads.
Clean reads were mapped to reference grapevine genome V2 using Bowtie. Mismatches no more than 2 bases were allowed in the alignment.
The gene expression level was calculated by using FPKM method.
Genome_build: http://genomes.cribi.unipd.it/DATA/V2/V2.1/
Supplementary_files_format_and_content: Results include length, excepted_count and FPKM and the description of gene for each sample were shown in xlsx table files.

organism: Vitis vinifera

source_name: grape berry

growth_protocol: Clusters of Vitis vinifera L. cv. Cabernet Sauvignon grapevines cultivated in Shanxi Academy of Agricultural Sciences Pomology Institute, Shanxi, China in 2015 were used for the study.

extract_protocol:
Three biological replicates for each sample were performed. A sub-sample of 50 berries were randomly selected from each biological replicate for RNA extraction. Total RNA was extracted from the frozen deseeded berries (whole pericarp) using a SpectrumTM Plant Total RNA Kit (Sigma-Aldrich, CA, USA).  RNA integrity and quality were assessed by analysis with the Aglient 2100 Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The 1000 mg/L ABA, 800 mg/L ABA and 100 mg/L NAA solutions containing 0.05% Tween 20 were applied at seven weeks after flowering (berry still hard and green, E-L 33 stage), with 0.05% Tween solution as the control. The spray of these solutions was performed at sunset to avoid the rapid evaporation of the solutions. After the first spray solution was absorbed, the second application were conducted ten hours later at the same day. A randomized block design was considered for this study, and each treatment or control was replicated in three plots of 50 vines. Each berry sample replicate included 500 berries collected from 50 vines. Sampling was performed at four E-L stages (E-L 34, E-L 35, E-L 36 and E-L 38) according to modified E-L system. Then, the samples were kept in dry ice and immediately transferred to laboratory. Before the extraction, samples were washed with distilled water to remove the unabsorbed ABA and NAA residues on berry surface.

tag: cultivar

value: Cabernet Sauvignon

tag: Stage


title: NAA100-E-L38-C_FPKM


title: wholeembryo_CLB_WAFHi1

source_name: whole embryo, CLB, WAF Hi 1

value: WAF Hi


title: wholeembryo_CLB_WAFHi3

source_name: whole embryo, CLB, WAF Hi 3


title: Ecoli_P2_T0_kinetic3

description: Cells were in P2 phase (glucose exhaustion), the sampling was performed just before rifampicin addition. It is the third kinetics out of 3 for this phase

source_name: E. coli in P2 phase, Sampling before rifampicin addition in kinetic 3


title: NAA100-E-L38-A_FPKM


title: Daxx_MII_WT_rep1


title: wholeembryo_CLB_WAFLo3

source_name: whole embryo, CLB, WAF Lo 3

value: WAF Lo


title: wholeembryo_CLB_WAFHi2

source_name: whole embryo, CLB, WAF Hi 2


title: wholeembryo_CLB_WAFLo2

source_name: whole embryo, CLB, WAF Lo 2


title: wholeembryo_AWB_CEWAFHi3

source_name: whole embryo, AWB, CEWAF Hi 3

value: AWB


title: Foxp3-GFP+Treg_WT_Rep3_RNA-seq

city: Cambridge

first: Mohammed-Firas

last: Sadiyah

address: The Old Schools, Trinity Ln

country: United Kingdom

institute: University of Cambridge

data_processing:
FastQ files underwent quality control with FastQC, adaptor trimming with Cutadapt and alignment to the NCBIM37 Mus musculus genome annotation with hisat2 using ClusterFlow pipelines
Differential gene expression analysis was performed using Cufflinks44 and differentially expressed genes were futher analysed using R
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values

source_name: Treg cells

extract_protocol:
Single-cell suspensions were purified by total CD4+ T cell enrichment followed by FACS-sorting
stored in 40 µl RNAlater™ Stabilization Solution at -80 °C
Samples were processed using the QIAshredder Kit (Qiagen) according to the manufacturer’s protocol
RNA was extracted from samples using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s protocol
RNA Libraries were prepared using the SmartSeq2 protocol on an automated Hamilton NGS-STAR library preparation system and sequenced using a HiSeq 2500 System (Illumina)

value: spleen

tag: age

value: post natal 18–21 weeks

tag: genotype

value: Bach2+/+ Foxp3EGFP-Cre-ERT2


title: wholeembryo_CLB_WAFLo1

source_name: whole embryo, CLB, WAF Lo 1

value: whole embryo

value: CLB


title: NAA100-E-L36-C_FPKM


title: Ecoli_P2_T4_kinetic2

description: Cells were in P2 phase (glucose exhaustion) the sampling was performed 4 min after rifampicin addition. It is the second kinetics out of 3 for this phase

source_name: E. coli in P2 phase, Sampling 4 minutes after rifampicin addition in kinetic 2


title: wholeembryo_AWB_CEWAFHi2

source_name: whole embryo, AWB, CEWAF Hi 2

value: CEWAF Hi


title: Ecoli_P2_T1_kinetic3

description: Cells were in P2 phase (glucose exhaustion) the sampling was performed 1 min after rifampicin addition. It is the third kinetics out of 3 for this phase

source_name: E. coli in P2 phase, Sampling 1 minute after rifampicin addition in kinetic 3


title: Ecoli_P2_T11_kinetic2

description: Cells were in P2 phase (glucose exhaustion) the sampling was performed 11 min after rifampicin addition. It is the second kinetics out of 3 for this phase

source_name: E. coli in P2 phase, Sampling 11 minutes after rifampicin addition in kinetic 2


title: Foxp3-GFP+Treg_WT_Rep2_RNA-seq


title: wholeembryo_AWB_CEWAFHi1

source_name: whole embryo, AWB, CEWAF Hi 1


title: NAA100-E-L36-B_FPKM


title: Ecoli_P2_T0_kinetic2

description: Cells were in P2 phase (glucose exhaustion), the sampling was performed just before rifampicin addition. It is the second kinetics out of 3 for this phase

source_name: E. coli in P2 phase, Sampling before rifampicin addition in kinetic 2


title: Ecoli_P2_T7_kinetic1

description: Cells were in P2 phase (glucose exhaustion), the sampling was performed 7 min after rifampicin addition. It is the first kinetics out of 3 for this phase

source_name: E. coli in P2 phase, Sampling 7 minutes after rifampicin addition in kinetic 1


title: wholeembryo_AWB_CEWAFLo2

source_name: whole embryo, AWB, CEWAF Lo 2

value: CEWAF Lo


title: wholeembryo_AWB_CEWAFLo3

source_name: whole embryo, AWB, CEWAF Lo 3


title: Ecoli_P2_T0.5_kinetic2

description: Cells were in P2 phase (glucose exhaustion) the sampling was performed 0.5 min after rifampicin addition. It is the second kinetics out of 3 for this phase

source_name: E. coli in P2 phase, Sampling 0.5 minute after rifampicin addition in kinetic 2


title: Foxp3-GFP+Treg_WT_Rep1_RNA-seq


title: NAA100-E-L36-A_FPKM

source_name: grape berry