title: D35_plus_b

city: La Jolla

first: Karl

last: Wahlin

state: CA

address: 9415 Campus Point Dr., #0946

department: Ophthalmology

institute: UC San Diego

data_processing:
Raw data mapped to genocde v25 release using TopHat v2.0.12
Differential gene expression based on negative binomial distribution with DeSeq2 in R
deSeq2 for gene statistics
Genome_build: Gencode v25
Supplementary_files_format_and_content: tab delimited file with normaized deSeq2 reads

source_name: Neural organoids

growth_protocol: Stem cells were maintained under hypoxic conditions in mTeSR1 media (Wahlin, Maroutti et al., 2017). Stem cells were differentiated into organoids using BE6.2-NIM (B27 + E6 at 2X concentration) (neural induction medium) consists of DMEM (#11965; Invitrogen) supplemented with 1% B27 vitamin A (-) (#12587010; Invitrogen) and 2X E6 supplement (38.8 mg/L insulin (#11376497001; Roche), +128mg/L L-ascorbic acid (#A8960; Sigma), 28μg/L selenium (#S5261; Sigma), 21.4 mg/L transferrin (#T0665; Sigma) and 38.8 mg/L NaHCO3). Osmolarity was raised +30mOsm to ~330-340mOsm) by adding 0.88 g/L NaCl (Ludwig, Bergendahl et al. 2006, Chen, Gulbranson et al. 2011). LTR (Long-Term Retina) medium was a 3:1 mix of DMEM:F12 (#11965, #11765; Invitrogen) supplemented with 1% B27 (#17504044; Invitrogen), 10% heat inactivated qualified-grade FBS (#16140071; Invitrogen), 1mM pyruvate (#11360; Invitrogen), 1xNEAA (#11140; Invitrogen), 1X Glutamax (#35050061; Invitrogen) and 1mM taurine (#T-8691; Sigma). For fluorescent live cell imaging, we substituted DMEM(#11965; Invitrogen) with Phenol red with FluoroBrite™ DMEM (#A1896701; Invitrogen) + 2mM glutamine that has no phenol red, HEPES, or sodium pyruvate.

extract_protocol:
Rneasy mini kit (Qiagen #74104), analyzed using Agilent 2100 DNA Bioanalyzer System, RIN value greater than 8 used for library preparation
Illumina Nextera librey prep synthesis kit

value: human induced pluripotent stem cell-derived organoids

tag: fluorescence

value: GFP+

tag: phenotype


title: FL_MPP_rep1

status: Public on Oct 25 2021

type: SRA

city: Oxford

first: Siobhan

last: Rice

address: Room 320, WIMM, JR Hospital/Headley Way

country: United Kingdom

institute: Weatherall Institute of Molecular Medicine

library_source: transcriptomic

data_processing:
RNA-seq reads were aligned to the hg38 genome using STAR
Read counts were determined using featureCounts (Subread package)
Genome_build: hg38

molecule: polyA RNA

organism: Homo sapiens

source_name: primary human FL

growth_protocol: crisprMLL-AF4 and control FL cells were maintained in StemLine II supplemented with 100ng/mL each of SCF, FLT3L and TPO during editing protocol and immediately transplanted into NSG mice via tail vein injection. Sorted FL cells were derived from primary human FL and never maintained in culture.

extract_protocol: RNA was extracted using the RNEasy mini kit (QIAGEN 74134). Poly A purification was conducted using the NEB Poly(A) mRNA magnetic isolation module as per the manufacturer’s protocol.

treatment_protocol: crisprMLL-AF4 FL cells were electrporated with Cas9-MLL and Cas9-AF4 ribonucleoproteins (RNP) to induce an MLL-AF4 chromosomal translocation, Control FL cells were electroporated with Cas9 or Cas9-MLL RNP only. Sorted FL cells were untreated

tag: sample type

value: primary human FL

tag: treatment

value: primary human FL cells were FACS sorted to isolate hematopoietic subpoulations

tag: cell type


title: FL_MPP_rep2


title: FL_HSC_rep2


title: ChIL-H3K27ac - CTX injurured TA - Day 7 - rep. 2

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

country: Japan

institute: Medical Institute of Bioregulation

library_source: genomic

data_processing:
Gene expression quantification (TPM estimation) was performed by Salmon "quant" with the default option.
The reads of ChIL-seq were mapped against the GRCm38 or GRCh38 reference genome using Bowtie2 with the default option.
Duplicated reads were discarded using samtools (rmdup) and the uniquely mapped reads were used for further analysis.
The bigWig files were generated using deepTools (version 3.4.1) with the command: bamCoverage -p 36 --binSize 100 --normalizeUsing CPM --smoothLength 1000.
Genome_build: GRCm38, GRCh38
Supplementary_files_format_and_content: CSV files include comma-delimited gene expression (TPM) matrices

molecule: genomic DNA

organism: Mus musculus

source_name: tibialis anterior muscle

extract_protocol:
Each cryo-tissue section (10 um) was placed onto u-plate 96 well bottom (Ibidi #89626) and the plate was stored at -80ºC freezer without backing to room temperature until use. Tissue section was fixed with 4%PFA in 0.3% TritonX-100/PBS for five minutes and washed with 0.3% TritonX-100/PBS. Double blocking were performed using blocking one (Nacalai #03953) and M.O.M blocking reagent (Vector Laboratories #BMK-2202) as instructed. The sections were incubated with primary antibody in M.O.M. protein concentrate/PBS at 4ºC overnight, followed by incubating with ChIL probe at same condition but in addition of NaCl at 0.5 M concentration.
ChIL-seq was performed according to ChIL (Harada et al., 2018) with some modifications. Longer incubation time is used for some steps (Extended Tn5 binding 1hr and fill-in step 2hrs),  Thermo T7 RNA polymerase (100 U per well; Toyobo), and 15 cycles of PCR amplification. Column purification (Zymo #D4013) and x0.5 volume of AMpure beads (Beckman Coulter) selection were performed to obtain 200-500 bp average of library.  For RNA-seq, total RNA was extracted from the cryo sections (up to five serial sections) using Direct-Zol kit (Zymo #R2063). The total of 10 ng RNA was used for library preparation using SMART-Seq Stranded Kit (Takara) as instructed.

treatment_protocol: Muscle regeneration studies were performed as previously reported (Ono et al., 2011), except for the injection of cardiotoxin (CTX) into the tibialis anterior (TA) muscle. Injured and intact TA muscles were sampled from five mice at day 0, 3, 5, 7 and 14 from mice after CTX injury. Day 0 mice were by needle injured controls.

tag: strain

tag: tissue

value: tibialis anterior muscle

tag: antibody

tag: time point


title: D35_minus_a

country: USA

molecule: total RNA

value: GFP-


title: D35_minus_c


title: ChIL-H3K27ac - CTX injurured TA - Day 7 - rep. 3


title: ChIL-H3K27ac - CTX injurured TA - Day 7 - rep. 1


title: FL_HSC_rep3


title: Jurkat_CRISPR_tRNA_day_20

city: Braunschweig

first: Andreas

last: Kloetgen

state: NI

address: Inhoffenstr 7

department: Department for Computational Biology of Infection Research

country: Germany

institute: Helmholtz Centre for Infection Research

description:
CRISPR_tRNA_library_normalized-results.tsv
CRISPR_tRNA_library_CERES-scores.tsv

data_processing:
Library strategy: CRISPR sgRNA screen
Trimming: Adapter sequences were first trimmed off using cutadapt, removing all untrimmed reads (parameters -e 0.1 -O 10 -m 20 –discard-untrimmed)
Counting: Trimmed 20bp reads were counted by exact matches with the sgRNA library sequences.
Normalization: Raw reads were intra-sample normalized with edgeR function cpm.
Differential analysis: First, log2 fold-changes based on CPM values between different valine conditions and repsective treatment days were calculated with a pseudocount of 0.1.
Gene summary: To summarize individual sgRNAs on a gene-level, we executed the R-package "ceres" to report essentiality scores per gene, using log2 fold-changes..
Genome_build: hg19
Supplementary_files_format_and_content: tsv file - per-sample CPM and differential CERES scores

source_name: Jurkat T-ALL cell line

extract_protocol:
Genomic DNA was isolated using Qiagen DNA purfication kit for tRNA screen and Takara Nucleospin Blood XL kit.
Libraries were prepared by amplification of the sgRNA with primers compatible for Illumina sequencing.

treatment_protocol: For the whole genome screen, the infected cells were cultured in standard or low valine media.

tag: cell line

value: Jurkat

tag: crispr library

value: tRNA-specific

tag: valine concentration

value: 20 days post transduction

tag: molecule subtype

value: CRISPR sgRNA


title: FL_HSC_rep1


title: control_rep3

source_name: human CD45+CD19+ FL cells sorted from the bone marrow of engrafted NSG mouse

value: control

value: primary human FL CD34+ cells were electroporated with Cas9 protein and MLL guide RNA only to cause a single cut in intron 11 of MLL (no effect) and engrafted into an NSG mouse

value: human CD45+CD19+ cells FACS sorted from the bone marrow of engrafted NSG mouse


title: D0A

source_name: Induced pluripotent stem cells

value: IMR90.4 human induced pluripotent stem cells


title: control_rep1

value: primary human FL CD34+ cells were electroporated with Cas9 protein only and engrafted into an NSG mouse


title: ChIL-H3K27ac - CTX injurured TA - Day 7 - rep. 5


title: ChIL-H3K27ac - CTX injurured TA - Day 5 - rep. 3


title: ChIL-H3K27ac - CTX injurured TA - Day 5 - rep. 4


title: Male_APPPS1-21_Abx+FMT (SS-HBD-32_S28)

city: Chicago

first: Priyam

last: Patel

state: IL

address: 750 North Lake Shore Drive, Rubloff 11-146

department: Quantitative Data Science Core

institute: Northwestern University

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned to mm10 using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited file with read counts per gene

source_name: Short-term ABX Tg mice study_sacrificed at 9 weeks

extract_protocol:
Total RNA was isolated using Trizol, phase separated by chloroform, and extracted by alcohol
RNA quality and quantity was assessed using the Agilent bio-analyzer. Strand-specific RNA-SEQ libraries were prepared using an TruSEQ mRNA RNA-SEQ library protocol (Illumina provided). Library quality and quantity was assessed using the Agilent bio-analyzer and libraries were sequenced using an Illumina NovaSEQ6000 (illumina provided reagents and protocols). Raw data was demultiplexed using Illumina’s bcl2fastq software and fastq.gz files were provided for analysis.

value: Cerebral cortex

tag: tissue dissection anatomy

value: dorsal side of the right hemisphere

tag: Sex

value: Male

value: Abx+FMT


title: D35_plus_a

value: human induced pluripotent stem cell-derived organoids

value: GFP+


title: D0B


title: ChIL-H3K27ac - CTX injurured TA - Day 5 - rep. 5

value: tibialis anterior muscle


title: Male_APPPS1-21_Abx+FMT (SS-HBD-34_S30)


title: crisprMLL-AF4_rep3

value: primary human FL CD34+ cells were CRISPR-Cas9 edited to induce an MLL-AF4 chromosomal translocation and engrafted into an NSG mouse


title: Male_APPPS1-21_Abx+FMT (SS-HBD-29_S25)


title: ChIL-H3K27ac - CTX injurured TA - Day 5 - rep. 2


title: NGP_DMSO_2

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

data_processing:
Reads were aligned to a reference genome containing the non-random chromosomes from hg19 and the sequences of ERCC probes using hisat2 with parameters --no-novel-juncs and -G set to a gene database file downloaded from RefSeq on 7/5/2017 to which positions of the ERCC probes were added.  Coverage of the genes in this list was calculated using htseq-count with parameters -i gene_id --stranded=reverse -f bam -m intersection-strict.
Supplementary_files_format_and_content: Counts files represent the number of reads quantified for each gene using htseq-count

source_name: Neuroblastoma

growth_protocol: Cells were grown in 6-well plates in RPMI media containing 10% FBS and 1% pen-strep. Cells were treated with DMSO or ATRA (5uM) for 6 days.

extract_protocol:
Libraries were prepared using Illumina TruSeq stranded specific sample preparation kits from 500ng of purified total RNA according to the manufacturer’s protocol. Finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 4200, and RT-qPCR using the Roche Kapa Biosystems library quantification kit according to manufacturer’s protocols. Indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq 550 with single-end 75bp reads by the Dana-Farber Cancer Institute Molecular Biology Core Facilities.
Cells were collected directly into Trizol and ERCC-spike in RNA was added directly to the suspension, normalized to cell number. RNA from the aqueous phase was then purified using QIAgen RNeasy columns according to the manufacturer’s protocol, and eluted in 30 uL RNase-free water.

value: NGP

tag: treatment protocol

value: DMSO, 6 days


title: Female_NonTg_Abx (merged_SS-HBD07_S6)

value: C57BL/6 (WT littermates from APPPS1-21 breedings)

value: Female

value: Abx


title: Male_APPPS1-21_Abx+FMT (SS-HBD-33_S29)


title: ChIL-H3K27ac - CTX injurured TA - Day 3 - rep. 1


title: ChIL-H3K27ac - CTX injurured TA - Day 3 - rep. 4


title: control_rep2

value: control


title: ChIL-H3K27ac - CTX injurured TA - Day 3 - rep. 2


title: Male_APPPS1-21_Abx+FMT (SS-HBD-30_S26)


title: ChIL-H3K27ac - CTX injurured TA - Day 3 - rep. 5


title: Male_APPPS1-21_Abx (SS-HBD-27_S24)


title: ChIL-H3K27ac - CTX injurured TA - Day 5 - rep. 1


title: NGP_DMSO_3


title: Male_APPPS1-21_Abx+FMT (SS-HBD-31_S27)


title: NGP_DMSO_1


title: NGP_ATRA_3

value: 5 uM ATRA, 6 days


title: Male_APPPS1-21_Abx (SS-HBD-26_S23)


title: crisprMLL-AF4_rep1

value: human CD45+CD19+ cells FACS sorted from the bone marrow of engrafted NSG mouse


title: ChIL-H3K27ac - CTX injurured TA - Day 3 - rep. 3


title: Male_APPPS1-21_Abx (SS-HBD-25_S22)


title: crisprMLL-AF4_rep2


title: NGP_ATRA_2


title: ChIL-H3K27ac - CTX injurured TA - Day 0 - rep. 5


title: ChIL-H3K27ac - CTX injurured TA - Day 0 - rep. 3


title: Male_APPPS1-21_Abx (SS-HBD-24_S21)


title: NBLS_DMSO_3

value: NBL-S


title: ChIL-H3K27ac - CTX injurured TA - Day 0 - rep. 4


title: NBLS_DMSO_2


title: Male_APPPS1-21_Abx (SS-HBD-23_S20)

value: Cerebral cortex


title: NGP_ATRA_1


title: Male_APPPS1-21_Abx (SS-HBD-22_S19)

value: dorsal side of the right hemisphere


title: ChIL-H3K27ac - CTX injurured TA - Day 0 - rep. 2


title: ChIL-H3K27ac - CTX injurured TA - Day 0 - rep. 1


title: NBLS_ATRA_3


title: NBLS_DMSO_1


title: Male_APPPS1-21_Vehicle (SS-HBD-19_S17)

value: Male

value: Vehicle


title: Male_APPPS1-21_Vehicle (SS-HBD-20_S18)


title: ChIL-Pol2S2PS5P - Testis - rep. 2

source_name: testis

value: testis


title: Male_APPPS1-21_Vehicle (SS-HBD-18_S16)


title: ChIL-Pol2S2PS5P - Testis - rep. 1


title: NBLS_ATRA_2


title: NBLS_ATRA_1


title: BE2C_DMSO_2


title: ChIL-Pol2S2PS5P - Liver - rep. 2

source_name: liver

value: liver


title: Male_APPPS1-21_Vehicle (SS-HBD-16_S14)


title: Male_APPPS1-21_Vehicle (SS-HBD-17_S15)


title: Male_APPPS1-21_Vehicle (SS-HBD-15_S13)


title: BE2C_DMSO_1


title: ChIL-Pol2S2PS5P - Liver - rep. 3


title: Female_APPPS1-21_Abx (SS-HBD-13_S12)


title: ChIL-Pol2S2PS5P - Heart - rep. 3

source_name: left ventricle

value: left ventricle


title: ChIL-Pol2S2PS5P - Liver - rep. 1


title: Female_APPPS1-21_Abx (SS-HBD-12_S11)


title: BE2C_ATRA_3


title: ChIL-Pol2S2PS5P - Testis - rep. 3


title: ChIL-Pol2S2PS5P - Heart - rep. 2


title: BE2C_ATRA_2


title: BE2C_DMSO_3


title: Female_APPPS1-21_Abx (SS-HBD-11_S10)


title: ChIL-Pol2S2PS5P - Heart - rep. 1


title: NGP_Ctrl_Input_MWZ5969 [Lab: Look]

data_processing:
Aligned using /usr/local/bin/bowtie with configuration -p 4 --best -k 2 -m 2 --sam -l 75
hg19
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1

growth_protocol: Cells were grown in 6-well plates in RPMI media containing 10% FBS and 1% pen-strep. Cells were treated with DMSO or ATRA (5uM) for 12 days.

extract_protocol:
Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
Lysates were clarified from sonicated nuclei and target bound fragments were isolated with antibody.

tag: chip antibody

tag: drug

value: DMSO

value: DMSO, 12 days


title: Control_No_ABX_8

city: Adelaide

first: Feargal

middle: J

last: Ryan

state: Adelaide

address: North Terrace

country: Australia

institute: SAHMRI

data_processing:
Quality control with Trimmomatic version 0.38
Gene count matrix was generated with FeatureCounts version 1.5.0-p2
Aligned to genome using HISAT2 version 2.1.0
Genome_build: mm10
Supplementary_files_format_and_content: FeatureCounts per gene counts

source_name: Liver

extract_protocol:
Liver portions were snap frozen and 500 mg sections were resuspended in trizol as described. RNA was extracted according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Liver

tag: antibiotics

tag: experimental group

value: Control


title: BE2C_ATRA_1


title: Female_APPPS1-21_Vehicle (SS-HBD-6_S6)

value: Female

tag: treatment


title: Female_APPPS1-21_Abx (SS-HBD-10_S9)

value: Abx


title: Female_APPPS1-21_Abx (SS-HBD-8_S7)


title: Control_No_ABX_7


title: NGP_ATRA_12d_RARA_MWZ5969 [Lab: Look]

tag: cell type

value: NGP

value: RARa

tag: antibody manu.

value: Abcam

tag: antibody catalog

tag: antibody lot

value: ATRA 12d

value: 5 uM ATRA, 12 days


title: Female_APPPS1-21_Vehicle (SS-HBD-5_S5)

tag: tissue

value: Cerebral cortex

value: dorsal side of the right hemisphere

tag: strain


title: Female_APPPS1-21_Abx (SS-HBD-9_S8)


title: Female_APPPS1-21_Vehicle (SS-HBD-4_S4)

value: Vehicle


title: Control_No_ABX_6


title: NGP_ATRA_12d_Input_MWZ5969 [Lab: Look]


title: Female_APPPS1-21_Vehicle (SS-HBD-3_S3)


title: Anti-CD40_ABX_14

value: ABX


title: NGP_ATRA_12d_H3K27ac_MWZ5969 [Lab: Look]


title: Female_APPPS1-21_Vehicle (SS-HBD-2_S2)


title: NBLS_DMSO_input_MZ_180616 [Lab: Look]

value: NBL-S


title: NGP_ATRA_12d_MEIS1_MWZ5969 [Lab: Look]


title: NBLS_DMSO_H3K27ac_MZ_180616 [Lab: Look]


title: NGP_Ctrl_H3K27ac_MWZ5969 [Lab: Look]


title: Female_APPPS1-21_Vehicle (SS-HBD-1_S1)


title: Anti-CD40_ABX_13


title: Anti-CD40_ABX_15


title: NBLS_ATRA_input_MZ_180616 [Lab: Look]


title: TALL3_0g_valine_total_RNA

data_processing:
Library strategy: Ribo-Seq
Trimming: Adatper sequences were first removed from each sequencing read using cutadapt version 1.18, keeping reads longer than 15bp (parameters: -m 15 -q 25).
ncRNA alignment: In order to remove ncRNA sequences, trimmed reads were first aligned against an ncRNA database downloaded from Ensembl Genes V85 using bowtie2 version 2.3.4. Only non-aligned reads were kept for further analyses.
Genome alignment: Remaining reads were aligned against the mouse reference genome sequence mm10/GRCm38 with STAR aligner version 2.5.0c
Read counting: Reads were counted per annotated gene exon with the STAR integrated counts function (-quantMode GeneCounts) using annotations from Ensembl Genes V85.
Normalization: Read counts were normalized using edgeR version 3.14.0 with the rpkm function and gene length information from Ensembl Genes V85.
Genome_build: mm10
Supplementary_files_format_and_content: tsv - FPKM list

source_name: mouse secondary transplant of T-ALL

extract_protocol:
Total RNA and Ribosome protected RNA was extracted using True Ribo-Seq profile kit from Illumina folllowing manufacturer's guidelines.
Libraries from Total RNA and Ribosome protected RNA was generated using  True Ribo-Seq profile kit from Illumina folllowing manufacturer's guidelines.

treatment_protocol: Mice secondrary transplanted with NOTCH-delta E tumors were fed either valine proficient control diet or valine deficient diet or valine defiecinet diet substituted with either 0.8g/L or 0.4g/L valine in drinking water. Mice were sacrificed 3 weeks in different diets and leuekmic cells were sorted from spleen using GFP as a marker and used for RNA isolation.

value: secondary transplant of T-ALL

value: 0.0g/kg valine diet

tag: rna fraction

value: total RNA

tag: mouse strain


title: BE2C_Ctrl_H3K27me3_MWZ7304 [Lab: Look]

value: DMSO

value: DMSO, 12 days


title: TALL3_0g_valine_RPF

tag: valine concentration

value: ribosome protected fragments


title: Anti-CD40_ABX_11

value: Liver


title: Control_ABX_4

value: Control


title: Anti-CD40_No_ABX_19


title: Anti-CD40_ABX_12


title: TALL3_0-4g_valine_RPF

value: 0.4g/kg valine diet


title: NBLS_ATRA_H3K27ac_MZ_180616 [Lab: Look]

value: Abcam


title: Anti-CD40_No_ABX_18


title: BE2C_Ctrl_H3K27ac_MWZ7304 [Lab: Look]


title: TALL3_0-4g_valine_total_RNA


title: BE2C_Ctrl_Input_MWZ7304 [Lab: Look]


title: BE2C_ATRA_input_MWZ6821 [Lab: Look]

value: ATRA 12d


title: Anti-CD40_No_ABX_20


title: Control_No_ABX_10


title: BE2C_ATRA_H3K27me3_MWZ7304 [Lab: Look]

value: 5 uM ATRA, 12 days


title: Control_ABX_5


title: Control_ABX_3


title: BE2C_ATRA_MEIS1_MWZ6821 [Lab: Look]


title: BE2C_ATRA_Input_MWZ7304 [Lab: Look]


title: Anti-CD40_No_ABX_17


title: TALL2_0g_valine_RPF


title: TALL3_0-8g_valine_total_RNA

value: 0.8g/kg valine diet


title: TALL3_0-8g_valine_RPF


title: TALL2_0g_valine_total_RNA


title: Control_No_ABX_9


title: TALL3_8g_valine_RPF

value: 8g/kg valine diet (control)


title: TALL2_0-8g_valine_RPF


title: ChIL- no antibody control (anti-mouse) - Testis

data_processing:
Gene expression quantification (TPM estimation) was performed by Salmon "quant" with the default option.
The reads of tsChIL-seq were mapped against the GRCm38 reference genome using Bowtie2 with the default option.
Duplicated reads were discarded using samtools (rmdup) and the uniquely mapped reads were used for further analysis.
The bigWig files were generated using deepTools (version 3.4.1) with the command: bamCoverage -p 36 --binSize 100 --normalizeUsing CPM --smoothLength 1000.
Genome_build: GRCm38
Supplementary_files_format_and_content: CSV files include comma-delimited gene expression (TPM) matrices

extract_protocol:
Each cryo-tissue section (10 um) was placed onto u-plate 96 well bottom (Ibidi #89626) and the plate was stored at -80ºC freezer without backing to room temperature until use. Tissue section was fixed with 4%PFA in 0.3% TritonX-100/PBS for five minutes and washed with 0.3% TritonX-100/PBS. Double blocking were performed using blocking one (Nacalai #03953) and M.O.M blocking reagent (Vector Laboratories #BMK-2202) as instructed. The sections were incubated with primary antibody in M.O.M. protein concentrate/PBS at 4ºC overnight, followed by incubating with ChIL probe at same condition but in addition of NaCl at 0.5 M concentration.
ChIL-seq was performed according to ChIL (Harada et al., 2018) with some modifications. Longer incubation time is used for some steps (Extended Tn5 binding 1hr and fill-in step 2hrs),  Thermo T7 RNA polymerase (100 U per well; Toyobo), and 15 cycles of PCR amplification. Column purification (Zymo #D4013) and x0.5 volume of AMpure beads (Beckman Coulter) selection were performed to obtain 200-500 bp average of library.  For RNA-seq, 10 ng of total RNA was used for library preparation using SMART-Seq Stranded Kit (Takara) as instructed.

value: testis

tag: antibody


title: ChIL- no antibody control (anti-rat) - Testis


title: TALL2_0-4g_valine_total_RNA


title: TALL3_0g_valine

data_processing:
Alignment: Sequencing reads were aligned against the reference genome sequences hg19 for human and mm10 for mouse using the STAR aligner. Only uniquely mapped reads were kept.
Read counting: STAR integrated function --quantMode GeneCounts was applied using Ensembl Genes V75 for human and Ensembl Genes V85 gene annotations. Only reverse-mapping read counts (RF) were utilized for downstream analyses.
Normalization: FPKM normalization was applied using edgeR after intra- and inter-sample normalization (“calcNormFactors” and “estimateTagwiseDisp”).
Genome_build: hg19 for human; mm10 for mouse
Supplementary_files_format_and_content: tsv-table of FPKM values

source_name: mouse leukemic cells from spleen

extract_protocol:
RNA was extracted using the RNeasy Mini Kit using Qiagen kit (Catalog no: 74106) folllowing manufacturer's guidelines.
The libraries were prepared using NEXTflex Rapid Directional RNA-Seq Kit from Bioo Scientific (Catalog no: 5138-07) folllowing manufacturer's guidelines.

treatment_protocol: Human cell line KOPTK1 was either treated with DMSO control or gamma-secretase inhibitor (Compound E, Alexis Bioscience, ALX-270-415-C250) for 72h. For the in vivo experiments, mice secondrary transplanted with NOTCH-delta E tumors were fed either valine proficient control diet or valine deficient diet or valine defiecinet diet substituted with either 0.8g/L or 0.4g/L valine in drinking water. Mice were sacrificed after 3 weeks in different diets and leuekmic cells were sorted from spleen using GFP as a marker and used for RNA isolation.

value: mouse leukemic cells from spleen


title: ChIL- no antibody control (anti-mouse) - Liver

value: liver


title: BE2C_ATRA_H3K27ac_MWZ7304 [Lab: Look]


title: Control_ABX_1

value: ABX


title: TALL3_04g_valine


title: TALL3_8g_valine_total_RNA

value: secondary transplant of T-ALL


title: ChIL-Pol2S5P - Testis - rep. 3


title: DKO241

first: Barbara

middle: L

last: Kee

state: Illinois

address: 924 E57th st

department: Pathology

institute: The University of Chicago

data_processing:
Raw sequence reads were trimmed using Trimmomatic v 0.33 (TRAILING:30 MINLEN:20)
Trimmed reads were aligned to mouse genome assembly mm10 with Tophat v 2.1.0.
Reads were assigned to genes using the htseq-count tool from HTSeq v 0.6.1 and gene annotations from Ensembl release 78.
The R package EdgeR was used to normalize the gene counts and to calculate differential expression statistics for each gene for each pairwise comparison of sample groups. Genes were considered differentially expressed if the |fold change| >= 2 and FDR < 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: normalized abundance measurements provided as edgeR output files

source_name: T cell leukemia cell line

growth_protocol: OPTI-MEM with 10%FBS, 50mM mercaptoethanol

extract_protocol:
RNA was extracted in Trizol Reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: no treatment

tag: source

value: Thymus

value: T cell leukemia cell line

tag: genotype

value: E2a-/-LefF/F LckCre+

value: FVB/NJ


title: SKO186.5


title: DKO170.2


title: TALL2_0-4g_valine_RPF

value: ribosome protected fragments


title: SKO163.5


title: TALL2_0-8g_valine_total_RNA

value: total RNA


title: Control_ABX_2

value: Liver

value: Control


title: TALL2_8g_valine_RPF


title: DKOTu3


title: DKO713


title: ChIL- no antibody control (anti-rat) - Heart

value: left ventricle


title: ChIL-Pol2S5P - Heart - rep. 3


title: ChIL-Pol2S5P - Heart - rep. 2


title: SKO132


title: ChIL- no antibody control (anti-mouse) - Heart


title: ChIL- no antibody control (anti-rat) - Liver


title: DKO102.4


title: TALL3_8g_valine


title: TALL2_8g_valine_total_RNA


title: ChIL-Pol2S5P - Testis - rep. 2


title: TALL2_0g_valine

value: 0.0g/kg valine diet


title: SKO156.6


title: DKO192.3


title: SC (controlled group)

city: Beijing

first: Guan

last: Li

email: umemaro@163.com, zzmbysy@sina.com

state: Beijing

address: 49 North Garden Road

country: China

institute: Peking University Third Hospital

description: samples were from 7-day sham operation controlled zygomatic maxillary suture

data_processing:
The Seurat pipeline clustering method for data preprocessing is Seurat 3.6 (R package). Cells with less than 200 genes, top 1% UMI or more than 20% mitochondrial gene ratio were considered abnormal and filtered out. PCA is used to reduce dimension and tsne is used to realize visualization.
Genome_build: Rnor_6.0.92 from ensembl database
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

organism: Rattus norvegicus

source_name: rat sham operation controlled zygomatic maxillary suture

growth_protocol: rats were feed in the SPF-level Laboratory Animal Room with normal diet

extract_protocol:
The tissue was transferred to the complete medium (aMEM + 20% FBS + P/s) and then crushed into cell suspension.Using single BD Rhapsody™ Cartridge Reagent Kit (Cat. 633731), the cell suspension (300-600 living cells per microliter determined by Count Star) were then further pooled and passed over a sample cartridge (400000847)for the BD Rhapsody to trap single cells. Processing for RNA isolation and cDNA library preparation according to the manufacturer's protocol.
Single-cell RNA-seq libraries were constructed according to the manufacture’s introduction, The libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100,000 reads per cell with pair-end 150 bp (PE150) reading strategy (performed by CapitalBio Technology, Beijing).

treatment_protocol: the rats were anesthetized with 10% chloral hydrate 4ml / kg, the facial skin was incised, part of masseter and temporal muscles were separated in order to expose part of the maxilla and zygoma. The nickel-titanium alloy wire, shaped into a W distractor, was drilled at the base of temporal bone and maxillary bone (spacing 1.2mm) respectively and tracted for seven days. The distrctor is made of 0.4mm nickel-titanium alloy wire by Jiyi (Beijing, China). After calibration, it can give 20g initial force between two holes spacing 1.2cm.The control group was only drilled without placing the distractor.

tag: age

value: 4 weeks


title: ChIL-Pol2S5P - Testis - rep. 1


title: SKO95


title: SKO137.1


title: ChIL-Pol2S5P - Liver - rep. 1


title: DKO548


title: TALL2_08g_valine

value: 0.8g/kg valine diet


title: TALL3_08g_valine


title: ChIL-H3K27ac - Testis - rep. 3

value: testis


title: TALL2_04g_valine

value: mouse leukemic cells from spleen

value: 0.4g/kg valine diet


title: SKO115.2


title: ChIL-Pol2S5P - Heart - rep. 1


title: ChIL-Pol2S5P - Liver - rep. 3

value: liver


title: TALL2_8g_valine

value: 8g/kg valine diet (control)


title: DKO79.9

value: Thymus


title: DO (experimental group)

description: samples were from 7-day distracted zygomatic maxillary suture

source_name: rat distracted zygomatic maxillary suture


title: ChIL-H3K27ac - Liver - rep. 3


title: ChIL-Pol2S5P - Liver - rep. 2


title: ChIL-H3K27ac - Testis - rep. 2


title: ChIL-H3K27ac - Liver - rep. 2


title: spinal cord astrocytes, LFNG-, EA23

city: Houston

first: Ekin

middle: Su

last: Akdemir

address: 1 Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Quality control was performed on concatenated fastq files using fastQC and multiQC. Paired end reads were mapped to the mouse genome (mm10) using STAR (v2.5.0a).
Reads Per Million (RPM) were calculated using GenomicAlignments (v1.16.0) and normalized using DESeq2 (v1.20.0).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPM values or raw counts for each sample

source_name: spinal cord astrocytes

extract_protocol:
Spinal cord was collected from LFNG-GFP  mice or ALDHL1L GFP C57BL/6J mice were dissected and dissociated, and astrocytes were isolated using FACS directly into QIAGEN RLT lysis buffer (Cat# 74004) with 1% ß-Mercaptoethanol. Bulk RNA was isolated using the RNeasy Micro Kit (74004, QIAGEN).
Illumina sequencing libraries were constructed from 10ng of total RNA using the Trio RNA-Seq System (0507-96, NuGEN).

value: spinal cord astrocytes

value: LFNG-GFP

tag: gfp status

value: LFNG-GFP negative cells


title: spinal cord astrocytes, LFNG+, EA28

value: LFNG-GFP positive cells


title: spinal cord astrocytes, LFNG-, EA21


title: ChIL-Hnf4alpha - Liver - rep. 3


title: spinal cord astrocytes, LFNG+, EA27


title: spinal cord astrocytes, ALDH-, EA25

value: ALDH1l1-GFP negative cells


title: spinal cord astrocytes, ALDH-, EA24


title: ChIL-H3K27ac - Heart - rep. 1


title: ChIL-Pol2S5P - Uninjured TA - excess depth

value: tibialis anterior muscle

tag: protocol

value: Uninjured TA

tag: time point

value: excess depth


title: ChIL-Pol2S5P - CTX injurured TA - Day 14 - rep. 4

value: CTX injurured TA

value: Day 14


title: ChIL-H3K27ac - Heart - rep. 2

value: left ventricle


title: ChIL-Hnf4alpha - Liver - rep. 2


title: spinal cord astrocytes, LFNG-, EA22


title: spinal cord astrocytes, ALDH+, EA18

value: ALDH1l1-GFP positive cells


title: ChIL-Pol2S5P - CTX injurured TA - Day 14 - rep. 1


title: ChIL-Pol2S5P - CTX injurured TA - Day 14 - rep. 3


title: ChIL-H3K27ac - Liver - rep. 1


title: Anti-CD40_No_ABX_16

value: Liver

tag: antibiotics

tag: experimental group


title: ChIL-Pol2S5P - CTX injurured TA - Day 7 - rep. 3

value: Day 7


title: MCF7_siOCT1 #1

type: RNA

city: Tokyo

first: Kotaro

last: Azuma

address: 7-3-1, Hongo, Bunkyo-ku

institute: University of Tokyo

hyb_protocol: After fragmentation and labeling, 1.8 ug of ss-cDNA was hybridized for 16 hr at 45°C  on a GeneChip (Clariom S Array, Human). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: Data analysis was performed by Transcriptome Analysis Console (TAC) 4.0 Software using SST-RMA method.

label: biotin

source_name: MCF-7 cells trasfected with siOCT1 #1

label_protocol: Fragmentation and biotinylation of ss-cDNA were performed according to the standard Affymetrix protocol from 150 ug total RNA.

growth_protocol: MCF-7 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) with 10% FBS and 1% penicillin-streptomycin at 37°C with 5% CO2.

extract_protocol: Total RNA was extracted from the cells for gene profiling 48 h after transfection of siRNA using Sepasol-RNA I Super G (Nacalai Tesque, Kyoto, Japan) according to manufacturer’s instruction.

treatment_protocol: Silencing of OCT1 was performed by small interfering RNA (siRNA) transfection (10 nM). Twp specific siRNAs targeting OCT1 (siOCT1 #1 and siOCT1 #2) and a control siRNA targeting firefly luciferase (siControl) were used. These siRNAs were transfected into breast cancer cells (MCF-7) at the time of seeding cells by reverse transfection method using Lipofectamine RNAiMAX (Invitogen, St. Louis, MO, USA).

tag: cell line


title: MCF7_siOCT1 #2

source_name: MCF-7 cells trasfected with siOCT1 #2


title: ChIL-Pol2S5P - CTX injurured TA - Day 5 - rep. 5

source_name: tibialis anterior muscle

value: Day 5


title: spinal cord astrocytes, LFNG+, EA26

tag: cell type


title: MCF7_siControl

source_name: MCF-7 cells trasfected with a control siRNA (siControl)


title: spinal cord astrocytes, ALDH+, EA16


title: ChIL-Pol2S5P - CTX injurured TA - Day 5 - rep. 4


title: ChIL-Pol2S5P - CTX injurured TA - Day 14 - rep. 2


title: ChIL-Hnf4alpha - Liver - rep. 1

value: liver


title: DP-Satb1KO-ChIP-rep1 [input]

city: Guangzhou

first: Hao

last: bingtao

address: ShataiNan Road, Baiyun District, Guangzhou, Guangdong Province

institute: Southern Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
ChIP-Seq data process pipline. Rawdata were filtered by fastp(v0.20.0) with default parameters, and reads were mapped to the mm10 genome assembly using bowtie2 (v2.3.5.1) with parameters (-p 6, --sensitive); Uniq mapped  ChIP-seq reads pairs were got after pcr duplication removing by Picard (v2.22.8) and samtools (v1.7); RPKM normalized BigWig files of  ChIP-Seq were generated by BEDtools(v2.29.2); Bed files of ChIP-Seq were got from Bam file by using HOMER (v4.10.4) with parameters (-style factor).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using bamCoverage with normalized values for each Sample,and bed files were generated using pos2bed.pl after peak calling using findPeaks.

source_name: Thymocytes

growth_protocol: All experiments involving mice were performed using protocols approved by  Southern Medical University Animal Studies Committee. Mice were on a C57Bl/6 genetic background . Animals were housed and bred in a specific pathogen-free animal facility.

extract_protocol: For ChIP-Seq, DP thymocytes were perforated and dealed with sonication. Protein-DNA particles were precipitated with antibody. DNA were purified by PCR Purification Kit.For library preparation, DNAseq libraries were made using Tn5 DNA Library preparation kit.

value: Thymus

value: DP thymocytes

tag: chip antibody


title: ChIL-H3K27ac - Testis - rep. 1

tag: tissue

value: testis


title: ChIL-Pol2S5P - CTX injurured TA - Day 5 - rep. 1

tag: strain


title: ChIL-Pol2S5P - CTX injurured TA - Day 7 - rep. 5


title: ChIL-Pol2S5P - CTX injurured TA - Day 7 - rep. 1


title: ChIL-Pol2S5P - CTX injurured TA - Day 7 - rep. 4


title: ChIL-Pol2S5P - CTX injurured TA - Day 7 - rep. 2


title: ChIL-Pol2S5P - CTX injurured TA - Day 14 - rep. 5


title: ChIL-Pol2S5P - CTX injurured TA - Day 5 - rep. 2


title: ChIL-Pol2S5P - CTX injurured TA - Day 3 - rep. 1

value: Day 3


title: ChIL-Pol2S5P - CTX injurured TA - Day 3 - rep. 4


title: ChIL-Pol2S5P - CTX injurured TA - Day 0 - rep. 4

value: Day 0


title: ChIL-Pol2S5P - CTX injurured TA - Day 3 - rep. 2


title: ChIL-Pol2S5P - CTX injurured TA - Day 0 - rep. 5


title: ChIL-Pol2S5P - CTX injurured TA - Day 5 - rep. 3


title: ChIL-Pol2S5P - CTX injurured TA - Day 3 - rep. 5


title: ChIL-Pol2S5P - CTX injurured TA - Day 0 - rep. 3


title: RNA-seq - CTX injurured TA - Day 14 - rep. 2

description:
Day14-L-2
CTX_TPMMatrix.csv.gz


title: RNA-seq - CTX injurured TA - Day 14 - rep. 5

description:
Day14-L-5
CTX_TPMMatrix.csv.gz


title: ChIL-Pol2S5P - CTX injurured TA - Day 0 - rep. 1


title: ChIL-Pol2S5P - CTX injurured TA - Day 3 - rep. 3


title: RNA-seq - CTX injurured TA - Day 7 - rep. 5

description:
Day7-L-5
CTX_TPMMatrix.csv.gz


title: RNA-seq - CTX injurured TA - Day 14 - rep. 1

description:
Day14-L-1
CTX_TPMMatrix.csv.gz


title: RNA-seq - CTX injurured TA - Day 14 - rep. 4

description:
Day14-L-4
CTX_TPMMatrix.csv.gz


title: L1_6h_SETD5

city: Akita

first: Yoshihiro

last: Matsumura

state: Akita

address: Hondo 1-1-1

department: Biochemistry and Metabolic Science

institute: Akita University Graduate School of Medicine

data_processing:
All bound DNA fragments were mapped UCSC build mm9 assembly of the mouse genome by the mapping program Bowtie2 based on the 5'-side 36-bp sequences.
Signals of ChIP-seq occupancy are presented as counts per million mapped reads (CPM) by using deepTools bamCoverage.
SICER2 program was used under the following parameters: window size 200 bp; gap size 400 bp (for H3K27ac and H3K4me1) and 600 bp (for SETD5-V5 and SETD5); E-value threshold, 100. SICER program was used under the following parameters: window size 200 bp; gap size 600 bp; E-value threshold, 100 for SETD5.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files

source_name: 3T3-L1 preadipocytes

growth_protocol: 3T3-L1 preadipocytes were maintained in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum at 37 °C. For adipocyte differentiation, two days after reaching confluence (day 0), 3T3-L1 preadipocytes were treated with differentiation medium containing insulin (1 μg/ml), 0.25 μM dexamethasone, and 0.5 mM isobutylmethylxanthine (MDI cocktail).

extract_protocol:
Sonicated nuclear fraction was incubated with each antibody and protein-DNA complexes were isolated.
Libraries were prepared according to Illumina's instructions.

value: SETD5 (IgG-F2104)

tag: day of hour of differentiation

value: 6 hr

tag: viral


title: RNA-seq - CTX injurured TA - Day 14 - rep. 3

description:
Day14-L-3
CTX_TPMMatrix.csv.gz

value: tibialis anterior muscle


title: L1_0h_SETD5

value: 0 hr


title: ChIL-Pol2S5P - CTX injurured TA - Day 0 - rep. 2

value: CTX injurured TA


title: RNA-seq - CTX injurured TA - Day 7 - rep. 4

description:
Day7-L-4
CTX_TPMMatrix.csv.gz


title: L1_0h_SETD5-V5_RepB


title: L1_6h_SETD5-V5_RepB


title: RNA-seq - CTX injurured TA - Day 7 - rep. 3

description:
Day7-L-3
CTX_TPMMatrix.csv.gz


title: L1_SETD5_D2_H3K27ac_RepB

value: Day 2


title: RNA-seq - CTX injurured TA - Day 7 - rep. 1

description:
Day7-L-1
CTX_TPMMatrix.csv.gz


title: RNA-seq - CTX injurured TA - Day 5 - rep. 4

description:
Day5-L-4
CTX_TPMMatrix.csv.gz


title: RNA-seq - CTX injurured TA - Day 7 - rep. 2

description:
Day7-L-2
CTX_TPMMatrix.csv.gz


title: RNA-seq - CTX injurured TA - Day 5 - rep. 3

description:
Day5-L-3
CTX_TPMMatrix.csv.gz


title: L1_0h_SETD5-V5_RepA


title: L1_SETD5_D0_H3K27ac_RepB


title: RNA-seq - CTX injurured TA - Day 5 - rep. 2

description:
Day5-L-2
CTX_TPMMatrix.csv.gz


title: RNA-seq - CTX injurured TA - Day 3 - rep. 5

description:
Day3-L-5
CTX_TPMMatrix.csv.gz


title: L1_SETD5_D0_H3K27ac_RepA


title: L1_6h_SETD5-V5_RepA


title: L1_E_D0_H3K27ac_RepA

value: Empty


title: RNA-seq - CTX injurured TA - Day 5 - rep. 5

description:
Day5-L-5
CTX_TPMMatrix.csv.gz


title: Ant-CXCL10 Antibody+GSK343 rep3

city: Birmingham

first: Narendra

last: Wajapeyee

state: AL

address: 720 20th Street South, Kaul 540A

department: Department of Biochemistry and Molecular Genetics

institute: University of Alabama at Birmingham

data_processing:
The base calling was performed using RTA 1.18.64.0
Reads were aligned to GRCm38/mm10 genome index and GRCm38/mm10 annotations using tophat version 2.1.0
Aligned read counts are estimated from alignment file and GRCm38/mm10 gtf using Htseq-count  version 0.6.0.
Sequenced reads were trimmed using Trimmomatic version 0.33 with parameters LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:15; and then mapped to mouse reference genome version mm10 using HISAT2 version 2.1.0 with parameters --mp 6,2 --rdg 5,3--rfg 5,3
Transcriptome assembly and gene expression quantification were performed using StringTie version 1.3.3b with default parameters to calculate FPKM values
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample for each gene

source_name: Mouse HEPA1-6 Tumors

growth_protocol: HEPA1-6 cells were subcuteneously injected into C57/BL6 and tumors were grown for 4 weeks.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen) as per the instruction from the manufacture and then purified using RNAeasy mini columns (Qiagen) as per the manufactures instructions.

treatment_protocol: C57/BL6 tumors injected with Control antibody or Anti-CXCL10 antibody was treated with or without EZH2 inhibitor GSK343

value: Tumor


title: Ant-CXCL10 Antibody+GSK343 rep4


title: RNA-seq - CTX injurured TA - Day 5 - rep. 1

description:
Day5-L-1
CTX_TPMMatrix.csv.gz


title: RNA-seq - CTX injurured TA - Day 3 - rep. 4

description:
Day3-L-4
CTX_TPMMatrix.csv.gz


title: L1_E_D0_H3K27ac_RepB


title: RNA-seq - CTX injurured TA - Day 3 - rep. 3

description:
Day3-L-3
CTX_TPMMatrix.csv.gz


title: L1_E_D2_H3K27ac_RepA


title: RNA-seq - CTX injurured TA - Day 3 - rep. 2

description:
Day3-L-2
CTX_TPMMatrix.csv.gz


title: RNA-seq - CTX injurured TA - Day 0 - rep. 5

description:
Day0-L-5
CTX_TPMMatrix.csv.gz


title: RNA-seq - CTX injurured TA - Day 3 - rep. 1

description:
Day3-L-1
CTX_TPMMatrix.csv.gz


title: L1_E_D2_H3K27ac_RepB


title: RNA-seq - CTX injurured TA - Day 0 - rep. 3

description:
Day0-L-3
CTX_TPMMatrix.csv.gz


title: Ant-CXCL10 Antibody rep4


title: L1_SETD5_D2_H3K27ac_RepA


title: RNA-seq - CTX injurured TA - Day 0 - rep. 4

description:
Day0-L-4
CTX_TPMMatrix.csv.gz


title: BE2C_DMSO_PHOX2B_MWZ8376

data_processing:
Library strategy: CUT&RUN-Seq
Aligned using /usr/local/bin/bowtie with configuration -p 4 --best -k 2 -m 2 --sam -l 75
hg19
Supplementary_files_format_and_content: bigWig files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment.

source_name: Neuroblastoma

growth_protocol: Cells were grown in T-75 flasks in RPMI media containing 10% FBS and 1% pen-strep. Cells were treated with DMSO or ATRA (5uM) for 12 days.

extract_protocol:
Purified  DNA was prepared for sequencing using to the Swift 2S automated library preparation kit according to the manufacturers protocol.
Chromatin coupled primary antibodies in situ were retrieved with Cutana ProteinA/G-Mnase (Epicypher) according to the manufacturers protocol.

tag: antibody manu.

value: SCBT

tag: antibody catalog

tag: antibody lot

tag: agent

value: DMSO


title: Ant-CXCL10 Antibody+GSK343 rep1


title: Ant-CXCL10 Antibody rep5


title: RNA-seq - CTX injurured TA - Day 0 - rep. 2

description:
Day0-L-2
CTX_TPMMatrix.csv.gz


title: Ant-CXCL10 Antibody rep3


title: BE2C_ATRA_MEIS1_MWZ8376

value: Abcam

value: ATRA, 5 microM


title: BE2C_ATRA_IgG_MWZ8376

value: IgG

value: Proteintech


title: g3_T3

city: Hohhot

first: Xiao

middle: dan

address: Xinhuadajie 005

institute: Inner Mongolia Medical University

data_processing:
Valid data were obtained after quality evaluation. Adaptor reads, low-quality reads, and reads that contained more than 5% N (N refers to base information that could not be determined) were removed from the original data.
Based on the Ensemble Genome and mRNA database, TopHat2 software (version 2.0.9) was used to compare a reference genome with the preprocessed valid data.
Based on the comparison results, the Cufflinks series program (version 2.1.1) was used to splice and annotate the sequence fragments and calculate the transcript expression levels.
The fragments per kilobase of transcript per million mapped reads (FPKM) method is used to represent the expression abundances of known genes in different samples, and an FPKM value of >0 was used as the detection standard for genes in this study.
The threshold of highly altered genes (HAGs) was set to P < 0.05.
Genome_build: GCA_000298735.2
Supplementary_files_format_and_content: Excel files include FPKM values/significant/genes for each sample; PDF files and JPEG files represent reference genome mapped reads statistics or GO/KEGG Enrichment.

organism: Ovis aries

source_name: oviduct mucosal epithelial cells

growth_protocol: The oviduct ampullae were cut longitudinally, and the mucosal epithelial cells were scraped after trypsin digestion, the cells were starved and cultured in serum-free and phenol red-free medium for 12 h to reduce any effects of serum and phenol red.

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

treatment_protocol: Samples were taken for RNA-sequencing (RNA-seq) after E2 ( 1 × 10-8 M) treatment for 0 (T0 control), 1.5 (T1 group), 3.5 (T2 group), and 5.5 h (T3 group).

tag: treatments

value: oviduct mucosal epithelial cells


title: g2_T3


title: RNA-seq - CTX injurured TA - Day 0 - rep. 1

description:
Day0-L-1
CTX_TPMMatrix.csv.gz


title: BE2C_DMSO_GATA3_MWZ8376

value: Cell Signaling


title: BE2C_ATRA_GATA3_MWZ8376


title: g1_T3


title: Ant-CXCL10 Antibody rep2


title: Ant-CXCL10 Antibody+GSK343 rep2


title: Ant-CXCL10 Antibody+GSK343 rep5


title: g3_T2


title: BE2C_DMSO_SOX4_MWZ8376

value: Sigma


title: Control Antibody+GSK343 rep4


title: Ant-CXCL10 Antibody rep1


title: g2_T2


title: g1_T2


title: Control Antibody+GSK343 rep2


title: BE2C_ATRA_SOX4_MWZ8376


title: Control Antibody+GSK343 rep5


title: Control Antibody+GSK343 rep3


title: g2_T1


title: Control Antibody+GSK343 rep1


title: BE2C_DMSO_IgG_MWZ8376


title: g3_T1


title: BE2C_ATRA_PHOX2B_MWZ8376


title: Control Antibody rep5


title: g1_T1


title: BE2C_DMSO_MEIS1_MWZ8376


title: Neuro-2A cells, siUpf1_2 (RNA-Seq)

city: Rochester

first: Tatsuaki

last: Kurosaki

state: NY

address: 601 Elmwood Avenue, Box 712

department: Biochemistry and Biophysics

institute: University of Rochester

data_processing:
Raw reads generated from the Illumina basecalls were demultiplexed using bcl2fastq version 2.19.0.
Quality filtering and adapter removal were performed using FastP version 0.20.0 with parameters "–length_required 35 –cut_front_window_size 1 –cut_front_mean_quality 13 –cut_front –cut_tail_window_size 1 –cut_tail_mean_quality 13 –cut_tail -w 8 -y –r -j".
Cleaned reads were mapped to the Mus musculus reference genome (GRCm38.p6 + Gencode-M22 Annotation) using STAR_2.7.0f and parameters "–twopass Mode Basic –runMode alignReads –outSAMtype BAM SortedByCoordinate –outSAMstrandField intronMotif –outFilterIntronMotifs RemoveNoncanonical".
Gene-level read quantification was derived using the subread-1.6.4 package (featureCounts) with a GTF annotation file (Gencode M22) and parameters "-s 2 -t exon -g gene_name".
Differential expression analysis was performed using DESeq2-1.22.1 with an adjusted P-value threshold of 0.05 within R version 3.5.1 (https://www.R-project.org/).
Genome_build: GRCm38.p6 + Gencode-M22 Annotation
Supplementary_files_format_and_content: text file with raw gene counts for all reference genes

source_name: siUpf1-treated N2A cells

growth_protocol: N2A mouse neuroblastoma cells  were cultured in Dulbecco’s Modified Eagle Medium/Nutrient Mixture F-12 (DMEM/F-12, Thermo Fisher Scientific) supplemented with 10% Fetal Bovine Serum (VWR).

extract_protocol:
RNA was extracted and purified using TRIzol reagent following manufacturer’s instructions (Thermo Fisher Scientific).
For RNA-seq library preparation using RNA from N2A cells, RNA concentration and quality were evaluated using a NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific) and a Bioanalyzer 2100 (Agilent), respectively. RNA-seq libraries were constructed using the TruSeq Stranded mRNA Library Prep Kit (Illumina) and 200 ng of RNA following manufacturer’s instructions. The quantity and quality of libraries were measured using a Qubit 4 Fluorometer (Thermo Fisher Scientific) and a 5300 Fragment Analyzer System (Agilent), respectively.

treatment_protocol: Cells (0.3×10^6/6-well plate) were transiently transfected with 60 pmol of control siRNA (Thermo Fisher Scientific) or Upf1 siRNA using the TransIT-X2 Dynamic Delivery System (Mirus Bio).

value: Neuro-2A (ATCC, CCL-131)

tag: treatment

value: Upf1 siRNA (5'- UCAAGGUUCCUGAUAAUUA-3')


title: Control Antibody rep4


title: g3_T0


title: Control Antibody rep3


title: g2_T0


title: Control Antibody rep2


title: Neuro-2A cells, siUpf1_1 (RNA-Seq)


title: Neuro-2A cells, siCtl_1 (RNA-Seq)

source_name: siCtl-treated N2A cells

value: Control siRNA (Silencer Negative Control #1; Thermo Fisher Scientific/Ambion)


title: g1_T0


title: Control Antibody rep1


title: H8_92_CI5200_FU_P3S2

status: Public on Oct 24 2021

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

data_processing:
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
STAR v2.5.2b  was to map reads to GRCh38 (Ensembl release 86) and obtain reads per gene counts (–quantMode Gene Counts)
Initial analysis indicated potential batch effects. As a result, analysis was limited to plates (P1S1,P3S2,P6S3) which contained cells from both SR and CI (SR-6,SR-2,SR-4,CI-9,CI-5,CI-3). Cells were filtered out if the library size and number of genes were 3 median absolute deviations away and if the percentage of mitochondrial reads was more than 3 absolute deviations. The Ig genes were filtered out.
The normalized expression values were obtained using the cpm function in edgeR library. log2(CPM+1) values were used for differential gene expression analysis.
Genome_build: GRCh38 (Ensembl release 86)
Supplementary_files_format_and_content: tab delimited text file containing raw read counts for each sample (in columns) and each annotated transcript (in rows).

source_name: derived from human PBMCs

extract_protocol:
RNA was purified from sorted single cells using RNACleanXP Solid Phase Reversible Immobilization (SPRI) beads (Beckman Coulter).
Full-length cDNA amplification of single cells was performed using the SMART-Seq v4 Ultra Low-Input RNA protocol. Amplified cDNA was fragmented using Illumina Nextera XT DNA Library Preparation kits and dual-indexed barcodes were added to each sample. Libraries were validated using an Agilent 4200 Tapestation, pooled, and sequenced at 101 SR on an Illumina HiSeq 3000 to an average depth of 1.67 M reads at the Yerkes NHP Genomics Core (http://www.yerkes.emory.edu/nhp_genomics_core/). The number of single cells sorted for each individual subject and their corresponding PCR plate ID is shown in Supplemental Table 2. We used a modified protocol for plate P2S23 where instead of using the Clontech SMART-Seq v4 kit, we used a version of the SMARter method with Clontech buffers as was previously described (58). The template switching oligos for full-length cDNA synthesis were obtained from Exiqon (Woburn, MA, USA) and the primers for cDNA synthesis from Integrated DNA Technologies (Skokie, IL, USA). The libraries for this plate were also sequenced twice.

value: memory B cells

tag: plateid

tag: donorid

tag: hcv infection outcome

value: persistence

value: peripheral blood


title: H9_86_CI5148_FU_P8S3_1


title: H9_93_CI5200_FU_P3S2


title: H8_92_SR5240_LA_P2S23

value: spontaneous clearance


title: H9_93_CI5200_FU_P4S2


title: H9_93_CI1457_LA_P9S3_9


title: H9_93_SR5240_LA_P2S23


title: Neuro-2A cells, siUpf1_3 (RNA-Seq)


title: H8_92_CI5200_FU_P4S2


title: H7_91_SR5240_LA_P2S23


title: H7_91_CI5200_FU_P4S2


title: H5_89_SR5240_LA_P2S23


title: H6_90_CI1457_LA_P9S3_9


title: H4_88_SR5240_LA_P2S23


title: H7_91_CI5200_FU_P3S2


title: H3_87_CI5200_FU_P4S2


title: H4_88_CI1457_FU_P11S4_1


title: H4_88_CI1457_LA_P9S3_9


title: H4_88_CI5200_FU_P4S2


title: H3_87_CI1457_LA_P9S3_9


title: H3_87_SR5240_LA_P2S23


title: H2_86_CI5200_FU_P3S2


title: H5_89_CI5200_FU_P3S2


title: H3_87_CI1457_FU_P11S4_1


title: H2_86_SR5240_LA_P2S23


title: H8_92_CI1457_LA_P9S3_9


title: H7_91_CI1457_FU_P11S4_1


title: H6_90_SR5240_LA_P2S23


title: Neuro-2A cells, siCtl_3 (RNA-Seq)


title: H6_90_CI5200_FU_P3S2


title: H1_85_CI5200_FU_P3S2


title: H1_85_SR5240_LA_P2S23


title: H1_85_CI1457_LA_P9S3_9


title: H11_95_CI5200_FU_P4S2


title: H10_94_SR5240_LA_P2S23


title: H10_94_CI1457_LA_P9S3_9


title: H6_90_CI1457_FU_P11S4_1


title: H5_89_CI1457_LA_P9S3_9


title: H5_89_CI5200_FU_P4S2


title: H9_93_CI1457_FU_P11S4_1


title: H8_92_CI1457_FU_P11S4_1


title: G9_81_CI1457_LA_P9S3_9


title: H3_87_CI5200_FU_P3S2


title: H4_88_CI5200_FU_P3S2


title: H10_94_CI5200_FU_P4S2


title: H2_86_CI1457_LA_P9S3_9


title: H1_85_CI1457_FU_P11S4_1


title: H10_94_CI5200_FU_P3S2


title: H6_90_CI5200_FU_P4S2


title: G9_81_SR5240_LA_P2S23


title: H8_85_CI5148_FU_P8S3_1


title: H5_89_CI1457_FU_P11S4_1


title: H10_87_CI5148_FU_P8S3_1


title: H7_91_CI1457_LA_P9S3_9


title: G9_81_CI5200_FU_P3S2


title: H2_86_CI1457_FU_P11S4_1


title: G9_81_CI5148_FU_P8S3_1


title: H10_94_CI1457_FU_P11S4_1


title: G9_81_CI1457_FU_P11S4_1


title: H12_96_CI5200_FU_P4S2


title: G9_81_CI5200_FU_P4S2


title: G8_80_CI5200_FU_P3S2


title: G8_80_CI1457_LA_P9S3_9


title: G8_80_CI5200_FU_P4S2


title: G7_79_SR5240_LA_P2S23


title: G8_80_SR5240_LA_P2S23


title: G8_80_CI5148_FU_P8S3_1


title: G8_80_CI1457_FU_P11S4_1


title: G7_79_CI5200_FU_P4S2


title: G7_79_CI5200_FU_P3S2


title: G7_79_CI1457_FU_P11S4_1


title: G7_79_CI1457_LA_P9S3_9


title: G6_78_CI1457_LA_P9S3_9


title: G6_78_CI5200_FU_P3S2


title: G6_78_SR5240_LA_P2S23


title: G7_79_CI5148_FU_P8S3_1


title: G5_77_CI5200_FU_P3S2


title: G6_78_CI1457_FU_P11S4_1


title: G5_77_CI5148_FU_P8S3_1


title: G5_77_CI5200_FU_P4S2


title: G5_77_SR5240_LA_P2S23


title: G6_78_CI5200_FU_P4S2


title: G6_78_CI5148_FU_P8S3_1


title: G5_77_CI1457_LA_P9S3_9


title: G4_76_CI5148_FU_P8S3_1


title: G4_76_CI5200_FU_P4S2


title: G3_75_CI5200_FU_P4S2


title: G4_76_SR5240_LA_P2S23


title: G4_76_CI1457_LA_P9S3_9


title: G4_76_CI5200_FU_P3S2


title: G4_76_CI1457_FU_P11S4_1


title: G5_77_CI1457_FU_P11S4_1


title: G3_75_CI1457_FU_P11S4_1


title: G2_74_SR5240_LA_P2S23


title: G3_75_CI5200_FU_P3S2


title: G3_75_CI5148_FU_P8S3_1


title: G2_74_CI5200_FU_P3S2


title: G3_75_CI1457_LA_P9S3_9


title: G2_74_CI1457_FU_P11S4_1


title: G1_73_CI5200_FU_P3S2


title: G1_73_SR5240_LA_P2S23


title: G1_73_CI5200_FU_P4S2


title: G1_73_CI1457_LA_P9S3_9


title: G1_73_CI5148_FU_P8S3_1


title: G12_84_CI1457_LA_P9S3_9


title: G11_83_CI5200_FU_P4S2


title: G3_75_SR5240_LA_P2S23


title: G10_82_SR5240_LA_P2S23


title: G2_74_CI1457_LA_P9S3_9


title: G10_82_CI5200_FU_P4S2


title: G2_74_CI5148_FU_P8S3_1


title: G10_82_CI5200_FU_P3S2


title: G12_84_SR5240_LA_P2S23


title: G12_84_CI5200_FU_P3S2


title: G1_73_CI1457_FU_P11S4_1


title: G12_84_CI5200_FU_P4S2


title: G10_82_CI1457_LA_P9S3_9


title: F9_69_SR5240_LA_P2S23


title: F9_69_CI5200_FU_P4S2


title: G11_83_SR5240_LA_P2S23


title: G12_84_CI5148_FU_P8S3_1


title: G12_84_CI1457_FU_P11S4_1


title: F9_69_CI5148_FU_P8S3_1


title: G11_83_CI1457_LA_P9S3_9


title: G11_83_CI5200_FU_P3S2


title: F9_69_CI1457_FU_P11S4_1


title: G2_74_CI5200_FU_P4S2


title: G10_82_CI5148_FU_P8S3_1


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title: F8_68_CI5200_FU_P3S2


title: F8_68_CI1457_LA_P9S3_9


title: F7_67_CI5200_FU_P4S2


title: F7_67_CI1457_FU_P11S4_1


title: F7_67_CI1457_LA_P9S3_9


title: G10_82_CI1457_FU_P11S4_1


title: F7_67_CI5148_FU_P8S3_1


title: F7_67_CI5200_FU_P3S2


title: F6_66_CI5200_FU_P3S2


title: F9_69_CI5200_FU_P3S2


title: G11_83_CI1457_FU_P11S4_1


title: F8_68_CI5200_FU_P4S2


title: F9_69_CI1457_LA_P9S3_9


title: F9_35_CI5076_FU_P1S1


title: F6_66_CI5148_FU_P8S3_1


title: F6_66_SR5240_LA_P2S23


title: F5_65_SR5240_LA_P2S23


title: F8_68_SR5240_LA_P2S23


title: G11_83_CI5148_FU_P8S3_1


title: F6_66_CI1457_FU_P11S4_1


title: F8_68_CI1457_FU_P11S4_1


title: F7_67_SR5240_LA_P2S23


title: F4_64_SR5240_LA_P2S23


title: F5_65_CI1457_FU_P11S4_1


title: F5_65_CI5200_FU_P4S2


title: F4_64_CI1457_LA_P9S3_9


title: F4_64_CI1457_FU_P11S4_1


title: F5_65_CI1457_LA_P9S3_9


title: F8_68_CI5148_FU_P8S3_1


title: F6_66_CI1457_LA_P9S3_9


title: F6_66_CI5200_FU_P4S2


title: F5_65_CI5200_FU_P3S2


title: F3_63_CI5200_FU_P3S2


title: F3_63_CI5200_FU_P4S2


title: F5_65_CI5148_FU_P8S3_1


title: F4_64_CI5200_FU_P3S2


title: F3_63_SR5240_LA_P2S23


title: F3_63_CI5148_FU_P8S3_1


title: F4_64_CI5200_FU_P4S2


title: F3_63_CI1457_FU_P11S4_1


title: F3_63_CI1457_LA_P9S3_9


title: F4_64_CI5148_FU_P8S3_1


title: F2_62_CI5148_FU_P8S3_1


title: F2_62_SR5240_LA_P2S23


title: F2_62_CI5200_FU_P4S2


title: F2_62_CI5200_FU_P3S2


title: F2_62_CI1457_LA_P9S3_9


title: F2_62_CI1457_FU_P11S4_1


title: F1_61_SR5240_LA_P2S23


title: F1_61_CI5200_FU_P3S2


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title: F12_72_SR5240_LA_P2S23


title: F1_61_CI1457_LA_P9S3_9


title: F1_61_CI1457_FU_P11S4_1


title: F12_72_CI5200_FU_P3S2


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title: F12_72_CI5200_FU_P4S2


title: F12_72_CI5148_FU_P8S3_1


title: F12_38_CI5076_FU_P1S1


title: F12_72_CI1457_LA_P9S3_9


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title: F12_72_CI1457_FU_P11S4_1


title: F11_71_CI5148_FU_P8S3_1


title: F11_71_CI5200_FU_P4S2


title: F11_71_CI1457_FU_P11S4_1


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title: F10_70_CI5200_FU_P4S2


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title: F11_71_CI5200_FU_P3S2


title: E8_56_CI5200_FU_P3S2


title: E8_56_CI5148_FU_P8S3_1


title: E8_41_CI5148_LA_P12S3_2


title: E8_56_CI1457_FU_P11S4_1


title: E8_56_CI1457_LA_P9S3_9


title: E7_55_CI5200_FU_P3S2


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title: E7_40_CI5148_LA_P12S3_2


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title: F10_36_CI5076_FU_P1S1


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title: E6_54_CI1457_FU_P11S4_1


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title: E6_54_CI1457_LA_P9S3_9


title: E6_54_CI5200_FU_P4S2


title: E6_54_CI5200_FU_P3S2


title: E5_53_SR5184_LA_P7S4_7


title: E6_54_SR5240_LA_P2S23


title: E6_27_CI5076_FU_P1S1


title: E6_54_SR5184_LA_P7S4_7


title: E5_53_SR5240_LA_P2S23


title: E5_53_CI5200_FU_P3S2


title: E5_53_CI5200_FU_P4S2


title: E5_53_CI1457_FU_P11S4_1


title: E7_28_CI5076_FU_P1S1


title: E4_52_CI5200_FU_P3S2


title: E4_52_SR5240_LA_P2S23


title: E4_52_SR5184_LA_P7S4_7


title: E4_52_CI1457_LA_P9S3_9


title: E3_51_CI5200_FU_P4S2


title: E3_51_SR5184_LA_P7S4_7


title: E3_51_SR5240_LA_P2S23


title: E5_53_CI5148_FU_P8S3_1


title: E4_37_CI5148_LA_P12S3_2


title: E4_52_CI5148_FU_P8S3_1


title: E3_51_CI5148_FU_P8S3_1


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title: E5_26_CI5076_FU_P1S1


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title: E3_51_CI5200_FU_P3S2


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title: E2_50_CI5200_FU_P4S2


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title: E2_50_SR5184_LA_P7S4_7


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title: E4_25_CI5076_FU_P1S1


title: E2_50_CI5148_FU_P8S3_1


title: E2_50_CI5200_FU_P3S2


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title: E1_49_SR5382_LA_P14S4_14


title: E1_49_CI5200_FU_P4S2


title: E2_50_SR5382_LA_P14S4_14


title: E1_49_CI5148_FU_P8S3_1


title: E2_50_CI1457_LA_P9S3_9


title: E1_49_CI1457_LA_P9S3_9


title: E1_49_CI1457_FU_P11S4_1


title: E3_51_CI1457_LA_P9S3_9


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title: E12_60_CI5148_FU_P8S3_1


title: E12_60_CI1457_LA_P9S3_9


title: E12_60_CI1457_FU_P11S4_1


title: E12_60_CI5200_FU_P4S2


title: E12_60_CI5200_FU_P3S2


title: E12_48_SR5159_LA_P6S3_6


title: E11_59_SR5240_LA_P2S23


title: E11_59_CI5200_FU_P3S2


title: E11_47_SR5159_LA_P6S3_6


title: E12_33_CI5076_FU_P1S1


title: E11_59_CI1457_FU_P11S4_1


title: E12_45_CI5148_LA_P12S3_2


title: E11_59_CI5148_FU_P8S3_1


title: E1_49_CI5200_FU_P3S2


title: E11_32_CI5076_FU_P1S1


title: E11_44_CI5148_LA_P12S3_2


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title: E10_58_CI5200_FU_P4S2


title: E10_58_CI5200_FU_P3S2


title: E11_59_CI5200_FU_P4S2


title: E10_58_CI1457_LA_P9S3_9


title: E10_58_CI1457_FU_P11S4_1


title: E10_43_CI5148_LA_P12S3_2


title: E10_31_CI5076_FU_P1S1


title: E10_46_SR5159_LA_P6S3_6


title: E1_22_CI5076_FU_P1S1


title: D9_45_CI5200_FU_P4S2


title: D9_45_SR5382_LA_P14S4_14


title: E10_58_CI5148_FU_P8S3_1


title: D9_45_SR5184_LA_P7S4_7


title: E11_59_CI1457_LA_P9S3_9


title: D9_45_CI5148_FU_P8S3_1


title: D9_45_CI5200_FU_P3S2


title: D9_45_SR5240_LA_P2S23


title: D9_45_CI1457_LA_P9S3_9


title: D9_45_CI1457_FU_P11S4_1


title: D8_44_SR5382_LA_P14S4_14


title: D8_44_SR5184_LA_P7S4_7


title: D8_44_SR5240_LA_P2S23


title: D9_33_CI5148_LA_P12S3_2


title: D8_44_CI5200_FU_P4S2


title: D8_44_CI5148_FU_P8S3_1


title: D8_44_CI5200_FU_P3S2


title: D8_44_CI1457_LA_P9S3_9


title: D8_44_CI1457_FU_P11S4_1


title: D8_32_CI5148_LA_P12S3_2


title: D7_43_SR5382_LA_P14S4_14


title: D8_41_SR5159_LA_P6S3_6


title: D7_43_SR5240_LA_P2S23


title: D7_43_SR5184_LA_P7S4_7


title: D7_43_CI5200_FU_P4S2


title: D7_43_CI5200_FU_P3S2


title: D7_43_CI5148_FU_P8S3_1


title: D7_43_CI1457_LA_P9S3_9


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title: A6_6_CI5076_LA_P12S3_2


title: A4_4_SR5213_LA_P14S4_14


title: A6_6_SR5209_LA_P1S1


title: A4_4_SR5240_LA_P3S2


title: A4_4_SR5209_LA_P1S1


title: A5_5_CI5200_LA_P13S3_3


title: A6_6_CI1457_FU_P11S4_1


title: A5_5_CI4674_LA_P10S3_10


title: A4_4_SR5184_LA_P7S4_7


title: A4_4_CI5200_FU_P4S2


title: A5_5_CI5076_LA_P12S3_2


title: A4_4_CI5200_LA_P13S3_3


title: A5_5_CI1457_FU_P11S4_1


title: A5_5_CI5200_FU_P4S2


title: A4_4_CI4715_FU_P6S3_6


title: A4_4_SR5159_LA_P2S23


title: A4_4_CI4674_LA_P10S3_10


title: A3_3_SR5213_LA_P14S4_14


title: A4_4_CI1457_FU_P11S4_1


title: A3_3_CI5200_FU_P4S2


title: A3_3_SR5184_LA_P7S4_7


title: A3_3_SR5240_LA_P3S2


title: A3_3_CI5148_FU_P8S3_1


title: A3_3_CI5076_LA_P12S3_2


title: A4_4_CI5148_FU_P8S3_1


title: A3_3_CI1457_LA_P9S3_9


title: A2_2_SR5213_LA_P14S4_14


title: A3_3_SR5159_LA_P2S23


title: A2_2_SR5209_LA_P1S1


title: A2_2_CI5148_FU_P8S3_1


title: A4_4_CI1457_LA_P9S3_9


title: A2_2_CI5200_FU_P4S2


title: A2_2_CI4674_LA_P10S3_10


title: A2_2_CI5200_LA_P13S3_3


title: A2_2_SR5240_LA_P3S2


title: A2_2_CI1457_LA_P9S3_9


title: A3_3_CI5200_LA_P13S3_3


title: A3_3_CI4715_FU_P6S3_6


title: A2_2_CI4715_FU_P6S3_6


title: A4_4_CI5076_LA_P12S3_2


title: A3_3_CI1457_FU_P11S4_1


title: A1_1_SR5184_LA_P7S4_7


title: A1_1_SR5213_LA_P14S4_14


title: A3_3_SR5209_LA_P1S1


title: A2_2_CI1457_FU_P11S4_1


title: A3_3_CI4674_LA_P10S3_10


title: A2_2_SR5159_LA_P2S23


title: A1_1_CI5148_FU_P8S3_1


title: A1_1_CI4715_FU_P6S3_6


title: A1_1_CI4674_LA_P10S3_10


title: A1_1_CI1457_LA_P9S3_9


title: A1_1_CI1457_FU_P11S4_1


title: A2_2_CI5076_LA_P12S3_2


title: A1_1_SR5240_LA_P3S2


title: A12_12_CI5200_FU_P4S2


title: A12_12_SR5159_LA_P2S23


title: A1_1_CI5076_LA_P12S3_2


title: A12_12_CI4715_FU_P6S3_6


title: A11_11_SR5213_LA_P14S4_14


title: A1_1_SR5159_LA_P2S23


title: A1_1_CI5200_FU_P4S2


title: A12_12_SR5240_LA_P3S2


title: A2_2_SR5184_LA_P7S4_7


title: A11_11_SR5159_LA_P2S23


title: A12_12_SR5184_LA_P7S4_7


title: B12_24_CI5148_FU_P8S3_1


title: A12_12_SR5209_LA_P1S1


title: A12_12_CI1457_FU_P11S4_1


title: A12_12_CI5148_FU_P8S3_1


title: A11_11_CI5200_FU_P4S2


title: A12_12_CI1457_LA_P9S3_9


title: A11_11_SR5209_LA_P1S1


title: A11_11_CI5148_FU_P8S3_1


title: A12_12_SR5213_LA_P14S4_14


title: A1_1_CI5200_LA_P13S3_3


title: A11_11_SR5240_LA_P3S2


title: A10_10_SR5213_LA_P14S4_14


title: A10_10_SR5184_LA_P7S4_7


title: A11_11_SR5184_LA_P7S4_7


title: A11_11_CI4674_LA_P10S3_10


title: A11_11_CI1457_LA_P9S3_9


title: A11_11_CI4715_FU_P6S3_6


title: A11_11_CI1457_FU_P11S4_1


title: A10_10_SR5209_LA_P1S1


title: A10_10_SR5159_LA_P2S23


title: A10_10_CI5200_FU_P4S2


title: A10_10_CI5148_FU_P8S3_1


title: A10_10_CI1457_LA_P9S3_9


title: A10_10_CI5200_LA_P13S3_3


title: A10_10_SR5240_LA_P3S2


title: A10_10_CI1457_FU_P11S4_1


title: A10_10_CI4715_FU_P6S3_6


title: E2.75_embryo_female_wt2_RNA

city: Heidelberg

first: Quentin

last: Gouil

state: VIC

address: Studley Road

institute: Olivia Newton-John Cancer Research Institute

description:
single-embryo RNA-seq
seRNA_seq_raw_counts.tsv
Control_Plate1_Collected_20190513_B1_RNA

data_processing:
as described in Wanigasuriya, Gouil et al. 2020 (https://doi.org/10.7554/eLife.55529)
Genome_build: mm10
Supplementary_files_format_and_content: RNA-seq: gene counts matrices. RRBS/WGBS: bismark coverage reports of mC and C counts (total and by allele)

source_name: E2.75 embryo

tag: mating

value: B6 SMCH/MMTV-Cre ♀ (FL/FL, +/+) X Cast ♂

tag: Sex

value: female

tag: age

value: embryo

tag: genotype

value: wt


title: E2.75_embryo_female_matdel1_RNA

description:
single-embryo RNA-seq
seRNA_seq_raw_counts.tsv
Test_Plate1_Collected_20190513_D2 _RNA

extract_protocol: as described in Wanigasuriya, Gouil et al. 2020 (https://doi.org/10.7554/eLife.55529)

value: B6 SMCH/MMTV-Cre ♀ (DEL/FL, T/+) X Cast ♂

tag: tissue

value: matdel


title: E2.75_embryo_female_wt4_RNA

description:
single-embryo RNA-seq
seRNA_seq_raw_counts.tsv
Control_Plate2_Collected_20190603_D3_RNA

tag: strain


title: E2.75_embryo_female_wt6_RNA

description:
single-embryo RNA-seq
seRNA_seq_raw_counts.tsv
Control_Plate2_Collected_20190603_H2_RNA


title: E2.75_embryo_female_matdel2_RNA

description:
single-embryo RNA-seq
seRNA_seq_raw_counts.tsv
Test_Plate1_Collected_20190513_F2 _RNA


title: E2.75_embryo_female_wt3_RNA

description:
single-embryo RNA-seq
seRNA_seq_raw_counts.tsv
Control_Plate1_Collected_20190513_B2_RNA


title: E2.75_embryo_female_matdel4_RNA

description:
single-embryo RNA-seq
seRNA_seq_raw_counts.tsv
Test_Plate2_Collected_20190603_D1 _RNA


title: E2.75_embryo_female_wt5_RNA

description:
single-embryo RNA-seq
seRNA_seq_raw_counts.tsv
Control_Plate2_Collected_20190603_F2_RNA


title: E2.75_embryo_female_matdel3_RNA

description:
single-embryo RNA-seq
seRNA_seq_raw_counts.tsv
Test_Plate2_Collected_20190603_B2 _RNA


title: E2.75_embryo_female_wt6_WGBS

description:
single-embryo WGBS
Control_Plate2_Collected_20190603_H2_WGBS


title: E2.75_embryo_female_wt1_RNA

description:
single-embryo RNA-seq
seRNA_seq_raw_counts.tsv
Control_Plate1_Collected_20190513_A1_RNA


title: E2.75_embryo_female_matdel3_WGBS

description:
single-embryo WGBS
Test_Plate2_Collected_20190603_B2_WGBS


title: E2.75_embryo_female_matdel2_WGBS

description:
single-embryo WGBS
Test_Plate1_Collected_20190513_F2_WGBS


title: E2.75_embryo_female_matdel4_WGBS

description:
single-embryo WGBS
Test_Plate2_Collected_20190603_D1_WGBS


title: E2.75_embryo_female_matdel1_WGBS

description:
single-embryo WGBS
Test_Plate1_Collected_20190513_D2_WGBS


title: A10_10_CI4674_LA_P10S3_10

tag: cell type


title: E2.75_embryo_female_wt5_WGBS

description:
single-embryo WGBS
Control_Plate2_Collected_20190603_F2_WGBS


title: E2.75_embryo_female_wt1_WGBS

description:
single-embryo WGBS
Control_Plate1_Collected_20190513_A1_WGBS


title: E2.75_embryo_female_wt3_WGBS

description:
single-embryo WGBS
Control_Plate1_Collected_20190513_B2_WGBS


title: E2.75_embryo_female_wt2_WGBS

description:
single-embryo WGBS
Control_Plate1_Collected_20190513_B1_WGBS


title: ChIPseq-H3K27me3_Input_6h

city: Dundee

first: Tom

last: Owen-Hughes

state: Tayside

address: Dow Street

department: School of Lifesciences, Gene Regulation and Expression

institute: University of Dundee

data_processing:
TT-seq: Fastq files were trimmed using Trim Galore 0.5.0 and CutAdapt 2.4 with default parameters   ATAC-seq: Fastq files were trimmed using trimmomatic-0.36 (CROP: 66) Mnase-seq: Fastq files were aligned to the mouse mm10 genome using bowtie2 with the parameter –X 1000 –x mm10. For each time point three different runs with two replicates each were used.
TT-seq:Sequence reads were aligned using STAR to the reference indexed GRCm38 genome including splice junctions (parameters: -outSAMtype BAM SortedByCoordinate -outSAMattributes All –quantMode GeneCounts TranscriptomeSAM) –outSAMFlagOR 243 –outSAMFlagAND 3852)    ATAC-seq: Alignment was performed using bowtie2-2.1.0 with the parameter –X 1000 –x mm10
ATAC-seq: Filtering was performed: samtools-0.1.18/samtools view -F 3852,
Normalisation was performed: RPM for mapped reads
ATAC-seq: Peaks were called using MACS2 callpeak function with the following parameters: -t "$1".bam -f BAM -n "$1"_MACS -g 1.87e9 -q 0.05 --broad -B ChIP-seq (EP300): macs2 callpeak -c Input.bam -t "$1".bam -f BAMPE -n "$1" -g 1.87e9 -q 0.2 (H3K27Ac) macs2 callpeak -c Input.bam -t "$1".bam -f BAMPE -n "$1" -g 1.87e9 -q 0.05 (H3K27me3) macs2 callpeak -c Input.bam -t "$1".bam -f BAMPE -n "$1" -g 1.87e9 -q 0.05 -broad
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files of combined replicates, normalised between time points

source_name: mouse embryonic stem cells E14

extract_protocol:
Cells were lysed in lysis buffer containing 1 % SDS, 10 mM EDTA, 50 mM Tris pH 8.1 and protease inhibitors. Cells were sonicated for 60 cycles (7.5 min total sonication time) at low setting using a Bioruptor (Diagenode). Sonicated lysates were then cleared by centrifugation for 10 min at high speed and 1/10 was used as input control.
Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina with multiplex oligos (#E7600).

value: mES TIR1, ARID1A-mini-auxin-inducible-GFP-tagged clone#57

value: 6h auxin

tag: molecule subtype

value: genomic DNA


title: E2.75_embryo_female_wt4_WGBS

description:
single-embryo WGBS
Control_Plate2_Collected_20190603_D3_WGBS


title: ChIPseq-H3K27me3_Input_162h

value: 162h auxin


title: ChIPseq-H3K27me3_Input_18h

value: 18h auxin


title: ChIPseq-H3K27me3_Input_2h

value: 2h auxin


title: ChIPseq-H3K27me3_Input_54h

value: 54h auxin


title: ChIPseq-H3K27me3_Input_0h

value: 0h auxin


title: ChIPseq-H3K27me3_mES_TIR1_ARID1A_mAID_162h_auxin rep_2

description:
H3K27me3_162h_dp_rm_1and2_norm.bw
H3K27me3_162h_2

extract_protocol:
Cells were lysed in lysis buffer containing 1 % SDS, 10 mM EDTA, 50 mM Tris pH 8.1 and protease inhibitors. Cells were sonicated for 60 cycles (7.5 min total sonication time) at low setting using a Bioruptor (Diagenode). Sonicated lysates were then cleared by centrifugation for 10 min at high speed, diluted 1/10 with dilution buffer (1 % Triton X-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris at pH 8.1, 0.1 % Brij-35) and incubated with 10 µl of anti H3K27me3 (CST, C36B11) overnight at 4°C. 50 μl of Protein A Dynabeads (Life Technologies) were pre-incubated with 0.5 % (w/v) BSA in PBS overnight. To capture antibody-bound protein-DNA complexes, lysates were incubated with the prepared beads for 4 hrs and subsequently washed twice with wash buffer I (0.1 % SDS, 1 % Triton X-100, 2 mM EDTA pH 8.0, 20 mM Tris pH 8.1, 150 mM NaCl), wash buffer II (0.1 % SDS, 1 % Triton X-100, 2 mM EDTA pH 8.0, 20 mM Tris pH 8.1, 500 mM NaCl), wash buffer III (0.25 mM LiCl, 1 % NP-40, 1 % sodium deoxycholate, 1 mM EDTA pH 8.0, 10 mM Tris pH 8.1) and TE buffer (10 mM Tris pH 8.1, 1 mM EDTA pH 8.0) in the cold. DNA was eluted using 1 % SDS, 100 mM NaHCO3 and reverse-crosslinked overnight before the clean up using AMpure XP beads.
Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina with multiplex oligos (#E7600).

tag: chip antibody

value: anti H3K27me3 (CST, ab9733)


title: ChIPseq-H3K27me3_mES_TIR1_ARID1A_mAID_162h_auxin rep_1

description:
H3K27me3_162h_dp_rm_1and2_norm.bw
H3K27me3_162h_1


title: ChIPseq-H3K27me3_mES_TIR1_ARID1A_mAID_54h_auxin rep_4

description:
H3K27me3_54h_dp_rm_norm.bw
H3K27me3_54h_4


title: ChIPseq-H3K27me3_mES_TIR1_ARID1A_mAID_54h_auxin rep_3

description:
H3K27me3_54h_dp_rm_norm.bw
H3K27me3_54h_3


title: ChIPseq-H3K27me3_mES_TIR1_ARID1A_mAID_54h_auxin rep_1

description:
H3K27me3_54h_dp_rm_norm.bw
H3K27me3_54h_1


title: ChIPseq-H3K27me3_mES_TIR1_ARID1A_mAID_54h_auxin rep_2

description:
H3K27me3_54h_dp_rm_norm.bw
H3K27me3_54h_2


title: ChIPseq-H3K27me3_mES_TIR1_ARID1A_mAID_18h_auxin rep_3

description:
H3K27me3_18h_dp_rm_norm.bw
H3K27me3_18h_3


title: ChIPseq-H3K27me3_mES_TIR1_ARID1A_mAID_18h_auxin rep_4

description:
H3K27me3_18h_dp_rm_norm.bw
H3K27me3_18h_4


title: ChIPseq-H3K27me3_mES_TIR1_ARID1A_mAID_6h_auxin rep_4

description:
H3K27me3_6h_dp_rm_norm.bw
H3K27me3_6h_4


title: ChIPseq-H3K27me3_mES_TIR1_ARID1A_mAID_18h_auxin rep_1

description:
H3K27me3_18h_dp_rm_norm.bw
H3K27me3_18h_1


title: ChIPseq-H3K27me3_mES_TIR1_ARID1A_mAID_6h_auxin rep_2

description:
H3K27me3_6h_dp_rm_norm.bw
H3K27me3_6h_2


title: ChIPseq-H3K27me3_mES_TIR1_ARID1A_mAID_2h_auxin rep_4

description:
H3K27me3_2h_dp_rm_norm.bw
H3K27me3_2h_4


title: ChIPseq-H3K27me3_mES_TIR1_ARID1A_mAID_2h_auxin rep_3

description:
H3K27me3_2h_dp_rm_norm.bw
H3K27me3_2h_3


title: ChIPseq-H3K27me3_mES_TIR1_ARID1A_mAID_6h_auxin rep_1

description:
H3K27me3_6h_dp_rm_norm.bw
H3K27me3_6h_1


title: ChIPseq-H3K27me3_mES_TIR1_ARID1A_mAID_0h_auxin rep_3

description:
H3K27me3_0h_dp_rm_norm.bw
H3K27me3_0h_3


title: ChIPseq-H3K27me3_mES_TIR1_ARID1A_mAID_0h_auxin rep_4

description:
H3K27me3_0h_dp_rm_norm.bw
H3K27me3_0h_4


title: ChIPseq-H3K27me3_mES_TIR1_ARID1A_mAID_2h_auxin rep_1

description:
H3K27me3_2h_dp_rm_norm.bw
H3K27me3_2h_1


title: A1_1_SR5209_LA_P1S1

value: memory B cells

value: peripheral blood


title: ChIPseq-H3K27ac_Input_18h


title: ChIPseq-H3K27me3_mES_TIR1_ARID1A_mAID_18h_auxin rep_2

description:
H3K27me3_18h_dp_rm_norm.bw
H3K27me3_18h_2


title: ChIPseq-H3K27ac_Input_0h


title: ChIPseq-H3K27me3_mES_TIR1_ARID1A_mAID_0h_auxin rep_1

description:
H3K27me3_0h_dp_rm_norm.bw
H3K27me3_0h_1


title: ChIPseq-H3K27ac_Input_54h


title: ChIPseq-EP300_mES_TIR1_ARID1A_mAID_0h_auxin rep_2 (repeat)

description:
p300_0h_no0-3_0-4_rep_dp_rm_norm_0.435.bw
p300_0h_2_rep

extract_protocol:
Cells were lysed in MNase lysis buffer (10 mM Tris pH7.5, 10 mM NaCl, 3mM MgCl2, 0.5% NP40, 0.15 mM spermine, 0.5 mM spermidine, plus Roche MiniComplete).and digested in MNase digest buffer (10 mM Tris pH7.5, 60 mM NaCl, 1 mM CaCl2, 0.15 mM spermine, 0.5 mM spermidine, 0.5 mM DTT) using 36 units of S7 MNase (Roche) for 20 minutes at 37°C. The digest was stopped by adding 50 mM EDTA and cells were spun down. Cell pellets were resuspended in ChIP buffer (SimpleChIP Enzymatic Chromatin IP Kit, CST). ChIP was performed following the manufacturer’s protocol with using 5 μg anti-EP300 antibody (sc-48343, Santa Cruz) .
Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina with multiplex oligos (#E7600).

value: anti EP300, sc-48343, Santa Cruz


title: ChIPseq-H3K27ac_Input_162h


title: ChIPseq-H3K27me3_mES_TIR1_ARID1A_mAID_6h_auxin rep_3

description:
H3K27me3_6h_dp_rm_norm.bw
H3K27me3_6h_3


title: ChIPseq-H3K27ac_mES_TIR1_ARID1A_mAID_18h_auxin rep_3

description:
H3K27Ac_18h_norm_0.89.bw
H3K27Ac_18h_3

extract_protocol:
Cells were lysed in lysis buffer containing 1 % SDS, 10 mM EDTA, 50 mM Tris pH 8.1 and protease inhibitors. Cells were sonicated for 60 cycles (7.5 min total sonication time) at low setting using a Bioruptor (Diagenode). Sonicated lysates were then cleared by centrifugation for 10 min at high speed, diluted 1/10 with dilution buffer (1 % Triton X-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris at pH 8.1, 0.1 % Brij-35) and incubated with 2 µg of anti H3K27ac antibody (Abcam, ab4729)  overnight at 4°C. 50 μl of Protein A Dynabeads (Life Technologies) were pre-incubated with 0.5 % (w/v) BSA in PBS overnight. To capture antibody-bound protein-DNA complexes, lysates were incubated with the prepared beads for 4 hrs and subsequently washed twice with wash buffer I (0.1 % SDS, 1 % Triton X-100, 2 mM EDTA pH 8.0, 20 mM Tris pH 8.1, 150 mM NaCl), wash buffer II (0.1 % SDS, 1 % Triton X-100, 2 mM EDTA pH 8.0, 20 mM Tris pH 8.1, 500 mM NaCl), wash buffer III (0.25 mM LiCl, 1 % NP-40, 1 % sodium deoxycholate, 1 mM EDTA pH 8.0, 10 mM Tris pH 8.1) and TE buffer (10 mM Tris pH 8.1, 1 mM EDTA pH 8.0) in the cold. DNA was eluted using 1 % SDS, 100 mM NaHCO3 and reverse-crosslinked overnight before the clean up using AMpure XP beads.
Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina with multiplex oligos (#E7600).

value: anti H3K27ac, Abcam ab4730


title: ChIPseq-H3K27ac_mES_TIR1_ARID1A_mAID_162h_auxin rep_2

description:
H3K27Ac_162h_norm_1.14.bw
H3K27Ac_162h_2


title: ChIPseq-H3K27ac_mES_TIR1_ARID1A_mAID_18h_auxin rep_4

description:
H3K27Ac_18h_norm_0.89.bw
H3K27Ac_18h_4


title: ChIPseq-H3K27ac_mES_TIR1_ARID1A_mAID_18h_auxin rep_2

description:
H3K27Ac_18h_norm_0.89.bw
H3K27Ac_18h_2


title: ChIPseq-H3K27ac_mES_TIR1_ARID1A_mAID_54h_auxin rep_2

description:
H3K27Ac_54h_norm.bw
H3K27Ac_54h_2


title: ChIPseq-H3K27ac_mES_TIR1_ARID1A_mAID_162h_auxin rep_4

description:
H3K27Ac_162h_norm_1.14.bw
H3K27Ac_162h_4


title: ChIPseq-H3K27ac_mES_TIR1_ARID1A_mAID_54h_auxin rep_3

description:
H3K27Ac_54h_norm.bw
H3K27Ac_54h_3


title: ChIPseq-H3K27me3_mES_TIR1_ARID1A_mAID_0h_auxin rep_2

description:
H3K27me3_0h_dp_rm_norm.bw
H3K27me3_0h_2


title: ChIPseq-H3K27ac_mES_TIR1_ARID1A_mAID_162h_auxin rep_3

description:
H3K27Ac_162h_norm_1.14.bw
H3K27Ac_162h_3


title: ChIPseq-H3K27ac_mES_TIR1_ARID1A_mAID_6h_auxin rep_4

description:
H3K27Ac_6h_norm_0.89.bw
H3K27Ac_6h_4


title: ChIPseq-H3K27me3_mES_TIR1_ARID1A_mAID_2h_auxin rep_2

description:
H3K27me3_2h_dp_rm_norm.bw
H3K27me3_2h_2


title: ChIPseq-H3K27ac_Input_6h


title: ChIPseq-H3K27ac_mES_TIR1_ARID1A_mAID_18h_auxin rep_1

description:
H3K27Ac_18h_norm_0.89.bw
H3K27Ac_18h_1


title: ChIPseq-H3K27ac_mES_TIR1_ARID1A_mAID_6h_auxin rep_3

description:
H3K27Ac_6h_norm_0.89.bw
H3K27Ac_6h_3


title: ChIPseq-H3K27ac_mES_TIR1_ARID1A_mAID_6h_auxin rep_2

description:
H3K27Ac_6h_norm_0.89.bw
H3K27Ac_6h_2


title: ChIPseq-H3K27ac_mES_TIR1_ARID1A_mAID_2h_auxin rep_3

description:
H3K27Ac_2h_norm_0.89.bw
H3K27Ac_2h_3


title: ChIPseq-H3K27ac_mES_TIR1_ARID1A_mAID_2h_auxin rep_1

description:
H3K27Ac_2h_norm_0.89.bw
H3K27Ac_2h_1


title: ChIPseq-H3K27ac_mES_TIR1_ARID1A_mAID_162h_auxin rep_1

description:
H3K27Ac_162h_norm_1.14.bw
H3K27Ac_162h_1


title: ChIPseq-H3K27ac_mES_TIR1_ARID1A_mAID_6h_auxin rep_1

description:
H3K27Ac_6h_norm_0.89.bw
H3K27Ac_6h_1


title: ChIPseq-H3K27ac_mES_TIR1_ARID1A_mAID_2h_auxin rep_4

description:
H3K27Ac_2h_norm_0.89.bw
H3K27Ac_2h_4


title: ChIPseq-H3K27ac_Input_2h


title: ChIPseq-EP300_Input_18h

description:
none
p300_Input_18h


title: ChIPseq-H3K27ac_mES_TIR1_ARID1A_mAID_0h_auxin rep_1

description:
H3K27Ac_0h_norm.bw
H3K27Ac_0h_1

value: anti H3K27ac, Abcam ab4729


title: ChIPseq-H3K27ac_mES_TIR1_ARID1A_mAID_0h_auxin rep_4

description:
H3K27Ac_0h_norm.bw
H3K27Ac_0h_4


title: ChIPseq-H3K27ac_mES_TIR1_ARID1A_mAID_0h_auxin rep_2

description:
H3K27Ac_0h_norm.bw
H3K27Ac_0h_2


title: ChIPseq-EP300_Input_6h

description:
none
p300_Input_6h


title: ChIPseq-H3K27ac_mES_TIR1_ARID1A_mAID_54h_auxin rep_4

description:
H3K27Ac_54h_norm.bw
H3K27Ac_54h_4


title: ChIPseq-EP300_Input_0h

description:
none
p300_Input_0h


title: ChIPseq-EP300_mES_TIR1_ARID1A_mAID_54h_auxin rep_3

description:
p300_54h_dp_rm_norm.bw
p300_54h_3


title: ChIPseq-H3K27ac_mES_TIR1_ARID1A_mAID_0h_auxin rep_3

description:
H3K27Ac_0h_norm.bw
H3K27Ac_0h_3


title: ChIPseq-EP300_Input_162h

description:
none
p300_Input_162h


title: ChIPseq-EP300_Input_2h

description:
none
p300_Input_2h


title: ChIPseq-EP300_mES_TIR1_ARID1A_mAID_162h_auxin rep_2

description:
p300_162h_dp_rm_norm.bw
p300_162h_2


title: ChIPseq-EP300_Input_54h

description:
none
p300_Input_54h


title: ChIPseq-H3K27ac_mES_TIR1_ARID1A_mAID_2h_auxin rep_2

description:
H3K27Ac_2h_norm_0.89.bw
H3K27Ac_2h_2


title: ChIPseq-EP300_mES_TIR1_ARID1A_mAID_18h_auxin rep_1

description:
p300_18h_dp_rm_norm.bw
p300_18h_1


title: ChIPseq-EP300_mES_TIR1_ARID1A_mAID_6h_auxin rep_4

description:
p300_6h_dp_rm_norm.bw
p300_6h_4


title: ChIPseq-EP300_mES_TIR1_ARID1A_mAID_162h_auxin rep_1

description:
p300_162h_dp_rm_norm.bw
p300_162h_1


title: ChIPseq-EP300_mES_TIR1_ARID1A_mAID_2h_auxin rep_4

description:
p300_2h_dp_rm_norm.bw
p300_2h_4


title: ChIPseq-EP300_mES_TIR1_ARID1A_mAID_54h_auxin rep_4

description:
p300_54h_dp_rm_norm.bw
p300_54h_4


title: ChIPseq-EP300_mES_TIR1_ARID1A_mAID_2h_auxin rep_1

description:
p300_2h_dp_rm_norm.bw
p300_2h_1


title: ChIPseq-EP300_mES_TIR1_ARID1A_mAID_18h_auxin rep_3

description:
p300_18h_dp_rm_norm.bw
p300_18h_3


title: ChIPseq-EP300_mES_TIR1_ARID1A_mAID_54h_auxin rep_1

description:
p300_54h_dp_rm_norm.bw
p300_54h_1


title: ChIPseq-EP300_mES_TIR1_ARID1A_mAID_18h_auxin rep_4

description:
p300_18h_dp_rm_norm.bw
p300_18h_4


title: ATACseq_mES_TIR1_ARID1A_untagged_2h_auxin rep_3

description:
ET-905-2h_ATAC_norm.bw
ET-905-2h-3

extract_protocol:
http://dx.doi.org/10.1038/protex.2017.096
Libraries were prepared according to Omni-ATAC-seq protocol (=extract protocol) using the Illumina Nextera DNA Library Prep Kit #15028212

value: mES TIR1 clone # 905


title: ATACseq_mES_TIR1_ARID1A_untagged_2h_auxin rep_2

description:
ET-905-2h_ATAC_norm.bw
ET-905-2h-2


title: ATACseq_mES_TIR1_ARID1A_untagged_18h_auxin rep_3

description:
ET-905-18h_ATAC_norm.bw
ET-905-18h-3


title: ChIPseq-EP300_mES_TIR1_ARID1A_mAID_54h_auxin rep_2

description:
p300_54h_dp_rm_norm.bw
p300_54h_2


title: ATACseq_mES_TIR1_ARID1Ako_rep1

description:
ARID1A-ko_ATAC_norm.bw
ARID1A-ko-1

value: mES TIR1 clone # 905, homozygous ARID1A ko

value: no auxin


title: ChIPseq-EP300_mES_TIR1_ARID1A_mAID_2h_auxin rep_2

description:
p300_2h_dp_rm_norm.bw
p300_2h_2

value: mES TIR1, ARID1A-mini-auxin-inducible-GFP-tagged clone#57


title: ChIPseq-EP300_mES_TIR1_ARID1A_mAID_0h_auxin rep_2

description:
p300_0h_no0-3_0-4_rep_dp_rm_norm_0.435.bw
p300_0h_2


title: ChIPseq-EP300_mES_TIR1_ARID1A_mAID_6h_auxin rep_3

description:
p300_6h_dp_rm_norm.bw
p300_6h_3

value: 6h auxin


title: ChIPseq-EP300_mES_TIR1_ARID1A_mAID_6h_auxin rep_1

description:
p300_6h_dp_rm_norm.bw
p300_6h_1

value: genomic DNA


title: ATACseq_mES_TIR1_ARID1Ako_rep2

description:
ARID1A-ko_ATAC_norm.bw
ARID1A-ko-2


title: ATACseq_mES_TIR1_ARID1Ako_rep3

description:
ARID1A-ko_ATAC_norm.bw
ARID1A-ko-3


title: ChIPseq-EP300_mES_TIR1_ARID1A_mAID_6h_auxin rep_2

description:
p300_6h_dp_rm_norm.bw
p300_6h_2


title: ChIPseq-EP300_mES_TIR1_ARID1A_mAID_0h_auxin rep_1

description:
p300_0h_no0-3_0-4_rep_dp_rm_norm_0.435.bw
p300_0h_1


title: ChIPseq-EP300_mES_TIR1_ARID1A_mAID_18h_auxin rep_2

description:
p300_18h_dp_rm_norm.bw
p300_18h_2


title: ATACseq_mES_TIR1_ARID1A_untagged_18h_auxin rep_1

description:
ET-905-18h_ATAC_norm.bw
ET-905-18h-1


title: ChIPseq-EP300_mES_TIR1_ARID1A_mAID_2h_auxin rep_3

description:
p300_2h_dp_rm_norm.bw
p300_2h_3


title: ATACseq_mES_TIR1_ARID1A_mAID_162h_auxin rep_3

description:
AAG57-162h_ATAC_norm_1.2.bw
AAG57-162h-3

value: 162h auxin


title: ATACseq_mES_TIR1_ARID1A_untagged_0h_auxin rep_3

description:
ET-905-0h_ATAC_norm.bw
ET-905-0h-3


title: ATACseq_mES_TIR1_ARID1A_untagged_2h_auxin rep_1

description:
ET-905-2h_ATAC_norm.bw
ET-905-2h-1


title: ATACseq_mES_TIR1_ARID1A_mAID_162h_auxin rep_1

description:
AAG57-162h_ATAC_norm_1.2.bw
AAG57-162h-1


title: ATACseq_mES_TIR1_ARID1A_mAID_162h_auxin rep_2

description:
AAG57-162h_ATAC_norm_1.2.bw
AAG57-162h-2


title: ATACseq_mES_TIR1_ARID1A_mAID_54h_auxin rep_3

description:
AAG57-54h_ATAC_norm_1.2.bw
AAG57-54h-3


title: ATACseq_mES_TIR1_ARID1A_untagged_18h_auxin rep_2

description:
ET-905-18h_ATAC_norm.bw
ET-905-18h-2

value: 18h auxin


title: ATACseq_mES_TIR1_ARID1A_mAID_54h_auxin rep_2

description:
AAG57-54h_ATAC_norm_1.2.bw
AAG57-54h-2


title: ATACseq_mES_TIR1_ARID1A_mAID_18h_auxin rep_3

description:
AAG57-18h_ATAC_norm_1.125.bw
AAG57-18h-3