title: Nrf2_HET_Rep1

city: Chapel Hill

first: Travis

last: Ptacek

state: NC

address: 5109 Neuroscience Research Building

institute: UNC Neuroscience Center Bioinformatics Core

data_processing:
Sequencing and base calling on the Illumina HiSeq 2500
Quality filtering was performed using FASTX v0.0.14 fastq_quality_filter for reads with 90% of bases having a quality of 20+
Reads aligned to reference genome using STAR v2.5.2b
Gene expression quantified using salmon v0.11.3
Differential gene expression tested using DESeq v1.22.2
Genome_build: mm9
Supplementary_files_format_and_content: Matrix of VST normalized counts from DESeq2 for all genes and samples

source_name: cultured oesophageal cells

extract_protocol:
TRIZOL (Invitrogen)
NEB NextUltra RNA Library Prep Kit (New England Biolabs) using the manufacturer's protocol

value: CRISPR/Cas9 microinjection

tag: crispr/cas9 cassette


title: Dppa_57_DNAm_CpG

status: Public on Jun 23 2020

type: SRA

city: Cambridge

first: Steven

middle: William

last: Wingett

state: Cambs

address: Francis Crick Avenue, Cambridge Biomedical Campus

department: Cell Biology

country: United Kingdom

institute: MRC Laboratory of Molecular Biology

library_source: genomic

data_processing:
Library strategy: NOMe-seq
EB RNA-seq raw FastQ data were trimmed with Trim Galore (version 0.4.4, default parameters) and mapped to the mouse GRCm38 genome assembly using Hisat2 version 2.1.0. Stable overexpression clone data used Trim Galore v0.5.0_dev and HiSat2 v2.1.0.
ChIP-seq Raw FastQ data were trimmed with Trim Galore v0.6.1 and aligned to mouse GRCm38 genome using Bowtie 2 v 2.3.2.
ATAC-seq Raw FastQ data were trimmed with Trim Galore (v0.5.0_dev) using standard parameters and aligned using Bowtie 2 v2.3.2.
NOME-seq Raw fastQ data were trimmed using Trim Galore version 0.4.4 using standard parameters, reads aligned using Bismark v0.18.2
All downstream data processing was performed using SeqMonk software (https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/).
Genome_build: mm10
Supplementary_files_format_and_content: The ChIP and ATAC is enrichment RPM over 1kb running windows. The RNA-seq is all genes RPM and the NOME-seq is 100CpG running window % methylation.  The files were generated using SeqMonk (exporting an annotated probe report).

molecule: genomic DNA

organism: Mus musculus

source_name: Dppa2/4 WT clone 57

growth_protocol: E14 mouse ESCs were grown using standard serum/LIF culture conditions (DMEM, 4,500 mg/L glucose, 4 mM L-glutamine, 110 mg/L sodium pyruvate, 15% fetal bovine serum, 1 U/mL penicillin, 1 mg/mL streptomycin, 0.1 mM nonessential amino acids, 50 mM b-mercaptoethanol, 103 U/mL LIF) at 37 degrees Celsius in normal oxygen, feeder-free on gelatin coated plates.

extract_protocol:
RNAseq: Total RNA was isolated using TriReagent (Sigma) or RNA-DNA allprep columns (Qiagen) 0.5-1mg DNAse treated (Thermo Fisher EN0525).
ChIPseq: Ten million cells were fixed in 1% formaldehyde (Fisher Scientific 28906) in DMEM (Invitrogen 41966-052) for 10 minutes, quenched in 0.125M glycine, and scraped off cell culture dishes using cell scrapers. Cells were lysed with buffers LB1 (50mM Hepes-KOH (pH 7.5), 140mM NaCl, 1mM EDTA, 10% Glycerol, 0.5% Igepal CA-630, 0.25% Triton-X 100), LB2 (10mM Tris-HCl (pH 8.0), 200mM NaCl, 1mM EDTA, 0.5mM EGTA), and LB3 (10mM Tris-HCl (pH 8.0), 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine, 1x Protease Inhibitors (Roche)) consecutively, before fragmenting chromatin by sonicating for 30 cycles of 30s ON high /30s OFF (Diagenode Bioruptor). For each ChIP, 5µg antibody (anti-Ash2l Bethyl Labs A300-489, anti-Ezh2 CST D2C9, anti-H2A.Z Abcam ab4174, anti-H3K4me3 Abcam ab8580, anti-H3K27me3 Active Motif AM39155, anti-IgG Abcam ab125938, anti-Ring1b CST D22F2) was pre-bound to protein G dynabeads (Invitrogen) and blocked with 0.5% BSA in PBS. Sonicated DNA was added to antibody-bound beads with 10% Triton-X 100 and incubated overnight at 4°C on a rotator. Beads and DNA were washed 6 times with RIPA buffer (50mM HEPES-KOH (pH 7.6), 1mM EDTA, 0.7% Na-Deoxycholate, 1% Igepal CA-630, 0.5M LiCl), followed by one wash in 1x TBS and overnight incubation at 65°C with elution buffer (50 mM Tris- HCl, pH 8; 10 mM EDTA; 1% SDS). For precipitation of chromatin, samples were treated with RNase A and Proteinase K. DNA was purified using MinElute PCR purification columns (Qiagen 28006) and eluted in 30µL of TE. DNA was quantified using HS DNA Qubit (ThermoFisher) or PicoGreen (ThermoFisher) assays.
ATACseq: 10,000 cells were trypsinised and immediately processed for ATACseq.
NOMEseq: Cells were fixed on 15cm plates wih Fixation solution (Active-Motif) for 10minutes at room temperature then processed according to Active Motif NOME-seq kit protocol.
RNAseq: Opposite strand-specific polyA RNA libraries were made using 1 µg of DNase- treated RNA at the Sanger Institute Illumina bespoke pipeline and sequenced using the Illumina HiSeq2 platform.
ChIPseq: libraries generated using MicroPlex Library Preparation Kit (Diagenode) following the manufacturer?s instructions. Libraries were quality controlled using bioanalyser HS DNA chips (Agilent) and single-end 50bp reads sequenced using the Illumina HiSeq2 sequencing platform.
ATACseq: ATAC-seq libraries were performed as previously described (Buenrostro, Wu, Chang, & Greenleaf, 2015) with the following modification to use on 10,000 cells: initial transposition reaction was performed with 10,000 cells, 10ml 2x TD buffer, 0.5ml Tn5 enzyme and 9.5ml H2O for 30minutes at 37 degrees Celsius. A total of 15 cycles of amplification were used. Two technical replicates were performed per clone, with 3 WT and 3 Dppa2/4 DKO clones used (total of 12 samples).
NOMEseq: Whole genome bisulfite libraries were generated using NOME-seq kit from Active Motif (103946) according to manufacturer?s instructions with 6 cycles of amplification for 2 WT clones (clones 57 and 58) and 1 Dppa2/4 DKO clone (clone 43).

treatment_protocol: Stable overexpression cell lines were generated using Lipofectamine 2000 on preplated cells and resistant cells selected with appropriate antibiotics for at least 1 week before sorting single cells into 96 well plates by flow cytometry using a BD Aria III or BD Influx high-speed cell sorter, and clonal expansion. CRISPR double knockout ESC line (clone 43) was described previously (M. Eckersley-Maslin et al., 2019), and additional CRISPR double knockout ESC lines (clone 37 and clone 53) generated as previously described (M. Eckersley-Maslin et al., 2019). For embryoid bodies, 2x106 mESCs were cultured on 10cm low-attachment dishes in standard ESC medium containing all described components except LIF.

tag: genotype

value: Dppa2/4 WT

tag: cell type

value: embryonic stem cell

tag: culture conditions

value: serum/LIF

tag: strain

value: CRISPR targetted E14 ESCs, contains MERVL::tdTomato reporter

tag: chip antibody


title: T47D-LTED

type: genomic

city: London

first: Alice

last: Gao

state: London

address: 237 Fulham Road

department: Breast Cancer Now

institute: The Institute of Cancer Research

description: basal

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the GeneChip® Scanner 3000 7G with AutoLoader.

data_processing:
SNPs were called using the Birdseed v2 algorithm (.CHP files), and copy number variations were called using the CN5 algorithm (.CNCHP files) using Affymetrix Genotyping Console 4.0 (Affymetrix). Sample table and .CNCHP data are based on genome build GRCh37 (hg19). HapMap samples were used as a reference.
Genotype Call (SNP call): AA, AB, BB, and NoCall; 'Signal' = Summarized signal

label: Biotin

organism: Homo sapiens

source_name: T47D-LTED, resistant to estrogen deprivation

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from target cell lines using QIAamp DNA mini kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

treatment_protocol: wt cells were treated long term with palobociclib until thay develop resistance.

tag: cell line

tag: compound

value: resistant to estrogen deprivation


title: Nrf2_WT_Rep2

country: USA

library_source: transcriptomic

molecule: polyA RNA

tag: treatment


title: Nrf2_WT_Rep1


title: TTP KO, 3h, replicate 3

city: Wien

first: Pavel

last: Kovarik

address: Dr.-Bohr-Gasse 9/4

department: Max Perutz Labs

country: Austria

institute: University of Vienna

data_processing:
Cutadapt (https://doi.org/10.14806/ej.17.1.200) was used for barcode, adapter and quality trimming.
Quality control was performed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
STAR version 2.5 (Dobin et al. 2013) was used to map all remaining reads to the GRCm38/mm10 mouse genome assembly.
Differential expression analysis was performed based on read counts using DESeq2 (Love et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: excel workbook files containing default DESeq2 result tables plus calculated individual FPKMs for each replicate

source_name: Bone marrow-derived dendritic cells

growth_protocol: Bone marrow-derived dendritic cells (BMDCs) were produced from bone marrow isolated from the femurs and tibias of 9-12 week old WT and TTP-/- mice.

extract_protocol:
Total RNA was extracted using QIAzol Lysis Reagent, which was followed by chloroform extraction. RNA was precipitated using Isopropanol and GlycoBlue, and was consequently subject to DNA digestion using DNase.
Libraries were prepared using SENSE mRNA-Seq Library Prep Kit V2 (Lexogen)

treatment_protocol: BMDCs were left untreated (0 h) or stimulated with 10 ng/ml lipopolysaccharide (LPS) for 3, 6 or 9 h.

value: Bone marrow-derived dendritic cells

value: TTP-/-

value: Lipopolysaccharide 3 hours


title: Ash2l_43

data_processing:
EB RNA-seq raw FastQ data were trimmed with Trim Galore (version 0.4.4, default parameters) and mapped to the mouse GRCm38 genome assembly using Hisat2 version 2.1.0. Stable overexpression clone data used Trim Galore v0.5.0_dev and HiSat2 v2.1.0.
ChIP-seq Raw FastQ data were trimmed with Trim Galore v0.6.1 and aligned to mouse GRCm38 genome using Bowtie 2 v 2.3.2.
ATAC-seq Raw FastQ data were trimmed with Trim Galore (v0.5.0_dev) using standard parameters and aligned using Bowtie 2 v2.3.2.
NOME-seq Raw fastQ data were trimmed using Trim Galore version 0.4.4 using standard parameters, reads aligned using Bismark v0.18.2
All downstream data processing was performed using SeqMonk software (https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/).
Genome_build: mm10
Supplementary_files_format_and_content: The ChIP and ATAC is enrichment RPM over 1kb running windows. The RNA-seq is all genes RPM and the NOME-seq is 100CpG running window % methylation.  The files were generated using SeqMonk (exporting an annotated probe report).

source_name: Dppa2/4 DKO clone 43

value: Dppa2/4 DKO

value: anti-Ash2l Bethyl Labs A300-489


title: wt-MCF7

description: basal

source_name: MCF7 under E2 maintenance

value: E2 maintenance


title: Nrf2_HET_Rep2


title: Hi-C_PPN5_rep1

city: Beijing

first: Ke

last: Zhang

state: Beijing

address: Haidian District

department: School of Life Sciences

country: China

institute: Tsinghua university

data_processing:
Basecalls performed using CASAVA version 1.8
For Hi-C samples: sisHi-C sequencing reads were mapped, processed and iteratively corrected using HiC-Pro, a pipeline developed by Servant et al. Briefly, the read pairs were mapped to the mm9 reference genome in a two-step approach with bowtie2. Then the invalid read pairs including dangling end, self-circle ligation and duplicates were discarded. The genome was divided into bins of specific length to generate the contact maps. For global detection of contacts, a 100Kb bin size and 300Kb bin size wereused and a 40Kb bin size was used for examination of local domain level contacts. The raw contact counts are normalized with iterative correction.
For RNA-seq samples: SMART-seq2 reads were aligned to the mm9 genome assembly using tophat2 version 2.1.1, then replicates were merged together, and transcript abundance (FPKM) were calculated based on Refseq annotation using cufflinks version 2.0.2.
Genome_build: mm9
Supplementary_files_format_and_content: The gene rpkm txt file contains FPKM value for all samples. While the validpair txt file indicates the paired interaction reads for each sample.

source_name: PPN5 SCNT embryos

extract_protocol:
The DNA extraction follows Hi-C protocol
Hi-C libraries were prepared using Hi-C protocal developed by Rao et al. with slightly modification
TruSeq

treatment_protocol: PPN5 SCNT embryos are collected 10 hours after activation.  MII oocytes were obtain at 13-14hrs after hCG injection. The spindle of oocyte was removed by the Piezo-driven (PrimeTech, Osaka, Japan) enucleation pipette on the Olympus inverted microscope (Tokyo, Japan), and the nuclei of donor cells were directly injected into the enucleated oocytes. The reconstructed oocytes were incubated in CZB medium for 1 hour before activation treatment. The cloned constructs were activated in Ca2+-free CZB medium supplemented with 10 mM SrCl2 (Sigma, Cat # 255521) and 5 μg/ml of cytochalasin B (Sigma, Cat # C-6762) for 4 hours. Cloned embryos were cultured in G1-Plus medium (Vitrolife, Cat # 10132) at 37.5 °C in an atmosphere of 5% CO2 in air. The first polar body was removed by enucleation pipette on the micromanipulator, while the zona pellucida was gently removed by treatment with acid Tyrode’s solution (Sigma, Cat # T-1788) for several minutes.

value: SCNT PPN5


title: Hi-C_PPN3_rep1

source_name: PPN3 SCNT embryos

treatment_protocol: PPN3 SCNT embryos are collected 6 hours after activation.  MII oocytes were obtain at 13-14hrs after hCG injection. The spindle of oocyte was removed by the Piezo-driven (PrimeTech, Osaka, Japan) enucleation pipette on the Olympus inverted microscope (Tokyo, Japan), and the nuclei of donor cells were directly injected into the enucleated oocytes. The reconstructed oocytes were incubated in CZB medium for 1 hour before activation treatment. The cloned constructs were activated in Ca2+-free CZB medium supplemented with 10 mM SrCl2 (Sigma, Cat # 255521) and 5 μg/ml of cytochalasin B (Sigma, Cat # C-6762) for 4 hours. Cloned embryos were cultured in G1-Plus medium (Vitrolife, Cat # 10132) at 37.5 °C in an atmosphere of 5% CO2 in air. The first polar body was removed by enucleation pipette on the micromanipulator, while the zona pellucida was gently removed by treatment with acid Tyrode’s solution (Sigma, Cat # T-1788) for several minutes.

value: SCNT PPN3


title: V6.5_ESC_MECP2-GFP_R168X_rep3

first: Charles

last: Li

state: MA

address: 455 Main Street

institute: Whitehead Institute for Biomedical Research

description:
V6.5_ESC_MECP2-GFP_WT_R168X.rsem.genes.results.counts.txt
V6.5_ESC_MECP2-GFP_WT_R168X.ERCC.DESeq2.resLFC.txt

data_processing:
RNA-seq reads were mapped using STAR aligner (v. 2.6.1a) to the murine RefSeq mm9 reference with ERCC spike-in reference sequences added. Alignment was performed using ENCODE long RNA-seq pipeline default parameters: --outFilterType BySJout, --outSAMattributes NH HI AS NM MD, --outFilterMultimapNmax 20, --outFilterMismatchNmax 999, --outFilterMismatchNoverReadLmax 0.05, --alignIntronMin 20, --alignIntronMax 1000000, --alignMatesGapMax 1000000, --alignSJoverhangMin 8, --alignSJDBoverhangMin 1, --sjdbScore 1. Gene expression values were quantified using RSEM (v. 1.2.31) with default parameters. Differential expression analysis was performed using DESeq2 (v. 1.24.0) with default parameters. Spike-in cell number normalization was performed by using ERCC spike-ins to estimate size factors used for DESeq2 library normalization. An FDR adjusted p-value cutoff of 0.1 was used to determine differentially expressed genes.
Genome_build: mm9
Supplementary_files_format_and_content: counts_RSEM
DESeq2 file represents the output results of differential expression analysis performed using DESeq2. File is organized as a table with each row representing a different gene. Columns represent the following: geneName, baseMean, log2FoldChange(WT/R168X), lfcSE, stat, pvalue, and padj.

molecule: total RNA

source_name: Embryonic stem cell

growth_protocol: MeCP2-GFP WT and R168X mutant V6.5 mouse embryonic stem cells (ESCs) were cultured in serum-free 2i/LIF media comprised of DMEM/F12 (Gibco 11320) supplemented with 0.5X N2 supplement (Gibco 17502), 0.5X B27 supplement (Gibco 17504), 2 mM L-glutamine (Gibco 25030), 1X MEM non-essential amino acids (Gibco 11140), 100 U/mL penicillin-streptomycin (Gibco 15140), 0.1 mM 2-mercaptoethanol (Sigma M7522), 3 µM CHIR99021 (Stemgent 04-0004), 1 µM PD0325901 (Stemgent 04-0006), and 1000 U/mL leukemia inhibitor factor (LIF) (ESGRO ESG1107). Prior to culturing cells, all tissue culture dishes were coated with 0.2% gelatin. The cells were grown in 37°C incubator maintaining 5% CO2 in a water-saturated atmosphere. Cell culture media were exchanged every 24 hours and cells were passaged every 2-3 days.

extract_protocol:
Cells were dissociated and counted. RNA was harvested from 2 million cell aliquots using the RNeasy Mini Plus kit (QIAGEN 74134) according to manufacturer's protocol. The amount of RNA extracted was quantified using a Nanodrop spectrophotometer (Thermo Scientific). A fixed amount of ERCC RNA Spike-In (Invitrogen 4456740) was added to each sample for use in cell number normalization. Samples were treated with DNA-free DNA Removal Kit (Invitrogen AM1906).
Library construction was performed by the Whitehead Institute Genome Technology Core using the KAPA RNA HyperPrep Kit with RiboErase (KAPA Biosystems K8562) according to manufacturer's protocol.

value: MECP2-GFP R168X

tag: gtcid


title: V6.5_ESC_MECP2-GFP_R168X_rep2


title: V6.5_ESC_MECP2-GFP_R168X_rep1


title: DBA/1 mice-12

type: RNA

city: Chengdu

first: Ling

last: Liu

state: Sichuan

address: Wai Nan Guo Xue Lane 37 #

department: Department of neurology

institute: West China Hospital, Sichuan University

description: Biological replicate 2 of 4

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

scan_protocol: Scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies).
Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR.

source_name: Brain tissue

label_protocol: mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen).

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: gender

value: male

tag: age

value: 5 weeks

tag: tissue

value: brainstem


title: RING1B_43

value: anti-Ring1b CST D22F2


title: DBA/1 mice-15

description: Biological replicate 3 of 4


title: C57BL/6 mice-12

description: Biological replicate 3 of 4


title: DBA/1 mice-17

description: Biological replicate 4 of 4


title: C57BL/6 mice-13

description: Biological replicate 4 of 4


title: DBA/1 mice-11

description: Biological replicate 1 of 4


title: SCC1_ctrl_SCNT_PPN1_rep2

description: SCC1_ctrl_SCNT_PPN1_rep12_allValidPairs.gz

data_processing:
Basecalls performed using CASAVA version 1.8
For RNA-seq samples: SMART-seq2 reads were aligned to the mm9 genome assembly using tophat2 version 2.1.1, then replicates were merged together, and transcript abundance (FPKM) were calculated based on Refseq annotation using cufflinks version 2.0.2.
For Hi-C samples: sisHi-C sequencing reads were mapped, processed and iteratively corrected using HiC-Pro, a pipeline developed by Servant et al. Briefly, the read pairs were mapped to the mm9 reference genome in a two-step approach with bowtie2. Then the invalid read pairs including dangling end, self-circle ligation and duplicates were discarded. The genome was divided into bins of specific length to generate the contact maps. For global detection of contacts, a 100Kb bin size was used and a 40Kb bin size was used for examination of local domain level contacts. The raw contact counts are normalized with iterative correction.
For ChIP-seq samples: the paired-end ChIP reads were aligned with the parameters: -t –q –N 1 –L 25 –X 1000 --no-mixed --no-discordant to mm9 reference genome by Bowtie (version 2.2.2). All unmapped reads, reads with low mapping quality (MAPQ < 20) and PCR duplicates were removed.
For CUT&RUN samples:the pair-end CUT&RUN reads were aligned to mm9 reference genome with random chromosome cleaned by Bowtie (version 2.2.2) under the parameters –t –q –N 1 –L 25. All unmapped reads, reads with low mapping quality (MAPQ < 20) and PCR duplicates were removed.
Genome_build: mm9
Supplementary_files_format_and_content: The gene rpkm txt file contains FPKM value for all samples.

extract_protocol:
The DNA extraction follows Hi-C protocol
Hi-C libraries were prepared using Hi-C protocal developed by Rao et al. with slightly modification

treatment_protocol: SCC1-AID-GFP mESCs were  treated without/with Auxin (500 μM) with the different time points. Sorting was then conducted using FACS Jazz to remove all the dead cells. Cells depleted of GFP fluorescence signals in auxin treatment group were collected as SCC1 KO (SCC1 -) groups, while the differentiated cells without the auxin treatment were collected as SCC1 WT (SCC1 +) groups. These cells are used as the SCNT donor cells. SCNT PPN1 embryos are collected 4 hours after the donor nucleus get injected into the enucleated MII oocytes. The reconstructed oocytes were incubated in CZB medium. The first polar body was removed by enucleation pipette on the micromanipulator, while the zona pellucida was gently removed by treatment with acid Tyrode’s solution (Sigma, Cat # T-1788) for several minutes.

tag: auxin treatment

value: no

value: SCC1 WT


title: V6.5_ESC_MECP2-GFP_WT_rep1

value: MECP2-GFP WT


title: SCC1_ctrl_SCNT_PPN1_rep1


title: V6.5_ESC_MECP2-GFP_WT_rep3


title: V6.5_ESC_MECP2-GFP_WT_rep2


title: SCC1_ctrl_diff_HiC_rep1

description: SCC1_ctrl_no_selection_diff_allValidPairs.gz

treatment_protocol: SCC1-AID-GFP mESCs were cultured in medium without LIF for 3 days and treated without/with Auxin (500 μM) for 1day. The differentiated cells were dissociated into single cells. Sorting was then conducted using FACS Jazz to remove all the dead cells. Cells depleted of GFP fluorescence signals in auxin treatment group were collected as SCC1 KO (SCC1 -) groups, while the differentiated cells without the auxin treatment were collected as SCC1 WT (SCC1 +) groups.


title: SCC1_auxin_SCNT_PPN1_rep2

description: SCC1_auxin_SCNT_PPN1_rep12_allValidPairs.gz

value: yes

value: SCC1 KO


title: Input_58_2

source_name: Dppa2/4 WT clone 58

value: Dppa2/4 WT

value: embryonic stem cell

value: serum/LIF

value: CRISPR targetted E14 ESCs, contains MERVL::tdTomato reporter


title: RING1B_58


title: Input_43

value: Dppa2/4 DKO


title: Input_58


title: Input_57


title: SKOG-HA- replicate2

city: Guangzhou

first: LI

last: LINPENG

address: KAIYUAN ROAD 190

institute: GIBH

data_processing:
Basecalls performed using CASAVA version 1.4
The sequencing reads were filtered by Trimmomatic (0.35), and then mapped to mouse reference sequence for mm10 using Bowtie2 (2.2.5).
Uniquely mapped reads were retained using Samtools (1.3.1) with parameters "-F 1804 -f 2 -q 30" and Picard tools MarkDuplicates (1.90)
peaks were called using MACS2 (2.1.0) callpeak module with parameters "-p 0.01 --nomodel --extsize 150 -B --SPMR --keep-dup all --call-summits" on  ChIP-seq data, and then only peaks with qvalue less than 1e-05 were keeped
Genome_build: mm10
Supplementary_files_format_and_content: Tracks of signal were computed using MACS2 bdgcmp module with parameter "-m ppois".The signal BigWig files were visualized using computeMatrix, plotHeatmap and plotProfile module in DeepTools (2.4.2)

source_name: mouse embryonic cell infection with retrovirus SKO+Glis1

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

value: ICR

value: mouse embryonic fibroblast cell

value: day 8 in reprogramming process

value: HA-tag(Cell Signaling, #3724)


title: T47D 991R

description: Palbociclib-resistant

source_name: T47D in E2 treated with Palbociclib (CDK4/6 inhibitor) until resistant


title: SKOG-Input


title: SKOG-HA- replicate1


title: SKOG-D8H3K27ac replicate2

value: day 5 in reprogramming process

value: H3K27Ac(Cell Signaling, #8173)


title: SKOG-D5H3K27ac replicate2


title: SKOF-D8H3K27ac replicate2

source_name: mouse embryonic cell infection with retrovirus SKO+Flag


title: C57BL/6 mice-10

description: Biological replicate 1 of 4

value: male

value: 5 weeks

value: brainstem


title: C57BL/6 mice-11

description: Biological replicate 2 of 4


title: SKOG-D8Input


title: SKOF-D5H3K27ac replicate2


title: SKOG-D8H3K27ac replicate1


title: SCC1_auxin_diff_HiC_rep1

description: SCC1_auxin_no_selection_diff_allValidPairs.gz


title: SKOG-D5Input


title: Input_36

source_name: Dppa2/4 DKO clone 36


title: MCF7-LTED

description: basal

source_name: MCF7-LTED, resistant to estrogen deprivation

value: resistant to estrogen deprivation


title: SCNT_mESC_ctrl_H3K9me3

description: SCNT_mESC_ctrl_H3K9me3_rep1_100bp_rpkm.tsv.gz

extract_protocol:
The DNA extraction follows ChIP-seq protocol
H3K27ac and H3K9me3 ChIP-seq in mESCs was performed as previously described (Brind’Amour et al., 2015; Liu et al., 2014). Briefly, mESCs were re-suspended in nuclear isolation buffer (Sigma). Depending on input size chromatin was fragmented for 5–7.5 min using MNase at 21 or 37 °C, and diluted in NChIP immunoprecipitation buffer (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 15 mM NaCl, 0.1% Triton X-100, 1 × EDTA-free protease inhibitor cocktail and 1 mM phenylmethanesulfonyl fluoride (Sigma)). Chromatin was pre-cleared with 5 or 10 μl of 1:1 protein A: G Dynabeads (Life Technologies) and then incubated with antibody (H3K9me3, abcam, cat # ab8898; H3K27ac, Active Motif, cat # 39133) overnight at 4 °C. Next, complexes were washed twice with 400 μl of ChIP wash buffer I (20 mM Tris-HCl, pH 8.0, 0.1% SDS, 1% Triton X-100, 0.1% deoxycholate, 2 mM EDTA and 150 mM NaCl) and twice with 400 μl of ChIP wash buffer II (20 mM Tris-HCl (pH 8.0), 0.1% SDS, 1% Triton X-100, 0.1%deoxycholate, 2 mM EDTA and 500 mM NaCl). Protein–DNA complexes were eluted in 30 μl of ChIP elution buffer (100 mM NaHCO3 and 1% SDS) for 1.5h at 68 °C. DNA was purified by phenol chloroform and ethanol-precipitated. Purified DNA was subjected to Tru-seq library construction using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S). The products were purified and size-selected with AMPure XP beads (Beckman Coulter, Cat # A63881).

treatment_protocol: SCC1-AID-GFP mESCs were  treated without/with Auxin (500 μM) with the different time points. Sorting was then conducted using FACS Jazz to remove all the dead cells. Cells depleted of GFP fluorescence signals in auxin treatment group were collected as SCC1 KO (SCC1 -) groups, while the differentiated cells without the auxin treatment were collected as SCC1 WT (SCC1 +) groups.

value: no

value: SCC1 WT

tag: antibody


title: H3K4me3_MC3

source_name: Dppa2/4 WT parental line (no CRISPR)

value: Dppa2/4 WT parental line (no CRISPR)

value: E14 ESCs, contains MERVL::tdTomato reporter

value: anti-H3K4me3 Abcam ab8580


title: SKOG-D5H3K27ac replicate1


title: SKOF-D8Input


title: SKOF-D8H3K27ac replicate1


title: Input_43_2

value: embryonic stem cell

value: serum/LIF

value: CRISPR targetted E14 ESCs, contains MERVL::tdTomato reporter


title: SCNT_mESC_ctrl_H3K27ac

description: SCNT_mESC_ctrl_H3K27ac_rep1_100bp_rpkm.tsv.gz


title: SCNT_mESC_auxin_6h_H3K9me3

description: SCNT_mESC_auxin_6h_H3K9me3_rep1_100bp_rpkm.tsv.gz

value: yes

value: SCC1 KO

tag: time point


title: SKOF-D5H3K27ac replicate1

value: ICR

value: mouse embryonic fibroblast cell


title: SCC1_auxin_SCNT_PPN1_rep1


title: SKOF-D5Input

value: day 5 in reprogramming process


title: SCNT_mESC_auxin_6h_H3K27ac

description: SCNT_mESC_auxin_6h_H3K27ac_rep1_100bp_rpkm.tsv.gz


title: SCNT_mESC_auxin_24h_H3K9me3

description: SCNT_mESC_auxin_24h_H3K9me3_rep1_100bp_rpkm.tsv.gz


title: Dppa_DKO_43B

value: Dppa2/4 DKO


title: 18907_N

city: Chicago

first: Yoav

last: GiladLi

state: IL

address: 920 e 58th St

department: Section of Genetic Medicine

institute: University of Chicago

description:
nuclear RNA
Yoruban Individuals

data_processing:
map to HG19 with WASP output mode. Remove reads not passing WASP multimapping.
Clean for mispriming by removing reads with 6 A's upstream of 7 of 10 As in upstream sequence.
Merge all BAM files and call peaks with inhouse scripts (avaialbe on github)
Assign PAS to genes using RefSeq annoations
Remove PAS used on average <5% in total or nuclear individuals
Genome_build: GRCh37
Supplementary_files_format_and_content: APAPAS_GeneLocAnno.5perc.bed: bed file with location of each PAS used at 5% in the total or nuclear fraction. Name column has peak unique number, gene, and PAS genic location. End corresponds to 5kb downstream of annotated 3' UTR
Supplementary_files_format_and_content: MetaDataSequencing.txt: file with relevant cell collection and sequencing metadata

source_name: Imortalized Lymphoblastoid cell line

growth_protocol: LCLs were grown in 15% FBS containing RPMI at 37 and 5% CO2. They were passagd 3 times, maintained at 8 X 10^5, and collected at concentration of 1 X 10^6.

extract_protocol:
The nuclear RNA was extracted using the first part of the nuclear isolation protocl from Mayer and Churchman. Once the sampes were pelleted in the nuclear wash buffer we resuspended in 700 ul of QIAzol lysis reagent and RNA isolation was complted using an miRNAEasy kit (Quiagen).
For each cell line we sampled both the total RNA in the cell, and the nucear RNA fraction through the ioslated nucleus.
3' RNA seq

treatment_protocol: Cells were collected and pelleted at 200 g for 5 min at 4C, washed with cold PBS, then spun again the same way.

tag: individual

value: Imortalized Lymphocyte

tag: Sex

value: F


title: H3K4me3_43

tag: genotype


title: H3K4me3_53

source_name: Dppa2/4 DKO clone 53

tag: cell type


title: 19138_T

description:
total RNA
Yoruban Individuals

value: M


title: 18907_T

description:
total RNA
Yoruban Individuals


title: TTP KO, 0h, replicate 2

value: Bone marrow-derived dendritic cells

value: TTP-/-

value: Untreated


title: 19101_N

description:
nuclear RNA
Yoruban Individuals


title: 19138_N

description:
nuclear RNA
Yoruban Individuals


title: H3K4me3_36

tag: culture conditions


title: 19101_T

description:
total RNA
Yoruban Individuals


title: SCNT_mESC_auxin_24h_H3K27ac

description: SCNT_mESC_auxin_24h_H3K27ac_rep1_100bp_rpkm.tsv.gz


title: H3K4me3_58

value: Dppa2/4 WT

tag: strain


title: H3K27me3_MC3

value: Dppa2/4 WT parental line (no CRISPR)

value: E14 ESCs, contains MERVL::tdTomato reporter

tag: chip antibody

value: anti-H3K27me3 Active Motif AM39155


title: 18913_T

description:
total RNA
Yoruban Individuals


title: 18913_N

description:
nuclear RNA
Yoruban Individuals


title: H3K27me3_58

value: embryonic stem cell

value: serum/LIF

value: CRISPR targetted E14 ESCs, contains MERVL::tdTomato reporter


title: mESC_SMC3_rep2

data_processing:
Library strategy: CUN&RUN
Basecalls performed using CASAVA version 1.8
For RNA-seq samples: SMART-seq2 reads were aligned to the mm9 genome assembly using tophat2 version 2.1.1, then replicates were merged together, and transcript abundance (FPKM) were calculated based on Refseq annotation using cufflinks version 2.0.2.
For Hi-C samples: sisHi-C sequencing reads were mapped, processed and iteratively corrected using HiC-Pro, a pipeline developed by Servant et al. Briefly, the read pairs were mapped to the mm9 reference genome in a two-step approach with bowtie2. Then the invalid read pairs including dangling end, self-circle ligation and duplicates were discarded. The genome was divided into bins of specific length to generate the contact maps. For global detection of contacts, a 100Kb bin size was used and a 40Kb bin size was used for examination of local domain level contacts. The raw contact counts are normalized with iterative correction.
For ChIP-seq samples: the paired-end ChIP reads were aligned with the parameters: -t –q –N 1 –L 25 –X 1000 --no-mixed --no-discordant to mm9 reference genome by Bowtie (version 2.2.2). All unmapped reads, reads with low mapping quality (MAPQ < 20) and PCR duplicates were removed.
For CUT&RUN samples:the pair-end CUT&RUN reads were aligned to mm9 reference genome with random chromosome cleaned by Bowtie (version 2.2.2) under the parameters –t –q –N 1 –L 25. All unmapped reads, reads with low mapping quality (MAPQ < 20) and PCR duplicates were removed.
Genome_build: mm9
Supplementary_files_format_and_content: The gene rpkm txt file contains FPKM value for all samples.

extract_protocol:
The DNA extraction follows CUT &RUN protocol
SMC3 CUT&RUN in mESCs was conducted as previously described (Skene and Henikoff, 2017). Briefly, samples were resuspended by washing buffer (HEPES-KOH, pH = 7.5, 20mM; NaCl, 150mM; Spermidine, 0.5mM and with Roche complete protease inhibitor) and incubated with concanavalin-coated magnetic beads (Polyscience, 86057) at 23°C for 10 mins. Next, the samples were resuspended by antibody buffer (washing buffer plus digitonin (Thermo, Cat # BN2006), freshly pre-heated, 0.005%~0.01%, tested for each batch; EDTA, pH = 8.0, 2mM) with SMC3 antibody (Abcam, Cat #ab9263) diluted at ratio of 1:100. After being incubated at 4°C for overnight, the samples were resuspended by washing buffer with pA-MNase (to a final concentration of 700ng/mL) and incubated at 4°C for 3 hours. The targeted digestion was then performed with CaCl2 treatment and quenched by stop buffer. Purified DNA was subjected to Tru-seq library construction using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S). The products were purified and size-selected with AMPure XP beads (Beckman Coulter, Cat # A63881).

value: no


title: 18862_T

description:
total RNA
Yoruban Individuals


title: 18862_N

description:
nuclear RNA
Yoruban Individuals


title: mESC_SMC3_rep1


title: H3K4me3_57

source_name: Dppa2/4 WT clone 57

value: anti-H3K4me3 Abcam ab8580


title: H3K27me3_57


title: SCC1_mesc_ctrl_RNA_rep2

extract_protocol:
The RNA extraction follows smart-seq2 protocol
The RNA-seq libraries were generated using the Smart-seq2 protocol as described previously with minor modification (Picelli et al., 2014). Cells were lysed in hypotonic lysis buffer (Amresco, M334), and the polyadenylated mRNAs were captured by the PolyT primers. After ~3–10 min lysis at 72 °C, the Smart-seq2 reverse transcription reactions were performed. After pre-amplification and AMPure XP beads purification, cDNAs were sheared by Covaris and were subject to Illumina TruSeq library preparation. All libraries were sequenced on Illumina HiSeq 2500 according to the manufacturer’s instruction.

value: SCC1 WT


title: 18856_T

description:
total RNA
Yoruban Individuals


title: 18856_N

description:
nuclear RNA
Yoruban Individuals


title: H3K27me3_53

value: Dppa2/4 DKO


title: 18852_T

description:
total RNA
Yoruban Individuals

value: Imortalized Lymphocyte


title: SCC1_mesc_ctrl_RNA_rep1


title: 18852_N

description:
nuclear RNA
Yoruban Individuals

value: F


title: H3K27me3_36


title: 18855_N

description:
nuclear RNA
Yoruban Individuals


title: SCC1_mesc_auxin_9h_RNA_rep1

value: yes

value: SCC1 KO


title: SCC1_mesc_auxin_6h_RNA_rep1


title: 18502_T

description:
total RNA
Yoruban Individuals


title: H2AZ_43

value: anti-H2A.Z Abcam ab4174


title: 18502_N

description:
nuclear RNA
Yoruban Individuals


title: SCC1_mesc_auxin_3h_RNA_rep1


title: 18522_N

description:
nuclear RNA
Yoruban Individuals

value: M


title: 18522_T

description:
total RNA
Yoruban Individuals


title: 18516_T

description:
total RNA
Yoruban Individuals


title: SCC1_mesc_auxin_24h_RNA_rep2


title: 18516_N

description:
nuclear RNA
Yoruban Individuals


title: 18510_T

description:
total RNA
Yoruban Individuals


title: EZH2_43

value: anti-Ezh2 CST D2C9


title: SCC1_mesc_auxin_24h_RNA_rep1


title: SCC1_mesc_auxin_1h_RNA_rep1


title: 18504_N

description:
nuclear RNA
Yoruban Individuals


title: EBset3_d9_clone58

description:
DNaseI treated total RNA
Processed_data_EB_RNAseq.txt

value: Dppa2/4 WT

value: embryoid body from day 9 of differentiation

value: EB differentiation media


title: 18504_T

description:
total RNA
Yoruban Individuals


title: 18498_T

description:
total RNA
Yoruban Individuals


title: EBset3_d9_clone43


title: 18855_T

description:
total RNA
Yoruban Individuals


title: SCC1_mesc_auxin_18h_RNA_rep1


title: EBset3_d7_clone58

value: embryoid body from day 7 of differentiation


title: 19207_N

description:
nuclear RNA
Yoruban Individuals


title: SCC1_mesc_auxin_12h_RNA_rep1


title: H2AZ_58

value: embryonic stem cell

value: serum/LIF


title: 18498_N

description:
nuclear RNA
Yoruban Individuals


title: EZH2_58

value: CRISPR targetted E14 ESCs, contains MERVL::tdTomato reporter


title: 19131_T

description:
total RNA
Yoruban Individuals


title: 19207_T

description:
total RNA
Yoruban Individuals


title: EBset3_d7_clone43


title: 19131_N

description:
nuclear RNA
Yoruban Individuals


title: SCC1_diff_ctrl_SCNT_PPN5_RNA_rep2

description: SCC1_ctrl_auxin_SCNT_L2C_PPN5_fpkm.txt.gz

value: no


title: EBset3_d4_clone58

value: embryoid body from day 4 of differentiation


title: 19140_N

description:
nuclear RNA
Yoruban Individuals


title: Dppa_DKO_36A

value: Dppa2/4 DKO


title: 19140_T

description:
total RNA
Yoruban Individuals

value: Imortalized Lymphocyte


title: 18510_N

description:
nuclear RNA
Yoruban Individuals


title: 19144_N

description:
nuclear RNA
Yoruban Individuals


title: EBset3_d3_clone58

value: embryoid body from day 3 of differentiation


title: 19144_T

description:
total RNA
Yoruban Individuals


title: SCC1_diff_ctrl_SCNT_late2cell_RNA_rep3

treatment_protocol: SCNT Late 2-cell embryos are collected 28 hours after the donor nucleus get injected into the enucleated MII oocytes. The reconstructed oocytes were incubated in CZB medium. The first polar body was removed by enucleation pipette on the micromanipulator, while the zona pellucida was gently removed by treatment with acid Tyrode’s solution (Sigma, Cat # T-1788) for several minutes.

value: SCC1 WT


title: EBset3_d4_clone43


title: 18912_N

description:
nuclear RNA
Yoruban Individuals

value: F


title: SCC1_diff_ctrl_SCNT_late2cell_RNA_rep2


title: 18912_T

description:
total RNA
Yoruban Individuals


title: SCC1_diff_ctrl_SCNT_late2cell_RNA_rep1


title: 19093_T

description:
total RNA
Yoruban Individuals


title: 19153_N

description:
nuclear RNA
Yoruban Individuals


title: 19153_T

description:
total RNA
Yoruban Individuals


title: SCC1_diff_ctrl_RNA_rep2

description: SCC1_diff_facs_select_noselect_fpkm.txt.gz


title: EBset3_d3_clone43


title: EBset3_d2_clone43

value: embryoid body from day 2 of differentiation


title: 19152_N

description:
nuclear RNA
Yoruban Individuals


title: SCC1_diff_ctrl_SCNT_PPN5_RNA_rep1


title: EBset3_d1_clone58

value: embryoid body from day 1 of differentiation


title: 19137_N

description:
nuclear RNA
Yoruban Individuals


title: SCC1_diff_auxin_SCNT_PPN5_RNA_rep2

value: yes

value: SCC1 KO


title: SCC1_diff_ctrl_RNA_rep1


title: 19137_T

description:
total RNA
Yoruban Individuals


title: EBset3_d1_clone43


title: EBset2_d9_clone_58

value: Dppa2/4 WT

value: embryoid body from day 9 of differentiation


title: SCC1_diff_auxin_SCNT_PPN5_RNA_rep1


title: 19200_N

description:
nuclear RNA
Yoruban Individuals

value: M


title: 19093_N

description:
nuclear RNA
Yoruban Individuals


title: 19171_N

description:
nuclear RNA
Yoruban Individuals


title: SCC1_diff_auxin_SCNT_late2cell_RNA_rep3


title: EBset2_d9_clone_43

value: EB differentiation media


title: 19171_T

description:
total RNA
Yoruban Individuals


title: 19200_T

description:
total RNA
Yoruban Individuals


title: 19160_N

description:
nuclear RNA
Yoruban Individuals


title: EBset3_d2_clone58


title: 19160_T

description:
total RNA
Yoruban Individuals


title: SCC1_diff_auxin_SCNT_late2cell_RNA_rep2


title: 18916_N

description:
nuclear RNA
Yoruban Individuals


title: EBset2_d7_clone58

value: embryoid body from day 7 of differentiation


title: SCC1_diff_auxin_SCNT_late2cell_RNA_rep1


title: 18916_T

description:
total RNA
Yoruban Individuals


title: EBset2_d7_clone43

value: CRISPR targetted E14 ESCs, contains MERVL::tdTomato reporter


title: SCC1_diff_auxin_RNA_rep2


title: 18909_T

description:
total RNA
Yoruban Individuals


title: 18909_N

description:
nuclear RNA
Yoruban Individuals


title: 19152_T

description:
total RNA
Yoruban Individuals


title: EBset2_d4_clone_58


title: SCC1_diff_auxin_RNA_rep1


title: EBset2_d4_clone_43


title: Abhd11 OE-2

city: Chongqing

first: Rui

last: Jian

address: Gaotanyan Street

department: Department of Histology and Embryology

institute: Third Military Medical University

description: Abhd11 OE ESCs cultured in the presence of 1000ng/ml Doxycyline

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, then mapped to mm10 whole genome using Hisat2(version:2.0.4).
Strings (version: 1.3.0) were used to count the number of Fragments for each gene after Hisat2 alignment, and then normalized by DESeq2 method. Finally, the count reads value of each gene was calculated.
Genome_build: mm10(GRCm38)

source_name: mESC

growth_protocol: murine ESCs were on 0.2% gelatin-coated plates in ESC maintenance medium containing high glucose Dulbecco-modified Eagle medium (DMEM), 5% fetal bovine serum (FBS), 15% KnockOut Serum Replacement (KSR), 2mM Glutamax, 1mM sodium pyruvate, 0.1mM  NEAA, 0.1mM b-mercaptoethanol, 100U/ml penicillin, 100U/ml streptomycin (all from Invitrogen) and 10ng/ml LIF (Millipore) at 37°C under 5% CO2

extract_protocol:
Total RNA was extracted using TRIzol Reagent(Invitrogen,Cat:15596026) and a miRNeasy Micro Kit (QIAGEN,Cat:217084) according the manufacturer's manual. The RNA quality were measured using Agilent 4200 TapeStation.
RNA samples were send to Genminix Informatic Ltd. (Shanghai, China) for mRNA sequencing on Illumina Hiseq platform (Illumina, San Diego, California, USA) with 6Gbps.

treatment_protocol: Control and Abhd11 KO ESCs were cultured in the absence of Doxycycline; Abhd11 RES ESCs were cultured in the presence of 1ng/ml Dox; Abhd11 OE ESCs were cultured in the presence of 1000ng/ml Dox.

value: mESC

tag: passage

value: passage 3

tag: phenotype

value: Abhd11 over-expression


title: EBset2_d3_clone58


title: 19210_N

description:
nuclear RNA
Yoruban Individuals

value: Imortalized Lymphocyte


title: Abhd11 OE-1


title: Abhd11 RES-2

description: Abhd11 Rescue ESCs cultured in the presence of 1ng/ml Doxycyline

value: Abhd11 rescue


title: EBset2_d2_clone_58


title: EBset2_d3_clone43

source_name: Dppa2/4 DKO clone 43

value: Dppa2/4 DKO

value: embryoid body from day 3 of differentiation


title: 19130_N

description:
nuclear RNA
Yoruban Individuals


title: Abhd11 RES-1


title: 18861_N

description:
nuclear RNA
Yoruban Individuals

value: F


title: 19119_T

description:
total RNA
Yoruban Individuals


title: 19130_T

description:
total RNA
Yoruban Individuals


title: 19210_T

description:
total RNA
Yoruban Individuals


title: 19119_N

description:
nuclear RNA
Yoruban Individuals


title: 18858_T

description:
total RNA
Yoruban Individuals


title: EBset2_d1_clone58

value: embryoid body from day 1 of differentiation


title: EBset2_d2_clone_43

value: embryoid body from day 2 of differentiation


title: Abhd11 KO(P3)-1

description: Abhd11 KO ESCs cultured in the absence of Doxycyline (passage 3)

value: Abhd11 knock-out


title: 19092_N

description:
nuclear RNA
Yoruban Individuals


title: Abhd11 KO(P3)-2


title: EBset2_d1_clone43


title: 18520_T

description:
total RNA
Yoruban Individuals


title: 18520_N

description:
nuclear RNA
Yoruban Individuals


title: 19092_T

description:
total RNA
Yoruban Individuals


title: 18519_N

description:
nuclear RNA
Yoruban Individuals


title: Abhd11 KO(P2)-2

description: Abhd11 KO ESCs cultured in the absence of Doxycyline (passage 2)

value: passage 2


title: Abhd11 KO(P2)-1


title: 18511_T

description:
total RNA
Yoruban Individuals


title: 18861_T

description:
total RNA
Yoruban Individuals


title: 18858_N

description:
nuclear RNA
Yoruban Individuals


title: EBset1_d9_clone43

value: embryoid body from day 9 of differentiation


title: Control-2

description: Control ESCs cultured in the absence of Doxycyline

value: control


title: ATAC_Reactivated_rep3

city: Rehovot

first: Asaf

last: Marco

address: Herzl 229

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
Illumina Casava1.7 software used for basecalling.
The raw fastq data of 40-bp paired-end sequencing reads were aligned to the mouse mm9 reference genome using Bowtie 2.0 in paired-end mode.
The Samtools collection was used to sort, remove PCR duplicates (rmdup), index BAM files (index), and calculate library statistics. BAM files were downsampled from properly aligned, paired and unique reads to 50M.
Open chromatin peaks were analyzed using MACS2 software (macs2 callpeak -t xxx.bam –broad -f BAMPE -g mm -q 0.05 –nomodel –keep-dup all -n –B –SPMR).
Differential peaks analysis between different conditions were identified by Diffbind v1.16.327 with default parameters and settings to use DESeq2 (cutoff; FDR < 0.01; fold changes > 1.5).
Genome_build: mm9
Supplementary_files_format_and_content: Normalized (RPKM) counts

source_name: Sorted neuronal nuclei

extract_protocol:
Hippocampal tissue was extracted and flash frozen. After extraction, samples were immediately homogenized in 0.5 mL ice cold PBS with protease inhibitors (Pi) (11836170001, Roche). The suspension was centrifuged at 1200 g, 4°C, for 5 minutes and the pellet was resuspended in 5 mL NF-1 hypotonic buffer (0.5% Triton X-100/0.1M Sucrose/5mM MgCl2/1mM EDTA/10mM Tris-HCl, pH 8.0, Pi). Pelleted nuclei were resuspended in and incubated with NeuN, Arc and GFP primary antibodies for overnight in 4°C. Unbound antibodies were washed out twice and nuclei were filtered with 40 µm mesh filter for FACS sorting.
ATAC seq libraries were prepared as previously described in Buenrostro, J. D, et al, Nat. Methods, 2013, with minor modification. Immediately follow sorting, cells were spun down (4°C, 1,600 x g for 15 min) and resuspended in fresh 50 ul cold lysis buffer (0.15% NP-40 instead of Igpal) and rocked on ice for 10 min. Next, tagmentation reaction was carried out in 25 ul volume (12.5 μl TD, 1.25 μl TDE1, 11.25 μl nuclease-free water), for 30 min at 37c with gentle rocking. Tagmented DNA fragments were amplified and barcoded using PCR reaction (1 cycle; 5min – 72c, 30sec – 98c, 10 cycles; 15sec – 98c, 30sec – 60c, 3min – 72c). Aamplified DNA was cleaned and purified using 1.8x AMPure beads.

treatment_protocol: In order to minimize the nonspecific eYFP label, one day prior to the contextual fear conditioning (CFC), mice were single housed in a 24h dark/dark room. In the next day, mice received one dose of 4-Hydroxytamoxifen, 1h before the CFC test. Following the behavioral task, mice were either euthanized after 1.5-2 h and brain were collected, or placed back into the dark room for the following 48 hr. After mice were taken out of the dark, they were returned to normal 12 hr (06:00–18:00) light-dark cycle, in the same room. 3 days later (total of 5 days after the CFC), half of the mice cohort were euthanized and brain were collected, while the other half returned to the testing room, where they exposed to the fear inducing cue (tone and context).

value: Hippocampus

value: ArcCreERT2 x R26R-STOP-floxed- yellow fluorescent protein (eYFP)

tag: treatment

value: Foot shock day 0, recall day 5, tissue collection day 7


title: ATAC_Reactivated_rep2

value: Foot shock day 0, recall day 5, tissue collection day 6


title: 19257_N

description:
nuclear RNA
Yoruban Individuals


title: Control-1

value: mESC

value: passage 3


title: 19239_T

description:
total RNA
Yoruban Individuals

value: Imortalized Lymphocyte

value: M


title: EBset1_d7_clone58

value: Dppa2/4 WT

value: embryoid body from day 7 of differentiation

value: EB differentiation media

value: CRISPR targetted E14 ESCs, contains MERVL::tdTomato reporter


title: Hi-C_SCC1_diff_con_rep2

source_name: SCC1-AID-mESC cell line

treatment_protocol: SCC1-AID-mESC cell line was generously provided by Dr. Robert Klose. mESCs were cultured in DMEM supplemented with 10 % Fetal Bovine Serum (FBS), MEM Non-Essential Amino Acids Solution (Gibco, Cat#. 111040050), GlutaMAX™ Supplement (Gibco, Cat # 35050061), 2-mercaptoethanol (Specialty media, Cat # ES-007-E), EmbryoMax 100X nucleosides (Millipore, Cat # ES-008-D), LIf (1000 U/ml, Millipore, Cat # ESG1107. For differentiation, ESCs were cultured in medium without LIF for 3 days. and treated without/with auxin (500 μM)(Nora et al., 2017) (Sigma, Cat # 6505-45-9) for 1 day. SCC1-AID differentiated cells were dissociated into single cells. Sorting was then conducted using FACS Jazz (BD Biosciences). Cells depleted of GFP fluorescence signals in auxin treatment group were collected as SCC1 KO groups, while the differentiated cells retaining relatively high GFP fluorescence signals without the auxin treatment were collected as SCC1 positive groups.

value: SCC1 WT


title: 19257_T

description:
total RNA
Yoruban Individuals

value: F


title: EBset1_d7_clone43

value: Dppa2/4 DKO


title: ATAC_Reactivated_rep1

value: Foot shock day 0, recall day 5, tissue collection day 5


title: ATAC_Late_rep4

value: Foot shock day 0, No recall, tissue collection day 5


title: 18519_T

description:
total RNA
Yoruban Individuals


title: EBset1_d9_clone58

value: embryoid body from day 9 of differentiation


title: 18511_N

description:
nuclear RNA
Yoruban Individuals


title: Hi-C_SCNT_8C_CC_rep2

source_name: SCNT 8-cell embryos

treatment_protocol: SCNT 8-cell embryos are collected 56 hours after the donor nucleus get injected into the enucleated MII oocytes. The reconstructed oocytes were incubated in CZB medium. The first polar body was removed by enucleation pipette on the micromanipulator, while the zona pellucida was gently removed by treatment with acid Tyrode’s solution (Sigma, Cat # T-1788) for several minutes.

value: SCNT 8-cell_CC


title: 19239_N

description:
nuclear RNA
Yoruban Individuals


title: Hi-C_SCC1_diff_auxin_rep2

description: EB_SCC1_auxin_rep12_allValidPairs.txt.gz

value: SCC1 KO


title: 19238_N

description:
nuclear RNA
Yoruban Individuals


title: ATAC_Late_rep2

value: Hippocampus

value: ArcCreERT2 x R26R-STOP-floxed- yellow fluorescent protein (eYFP)


title: 19225_T

description:
total RNA
Yoruban Individuals


title: EBset1_d4_clone43

value: embryoid body from day 4 of differentiation


title: EBset1_d4_clone58


title: EBset1_d3_clone58

value: embryoid body from day 3 of differentiation


title: ATAC_Late_rep3


title: Hi-C_SCNT_8C_MEF_rep2

value: SCNT 8-cell_MEF


title: EBset1_d3_clone43


title: ATAC_Late_rep1


title: EBset1_d2_clone58

value: Dppa2/4 WT

value: embryoid body from day 2 of differentiation


title: ATAC_Early_rep3

value: Foot shock day 0, No recall, tissue collection day 0


title: Hi-C_SCNT_8C_MEF_rep1


title: EBset1_d2_clone43

value: EB differentiation media

value: CRISPR targetted E14 ESCs, contains MERVL::tdTomato reporter


title: 19223_T

description:
total RNA
Yoruban Individuals

value: Imortalized Lymphocyte

value: M


title: Hi-C_SCNT_Late2C_rep2

source_name: SCNT Late 2-cell embryos

value: SCNT Late-2cell


title: ATAC_Early_rep2


title: 19238_T

description:
total RNA
Yoruban Individuals

value: F


title: EBset1_d1_clone58

value: embryoid body from day 1 of differentiation


title: Hi-C_SCNT_Late2C_rep1


title: ATAC_Early_rep1


title: 19223_N

description:
nuclear RNA
Yoruban Individuals


title: Hi-C_PPN5_rep2

source_name: PPN5 SCNT embryos

value: SCNT PPN5


title: 19209_T

description:
total RNA
Yoruban Individuals


title: ATAC_Basal_rep4


title: E14+GFP_c2_3

description:
DNaseI treated total RNA
Processed_data_OE_RNAseq.txt

source_name: GFP stable overexrpession clone 2

value: GFP stable overexrpession

value: embryonic stem cell

value: serum/LIF

value: E14 ESC


title: Hi-C_SCNT_8C_CC_rep1

value: SCNT 8-cell_CC


title: Hi-C_PPN3_rep2

source_name: PPN3 SCNT embryos

value: SCNT PPN3


title: E14+GFP_c2_2


title: 19193_T

description:
total RNA
Yoruban Individuals


title: EBset1_d1_clone43

value: Dppa2/4 DKO


title: ATAC_Basal_rep2

value: Hippocampus

value: ArcCreERT2 x R26R-STOP-floxed- yellow fluorescent protein (eYFP)


title: 19209_N

description:
nuclear RNA
Yoruban Individuals


title: 19193_N

description:
nuclear RNA
Yoruban Individuals


title: 19225_N

description:
nuclear RNA
Yoruban Individuals


title: ATAC_Basal_rep3

value: Foot shock day 0, No recall, tissue collection day 0


title: ATAC_Basal_rep1


title: E14+GFP_c1_3

source_name: GFP stable overexrpession clone 1


title: 19141_T

description:
total RNA
Yoruban Individuals


title: RNA_SCNT_8C_MEF_rep3

data_processing:
Basecalls performed using CASAVA version 1.8
For RNA-seq samples: SMART-seq2 reads were aligned to the mm9 genome assembly using tophat2 version 2.1.1, then replicates were merged together, and transcript abundance (FPKM) were calculated based on Refseq annotation using cufflinks version 2.0.2.
Genome_build: mm9
Supplementary_files_format_and_content: The gene rpkm txt file contains FPKM value for all samples.

source_name: embryo

extract_protocol:
The RNA extraction follows smart-seq2 protocol
The RNA-seq libraries were generated using the Smart-seq2 protocol as described previously with minor modification (Picelli et al., 2014). Cells were lysed in hypotonic lysis buffer (Amresco, M334), and the polyadenylated mRNAs were captured by the PolyT primers. After ~3–10 min lysis at 72 °C, the Smart-seq2 reverse transcription reactions were performed. After pre-amplification and AMPure XP beads purification, cDNAs were sheared by Covaris and were subject to Illumina TruSeq library preparation. All libraries were sequenced on Illumina HiSeq 2500 according to the manufacturer’s instruction.
Nextera

tag: developmental stage

value: SCNT 8-cell_MEF

value: embryo


title: Mix

first: Sebastian

last: Pott

state: Il

address: 920 58th Street

department: Human Genetics

description:
Drop-seq
Mix represents sample in which cells with Wt and Mut genotypes, Mesp1Cre-sorted E7.5 mesoderm from Mesp1-Cre/+;R26-tdTomato/+ embryos and Mesp1Cre-sorted E7.5 mesoderm from Mesp1-Cre/+;R26-Gli3R-IRES-Venus/+ embryos, respectively, were pooled during sorting. The proportion of cells from either genotype was approximately 50/50 at the outset, based on FACS counting.

data_processing:
Drop-seq libaries were processed using a custom pipeline (https://github.com/sebpott/dropseq_pipeline), major steps are described below.
For each sample a whiltelist of barcodes likely corresponding to  cells was obtained using  umi_tools whitelist with --error-correct-cell --filter-cell-barcode set.
Read 1:  Barcode and UMI follow the initial dropseq protocol, CCCCCCCCCCCCNNNNNNNN, where the first 12 nucleotides (C) correspond to the cell barcode and the last 8 (N) correspond to the UMI.
Read 2 was trimmed of adaptor sequences using cutadapt with --minimum-length 30 -a AAAAAA -g AAGCAGTGGTATCAACGCAGAGTGAATGGG
reads were aligned using STAR v with the following settings: --outFilterMultimapNmax 1 --outSAMtype BAM SortedByCoordinate --outStd BAM_SortedByCoordinate
aligned reads were assigned to trasncripts using featurecounts (-R BAM)
gene counts for each cell were obtained using umi_tools count (--wide-format-cell-counts --per-gene --gene-tag=XT --per-cell)
Genome_build: mm10
Supplementary_files_format_and_content: matrix files of transcript counts for each samples with rows correspoinding to genes and columns to cells, barcode whitelist files containing cell barcodes accepted as cells.

source_name: Mesp1Cre-sorted E7.5 mesoderm from Mesp1-Cre/+;R26-tdTomato/+ embryos, Mesp1-Cre/+;R26-Gli3R-IRES-Venus/+ embryos

extract_protocol:
Embryos used for Drop-seq profiling were harvested at E8.25 in 1x ice cold PBS, pooled with their littermates, dissociated with TrypLE (Fisher) reagent for 10 minutes at 37C while shaking at 1,400 rpm in a Fisher Thermomixer, followed by inactivation by addition of 10% FBS in 1x PBS. Cells were spun down at 800 x g for 5 minutes, re-suspended in 10% FBS with a Near-IR dead dye (Life Technologies) and strained through a 40µm mesh prior to FACS. Mesp1Cre-marked cells were isolated by FACS and collected in cold 1x PBS; 0.01%BSA solution.
Drop-seq protocol was performed according to Macosko et al. with the modification that a custom-built 90 μm Drop-seq microfluidic device was used for droplet generation, creating droplets smaller than the standard Drop-seq protocol

value: Mesp1Cre-marked cells isolated by FACS

value: Mixed sample (WT and Mut)


title: Hi-C_PPN1_rep1

source_name: PPN1 SCNT embryos

treatment_protocol: PPN1 SCNT embryos are collected 4 hours after activation.  MII oocytes were obtain at 13-14hrs after hCG injection. The spindle of oocyte was removed by the Piezo-driven (PrimeTech, Osaka, Japan) enucleation pipette on the Olympus inverted microscope (Tokyo, Japan), and the nuclei of donor cells were directly injected into the enucleated oocytes. The reconstructed oocytes were incubated in CZB medium for 1 hour before activation treatment. The cloned constructs were activated in Ca2+-free CZB medium supplemented with 10 mM SrCl2 (Sigma, Cat # 255521) and 5 μg/ml of cytochalasin B (Sigma, Cat # C-6762) for 4 hours. Cloned embryos were cultured in G1-Plus medium (Vitrolife, Cat # 10132) at 37.5 °C in an atmosphere of 5% CO2 in air. The first polar body was removed by enucleation pipette on the micromanipulator, while the zona pellucida was gently removed by treatment with acid Tyrode’s solution (Sigma, Cat # T-1788) for several minutes.

value: SCNT PPN1


title: Mut rep2

description: Drop-seq

source_name: Mesp1Cre-sorted E8.25 mesoderm from Mesp1-Cre/+;R26-Gli3R-IRES-Venus/+ embryos

value: Mut


title: 19141_N

description:
nuclear RNA
Yoruban Individuals

source_name: Imortalized Lymphoblastoid cell line

value: Imortalized Lymphocyte

value: M


title: 18870_T

description:
total RNA
Yoruban Individuals

value: F


title: E14+GFP_c1_1

value: GFP stable overexrpession

value: embryonic stem cell

value: serum/LIF


title: RNA_SCNT_8C_MEF_rep1


title: Mut rep1

description: Drop-seq


title: E14+Dppa4_c6_3

source_name: Dppa4-GFP stable overexpression clone 6

value: Dppa4-GFP stable overexpression

value: E14 ESC


title: RNA_SCNT_Late2C_rep2

value: SCNT Late-2cell


title: 18870_N

description:
nuclear RNA
Yoruban Individuals


title: Hi-C_PPN1_rep2


title: WT rep2

description: Drop-seq

source_name: Mesp1Cre-sorted E8.25 mesoderm from Mesp1-Cre/+;R26-tdTomato/+ embryos

value: WT


title: E14+GFP_c2_1


title: 18853_T

description:
total RNA
Yoruban Individuals


title: RNA_SCNT_Late2C_rep1


title: E14+Dppa4_c6_2


title: E14+Dppa4_c6_1


title: WT rep1

description: Drop-seq


title: 18853_N

description:
nuclear RNA
Yoruban Individuals


title: RNA_PPN5_rep2

value: SCNT PPN5


title: 18508_T

description:
total RNA
Yoruban Individuals


title: E14+Dppa4_c5_3

source_name: Dppa4-GFP stable overexpression clone 5


title: Mouse_proB_WT_Ythdf2_RIP_rep2

first: Ruitu

last: Lyu

address: 929 E 57th Street

department: Chemistry

institute: The University of Chicago

data_processing:
MeRIP-seq
Base-calling was performed using CASAVA.
MeRIP-seq and Input sequencing data were sent to trim-galore to remove low quality reads and adaptor sequence contaminants under default parameters except for “–length 50,”
Remaining reads were then aligned to the mouse transcriptome annotation based on mm9 assembly using hisat2 aligner (v2.1.0), default parameters were used.
m6A peaks and Mett14 dependent  m6A  peaks were identified using exomePeak R/Bioconductor package with default parameters.
Profiles of m6A tag density in Ctrl and Mett14KO proB cells on m6A peaks are generated by plotProfile tool in deeptools 2.0 tool suite.
Genome_build: mm9
Supplementary_files_format_and_content: bed
RIP-Seq
Base-calling was performed using CASAVA.
RIP-seq and Input sequencing reads were aligned to the mouse transcriptome annotation based on mm9 assembly using hisat2 aligner (v2.1.0), default parameters were used.
Fpkm value of samples were generated by cufflinks
Reads count of samples were called by featureCounts function in Rsubread package
Genome_build: mm9
Supplementary_files_format_and_content: csv

source_name: proB cell

growth_protocol: B220+ cells were enriched and cultured in the presence of IL-7 for 5 days.  WT and Mettl14 KO CD19+CD2-Igκ/λ- cells were sorted and subject to m6A-seq analysis (n=2 for WT group and n=1, pooled from 3 mice, for Mettl14 KO group).

extract_protocol:
Total RNA was extracted with Trizol, polyA RNA was enriched with the Dynabeads mRNA Purification Kit (cat# 61006), RNA was fragmented to ~200nt with sonication, and m6A IP was performed with the EpiMark N6-Methyladenosine Enrichment Kit (cat# E1610S)
Library constructed with the SMARTer Stranded Total RNA-Seq Kit v.2 (cat# 634412)

value: wild type


title: E14+GFP_c1_2

extract_protocol:
RNAseq: Total RNA was isolated using TriReagent (Sigma) or RNA-DNA allprep columns (Qiagen) 0.5-1mg DNAse treated (Thermo Fisher EN0525).
ChIPseq: Ten million cells were fixed in 1% formaldehyde (Fisher Scientific 28906) in DMEM (Invitrogen 41966-052) for 10 minutes, quenched in 0.125M glycine, and scraped off cell culture dishes using cell scrapers. Cells were lysed with buffers LB1 (50mM Hepes-KOH (pH 7.5), 140mM NaCl, 1mM EDTA, 10% Glycerol, 0.5% Igepal CA-630, 0.25% Triton-X 100), LB2 (10mM Tris-HCl (pH 8.0), 200mM NaCl, 1mM EDTA, 0.5mM EGTA), and LB3 (10mM Tris-HCl (pH 8.0), 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine, 1x Protease Inhibitors (Roche)) consecutively, before fragmenting chromatin by sonicating for 30 cycles of 30s ON high /30s OFF (Diagenode Bioruptor). For each ChIP, 5µg antibody (anti-Ash2l Bethyl Labs A300-489, anti-Ezh2 CST D2C9, anti-H2A.Z Abcam ab4174, anti-H3K4me3 Abcam ab8580, anti-H3K27me3 Active Motif AM39155, anti-IgG Abcam ab125938, anti-Ring1b CST D22F2) was pre-bound to protein G dynabeads (Invitrogen) and blocked with 0.5% BSA in PBS. Sonicated DNA was added to antibody-bound beads with 10% Triton-X 100 and incubated overnight at 4°C on a rotator. Beads and DNA were washed 6 times with RIPA buffer (50mM HEPES-KOH (pH 7.6), 1mM EDTA, 0.7% Na-Deoxycholate, 1% Igepal CA-630, 0.5M LiCl), followed by one wash in 1x TBS and overnight incubation at 65°C with elution buffer (50 mM Tris- HCl, pH 8; 10 mM EDTA; 1% SDS). For precipitation of chromatin, samples were treated with RNase A and Proteinase K. DNA was purified using MinElute PCR purification columns (Qiagen 28006) and eluted in 30µL of TE. DNA was quantified using HS DNA Qubit (ThermoFisher) or PicoGreen (ThermoFisher) assays.
ATACseq: 10,000 cells were trypsinised and immediately processed for ATACseq.
NOMEseq: Cells were fixed on 15cm plates wih Fixation solution (Active-Motif) for 10minutes at room temperature then processed according to Active Motif NOME-seq kit protocol.
RNAseq: Opposite strand-specific polyA RNA libraries were made using 1 µg of DNase- treated RNA at the Sanger Institute Illumina bespoke pipeline and sequenced using the Illumina HiSeq2 platform.
ChIPseq: libraries generated using MicroPlex Library Preparation Kit (Diagenode) following the manufacturer?s instructions. Libraries were quality controlled using bioanalyser HS DNA chips (Agilent) and single-end 50bp reads sequenced using the Illumina HiSeq2 sequencing platform.
ATACseq: ATAC-seq libraries were performed as previously described (Buenrostro, Wu, Chang, & Greenleaf, 2015) with the following modification to use on 10,000 cells: initial transposition reaction was performed with 10,000 cells, 10ml 2x TD buffer, 0.5ml Tn5 enzyme and 9.5ml H2O for 30minutes at 37 degrees Celsius. A total of 15 cycles of amplification were used. Two technical replicates were performed per clone, with 3 WT and 3 Dppa2/4 DKO clones used (total of 12 samples).
NOMEseq: Whole genome bisulfite libraries were generated using NOME-seq kit from Active Motif (103946) according to manufacturer?s instructions with 6 cycles of amplification for 2 WT clones (clones 57 and 58) and 1 Dppa2/4 DKO clone (clone 43).


title: RNA_SCNT_8C_MEF_rep2

value: SCNT 8-cell_MEF

value: embryo


title: RNA_PPN5_rep1


title: 18508_N

description:
nuclear RNA
Yoruban Individuals


title: E14+Dppa4_c5_2


title: Mouse_proB_WT_Ythdf2_RIP_Input_rep2


title: E14+Dppa4_c5_1


title: RNA_PPN3_rep2

value: SCNT PPN3


title: 18505_T

description:
total RNA
Yoruban Individuals


title: Mouse_proB_WT_Ythdf2_RIP_Input_rep1


title: E14+Dppa2_c5_3

source_name: Dppa2-GFP stable overexpression clone 5

value: Dppa2-GFP stable overexpression


title: RNA_PPN1_rep2

value: SCNT PPN1


title: Mouse_proB_Mettl14KO_Ythdf2_RIP_rep1

value: Mettl14 Knockout


title: E14+Dppa2_c5_2


title: E14+Dppa2_c5_1


title: RNA_PCC_rep2

treatment_protocol: PCC SCNT embryos are collected one hour after the donor nucleus get injected into the enucleated MII oocytes. The reconstructed oocytes were incubated in CZB medium. The first polar body was removed by enucleation pipette on the micromanipulator, while the zona pellucida was gently removed by treatment with acid Tyrode’s solution (Sigma, Cat # T-1788) for several minutes.

value: SCNT PCC


title: 18501_T

description:
total RNA
Yoruban Individuals

value: Imortalized Lymphocyte

value: M


title: 18501_N

description:
nuclear RNA
Yoruban Individuals


title: E14+Dppa2_c3_3

source_name: Dppa2-GFP stable overexpression clone 3

value: embryonic stem cell


title: 18499_T

description:
total RNA
Yoruban Individuals


title: Mouse_proB_Mettl14KO_Ythdf2_RIP_Input_rep1


title: Mouse_proB_Mettl14KO_m6A_IP.rep1

data_processing:
Library strategy: MeRIP-seq
MeRIP-seq
Base-calling was performed using CASAVA.
MeRIP-seq and Input sequencing data were sent to trim-galore to remove low quality reads and adaptor sequence contaminants under default parameters except for “–length 50,”
Remaining reads were then aligned to the mouse transcriptome annotation based on mm9 assembly using hisat2 aligner (v2.1.0), default parameters were used.
m6A peaks and Mett14 dependent  m6A  peaks were identified using exomePeak R/Bioconductor package with default parameters.
Profiles of m6A tag density in Ctrl and Mett14KO proB cells on m6A peaks are generated by plotProfile tool in deeptools 2.0 tool suite.
Genome_build: mm9
Supplementary_files_format_and_content: bed
RIP-Seq
Base-calling was performed using CASAVA.
RIP-seq and Input sequencing reads were aligned to the mouse transcriptome annotation based on mm9 assembly using hisat2 aligner (v2.1.0), default parameters were used.
Fpkm value of samples were generated by cufflinks
Reads count of samples were called by featureCounts function in Rsubread package
Genome_build: mm9
Supplementary_files_format_and_content: csv


title: 18499_N

description:
nuclear RNA
Yoruban Individuals


title: RNA_PCC_rep1


title: E14+Dppa2_c3_2

value: serum/LIF


title: Mouse_proB_WT_Ythdf2_RIP_rep1


title: 18486_T

description:
total RNA
Yoruban Individuals


title: Mouse_proB_WT_Input.rep2


title: RNA_PPN3_rep1


title: WT_4h_rep3

city: Planegg-Martinsried

first: Vigo

last: Heissmeyer

state: Bayern

address: Großhaderner Str. 9

department: Institute for Immunology

country: Germany

institute: Ludwig-Maximilians-Universität

data_processing:
The reads were mapped with STAR1 (version 2.3.1z4) against the mouse genome (GRCm38)
Read counts for genes were derived in two ways: 1. counting read pairs fully contained within annotated genes and 2. counting only read pairs fully consistent with at least one annotated transcript using the ENSEMBL2 annotation GRCm38.75.
Differential analysis: Based on these two count types we   performed a robust differential analysis: we derived three down-sampled count variants: (i) raw read  counts (ii) unique fragment counts (i.e. read pairs mapped exactly to the same genomic positions are only counted once) and (iii) down-sampled counts as proposed in Erhard and Zimmer3. We performed then on all resulting 6 count tables differential analysis using four methods: DESeq4, edgeR5, limma6 and empiRe7. The resulting 6x4=24 outcomes with estimated log2(FC) (FC = fold change) values and multiple-testing corrected p-values were then in turn used to derive a conservative combined differential analysis table: for every gene in a given condition pair we selected the least significant (maximum) p-value (columns with suffix worst_fdr) from these 24 combinations and the weakest log2(FC) (i.e. the one with minimum abs(log2(FC))) (columns log2fc). If the direction of the log2(FC) estimates  was inconsistent (i.e. some where > 0 and some <0) we set the corresponding log2(FC) to zero.
Genome_build: GRCm38
Supplementary_files_format_and_content: roquin_regnase_tcell_knockout_timecourses_with_readinfos.csv (For each gene normed counts per sample (replicate data in columns with suffix counts, robust log2fc-s and fdr-s (see data processing steps above))

source_name: CD4 T cells

growth_protocol: CD4 T cells were isolated from spleens of Cd4-Cre-ERt2 (WT), Rc3h1/2 fl/fl; Cd4-Cre-ERt2 (iDKO), Zc3h12a fl/fl; Cd4-Cre-ERt2 (iKO) or Rc3h1/2 fl/fl; Zc3h12a fl/f; Cd4-Cre-ERt2 (iTKO) mice and the KO of respective genes induced via 4´-OH-tamoxifen treatment.  Afterwards, the T cells were activated in vitro with anti-CD3/28 under Th1 conditions for 40h, cultivated for further 2 days in IL-2 containing media, and with or without restimulation with anti-CD3/28 subjected for RNA isolation and RNA Seq.

extract_protocol:
T cells were pelleted, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using Universal RNA-Seq Library Preparation Kit (NuGEN)

treatment_protocol: T cells were either left untreated (0h) or restimulated for 1h, 2h or 4 with anti-CD3/28.

value: spleen

value: Splenic CD4 T cells

value: Cd4-Cre-ERt2 (WT)

value: Restimulation with anti-CD3/28 for 4h


title: Mouse_proB_WT_Input.rep1


title: WT_4h_rep4


title: E14+Dppa2_c3_1

treatment_protocol: Stable overexpression cell lines were generated using Lipofectamine 2000 on preplated cells and resistant cells selected with appropriate antibiotics for at least 1 week before sorting single cells into 96 well plates by flow cytometry using a BD Aria III or BD Influx high-speed cell sorter, and clonal expansion. CRISPR double knockout ESC line (clone 43) was described previously (M. Eckersley-Maslin et al., 2019), and additional CRISPR double knockout ESC lines (clone 37 and clone 53) generated as previously described (M. Eckersley-Maslin et al., 2019). For embryoid bodies, 2x106 mESCs were cultured on 10cm low-attachment dishes in standard ESC medium containing all described components except LIF.

value: E14 ESC


title: Dppa_WT_serum_Mc3_C

description:
DNaseI treated total RNA
Processed_data_ESC_RNAseq_RPM_allgenes.txt

source_name: Dppa2/4 WT parental line (no CRISPR)

value: Dppa2/4 WT parental line (no CRISPR)

value: E14 ESCs, contains MERVL::tdTomato reporter


title: 18505_N

description:
nuclear RNA
Yoruban Individuals

value: F


title: 18486_N

description:
nuclear RNA
Yoruban Individuals


title: WT_4h_rep2


title: RNA_PPN1_rep1

value: embryo


title: Dppa_WT_serum_Mc3_B


title: Mouse_proB_WT_m6A_IP.rep1

value: wild type


title: WT_4h_rep1


title: WT_2h_rep4

value: Restimulation with anti-CD3/28 for 2h


title: T47D_ULA_1

city: Pittsburgh

first: Kevin

last: Levine

state: Pennsylvania

address: 204 Craft Ave

institute: University of Pittsburgh

data_processing:
Raw sequence data were mapped to hg38 genome (ensembl release version 82) and transcript counts were quantified with Salmon (version 0.8.2)
Transcript counts were converted to gene-level counts using tximport and biomaRt with hsapiens_gene_ensembl, sep2015.archive.ensembl.org
Genome_build: hg38
Supplementary_files_format_and_content: csv file containing gene counts for all samples using salmon and tximport

growth_protocol: MDA-MB-134-VI (MM134) and SUM44PE (SUM44) ILC cell lines and MCF7 and T47D IDC cell lines were grown in 2D or ultra-low attachment (ULA) plates for 24 hours

extract_protocol:
RNA was isolated using Illustra RNAspin Mini Kit
TruSeq Stranded Total RNA Library Prep Kit was used for library preparation according to Illumina standard protocols

tag: cell line

value: invasive ductal carcinoma (IDC) cell line

tag: culture type

value: ultra-low attachment (ULA) suspension


title: SKO+Flag  day 8 replicate 1

data_processing:
Illumina bcl2fastq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments per Kilobase per Millon Mapped Fragments (FPKM) were calculated using a protocol from Trapnell,C.et al, 2010(replicate 1);Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009(replicate 2). In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM /rpkm values for each Sample ...

source_name: mouse embryonic cell infection with retrovirus SKO+Flag

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

tag: genotype/variation

value: SKO+Flag

value: ICR

tag: tissue

value: mouse embryonic fibroblast cell

tag: age

value: day 8 in reprogramming process


title: WT_2h_rep3

value: spleen


title: T47D_ULA_3


title: T47D_ULA_2


title: Dppa_WT_serum_58_B

data_processing:
EB RNA-seq raw FastQ data were trimmed with Trim Galore (version 0.4.4, default parameters) and mapped to the mouse GRCm38 genome assembly using Hisat2 version 2.1.0. Stable overexpression clone data used Trim Galore v0.5.0_dev and HiSat2 v2.1.0.
ChIP-seq Raw FastQ data were trimmed with Trim Galore v0.6.1 and aligned to mouse GRCm38 genome using Bowtie 2 v 2.3.2.
ATAC-seq Raw FastQ data were trimmed with Trim Galore (v0.5.0_dev) using standard parameters and aligned using Bowtie 2 v2.3.2.
NOME-seq Raw fastQ data were trimmed using Trim Galore version 0.4.4 using standard parameters, reads aligned using Bismark v0.18.2
All downstream data processing was performed using SeqMonk software (https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/).
Genome_build: mm10
Supplementary_files_format_and_content: The ChIP and ATAC is enrichment RPM over 1kb running windows. The RNA-seq is all genes RPM and the NOME-seq is 100CpG running window % methylation.  The files were generated using SeqMonk (exporting an annotated probe report).

source_name: Dppa2/4 WT clone 58

value: Dppa2/4 WT

value: embryonic stem cell

value: serum/LIF

value: CRISPR targetted E14 ESCs, contains MERVL::tdTomato reporter


title: Dppa_WT_serum_58_C


title: Dppa_WT_serum_Mc3_A

value: Dppa2/4 WT parental line (no CRISPR)


title: WT_2h_rep2

value: Splenic CD4 T cells

value: Cd4-Cre-ERt2 (WT)


title: Dppa_WT_serum_58_A


title: WT_2h_rep1


title: SKO+Glis1 day 8 replicate 1

source_name: mouse embryonic cell infection with retrovirus SKO+Glis1


title: T47D_2D_1

value: attached (2D)


title: T47D_2D_2


title: Dppa_WT_serum_57_C

source_name: Dppa2/4 WT clone 57


title: Mouse_proB_WT_m6A_IP.rep2

value: wild type

tag: antibody


title: KO H3K9ac_ChIPSeq

city: Detroit

first: Qing-Sheng

last: Mi

state: Michigan

address: One Ford Place

department: Dermatology

institute: Henry Ford Health System

data_processing:
bcl2fastq v2.20.0.422 conversion software used for basecalling.
Raw ChIP-seq reads were quality checked using the software FastQC version v0.10.1 and processed using BBDuk (v36.19) and seqtk (v1.2-r94, https://github.com/lh3/seqtk) to trim the adapters and low-quality bases, respectively.
The trimmed reads were then aligned to the mouse mm10 genome sequence using Bowtie2 (v2.2.5) and only uniquely matching reads were retained.
Mapping results of each ChIP and the input sample were subjected to ChIP enriched peak calling using the MACS2 (v2.1.1.20160309).
Peak annotation was conducted using ChIPseeker.
Genome_build: mm10
Supplementary_files_format_and_content: Excel files include PeakID, chromosome, start and end site, strand, peak score, focus ratio/region size, annotation, detailed annotation, distance to TSS, nearest promoterID, Entrez ID, nearest Unigene, nearest Refseq, nearest Ensembl, gene name, gene alias, gene description, gene type, fold_enrichment, -LOG10(pvalue), -LOG10(qvalue) and pileup for each Sample.
Supplementary_files_format_and_content: bedGraph files

source_name: alveolar macrophage

extract_protocol:
The CD45+CD11c+SiglecF+  lung alverolar macrophages (AMs) were sorted by FACS Aria II flow cytometer. Cell pellets from the freshly isolated AMs were directly frozen at -80°C. The samples were then submitted to EpiGentek for ChIP, library preparation, and sequencing.
The cells were fixed with 1% formaldehyde and chromatin was isolated using ChromaFlashTM Chromatin Extraction Kit. Chromatin was sheared using the Episonic2000 Sonicatin System. ChIP was performed using an antibody against HDAC3, H3K27ac or H3K9ac on the chromatin and Input DNA (without immunoprecipitation) was used as background. After adapter linking, library was size-selected (100-300 bp) and PCR-amplified. Ten nanomolar of sample libraries were provided for next generation sequencing.

value: FVB/NJ backcross to C57BL/6 over 10 generations

value: lung

value: alveolar macrophage

value: 8-12 weeks

value: HDAC3 KO

value: H3K9ac (Epigentek, Cat. #A4022)


title: WT H3K9ac_ChIPSeq

value: wild-type


title: Dppa_WT_serum_57_B


title: input DNA


title: KO H3K27ac_ChIPSeq

value: H3K27ac (Epigentek, Cat. #A4753)


title: WT_1h_rep4

value: spleen

value: Restimulation with anti-CD3/28 for 1h


title: WT_1h_rep3


title: SUM44_ULA_2

value: Invasive lobular carcinoma (ILC) cell line

value: ultra-low attachment (ULA) suspension


title: WT_1h_rep2


title: T47D_2D_3

value: invasive ductal carcinoma (IDC) cell line


title: SUM44_ULA_1


title: WT_1h_rep1

value: Splenic CD4 T cells


title: Dppa_DKO_serum_53_B

source_name: Dppa2/4 DKO clone 53

value: Dppa2/4 DKO

value: embryonic stem cell

value: serum/LIF

value: CRISPR targetted E14 ESCs, contains MERVL::tdTomato reporter


title: WT H3K27ac_ChIPSeq

value: FVB/NJ backcross to C57BL/6 over 10 generations

value: lung


title: SUM44_2D_3

value: attached (2D)


title: Dppa_DKO_serum_53_C


title: WT HDAC3_ChIPSeq

value: alveolar macrophage

value: 8-12 weeks

value: HDAC3 (Abcam, Cat# ab7030)


title: KO HDAC3_ChIPSeq

value: HDAC3 KO


title: Dppa_DKO_serum_53_A


title: SUM44_2D_2


title: WT_0h_rep4

value: spleen

value: Cd4-Cre-ERt2 (WT)

value: untreated


title: Dppa_DKO_serum_43_C

source_name: Dppa2/4 DKO clone 43


title: WT_0h_rep2


title: LungMF KO scRNASeq

data_processing:
Paired-end read counts for all known murine genes underwent barcode and unique molecular identifier (UMI) deconvolution, and were subsequently aligned to the mm10 reference genome using the 10X Cell RangerTM [v2.1] pipeline.
2,000-3,000 cells were captured, with 53,000-73,000 mean reads per cell, with 1,200-1,300 median genes per cell. Datasets were subsequently analyzed using R package Seurat’s Canonical Correlation Analysis (CCA) workflow to characterize the differences between pooled samples.
The following quality control metrics were employed. To identify potential doublets, cells expressing uncharacteristically high numbers of genes (>2,500) were excluded (double the median number of genes). Low quality cells were excluded based on a low number of genes detected (<300) or having high mitochondrial genetic content (>5.0%). Additionally, uninteresting sources of variation within the data were removed. Genes removed include sex specific genes (Xist and all Y chromosome genes), ribosomal structural proteins (as identified by gene ontology term GO:0003735 and RPG: Ribosomal Protein Gene database (41), non-coding rRNAs, Hbb, and genes expressed in < 3 cells.
Samples have 3 fastq files associated with them with a tag in the filename such R1,R1, I1. The I1 contains the sample index. The R1 contains the 10x barcode (16 base pairs) followed by UMI (10 bp). The R2 contains the transcript read.
Genome_build: mm10
Supplementary_files_format_and_content: [LGF_1.data.txt, LGF_2.data.txt]  The data slot stores normalized and log-transformed single cell expression. This maintains the relative abundance levels of all genes, and contains only zeros or positive values. This data is used for visualizations, such as violin and feature plots, most differential expression tests, finding high-variance genes, and as input to ScaleData.
[LGF_1.scale.data.txt, LGF_2.scale.data.txt]  The scale.data slot represents a cell’s relative expression of each gene, in comparison to all other cells. Therefore this matrix contains both positive and negative values. This data is used as input for dimensional reduction techniques, and is displayed in heatmaps

extract_protocol:
The CD45+CD11c+SiglecF+  lung alverolar macrophages (AMs) were sorted by FACS Aria II flow cytometer. 5,000 FACS-sorted cells were loaded into each reaction for gel bead-in-emulsion (GEM) generation and cell barcoding.
Single cell sequencing libraries were generated using the 10X Genomics Chromium Single Cell 3’ Reagent Kit (v2 Chemistry) and Chromium Single Cell Controller. Reverse transcription of the GEM (GEM-RT) was performed in a Thermocycler (Veriti™ 96-Well Fast Thermal Cycler, Applied Biosynthesis; 53 °C 45 min, 85 °C 5 min, 4 °C hold). cDNA amplification was performed after GEM-RT cleanup with Dynabeads MyOne Silane (Thermo Fisher Scientific) with the same Thermocycler (98 °C 3 min; 98 °C 15 sec, 67 °C 20 sec, 72 °C 1 min, repeat 12 cycles; 72 °C 1 min, 4 °C hold). Amplified cDNA is cleaned up with SPRIselect Reagent Kit (Beckman Coulter) and followed by library construction procedure, including fragmentation, end repaired, adaptor ligation, and library amplification. A Bioanalyzer (Agilent) was used for library quality control. Libraries were sequenced on an Illumina HiSeq4000 using paired-end flow cell: Read 1, 26 cycles, i7 index 8 cycles; Read 2: 98 cycles.


title: SUM44_ULA_3

value: Invasive lobular carcinoma (ILC) cell line

value: ultra-low attachment (ULA) suspension


title: SUM44_2D_1


title: WT_0h_rep3

value: Splenic CD4 T cells


title: Dppa_DKO_serum_43_A

value: Dppa2/4 DKO


title: MM134_ULA_3


title: WT_0h_rep1


title: LungMF E18.5 HDAC3 KO-3

description:
LG MF E18.5 Expression Browser Raw.xlsx
80335

data_processing:
bcl2fastq v2.17.1.14 conversion software used for basecalling.
The RNA-Seq reads were aligned to the mouse GRCm38/mm10 reference genome using Biomedical Genomics Workbench 4 (QIAGEN).
The expression levels for each sample were quantified and normalized usingBiomedical Genomics Workbench 4 (QIAGEN).
Genome_build: mm10
Supplementary_files_format_and_content: Excel file includes gene name, chromosome, region, identifier, KO vs. WT-Max group means, KO vs. WT-Fold change, KO vs. WT-Log fold change, KO vs. WT-P-value, KO vs. WT-FDR p-value, KO vs. WT- FDR-Bonferroni, Total counts and RPKM values for each Sample

source_name: fetal lung immature alveolar macrophage (preAM)

extract_protocol:
The CD45+F4/80loCD11blo lung preAMs were sorted by FACS Aria II flow cytometer. Total RNA was extracted from the sorted cells with miRCURY RNA Isolation Kit - Cell & Plant (Exiqon). cDNA library was generated using SMART-Seq v4 Ultra Low Input RNA Kit (Clontech).
cDNA was pre-amplified by a thermal cycler (Applied Biosystem) using 12-14 cycles and sheered into 150-400 bp fragments using Bioruptor Pico sonicator (Diagenode). The DNA ends were repaired using End-It™ DNA End-Repair Kit (Epicentre). The end repaired DNA fragments were ligated to adaptors by T4 ligase (NEB) after a single “A” was added at 3’ by Klenow Fragment (3’→5’ Exo-) (NEB). MinElute Reaction Cleanup Kit (Qiagen) was used for DNA cleanup after each step. Illumina P5 and P7 primers with individual adaptors were used for final library amplification. The 150-400 bp final product was purified on a 2% E-gel (Thermo Fisher Scientific).

value: embryonic day 18.5


title: Dppa_WT_serum_57_A

value: Dppa2/4 WT

value: embryonic stem cell

value: serum/LIF


title: LungMF WT scRNASeq

value: FVB/NJ backcross to C57BL/6 over 10 generations

value: lung

value: wild-type


title: Dppa_DKO_serum_36_C

source_name: Dppa2/4 DKO clone 36

value: CRISPR targetted E14 ESCs, contains MERVL::tdTomato reporter


title: TKO_4h_rep4

value: Rc3h1/2 fl/fl; Zc3h12a fl/fl; Cd4-Cre-ERt2 (TKO)

value: Restimulation with anti-CD3/28 for 4h


title: LungMF E18.5 HDAC3 KO-2

description:
LG MF E18.5 Expression Browser Raw.xlsx
80334

value: fetal lung immature alveolar macrophage (preAM)

value: HDAC3 KO


title: Dppa_DKO_serum_36_B


title: MM134_ULA_1


title: TKO_4h_rep3

value: spleen


title: LungMF E18.5 HDAC3 KO-1

description:
LG MF E18.5 Expression Browser Raw.xlsx
80333


title: Dppa_DKO_serum_36_A


title: MM134_2D_3

value: Invasive lobular carcinoma (ILC) cell line

value: attached (2D)


title: TKO_4h_rep2

value: Splenic CD4 T cells


title: LungMF E18.5 WT-3

description:
LG MF E18.5 Expression Browser Raw.xlsx
80332


title: MM134_2D_2


title: SKO+Flag  day 8 replicate 2

description: rpkm.anno

value: SKO+Flag

value: ICR

value: mouse embryonic fibroblast cell

value: day 8 in reprogramming process


title: TKO_4h_rep1


title: LungMF E18.5 WT-2

description:
LG MF E18.5 Expression Browser Raw.xlsx
80331

value: embryonic day 18.5


title: MM134_2D_1


title: LungMF E18.5 WT-1

description:
LG MF E18.5 Expression Browser Raw.xlsx
80330

value: FVB/NJ backcross to C57BL/6 over 10 generations


title: BloodSample144Chemo: 1Radiation: 1

city: Los Angeles

first: Mary

middle: Elizabeth

last: Sehl

state: CA

address: 100 UCLA Medical Plaza, Suite 550

department: Medicine / Hematology-Oncology

institute: UCLA

hyb_protocol: Illumina protocol

scan_protocol: Illumina protocol

data_processing: Noob normalization using preprocessNoob in the minfi R package

label: Cy3, Cy5

source_name: BloodSample144Chemo: 1Radiation: 1

label_protocol: Bisulfite conversion was performed on 500 ng of DNA using the llumina Infinium Methylation Assay protocol in the EZ DNA Methylation kit (Zymo Research). Next the samples were loaded onto the Infinium Human MethylationEPIC BeadChip

extract_protocol: Genomic DNA of whole blood samples

tag: time point

tag: chemotherapy any

tag: radiationtherapy any

tag: female

tag: batch number


title: BloodSample143Chemo: 1Radiation: 1

source_name: BloodSample143Chemo: 1Radiation: 1


title: MCF7_ULA_3

tag: cell type

value: invasive ductal carcinoma (IDC) cell line

value: ultra-low attachment (ULA) suspension


title: BloodSample142Chemo: 1Radiation: 1

source_name: BloodSample142Chemo: 1Radiation: 1


title: MCF7_ULA_2


title: MCF7_ULA_1


title: MM134_ULA_2


title: TKO_2h_rep3

tag: strain

tag: genotype

value: Restimulation with anti-CD3/28 for 2h


title: TKO_2h_rep1

value: Rc3h1/2 fl/fl; Zc3h12a fl/fl; Cd4-Cre-ERt2 (TKO)


title: TKO_2h_rep2


title: TKO_2h_rep4


title: MCF7_2D_3


title: BloodSample140Chemo: 0Radiation: 1

source_name: BloodSample140Chemo: 0Radiation: 1


title: TKO_1h_rep4

value: Restimulation with anti-CD3/28 for 1h


title: MCF7_2D_2


title: SKO+Glis1 day 8 replicate 2

description: rpkm.anno


title: TKO_1h_rep3


title: OCI-AML3 alone rep 3

city: Houston

first: Venkata

middle: Lokesh

last: Battula

state: Texas

address: 1515 holcombe blvd

department: Leukemia

institute: MD Anderson Cancer Center

data_processing:
Samples were sequenced on the HiSeq Sequencing System by the Sequencing and Microarray Core facility at MD Anderson Cancer Center
Sequence reads were mapped to human genomics (build hg19) with bowtie2 aligner using RSEM software
The EdgeR package in R software was used to compare the differential expression between OCI-AML3 cells cultured alone or with BM-MSCs
Genes with adjusted p values less than 0.05 and absolute fold changes larger than 2 were considered significant
Genome_build: build hg19
Raw data file format and content: Raw data are unavailable for this submission because the files had been permanantly deleted prior to the submission date

source_name: OCI-AML3 leukemia cell line

growth_protocol: OCI-AML3 cells were cultured in RPMI medium supplemented with fetal bovine serum 10% and 1% penicillin/streptomycin. Human marrow stromal cells were isolated from bone marrow harvested from healthy patient donors for use in allogeneic stem cell transplantation

extract_protocol:
Five million cells were lysed in Trizol reagent overnight at -80°C,  total RNA was isolated by ethanol precipitation
RNA libraries were prepared for sequencing using standard illumina protocols

treatment_protocol: OCI-AML3 cells were cultured in tissue culture flasks with or without bone marrow stromal cells at 5:1 ratio for 3 to 5 days in CO2 incubator

value: Adult Acute myeloid leukemia cell line derived from a 57 year old male

tag: condition

value: seeded alone


title: OCI-AML3 with BM-MSCs rep 3

description: Raw data are unavailable for this submission because the files had been permanantly deleted prior to the submission date

source_name: OCI-AML3 leukemia cell line with human marrow stromal cells

value: seeded with human bone marrow stromal cells derived from healthy donors at 5:1 ratio


title: OCI-AML3 with BM-MSCs rep 1

source_name: OCI-AML3 leukemia cell line co-cultured with human marrow stromal cells


title: OCI-AML3 with BM-MSCs rep 2


title: BloodSample139Chemo: 1Radiation: 1

source_name: BloodSample139Chemo: 1Radiation: 1


title: MCF7_2D_1


title: TKO_1h_rep2

source_name: CD4 T cells

value: spleen

tag: treatment


title: BloodSample138Chemo: 1Radiation: 1

source_name: BloodSample138Chemo: 1Radiation: 1


title: OCI-AML3 alone- rep 1


title: TKO_1h_rep1


title: BloodSample137Chemo: 1Radiation: 1

source_name: BloodSample137Chemo: 1Radiation: 1


title: BloodSample141Chemo: 0Radiation: 1

source_name: BloodSample141Chemo: 0Radiation: 1


title: BloodSample136Chemo: 1Radiation: 1

source_name: BloodSample136Chemo: 1Radiation: 1


title: NAM_treated AT3 tumor Rep 2

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

data_processing:
Sequencing, data quality, reads repartition (e.g., for potential ribosomal contamination), and insert size estimation were performed using FastQC, Picard-Tools, Samtools and rseqc
Reads were mapped using STAR_2.4.0
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file includes deseq2 normalized expression values for each gene and for each sample. Annotations from Mouse FAST DB v2016_1 were also provide

source_name: mammary gland tumor

growth_protocol:
M/D: Fifty mg slow-release (90 days) medroxyprogesterone acetate (MPA) pellets (Innovative Research of America) were implanted subcutaneously by surgery into 6-9 week-old female (day 0). Mice were administered 200 µL of a 5 mg mL-1 7,12-dimethylbenz[a]anthracene (DMBA; from Sigma-Aldrich) solution in corn oil (Sigma-Aldrich), by oral gavage once a week on weeks 1, 2, 3, 5, 6 and 7 after implantation of the MPA pellet. When tumors reached 0.25cm2 the animals were randomized to the different treatment groups.
AT3: For tumorigenicity assays, 1.0 x 10^6 AT3 cells were injected subcutaneously. When tumors reached 0.25cm2 the animals were randomized to the different treatment groups.

extract_protocol:
Tumors were removed from the mice and RNA freshly extracted using Qiagen RNeasy kits.
mRNA libraries were prepared using the Truseq mRNA library prep kit (Illumina) and sequenced in paired end mode (2X75)

treatment_protocol: 0.5 % NAM was added to the drinking water for 10 days. Drinking water was changed once a week

tag: agent

value: NAM


title: TKO_0h_rep4

value: Splenic CD4 T cells

value: untreated


title: NAM_treated AT3 tumor Rep 1


title: BloodSample135Chemo: 1Radiation: 1

source_name: BloodSample135Chemo: 1Radiation: 1


title: OCI-AML3 alone rep 2

tag: cell line


title: Untreated AT3 tumor Rep 3


title: TKO_0h_rep2


title: IP XL1

city: Singapore

first: Polly Leilei

last: Chen

address: #12-01, MD6, 14 Medical Drive

department: Department of Anatomy

country: Singapore

institute: Cancer Science Institute of Singapore NUS

description:
IP of DAP3 replicate 1
Paired-end 50bp
processed data file: DAP3_eCLIP-seq_peaks.xlsx

data_processing:
Library strategy: eCLIP-seq
Raw data starting from fastq files are processed and analyzed by using CSI NGS Portal: https://csibioinfo.nus.edu.sg/csingsportal
eCLIP pipeline developed by Gene Yeo's lab was used to identify the peaks. The full protocol is available here: https://github.com/YeoLab/eclip
The peaks were annotated by ANNOVAR for the genes and the genomic regions. For the annotation, the mid-point (i.e. the base at the center) of the peaks are used rather than the entire region for simplicity.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: DAP3_eCLIP-seq_peaks.xlsx: The processed data file contains the peaks identified by eCLIP-Seq pipeline and the gene annotations added by ANNOVAR.

source_name: human esophageal squamous carcinoma cells

growth_protocol: RPMI medium 10% FBS.

extract_protocol:
Cell lysate was harvested according to eCLIP protocol.
Library was prepared according to eCLIP protocol.

value: esophageal squamous carcinoma cell line


title: IP XL2

description:
IP of DAP3 replicate 2
Paired-end 50bp
processed data file: DAP3_eCLIP-seq_peaks.xlsx


title: BloodSample134Chemo: 0Radiation: 1

source_name: BloodSample134Chemo: 0Radiation: 1


title: NAM_treated AT3 tumor Rep 3


title: Untreated AT3 tumor Rep 2


title: TKO_0h_rep1


title: BloodSample133Chemo: 1Radiation: 1

source_name: BloodSample133Chemo: 1Radiation: 1


title: KO_4h_rep4

value: Zc3h12a fl/fl; Cd4-Cre-ERt2 (KO)

value: Restimulation with anti-CD3/28 for 4h


title: Input XL2

description:
Size-matched input of DAP3 replicate 2
Paired-end 50bp
processed data file: DAP3_eCLIP-seq_peaks.xlsx


title: 3′-tag RNA-seq WT neuron

city: San Francisco

first: Ruilin

last: Tian

address: 675 Nelson Rising Lane, 3rd Floor

department: Institute for Neurodegenerative Diseases

institute: University of California, San Francisco

description:
3′-tag RNA-seq
WT_vs_PSAPKO.csv

data_processing:
For CROP-seq, Cellranger (version 3.1.0,10X Genomics) with default parameters was used to align reads and generate digital expression matrices from single-cell sequencing data. For 3'-tag RNA-seq, Salmon v0.14.1 was used to obtain transcript abundance counts
For CROP-seq, the Scanpy package (version 1.4.6) (Wolf et al., 2018) implemented in Python was used for downstream analysis of the digital expression matrices with mapped sgRNA identities. For 3'-tag RNA-seq, Gene-level count estimates were obtained using tximport v1.8.0
Differential gene expression analysis using DESeq2 v1.20.0
Genome_build: GRCh38
Supplementary_files_format_and_content: For the 3'-tag RNA seq data, files containing gene Enzemble ID, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj and Gene symbol are provided in Comma-separated values (.csv) format. For the CROP-seq data, expression matrices output by cellranger are provided in .h5 format.

source_name: Human iPSC-derived neuron

growth_protocol: Neuronal Medium without antioxidants

extract_protocol:
RNA was extracted using the Quick-RNA Miniprep Kit (Zymo; Cat. No. R1054), and RNA concentrations were determined with the Qubit RNA HS Assay Kit (Invitrogen; Cat. No. Q32855) on a Qubit 2.0 Fluorometer (Invitrogen; Cat. No. Q32866)
Libraries were prepared by UC Davis Genome Center according to the 3'-Tag RNA seq protocol

value: human neuron

value: WT