title: H3K27ac wtEpiSCs 24h rep1

description: ChIP-seq

data_processing:
Mapping: Bowtie (1.1.0), parameters: -m 1 --best --strata --chunkmbs 512 -S –phred64-quals -q -l 40 -n 1
Read cleanup: Samtools (0.1.19), SAM files were converted to BAM files with and duplicate reads were removed with rmdup
Peak calling: MACS2 (2.1.0), parameters: callpeak -B -p 1e-5 -g mm –SPMR --nomodel --extsize 300 --llocal 100000
Input control: Input_wtEpiSCs_15min_fix2
Peak calling on pooled: H3K27ac wtEpiSCs 24h rep1 & H3K27ac wtEpiSCs 24h rep2
Input control for pooled: Input_wtEpiScs_10min_fix1
genome build: mm9
processed data files format and content: bed and bw

source_name: H3K27ac wtEpiSCs 24h rep1

extract_protocol:
Crosslinking 10mins RT, lysis, sonication and immunoprecipiation following standard procedures.
Illumina Truseq DNA library protocol

value: Abcam, ab4729


title: Input wtEpiSCs 10min fix1

status: Public on Dec 20 2016

type: SRA

city: Utrecht

first: Jacqueline

last: Deschamps

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: ChIP-seq

library_source: genomic

data_processing:
Mapping: Bowtie (1.1.0), parameters: -m 1 --best --strata --chunkmbs 512 -S –phred64-quals -q -l 40 -n 1
Read cleanup: Samtools (0.1.19), SAM files were converted to BAM files with and duplicate reads were removed with rmdup
Peak calling: MACS2 (2.1.0), parameters: callpeak -B -p 1e-5 -g mm –SPMR
genome build: mm9
processed data files format and content: bed and bw

molecule: genomic DNA

organism: Mus musculus

source_name: Input wtEpiSCs 10min fix1

growth_protocol: Pre-streak embryos (E6.0) were isolated in M2 medium; extraembryonic tissue and surrounding primitive endoderm was removed. Explants were put on MEFs and cultured in presence of Wnt inhibitor IWP2 (2 µM, Sigma Aldrich, dissolved in DMSO) in medium containing 20% KOSR, 77% DMEM/F12, 1x penicillin/streptomycin (100 units/mL, Thermo Fisher Scientific), 2 mM L-glutamine, 1x non-essential amino acids, 0.01% β-mercaptoethanol, Fgf-basic (12 ng/mL, ThermoFisher Scientific ), Activin A (20 ng/mL, R&D Systems).  MEF-free culture took place on surface coated by fibronectin (ThermoFisher Scientific) in medium containing 48% DMEM/F12, 48% Neurobasal Medium 1% B27 Supplement, 0.5% N2 Supplement B (all Thermo Fisher Scientific), 1x penicillin/streptomycin, Fgf-basic (12 ng/mL), Activin A (20 ng/mL), IWP2 (2 µM), 0.01% β-mercaptoethanol. Medium was refreshed on daily basis.

extract_protocol:
Crosslinking 10mins RT, lysis, sonication following standard procedures.
Illumina Truseq DNA library protocol

treatment_protocol: Wnt and Fgf stimulation was done after at least two passages feeder-free culturing by withdrawal of IWP2 and addition of Chiron (3 µM) and Fgf8 (120ng/ml).

tag: tissue

value: EpiSCs

tag: antibody

tag: treatment


title: Input wtEpiSCs 15min fix1

description: ChIP-seq

source_name: Input wtEpiSCs 15min fix1

extract_protocol:
Crosslinking 15mins RT, lysis, sonication following standard procedures.
Illumina Truseq DNA library protocol


title: 4C-seq Fzd10 0h EpiSCs

data_processing:
Library strategy: 4C-seq
The initial step in the 4C-seq analysis is the alignment of the sequencing reads to a reduced genome of sequences that flank DpnII sites (4C fragment ends), using custom Perl scripts. Due to their ambiguous nature in reporting contacts, repetitive fragment ends were excluded from subsequent analysis. The reduced genome was based on mouse genome mm9.
genome build: mm9
processed data files format and content: wig

source_name: 4C-seq Fzd10 0h EpiSCs

extract_protocol:
The initial steps of the 4C procedure, as published before (Simonis et al., 2006, Nature Genetics (PMID 17033623)), remain unchanged. Cells are cross-linked using 2% formaldehyde for 10 min at room temperature in PBS 10% FCS and nuclei are isolated, after which chromatin is digested with DpnII and subsequently ligated. After reversal of the cross-links, the DNA is purified and treated with the second restriction enzyme treatment (Csp6I). After a second re-ligation step, the sample is purified and a 4C PCR is performed.
4C PCR

treatment_protocol: Wnt stimulation was done after at least two passages feeder-free culturing by withdrawal of IWP2 and addition of Wnt3a (Cell Guidance Systems, 125 ng/mL) or Chiron (3 µM).


title: Input wtE9.5Anterior 10min fix1

description: ChIP-seq

source_name: Input wtE9.5Anterior 10min fix1

extract_protocol:
Crosslinking 10mins RT, lysis, sonication according to Amin and Bobola (2014).
Illumina Truseq DNA library protocol

value: E9.5 embryo anterior


title: Cdx2 wtEpiSCs 24h rep2

description: ChIP-seq

data_processing:
Mapping: Bowtie (1.1.0), parameters: -m 1 --best --strata --chunkmbs 512 -S –phred64-quals -q -l 40 -n 1
Read cleanup: Samtools (0.1.19), SAM files were converted to BAM files with and duplicate reads were removed with rmdup
Peak calling: MACS2 (2.1.0), parameters: callpeak -B -p 1e-5 -g mm –SPMR
Input control: Input_wtEpiSCs_15min_fix2
Peak calling on pooled: Cdx2_wtEpiSCs_24h_rep1 & Cdx2_wtEpiSCs_24h_rep2
Input control for pooled: Input_wtEpiSCs_15min_fix1 & Input_wtEpiSCs_15min_fix2 pooled
genome build: mm9
processed data files format and content: bed and bw

source_name: Cdx2 wtEpiSCs 24h rep2

extract_protocol:
Crosslinking 15mins RT, lysis, sonication and immunoprecipiation following standard procedures.
Illumina Truseq DNA library protocol

value: Biogenex, MU392A-UC (CDX2-88)


title: CBP-P300 WTEpiSCs 24h rep1

description: ChIP-seq

data_processing:
Mapping: Bowtie (1.1.0), parameters: -m 1 --best --strata --chunkmbs 512 -S –phred64-quals -q -l 40 -n 1
Read cleanup: Samtools (0.1.19), SAM files were converted to BAM files with and duplicate reads were removed with rmdup
Peak calling: MACS2 (2.1.0), parameters: callpeak -B -p 1e-5 -g mm –SPMR
Input control: Input_wtEpiSCs_15min_fix3
genome build: mm9
processed data files format and content: bed and bw

source_name: CBP-P300 WTEpiSCs 24h rep1

value: Cell Signaling Technology, #4771


title: H3K27ac wtE9.5Anterior tissue rep1

description: ChIP-seq

data_processing:
Mapping: Bowtie (1.1.0), parameters: -m 1 --best --strata --chunkmbs 512 -S –phred64-quals -q -l 40 -n 1
Read cleanup: Samtools (0.1.19), SAM files were converted to BAM files with and duplicate reads were removed with rmdup
Peak calling: MACS2 (2.1.0), parameters: callpeak -B -p 1e-5 -g mm –SPMR --nomodel --extsize 300 --llocal 100000
Input control: Input_wtE9.5Anterior_10min_fix1
genome build: mm9
processed data files format and content: bed and bw

source_name: H3K27ac wtE9.5Anterior tissue rep1

extract_protocol:
Crosslinking 10mins RT, lysis, sonication and immunoprecipiation according to Amin and Bobola (2014).
Illumina Truseq DNA library protocol

value: Abcam, ab4729 **Nb. The batch of H3K27ac Ab used for this experiment cross-reacts with H3K9ac. Therefore this dataset was not used in the manuscript.**


title: Cdx2 wtEpiSCs 24h rep1

description: ChIP-seq

data_processing:
Mapping: Bowtie (1.1.0), parameters: -m 1 --best --strata --chunkmbs 512 -S –phred64-quals -q -l 40 -n 1
Read cleanup: Samtools (0.1.19), SAM files were converted to BAM files with and duplicate reads were removed with rmdup
Peak calling: MACS2 (2.1.0), parameters: callpeak -B -p 1e-5 -g mm –SPMR
Input control: Input_wtEpiSCs_15min_fix1
Peak calling on pooled: Cdx2_wtEpiSCs_24h_rep1 & Cdx2_wtEpiSCs_24h_rep2
Input control for pooled: Input_wtEpiSCs_15min_fix1 & Input_wtEpiSCs_15min_fix2 pooled
genome build: mm9
processed data files format and content: bed and bw

source_name: Cdx2 wtEpiSCs 24h rep1


title: H3K27ac wtEpiSCs 24h rep2

description: ChIP-seq

data_processing:
Mapping: Bowtie (1.1.0), parameters: -m 1 --best --strata --chunkmbs 512 -S –phred64-quals -q -l 40 -n 1
Read cleanup: Samtools (0.1.19), SAM files were converted to BAM files with and duplicate reads were removed with rmdup
Peak calling: MACS2 (2.1.0), parameters: callpeak -B -p 1e-5 -g mm –SPMR --nomodel --extsize 300 --llocal 100000
Input control: Input_wtEpiSCs_10min_fix1
Peak calling on pooled: H3K27ac wtEpiSCs 24h rep1 & H3K27ac wtEpiSCs 24h rep2
Input control for pooled: Input_wtEpiScs_10min_fix1
genome build: mm9
processed data files format and content: bed and bw

source_name: H3K27ac wtEpiSCs 24h rep2


title: H3K27ac wtE9.5Tailbud tissue rep1

description: ChIP-seq

source_name: H3K27ac wtE9.5Tailbud tissue rep1

value: E9.5 embryo tailbud

value: Abcam, ab4729 **Nb. The batch of H3K27ac Ab used for this experiment cross-reacts with H3K9ac. Therefore this dataset was not used in the manuscript**


title: glucagon (10nM) + corticosterone (1.7uM), 1hr GR ChIP-seq rep#1

city: Bethesda

first: Songjoon

last: Baek

state: MD

address: 41 Library Drive

department: CCR

country: USA

institute: NCI / NIH

data_processing:
Illumina Casava 1.8 software was used for basecalling and alignment.
Areas of enrichment were identified using DNase2Hotspots software(htrceforge.net/projects/dnase2hotspots/) software with FDR 0%.
Raw signal density graphs were generated by counting tags at each genomic coordinate after extending the length of sequences to 150bp by strands.
Genome_build: mm9 (NCBI 37)
Supplementary_files_format_and_content: comma-delimited (CSV)  text files include genomic locations (Chromosome, start,  end ), z-score, p-value and the maximum density of hotspots. Bedgraph files contain genomic locations and normalized tag density profiles.

source_name: primary mouse hepatocytes

growth_protocol: mice maintained according to NIH guidelines under 12-hr light-dark cycles (light on at 6:00AM). Hepatocytes isolated by the two-step collagenase perfusion technique

extract_protocol: crosslinked material was lyzed and sonicated. Chromatin precipitated with antibody and DNA was purified by ethanol precipitation

treatment_protocol: mice were fasted for 24 or 10 hrs or fed ad lib. Hepatocytes treated with glucagon (10nM) or glucagon (10nM) + corticosterone (1.7uM) for 1hr

tag: strain

tag: chip antibody

value: cocktail of GR Abs (3.3ul of each Ab):PA1-511A (ThermoScientific),  MA1-510 (ThermoScientific), M-20 (sc-1004, Santa Cruz)


title: glucagon (10nM), 1hr ChIP-seq rep#1

value: CREB (48H2) Rabbit mAb #9197


title: NT - untreated CREB ChIP-seq


title: glucagon (10nM) + corticosterone (1.7uM), 1hr ChIP-seq rep#1


title: fasted 24 hr CEBPb ChIP-seq rep#3

source_name: liver


title: fasted 24 hr CEBPb ChIP-seq rep#2


title: NRI2_1

city: Minneapolis

first: Nuri

middle: Alpay

last: Temiz

state: MN

address: 2231 6th St SE

department: Masonic Cancer Center

institute: University of Minnesota

library_source: transcriptomic

data_processing:
Initial QC performed using FastQC v 0.11.2
Tophat v 2.0.13 was used to align samples
Cufflinks v 2.2.1 was used to generate abundances and fpkm values with max-bundle-frans <10000000>
Genome_build: mm9
Supplementary_files_format_and_content: matrix of fpkm values per sample

molecule: total RNA

source_name: aml

growth_protocol: total RNA was extracted using RNeasy Midi Kit

extract_protocol: average insert size of 200 selected

treatment_protocol: TruSeq RNA v2

value: NRAS(V12) and Mll-AF9 AML tail injection to SCID Beige mouse

tag: tumor

value: NRAS independent


title: NRI2_3


title: NRI2_2


title: fasted 24 hr CEBPb ChIP-seq rep#1


title: NRI1_2


title: fed CEBPb ChIP-seq rep#3


title: NRI1_3


title: Input wtE9.5Tailbud 10min fix1

description: ChIP-seq

source_name: Input wtE9.5Tailbud 10min fix1


title: glucagon (10nM) + corticosterone (1.7uM), 1hr GR ChIP-seq rep#2


title: NRD1_3

value: NRAS dependent


title: NRD1_2


title: glucagon (10nM) + corticosterone (1.7uM), 1hr ChIP-seq rep#2


title: fed CEBPb ChIP-seq rep#1


title: NRD1_1


title: RNASeq_Mut_p13_rep3

city: Haining

first: Chaochen

last: Wang

address: 718 East Haizhou Rd

department: ZJU-UoE Institute

country: China

institute: Zhejiang University

description: processed data file: RNASeq_fpkm_p13.txt

data_processing:
Basecalls performed using the CASAVA software
ChIP-seq and Dnase-seq reads were aligned to the mm9 genome assembly using the Bowtie2 program (Langmead et al., Nature method, 2012)
RNA-seq reads were aligned to the mm9 genome assembly using the STAR program (Dobin et al., Bioinformatics, 2012). Fpkm values were calculated using DESeq2.
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-seq: BedGraph files can be used to check ChIP-seq peaks through the UCSC genome browser.
Supplementary_files_format_and_content: Dnase-seq: BedGraph files can be used to check DNase-seq peaks through the UCSC genome browser.
Supplementary_files_format_and_content: RNA-Seq: fpkm table contains the fpkm value for each gene.

growth_protocol: C57BL/6 mice were purchased from Charles River and used as WT controls.Socs2-Δs (Mut) mice were generated by CRIPSR/Cas9 genome editing. All animals were handled and housed in accordance with the guidelines of the NIH and experiments were approved by the ACUC of NIDDK.

extract_protocol:
Poly(A) RNA were purified twice with Trizol and RNeasy® Plus Mini Kit (Qiagen). cDNA was synthesized using SuperScript II (Invitrogen) and TruSeq RNA Sample Preparation Kit (Illumina).
Libraries were prepared for sequencing using standard Illumina protocols.

value: Mammary gland

tag: time

value: pregnancy day of 13

tag: genotype/variation

value: wild type


title: NRI1_1


title: RNASeq_WT_p13_rep2


title: RNASeq_WT_p13_rep3


title: RNASeq_Mut_p13_rep2


title: RNASeq_WT_p13_rep4


title: RNASeq_WT_p13_rep1


title: glucagon (10nM), 1hr ChIP-seq rep#2


title: fed CEBPb ChIP-seq rep#2


title: Dnase-seq_Mut_p13

description: Dnase-seq

extract_protocol:
Frozen tissue was ground into powder and homogenized with buffer A (15mM Tris-HCl PH 8.0, 15 mM NaCl, 60 mM KCl, 1mM EDTA, 0.5mM EGTA, 0.15mM Spermine, 0.5mM Spermidine, 0.5mM DTT, 1mM PMSF with proteinase inhibitors). After cells were lysated, nucleuses were collected, counted and re-suspended in Dnase buffer. 10U Dnase I (New England Biolab) was used to digest 10 million nucleuses at 37C0 for 5 minutes followed by proteinase K digestion. Genomic DNA was then purified. 50 bp and -100 bp DNA fragments were selected for further library construction and sequencing.
Libraries were prepared for sequencing using standard Illumina protocols.


title: MA9.3ITD-shFTO_RNA-seq

city: Monrovia

first: Jianjun

last: Chen

state: CA

department: Systems Biology

institute: Beckman Research Institute of City of Hope

data_processing:
sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
the FPKM were calculated using Cufflinks with default parameters
Genome_build: GRCh38
Supplementary_files_format_and_content: Cufflinks output, tab-delimited text files include FPKM values for each Sample , The first line contains column names separated by the tab character.

molecule: polyA RNA

organism: Homo sapiens

source_name: MA9.3ITD cell

extract_protocol:
RNA was extracted by Trizol. Polyadenylated RNA was extracted using FastTrack MAC Maxi mRNA isolation kit (Invitrogen)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: cell type

value: acute monocytic leukemia (AML) cells

tag: tissue source

value: peripheral blood

tag: cell line info.

value: human CD34+ hematopoietic stem/progenetor cells stably infected by MLL-AF9 and FLT3-ITD

tag: transduced with

value: pLKO.1-shFTO; shFTO


title: Dnase-seq_Mut_I1

description: Dnase-seq

value: Involution day 1


title: ChIPSeq_GR_Mut_p13

extract_protocol:
Frozen-stored mammary tissues from virgin or p13 were broken into powder with mortar and pestle. Nuclei were extracted in Farnham lysis buffer (5mM PIPES pH8.0, 85mM KCl, 0.5% NP-40 and protease inhibitors). Antibodies against STAT5A (Santa Cruz, sc-1081), H3K27ac (Abcam, Ab4729), GR (Thermo Scientific, PA1-511A) were used for ChIP.
Libraries were prepared for sequencing using standard Illumina protocols.

value: anti-GR (ThermoFisher, PA1-511A)


title: MethylC-seq_CO_60d_B

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
RNA-seq: The reads were mapped to gencode V10 annotation and hg19 reference genome with Tophat2 2.0.13 (Kim et al., 2013). Mitochondrial and rRNA annotations were removed from the GTF file. Mapped RNA-seq reads were counted and summarized to the gene level with HTSeq 0.6.1 using parameters ‘-s reverse -a 10 -t exon -i gene_name -m union’ (Anders et al, 2015). Differentially expressed genes were identified with EdgeR with FDR < 0.05 and Fold Change >= 2 (Robinson et al., 2010).
MethylC-seq reads were mapped to hg19 reference genome using MethylPy (https://bitbucket.org/schultzmattd/methylpy/wiki/Home, Lister et al., 2013; Schultz et al., 2015). Significantly methylated cytosine sites were identified using a binomial test for each tri-nucleotide context with FDR < 0.01 (corrected by benjamini hochberg method for multiple testing) as described in Ma et al., 2014.
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text files of gene expression levels (RPKM) estimated using edgeR 3.8.6
Supplementary_files_format_and_content: tab delimited text files of methylcytosine calls; columns in allc files are: column 1 - chromosome; column 2 - position; column 3 - strand; column 4 - class; column 5 - mC reads; column 6 - total reads; column 7 - methylated (Boolean value indicating the result of statistical test for methylated cytosines)

source_name: Cerebral organoids, 60 days differentiation

growth_protocol: COs were generated following exactly the previously established protocol and using an orbital shaker for agitation (Lancaster et al. 2013; Lancaster and Knoblich 2014). For RNA-seq analysis, the following samples were collected from each of two independent batches: H9 hES day 0 (remaining cells from EB generation), 5 pooled EBs day 18, 3 pooled COs day 40, 3 pooled COs day 60. Samples were homogenized in 1 ml Trizol reagent (Thermo, cat. #15596026) and RNA was extracted according to manufacturer instructions. 1 μl GlycoBlue (Thermo cat. # AM9516) was added during isopropanol precipitation to facilitate RNA pellet visualization. For DNA methylation analysis, the following samples were collected from each of two independent batches: H9 hES day 0 (remaining cells from EB generation), 3 pooled EBs day 16, 3 pooled COs day 40, 3 pooled COs day 60. DNA was collected using the DNeasy kit from Qiagen and DNA was eluted in 200 μl of water, except for the EB16 day sample, which was eluted in 100 μl because of the small size of the sample at that time point.

extract_protocol: A detailed protocol for MethylC-seq libraries preparation can be found in Urich et al., (2015). MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing. Nat Protoc 10, 475-483.

tag: Sex

value: Female

tag: cell line source

value: human embryonic stem cell line

tag: cell subtype


title: MethylC-seq_Fetal_Ctx

source_name: Middle frontal gyrus from 19w gestation human brain

extract_protocol:
For DNA and RNA extraction, the tissue was frozen in liquid nitrogen and homogenized by grinding with pestle and mortar. DNA was extracted using DNeasy Blood & Tissue Kit (Qiagen cat. # 69504).
A detailed protocol for MethylC-seq libraries preparation can be found in Urich et al., (2015). MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing. Nat Protoc 10, 475-483.

value: Male


title: MA9.3ITD-shNS_RNA-seq

value: pLKO.1 empty vertor; shNS


title: MethylC-seq_CO_40d_A

source_name: Cerebral organoids, 40 days differentiation


title: RNASeq_Mut_p13_rep1


title: Dnase-seq_WT_I1

description: Dnase-seq


title: m6A-seq shFTO

data_processing:
sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
m6A-seq reads were aligned to the GRCh38 genome assembly using Tophat 2.1.1
peaks were called using MACS2 and exomePeak. Only the peaks called by both the two tools are retained for further analysis.
the m6A peaks were annotated using an ad hoc perl script.
GSEA and DAVID tool were used to perform pathway enrichment analysis
Genome_build: GRCh38
Supplementary_files_format_and_content: bigwig files were generated by MACS2 and bedGraphToBigWig. BedWig files can be uploaded to UCSC Genome Browser for visualization

extract_protocol:
RNA was extracted by Trizol. Polyadenylated RNA was extracted using FastTrack MAC Maxi mRNA isolation kit (Invitrogen)
RNA fragmentation, m6A-Seq and library preparation were performed according to previous protocals (Dan et al., 2012)

value: acute monocytic leukemia

value: m6A antibody


title: m6A-seq shNS


title: ChIPSeq_STAT5_Mut_L1

value: Lactation day 1

value: anti-STAT5A (Santa Cruz, sc-1081)


title: MethylC-seq_EB_B

source_name: Embryoid body derived from H9 hESC

value: Embryoid body derived from H9 hESC


title: ChIPSeq_H3K27ac_Mut_p13

value: Mammary gland

value: pregnancy day of 13

value: anti-H3K27ac (Abcam, ab4729)


title: RNA-seq_CO_60d_B

description: processed data file: CO_FetalCtx_RPKM.tsv

extract_protocol: Stranded RNA-seq libraries were constructed with Truseq Stranded mRNA LT kit (Illumina, RS-122-2101 and RS-122-2102) and were sequenced on Illumina HiSeq 2500 with 100 bases single-ended reads.

value: Cerebral organoids, 60 days differentiation


title: Input 1

city: Aurora

first: Lori

last: Sussel

state: CO

address: 1775 Aurora Ct.

institute: University of Colorado

data_processing:
ChIP-Seq data was analyzed using the standard ChIP-Seq pipeline developed at the NYU Applied Bioinformatics Core, which is called  'HiC-Bench' available on GitHub at https://github.com/NYU-BFX/hic-bench.
The mm9 reference genome was used with ENSEMBL version 59. Peaks were called with MACS (version 2.0.10.20131216) with reads extended by 400bp while bypassing the standard model and a qvalue cutoff of 0.01.
Peaks were annotated with GenomicTools (http://www.ncbi.nlm.nih.gov/pubmed/22113082) included in the ChIP-Seq pipeline, allowing for 100kb upstream and downstream overlaps.
HOMER version 4.6 was used for motif discovery with a region size of 200bp.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files contain the alignment for each sample and were generated with Bedtools version 2.22.0

source_name: MIN6 cells

growth_protocol: MIN6 cells were  generated in 150mm TC treated culture dish (Corning) on DMEM  medium supplemented with 15% fetal bovine serum and penicillin streptomycin.

extract_protocol:
Lysates were clarified from sonicated nuclei and Nkx2.2-DNA complexes were isolated with Nkx2.2 antibody.
Libraries were prepared as per instructions of the Kapa Hyper kit (Illumina)

value: Insulinoma derive pancreatic beta cells

tag: chip  antibody


title: ChIPSeq_H2K27ac_Mut_L1

tag: tissue


title: MethylC-seq_CO_40d_B

value: Cerebral organoids, 40 days differentiation


title: ChIPSeq_STAT5_Mut_p13


title: Input 3


title: Input 2


title: MethylC-seq_EB_A


title: RNA-seq_CO_40d_B


title: MethylC-seq_H9_A

source_name: H9 human embryonic stem cell


title: RNA-seq_CO_40d_A


title: MethylC-seq_H9_B


title: mutant 1 LG1405

data_processing:
RTA (Illumina) was used for base calling
CASAVA (version 1.8.2) was used for converting BCL to fastq format, coupled with adaptor trimming
Reads were mapped  to a reference genome (Mouse: UCSC/mm9) using Tophat (Trapnell C et al 2009 Bioinformatics) (version 2.0.4) with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10).
Relative abundance (aka expression level) of genes and splice isoforms was determined using cufflinks (Trapnell C et al 2010 Nature Biotech) (version 2.0.2) with default settings.
Differentially expressed genes were calculated using Deseq (Anders S et al 2010 Genome Biology).
Genome_build: mm9
Supplementary_files_format_and_content: csv-files includse FPKM values for all genes/isoforms in a sample
Supplementary_files_format_and_content: csv-file includes DeSeq analysis for all samples

source_name: pancreatic islets

extract_protocol:
Pancreatic islets were isolated through collagenase treatment and total RNA was isolated using QIAGEN RNeasy Micro kit. Libraries were prepared from total RNA (RIN>8) with the TruSeq RNA prep kit (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: sample name

tag: genotype

value: Nkx2.2 flox/flox; RipCre/+; Rosa26Tomato/Rosa26Tomato

value: pancreatic islets


title: Dnase-seq_WT_p13

description: Dnase-seq

tag: strain

value: wild type


title: RNA-seq_Fetal_Ctx

extract_protocol:
For DNA and RNA extraction, the tissue was frozen in liquid nitrogen and homogenized by grinding with pestle and mortar. RNA was extracted using RNeasy Lipid Tissue Mini kit (Qiagen cat. # 74804).
Stranded RNA-seq libraries were constructed with Truseq Stranded mRNA LT kit (Illumina, RS-122-2101 and RS-122-2102) and were sequenced on Illumina HiSeq 2500 with 100 bases single-ended reads.

value: Middle frontal gyrus from 19w gestation human brain


title: control 1 LG1401


title: Nkx2_2-2


title: Nkx2_2-3


title: Nkx2_2-1


title: RNA-seq_H9_A

value: Female

value: human embryonic stem cell line


title: RNA-seq_CO_60d_A


title: RNA-seq_H9_B


title: MethylC-seq_CO_60d_A


title: mutant 3 LG8737

value: Nkx2.2 flox/flox; RipCre/+; Rosa26Tomato/+


title: fasted 24 hr GR ChIP-seq rep#2

tag: chip antibody

value: cocktail of GR Abs (3.3ul of each Ab):PA1-511A (ThermoScientific),  MA1-510 (ThermoScientific), M-20 (sc-1004, Santa Cruz)


title: control 3 LG8736

value: Nkx2.2 flox/flox


title: RNA-seq_EB_A


title: CD24plusplus2

city: Stanford

first: Howard

last: Chang

address: 269 Campus Drive

department: Dermatology

institute: Stanford University

description:
CD24plus-CD24plus
Started from a CD24 positive K562 cell population. Re-sorted after 5 days for CD24. CD24 positive at day5. Replicate2

data_processing:
fastq files were aligned to the hg19 genome using Bowtie2 using the following specifications -S -X2000 -p10 -m1 --very-sensitive
Duplicates were removed and library size was estimated using PICARD tools
peaks were called using MACS2 with the --nomodel setting
Genome_build: hg19
Supplementary_files_format_and_content: bw files for UCSC upload  were generated using bedtools

extract_protocol:
Tagmentation was performed as previously described (Buenrostro et al., 2013)
Purified DNA was barcoded using a single unique adapter (i5)

value: CML cell line


title: fasted 24 hr GR ChIP-seq rep#1


title: control 2 LG437

value: Nkx2.2 flox/flox; Rosa26Tomato/+


title: fed GR ChIP-seq rep#2


title: RNA-seq_EB_B

value: Embryoid body derived from H9 hESC


title: fed GR ChIP-seq rep#1


title: CD24plusminus1

description:
CD24plus-CD24minus
Started from a CD24 positive K562 cell population. Re-sorted after 5 days for CD24. CD24 negative at day5. Replicate1


title: CD24plusplus1

description:
CD24plus-CD24plus
Started from a CD24 positive K562 cell population. Re-sorted after 5 days for CD24. CD24 positive at day5. Replicate1


title: CD24minusplus1

description:
CD24minus-CD24plus
Started from a CD24 negative K562 cell population. Re-sorted after 5 days for CD24. CD24 positive at day5. Replicate1


title: WT 2 IP

data_processing:
m6A-seq reads were aligned to the hg19 genome assembly using Tophat 2.0.12 with default parameters.
peaks were called using MACS and exomePeak. Only the peaks called by both the two tools are retained for further analysis.
The m6A peaks were annotated using an ad hoc perl script. The RNA-Seq reads were normalized using RSEM method. EBSeq was used to find differentially expressed genes.
DAVID tool was used to perform pathway enrichment analysis
Genome_build: hg19
Supplementary_files_format_and_content: BedGraph files were generated by homer. BedGraphfiles can be uploaded to UCSC Genome Browser for visualization

source_name: Mono mac6 cell

tag: tumor

value: acute monocytic leukemia

value: peripheral blood

tag: antibody


title: WT 2 input

value: input


title: FTO+ 1 IP


title: FTO+ 2 IP


title: WT 1 IP


title: WT 1 input


title: FTO+ 2 input


title: CD24minusminus2

description:
CD24minus-CD24minus
Started from a CD24 negative K562 cell population. Re-sorted after 5 days for CD24. CD24 negative day5. Replicate2


title: CD24minusminus1

description:
CD24minus-CD24minus
Started from a CD24 negative K562 cell population. Re-sorted after 5 days for CD24. CD24 negative day5. Replicate1


title: fed rep#2 RNA-seq

data_processing:
Basecalls were performed using RTA 1.12.4.2
Demultiplexing was performed by Casava 1.8.2 allowing 1 mismatch
Alignment was performed by Tophat2 (v2.0.8) with -r 10 --mate-std-dev 200 options
Genome_build: mm9
Supplementary_files_format_and_content: fpkm_tracking files including FPKM values for the analysis of gene expression

extract_protocol: Total RNA was isolated using NucleoSpin kit (Macherey-Nagel). When isolating RNA from primary hepatocytes, 350 µl of lysis buffer was directly applied on plate. When isolating RNA from liver, 30mg of tissue was homogenized in 600 µl of lysis buffer using TissueRuptor (Qiagen).

treatment_protocol: mice were fasted for 24 hrs or fed ad lib. Hepatocytes treated with glucagon (10nM) for 3 hr.


title: fasted 24 hrs rep#2 RNA-seq


title: fed rep#1 RNA-seq


title: fasted 24 hrs rep#1 RNA-seq


title: fasted 24h DHS-seq rep#3

growth_protocol: mice maintained according to NIH guidelines under 12-hr light-dark cycles (light on at 6:00AM)

extract_protocol: on 6:00am mice were euthanized by cervical dislocation and liver was excised. isolated nuclei from fresh livers were treated with DNase-I and DNA fragments of 100-500 bp from a chromatin digestion with 40 U/ml DNase were purified using sucrose gradients. DNA was precipitated and reconstituted in nuclease free H2O

treatment_protocol: mice were fasted for 24 hrs or fed ad lib


title: fasted 24h DHS-seq rep#2


title: CD24plusminus2

description:
CD24plus-CD24minus
Started from a CD24 positive K562 cell population. Re-sorted after 5 days for CD24. CD24 negative at day5. Replicate2


title: fed rep#3 RNA-seq


title: fasted 24h DHS-seq rep#1


title: 5'GRO-seq with fragmentation

first: Long

last: Vo ngoc

state: California

address: 9500 Gilman Dr

institute: UCSD

description: run-on RNA

data_processing:
Library strategy: GRO-Seq
Adapter sequences were removed from 5'-GRO-seq reads with homerTools trim.
The resulting reads were mapped to the hg19 human genome by using Bowtie2 with the default settings.
High quality reads (MAPQ ≥ 10) were selected and the location of the 5’ end of each read was then retrieved and pile-ups were calculated at these genomic positions.
FocusTSS was used to call TSS peaks
Genome_build: hg19
Supplementary_files_format_and_content: Bed files; score in column #5 represent read count for the peak; FI value is comprised in the peak name in column #4

source_name: human breast carcinoma cells

growth_protocol: MCF-7 cells (ATCC) were maintained in DMEM (ATCC) supplemented with 10% FBS (ATCC), 15 μg/mL bovine insulin (Sigma-Aldrich), 50 U/mL penicillin (ThermoFisher), and 50 μg/mL streptomycin (ThermoFisher).

extract_protocol:
Two 5’-GRO-seq experiments were carried out by variation of the procedure described in Duttke et al. (2015) and Hetzel et al. (2016). We were curious with regard to whether the RNA fragmentation step would affect the 5'-GRO-seq data, and we therefore performed one experiment with the RNA fragmentation and other experiment without the RNA fragmentation. As shown in Supplemental Fig. S2, we obtained similar results from the two experiments, and thus used both datasets for our analyses. For each experiment, nuclear run-on reactions were performed with 107 MCF-7 nuclei in the presence of BrUTP (Sigma Aldrich) for labeling of the RNA. Trizol LS (Fisher Scientific) was used to terminate the reaction and to extract the RNA.
For 5’-GRO-seq with fragmentation, RNA was hydrolyzed by Zn(II)-mediated fragmentation (Ambion). BrU-labeled transcripts were immunoprecipitated with anti-BrdU agarose beads (Santa Cruz Biotech) and extracted with Trizol LS. The resulting RNA was incubated with T4 polynucleotide kinase (NEB) in low pH buffer followed by treatment with calf intestinal alkaline phosphatase (CIP; NEB) to achieve 5’ and 3’ dephosphorylation. A second BrU enrichment was performed, and 5’-monophosphate-RNAs were removed with Terminator 5’-phosphate-dependent exonuclease (Epicentre), as described in Hetzel et al. (2016). The RNA was subjected to a second round of dephosphorylation with CIP (NEB). Decapping and library preparation were performed as described in Hetzel et al. (2016).
For 5’-GRO-seq without RNA fragmentation, the run-on step was followed by RNA extraction with Trizol. BrU-labeled transcripts were immunoprecipitated with anti-BrdU agarose beads. RNA was dephosphorylated with CIP (NEB), and subjected to a second round of BrU enrichment that was followed by a second round of CIP (NEB). Decapping and library preparation were performed as described in Hetzel et al. (2016).
It might be noted that these experiments involve the ligation of an adapter (GTTCAGAGTTCTACrArGUrCrCrGrArCrGrAUrC) to the 5' end of the transcripts. The ligation step has been found to exhibit sequence bias (Jayaprakash et al. 2011). Hence, it might alter the relative amounts of different transcripts, but would not affect the accuracy of the mapping of the 5' ends of the transcripts.
The Small RNA Library Prep Set (New England Biolabs) was used for final library preparation with modifications as described in Hetzel et al. 2016


title: fed DHS-seq rep#2


title: 5'GRO-seq without fragmentation

description: run-on RNA


title: RH18 MYF5

first: Javed

last: Khan

address: 37 Convent Dr.

department: Genetics Branch

institute: NCI, NIH

data_processing:
ChIP enriched DNA reads were mapped to reference genome (hg19) using BWA version 0.7.10
The ChIP-seq peaks were called by MACS2 version 2.1.0.
Genome_build: Hg19
Supplementary_files_format_and_content: peak files are tab delimited text files for each sample.

source_name: RH18 Fusion Negative Rhabdomyosarcoma cell line

growth_protocol: Cell lines were grown in DMEM supplemented with 10%FBS and Pen/Strep.

extract_protocol:
DNA was extracted from ChIP-seq samples prepared following the Active Motif ChIP-IT High Sensitivity kit protocol.
Standard Illumina barcodes were introduced during library preparation

treatment_protocol: ChIP samples harvested after 1% formaldehyde fixation for 12 minutes, sonicated, processed and ChIP-enriched via standard protocols (Active Motif ChIP-IT HS kit) with indicated antibodies.

value: Myf-5, Santa Cruz (C-20) cat# sc-302

tag: enrichment target

tag: target function

value: Transcription Factor


title: RH18 H3K27ac

value: H3K27ac (Active Motif, 39133)

value: Active enhancers


title: RD Fusion Negative Rhabdomyosarcoma cell line input

value: control


title: fasted 24 hrs H3K27ac ChIP-seq rep#1

extract_protocol: crosslinked material was lyzed and sonicated. Chromatin precipitated with antibody and DNA was purified by ethanol precipitation


title: HCT116_shRNA#3_3 - RNAseq

city: Boston

first: Paloma

last: Cejas

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana Farber Cancer Institute

description:
CNOT3_depleted_3
RNAseq
Total RNA was extracted with TRIzol reagent (Invitrogen) and the RNeasy Mini Kit (Qiagen). RNA was treated with the Turbo DNA-free kit (Ambion) to remove genomic DNA.   RNA-seq libraries were prepared from 300 ng RNA using the TruSeq RNA Sample Preparation kit (Illumina) and 75-bp single-end sequences were obtained on a NextSeq 500 Instrument (Illumina).

data_processing:
Alignment: For ChIPseq experiments we used Bowtie2 (2.1.0) with settings (--no-unal). For RNAseq we used Tophat, version 2.0.9, default options.
ChIPseq analyses: For peak calling we used MACS2 using Q:0.01.
RNAseq analyses: normalized and differential expression: Cufflinks, version 2.2.1; settings: -b, -u, and default; Cuffmerge was used with reference gtf and default settings; Cuffquant was used with default settings; Cuffnorm was used with default settings; Cuffdiff was used with -b, -u and default settings.
Genome_build: Hg19
Supplementary_files_format_and_content: ChIPseq: Wiggle files were generated by NPS software using parameters by default. Bed files (the 5 columns are 1: chromosome, 2: start location, 3: end location, 4: peak number, 5: score).
Supplementary_files_format_and_content: RNAseq: Individual samples have an FPKM gene tracking file from Cufflinks, estimating transcript abundance for that sample, along with confidence intervals.  There are two processed data matrices that apply to all the samples.  There exists a differential expression table, prepared using Cuffdiff with an FDR of 5%, which contains average normalized FPKM values for Controls infected with a non specific NS_shRNA construct (Scr) and CNOT3-depleted by infection with shRNA_#3 construct (silenced), as well as fold change in expression, P-values, and Q-values corrected for multiple hypothesis testing.

source_name: Colorectal cancer cell line

growth_protocol: Sections of snap-frozen tissues were either micrococcal nuclease treated or cross-linked with 1% formaldedyde for 20 minutes and sonicated for ChIPseq experiments followed b ChIP with 10ug of antibody. HCT116 cells were cross-linked with 1% formaldehyde for 20 min at 37oC, followed by ChIP with 10 µg CNOT3 for ChIPseq. For RNAseq experiments cells were washed with PBS and total RNA was extracted with TRIzol reagent (Invitrogen) and the RNeasy Mini Kit (Qiagen). RNA was treated with the Turbo DNA-free kit (Ambion) to remove genomic.

extract_protocol:
ChIPseq: Lysates were clarified from micrococcal nuclease digested or sonicated or and histone-DNA or CNOT3-DNA complexed were  isolated with antibody.
RNAseq: Total RNA was extracted with TRIzol reagent (Invitrogen) and the RNeasy Mini Kit (Qiagen). RNA was treated with the Turbo DNA-free kit (Ambion) to remove genomic DNA.
For ChIPseq:ThruPLEX-FD kits (Rubicon Genomics) was used and 50 bp single-end reads were sequenced on a HiSeq2000 instrument (Illumina).
For RNAseq: TruSeq RNA Sample Preparation Kit (Illumina) was used according to the manufacturer's instructions and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

tag: cell line

tag: genotype/variation

value: CNOT3 depleted


title: RH18 input


title: fasted 24 hrs rep#3 RNA-seq


title: HCT116_NS_shRNA_2 - RNAseq

description:
Control_2
RNAseq
Total RNA was extracted with TRIzol reagent (Invitrogen) and the RNeasy Mini Kit (Qiagen). RNA was treated with the Turbo DNA-free kit (Ambion) to remove genomic DNA.   RNA-seq libraries were prepared from 300 ng RNA using the TruSeq RNA Sample Preparation kit (Illumina) and 75-bp single-end sequences were obtained on a NextSeq 500 Instrument (Illumina).

value: Control


title: fasted 10 hrs H3K27ac ChIP-seq rep#3


title: fed H3K27ac ChIP-seq rep#2


title: fasted 24 hrs H3K27ac ChIP-seq rep#3


title: FTO+ 1 input


title: HCT116_NS_shRNA_1 - RNAseq

description:
Control_1
RNAseq
Total RNA was extracted with TRIzol reagent (Invitrogen) and the RNeasy Mini Kit (Qiagen). RNA was treated with the Turbo DNA-free kit (Ambion) to remove genomic DNA.   RNA-seq libraries were prepared from 300 ng RNA using the TruSeq RNA Sample Preparation kit (Illumina) and 75-bp single-end sequences were obtained on a NextSeq 500 Instrument (Illumina).


title: fed DHS-seq rep#3


title: fed DHS-seq rep#1


title: fasted 24 hrs H3K27ac ChIP-seq rep#2


title: RD Fusion Negative Rhabdomyosarcoma cell line H3K27ac


title: HCT116_shRNA#3_2 - RNAseq

description:
CNOT3_depleted_2
RNAseq
Total RNA was extracted with TRIzol reagent (Invitrogen) and the RNeasy Mini Kit (Qiagen). RNA was treated with the Turbo DNA-free kit (Ambion) to remove genomic DNA.   RNA-seq libraries were prepared from 300 ng RNA using the TruSeq RNA Sample Preparation kit (Illumina) and 75-bp single-end sequences were obtained on a NextSeq 500 Instrument (Illumina).


title: mutant 2 LG435

value: pancreatic islets


title: fasted 10 hrs H3K27ac ChIP-seq rep#2


title: D7-2

first: Laertis

last: Ikonomou

address: 670 Albany St

department: Center for Regenerative Medicine

institute: Boston University

description: RNA extracted from mES derived cells

data_processing:
The fastq files were aligned against mm9 reference genome with Tophat v2.0.4
HTSeq is used to quantify read count per gene from aligned BAM files
The edgeR package in R was used to perform differential analysis between D14 and D1, D7 and D1, D14 and D7 with a FDR cutoff at 0.05.
Genome_build: mm9
Supplementary_files_format_and_content: text file with raw read count

source_name: Mouse Embryonic Stem Cells

extract_protocol:
Cells were harvested from wells and RNA was extracted using using QIAshredder columns (QIAGEN, 79656) and the RNeasy Plus Mini Kit (QIAGEN, 74136) according to the QIAGEN manual instructions. Purified RNA was eluted in 30 µl nuclease-free water.
Sequencing libraries were prepared from total RNA samples using Illumina® TruSeq® RNA Sample Preparation Kit v2. Briefly, the mRNA was isolated using magnetic bead-based poly(A) selection, fragmented, and randomly primed for reverse transcription, followed by second-strand synthesis to create double-stranded cDNA fragments. These cDNA fragments were then end-repaired, added with a single ‘A’ base, and ligated to Illumina® Paired-End sequencing adapters. The products were purified and PCR-amplified to create the final cDNA library. The libraries from individual samples were pooled in groups of four for cluster generation on the Illumina® cBot using Illumina® TruSeq® Paired-End Cluster Kit. Each sample was sequenced four per lane on the Illumina® HiSeq 2500 to generate more than 25 million Paired-End 100-bp reads.

treatment_protocol: Dox was added at a concentration of 1 μg/ml to the cell culture media to activate expression of the Tet-On Nkx2-1 transgene

tag: differentiation stage

value: Day 7

tag: developmental stage

value: Anterior Foregut Endoderm

tag: treatment

value: Dox D6-D7

tag: source tissue

value: Embryonic Stem Cells


title: fasted 10 hrs H3K27ac ChIP-seq rep#1


title: D1-2

description: RNA extracted from mES derived cells

value: Day 1

value: Pluripotent

value: Dox D0-D1


title: PRO20150916_C1_95

status: Public on Dec 19 2016

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

data_processing:
Cutadapt-1.2.1 of 3p adaptor 'CTGTCTCTTATACACATCT',
Discarding of trimmed reads with length < 50b,
Filtering of reads not starting with a perfect 14b 5p adaptor 'AAGTCGCAGGGTTG', then a well formatted HUMI sequence (we require a well formated N4H4 HUMI in this N6H4 HUMI experiment) followed by at least 3 'G' before cDNA sequence,
Extraction of 5p adaptor, UMI and strech of 'G',
Mapping with STAR_2.4.0a versus hg19 using encodeproject.org RNA-seq options "--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000"
Drop-seq_tools-1.0 dropseq.jar tool for tagging with Gene information from Ensembl release GRCh37.75, then DigitalExpression calling with default parameters (edit distance=1).
Genome_build: hg19
Supplementary_files_format_and_content: PRO20150916_C1_dge_ed1.txt: quantifcation file containing for each gene detected in at least one sample the number of mRNA (unique molecular identifier) molecules counted for this gene.

source_name: respiratory epithelium

growth_protocol: Culture was performed according to Marcet et al (https://www.ncbi.nlm.nih.gov/pubmed/21602795) with time of differentiation equal to 33 days (air liquid interface), except that the differentiation medium was PneumaCult™-ALI Medium (StemCell Technologies, Vancouver, BC, V6A 1B6, Canada).

extract_protocol:
HNEC cells were loaded onto a Fluidigm 96 cell IFC and lyzed with 0.2% w/v Tween 20, 1 U/ul Promega RNAsin RNAse inhibitor, 2 µM reverse transcription primer (TGCGGTATCTAAAGCGGTGAGT(30)VN), 2.5 mM dNTPs, 1x C1 loading reagent (Fluidigm), ERCC Spike-In Mix 1 @ 20,000 molecules/cell (Life Technologies). Cells were lyzed for 10 min at room temperature followed by 3 min at 70°C and 3 min at 10°C.
Cells were processed in a 96 cell Fluidigm C1 IFC. Reverse transcription: 18 nl of 1.75 x  reverse transcription mix, 8.75 mM DTT, 1.75 M Betaine, 10.5 mM MgCl2, 1.75 uM template switching oligonucleotide (GCAATGAAGTCGCAGGGTTGN(4)H(4)rGrGrG), 0.5 U/ul Promega RNAsin, 5.5 U/ul Life Technologies Superscript II reverse transcriptase, 1x C1 loading reagent were added to each lysed cell and incubated for 10 min at 25°C, 90 min at 42°C, 15 min at 70°C. PCR amplification: 270 nl 1.15 x KAPAHiFi HotStart Ready Mix, 55 nM barcode primer (TGCGGTATCTAAAGCGGTGAGCCATCTCATCCCTGCGTGTCTCCGACTCAG<index>GCAATGAAGTCGCAGGGTTG, indices were standard ion torrent barcodes) and 1.1 µM biotinylated PCR primer were back-loaded to each cell. PCR amplification was for 3 min at 98°C followed by 18 cycles at 98°C for 20 sec, 64°C for 15 sec, 72°C for 6 min, and a final extension at 72°C for 5 min. Fragmentation and library preparation: Barcoded, amplified cDNA from all cells was pooled and fragmented by tagmentation with EzTn5 transposase (Epicentre) and Tn5 mosaic end duplexes (upper: 5’-AGA TGT GTA TAA GAG ACA-3’, lower: 5’-PhosCTG TCT CTT ATA CAC ATC T-3’), 5’ terminal (biotinylated) fragments were isolated with streptavidin beads and Ion Torrent adapter sequences were added by PCR (Primers: CCATCTCATCCCTGCGTGTCTC, 0.5 μM; CCACTACGCCTCCGCTTTCCTC, 0.5 μM; CCACTACGCCTCCGCTTTCCTCTCTATGGGCAGTCGGTGATAGATGTGTATAAGAGACAG,  0.125 μM).
5' selective, oligo-dT-primed RNA-seq based on the SmartSeq technique.

tag: cell type

value: human nasal epithelial cell (HNEC)

tag: imaging

tag: qccode


title: HCT116_NS_shRNA_3 - RNAseq

description:
Control_3
RNAseq
Total RNA was extracted with TRIzol reagent (Invitrogen) and the RNeasy Mini Kit (Qiagen). RNA was treated with the Turbo DNA-free kit (Ambion) to remove genomic DNA.   RNA-seq libraries were prepared from 300 ng RNA using the TruSeq RNA Sample Preparation kit (Illumina) and 75-bp single-end sequences were obtained on a NextSeq 500 Instrument (Illumina).


title: PRO20150916_C1_94

value: debris


title: fed H3K27ac ChIP-seq rep#3

source_name: liver


title: D14-3

description: RNA extracted from mES derived cells

value: Day 14

value: Early Thyroid Progenitors


title: D14-2

description: RNA extracted from mES derived cells


title: fed H3K27ac ChIP-seq rep#1


title: PRO20150916_C1_91


title: D7-3

description: RNA extracted from mES derived cells


title: D14-1

description: RNA extracted from mES derived cells


title: PRO20150916_C1_90


title: PRO20150916_C1_88

value: empty


title: PRO20150916_C1_86


title: PRO20150916_C1_84


title: PRO20150916_C1_83


title: PRO20150916_C1_82


title: PRO20150916_C1_96


title: HCT116_shRNA#3_1 - RNAseq

description:
CNOT3_depleted_1
RNAseq
Total RNA was extracted with TRIzol reagent (Invitrogen) and the RNeasy Mini Kit (Qiagen). RNA was treated with the Turbo DNA-free kit (Ambion) to remove genomic DNA.   RNA-seq libraries were prepared from 300 ng RNA using the TruSeq RNA Sample Preparation kit (Illumina) and 75-bp single-end sequences were obtained on a NextSeq 500 Instrument (Illumina).


title: D1-1

description: RNA extracted from mES derived cells


title: PRO20150916_C1_79


title: PRO20150916_C1_93


title: PRO20150916_C1_80


title: PRO20150916_C1_76

value: dead


title: PRO20150916_C1_81


title: PRO20150916_C1_92


title: PRO20150916_C1_74


title: PRO20150916_C1_71


title: PRO20150916_C1_70


title: PRO20150916_C1_89


title: PRO20150916_C1_67


title: PRO20150916_C1_65


title: PRO20150916_C1_87

value: nodata


title: PRO20150916_C1_85


title: D7-1

description: RNA extracted from mES derived cells


title: PRO20150916_C1_78


title: PRO20150916_C1_77


title: PRO20150916_C1_62


title: PRO20150916_C1_61


title: PRO20150916_C1_59


title: PRO20150916_C1_63


title: PRO20150916_C1_58


title: PRO20150916_C1_73


title: PRO20150916_C1_72


title: PRO20150916_C1_69


title: PRO20150916_C1_68


title: PRO20150916_C1_66


title: PRO20150916_C1_75


title: PRO20150916_C1_64


title: PRO20150916_C1_50


title: PRO20150916_C1_51


title: PRO20150916_C1_49


title: PRO20150916_C1_60


title: PRO20150916_C1_45


title: PRO20150916_C1_43


title: PRO20150916_C1_42


title: PRO20150916_C1_57


title: PRO20150916_C1_56


title: PRO20150916_C1_55


title: PRO20150916_C1_53


title: PRO20150916_C1_54


title: PRO20150916_C1_41


title: PRO20150916_C1_48


title: PRO20150916_C1_47


title: PRO20150916_C1_36


title: PRO20150916_C1_46


title: PRO20150916_C1_44


title: PRO20150916_C1_52


title: PRO20150916_C1_35


title: PRO20150916_C1_31


title: PRO20150916_C1_30


title: PRO20150916_C1_38


title: PRO20150916_C1_32


title: PRO20150916_C1_33


title: PRO20150916_C1_29


title: PRO20150916_C1_40


title: PRO20150916_C1_27


title: PRO20150916_C1_26


title: CD24minusplus2

description:
CD24minus-CD24plus
Started from a CD24 negative K562 cell population. Re-sorted after 5 days for CD24. CD24 positive at day5. Replicate2

value: CML cell line


title: PRO20150916_C1_25


title: PRO20150916_C1_22


title: PRO20150916_C1_21


title: PRO20150916_C1_37


title: PRO20150916_C1_39


title: PRO20150916_C1_24


title: PRO20150916_C1_20


title: PRO20150916_C1_18


title: PRO20150916_C1_23


title: PRO20150916_C1_16


title: PRO20150916_C1_19


title: PRO20150916_C1_14


title: PRO20150916_C1_34


title: PRO20150916_C1_13


title: PRO20150916_C1_28


title: PRO20150916_C1_8


title: PRO20150916_C1_9


title: PRO20150916_C1_12


title: PRO20150916_C1_7


title: PRO20150916_C1_11


title: PRO20150916_C1_6


title: PRO20150916_C1_5


title: PRO20150916_C1_4


title: PRO20150916_C1_3


title: PRO20150916_C1_1


title: PRO20150814_C1_96

data_processing:
Cutadapt-1.2.1 of 3p adaptor 'CTGTCTCTTATACACATCT',
Discarding of trimmed reads with length < 50b,
Filtering of reads not starting with a perfect 14b 5p adaptor 'AAGTCGCAGGGTTG', then a well formatted HUMI sequence (we require a well formated N4H4 HUMI in this N6H4 HUMI experiment) followed by at least 3 'G' before cDNA sequence,
Extraction of 5p adaptor, UMI and strech of 'G',
Mapping with STAR_2.4.0a versus hg19 using encodeproject.org RNA-seq options "--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000"
Drop-seq_tools-1.0 dropseq.jar tool for tagging with Gene information from Ensembl release GRCh37.75, then DigitalExpression calling with default parameters (edit distance=1).
Genome_build: hg19
Supplementary_files_format_and_content: PRO20150814_C1_dge_ed1.txt: quantifcation file containing for each gene detected in at least one sample the number of mRNA (unique molecular identifier) molecules counted for this gene.

growth_protocol: Culture was performed according to Marcet et al (https://www.ncbi.nlm.nih.gov/pubmed/21602795) with time of differentiation equal to 52 days (air liquid interface). Culture medium was differentiation medium consisting of 1:1 DMEM (Invitrogen, Gibco) and bronchial epithelial basal medium (Lonza) with the Clonetics complements for human Epidermal Growth Factor (hEGF) (0.5 ng ml 1), epinephrine (5 g ml 1), bovine pituitary extract (BPE).


title: PRO20150916_C1_2


title: PRO20150814_C1_95


title: PRO20150916_C1_17


title: PRO20150814_C1_94


title: PRO20150814_C1_93


title: PRO20150814_C1_92


title: PRO20150814_C1_91


title: PRO20150814_C1_89


title: PRO20150814_C1_87


title: PRO20150814_C1_90


title: PRO20150916_C1_15


title: PRO20150814_C1_88


title: PRO20150916_C1_10


title: PRO20150814_C1_85


title: PRO20150814_C1_86


title: PRO20150814_C1_84


title: PRO20150814_C1_82


title: PRO20150814_C1_83


title: PRO20150814_C1_81


title: PRO20150814_C1_80


title: PRO20150814_C1_79


title: PRO20150814_C1_78


title: PRO20150814_C1_76


title: PRO20150814_C1_77


title: PRO20150814_C1_75


title: PRO20150814_C1_74

value: weird green + debris


title: PRO20150814_C1_69


title: PRO20150814_C1_70

value: weird


title: PRO20150814_C1_68


title: PRO20150814_C1_71

value: red + green


title: PRO20150814_C1_67


title: PRO20150814_C1_65


title: PRO20150814_C1_62


title: PRO20150814_C1_63


title: PRO20150814_C1_64


title: PRO20150814_C1_59


title: PRO20150814_C1_57

value: big


title: PRO20150814_C1_56

value: not stain


title: PRO20150814_C1_55


title: PRO20150814_C1_53


title: PRO20150814_C1_60


title: PRO20150814_C1_52


title: PRO20150814_C1_54


title: PRO20150814_C1_51


title: PRO20150814_C1_58


title: PRO20150814_C1_49


title: PRO20150814_C1_72


title: PRO20150814_C1_73

value: 1 cell in + 1 cell out


title: PRO20150814_C1_47


title: PRO20150814_C1_48


title: PRO20150814_C1_66


title: PRO20150814_C1_45


title: PRO20150814_C1_61


title: PRO20150814_C1_42


title: PRO20150814_C1_43


title: PRO20150814_C1_41


title: PRO20150814_C1_44


title: PRO20150814_C1_40


title: PRO20150814_C1_39


title: PRO20150814_C1_38


title: PRO20150814_C1_37


title: PRO20150814_C1_35


title: PRO20150814_C1_34


title: PRO20150814_C1_36


title: PRO20150814_C1_33


title: PRO20150814_C1_32


title: PRO20150814_C1_50


title: PRO20150814_C1_31


title: PRO20150814_C1_30


title: PRO20150814_C1_29


title: PRO20150814_C1_46


title: PRO20150814_C1_25

value: 1green+debris red


title: PRO20150814_C1_28


title: PRO20150814_C1_24


title: PRO20150814_C1_27


title: PRO20150814_C1_23


title: PRO20150814_C1_22


title: PRO20150814_C1_26


title: PRO20150814_C1_20


title: PRO20150814_C1_18


title: PRO20150814_C1_19


title: PRO20150814_C1_16


title: PRO20150814_C1_15


title: PRO20150814_C1_21


title: PRO20150814_C1_17

value: Debris


title: PRO20150814_C1_11


title: PRO20150814_C1_12


title: PRO20150814_C1_8


title: PRO20150814_C1_9

value: 1cell in + 1 cell out


title: PRO20150814_C1_7

value: human nasal epithelial cell (HNEC)


title: PRO20150814_C1_6


title: PRO20150814_C1_4

value: green + red


title: PRO20150814_C1_5


title: PRO20150814_C1_3


title: PRO20150814_C1_1


title: PRO20160225_C1_95

data_processing:
Cutadapt-1.2.1 of 3p adaptor 'CTGTCTCTTATACACATCT',
Discarding of trimmed reads with length < 50b,
Filtering of reads not starting with a perfect 14b 5p adaptor 'AAGTCGCAGGGTTG', then a well formatted HUMI sequence. The UMI sequence was N6H4. We analyzed only N4H4 part of the UMI for compatibility with replicates where a N4H4 UMI was used.  We require a well formated N4H4 HUMI followed by at least 3 'G' before cDNA sequence
Extraction of 5p adaptor, UMI and strech of 'G',
Mapping with STAR_2.4.0a versus hg19 using encodeproject.org RNA-seq options "--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000"
Drop-seq_tools-1.0 dropseq.jar tool for tagging with Gene information from Ensembl release GRCh37.75, then DigitalExpression calling with default parameters (edit distance=1).
Genome_build: hg19
Supplementary_files_format_and_content: PRO20160225_C1_dge_ed1_76cells.txt: quantifcation file containing for each gene detected in at least one sample the number of mRNA (unique molecular identifier) molecules counted for this gene.

growth_protocol: HEK293 cells were cultured in DMEM medium supplemented with glutamine and 10% fetal calf serum.

extract_protocol:
HEK-293 cells were loaded onto a Fluidigm 96 cell IFC and lyzed with 0.2% w/v Tween 20, 1 U/ul Promega RNAsin RNAse inhibitor, 2 µM reverse transcription primer (TGCGGTATCTAAAGCGGTGAGT(30)VN), 2.5 mM dNTPs, 1x C1 loading reagent (Fluidigm), ERCC Spike-In Mix 1 @ 20,000 molecules/cell (Life Technologies). Cells were lyzed for 10 min at room temperature followed by 3 min at 70°C and 3 min at 10°C.
Cells were processed in a 96 cell Fluidigm C1 IFC. Reverse transcription: 18 nl of 1.75 x  reverse transcription mix, 8.75 mM DTT, 1.75 M Betaine, 10.5 mM MgCl2, 1.75 uM template switching oligonucleotide (GCAATGAAGTCGCAGGGTTGN(4)H(4)rGrGrG), 0.5 U/ul Promega RNAsin, 5.5 U/ul Life Technologies Superscript II reverse transcriptase, 1x C1 loading reagent were added to each lysed cell and incubated for 10 min at 25°C, 90 min at 42°C, 15 min at 70°C. PCR amplification: 270 nl 1.15 x KAPAHiFi HotStart Ready Mix, 55 nM barcode primer (TGCGGTATCTAAAGCGGTGAGCCATCTCATCCCTGCGTGTCTCCGACTCAG<index>GCAATGAAGTCGCAGGGTTG, indices were standard ion torrent barcodes) and 1.1 µM biotinylated PCR primer were back-loaded to each cell. PCR amplification was for 3 min at 98°C followed by 18 cycles at 98°C for 20 sec, 64°C for 15 sec, 72°C for 6 min, and a final extension at 72°C for 5 min. Fragmentation and library preparation: Barcoded, amplified cDNA from all cells was pooled and fragmented by tagmentation with EzTn5 transposase (Epicentre) and Tn5 mosaic end duplexes (upper: 5’-AGA TGT GTA TAA GAG ACA-3’, lower: 5’-PhosCTG TCT CTT ATA CAC ATC T-3’), 5’ terminal (biotinylated) fragments were isolated with streptavidin beads and Ion Torrent adapter sequences were added by PCR (Primers: CCATCTCATCCCTGCGTGTCTC, 0.5 μM; CCACTACGCCTCCGCTTTCCTC, 0.5 μM; CCACTACGCCTCCGCTTTCCTCTCTATGGGCAGTCGGTGATAGATGTGTATAAGAGACAG,  0.125 μM).
5' selective, oligo-dT-primed RNA-seq based on the SmartSeq technique.


title: PRO20160225_C1_94


title: PRO20160225_C1_92


title: PRO20160225_C1_90


title: PRO20160225_C1_91


title: PRO20160225_C1_89


title: PRO20160225_C1_88


title: PRO20150814_C1_14


title: PRO20150814_C1_13


title: PRO20160225_C1_85


title: PRO20150814_C1_10


title: PRO20160225_C1_82


title: PRO20160225_C1_81


title: PRO20160225_C1_79


title: PRO20160225_C1_75


title: PRO20160225_C1_80


title: PRO20160225_C1_84


title: PRO20160225_C1_77


title: PRO20160225_C1_71


title: PRO20150814_C1_2


title: PRO20160225_C1_73


title: PRO20160225_C1_87


title: PRO20160225_C1_68


title: PRO20160225_C1_69


title: PRO20160225_C1_96


title: PRO20160225_C1_74


title: PRO20160225_C1_65


title: PRO20160225_C1_63


title: PRO20160225_C1_66


title: PRO20160225_C1_61


title: PRO20160225_C1_60


title: PRO20160225_C1_59


title: PRO20160225_C1_56


title: PRO20160225_C1_57


title: PRO20160225_C1_55


title: PRO20160225_C1_67


title: PRO20160225_C1_53


title: PRO20160225_C1_51


title: PRO20160225_C1_44


title: PRO20160225_C1_48


title: PRO20160225_C1_46


title: PRO20160225_C1_54


title: PRO20160225_C1_50


title: PRO20160225_C1_49


title: PRO20160225_C1_40


title: PRO20160225_C1_33


title: PRO20160225_C1_34


title: PRO20160225_C1_64


title: PRO20160225_C1_38


title: PRO20160225_C1_36


title: PRO20160225_C1_35


title: PRO20160225_C1_62


title: PRO20160225_C1_32


title: PRO20160225_C1_30


title: PRO20160225_C1_31


title: PRO20160225_C1_29


title: PRO20160225_C1_26


title: PRO20160225_C1_25


title: PRO20160225_C1_28


title: PRO20160225_C1_27


title: PRO20160225_C1_22


title: PRO20160225_C1_23


title: PRO20160225_C1_18


title: PRO20160225_C1_42


title: PRO20160225_C1_16


title: PRO20160225_C1_17


title: PRO20160225_C1_39


title: PRO20160225_C1_13


title: PRO20160225_C1_15


title: PRO20160225_C1_12


title: PRO20160225_C1_10


title: PRO20160225_C1_9


title: PRO20160225_C1_7


title: PRO20160225_C1_11


title: PRO20160225_C1_8


title: PRO20160225_C1_2


title: PRO20160225_C1_3


title: PRO20160225_C1_6


title: PRO20150702_C1_88

data_processing:
Cutadapt-1.2.1 of 3p adaptor 'CTGTCTCTTATACACATCT',
Discarding of trimmed reads with length < 50b,
Filtering of reads not starting with a perfect 14b 5p adaptor 'AAGTCGCAGGGTTG', then a well formatted HUMI sequence (N4H4) followed by at least 3 'G' before cDNA sequence,
Extraction of 5p adaptor, UMI and strech of 'G',
Mapping with STAR_2.4.0a versus hg19 using encodeproject.org RNA-seq options "--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000"
Drop-seq_tools-1.0 dropseq.jar tool for tagging with Gene information from Ensembl release GRCh37.75, then DigitalExpression calling with default parameters (edit distance=1).
Genome_build: hg19
Supplementary_files_format_and_content: PRO20150702_C1_dge_ed1_38cells.txt: quantifcation file containing for each gene detected in at least one sample the number of mRNA (unique molecular identifier) molecules counted for this gene.


title: PRO20160225_C1_1


title: PRO20160225_C1_5


title: PRO20150702_C1_84


title: PRO20150702_C1_82


title: PRO20150702_C1_85


title: PRO20150702_C1_81


title: PRO20150702_C1_83


title: PRO20150702_C1_71


title: PRO20150702_C1_68


title: PRO20150702_C1_66


title: PRO20150702_C1_65


title: tph2-/-  AGM-2

city: beijing

first: Lv

last: Junhua

state: beijing

address: 1 Beichen West Road, Chaoyang District

institute: INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES

description:
AGM of  tph2-/- rep2
164-7

data_processing:
Reads were aligned to the GRCm38 genome assembly using TopHat v2.0.9
For each sample, reads counts of all genes were computed using HTSeq v0.5.3p9
Identifieded differentially expressed genes with R package DEGseq
Genome_build: GRCm38
Supplementary_files_format_and_content: Gene expression for each gene of all samples

source_name: mouse

extract_protocol:
The total RNA was extracted using TRNzol  (Tiangen, Beijing) using the AGMs from two littermate pairs of tph2+/+, tph2+/- or tph2-/- at E11.5
Approximately 1 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 (Illumina) in paired-read mode, creating reads with a length of 150 bp.

value: AGM cells

tag: age

tag: tissue

value: embryos


title: PRO20150702_C1_64


title: PRO20150702_C1_62


title: tph2-/-  AGM-1

description:
AGM of  tph2-/- rep1
164-2

tag: strain


title: PRO20150702_C1_58


title: tph2+/-  AGM-2

description:
AGM of  tph2+/- rep2
164-4


title: tph2+/-  AGM-1

description:
AGM of  tph2+/- rep1
164-3


title: PRO20150702_C1_54


title: PRO20150702_C1_48


title: PRO20150702_C1_46


title: PRO20150702_C1_49


title: tph2+/+  AGM-2

description:
AGM of  tph2+/+ rep2
164-8


title: PRO20150702_C1_31


title: tph2+/+  AGM-1

description:
AGM of  tph2+/+ rep1
164-6


title: PRO20150702_C1_29


title: PRO20150702_C1_39


title: PRO20150702_C1_43


title: PRO20150702_C1_36


title: PRO20150702_C1_45


title: PRO20150702_C1_69


title: PRO20150702_C1_22


title: PRO20150702_C1_26


title: PRO20150702_C1_27


title: PRO20150702_C1_20


title: PRO20150702_C1_19


title: PRO20150702_C1_18


title: PRO20150702_C1_35


title: PRO20150702_C1_1


title: PRO20150702_C1_12


title: PRO20150702_C1_16


title: PRO20150702_C1_56


title: PRO20150702_C1_9


title: PRO20150702_C1_7


title: PRO20150702_C1_6


title: PRO20151215_C1_85

data_processing:
Cutadapt-1.2.1 of 3p adaptor 'CTGTCTCTTATACACATCT',
Discarding of trimmed reads with length < 50b,
Filtering of reads not starting with a perfect 14b 5p adaptor 'AAGTCGCAGGGTTG', then a well formatted HUMI sequence (N4H4) followed by at least 3 'G' before cDNA sequence,
Extraction of 5p adaptor, UMI and strech of 'G',
Mapping with STAR_2.4.0a versus hg19,
Drop-seq_tools-1.0 dropseq.jar tool for tagging with Gene information from Ensembl release GRCh37.75, then DigitalExpression calling with default parameters (edit distance=1).
Genome_build: hg19
Supplementary_files_format_and_content: PRO20151215_C1_dge_ed1.txt: quantifcation file containing for each gene detected in at least one sample the number of mRNA (unique molecular identifier) molecules counted for this gene.


title: PRO20151215_C1_80


title: PRO20151215_C1_75


title: PRO20151215_C1_73


title: PRO20151215_C1_74


title: PRO20151215_C1_86


title: PRO20151215_C1_87


title: PRO20151215_C1_69


title: PRO20151215_C1_62


title: PRO20151215_C1_53


title: PRO20151215_C1_55


title: PRO20151215_C1_57


title: PRO20151215_C1_67


title: PRO20151215_C1_52


title: PRO20151215_C1_51


title: PRO20151215_C1_56


title: PRO20151215_C1_50


title: PRO20151215_C1_48


title: PRO20151215_C1_40


title: PRO20151215_C1_39


title: PRO20151215_C1_44


title: PRO20151215_C1_31


title: PRO20151215_C1_34


title: PRO20151215_C1_33


title: PRO20151215_C1_35


title: PRO20151215_C1_32


title: PRO20151215_C1_28


title: PRO20151215_C1_27


title: PRO20151215_C1_23


title: PRO20151215_C1_22


title: PRO20151215_C1_20


title: PRO20151215_C1_18


title: PRO20151215_C1_21


title: PRO20151215_C1_16


title: PRO20151215_C1_15


title: PRO20151215_C1_43


title: PRO20151215_C1_45


title: PRO20151215_C1_9


title: PRO20151215_C1_14


title: PRO20151215_C1_8


title: PRO20151215_C1_10


title: PRO20151215_C1_5


title: PRO20151215_C1_2


title: PRO20151215_C1_7


title: PRO20150702_BatchB_replicate3

data_processing:
Cutadapt-1.2.1 of 3p adaptor 'CTGTCTCTTATACACATCT',
Discarding of trimmed reads with length < 50b,
Filtering of reads not starting with a perfect 14b 5p adaptor 'AAGTCGCAGGGTTG', then a well formatted HUMI sequence (N4H4) followed by at least 3 'G' before template sequence,
Extraction of 5p adaptor, UMI and strech of 'G',
Mapping with STAR_2.4.0a versus hg19,
Drop-seq_tools-1.0 dropseq.jar tool for tagging with Gene information from Ensembl release GRCh37.75, then DigitalExpression calling with default parameters (edit distance=1).
Genome_build: hg19
Supplementary_files_format_and_content: PRO20150626_0207_dge_ed1.txt: quantifcation file containing for each gene detected in at least one sample the number of mRNA molecules counted for this gene.

extract_protocol:
1000 HEK-293 cells in 4.5 ul C1 wash buffer (Fluidigm) were lysed with 9 ul of lysis buffer (0.2% w/v Tween 20, 1 U/ul Promega RNAsin RNAse inhibitor, 2 µM reverse transcription primer (TGCGGTATCTAAAGCGGTGAGT(30)VN), 2.5 mM dNTPs, 1x C1 loading reagent (Fluidigm), ERCC Spike-In Mix 1 @ 20,000 molecules/cell (Life Technologies). The sample was incubated for 10 min at room temperature followed by 3 min at 70°C and 3 min at 10°C.
Reverse transcription: 18 ul of 1.75 x  reverse transcription mix, 8.75 mM DTT, 1.75 M Betaine, 10.5 mM MgCl2, 1.75 uM template switching oligonucleotide (GCAATGAAGTCGCAGGGTTGN(4)H(4)rGrGrG), 0.5 U/ul Promega RNAsin, 5.5 U/ul Life Technologies Superscript II reverse transcriptase, 1x C1 (Fluidigm) loading reagent were added to the lysed cells and the sample was incubated for 10 min at 25°C, 90 min at 42°C, 15 min at 70°C and kept below 10°C until PCR amplification.   PCR amplification and barcoding: One tenth of the reverse transcription (3.15 µl, 100 cells) was mixed with 27 µl 1.15 x Kappa KAPAHiFiHiFi HotStart Ready Mix, 55 nM barcode primer (TGCGGTATCTAAAGCGGTGAGCCATCTCATCCCTGCGTGTCTCCGACTCAG<index>GCAATGAAGTCGCAGGGTTG, indices are Ion Torrent standard indices),  1.1 µM biotinylated PCR primer (Bio-TGCGGTATCTAAAGCGGTGAG). For PCR amplification samples were incubated 3 min at 98°C followed by 18 cycles at 98°C for 20 sec, 64°C for 15 sec, 72°C for 6 min, and a final extension at 72°C for 5 min. Fragmentation and library preparation: PCR products were fragmented by tagmentation with EzTn5 transposase (Epicentre) and Tn5 mosaic end duplexes (upper: 5’-AGA TGT GTA TAA GAG ACA-3’, lower: 5’-PhosCTG TCT CTT ATA CAC ATC T-3’), 5’ terminal (biotinylated) fragments were isolated with streptavidin beads and and Ion Torrent adapter sequences were added by PCR (Primers: CCATCTCATCCCTGCGTGTCTC, 0.5 μM; CCACTACGCCTCCGCTTTCCTC, 0.5 μM; CCACTACGCCTCCGCTTTCCTCTCTATGGGCAGTCGGTGATAGATGTGTATAAGAGACAG,  0.125 μM).
5' selective, oligo-dT-primed RNA-seq based on the SmartSeq technique.

tag: batch

value: B


title: PRO20150702_BatchB_replicate1


title: PRO20151215_C1_38


title: PRO20151215_C1_3


title: PRO20150702_BatchB_replicate2


title: PRO20150626_BatchA_replicate2

value: A


title: merged_Hyl-2-G3

city: Denton

first: Rajeev

middle: K.

last: Azad

state: Texas

address: 1155 Union Circle #305220

institute: University of North Texas

data_processing:
Used Tophat and Bowtie for read alignment onto Caenorhabditis elegans reference genome and Cufflinks for obtaining the FPKMs and assessment of significance of fold change
Genome_build: C. elegans genome build WS195
Supplementary_files_format_and_content: Tab-delimited file (opens in Excel); FPKMs for wild-type Bristol (N2), hyl-2(tm2031), glucose-fed N2, and glucose-fed hyl-2(tm2031)

organism: Caenorhabditis elegans

source_name: Whole animal

growth_protocol: The wild-type Bristol (N2) and hyl-2(tm2031) strains were cultured using NGM plates seeded with E. coli (OP50 or HT115) and raised at 20ºC. To obtain animals of the specified stage of development for each experiment as noted below, one-day old adult hermaphrodites were allowed to lay eggs on a plate (1-2 hours), and anatomical markers such as gonad morphology and time post molting stage were used to identify the developmental stage of the subsequent offspring.

extract_protocol:
4 volumes of Trizol per volume of animals were added. The tubes were immediately frozen in liquid nitrogen, thawed and briefly vortexed; this step was repeated and then followed by a 5-minute incubation at room temperature. To each tube 0.2 ml of chloroform per 1 ml of Trizol was added, mixed gently, for 15 seconds, incubated at room temperature for 2-3 minutes, and then centrifuged at 12,000g for 15 minutes at 4ºC. The colorless upper phase was transferred to an RNase free tube. RNA was then purified using an Ambion PureLink RNA Mini Kit (Cat#12183018A). Following RNA purification, the RNA was treated with DNase I (Life Technologies Cat# 12185010), quantified using a NanoDrop Spectrophotometer and stored at -80ºC.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Animals (N2 and hyl-2) were fed a glucose-supplemented diet. Glucose (Sigma) solution is spread evenly, fully covering the entire plate, and allowed to dry before being seeded with bacteria (OP50, HT115 or appropriate RNAi strain).

tag: Stage

value: young non gravid adult hermaphrodite

tag: diet

value: OP50 and glucose


title: merged_Hyl-2-G2


title: MCF10a_rep5

city: Charlottesville

first: Michael

last: Guertin

state: Virginia

address: 1340 Jefferson Park Ave

institute: University Of Virginia

data_processing:
library strategy: ATAC-seq
Align with bowtie2
Merge bam files for all replicates
Normalize and create BedGraph, bigWig
Peak calling with hotspot (standard paramters)
Genome_build: hg38
Supplementary_files_format_and_content: bedGraph and bigWig file for merged replicates, hotspot file with spots calculated by hotspot with fdr <0.01

source_name: mammary epithelial cell line

growth_protocol: MCF10A cells were cultured in Dulbecco’s modified Eagle’s medium DMEM (Invitrogen) with 5% horse serum (Invitrogen), 1% penicillin/streptomycin (Invitrogen), 20 ng/ml EGF (Peprotech), 0.5 μg/ml hydrocortisone(Sigma), 100 ng/ml cholera toxin (Sigma) and 10 μg/ml insulin (Sigma) . Cells were grown in a humidified incubator at 37°C with 5% CO2.

extract_protocol:
Cell lysis in hypotonic solution
nextera kit

treatment_protocol: baseline

value: mammary epithelial cell line

tag: cell status

value: Healthy cells with passage number < 30


title: PRO20150626_BatchA_replicate1


title: MCF10a_rep6


title: MCF10a_rep3


title: PRO20151215_C1_17


title: MCF10a_rep1


title: HEK bulk rep2

data_processing:
Cutadapt-1.2.1 of 3p adaptor 'CTGTCTCTTATACACATCT',
Discarding of trimmed reads with length < 50b,
Filtering of reads not starting with a well formatted HUMI sequence (N6H4) followed by at least 3 'G' before template sequence,
Extraction of UMI and strech of 'G',
Mapping with STAR_2.4.0a versus hg19,
Drop-seq_tools-1.0 dropseq.jar tool for tagging with Gene information from Ensembl release GRCh37.75, then DigitalExpression calling with default parameters (edit distance=1).
Genome_build: hg19
Supplementary_files_format_and_content: NS20160217_dge_ed1.txt: quantifcation file containing for each gene detected in at least one sample the number of mRNA molecules counted for this gene.

extract_protocol:
1000 HEK-293 cells in 4.5 ul C1 wash buffer (Fluidigm) were lysed with 9 ul of lysis buffer (0.2% w/v Tween 20, 1 U/ul Promega RNAsin RNAse inhibitor, 2 µM reverse transcription primer (AGGGTAATCGTCGGTGTCCAT(30)VN), 2.5 mM dNTPs, 1x C1 loading reagent (Fluidigm), ERCC Spike-In Mix 1 @ 20,000 molecules/cell (Life Technologies). The sample was incubated for 10 min at room temperature followed by 3 min at 70°C and 3 min at 10°C.
Reverse transcription: 18 ul of 1.75 x  reverse transcription mix, 8.75 mM DTT, 1.75 M Betaine, 10.5 mM MgCl2, 1.75 uM template switching oligonucleotide (rGrCrArArUrGrArArGrUrCrGrCrArGrGrGrUrUrGN(6)H(4)rGrGrG), 0.5 U/ul Promega RNAsin, 5.5 U/ul Life Technologies Superscript II reverse transcriptase, 1x C1 (Fluidigm) loading reagent were added to the lysed cells and the sample was incubated for 10 min at 25°C, 90 min at 42°C, 15 min at 70°C and kept below 10°C until PCR amplification.   PCR amplification and barcoding: One tenth of the reverse transcription (3.15 µl, 100 cells) was mixed with 27 µl 1.15 x Kappa KAPAHiFiHiFi HotStart Ready Mix, 55 nM barcode primer (TGCGGTATCTAAAGCGGTGAG<index>ACACTCTTTCCGCAATGAAGTCGCAGGGTTG, indices are Illumina Truseq indices),  1.1 µM biotinylated PCR primer (Bio-TGCGGTATCTAAAGCGGTGAG),  reverse PCR primer (1.1 uM, AGGGTAATCGTCGGTGTCCA). For PCR amplification samples were incubated 3 min at 98°C followed by 18 cycles at 98°C for 20 sec, 64°C for 15 sec, 72°C for 6 min, and a final extension at 72°C for 5 min. Library preparation: PCR products were fragmented by tagmentation with EzTn5 transposase (Epicentre) and Tn5 mosaic end duplexes (upper: 5’-AGA TGT GTA TAA GAG ACA-3’, lower: 5’-PhosCTG TCT CTT ATA CAC ATC T-3’), 5’ terminal fragments were isolated with streptavidin beads and Illumina adapter sequences were added by PCR (Primers: AATGATACGGCGACCACCGAGAT, 0.5 μM; AATGATACGGCGACCACCGAGATCTACACCACAGTTGAGTGCGGTATCTAAAGCGGTGAG, 0.125 μM; CAAGCAGAAGACGGCATACGAGAT, 0.5 μM; CAAGCAGAAGACGGCATACGAGATGTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG,  0.125 μM).
5' selective, oligo-dT-primed RNA-seq based on the SmartSeq technique. Libraries were sequenced with custom sequencing primers.  Custom read1 seq. Primer: ACACTCTTTCCGCAATGAAGTCGCAGGGTTG; Custom read2 seq. Primer: GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG;  Custom index seq. Primer: CCACAGTTGAGTGCGGTATCTAAAGCGGTGAG


title: HEK bulk rep3


title: merged_Hyl-2-G1


title: merged_Hyl-2-2

value: OP50 food


title: merged_Hyl-2-1


title: HEK bulk rep1


title: AUAWT3

city: Madrid

first: Manuel

middle: J

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

description:
PolyA RNA
AUAWT3_59
Processed data file: matrix_table.txt

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2.
Sequencing adaptor contaminations were removed from reads using Cutadapt v1.3.
Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3.
Genome_build: GRCm38 assembly, Ensembl genebuild 70
Supplementary_files_format_and_content: matrix_table.txt: Tab-delimited text file contains ENSEMBL gene Ids and TMM-Normalized counts per million for each sample.

source_name: Embryonic heart, control

growth_protocol: Experiments were conducted with E12.5 mouse embryos with C57BL/6 background.

extract_protocol:
Total RNA was extracted from ventricular embryonic tissue collected from embryonic hearts by removing atria and valve region using QIAzol Lysis Reagent (Qiagen; CA; USA) and miRNeasy Mini Kit (Qiagen; CA; USA).
RNA was quantified and purity checked using a NanoDrop ND-1000 (Thermo Scientific; MA; USA). RNA integrity was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies; CA; USA). 500 ng of total RNA were used with the TruSeq RNA Sample Preparation v2 Kit (Illumina; CA; USA) to construct index-tagged cDNA libraries.
RNA-Seq libraries were sequenced (single-end mode and length of 75 bp) on the Genome Analyzer IIx system using the standard RNA sequencing protocol in the TruSeq SBS kit v5.

tag: strain/background

value: Vhl(flox/flox) / Nkx2.5(+/+)

value: Heart (embryonic ventricular tissue)

tag: litter


title: AUAWT2

description:
PolyA RNA
AUAWT2_45
Processed data file: matrix_table.txt

tag: genotype/variation


title: AUAKO3

description:
PolyA RNA
AUAKO3_47
Processed data file: matrix_table.txt

source_name: Embryonic heart, Vhl KO

value: Vhl(flox/flox) / Nkx2.5(Cre/+)


title: AUAKO1

description:
PolyA RNA
AUAKO1_8
Processed data file: matrix_table.txt


title: merged_N2-2

value: N2 wild type


title: merged_N2-G1


title: merged_N2-1


title: merged_N2-G2


title: AUAWT1

description:
PolyA RNA
AUAWT1_7
Processed data file: matrix_table.txt


title: Post-H/S probe 2 CHART_B2

city: Winnipeg

first: Athanasios

last: Zovoilis

state: MB

address: 745 Bannatyne Ave

department: Biochemistry and Medical Genetics

country: Canada

institute: University of Manitoba

description: library strategy: Chart-seq

data_processing:
Base calling was performed based on the respective Illumina pipeline of either HiSeq or MiSeq system.
Trimming of adapter sequences was performed using cutadapt (DOI: http://dx.doi.org/10.14806/ej.17.1.200)  for the following adapter sequences: Short-RNA sequencing: AAGATCGGAAGAGCACACGTCT.  Paired end RNA sequencing: AAGATCGGAAGAGCACACGTCT  and  AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT for read 1 and read 2, respectively.
Mapping to the mm9 mouse genome: Raw short-RNA-seq, CHART-seq, ChIP-seq reads and the respective  sequenced input reads were mapped against mouse mm9 genome using default parameters of  bwa.0.5.5 (PMID: 20080505).  RNA sequencing reads were mapped against mouse mm9 transcriptome using tophat-2.1.0 (PMID:19289445) with the following parameters: bowtie1 -r -100 -N 20 --read-gap-length 10 --segment-mismatches 3  --read-edit-dist 20.
ChIP-seq/CHART-seq noise filtering: Using in home scripts and bedtools (PMID: 20110278) the resulting sam files were converted to bed files and enriched genomics regions against the input were filtered using SICER (PMID: 24743992) with a window and gap parameter of 300 and an FDR 0.05. Subsequently, CHART-seq reads of the B2 probe were filtered further against enriched regions of the negative CHART probe. The resulting filtered reads are presented as processed data files ending in *filtered.bed.
Short-RNA-seq 5'ends: 5' end genomic co-ordinates of the short-RNA-sequencing reads were extracted using in home text parsing scripts  from the bed files created as described in the previous step.  The resulting 5 end read files consisting of three columns (1st: Chr name, 2nd: position, 3rd: strand orientation of the reads' 5'end) were mapped and plotted against the B2 repeat start gemonic co-ordinates as defined by Repeat Masker for mm9 using Seqmonk. Subsequently read counts were normalized as described below. These are presented as processed data files ending in *5ends.txt in which the first column is the absolute distance in nt from repeat start and the second column is the relative read counts. We used the number of reads at position +1 as an internal normalization control. Alternatively, we normalized the number of cut sites to (i) total B2 RNA levels from the respective conventional RNA-seq performed in parallel, in order to exclude increased B2 expression as a confounding factor; and (ii) to tRNA levels which are POL-II-independent. Both normalization methods yielded similar conclusions. Because of single-end 50 nt sequencing, full length B2 RNA or fragments of >50 nt in short-RNA-seq would appear as 50-nt reads. In order to get a better insight into such cases we have also sequenced the short-RNA libraries with miseq in order to produce single end 200nt long reads that would span the full length of B2 RNA. These files include in their name the "short-RNA-longer_reads" term.
RNAseq:Using bedtools, sam files were converted to bedgraph files scaled for the total number of reads per sample and subsequently to bigwig (bw) files using the UCSC wigToBigWig utility.
Genome_build: mm9
Supplementary_files_format_and_content: Bed files represent CHIP-seq or CHART-seq reads filtered against the input using SICER and in case of CHART also against the negative probe CHART sample. Txt files represent the relative counts (2nd column) of the mapped read 5'end of the sequenced short-RNAs (both rep1 and rep2) with regard to the start of the B2 loci (Repeat Masker). Big files represent read counts scaled to the total number of mapped reads.

source_name: NIH/3T3 cells

growth_protocol: NIH/3T3: DMEM plus Glutamax, 10%FBS, 1% Pen/Strep. ES cells:15% FBS, 1%Pen/Strep, high-glucose DMEM+GlutaMAX with supplemented with LIF and cultured on inactivated mouse embryonic fibroblasts feeder layers.

extract_protocol:
RNA: Trizol followed by depletion of ribosomal RNA using the ribominus V2 kit (Life technologies) and  size selection using the mirVana separation kit (Life technologies), DNA: Phenol-Chloroform
Libraries were prepared according to NEB instructions accompanying the following kits: ChIP/CHART-sequencing: NEBNext ChIP-seq library Prep Master MIX set, Short-RNA-sequencing:NEBnext  small RNA library construction kit (NEB), RNA-sequencing: NEBNext Ultra directional RNA library kit (NEB)

treatment_protocol: Heat Shock (45C) 15 minutes. Transfection with LNAs against B2 RNA (500nM) and Ezh2(25nM) for 24h.

value: Fibroblast

tag: passages

tag: chart probe

value: B2 RNA probe 2


title: MCF10a_rep2

tag: cell line


title: merged_Hyl-2-3


title: Pre-H/S rep 2 InputForSuz12_ChIPSeq

tag: chip antibody


title: Post-H/S rep 2 InputForSuz12_ChIPSeq

tag: cell type


title: Pre-H/S rep 1 InputForSuz12_ChIPSeq


title: MP100_PB5 [TGP69]

city: Osaka

first: Ko

last: Omura

address: 2-1-6 Kashima yodogawa-ku

country: Japan

institute: Astellas Pharma Inc.

data_processing:
The obtained tag sequences were mapped onto rat genome (NCBI Rn4) using BioScope 1.3.1 (Life Technologies).
For promoter analysis, arbitrary tag count values were calculated following formula and used as each gene DNA methylation state; normalized values = (number of sequence reads from 4500 bp upstream to 1125 bp downstream of transcription start site of each gene) * 50,000,000 / total coverage number.
Using summed mapped tags of 5 animals in whole genome as one sample, global identification of altered DNA methylation regions and obtaining DNA methylation status of RT1-CE5 were performed using Avadis NGS version 1.4.5 (Strand Life Sciences®, Bangalore, India).
Peak detection algorithm for ChIP analysis was applied to identify the peaks that significantly changed the tag number. Detecting condition: algorithm: enrichment peak detection, enrichment factor: 5, Window size (bp): 100, Minimum reads in window = 10, Window slide size (bp): 50, Minimum region size (bp): 150, Minimum reads in region = 15, Upstream padding distance for genes: 5000.
Genome_build: Rn4
Supplementary_files_format_and_content: Region_4500_1125 files were generated using microsoft Excel.; Scores represent DNA methylation state in promoter of each gene.; peak detection file was generated using Avadis NGS 1.4.5.; Enrichment factor represent hypo/hypermethylated region in livers treated with 30mg/kg of DEN compared with PB group.

organism: Rattus norvegicus

extract_protocol:
Liver DNA samples were obtained and soaked in RNAlater (Life Technologies) to stabilize DNA. Genomic DNA from 5 rat livers of each group was isolated using QIAamp® DNA Mini Kit (Qiagen, Hilden, Germany). Methylated genomic DNA were enriched by MethylMiner methylated DNA enrichment kit (Life Technologies).
For construction of standard fragment libraries, SOLiD Fragment Library Construction Kit (Life Technologies) was utilized. After ligation of adaptor to both end of each fragment, each DNA library was selected by its size (inserts were approximately 250 bp) using SOLiD Library Size Selection kit before nick translation, PCR amplification, bead attachment and emulsion PCR. Library was 50 base read sequenced using SOLiD 4 Analyzer.

treatment_protocol: The animals were treated for 1 or 2 weeks (30 mg/kg of DEN were treated for 1 week because of marked body weight loss) and withdrawn for 2 weeks, then, 500 ppm of phenobarbital was given in drinking water. One week after PB promotion, partial hepatectomy was carried out for all animals. After 6 weeks PB promotion, the animals were euthanized.

tag: initiation/promotion

value: 100mg/kg methapyrilene

tag: promotion

value: 500ppm phenobarbital

tag: timing of sampling

value: terminal euthanasia


title: APAP1000_PB5 [TGP70]

value: 1000mg/kg acetaminophen


title: APAP1000_PB4 [TGP60]


title: APAP1000_PB3 [TGP59]


title: Pre-H/S probe 2 CHART_B2

description: library strategy: Chart-seq


title: MP100_PB4 [TGP58]


title: APAP1000_PB2 [TGP40]


title: merged_N2-G3


title: Post-H/S rep 2 Suz12_ChIPSeq

value: Suz12 (Active motif, catalog# 39357, lot# 28612003)


title: Post-H/S rep 1 Suz12_ChIPSeq


title: merged_N2-3


title: MP100_PB3 [TGP57]


title: Pre-H/S rep 2 Suz12_ChIPSeq


title: Pre-H/S rep 1 Suz12_ChIPSeq


title: mouseEScells Short-RNA-seq

description:
Short-RNA-seq
Processed data file: mouseEScells-short-RNA-5ends.txt

source_name: ES cells

value: Embryonic Stem cells


title: TAA45_PB5 [TGP68]

value: 45mg/kg thioacetamide


title: TAA45_PB4 [TGP56]


title: 20OD

city: Orlando

first: Augusto

last: Schneider

state: FL

address: 6900 Lake Nona Blvd

department: Burnett School of Biomedical Sciences

institute: University of Central Florida

data_processing:
IlluminaCasava1.8 software was used for basecalling; all reads use phred33 quality scores.
Sequence reads were processed using sRNAToolBox, available at: http://bioinfo5.ugr.es/srnatoolbox/. Refernce: Rueda et al. (2015) - doi: 10.1093/nar/gkv555.
The data have not been further normalized or manipulated, so that each user can perform sample (library) depth and other normalization using software such as DESeq or edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file include RPM values for each sample in separate columns processed by EdgeR.

source_name: Ovary

extract_protocol:
Ovaries were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. RNA was extracted according to Matkovich & Dorn (2015; Gary R. Skuse and Maureen C. Ferran (eds.), Cardiomyocytes: Methods and Protocols, Methods in Molecular Biology, vol. 1299, DOI 10.1007/978-1-4939-2572-8_3) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Ames dwarf

tag: age

value: 22 months

tag: genotype

value: df/df


title: MP100_PB2 [TGP38]

tag: strain


title: APAP1000_PB1 [TGP39]


title: 19OD


title: TAA45_PB2 [TGP20]


title: 18OD


title: TAA45_PB1 [TGP19]


title: 16OD


title: Post-H/S rep 1 InputForSuz12_ChIPSeq


title: 22NO

value: N/df


title: 15NO


title: DEN30_PB4 [TGP54]

value: 30mg/kg diethylnitrosamine


title: 14NO


title: DEN30_PB5 [TGP67]


title: 13NO


title: DEN30_PB3 [TGP53]


title: AUAKO2

description:
PolyA RNA
AUAKO2_46
Processed data file: matrix_table.txt

tag: developmental stage

tag: tissue

value: Heart (embryonic ventricular tissue)


title: 10YD

value: 6 months


title: 12NO


title: DEN30_PB1 [TGP17]


title: 23OD


title: 9YD


title: DEN3_PB4 [TGP36]

value: 3mg/kg diethylnitrosamine


title: DEN3_PB3 [TGP35]


title: DEN30_PB2 [TGP18]


title: DEN3_PB5 [TGP66]


title: 8YD


title: 7YD


title: MP100_PB1 [TGP37]


title: DEN3_PB2 [TGP16]


title: TAA45_PB3 [TGP55]


title: DEN3_PB1 [TGP15]


title: 6YD


title: MC_PB5 [TGP52]

value: 0.5% methylcellulose


title: 21NY


title: MC_PB4 [TGP34]


title: 4NY


title: MC_PB1 [TGP13]


title: 2NY


title: MC_PB2 [TGP14]


title: dKD_SMG7_rescue3

city: Bern

first: Oliver

last: Muehlemann

address: Freiestrasse 6

country: Switzerland

institute: University of Bern

description: batchB

data_processing:
quality trimming with Trimmomatic
mapping with TopHat, GTF: Ensembl release 84
counting with HTSeq: reverse strand, union mode
Genome_build: GRCh38
Supplementary_files_format_and_content: gene_counts.csv contains the number of mapped reads assigned to every gene in each condition

extract_protocol:
Total RNA was extracted using the GenElute Mammalian Total RNA Miniprep Kit (Sigma-Aldrich).
Illumina TruSeq Stranded mRNA (chemistry v3), with polyA selection.

value: HeLa cells

tag: gene kd

value: SMG6, SMG7

tag: gene rescue


title: 3NY


title: MC_water5 [TGP51]

value: water


title: dKD_SMG7_rescue1

description: batchB


title: dKD_SMG7_rescue2

description: batchB


title: MC_water3 [TGP31]

value: terminal euthanasia


title: dKD_SMG6_rescue3

description: batchB


title: MC_water4 [TGP32]


title: MC_water1 [TGP11]


title: MC_water2 [TGP12]


title: dKD_SMG6_rescue2

description: batchB


title: Post-H/S rep 2 Short-RNA-seq

description:
Short-RNA-seq
Processed data file: PostHS-short-RNA-5ends.txt

source_name: Post-H/S Short-RNA-seq

value: NIH/3T3 Fibroblasts


title: 5NY


title: B2LNA rep 1 Short-RNA-seq

description:
Short-RNA-seq
Processed data file: B2LNA-short-RNA-5ends.txt

source_name: B2LNA Short-RNA-seq


title: dKD_SMG6_rescue1

description: batchB


title: Post-H/S rep 1 Short-RNA-seq


title: Pre-H/S rep 1 Short-RNA-seq

description:
Short-RNA-seq
Processed data file: PreHS-short-RNA-5ends.txt

source_name: Pre-H/S Short-RNA-seq


title: APAP1000_PB4 [TGP50]

value: 1000mg/kg acetaminophen

value: 500ppm phenobarbital

value: partialhepatectomy


title: CHART-Input-PostHS-rep2

description: library strategy: Chart-seq

source_name: CHART-Input-PostHS


title: MC_PB3 [TGP33]


title: dKD3

description: batchB


title: dKD2

description: batchB


title: UPF1_CLIP_rep1

data_processing:
quality trimming with Trimmomatic
mapping with TopHat, GTF: Ensembl release 77
counting with HTSeq: strand specific, union mode
Genome_build: GRCh38
Supplementary_files_format_and_content: CLIP-seq_gene_counts.csv contains the number of mapped reads assigned to every gene

source_name: HeLa cells

extract_protocol:
After cell lysis in 3 mL hypotonic lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 2 mM EDTA, 0.5% (v/v) Triton X-100, Halt Protease Inhibitor Cocktail), and removal of cell debris by centrifugation, the supernatant was adjusted to 160 mM NaCl and incubated with 30 U RNase I (Ambion) and 15 U Turbo DNase (Ambion) at 37 °C for 7.5 minutes. 160 μL Dynabeads Protein G were incubated with 18 μg of mouse anti-FLAG M2 antibody (Sigma Aldrich), washed and resuspended in 1 mL hypotonic lysis buffer and incubated with the cell lysate at 4 °C for 1.5 hours. The beads were then washed three times with IP-buffer (50 mM HEPES-NaOH pH 7.5, 300 mM KCl, 0.05% (v/v) NP-40, Halt Protease Inhibitor Cocktail).
Illumina TruSeq Stranded mRNA.

treatment_protocol: Knockdown of endogenous UPF1 was induced in HeLa tTR-KRAB-shUPF1 cells (Metze et al., RNA 2013) by addition of 5 mg/mL doxycycline and 8x10e6 cells were transiently transfected with 4 mg of a pcDNA3 expression plasmid encoding a C-terminally Flag-tagged, RNAi-resistant version of UPF1 using 30 mL of Lipofectamine 2000. 44 hours post transfection, cells were washed and cross-linked in ice-cold PBS applying 150 mJ/cm2 UV-C light (Bio-Link BLX-E, 254 nm).

value: HeLa

value: expressing C-terminally flag tagged-UPF1 under endogenous UPF1 knockdown

tag: antibody


title: UPF1_CLIP_rep2

tag: genotype/variation

value: mouse anti-FLAG M2 antibody (Sigma Aldrich)


title: Ezh2-LNA rep 1 Short-RNA-seq

description:
Short-RNA-seq
Processed data file: Ezh2-LNA-short-RNA-5ends.txt

source_name: Ezh2-LNA Short-RNA-seq

tag: passages


title: APAP1000_PB3 [TGP49]


title: CHART-Input-PostHS-rep1

description: library strategy: Chart-seq


title: CHART-Input-PreHS-rep2

description: library strategy: Chart-seq

source_name: CHART-Input-PreHS


title: dKD1

description: batchB


title: CHART-Input-PreHS-rep1

description: library strategy: Chart-seq


title: Pre-H/S rep 2 Short-RNA-seq


title: SMG7_rescue3

description: batchB


title: SMG7_rescue2

description: batchB


title: MP100_PB5 [TGP64]

value: 100mg/kg methapyrilene


title: MP100_PB4 [TGP48]


title: SMG7_rescue1

description: batchB


title: SMG7_KD3

description: batchB


title: CHART-Negative-rep1

description: library strategy: Chart-seq

source_name: CHART-Negative

tag: chart probe

value: Negative probe


title: MP100_PB3 [TGP47]

source_name: liver


title: CHART-Negative-rep2

description: library strategy: Chart-seq


title: APAP1000_PB1 [TGP29]


title: SMG7_KD1

description: batchB


title: Pre-H/S rep 2 CHART_B2

description: library strategy: Chart-seq

source_name: Pre-H/S CHART_B2

value: B2 RNA probe 1


title: SMG7_KD2

description: batchB


title: Post-H/S rep 2 CHART_B2

description: library strategy: Chart-seq

source_name: Post-H/S CHART_B2


title: scr6

description: batchB

value: scramble


title: MP100_PB2 [TGP28]


title: TAA45_PB5 [TGP63]

value: 45mg/kg thioacetamide


title: MP100_PB1 [TGP27]


title: Post-H/S rep 1 CHART_B2

description: library strategy: Chart-seq


title: scr5

description: batchB


title: Pre-H/S rep 1 CHART_B2

description: library strategy: Chart-seq


title: APAP1000_PB2 [TGP30]


title: TAA45_PB4 [TGP46]


title: Post-H/S rep 2 Input_ChIPSeq

source_name: Post-H/S Input_ChIPSeq


title: scr4

description: batchB


title: Pre-H/S rep 2 Input_ChIPSeq

source_name: Pre-H/S Input_ChIPSeq


title: SMG6_rescue3

description: batchA


title: Post-H/S rep 2 Pol II S2P_ChIPSeq

source_name: Post-H/S Pol II S2P_ChIPSeq

value: Pol II S2P panel (Abcam, catalog# ab103968, lot# 139798-3)


title: TAA45_PB2 [TGP10]


title: B2LNA rep 2 Pol II S2P_ChIPSeq

source_name: B2LNA Pol II S2P_ChIPSeq


title: SMG6_rescue2

description: batchA

value: HeLa cells


title: TAA45_PB1 [TGP09]


title: SMG6_KD3

description: batchA


title: SMG6_rescue1

description: batchA


title: DEN30_PB5 [TGP62]

value: 30mg/kg diethylnitrosamine


title: APAP1000_PB5 [TGP65]


title: Pre-H/S rep 2 Pol II S2P_ChIPSeq

source_name: Pre-H/S Pol II S2P_ChIPSeq


title: DEN30_PB3 [TGP43]


title: Post-H/S rep 2 Ezh2_ChIPSeq

source_name: Post-H/S Ezh2_ChIPSeq

value: Ezh2 (D2C9) (Cell Signaling Technology, catalog# 5246S, lot# 6)


title: SMG6_KD1

description: batchA


title: SMG6_KD2

description: batchA


title: UPF1_rescue3

description: batchA


title: DEN30_PB1 [TGP07]


title: Pre-H/S rep 2 Ezh2_ChIPSeq

source_name: Pre-H/S Ezh2_ChIPSeq


title: Pre-H/S rep 2 H3K27me3_ChIPSeq

source_name: Pre-H/S H3K27me3_ChIPSeq

value: H3K27me3 (Active Motif, catalog# 39155, lot# 23813016)


title: DEN30_PB2 [TGP08]


title: TAA45_PB3 [TGP45]


title: UPF1_rescue2

description: batchA


title: Dentate Gyrus RNAseq [dentategytusWTIE]

city: Newcastle upon Tyne

first: David

last: Elliott

address: 1 Central parkway

department: Institute of Genetic Medcine

country: United Kingdom

institute: Newcastle University

data_processing:
Data filtering; seqtk 1.0; Trim-galore 0.3.5; Perl script to remove poly-N tails
Mapping; Tophat2 2.0.8b.Linux_x86_64
Counting reads mapped to genes; BEDTools 2.17.0
Testing for differentially expressed genes; DESeq2 1.0.19
Counting reads mapped to exons; dexseq_count.py
Testing for differentially used exons; DEXSeq 1.6.0
Genome_build: mm10
Supplementary_files_format_and_content: Tab-deleimited text files Gene count file and exon count files

source_name: Wild type_Dentate Gyrus

growth_protocol: adult mice, kept under standard conditions, and dissected

extract_protocol:
Qiagen Rneasy plus kit
Illumina TruSeq mRNA library preparation

treatment_protocol: No special treatment

tag: strain background

value: Tstar null allele backcrossed onto the C57Bl6 background for 8 generations

value: wild type

value: adult

value: Dentate Gyrus


title: UPF1_rescue1

description: batchA


title: Ammon's Horn RNAseq [595596KOIE]

source_name: Knockout_Ammon's horm

value: Khdrbs3 Knockout

value: Ammon's Horn


title: UPF1_KD3

description: batchA


title: DEN3_PB4 [TGP26]

value: 3mg/kg diethylnitrosamine

value: 500ppm phenobarbital

value: partialhepatectomy


title: DEN3_PB3 [TGP25]


title: DEN30_PB4 [TGP44]


title: Post-H/S rep 2 H3K27me3_ChIPSeq

source_name: Post-H/S H3K27me3_ChIPSeq

value: NIH/3T3 Fibroblasts

tag: chip antibody


title: UPF1_KD2

description: batchA

tag: cell type


title: Ammon's Horn RNAseq [498501KOIE]


title: DEN3_PB2 [TGP06]

tag: initiation/promotion


title: DEN3_PB1 [TGP05]

tag: promotion


title: Ammon's Horn RNAseq [611WTIE]

source_name: Wild type_Ammon's horm


title: MC_PB5 [TGP42]

value: 0.5% methylcellulose

tag: timing of sampling


title: UPF1_KD1

description: batchA


title: scr3

description: batchA

value: scramble


title: Ammon's Horn RNAseq [494499WTIE]

tag: age


title: Ammon's Horn RNAseq [519609WTIE]


title: DEN3_PB5 [TGP61]


title: MC_PB4 [TGP24]


title: scr1

description: batchA


title: scr2

description: batchA


title: MC_PB3 [TGP23]


title: MC_PB1 [TGP03]


title: MC_PB2 [TGP04]


title: MC_water3 [TGP21]

value: water


title: uncntl-2

city: Heidelberg

first: Benjamin

middle: Andrew

last: Story

address: Meyerhofstrasse 1

department: Genomics

country: Germany

institute: European Molecular Biology Laboratory (EMBL)

data_processing:
Basecalls performed using CASAVA version 1.4
Alignment to the human genome using TopHat v 2.0.13
Analysis of alternative splicing event differences using MISO v0.5.2
Genome_build: Ensembl hg19 v67
Supplementary_files_format_and_content: Pairwise comparisons of alternative splicing events, MISO output

source_name: HeLa cells

growth_protocol: HeLa-HIV cells (uninduced with doxycyclin) were grown in the presence of Iscove's Eagle medium + 10% fetal bovine serum grown at 37˚C in 5% CO2. 24 hour incubation of cells with 1C8 at the indicated concentrations.

extract_protocol:
Total RNA was purified using the RNAeasy mini kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols
TrueSeq library from Illumina for RNA-Seq

tag: drug treatment


title: uncntl-4

treatment_protocol: 24 hour incubation of cells with 1C8 at the indicated concentrations


title: MC_water5 [TGP41]

tag: strain


title: MC_water4 [TGP22]