title: Neurons #2

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

data_processing:
Data were aligned to mm9 genome using Bismark v0.7.4 with default settings
bedgraph files were generated by Bismark software
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph files containing the methylation profiles

source_name: cerebral cortex at day 15.5 of embryonic development

extract_protocol:
DNA was isolated by using phenol -choloroform protocol followed by ethanol precipitation.
In order to generate the whole genome libraries with bisulfite converted DNA, neural cell DNA was sonicated to approx. 150 bp DNA fragments. Further, DNA was end repaired by using End-It- DNA End-Repair Kit (Epicentre) and linker ligated with T4 ligase (NEB). The linked ligated DNA was bisulfite converted by using EZ DNA Methylation-Gold™ Kit according to manufacture instructions (Zymo Research) and amplified with Pfu Turbo polymerase (Agilent). Sequencing was performed in Integrative Genomic Core at City of Hope.

treatment_protocol: We used a double transgenic reporter system to purify NPCs and neurons from E15.5 mouse cortex. We used heterozygous nestin-GFP mice and homozygous Dcx-RFP mice to obtain littermate embryos that are positive for both GFP and RFP and also RFP single positive embryos. These embryos were used for obtaining GFP+RFP- cells (NPCs) and RFP+ cells (neurons), respectively, from the same mouse litters.

tag: sample type

value: FACS purified cells

value: Cortical Neurons


title: PBMCs sample_PCH009RNP

status: Public on Dec 31 2017

type: SRA

city: Atlanta

first: Monica

middle: L.

last: Rojas-Peña

state: GA

address: 310 Ferst Dr.

department: School of Biology

country: USA

institute: Georgia Institute of Technology

library_source: transcriptomic

data_processing:
The raw RNA-Seq reads for each sample were aligned to the reference human genome (hg19) using Bowtie as the short read aligner, and splice junctions were identified using TopHat
Estimation of Transcript abundance was estimated at the level of the whole gene as counts per million (cpm) values using the tool htseq-count of the open source python package HTSeq (Andres et al. 2015).
The final dataset consists of 55 RNAseq single end 100bp samples with a total of 13,282 genes that had a cpm of 1 or more in at least 3 of the samples.
cpm values were normalized using the Trimmed of the M-values (TMM) procedure with the edgeR package from Bioconductor and transformed to logarithm base 2.
Genome_build: hg19
Supplementary_files_format_and_content: excel file include normalize expression values matrix for all samples

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral blood mononuclear cells (PBMCs)

extract_protocol:
Whole blood mRNA was extracted using TempusTM Blood RNA Tube isolation kits provided by the manufacturer Applied Biosystems, and the quality was determined based on the Agilent Bioanalyzer 2100 RNA Integrity score (RIN).
Illumina RNA seq kit was used for sequence library preparation using the Illumina TruSeq RNA Sample Prep Guide: Low Throughput (LT) Protocol.

tag: tissue

value: blood

tag: cell type

value: PBMC

tag: gender

value: F

tag: age

tag: time

value: PreChallenge

tag: group

value: RASNP

tag: protected/suceptibible/duffy

value: Suceptible


title: PBMCs sample_PCH005RNP

value: M


title: Neural progenitor cells #1

state: CA

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

value: Neural progenitor cells


title: ARC-D-Fed-313

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

country: United Kingdom

institute: University of Cambridge

description:
laser-captured hypothalamic nucleus (region)
cpm_del.txt

data_processing:
Basecalls performed using CASAVA 1.7
Reads were aligned to the mouse genome (GRCm38) using Tophat v2.0.11
Counts were determined using Cufflinks v2.2.1
Count normalisation was performed using the edgeR and limma packages in R.
Genome_build: GRCm38
Supplementary_files_format_and_content: Counts per Million (CPM) matrix in tab-delimited text

source_name: arcuate nucleus

extract_protocol:
Hypothalamic nuclei were laser-capture microdissection from cryosections using a P.A.L.M Microlaser system, and RNA extracting using the miRNeasy micro RNA extraction kit (Qiagen).
Total RNA was amplified using an Ovation RNA-Seq System V2 (NuGEN), after which cDNA libraries were prepared using the Encore Rapid DR Multiplex System (NuGEN).

treatment_protocol: Male mice with a paternal Snord116 deletion (B6(Cg)-Snord116tm1.1Uta/J - JAX stock no 008149) were either ad-libitum fed or fasted for 24-hours prior to brain dissection.

tag: strain

tag: nutritional state

value: Fed

tag: batch


title: Neurons #1


title: ARC-D-Fast-311

value: Fast


title: PBMCs sample_PCH084F

value: Fy

value: Duffy Fy(-)


title: ARC-D-Fast-305


title: PBMCs sample_PCH010RP

value: RASP

value: Protected


title: PBMCs sample_PCH075F


title: PBMCs sample_PCH066F


title: PBMCs sample_PCH058F


title: PBMCs sample_PCH002CP

value: Ctrl


title: P2_Non-Mes_H19-C-rep3

description:
Mus musculus post natal day 2 non-mesenchymal cells-Controls 2 (H19DMD+/+; Nkx3.2+/Cre)
data2.tsv
SLX-9736.L2DRBC14

data_processing:
Reads were aligned to the GRCm38/Ensembl V54 transcriptome using Tophat v2.0.8 with default parameters
FPKM values and differential gene expression were determined using CuffLinks v2.2.1 using default parameters
Genome_build: GRCm38
Supplementary_files_format_and_content: Fastq files for raw data and raw count values in tab-delimted txt format

source_name: pancreas

extract_protocol:
P2 pancreata were dissected and dissociated into single cells using trypsin-EDTA. Cells were then isolated by FACS into mesenchymal cells (YFP+) and non-mesenchymal cells (YFP-). Total RNA was extracted using RNEasy Micro kit (Qiagen-74004)
2ng total RNA was whole-transcriptome amplified using the Ovation RNA–seq System V2 (NuGEN). 2 ?g amplified cDNA was then used to prepare the RNA–seq libraries using the Ovation Rapid DR Library System (NuGEN).
RNA-seq using Illumina HiSeq 2500 system for single-end 50-bp sequencing

value: non-mesenchymal cells

value: post natal day 2

tag: genotype

value: Controls 2 (H19DMD+/+; Nkx3.2+/Cre)


title: P2_Non-Mes_H19-KO-rep2

description:
Mus musculus post natal day 2 non-mesenchymal cells-Mutants 2 (H19DMDfl/+; Nkx3.2+/Cre)
data2.tsv
SLX-9736.L2DRBC06

value: Mutants 2 (H19DMDfl/+; Nkx3.2+/Cre)


title: P2_Non-Mes_H19-KO-rep1

description:
Mus musculus post natal day 2 non-mesenchymal cells-Mutants 2 (H19DMDfl/+; Nkx3.2+/Cre)
data2.tsv
SLX-9736.L2DRBC05


title: PBMCs sample_PCH065C

value: blood

value: PBMC


title: P2_Non-Mes_H19-C-rep2

description:
Mus musculus post natal day 2 non-mesenchymal cells-Controls 2 (H19DMD+/+; Nkx3.2+/Cre)
data2.tsv
SLX-9736.L2DRBC13


title: Neural progenitor cells #2

value: FACS purified cells


title: PBMCs sample_DGS025RP

value: F

value: Diagnosis


title: P2_Non-Mes_H19-C-rep4

description:
Mus musculus post natal day 2 non-mesenchymal cells-Controls 2 (H19DMD+/+; Nkx3.2+/Cre)
data2.tsv
SLX-9736.L2DRBC16


title: PBMCs sample_PCH006RNP

value: M

value: PreChallenge

value: RASNP

value: Suceptible


title: PBMCs sample_DGS012RP


title: PBMCs sample_DGS010RP


title: P2_Mes_H19-KO-rep3

description:
Mus musculus post natal day 2 mesenchymal cells-Mutants 2 (H19DMDfl/+; Nkx3.2+/Cre)
data2.tsv
SLX-9736.L2DRBC03

value: mesenchymal cells


title: PBMCs sample_DGS007RP

value: RASP


title: P2_Mes_H19-KO-rep4

description:
Mus musculus post natal day 2 mesenchymal cells-Mutants 2 (H19DMDfl/+; Nkx3.2+/Cre)
data2.tsv
SLX-9736.L2DRBC04


title: PBMCs sample_PCH011RNP


title: P2_Mes_H19-KO-rep1

description:
Mus musculus post natal day 2 mesenchymal cells-Mutants 2 (H19DMDfl/+; Nkx3.2+/Cre)
data2.tsv
SLX-9736.L2DRBC01


title: P2_Mes_H19-KO-rep2

description:
Mus musculus post natal day 2 mesenchymal cells-Mutants 2 (H19DMDfl/+; Nkx3.2+/Cre)
data2.tsv
SLX-9736.L2DRBC02


title: PBMCs sample_PCH038F

value: Fy

value: Duffy Fy(-)


title: PBMCs sample_DGS026RNS


title: PBMCs sample_DGS017RNP


title: P2_Mes_H19-C-rep3

description:
Mus musculus post natal day 2 mesenchymal cells-Controls 2 (H19DMD+/+; Nkx3.2+/Cre)
data2.tsv
SLX-9736.L2DRBC11


title: P2_Mes_H19-C-rep2

description:
Mus musculus post natal day 2 mesenchymal cells-Controls 2 (H19DMD+/+; Nkx3.2+/Cre)
data2.tsv
SLX-9736.L2DRBC10


title: PBMCs sample_DGS021RNP


title: P2_Non-Mes_H19-C-rep1

description:
Mus musculus post natal day 2 non-mesenchymal cells-Controls 2 (H19DMD+/+; Nkx3.2+/Cre)
data2.tsv
SLX-9736.L2DRBC12

value: non-mesenchymal cells


title: P2_Mes_H19-C-rep1

description:
Mus musculus post natal day 2 mesenchymal cells-Controls 2 (H19DMD+/+; Nkx3.2+/Cre)
data2.tsv
SLX-9736.L2DRBC09

value: post natal day 2


title: PBMCs sample_DGS011RNP


title: PBMCs sample_DGS009RNP


title: P2_Mes_H19-C-rep4

description:
Mus musculus post natal day 2 mesenchymal cells-Controls 2 (H19DMD+/+; Nkx3.2+/Cre)
data2.tsv
SLX-9736.L2DRBC15

value: Controls 2 (H19DMD+/+; Nkx3.2+/Cre)


title: PBMCs sample_DGS084F


title: Scrambled control shRNA_1

city: New York

first: Martin

middle: J.

last: Walsh

state: NY

address: One Gustave L. Levy Pl.

department: Structural and Chemical Biology

institute: Mount Sinai School of Medicine

data_processing:
After filtering contaminant (aligned) reads, the reads with good quality were aligned to several human reference databases including hg19 genome, RefSeq exons, splicing junctions using BWA alignment algorithm.
The filtered reads that are uniquely aligned to the exon and splicing-junction sites for each transcript were then counted as expression level for a corresponding transcript
and was further subjected to log2 transformation and global median normalization, to compare transcripts levels among distinct samples.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized values for each transcript in each sample

source_name: Scrambled control shRNA (control for WDR77 shRNA)

growth_protocol: The human breast cancer cell line, MDA-MB-231 was obtained from ATCC and cultured in Dulbecco’s modified essential medium (DMEM) containing 10% fetal bovine serum (FBS) and passaged one or two times a week.

extract_protocol:
Total RNA was extracted using the RNEasy kit (Qiagen) and treated with RNAse free Dnase-I (Qiagen)
RNA-seq libraries were prepared from RNEasy extracted RNA samples from which rRNA was removed using Ribo-ZeroTM and following the TruSeq Stranded Total RNA Sample Prep kit protocol (Illumina).

treatment_protocol: Cells were infected with either control or WDR77 or PRMT5 shRNA. 4 days post-infection, cells were selected with 1mg/mL puromycin (Sigma) for 5 more days and harvested for RNA extraction

tag: cell line

value: breast cancer cell line MDA-MB-231

tag: infection

value: Scrambled control shRNA_1

tag: treatment

value: Infected cells were selected with puromycin (1mg/mL) for 5 days


title: PRMT5 shRNA

source_name: PRMT5 shRNA

value: PRMT5 shRNA


title: DMSO-treated

data_processing:
After filtering contaminant (aligned) reads, the reads with good quality were aligned to several human reference databases including hg19 genome, RefSeq exons, splicing junctions using BWA alignment algorithm.
The filtered reads that are uniquely aligned to the exon and splicing-junction sites for each transcript were then counted as expression level for a corresponding transcript
and was further subjected to log2 transformation  and global median normalization, to compare transcripts levels among distinct samples.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized values for each transcript in each sample

treatment_protocol: MDA-MB-231 cells were treated with 5µM DMSO or 5µM HPTB for 4 hours at 37°C

value: 5µM DMSO for 4 hours at 37°C


title: PBMCs sample_DGS075F

value: blood

value: PBMC

value: F

value: Diagnosis


title: PBMCs sample_DGS066F


title: PBMCs sample_DGS058F


title: Scrambled control shRNA_2

source_name: Scrambled control shRNA (control for PRMT5 shRNA)

value: Scrambled control shRNA_2


title: PRMT5_ChIP-seq

data_processing:
Basecalls performed using CASAVA version 1.4
read sequences were done QC filtering by FASTX ( -q 20 -p 90 )
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie2
peaks were called using MACS2 using Input as control with the following setting: QVALUE threshold (0.05), MFOLD (5, 50).
Genome_build: hg19
Supplementary_files_format_and_content: bed files were generated using MACS.

extract_protocol:
After cross-linking cells for 10 min with 1% formaldehyde and sonicating chromatin with a Diagenode Bioruptor, chromatin was immunoprecipitated using 5 µg of PRMT5 (Bethyl Labs, A300-849A) or 5 µg of rabbit serum for 1mg protein.
ChIP-DNA was end repaired with T4 DNA polymerase and polynucleotide kinase. An A-base was added to the end-repaired DNA fragments. Solexa adaptors were ligated to the ChIP DNA fragments and 200-300bp size fractions were excised from 2% agarose gel stained with GelStar. Adaptor-modified fragments were enriched by 16 cycles of PCR amplification. The DNA library prep was validated in Bioanalyzer for quantity and size.

treatment_protocol: No treatment

value: no treatment

tag: chip antibody

value: PRMT5 (Bethyl Labs A300-849A)


title: Input_ChIP-seq

source_name: Input

value: none (input)


title: PBMCs sample_DGS020C

value: M

value: Ctrl

value: Suceptible


title: PBMCs sample_DGS002CP

value: Protected


title: PBMCs sample_B012RP

value: Baseline

value: RASP


title: P2_Mes_Igf2-KO-rep3

description:
Mus musculus post natal day 2 mesenchymal cells-Mutants 1 (Igf2+/fl; Nkx3.2Cre/+)
data1.tsv
SLX-8880.L2DRBC03

value: mesenchymal cells

value: post natal day 2

value: Mutants 1 (Igf2+/fl; Nkx3.2Cre/+)


title: P2_Mes_Igf2-KO-rep2

description:
Mus musculus post natal day 2 mesenchymal cells-Mutants 1 (Igf2+/fl; Nkx3.2Cre/+)
data1.tsv
SLX-8880.L2DRBC02


title: PBMCs sample_B010RP

value: blood


title: WDR77 shRNA

source_name: WDR77 shRNA

value: breast cancer cell line MDA-MB-231

value: WDR77 shRNA

value: Infected cells were selected with puromycin (1mg/mL) for 5 days


title: HPTB-treated

value: 5µM HPTB for 4 hours at 37°C


title: P2_Mes_Igf2-KO-rep1

description:
Mus musculus post natal day 2 mesenchymal cells-Mutants 1 (Igf2+/fl; Nkx3.2Cre/+)
data1.tsv
SLX-8880.L2DRBC01


title: PBMCs sample_B007RP

value: PBMC

value: F


title: PBMCs sample_B026RNS

value: RASNP


title: PBMCs sample_B001RP


title: P2_Mes_Igf2-C-rep4

description:
Mus musculus post natal day 2 mesenchymal cells-Controls 1 (Igf2+/+; Nkx3.2Cre/+)
data1.tsv
SLX-8880.L2DRBC12

value: Controls 1 (Igf2+/+; Nkx3.2Cre/+)


title: PBMCs sample_DGS005RNP

value: M

value: Diagnosis


title: P2_Mes_Igf2-C-rep3

description:
Mus musculus post natal day 2 mesenchymal cells-Controls 1 (Igf2+/+; Nkx3.2Cre/+)
data1.tsv
SLX-8880.L2DRBC11


title: PBMCs sample_B021RNP

value: Suceptible


title: P2_Mes_Igf2-C-rep2

description:
Mus musculus post natal day 2 mesenchymal cells-Controls 1 (Igf2+/+; Nkx3.2Cre/+)
data1.tsv
SLX-8880.L2DRBC10


title: PBMCs sample_B017RNP

value: Baseline


title: P2_Mes_Igf2-C-rep1

description:
Mus musculus post natal day 2 mesenchymal cells-Controls 1 (Igf2+/+; Nkx3.2Cre/+)
data1.tsv
SLX-8880.L2DRBC09


title: PBMCs sample_B005RNP


title: PBMCs sample_B006RNP


title: p53-WT-ATRX-fl-ctrl-C

city: Houston

first: Jason

middle: T

last: Huse

state: TX

address: 1515 Holcombe Blvd

department: Department of Pathology

institute: University of Texas MD Anderson Cancer Center

data_processing:
Basecalls performed using CASAVA version 1.4
Alignment was done using Tophat version 2.1.1
Tuxedo suite was used for downstream analysis
Differential experssion was obtained using DESeq
Genome_build: mm9
Supplementary_files_format_and_content: DESeq normalized values for all genes

source_name: Tp53+/+, Atrx+ NPC

growth_protocol: Forebrains were removed from p1 mouse pups and mechanically homogenized by repetitive pipetting in NeuroCult Basal Medium containing NeuroCult Proliferation Supplement, 20 ng/ml EGF, 10 ng/ml basic FGF, 2 μg/ml heparin  (Stemcell Technologies), 50 units/ml penicillin, and 50 μg/ml streptomycin (Thermo Fisher Scientific).  Homogenized samples were then cultured in a humidified incubator at 5% CO2 and 37 °C. At the time of experiment, cells were in a logarithmic growth phase.

extract_protocol:
Total RNA was extracted from pelleted cells in exponential growth phase
RNA libraries were prepared for sequencing using standard Illumina protocols

value: forebrain

value: Neuroepithelial progenitor cell

tag: passage

value: mixed


title: PBMCs sample_B084F

value: Fy

value: Duffy Fy(-)


title: p53-WT-ATRX-fl-ctrl-B


title: p53-WT-ATRX-KO-B

source_name: Tp53+/+, Atrx- NPC


title: PBMCs sample_B066F

value: blood


title: p53-WT-ATRX-KO-A


title: p53-KO-ATRX-fl-ctrl-B

source_name: Tp53-/-, Atrx+ NPC


title: PBMCs sample_B038F


title: PBMCs sample_B058F


title: PBMCs sample_B020C

value: Ctrl


title: PBMCs sample_B065C


title: p53-KO-ATRX-KO-C

source_name: Tp53-/-, Atrx- NPC


title: PBMCs sample_B002CP

value: Protected


title: p53-KO-ATRX-KO-B


title: PBMCs sample_B009RNP


title: p53-KO-ATRX-fl-ctrl-A


title: PBMCs sample_B011RNP


title: p53-KO-ATRX-KO-A


title: p53-WT-ATRX-fl-ctrl-A


title: p53-/-ATRX-  H3.3_B

description: p53-/-ATRX-  H3.3_B

data_processing:
Basecalls performed using CASAVA version 1.4
Alignment was done using BWA to the reference genome
Duplicates were removed using PicardTools 'MarkDuplicates.jar'
Peaks were called using macs2 with default parameters on the paired mode with corresponding input as control
Peaks in the negative controls were subtracted
Genome_build: mm9
Supplementary_files_format_and_content: bed files containing peaks for Tp53-/- and Tp53-/- Atrx- samples

extract_protocol:
Lysates were clarified from sonicated nuclei and H3.3-DNA complexes were isolated with antibody.
Histone H3.3 chromatin immunoprecipitation was performed following the manufacturer instructions of Magna ChIP A Chromatin Immunoprecipitation Kit using 10 μg of Anti-Histone H3.3 antibody (Millipore).  Sequencing libraries were prepared using the Kapa Hyper library Prep kit (Roche) with library amplification primer mix and sequenced as 50 base pair reads by single-read format on an Illumina HiSeq 2500 (v4 chemistry) with a maximum of 7 samples per lane

value: Anti-Histone H3.3 antibody (Millipore)


title: Lead3_D9

city: Cleveland

first: Peng

last: Jiang

state: OH

address: 2121 Euclid Ave

institute: Cleveland State University

description: Time Course - NPCs

data_processing:
FASTQ files were generated by CASAVA (v1.8.2).
Reads were mapped to the human transcriptome (RefGene v1.1.17) using Bowtie 0.12.8 (Langmead et al. 2009) allowing up to 2-mismatches and a maximum of 200 multiple hits.
The gene expected read counts and TPMs were estimated by RSEM (v1.2.3)
Genome_build: hg19
Supplementary_files_format_and_content: [.txt] gene expression values

growth_protocol: NPCs were derived with a modified protocol from a previously reported protocol (Chambers et al. 2009).

extract_protocol:
Samples were collected at indicated time points by lysing cells directly on the plate with 350ul RLT buffer.
Cells were lysed in 350ul of the Qiagen Buffer RLT (79216). Total RNA was isolated using the Qiagen RNeasy 96 Kit (74181) and quantified with the ThermoFisher Scientific Quant-It RNA Assay Kit (Q33140) and the Agilent Bioanalyzer RNA 6000 Pico Kit (5067-1513).
cDNA libraries were prepared with 100 ng of input total RNA and indexed with the Illumina TruSeq RNA Prep Kit v2 (RS-122-2001 and RS-122-2002). Indexed cDNA libraries were pooled and sequenced on an Illumina HiSeq2500 with single end 51 bp reads.

treatment_protocol: NPCs were thawed and expanded in neural expansion medium for 5 days before they were harvested by Accutase treatment.

tag: agent

value: Lead

tag: dose

value: neural progenitor cells (NPCs)


title: p53-WT-ATRX-KO-C

tag: tissue

tag: cell type


title: p53-/-Atrx- H3.3_3

description: p53-/-Atrx- H3.3_3


title: Lead3_D6

description: Time Course - NPCs


title: p53-/- ATRX- H3.3_A

description: p53-/- ATRX- H3.3_A


title: Lead3_D7

description: Time Course - NPCs


title: p53-/-Atrx- H3.3_2

description: p53-/-Atrx- H3.3_2


title: Lead3_D5

description: Time Course - NPCs


title: PBMCs sample_DGS001RP

value: PBMC

tag: gender

value: F

tag: age

value: RASP


title: PBMCs sample_B075F

tag: time

tag: group


title: Lead3_D4

description: Time Course - NPCs


title: p53-KO-ATRX-fl-ctrl-C

tag: strain


title: p53-/-Atrx- Input_3

description: p53-/-Atrx- Input_3

value: none (input)


title: p53-/-Atrx- H3.3_1

description: p53-/-Atrx- H3.3_1


title: Lead3_D3

description: Time Course - NPCs


title: p53-/- ATRX- H3.3

description: p53-/- ATRX- H3.3


title: Lead3_D8

description: Time Course - NPCs


title: Lead3_D25

description: Time Course - NPCs


title: Lead3_D26

description: Time Course - NPCs


title: Lead3_D24

description: Time Course - NPCs


title: p53-/-Atrx- Input_1

description: p53-/-Atrx- Input_1


title: p53-/- H3.3_B

description: p53-/- H3.3_B

source_name: Tp53-/- NPC


title: Lead3_D23

description: Time Course - NPCs


title: p53-/- H3.3_A

description: p53-/- H3.3_A


title: p53-/- H3.3_3

description: p53-/- H3.3_3


title: Lead3_D2

description: Time Course - NPCs


title: p53-/- H3.3_2

description: p53-/- H3.3_2


title: Lead3_D22

description: Time Course - NPCs


title: Lead3_D21

description: Time Course - NPCs


title: p53-/- H3.3

description: p53-/- H3.3


title: p53-/- H3.3_1

description: p53-/- H3.3_1


title: p53-/- Input_3

description: p53-/- Input_3


title: Lead3_D1

description: Time Course - NPCs


title: p53-/- Input_2

description: p53-/- Input_2


title: Lead3_D19

description: Time Course - NPCs


title: p53-/-Atrx- Input_2

description: p53-/-Atrx- Input_2


title: Lead3_D20

description: Time Course - NPCs


title: Lead3_D18

description: Time Course - NPCs


title: Lead3_D17

description: Time Course - NPCs


title: p53-/- Input_1

description: p53-/- Input_1


title: Lead3_D16

description: Time Course - NPCs


title: p53+/+ ATRX -/-_Input

description: This is a negative control sample. No processed data available for this sample.

data_processing:
Basecalls performed using CASAVA version 1.4
Alignment was done using BWA to the reference genome
Duplicates were removed using PicardTools 'MarkDuplicates.jar'
Peaks were called using macs2 with default parameters on the paired mode with corresponding input as control
Peaks in the negative controls were subtracted
Genome_build: mm9
Supplementary_files_format_and_content: bed files containing peaks for p53+ and p53- samples

extract_protocol:
Lysates were clarified from sonicated nuclei and ATRX-DNA complexes were isolated with antibody.
ATRX ChIP was performed as previously described (Law et al., 2010). Cells were fixed with 2 mM EGS (Pierce) for 45 min at room temperature in PBS. Formaldehyde was then added to 1% for 20 min and quenched with 125 mM glycine. Chromatin was sonicated with a Bioruptor Plus (Diagenode) to generate DNA fragments under 500 bp and lysates were immunoprecipitated with 40 μg ATRX H300 antibody or rabbit IgG control (Santa Cruz Biotechnology).


title: p53-/-_Input 3


title: p53+/+ ATRX -/-_ATRX

value: ATRX H300 antibody (Santa Cruz)


title: Lead3_D15

description: Time Course - NPCs


title: p53-/-_ Input 2


title: Lead3_D13

description: Time Course - NPCs


title: Lead3_D12

description: Time Course - NPCs


title: p53-/-_ATRX 2


title: p53-/-_ATRX 3


title: Lead3_D11

description: Time Course - NPCs


title: p53-/-_ Input 1


title: Lead3_D14

description: Time Course - NPCs


title: Lead30_D8

description: Time Course - NPCs


title: p53+/+_Input 3

source_name: Tp53+/+ NPC


title: p53+/+_Input 1


title: p53+/+_ATRX 3


title: Lead30_D6

description: Time Course - NPCs


title: p53+/+_Input 2


title: Lead3_D10

description: Time Course - NPCs


title: Lead30_D7

description: Time Course - NPCs


title: Lead30_D4

description: Time Course - NPCs


title: Lead30_D9

description: Time Course - NPCs


title: Lead30_D5

description: Time Course - NPCs


title: p53+/+_ ATRX 2


title: Lead30_D3

description: Time Course - NPCs


title: p53+/+_ATRX 1


title: Tp53-/-, Atrx- ATAC 3

data_processing:
Basecalls performed using CASAVA version 1.4
Alignment was done using BWA to the reference genome
Duplicates were removed using PicardTools 'MarkDuplicates.jar'. The submitted raw files (bam format) were 'sorted, cleaned, removed_duplicates'.
Peaks were called using Zinba with default parameters after creating tag alignment and basecount files
wig files were created using the command -  samtools pileup ${bam_file} | perl -ne 'BEGIN{print "track type=wiggle_0 name=fileName description=fileName\n"};($c, $start, undef, $depth) = split; if ($c ne $lastC) { print "variableStep chrom=$c\n"; };$lastC=$c;n ext unless $. % 10 ==0;print "$start\t$depth\n" unless $depth<3;' > ${DIRECTORY}/${sample}.wig
Genome_build: mm9
Supplementary_files_format_and_content: bed files containing peaks information and wig files with variable step where scores represent read depth

source_name: Tp53-/- , Atrx- NPC

extract_protocol:
Resuspend pelleted cells in lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) before proceeding to ATAC-seq protocol
ATAC-Seq was performed on mNPCs as previously described (Buenrostro et al., 2013).  Libraries were prepared from fresh cells and sequenced as paired end 50 reads on a HiSeq 2500 with version 4 chemistry and 6 samples per lane (~50 million paired end reads per sample).


title: Lead30_D2

description: Time Course - NPCs


title: Lead30_D26

description: Time Course - NPCs


title: Tp53-/-, Atrx- ATAC 1


title: p53-/-_ATRX 1


title: Tp53-/-, Atrx- ATAC 2


title: SGE_ATAC_124

city: Tempe

first: Noah

last: Snyder-Mackler

state: AZ

address: 427 East Tyler Mall

institute: Arizona State University

data_processing:
Library strategy: ATAC-Seq
Reads were mapped to MacaM using the bwa-mem algorithm with default settings
Open chromatin regions were identified using MACS2 (--nomodel --keep-dup all -q 0.05 -f BAMPE) after merging data from all three samples into a single alignment file and removing all reads that mapped to the mitochondria. We called peaks at a 5% FDR threshold
Genome_build: MacaM
Supplementary_files_format_and_content: [.bed] peaks

organism: Macaca mulatta

source_name: peripheral blood mononuclear cells

growth_protocol: we drew 4 mL of blood from each female and purified the PBMC fraction using density gradient centrifugation.

extract_protocol:
ATAC-seq libraries were prepared from 50,000 cells per sample as described in Buenrostro et al 2013, but skipping the cell lysis step, which has been shown to reduce the proportion of mitochondrial reads in the final library.
Libraries were barcoded, multiplexed, and sequenced on an Illumina NextSeq using paired-end, 38 bp reads.

treatment_protocol: PBMCs were seeded at 500,000 cells per mL of media and incubated at 35C for 90 minutes.

value: peripheral blood mononuclear cells

tag: study phase

value: phase 2


title: SGE_ATAC_114


title: SGE_ATAC_130


title: Tp53-/- ATAC 3

value: forebrain

value: Neuroepithelial progenitor cell


title: Lead30_D25

description: Time Course - NPCs


title: Lead30_D23

description: Time Course - NPCs


title: C5_1A_L1

city: Brisbane

first: Jianhua

last: Guo

address: Research Road, Level 4 Gehrmann Building

department: Australian Centre for Water and Environmental Biotechnology

country: Australia

institute: University of Queensland

description: 50mg/L CuO NPs addition

data_processing:
NGS QC Toolkit (v2.3.3) was used to do the quality control and tag removal to generate the clean sequence reads; the resulting clean reads no shorter than 75 bp were used for downstream analyses.
The cleaned sequence reads for each sample were aligned to the PAO1 reference genome (NC_002516) using SeqAlto
Strand-specific coverage for each gene was calculated and differential expression analysis was conducted using the cuffdiff command in Cufflinks (version 2.2.1)
Statistic analyses and visualization were conducted using the cummeRbund package in R (http://compbio.mit.edu/cummeRbund/). Gene expression was calculated as reads per kilobase of a gene per million mapped reads (RPKM), a normalized value derived from the frequency of detection and the length of a given gene (Cole Trapnell, Nature Protocols, 2012) Differences in fold-change values were calculated between control and FNA-treated samples (4 μg-N/L) by determining the log2 fold-change (LFC) of the RPKM values determined from experiments run on two separate occasions.
Genome_build: NC_002516
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Pseudomonas aeruginosa

source_name: Bacteria

growth_protocol: P. aeruginosa PAO1 strain was activated according to the supplier (DSMZ) and grown on tryptic soy agar (TSA) plates at 30 ºC for 26 hours. One colony was then selected and transferred to tryptic soy broth (TSB) medium and incubated shaken at 150 rpm and 30 ºC for another 26 hours. Afterwards, 5 mL of the bacterium suspension was transferred into the serum bottles containing 150 mL of sterile anaerobic Glycerol modified M9 (GLYM9) medium in an anaerobic chamber. After 26 hours’ incubation, optical density at 600 nm (OD600) was measured and then adjusted to 0.5. Then 10 mL of this inoculum standard was transferred into 150 mL of sterile anaerobic GLYM9 medium in serum bottles in an anaerobic chamber and then incubated at 30 ˚C while shaken at 150 rpm. GLYM9 medium used in this study contained 10 g/L glycerol, 0.2 g/L yeast extract, 0.2 M phosphate buffer, 9 mM NaCl, 38 mM NH4Cl, 2 mM MgSO4•3H2O, 100 μM CaCl2•2H2O and 30 mM NaNO3 with the pH adjusted to 6.3±0.

extract_protocol:
The total RNA extraction was performed at 13 hours incubation, that is 2 hours after nanoparticle exposure. The bacteria suspension of 6 mL from each serum bottle was collected and centrifuged at 14,000 rpm for 5 minutes at 4 oC, the supernatant was discarded and the pellets were immediately frozen in the liquid nitrogen before storing at -80ºC for later RNA extraction. Total RNA extraction was performed using the QIAGEN miRNeasy Mini Kit (Catalog number: 217004) according to the manufacturer’s instructions except adding an extra beat-beading step to ensure the complete lysis of the bacterial cells.
Strand-specific cDNA library construction

treatment_protocol: Eleven hours after the inoculation when the culture was in its early exponential phase of growth (OD of 0.2~0.3), a volume of a stock CuO nanoparticles solution was added to reach the initial nanoparticle concentration of 0.1, 1, 10 and 50 mg/L. Control cultures, with no nanoparticle addition, had the same volume of GLYM9 medium added.

value: wild type

tag: incubation time

value: 13 hours incubation after the standard inoculation, that is 2 hours after CuO NPs addition

tag: nanoparticle level

value: 50 mg/L CuO NPs


title: Lead30_D24

description: Time Course - NPCs


title: Tp53-/- ATAC 2

value: mixed

tag: genotype


title: Tp53-/- ATAC 1


title: Lead30_D22

description: Time Course - NPCs


title: C3_1A_L1

description: 10mg/L CuO NPs addition

value: 10 mg/L CuO NPs


title: P2_Non-Mes_H19-KO-rep3

description:
Mus musculus post natal day 2 non-mesenchymal cells-Mutants 2 (H19DMDfl/+; Nkx3.2+/Cre)
data2.tsv
SLX-9736.L2DRBC07

value: non-mesenchymal cells

value: post natal day 2

value: Mutants 2 (H19DMDfl/+; Nkx3.2+/Cre)


title: AOS-16 RNA-Seq

city: Shanghai

first: Xiaobai

last: Zhang

address: 1239 Siping Road

country: China

institute: Tongji University

data_processing:
RNA-seq reads were aligned to the UCSC mouse genes (mm9) using Tophat (version 2.0.13). Only the uniquely mapped reads were retained for analysis in this study.
We used Cuffdiff (version 2.2.1) to calculate the expression abundance of each gene as fragments per kilobase per million mapped reads (FPKM).
Genome_build: mm9
Supplementary_files_format_and_content: The processed data file is a tab-delimited file showing gene expresssion levels with FPKM.

molecule: polyA RNA

source_name: Androgenetic haploid embryonic stem cells (AG-haESCs)

growth_protocol: The specific pathogen free (SPF) grade mice were housed in the animal facility of Tongji University. 8-10 week old BDF1 hybrid mice that used to collect MⅡ oocyte were obtained from mating of C57BL/6 female with male DBA/2. All animal procedures were performed under the ethical guidelines of Tongji University. Injection of sperm into anucleated oocyte was conducted as previously described7. Spindle of MII oocyte were removed using a piezo-drill micromanipulator and injected with a sperm head following activation by SrCl2 for 4-6 hr. Then reconstructed embryo were cultured in G1 plus medium and developed to blastocyst. Blastocyst were planted on feeder in 15% KSR Konckout DMEM supplement with 2i. After 6-8 days in culture, the outgrowths were passaged and cultured in 2i ESM with feeder. G0/G1 haploid cells were sorted through staining of 15µg/ml Hoechst 33342 regularly. Analytic flow profiles were recorded by BD FACS AriaⅡ. For diploidization analysis, every group prepared 5 cell sample of 12-well and analyzed by staining of 15µg/ml Hoechst 33342, each sample recorded 5×10^5 cells by BD FACS AriaⅡ.

extract_protocol:
The cell used for RNA-seq were collection of G0/G1 cell through FACS and washed by DPBS.RNA were extracted by QIAGEN Allprep DNA/RNA mini Kit.
RNA libraray were constructed used KAPA stranded mRNA-seq kit illumina platform and sequenced at the Berry genomic corporation.

value: F1 hybrid C57BL/6 X DBA/2


title: Lead30_D20

description: Time Course - NPCs

value: Lead

value: neural progenitor cells (NPCs)


title: C1_1A_L1

description: 1mg/L CuO NPs addition

value: 13 hours incubation after the standard inoculation

value: 1 mg/L CuO NPs


title: P2_Non-Mes_H19-KO-rep4

description:
Mus musculus post natal day 2 non-mesenchymal cells-Mutants 2 (H19DMDfl/+; Nkx3.2+/Cre)
data2.tsv
SLX-9736.L2DRBC08


title: Round_sperm RNA-Seq

source_name: Round sperm

value: sperm


title: AOS-14 RNA-Seq

value: Androgenetic haploid embryonic stem cells (AG-haESCs)


title: Lead30_D21

description: Time Course - NPCs


title: Lead30_D1

description: Time Course - NPCs


title: c2

city: Munich

first: Stefan

last: Krebs

address: Feodor-Lynen-Str. 25

department: Gene Center

country: Germany

institute: Ludwig-Maximilian University

data_processing:
Basecalling was done by RTA1.17.21.3
reads were mapped to the plasmid used for transfection in order to remove reads derived from residual plasmid DNA. Unmapped reads were used as input for the further steps
reads were aligned to the human genome by Tophat v1.4.0 with hg19 and a gtf file with gene annotations downloaded from the igenomes website (http://support.illumina.com/sequencing/sequencing_software/igenome.html)
reads overlapping with annotated genes were counted with HTseq count
variance stabilisation and differential gene expression were done by DESeq
Genome_build: hg19
Supplementary_files_format_and_content: raw count table from HTseq count

source_name: melanoma cell line

growth_protocol: 1x106 1205Lu metastatic melanoma cells were seeded in a T75 flask and cultivated overnight at 37°C and 5% CO2 in Tu2% medium.

extract_protocol:
Total RNA was isolated with DirectZol Kit (Zymo Research) according to the accompanying instructions
125 ng of total RNA were used for library construction with Nugen Encore Complete RNAseq library system following the manufacturer's protocol

treatment_protocol: 7.8 µg plasmid DNA (pCMV6-SOX10 or pCMV6 control) per flask were transiently transfected using 23.5 µl FuGENE® 6 transfection reagent (Promega, Madison, Wisconsin, USA) in 366 µl Opti-MEM reduced serum medium (Gibco by life technologies, Carlsbad, California, USA) and 7.8 ml Tu2% medium on top of the cells. Twenty-four hours later, cells were harvested in 1 ml QIAzol (Qiagen, Hilden, Germany).

tag: cell line

tag: tumor stage

value: metastatic


title: c3

tag: treatment


title: c1


title: Z2_1A_L1

description: NO CuO NPs addition

value: control (0 mg/L CuO NPs)


title: Lead30_D18

description: Time Course - NPCs


title: Lead30_D19

description: Time Course - NPCs


title: s3


title: A129-2 RNA-Seq


title: s2


title: Lead30_D17

description: Time Course - NPCs


title: Ctrl_E13.5_MedialDorsalTelencephalon_Rpl5

city: Freiburg

first: Henriette

last: Franz

address: Alberstr: 17

department: Anatomy and Cellbiology

institute: University Freiburg

description:
Control E13.5 Medial dorsal telencephalon Biological replicate 5
2 medial dorsal telencephalon samples were pooled and sequenced on 3 different lanes

data_processing:
Sequencer: HiSeq2500/75 M reads per sample/Max read length 2x150bp
Automatic detection and trimming of adapters were done using TrimGalore (version 0.2.8) and cut out of the 3' end bases with Phred quality score less than 28.
Usage of TopHat2 (version 2.0.9) (Kim et al., 2013) for alignment to mouse genome build mm10.
Mapping to annotations from Ensembl FTP release 79
After htseq count (version 0.6.0) differential gene expression analysis was performed using the DESeq2 (version 1.6.1)
Genome_build: mm10

source_name: Medial dorsal telencephalon E13.5

extract_protocol:
For RNA extraction the tissue was homogenized by shearing force followed by QIAshredder Kit (#79654, Qiagen, Germany). Cells were homogenized by QIAshredder only. The total RNA was extracted using RNAeasy Mini Kit (#74104, Qiagen, Germany) including an on-column DNAse digestion (#79254, Qiagen, Germany).
Library and sequencing performed by Eurofins: stranded RNA-Seq: TruSeq stranded total RNA sample preparation GOLD (RS-122-2301)

tag: developmental stage

value: Medial dorsal telencephalon


title: Ctrl_E13.5_MedialDorsalTelencephalon_Rpl3

description:
Control E13.5 Medial dorsal telencephalon Biological replicate 3
2 medial dorsal telencephalon samples were pooled and sequenced on 3 different lanes


title: s1


title: Ctrl_E13.5_MedialDorsalTelencephalon_Rpl4

description:
Control E13.5 Medial dorsal telencephalon Biological replicate 4
2 medial dorsal telencephalon samples were pooled and sequenced on 3 different lanes


title: Lead30_D16

description: Time Course - NPCs

tag: agent


title: Ctrl_E13.5_MedialDorsalTelencephalon_Rpl2

description:
Control E13.5 Medial dorsal telencephalon Biological replicate 2
2 medial dorsal telencephalon samples were pooled and sequenced on 3 different lanes


title: Lead30_D15

description: Time Course - NPCs

tag: dose


title: Foxg1-KO_heterocygots_E13.5_MedialDorsalTelencephalon_Rpl5

description:
Foxg1-KO heterocygot E13.5 Medial dorsal telencephalon Biological replicate 5
3 medial dorsal telencephalon samples were pooled and sequenced on 3 different lanes

tag: tissue


title: Ctrl_E13.5_MedialDorsalTelencephalon_Rpl1

description:
Control E13.5 Medial dorsal telencephalon Biological replicate 1
2 medial dorsal telencephalon samples were pooled and sequenced on 3 different lanes


title: Lead30_D14

description: Time Course - NPCs

tag: cell type


title: Lead30_D12

description: Time Course - NPCs


title: Lead30_D13

description: Time Course - NPCs


title: Lead30_D11

description: Time Course - NPCs


title: Foxg1-KO_heterocygots_E13.5_MedialDorsalTelencephalon_Rpl4

description:
Foxg1-KO heterocygot E13.5 Medial dorsal telencephalon Biological replicate 4
3 medial dorsal telencephalon samples were pooled and sequenced on 3 different lanes


title: Foxg1-KO_heterocygots_E13.5_MedialDorsalTelencephalon_Rpl3

description:
Foxg1-KO heterocygot E13.5 Medial dorsal telencephalon Biological replicate 3
3 medial dorsal telencephalon samples were pooled and sequenced on 3 different lanes


title: Reoxygenation rep2

city: Taipei

first: Liang-Chuan

last: Lai

state: Taiwan

address: 1 Jen-Ai Road, Sec 1

department: Physiology

country: Taiwan

institute: National Taiwan University

data_processing:
RNA-seq reads were aligned to the hg19 genome assembly using Tophat version 2.0.9 with parameters -p 12 --library-type fr-firststrand
Cufflinks verson 2.2.1 was then applied to assemble transcripts and quantify their abundance in terms of FPKM (fragments per kilobase of transcript per million fragments mapped)
All possible lncRNA from transcripts assembly were annotated based on the LNCipedia database (http://www.lncipedia.org/)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: MCF-7 cells

growth_protocol: MCF-7, the breast cancer cell line was maintained in Dulbecco’s modified Eagle’s medium (DMEM) (GIBCO, Carlsbad, CA, USA). It was supplemented with 10% fetal bovine serum (FBS) (GIBCO) and 1% penicillin-streptomycin-amphotericin solution (Biological Industries, Beit-Haemek, Israel). It was incubated at 37 °C in a humidified atmosphere with 5% CO2

extract_protocol:
Total RNA was extracted by TRIpure reagent (Roche Diagnostics, Branchburg, NJ, USA) according to the manufacturer’s protocol.
The total RNA extracted from MCF-7 were digested to 180 bp fragments after removing out rRNA by Ribo-Zero Gold kit (Illumina, San Diego, CA). The fragments of RNA were reverse-transcribed to cDNA by TruSeq Stranded total RNA kit (Illumina), then the specific adapters were ligated to the both ends of these cDNA fragments and become sequencing library.

treatment_protocol: Normoxia:21%O2 24h  Hypoxia:0.5%O2 24h  Re-oxygenation:0.5%O2 24h shift to 21%O2 24h

value: breast cancer cell

tag: passages

tag: oxygen status

value: reoxygenation


title: Lead30_D10

description: Time Course - NPCs


title: Normoxia rep3

value: normoxia


title: Foxg1-KO_heterocygots_E13.5_MedialDorsalTelencephalon_Rpl1

description:
Foxg1-KO heterocygot E13.5 Medial dorsal telencephalon Biological replicate 1
3 medial dorsal telencephalon samples were pooled and sequenced on 3 different lanes


title: Normoxia rep2


title: Reoxygenation rep1


title: Normoxia rep1


title: Control_D9

description: Time Course - NPCs

value: Control


title: Foxg1-KO_homocygots_E13.5_MedialDorsalTelencephalon_Rpl4

description:
Foxg1-KO homocygot E13.5 Medial dorsal telencephalon Biological replicate 4
3 medial dorsal telencephalon samples were pooled and sequenced on 3 different lanes


title: Control_D8

description: Time Course - NPCs


title: Hypoxia rep2

value: hypoxia


title: Control_D6

description: Time Course - NPCs


title: Control_D7

description: Time Course - NPCs


title: Foxg1-KO_homocygots_E13.5_MedialDorsalTelencephalon_Rpl3

description:
Foxg1-KO homocygot E13.5 Medial dorsal telencephalon Biological replicate 3
3 medial dorsal telencephalon samples were pooled and sequenced on 3 different lanes


title: Foxg1-KO_homocygots_E13.5_MedialDorsalTelencephalon_Rpl2

description:
Foxg1-KO homocygot E13.5 Medial dorsal telencephalon Biological replicate 2
3 medial dorsal telencephalon samples were pooled and sequenced on 3 different lanes


title: Control_D5

description: Time Course - NPCs


title: Hypoxia rep1


title: early involution

city: Taian

first: zb

last: Ji

address: Daizong street

institute: shandong agricultural university

data_processing:
Run Solexa pipeline [*fq]
Remove low qulity reads strictly
Trim 3' adaptor sequence
Remove 5' adaptor contaminants
Plot data distribution
Remove too small and polyA
Supplementary_files_format_and_content: This file contains clean tags, 18-30 nt, tab delimited, length | number | sequence

organism: Capra hircus

source_name: I-primary

extract_protocol:
size fractionation (18-30 nt)
5' adaptor ligation, 3' adaptor ligation, RT-PCR, Solexa sequencing

value: mammary gland

value: early involution (5th day after forced weaning at late lactation, 218 day after parturition)


title: Control_D3

description: Time Course - NPCs


title: early lactation

source_name: L-primary

value: early lactation (10th day after parturition)


title: Foxg1-KO_homocygots_E13.5_MedialDorsalTelencephalon_Rpl1

description:
Foxg1-KO homocygot E13.5 Medial dorsal telencephalon Biological replicate 1
3 medial dorsal telencephalon samples were pooled and sequenced on 3 different lanes


title: Dot1l-cKO_E14.5_DorsalTelencephalon_Rpl4

description: Dot1l-cKO Mus Musculus dorsal telencephalon E14.5 biological replicate 4

data_processing:
Sequencer: HiSeq2500/8 lanes/ 200 M reads per lane/Max read length 2x150bp
Automatic detection and trimming of adapters were done using TrimGalore (version 0.2.8) and cut out of the 3' end bases with Phred quality score less than 28.
Usage of TopHat2 (version 2.0.9) (Kim et al., 2013) for alignment to mouse genome build mm10.
Mapping to annotations from Ensembl FTP release 79
After htseq count (version 0.6.0) differential gene expression analysis was performed using the DESeq2 (version 1.6.1)
Genome_build: mm10

source_name: Dorsal telencephalon E14.5

extract_protocol:
For RNA extraction the tissue was homogenized by shearing force followed by QIAshredder Kit (#79654, Qiagen, Germany). Cells were homogenized by QIAshredder only. The total RNA was extracted using RNAeasy Mini Kit (#74104, Qiagen, Germany) including an on-column DNAse digestion (#79254, Qiagen, Germany).
stranded RNA-Seq: TruSeq stranded total RNA sample preparation GOLD (RS-122-2301)

value: Foxg1Cre:Cre/+; Dot1l-cKO f/f

value: Dorsal telencephalon


title: Reoxygenation rep3


title: Foxg1-KO_heterocygots_E13.5_MedialDorsalTelencephalon_Rpl2

description:
Foxg1-KO heterocygot E13.5 Medial dorsal telencephalon Biological replicate 2
3 medial dorsal telencephalon samples were pooled and sequenced on 3 different lanes


title: Dot1l-cKO_E14.5_DorsalTelencephalon_Rpl2

description: Dot1l-cKO Mus Musculus dorsal telencephalon E14.5 biological replicate 2


title: Control_D26

description: Time Course - NPCs

value: neural progenitor cells (NPCs)


title: Dot1l-cKO_E14.5_DorsalTelencephalon_Rpl3

description: Dot1l-cKO Mus Musculus dorsal telencephalon E14.5 biological replicate 3


title: Dot1l-cKO_E14.5_DorsalTelencephalon_Rpl5

description: Dot1l-cKO Mus Musculus dorsal telencephalon E14.5 biological replicate 5


title: Dot1l-cKO_E14.5_DorsalTelencephalon_Rpl1

description: Dot1l-cKO Mus Musculus dorsal telencephalon E14.5 biological replicate 1


title: Hypoxia rep3


title: Control_D25

description: Time Course - NPCs


title: Control_D24

description: Time Course - NPCs


title: Control_D23

description: Time Course - NPCs


title: Control_D22

description: Time Course - NPCs


title: Ctrl_E14.5_DorsalTelencephalon_Rpl4

description: Control Mus Musculus dorsal telencephalon E14.5 biological replicate 4

value: Foxg1Cre:+/+; Dot1l-cKO f/+


title: Ctrl_E14.5_DorsalTelencephalon_Rpl5

description: Control Mus Musculus dorsal telencephalon E14.5 biological replicate 5


title: Ctrl_E14.5_DorsalTelencephalon_Rpl3

description: Control Mus Musculus dorsal telencephalon E14.5 biological replicate 3


title: Ctrl_E14.5_DorsalTelencephalon_Rpl2

description: Control Mus Musculus dorsal telencephalon E14.5 biological replicate 2


title: Control_D21

description: Time Course - NPCs


title: H3K79me2_ChIPseq_Cortex_Rpl3

description: H3K79me2, ChIPseq, Mus Musculus cortex, biological replicate 3

data_processing:
Sequencer: HiSeq2500/8 lanes/ 200 M reads per lane/Max read length 2x150bp
Raw data processed with Illumina bcl2fastq2 v1.8.4 to fastq files
Reads were directly mapped with Bowtie2 v2.2.0 without trimming
Picard MarkDuplicates was used to remove read duplicates before peak calling with MACS2 v2.1.0 (for broad peaks)
Genome_build: mm10

source_name: Cortex E12.5

extract_protocol:
Roidl et al, Stem Cells. 2016 Jan;34(1):233-45. doi: 10.1002/stem.2187.
1 - ChIP-Seq: NEBNext® Ultra DNA Library Prep Kit for Illumina® (E7370S/L)

value: NMRI

value: Wildtype

value: Cortex


title: Control_D4

description: Time Course - NPCs


title: Ctrl_E14.5_DorsalTelencephalon_Rpl1

description: Control Mus Musculus dorsal telencephalon E14.5 biological replicate 1


title: Foxg1-KO_homocygots_E13.5_MedialDorsalTelencephalon_Rpl5

description:
Foxg1-KO homocygot E13.5 Medial dorsal telencephalon Biological replicate 5
3 medial dorsal telencephalon samples were pooled and sequenced on 3 different lanes


title: Control_D19

description: Time Course - NPCs


title: Control_D20

description: Time Course - NPCs


title: Control_D2

description: Time Course - NPCs


title: H3K79me2_ChIPseq_Cortex_Rpl2

description: H3K79me2, ChIPseq, Mus Musculus cortex, biological replicate 2


title: Control_D16

description: Time Course - NPCs


title: Control_D18

description: Time Course - NPCs


title: Input_Cortex_Rpl3

description: Input, Mus Musculus cortex, biological replicate 3


title: Input_Cortex_Rpl2

description: Input, Mus Musculus cortex, biological replicate 2


title: Input_Cortex_Rpl1

description: Input, Mus Musculus cortex, biological replicate 1


title: Control_D15

description: Time Course - NPCs


title: Control_D14

description: Time Course - NPCs


title: Control_D13

description: Time Course - NPCs


title: D5.5WT

city: Chongqing

first: Qingliang

last: ZOU

address: Tiansheng road

institute: Southwest university

data_processing:
Raw data were filtered to obtain clean data using Perl scripts. Reference genome and annotations were downloaded from the ENSEMBL website (http://www.ensembl.org/index.html).
Reference genome library was built using the Bowtie2 v2.2.3 software, and clean data was aligned to the library using the TopHat v2.0.12 software.
Gene expression levels were calculated by the RPKM method using the HTSeq v0.6.0 software.
Genes with P value<0.05 and |log2 ratio|≥1 were identified as differentially expressed genes using the DESeq (v1.16.0) software
These data were then subject to GO (gene ontology, http://geneontology.org/) analyses and aligned to KEGG (Kyoto Encyclopedia of Genes and Genomes, http://www.kegg.jp/) database to build pathway maps.
Genome_build: zv9
Supplementary_files_format_and_content: [rpkm.xls] tab-delimited text file includes RPKMs for each Sample.  [Table_s1.xls] foldChange between developmental stages in each genotype cells.

organism: Danio rerio

source_name: Hepatocytes

extract_protocol:
Total RNA was harvested using Trizol reagent.
cDNA libraries were generated from these sorted cells using the Smart-seq2 protocol.

treatment_protocol: Choose two different stages (5.5 and 7.5 dpf)  of zc3h8-/- mutant and wild-type group larves which hepatocytes were markerd by Tg(lfabp:Dendra2-NTR) transgenic line, and the zebrafish livers samples were respectively dissected, collected, and homogenized in 1 ml 0.5% trypsin at 4 °C. The homogenized cell suspension was centrifuged at 1000x g at 4 °C for 5 minutes. Then, the supernatant was removed and the cell pellet was resuspended in PBS, followed by cell sorting by flow cytometry (Moflo XDP, Beckman).

value: ABGO

value: liver

value: 5.5 dpf


title: D7.5MUT

value: 7.5 dpf


title: D5.5MUT


title: Control_D12

description: Time Course - NPCs


title: Control_D11

description: Time Course - NPCs


title: Control_D10

description: Time Course - NPCs


title: Control_D0

description: Time Course - NPCs


title: Control_D1

description: Time Course - NPCs


title: 164 KO

city: Verona

first: Nicola

last: Vitulo

state: Verona

address: Ca' Vignal 1, Strada Le Grazie 15

department: Department Biotechnology

country: Italy

institute: University of Verona

description: AGN

data_processing:
Reads preposessing was performed using cutadapt to remove adapter sequence. The minimum sequence length was set to 16
Reads were aligned on the reference genome using a two step procedures: at first reads were aligned using STAR program version 2.3.0e . The unmapped reads were aligned using bowtie2 version 2.2.2.1 setting the flag --local and --very-sensitive-local
Gene quantification was performed using htseq-count
raw counts were adjust for GC-content effect and to account for the different depth of sequencing usingfull quantile normalization implemented in EdaSeq R package
Differentially expressed genes were found using EdgeR R package setting the p-value < 0.05 after FDR correction
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text file containing the normalized reads counts for all the samples.

source_name: splenic B cells

extract_protocol:
spleen was taken from sacrificed mice and smashed to obtain a cell suspensions. B cells were isolated using magnetic separation and total RNA was prepared using QIAGEN RNeasy kit (#74106)
Total RNA samples were processed according to Dynabeads® mRNA DIRECTTM Purification Kit (Ambion) to isolate mRNA. The template library was prepared using the Ion Total RNA-Seq Kit v2 (Life Technologies). Quantity and size distribution of the library were analyzed using the Agilent Bioanalyzer 2100 DNA HS chip. Emulsion PCR using 10microl of 100pM library was performed using an OneTouch 2 instrument (Life Technologies) with an Ion PI Template OT2 200 kit following the manufacturer’s instructions. The enrichment of template library was achieved using the Ion OneTouch ES enrichment system (Life Technologies). Ion Proton sequencer and IPv2 chip were prepared according to the manufacturer’s recommendations.

value: Csnk2b-/- (KO)

value: spleen

tag: age

value: 8 weeks


title: 154 KO

description: AGL


title: Control_D17

description: Time Course - NPCs

value: Control


title: H3K79me2_ChIPseq_Cortex_Rpl1

description: H3K79me2, ChIPseq, Mus Musculus cortex, biological replicate 1


title: MCF7_E2+Dex_75 mins (15 min E2 and 60 min E2+Dex)_INPUT_rep1

city: Chicago

first: Hari

last: Singhal

state: IL

address: 929 E 57th St

department: Ben May Department for Cancer Research

institute: University of Chicago

description: ChIP-seq and reChIP-seq

data_processing:
The FASTQ files were filtered and good quality reads were groomed and subsequently aligned to HG19 genome build using Bowtie2
The output from Bowtie2 (BAM files) was subjected to MACS14 to call ChIP-seq peaks. Corresponding inputs for each of the treatment conditions were used as the background.
If needed, the ChIP-seq peaks thus obtained were filtered based on false discovery rates and height of the peaks.
Vehicle treated ChIP-peaksets were subtracted from the hormone-treated ChIP-peaksets.
Genome_build: HG19
Supplementary_files_format_and_content: BED files

source_name: Breast cancer cells

growth_protocol: Cells were cultured for 48 hours in charcoal-stripped serum media to deprive them of steroids.

extract_protocol:
Hormone-treated were harvested and ChIP was performed as per the directions provided in materials and method (ChIP and ChIP-sequencing).
ChIP-seq libraries were prepared using Kapa ChIP-seq kits.
Details of library preparation strategy are provided in the materials and methods section (ChIP and ChIP-seq) of the paper.

treatment_protocol: Steroid-deprived cell models were treated with 10 nM estradiol, 10 nM NR3C ligand (progesterone (PR), dexamethasone (GR), DHT (AR) or aldosterone (MR)) or 10 nM of both the hormones for the above-mentioned time.

tag: tissue type

value: ER+/PR+ MCF7 cell models

tag: er/pr status

value: ER+/PR+

tag: drug treatment

value: 10nM Estradiol + 10 nM Dexamethasone

tag: hormone exposure time

value: 75 minutes (15 min E2 and 60 min E2+Dexamethasone)

tag: chip antibody

value: none (INPUT)


title: MCF7_E2_75 mins_INPUT_rep2

description: ChIP-seq and reChIP-seq

value: 10 nM Estradiol

value: 75 minutes


title: MCF7_E2+Dex_75 mins (15 min E2 and 60 min E2+Dex)_INPUT_rep2

description: ChIP-seq and reChIP-seq


title: MCF7_Dex_60 mins_INPUT_rep2

description: ChIP-seq and reChIP-seq

value: 10 nM Dexamethasone

value: 60 minutes


title: 32 WT

description: AGK

tag: strain

tag: genotype

value: Csnk2b+/+ (WT)


title: 157 KO

description: AGM


title: 31 WT

description: AGJ


title: DNMT_1028nB [ATAC-seq]

first: Benjamin

middle: G

last: Barwick

address: 1365 Clifton Rd. NE WCI-C 4th Floor Benches 36-37

department: Hematology and Medical Oncology

institute: Emory University

description:
ATAC-seq (Assay for Transposase Accessible Chromatin-sequencing)
Processed data file: diff.MACS2_nomodel.union.rppm.cov.minFc.2.txt

data_processing:
ATAC-seq FASTQ files were aligned to the murine genome (mm9) using bowtie (v.1.1.1).
PCR duplicates were identified using Picard (v.1.127).
Enriched regions were determined with MACS2 (v.2.1.0.20140616) with the following parameters "-g mm --nomodel -n -q 0.01".
All peaks in any sample were combined in R/Bioconductor (v.3.2.3) using the Genomic Ranges package (v.1.22.4).
Data were normalized for reads per peak per million (RPPM) = reads x 106 / (total # of reads x fraction of reads in peaks).
Differential peaks were called with EdgeR (v.3.12.1) imposing a 2 fold-change difference.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: diff.MACS2_nomodel.union.rppm.cov.minFc.2.txt: Tab-delimited text file includes a summary of RPPM values per peak and differential stats.

source_name: naïve B cell (B220+ Fas- GL7-), Dnmt3-deficient

extract_protocol:
Cells were pelleted at 500g for 10 min and lysed in nuclei lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL).
Nuclei were pelleted at 500g for 30 min and tagmented with Tn5 (Illumina) for 60 min at 37°C prior to protein digestion with 2 mL 10 mg/mL Proteinase K at 40°C for 40 minutes. Libraries were size selected with SPRI beads (AMPure) prior to 12 rounds of PCR amplification.

tag: background/strain

tag: genotype/variation

tag: gender

value: male

value: lymph node

value: naive B cell (B220+ Fas- GL7-)


title: DNMT_1026nB [ATAC-seq]


title: 28 WT

description: AGI


title: MCF7_Dex_60 mins_INPUT_rep1

description: ChIP-seq and reChIP-seq


title: DNMT_1024BMPC [ATAC-seq]

description:
we have removed this sample from our analysis due to an aberrant number of reads in peaks, which we believe is attributable to a technical issue.
ATAC-seq (Assay for Transposase Accessible Chromatin-sequencing)

source_name: bone marrow plasma cell (CD138+), Dnmt3-deficient

value: female

value: bone marrow

value: bone marrow plasma cell (CD138+)


title: MCF7_Vehicle_60 mins_INPUT_rep1

description: ChIP-seq and reChIP-seq

value: Vehicle


title: D7.5WT

value: ABGO

value: liver

tag: developmental stage

value: 7.5 dpf


title: In7 (RRBS)

city: Los Angeles

first: Xia

last: Yang

address: 2000 Terasaki Life Sciences Bldg, 610 Charles E. Young Drive East

department: IBP

institute: UCLA

description: replicate 1

data_processing:
Reads were trimmed to remove the adapter sequences and low quality bases.
Bisulfite-converted reads were aligned to aligned to rat genome (UCSC assembly 5.0) using using the bisulfite aligner BS Seeker2, which utilizes the short read aligner Bowtie. As bisulfite treatment converted unmethylated cytosines (Cs) to thymines (Ts), we estimated the methylation level at each covered cytosine by methylation percentage which was calculated as NC/(NC + NT), where NC is the number of methylated reads and NT is the number of unmethylated reads
Genome_build: rn5
Supplementary_files_format_and_content: tab-delimited text files including the methylation level of cytosines in CpG, CHH and CHG context. The 8 fields in the files are (1) chromosome, (2) nucleotide on Watson (+) strand, (3) position, (4) context (CG/CHG/CHH), (5) dinucleotide-context (CA/CC/CG/CT), (6) methylation-level = #_of_C / (#_of_C + #_of_T)., (7) #_of_C (methylated C, the count of reads showing C here), (8) = #_of_C + #_of_T (all Cytosines, the count of reads showing C or T here)

organism: Rattus norvegicus

source_name: rat frontal cortex

extract_protocol:
Geome DNA was extracted with Qiagen AllPrep DNA/RNA Mini Kit. Quantity and quality of DNA were checked using Nanodrop (Thermo Fisher Scientific, MA, USA), Qubit RNA assay (Life Technologies, NY, USA) and gel electrophoresis
Reduced representation bisulfite sequencing (RRBS) libraries were constructed as described previously with some modifications (Chen, P.Y. et al. Physiol Genomics 45, 565-576). Briefly, about 1,000 ng genomic DNA was digested with the MspI enzyme. Digested DNA was then purified, end-repaired, and adenylated, followed by ligation to Illumina TruSeq barcode adapters (Illumina Inc, CA, USA). Fragments of 150-300 bp in size were selected, bisulfite-treated, and sequenced using an Illumina Hiseq 2500 System (Illumina Inc, CA, USA).

tag: treatment

value: high fat diet + injection of 5-AzaD in PBS

value: Sprague Dawley

value: frontal cortex


title: DNMT_1021BMPC [ATAC-seq]

source_name: bone marrow plasma cell (CD138+), Dnmt3-sufficient

tag: tissue


title: MCF7_E2+DHT_45 mins_INPUT

description: ChIP-seq and reChIP-seq

value: ER+/PR+ MCF7 cell models

value: ER+/PR+

value: 10nM Estradiol + 10 nM DHT

value: 45 minutes

value: none (INPUT)


title: DNMT_1020BMPC [ATAC-seq]

tag: cell type


title: In5 (RRBS)

description: replicate 1


title: MCF7_DHT_45 mins_INPUT

description: ChIP-seq and reChIP-seq

value: 10 nM DHT


title: DNMT_1018BMPC [ATAC-seq]


title: HFD4 (RRBS)

description: replicate 1

value: high fat diet + PBS


title: DNMT_1016BMPC [ATAC-seq]

value: female


title: MCF7_E2_45 mins_INPUT

description: ChIP-seq and reChIP-seq

value: 10 nM Estradiol


title: DNMT_1012nB [ATAC-seq]

source_name: naïve B cell (B220+ Fas- GL7-), Dnmt3-sufficient

value: male

value: lymph node

value: naive B cell (B220+ Fas- GL7-)


title: HFD3 (RRBS)

description: replicate 1


title: MCF7_Vehicle_45 mins_INPUT

description: ChIP-seq and reChIP-seq

value: Vehicle


title: MCF7_E2+Aldosterone_45 mins_ERChIP

description: ChIP-seq and reChIP-seq

value: 10nM Estradiol + 10 nM Aldosterone

value: anti-ER (SC biotech HC-20, cat# SC-543, lot# F0515)


title: HFD1 (RRBS)

description: replicate 1

value: Sprague Dawley


title: HFD2 (RRBS)

description: replicate 1

value: frontal cortex


title: MCF7_Aldosterone_45 mins_ERChIP

description: ChIP-seq and reChIP-seq

value: ER+/PR+ MCF7 cell models

value: 10 nM Aldosterone


title: MCF7_E2_75 mins_INPUT_rep1

description: ChIP-seq and reChIP-seq

value: ER+/PR+

value: 75 minutes


title: In6 (RRBS)

description: replicate 1

value: high fat diet + injection of 5-AzaD in PBS


title: HF8 (RRBS)

description: replicate 1

value: high fat diet


title: MCF7_E2_45 mins_ERChIP

description: ChIP-seq and reChIP-seq

value: 45 minutes


title: M1neg [ATAC-seq]

source_name: PE-specific germinal center B cell (B220+ Fas+ GL7+ PE+), Dnmt3-sufficient


title: DNMT_1008nB [ATAC-seq]


title: DNMT_1009nB [ATAC-seq]


title: DNMT_1019BMPC [ATAC-seq]

value: female

value: bone marrow

value: bone marrow plasma cell (CD138+)


title: HF5 (RRBS)

description: replicate 1


title: In3 (RRBS)

description: replicate 1


title: HF6 (RRBS)

description: replicate 1


title: MCF7_Vehicle_45 mins_ERChIP (I2)

description: ChIP-seq and reChIP-seq


title: F2neg [ATAC-seq]

value: lymph node

value: PE-specific germinal center B cell (B220+ Fas+ GL7+ PE+)


title: HF7 (RRBS)

description: replicate 1


title: M1pos [ATAC-seq]

source_name: PE-specific germinal center B cell (B220+ Fas+ GL7+ PE+), Dnmt3-deficient

value: male


title: F3pos [ATAC-seq]


title: CON4 (RRBS)

description: replicate 1

value: chow diet


title: CON3 (RRBS)

description: replicate 1


title: MCF7_E2_75 mins_ERChIP

description: ChIP-seq and reChIP-seq

value: 10 nM Estradiol

value: anti-ER (SC biotech HC-20, cat# SC-543, lot# F0515)


title: F2pos [ATAC-seq]


title: MCF7_Vehicle_60 mins_ERChIP

description: ChIP-seq and reChIP-seq

value: Vehicle

value: 60 minutes


title: F1pos [ATAC-seq]


title: CON1 (RRBS)

description: replicate 1

value: Sprague Dawley

value: frontal cortex


title: In7 (RNA-Seq)

description: replicate 1

data_processing:
Paired-end RNA-Seq reads were analyzed using the Tuxedo tool package comprised of Tophat/Bowtie, Cufflinks, and Cuffdiff. Specifically, we used TopHat2/Bowtie2 which allows alignment across splice junctions to map reads to the rat genome (UCSC assembly 5.0) and to discover transcript splice sites. Cufflinks were then used to assemble the aligned reads onto transcripts, and Cuffdiff was used to compare the aligned reads between different treatment groups to identify genes and gene transcripts that are differentially expressed. Multiple hypothesis testing was corrected using the Benjamini-Hochberg method to estimate false discover rate (FDR).
Genome_build: rn5
Supplementary_files_format_and_content: tab-delimited text files include FPKM values and status ("FAIL","HIGHDATA","LOWDATA","OK",etc.) for each sample

extract_protocol:
Total RNA was extracted with Qiagen AllPrep DNA/RNA Mini Kit. Quantity and quality of RNA were checked using Nanodrop (Thermo Fisher Scientific, MA, USA), Bioanalyzer (Agilent Technologies, CA, USA) and Qubit RNA assay (Life Technologies, NY, USA).
The RNA-Seq libraries were prepared followed the standard Illumina protocol (http://support.illumina.com/sequencing/documentation.ilmn). Briefly, about 1,000 ng total RNA was first enriched for mRNA by poly-A selection, then fragmented, and reverse transcribed using random hexamer-primers to generate first-strand cDNA. Second-strand cDNA was then generated using RNase H and DNA polymerase. Fragments of 200-400 bp in size were next enriched through PCR and multiplex barcodes were also added. Sequencing was performed on HiSeq 2500 (Illumina Inc, CA, USA). Data quality check was done on Sequencing Analysis Viewer and demultiplexing was performed with CASAVA 1.8.2 (Illumina Inc, CA, USA).


title: MCF7_DHT_45 mins_ERChIP

description: ChIP-seq and reChIP-seq

value: ER+/PR+ MCF7 cell models

value: ER+/PR+

value: 10 nM DHT


title: Dnmt3_913 [RRBS]

description:
Reduced Representation Bisulfite Sequencing (RRBS)
Processed data file: DML.Sample.group.common.coverage.10.annot.sig.0.01.txt

data_processing:
RRBS FASTQ files were aligned to the in silico bisulfite converted genome (mm9) using Bismark (v.0.13.1) with the Bowtie2 (v.2.2.4) option.
Binary Alignment Map (BAM) files were parsed to derive DNA methylation calls that were collapsed to the CpG level using custom R scripts that made use of the ‘Rsamtools’ (v.1.22.0) and ‘data.table’ (v.1.9.6) packages (available upon request)
Data were summarized for CpGs that were covered at 10x in all samples and CpGs that were covered at 10x by all groups
Differentially methylated loci were determined in R/Bioconductor (v.3.2.3) with DSS (v.2.10.0) for all CpGs with 10x coverage in all groups.  A mininum FDR of 0.01 and change in DNA methylation of 20% were imposed to be considered significant.
genome build: mm9
DML.Dnmt3.Group.common.10.annot.sig.0.05.csv.gz: summary of unmethylated reads, methylated reads, and average methylation level, and differential statistics between Dnmt3ab-deficient and Dnmt3ab-sufficient cell types, for CpGs with at least 10X coverage per group
DML.Cell.Group.common.10.annot.0.05.csv.gz: summary of unmethylated reads, methylated reads, and average methylation level, and differential statistics between Cell types while controlling for Dnmt3ab-specific effects, for CpGs with at least 10X coverage per group

extract_protocol:
Overnight digestion in Proteinase K and RNase followed by isolation with Phenol Chloroform and isoamyl alcohol and ethanol precipitation.
Reduced Representation Bisulfite Sequencing (RRBS) libraries were made from 20 ng of DNA that was digested overnight with 20 U MspI (New England Biolabs) and 20 U TaqI following the manufacturer's protocol. Digested DNA was purified using a 1.8X Solid Phase Reversible Immobilization (SPRI) clean-up with Agencourt AMPure XP beads (Beckman Coulter). Illumina compatible sequencing adaptors were used and contained fully methylated cytosine residues and were designed similar to those previously described (Barwick et al. 2016, PMID: 27500631) and synthesized by Integrated DNA Technologies. DNA was end-repaired and A-tailed and sequencing adaptors were ligated using the Hyper Prep Kit (KAPA Biosystems) following the manufacturer's protocol. Adaptor-ligated DNA was bisulfite treated using the EpiTect Bisulfite Kit (Qiagen), modifying the manufacturer's protocol by extending the denaturation thermocycler step from 5 to 10 minutes at 99ᵒC. Adaptor-ligated bisulfite treated libraries were amplified 10-15 times using HiFi Uracil+ Polymerase (KAPA Biosystems) and library concentration was estimated using the KAPA quantification kit (KAPA Biosystems). Size was estimated using a high sensitivity DNA chip (Agilent Technologies) at the Emory Integrated Genomics Core. Libraries were sequenced using 50 bp paired-end reads on a HiSeq2500 by the Genome Technology Center at New York University (NYU).

tag: strain/background


title: Dnmt3_914 [RRBS]


title: CON2 (RRBS)

description: replicate 1


title: MCF7_E2+Dexamethasone_75 mins (15 min E2 and 60 min E2+Dex)_ERChIP

description: ChIP-seq and reChIP-seq

value: 10nM Estradiol + 10 nM Dexamethasone

value: 75 minutes (15 min E2 and 60 min E2+Dexamethasone)


title: MCF7_Dexamethasone_60 mins_ERChIP

description: ChIP-seq and reChIP-seq

value: 10 nM Dexamethasone


title: Dnmt3_912 [RRBS]

value: bone marrow

value: bone marrow plasma cell (CD138+)


title: In6 (RNA-Seq)

description: replicate 1

value: high fat diet + injection of 5-AzaD in PBS


title: In5 (RNA-Seq)

description: replicate 1


title: In3 (RNA-Seq)

description: replicate 1


title: MCF7_E2_45 mins_ERChIP (H4)

description: ChIP-seq and reChIP-seq

value: 45 minutes


title: T47D-B_R5020_45 mins_INPUT

description: ChIP-seq and reChIP-seq

data_processing:
The FASTQ files were filtered and good quality reads were groomed and subsequently aligned to HG19 genome build using Bowtie2
The output from Bowtie2 (BAM files) was subjected to MACS14 to call ChIP-seq peaks. Corresponding inputs for each of the treatment conditions were used as the background.
If needed, the ChIP-seq peaks thus obtained were filtered based on false discovery rates and height of the peaks.
Vehicle treated ChIP-peaksets were subtracted from the hormone-treated ChIP-peaksets. For reChIP-seq, the reChIP peaks obtained after vehicle treatment as well as the reChIP peaks observed upon second pulldown with control IgG were used as controls. Hence, both of the reChIP controls were subtracted from the reChIP-signal obtained on joint estradiol plus R5020 treatment.
Genome_build: HG19
Supplementary_files_format_and_content: BED files

extract_protocol:
Hormone-treated were harvested and ChIP was performed as per the directions provided in materials and method (ChIP and ChIP-sequencing; reChIP and reChIP-sequencing)
ChIP-seq and reChIP-seq libraries were prepared using Kapa ChIP-seq kits.
Details of library preparation strategy are provided in the materials and methods section (ChIP and ChIP-seq; reChIP and reChIP-seq) of the paper.

treatment_protocol: Steroid-deprived cell models were treated with 10 nM estradiol, 10 nM R5020 or 10 nM of both the hormones for 45 minutes.

value: ER+/PRA-/PRB+ T47D cell models

value: ER+/PRA-/PRB+

value: none (INPUT)


title: T47D-B_E2+R5020_45 mins_INPUT

description: ChIP-seq and reChIP-seq

value: 10nM Estradiol + 10 nM R5020


title: Dnmt3_911 [RRBS]

value: female


title: HFD4 (RNA-Seq)

description: replicate 1

value: high fat diet + PBS

value: Sprague Dawley


title: Dnmt3_910 [RRBS]


title: Dnmt3_909 [RRBS]

value: male


title: M1pos [RRBS]

value: lymph node

value: PE-specific germinal center B cell (B220+ Fas+ GL7+ PE+)


title: T47D-B_E2_45 mins_INPUT

description: ChIP-seq and reChIP-seq

value: 10 nM Estradiol


title: HFD3 (RNA-Seq)

description: replicate 1

value: frontal cortex


title: F3pos [RRBS]


title: HFD2 (RNA-Seq)

description: replicate 1


title: MCF7_E2+DHT_45 mins_ERChIP

description: ChIP-seq and reChIP-seq

value: ER+/PR+ MCF7 cell models

value: ER+/PR+

value: 10nM Estradiol + 10 nM DHT

value: anti-ER (SC biotech HC-20, cat# SC-543, lot# F0515)


title: T47D-B_E2+R5020_45 mins_ER_ChIP

description: ChIP-seq and reChIP-seq

value: 45 minutes


title: T47D-B_E2+R5020_45 mins_PR_ChIP

description: ChIP-seq and reChIP-seq

value: ER+/PRA-/PRB+ T47D cell models

value: anti-PR (inhouse KD68)


title: HF7 (RNA-Seq)

description: replicate 1

value: high fat diet


title: MCF7_Vehicle_45 mins_ERChIP (H2)

description: ChIP-seq and reChIP-seq

value: Vehicle


title: HF8 (RNA-Seq)

description: replicate 1


title: F3neg [RRBS]

value: female


title: T47D-B_R5020_45 mins_ER_ChIP

description: ChIP-seq and reChIP-seq

value: ER+/PRA-/PRB+


title: M1neg [RRBS]


title: F2neg [RRBS]


title: T47D-B_R5020_45 mins_PR_ChIP

description: ChIP-seq and reChIP-seq


title: CON4 (RNA-Seq)

description: replicate 1

value: chow diet

value: Sprague Dawley


title: HF6 (RNA-Seq)

description: replicate 1


title: T47D-B_E2_45 mins_ER_ChIP

description: ChIP-seq and reChIP-seq


title: T47D-B_E2_45 mins_PR_ChIP

description: ChIP-seq and reChIP-seq


title: T47D-B_Vehicle_45 mins_INPUT

description: ChIP-seq and reChIP-seq

value: none (INPUT)


title: T47D-B_Vehicle_45 mins_ER_ChIP

description: ChIP-seq and reChIP-seq


title: Dnmt3_736 [RRBS]

value: male

value: lymph node

value: naive B cell (B220+ Fas- GL7-)


title: Dnmt3_734 [RRBS]


title: CON2 (RNA-Seq)

description: replicate 1

value: frontal cortex


title: CON3 (RNA-Seq)

description: replicate 1


title: Dnmt3_705 [RRBS]


title: T47D-A_E2+R5020_45 mins_INPUT

description: ChIP-seq and reChIP-seq

value: ER+/PRA+/PRB- T47D cell models

value: ER+/PRA+/PRB-

value: 10nM Estradiol + 10 nM R5020


title: CON1 (RNA-Seq)

description: replicate 1


title: T47D-A_R5020_45 mins_INPUT

description: ChIP-seq and reChIP-seq

value: 45 minutes


title: T47D-B_Vehicle_45 mins_PR_ChIP

description: ChIP-seq and reChIP-seq

value: ER+/PRA-/PRB+ T47D cell models


title: F2pos [RRBS]

value: PE-specific germinal center B cell (B220+ Fas+ GL7+ PE+)


title: HFD1 (RNA-Seq)

description: replicate 1

value: high fat diet + PBS


title: Dnmt3_702 [RRBS]


title: HF5 (RNA-Seq)

description: replicate 1

value: high fat diet


title: T47D-A_Vehicle_45 mins_INPUT

description: ChIP-seq and reChIP-seq

value: Vehicle


title: T47D-A_E2+R5020_45 mins_ER_ChIP

description: ChIP-seq and reChIP-seq

value: anti-ER (SC biotech HC-20, cat# SC-543, lot# F0515)


title: T47D-A_E2+R5020_45 mins_PR_ChIP

description: ChIP-seq and reChIP-seq

value: anti-PR (inhouse KD68)


title: Dnmt3_914 [RNA-seq]

description:
mRNA
Processed data file: diff.geneFpkm.exon.glm.LogFc.1.txt

data_processing:
RNA-seq data was mapped back to the UCSC mouse genome mm9 using Tophat254 (v.2.0.13) with the following parameters "-p 8 -N2 -max-multihits 1 -read-gap-length 1" and the UCSC Known Genes mm9 transcript file as a guide. The 92 ERCC sequences were added to the mm9 genome as artificial chromosomes.
PCR duplicates were determined using Picard (http://broadinstitute.github.io/picard/) and removed from subsequent analyses.
Reads that uniquely overlapped mm9 exons were determined in R (v.3.2.2) using the 'summarizeOverlaps' function in mode 'IntersectionNotEmpty' of the 'GenomicAlignments' package (v.1.6.3).
Reads per million (RPM) were calculated for each gene based on the number reads in all potential exons for a given gene and the total number of uniquely mappable reads per sample.
Fragments per kilobase per million (FPKM) were calculated based on RPM and the total size of non-overlapping exons for a gene.
Differentially expressed genes were determined with EdgeR (v.3.12.1) by imposing a minimum absolute log2 fold-change of 1 and an FDR less than 0.01.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: diff.geneFpkm.exon.glm.LogFc.1.txt: Tab-delimited text file includes normalized read counts (that map to exons) expressed in fragments per kilobase per million (FPKM) for UCSC mm9 KnownGenes, and a summary of differential statistics.

extract_protocol:
For RNA-seq analysis, 5,000 cells were sorted into RLT buffer (Qiagen) with 1% 2-mercaptoethanol (Sigma), vortexed and snap frozen. RNA was extracted using RNeasy Micro Kit (Qiagen) following the manufacturer's protocol. DNA was removed with on-column DNase digestion.
The Smarter Clontech Ultralow HV kit with the Advantage 2 for 13 cycles of amplification was used for cDNA synthesis followed by the Illumina Nextera kit with 12 cycles of amplification.

value: bone marrow

value: bone marrow plasma cell (CD138+)


title: Dnmt3_704 [RRBS]

value: female


title: T47D-A_R5020_45 mins_ER_ChIP

description: ChIP-seq and reChIP-seq


title: Contact_Fixed_2

city: Stanford

first: Jose

middle: Ramon

last: Dinneny

state: United States

address: 260 Panama St

department: Plant Biology

institute: Carnegie Institution for Science, Department of Plant Biology

data_processing:
Unmapped post-filter reads were pre-processed using Scythe v0.981 and Cutadapt v1.3 to remove Illumina sequencing adapters, and Sickle v1.0 for quality trimming.
Reads which were still paired after pre-processing were mapped to B73 maize genome (AGPv3, Ensembl 21) using TopHat v2.0.9
Transcripts were assembled using Cufflinks v2.1.1 and Cuffmerge.
Differential expression was tested using Cuffdiff v2.2.1
Differential expression was also measured using DESeq2; BAM files were converted to sorted SAM files using Samtools v0.1.19, transcript counts were calculated using HTSeq 0.5.4p3, and differential expression was measured using DESeq2 v1.14.0.
Genome_build: Zea mays B73 genome (AGPv3, Ensembl 21)
Supplementary_files_format_and_content: genes_read_group_tracking_with_GRMZM.csv: comma-separated CSV with FPKM values from Cuffdiff for each gene in each sample. RNA-seq significant genes.xlsx: Excel spreadsheet of genes which were significantly differentially expressed between the air and contact sides, including functional annotations.

organism: Zea mays

source_name: Primary root

growth_protocol: Seeds were sterilized using a heat/bleach treatment (5 min incubation in 55°C water bath, 20 min incubation in 20% commercial bleach + 0.1% Tween-20 (Sigma), 5-7 washes with autoclave-sterilized deionized water) and germinated on autoclave-sterilized 100-lb germination paper (Anchor Paper Company) soaked with autoclaved deionized water for 2 days. Germinated seedlings were transferred to autoclave-sterilized agar media containing 1% w/v agar (BD, Difco), 1/2X Murashige & Skoog basal salts (Caisson Labs), and 0.5 g/l MES hydrate (Sigma-Aldrich) in 120 X 120 X 17-mm square plastic plates (USA Scientific). Agar plates were incubated vertically in a growth chamber (Percival, CU41L4) under 16 h light (29°C, 100-µE light) / 8 h dark (24°C) cycle.

extract_protocol:
RNA was isolated using the ZR Plant RNA MiniPrep™ kit (Zymo Research). Tissues were homogenized using a FastPrep®-24 (MP Biomedicals), twice for 30 s at 6.0 m/s. On-column DNase digest was done using RNase-Free DNase Set (50) kit (QIAGEN). Ribosomal RNA was removed using the RiboZero™ Magnetic Kit for Plant Seed/Root (Epicentre), followed by cleanup using the Zymo RNA Clean & Concentrator™-5 kit (Zymo Research).
Sequencing libraries were prepared using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (New England Biolabs).

treatment_protocol: Primary roots of seedlings 3 days post-imbibition were manually dissected using an X-ACTO® #1 precision knife with #11 blades under a dissection microscope (Olympus SZ61 with Schott ACE light source). Competent- and fixed-zone tissues were taken from 0-5 and 5-15 mm from the root tip, respectively. Tissue segments were cut longitudinally to separate the air and contact sides of the root. 3 biological replicates were collected for each tissue type, with each replicate composed of tissue pooled from 2 seedlings. Tissues were flash-frozen in liquid nitrogen and stored at -80°C until processed.

tag: inbred line

value: Primary root

tag: root side

value: Contact

tag: developmental zone

value: Fixed

tag: biological replicate


title: T47D-A_R5020_45 mins_PR_ChIP

description: ChIP-seq and reChIP-seq

tag: tissue type

value: ER+/PRA+/PRB- T47D cell models

tag: er/pr status

tag: drug treatment


title: Dnmt3_703 [RRBS]

city: Atlanta

value: lymph node

value: naive B cell (B220+ Fas- GL7-)


title: Dnmt3_912 [RNA-seq]

value: male


title: Dnmt3_911 [RNA-seq]


title: RNAs from buckwheat seed developmental stage 5

city: Hefei

first: cong

middle: bing

last: fang

state: Anhui

address: No. 130 Changjiang West Road

department: School of Horticulture

institute: Anhui Agricultural University

data_processing: Raw sequences were transformed into clean tags through removing adaptor sequence,low-quality sequences (tags with unknown sequences [“N”]), empty reads (sequence with only adaptor sequences but no tags), too-long or too-short tags, and tags with a copy number of 1 (probably a sequencing error). A preprocessed database of all possible CATG+ 17-nucleotide tag sequences was created using our transcriptome reference database. For annotation, all tags were mapped to the reference sequences and only allowed no more than 1 nucleotide mismatch.Clean tags mapped to reference sequences from multiple genes were filtered,and the remaining clean tags were designed as unambiguous tags. For gene expression analysis, the number of unambiguous clean tags for each gene was calculated and then normalized to the number of transcripts per million tags (TPM). The gene ontology (GO) classification system was used to determine the possible functions of all genes tagged.

organism: Fagopyrum esculentum

growth_protocol: Plants were grown under normal orchard conditions.

extract_protocol: Beads with Oligo(dT) are used to isolate poly(A) mRNA after total RNA is collected from pear fruits . Fragmentation buffer is added for interrupting mRNA to short fragments. Taking these short fragments as templates, random hexamer-primer is used to synthesize the first-strand cDNA. The second-strand cDNA is synthesized using buffer, dNTPs, RNaseH and DNA polymerase I, respectively. Short fragments are purified with QiaQuick PCR extraction kit and resolved with EB buffer for end reparation and adding poly(A). After that, the short fragments are connected with sequencing adapters. And, after the agarose gel electrophoresis, the suitable fragment are selected for the PCR amplification as templates. At last, the library could be sequenced using Illumina HiSeq™ 2000.

tag: authority

value: Fagopyrum esculentum Moench.

tag: development stage

value: buckwheat seed developmental stage 5


title: RNAs from buckwheat seed developmental stage 3

value: buckwheat seed developmental stage 3


title: RNAs from buckwheat seed developmental stage 2

value: buckwheat seed developmental stage 2


title: T47D-A_E2_45 mins_ER_ChIP

description: ChIP-seq and reChIP-seq

value: ER+/PRA+/PRB-

value: 10 nM Estradiol

tag: hormone exposure time

value: 45 minutes

tag: chip antibody


title: M1pos [RNA-seq]

tag: background/strain

tag: genotype/variation

tag: gender

value: PE-specific germinal center B cell (B220+ Fas+ GL7+ PE+)


title: Contact_Fixed_1

tag: tissue


title: RNAs from buckwheat seed developmental stage 1

value: buckwheat seed developmental stage 1


title: M1neg [RNA-seq]

tag: cell type


title: T47D-A_E2_45 mins_PR_ChIP

description: ChIP-seq and reChIP-seq

value: anti-PR (inhouse KD68)


title: T47D-A_Vehicle_45 mins_ER_ChIP

description: ChIP-seq and reChIP-seq

value: Vehicle

value: anti-ER (SC biotech HC-20, cat# SC-543, lot# F0515)


title: Contact_Fixed_0

value: Primary root

value: Contact

value: Fixed


title: Contact_Competent_2

value: Competent


title: F3pos [RNA-seq]

value: female

value: lymph node


title: T47D-A_Vehicle_45 mins_PR_ChIP

description: ChIP-seq and reChIP-seq

value: ER+/PRA+/PRB- T47D cell models


title: Dnmt3_910 [RNA-seq]

value: bone marrow

value: bone marrow plasma cell (CD138+)


title: T47D-A_E2_45 mins_INPUT

description: ChIP-seq and reChIP-seq

value: ER+/PRA+/PRB-

value: none (INPUT)


title: Dnmt3_909 [RNA-seq]

value: male


title: Contact_Competent_0


title: Contact_Competent_1


title: T47D-B_R5020_45 mins_PRB_INPUT_reChIP

description: ChIP-seq and reChIP-seq

value: ER+/PRA-/PRB+ T47D cell models

value: ER+/PRA-/PRB+

value: 45 minutes


title: RNAs from buckwheat seed developmental stage 4

value: Fagopyrum esculentum Moench.

value: buckwheat seed developmental stage 4


title: T47D-B_Vehicle_45 mins_PRB_INPUT_reChIP

description: ChIP-seq and reChIP-seq

value: Vehicle


title: F2pos [RNA-seq]

value: PE-specific germinal center B cell (B220+ Fas+ GL7+ PE+)


title: T47D-A_Vehicle_45 mins_PRA_INPUT_reChIP

description: ChIP-seq and reChIP-seq


title: Dnmt3_736 [RNA-seq]

value: naive B cell (B220+ Fas- GL7-)


title: F3neg [RNA-seq]


title: T47D-Vehicle_45 mins_PR_INPUT_reChIP

description: ChIP-seq and reChIP-seq

value: ER+/PR+ T47D cell models

value: ER+/PR+


title: Air_Competent_2

value: Primary root

value: Air

value: Competent


title: Air_Fixed_0

value: Fixed


title: Air_Fixed_2


title: Dnmt3_704 [RNA-seq]

value: female

value: lymph node


title: F2neg [RNA-seq]


title: T47D-B_Vehicle_45 mins_ERIgG(Control)_reChIP

description:
ChIP-seq and reChIP-seq
processed data file: T47D_PRB(reChIP)_ERPRBComplexes_R5020_AZ9 (subtracted Veh and IgG).bed

value: anti-ER (SC biotech HC-20, cat# SC-543, lot# F0515) plus anti-rabbit IgG Control (cat# sc-2027, lot# E2914 or H2615)


title: T47D-A_R5020_45 mins_PRA_INPUT_reChIP

description: ChIP-seq and reChIP-seq

value: ER+/PRA+/PRB- T47D cell models

value: ER+/PRA+/PRB-

value: none (INPUT)


title: Air_Fixed_1


title: Air_Competent_1


title: Air_Competent_0


title: Dnmt3_734 [RNA-seq]

value: male


title: T47D-R5020_45 mins_PR_INPUT_reChIP

description: ChIP-seq and reChIP-seq

value: 45 minutes


title: Dnmt3_705 [RNA-seq]


title: T47D-B_R5020_45 mins_ERPRBComplex_reChIP

value: ER+/PRA-/PRB+ T47D cell models

value: ER+/PRA-/PRB+

value: anti-ER (SC biotech HC-20, cat# SC-543, lot# F0515) plus anti-PR (inhouse KD68)


title: JR3890-MeCP2_KO

city: Cambridge

first: Rahul

last: Karnik

state: MA

address: 419 Broadway

data_processing:
Sequence reads were aligned to the mouse genome (mm9) using bsmap.
CpG level methylation calls were calculated using mcall from the MOABS package.
Genome_build: mm9
Supplementary_files_format_and_content: [.bed] chrom,start,end,ratio,totalC,methC,strand,next,Plus,totalC,methC,Minus,totalC,methC, localSeq

source_name: whole brain

extract_protocol: 200 ng of genomic DNA was fragmented using a Covaris S2 for 6 min according to the following program: duty cycle 5%; intensity 5; cycle per burst 200. The sheared DNA was purified using the DNA Clean & Concentrator kit from Zymo Research per the manufacturer’s recommendations. Bisulfite conversion of DNA was then conducted using the EZ DNA Methylation-Gold kit (Zymo Research) followed the instructions, eluting to 15 μl low TE buffer. To minimize continual loss during storage, the converted DNA was immediately processed for generating WGBS libraries using the Accel-NGS Methyl-Seq DNA library kit (Swift Biosciences) following the manufacturer’s protocol.

tag: strain

value: MeCP2 KO


title: JR664-C57BL_1BJ_WT

value: wild type


title: T47D-B_Vehicle_45 mins_ERPRBComplex_reChIP

value: Vehicle


title: Dnmt3_703 [RNA-seq]

value: naive B cell (B220+ Fas- GL7-)


title: 10 μM PCB153-2

city: Woods Hole

first: Neelakanteswar

last: Aluru

address: 45 Water Street

department: Biology

institute: Woods Hole Oceanographic Institution

data_processing:
Trimming adaptor sequences using Trimmomatic
Mapping the reads to the genome (Ensembl version 84) using STARaligner
Counting the reads using Htseq-count
Statistical analysis was done using edgeR
Genome_build: GRCz10
Supplementary_files_format_and_content: Text file of count data for each gene

source_name: 10 μM PCB153

extract_protocol:
Total RNA was isolated using the Aurum total RNA mini kit (BioRad, Herculus, CA)
The Illumina Truseq Stranded total RNA library prep kit with Ribo-Zero Gold was used for library preparation

treatment_protocol: Zebrafish embryos were exposed to either DMSO (0.1%; solvent control) or three different concentrations of PCB153 (0.1, 1 and 10 μM) from 4 hours post-fertilization (hpf) to 120 hpf.

tag: agent

tag: concentration

value: 10 μM

tag: age

value: 5 days post-fertilization

tag: developmental stage

value: larval

value: Whole Animal


title: T47D-A_Vehicle_45 mins_ERIgG(Control)_reChIP

description:
ChIP-seq and reChIP-seq
processed data file: T47D_PRA(reChIP)_ERPRAComplexes_R5020_AZ5 (subtracted Veh and IgG).bed

tag: tissue type

value: anti-ER (SC biotech HC-20, cat# SC-543, lot# F0515) plus anti-rabbit IgG Control (cat# sc-2027, lot# E2914 or H2615)


title: T47D-B_R5020_45 mins_ERIgG(Control)_reChIP

tag: er/pr status


title: T47D-A_R5020_45 mins_ERIgG(Control)_reChIP

value: ER+/PRA+/PRB- T47D cell models

tag: drug treatment


title: T47D-A_Vehicle_45 mins_ERPRAComplex_reChIP

value: ER+/PRA+/PRB-


title: 1 μM PCB153-4

source_name: 1 μM PCB153

value: 1 μM


title: 10 μM PCB153-1


title: Dnmt3_702 [RNA-seq]

value: female

value: lymph node


title: Dnmt3_913 [RNA-seq]

value: male

value: bone marrow

value: bone marrow plasma cell (CD138+)


title: 10 μM PCB153-4


title: 10 μM PCB153-3


title: T47D-A_R5020_45 mins_ERPRAComplex_reChIP

value: 45 minutes

value: anti-ER (SC biotech HC-20, cat# SC-543, lot# F0515) plus anti-PR (inhouse KD68)


title: 1 μM PCB153-2


title: 0.1 μM PCB153-3


title: T47D-R5020_45 mins_ERIgG(Control)_reChIP

description:
ChIP-seq and reChIP-seq
processed data file: T47D_PR(reChIP)_ERPRComplexes_R5020_AZ1 (subtracted Veh and IgG).bed

value: ER+/PR+ T47D cell models

value: ER+/PR+


title: T47D-Vehicle_45 mins_ERIgG(Control)_reChIP

value: Vehicle


title: T47D-R5020_45 mins_ERPRComplex_reChIP


title: G4.2_Ko_Rep2

city: Parkville

first: Belinda

last: Phipson

state: VIC

address: 1G Royal Parade

department: Bioinformatics

institute: WEHI

data_processing:
Fastq files were generated using the bcl to fastQ converter 2.17.
The raw reads were mapped to the mouse genome (mm10) using the STAR aligner version 2.4.0h1 in the two pass mapping mode
The mapped reads were quantified at the gene level using featureCounts version 1.4.6 using GENCODE VM4 comprehensive annotation
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text file with Gene symbol and Gene length in the first two columns, followed by 33 columns containing counts for each sample

source_name: knockout_E11.5_whole kidney

extract_protocol:
RNA were extracted using QIAGEN RNeasy micro kit after snap-freezing fresh tissue in 1.5ml tube on dry ice.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: knockout

tag: Sex

value: embyronic whole kidney

tag: batch


title: G6.3_Ko_Rep2


title: T47D_PRB_E2+R5020_RNAseq

description:
Cell models RNA-seq
processed data file: T47D-PRB_RNAseq.csv

data_processing:
The FASTQ files were filtered and good quality reads were groomed and subsequently aligned to HG19 genome build using TopHat.
Relative expression of transcripts were calculated by subjecting TopHat output (BAM files) to Cufflinks package.
Cufflinks assemblies obtained from Cufflinks package were merged using cuffmerge. For every model system, cufflink assemblies of each of the treatments were merged with the cufflinks assemblies of the respective vehicle-treated samples.
The output from Cuffmerge along with the corresponding TopHat output (BAM files) were subjected to Cuffdiff to calculate transcript expression.
Genes that were up or down regulated by at least two fold were used for downstream analyses.
Genome_build: HG19
Supplementary_files_format_and_content: CSV includes RPKM values for each of the treatment conditions (E2, R5020 or E2+R5020) versus control treatment. Union of all estrogen and progestin-regulated genes for the respective samples is provided.

extract_protocol:
Hormone-treated cells were homogenized and total RNA was extracted using Qiagen RNAeasy kit
PolyA tail selection was performed on 250 ng of total RNA. RNA-seq libraries were prepared using NEBNext kit.
Details of library preparation strategy are provided in the materials and methods section (RNA expression and RNA-sequencing) of the paper.

treatment_protocol: Steroid-deprived cell models were treated with 10 nM estradiol, 10 nM R5020 or 10 nM of both the hormones for 12 hours.

value: ER+/PRA-/PRB+ T47D cell models

value: ER+/PRA-/PRB+

value: 10nM Estradiol + 10 nM R5020

tag: hormone exposure time

value: 12 Hours


title: 0.1 μM PCB153-4

value: 5 days post-fertilization

value: larval

value: Whole Animal


title: 1 μM PCB153-3

value: 1 μM


title: 0.1 μM PCB153-1


title: 0.1 μM PCB153-2


title: 1 μM PCB153-1


title: G3.6_wt_Rep2

source_name: wildtype_E11.5_whole kidney

value: wildtype

value: female


title: DMSO treated-4

source_name: DMSO treated

value: DMSO

value: control


title: T47D-Vehicle_45 mins_ERPRComplex_reChIP

value: ER+/PR+ T47D cell models

value: 45 minutes

tag: chip antibody

value: anti-ER (SC biotech HC-20, cat# SC-543, lot# F0515) plus anti-PR (inhouse KD68)


title: G3.3_Het_Rep2

source_name: heterozygous_E11.5_whole kidney

value: heterozygous


title: T47D_PRB_E2_RNAseq

value: 10 nM Estradiol


title: T47D_PRB_Vehicle_RNAseq

value: ER+/PRA-/PRB+ T47D cell models

value: Vehicle


title: DMSO treated-2


title: T47D_PRA_E2+R5020_RNAseq

description:
Cell models RNA-seq
processed data file: T47D-PRA_RNAseq.csv

value: ER+/PRA+/PRB- T47D cell models

value: ER+/PRA+/PRB-

value: 10nM Estradiol + 10 nM R5020


title: G3.2_Het_Rep2

value: embyronic whole kidney


title: T47D_PRA_R5020_RNAseq

value: 12 Hours


title: G1.7_wt_Rep2


title: DMSO treated-3

value: 5 days post-fertilization

value: larval

value: Whole Animal


title: T47D_PRB_R5020_RNAseq

value: ER+/PRA-/PRB+


title: DMSO treated-1

value: DMSO

value: control


title: G1.5_wt_Rep2

value: wildtype

value: male


title: T47D_PRA_E2_RNAseq


title: Mutant_TCDD_16

data_processing:
Raw data files were trimmed using cutadapt
Trimmed reads were aligned to the genome using tophat2
Bam files were sorted using samtools
HTseq-count (union) was used to obtain the counts mapped to individual genes
edgeR was used to statistical analysis
Genome_build: GRCz10 version 84 (Danio_rerio.GRCz10.dna.toplevel.fa.gz/ Danio_rerio.GRCz10.84.gtf.gz)
Supplementary_files_format_and_content: HTseq-count data is in text format

source_name: ahrra null mutants TCDD exposed embryos

growth_protocol: ahrra null embryos were generated using zinc finger nuclease approach.

extract_protocol:
Total RNA from 72 hpf embryos was isolated using BioRad Aurum kit.
Unstranded libraries were constructed using Illumina's Truseq kit.

treatment_protocol: Wildtype and ahrra-null zebrafish embryos were exposed to either carrier control (0.01% DMSO) or 2nM TCDD for 1 hour at 6 hours post-fertilization. At the end of the exposure, embryos were thoroughly rinsed in fresh 0.3x Danieu's solution and maintained until 72 hpf.

tag: time point

value: 72 hpf embryos

tag: treatment

value: TCDD

value: Tupfel longfin


title: Mutant_TCDD_15


title: G6.2_Ko_Rep1

tag: genotype/variation

value: knockout

value: female


title: G1.1_Het_Rep2

value: heterozygous

tag: tissue


title: G6.1_Ko_Rep1


title: Mutant_TCDD_14


title: Mutant_TCDD_13


title: Mutant_DMSO_12

source_name: ahrra null mutants DMSO exposed embryos


title: Mutant_DMSO_11


title: G4.6_wt_Rep1


title: G5.1_wt_Rep1


title: G4.5_wt_Rep1


title: CO2 Deprivation 24h sample 2

last: Fan

address: 130 Meilong Road

institute: East China University of Science & Technology

data_processing:
Default parameters were used to pass reads using Illumina quality-control pipeline. All the filtered reads were trimmed. The processed sequence files were then mapped to the assembled genome by TopHat with a tolerance of up to 2 mismatches and 3 indels.
For each of the mRNA-seq datasets, the transcript relative abundance (TRA) was expressed as the numbers of aligned reads to annotated gene models using HTSeq method and then normalized to RPKM values
Genome_build: de novo assembly
Supplementary_files_format_and_content: text file of gene RPKM values. A file of FASTA sequences and the gff genome annotation are available on the series record.

organism: Auxenochlorella pyrenoidosa

source_name: whole cells_CO2 deprivation 24h

growth_protocol: Chlorella cells were cultivated photoautotrophically with 5% CO2.

extract_protocol:
the total RNA was isolated using TRIzol Reagent (Invitrogen) according to manufacturer’s instructions.
The RNA samples were cleaned up using RNeasy columns (Qiagen, http://www.qiagen.com) following the manufacturer’s instruction. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.

treatment_protocol: After five days cultivation, the broth was then transferred to air environment for CO2 deprivation (bubbled with air).


title: CO2 Deprivation 1h sample 2

source_name: whole cells_CO2 deprivation 1h


title: CO2 Deprivation 4h sample 1

source_name: whole cells_CO2 deprivation 4h


title: G5.4_Ko_Rep1


title: CO2 Deprivation 4h sample 2


title: CO2 Deprivation 1h sample 1


title: G4.4_Het_Rep1


title: Mutant_DMSO_9


title: Wildtype_TCDD_8

source_name: Wildtype TCDD exposed embryos


title: CO2 Deprivation 0h sample 2

source_name: whole cells_CO2 deprivation 0h


title: Mutant_DMSO_10


title: Wildtype_TCDD_7


title: G1.1_Het_Rep1


title: T47D_PRA_Vehicle_RNAseq

source_name: Breast cancer cells

value: ER+/PRA+/PRB- T47D cell models

value: ER+/PRA+/PRB-

value: Vehicle


title: G4.3_Het_Rep1

value: embyronic whole kidney


title: Wildtype_DMSO_4

source_name: Wildtype DMSO exposed embryos


title: CO2 Deprivation 0h sample 1