title: Histone3-K27me3 ChIPSeq 1

description: anti-Histone3-K27me3 antibody


title: Pancreas-anti-Ptf1aJEJ-J2

status: Public on Sep 01 2016

type: SRA

city: Dallas

first: Galvin

last: Swift

state: TX

address: 6000 Harry Hines Blvd

department: Molecular Biology

country: USA

institute: U TX Southwestern Medical Center

library_source: genomic

data_processing:
ChIP-seq reads were aligned by using bowtie -v --best -p -q
Peaks were called using HOMER with the following setting: Enrichment Fold (4), Poisson, pValue = 1e-4 .
Peaks of replicates were merged by using SAMTOOLS intersectBed command with default setup (at least 1 bp overlap between 2 peaks)
Genes associated with peaks were defined by using GREAT
Genome_build: mm9
Supplementary_files_format_and_content: .txt Bedtool output of merged peak coordinates.

molecule: genomic DNA

organism: Mus musculus

source_name: pancreas

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with Ptf1a antibodies.
Standard Illumina ChIP-seq

tag: strain

tag: tissue

value: pancreas

tag: chip antibody

value: PTF1A antiboby from JE Johnson


title: Animal9_Female_Liver_Sequencing batch 1

city: Indianapolis

first: Aaron

middle: Thomas

last: Smith

state: IN

address: Lilly Corporate Center

department: Investigative Toxicology

institute: Eli Lilly

description:
Sequencing batch 1 from sample Animal9_Female_Liver
US-1458635_AD2C4RACXX_US-1458635_GATCAG_L001_R1_001

library_source: transcriptomic

data_processing:
FastQ files were processed to remove adaptor sequence and discard reads < 17bp in length with cutadapt v. 1.4.1 [23] with options –a TGGAATTCTCGGGTGCCAAGG –quality-base 33 –q 20 –match-read-wildcards –m 17. All trimmed reads that contained an ‘N’ were discarded. Identical sequences from the same sample were combined into a single sequence in the form expected by miRDeep2
Quantifier.pl from the mirdeep2 package [v. 2.0.0.5 ] was used to generate miR alignment files (.mrd files) against known miRs from miRbase 20 with options –P –p <org>_hairpin.fa –m <org>_mature.fa –r trimmed_reads.fa –d. This was done separately for rat, mouse, human, and C. elegans known miRs.
The .mrd files were then parsed with a custom Perl script as follows. Each isomiR sequence in an alignment was associated with the corresponding mature miR identifier. If it aligned to a miRNA precursor, but not with an expected mature miR sequence, it was identified as <miR>-pre to indicate this. Usually these correspond with reverse strand miRs that have not yet been annotated as alternate mature forms. Sometimes these appear to be microRNA offset RNAs [25] and sometimes they appear to represent incompletely processed sequence. If a given sequence was identified as aligning with more than one precursor, it was associated with all potential names as a composite name. That is, a sequence that aligned to both let-7a-5p and let-7f-5p was assigned to the composite mature miR let-7a-5p;let-7f-5p to indicate for subsequent analyses that this identification was ambiguous. All sequences that had not yet been identified against known rat miRs were then looked for in the analysis with respect to known mouse miRs, and so on against human and finally C. elegans miRs. This process allows for identification of conserved rodent miRs that have not yet been annotated in rat, and against conserved mammalian miRs that have not yet been annotated in rat and mouse. The comparison with C. elegans was to identify spiked in C. elegans miRs (not used in this data set).
In parallel to the above identification of known miRs, we used miRDeep2’s novel miR identification process as well. We aligned all the unique trimmed fasta reads to the RN5 reference rat genome with miRDeep2’s mapper.pl script with default parameters and then used the miRDeep2.pl script to generate novel miR predictions and .mrd files. The .mrd files were parsed as above to assign miR names to each unique read. We then attempted to identify and merge novel predictions that were identical to known miRs as follows. If the same read sequence identified a miR in the novel analysis and in the known analysis and the known miR appeared in miRDeep’s .mrd file, we assumed that this was a duplicate identification and changed the miR name from that reported by miRDeep (chr# followed by a unique ID) to that of the known miR. Otherwise, we assumed that the novel prediction might be different from the known miR identification and added it to the list of potential identifications for the sequence. So, for example, a sequence which was aligned by miRDeep2 to a predicted miR on chrX and also identified as miR-450a is identified as “chrX_48156-5p;miR-450a-5p” because miRDeep2 does not show miR-450a as aligned to this predicted miR, indicating that these are two potentially distinctsources of this sequence. Finally, the counts associated with each unique sequence are summed for each named miR (including complex, multi-named miRs) for each sample and these are reported as the miR level counts.
Genome_build: Rn5 for novel miR identification, mirbase 20 for known miR identification
Supplementary_files_format_and_content: Tab delimited text files with raw count information at either the mature miR level or isomiR level. Both files also contain the source of the predictiion that the indicated counts go with the indicated miR or isomiR.

molecule: total RNA

organism: Rattus norvegicus

growth_protocol: Naïve Sprague Dawley rats ,12-13 weeks old, were used for organ isolation.

extract_protocol:
RNA was purified using the miRNAeasy protocol from Qiagen (Kit cat# 217004).
Library construction was performed according to Illumina’s TruSeq small RNA sample prep protocol (Cataloge # RS-200-0048) using a HiSeq2000.  Briefly, RNA was extracted from tissues using the miRNeasy protocol. Libraries were constructed using the Illumina TruSeq small RNA preparation guide which entails ligation of adapters on the 3' and 5' ends of the RNA molecules.  The libraries were quantitated using RiboGreen and were size selected through gel electrophoresis and libraries consistent with the size of miRNAs were gel purified.  Sequencing was performed with each sample receiving 4-5 million, 30bp, single-end reads. generated

value: Sprague Dawley

tag: animal id

tag: age

value: 12-13 weeks

tag: gender

value: female

value: Liver

tag: rin


title: Histone3-K27me3 ChIPSeq 4

description: anti-Histone3-K27me3 antibody

data_processing:
Illumina HiSeq Control Software version 2.0.10.0 used for basecalling
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie v0.12.9 with parameters -m 1 -v 2 --best --strata
Peaks were called using HOMER through "findpeaks" function with -style factor and default parameters for K ChIP sample and -F 3 -P 0.01 -L 3 -fdr 0.05 -style factor for J ChIP sample
Common peaks between K ChIP and J ChIP samples were found using BedTools v2.25.0 "intersectBed" command using default settings
for Heat Map Figure 4E.  Macs2 command line macs2 callpeak -t *.bam -c input.bam --gsize=1.87e9 --broad --broad-cutoff 0.1 -B
Genome_build: mm9

extract_protocol:
Lysates were clarified from sonicated nuclei and MIST1-DNA complexes were isolated with antibody.
DNA libraries were prepared for sequencing using standard Illumina True-seq protocols


title: Animal11_Female_Stomach_Non-Glandular_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal11_Female_Stomach_Non-Glandular
US-1466225_AD1GBMACXX_US-1466225_CGATGT_L006_R1_001


title: Animal8_Female_WholeBlood_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal8_Female_WholeBlood
US-1459892_AD1GBMACXX_US-1459892_CTTGTA_L003_R1_001

value: WholeBlood


title: cuc2-3_2

city: evry

first: remi

last: bounon

state: essonne

address: 2 avenue Gaston Crémieux

department: BAP

country: France

institute: INRA

data_processing:
default parameters to Torrent Suite Software version 4.0.2
Mapping with Bowties2 on messager RNA TAIR 10 reference (parameters : no MultiHit, local reads mapping, TAIR 10 refrence with one gene model)
Genome_build: Arabidopsis thaliana TAIR 10
Supplementary_files_format_and_content: our processed data files contain 3 comment lines corresponding to the time of processing, the number of reads parsed and the number of reads mapped. An example is shown below: #sam2pkm :2014-02-14 11:16:22.632693 # total read parsed : 34170794 # total read mapped : 28674853. Then the column headers #id    len    nb_single : "id" corresponds to the locus identifier (Arabidopsis Genome Initiative code); "len" corresponds to the length of the gene model in nt;"nb_single" corresponds to the number of reads mapped on the gene model

organism: Arabidopsis thaliana

growth_protocol: Media_soil/Hygrometry_65%/Temperature_21°C/Light_Short day conditions (8h light -16h dark)

extract_protocol:
extraction-MirVana_fm_1560.pdf
RNA libraries were prepared for sequencing using standard LifeTechnologies protocols for Ion Torrent Proton (4476286_Ion Total RNA-Seq Kit v2_UG_RevE.pdf)
RNA Seq in Stranded Single End, sizing 230bp, messager RNA selection (DynabeadsmRNADIRECTMicro_UG_Rev004.pdf)

treatment_protocol: no treatment

tag: organ

value: aerial

value: 21 days

tag: ecotype

tag: genotype


title: Pancreas-anti-Ptf1aRJM-MA_7

value: PTF1A antiboby from RJ MacDonald


title: Animal10_Female_Cerebrum_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal10_Female_Cerebrum
US-1458927_AD1GBMACXX_US-1458927_TAGCTT_L002_R1_001

value: Cerebrum


title: 6d_cKO2

data_processing:
Illumina HiSeq Control Software version 2.0.10.0 used for basecalling
Sequences were mapped to mm9 mouse genome using TopHat v2.0.4 (by use of Bowtie v0.12.7.0) with parameters --no-novel-juncs --segment -length 25 --segment-mismatches 3
Sequences per gene were counted using Samtools ( v0.1.18.0) /HTSeq (v0.6.0)
Counts-per-million (CPM) were calculated using TMM normalization according to Robinson et al., Bioinformatics, 2010. Data set was filtered for minimal expression by "keep <- rowSums(cpm(d)) >= 3"
Differential gene expression analysis was performed with edgeR v3.0.8 (FDR < 0.05)
Genome_build: mm9
Supplementary_files_format_and_content: Normalized counts-per-million (CPM) for each sample in tab-delimited text file
Supplementary_files_format_and_content: EdgeR results as .xlxs spreadsheets, all results as DE_Ptf1a_cKO 6-day, and fdr < 0.05.

extract_protocol:
RNA preparation:  pancreas was homogenized in 4 M Guanidine Thiocyanate, 0.1 M Tris HCl pH 7.5, 1% 2-mercaptoethanol with a Tekmar Tissuemizer.  RNA was isolated from an aliquot of the homogenate by addition of N-Lauroylsarcosine sodium salt to 0.5%, Potassium Acetate pH 5.5 to 0.1 M, and Acetic Acid to 0.08 M, followed by addition of 0.75 volume ethanol while vortexing.  RNA was allowed to precipitate from the solution at -20 C for at least 1 hour, collected by centrifugation at 12,000 g for 5', and the RNA pellet resuspended in Trizol (equal volume to starting homogenate).  Subsequent steps were as per manufacturer's protocol (Life Technologies).
RNA libraries were prepared for sequencing using standard Illumina True-seq protocols

treatment_protocol: Tamoxifen treatment: On day 0, 1, 2, mice received 0.25 mg tamoxifen/g mouse at 50 mg/ml in corn oil by gavage.  Mice were sacrificed on day 6.


title: Histone3-K27me3 ChIPSeq 3

description: anti-Histone3-K27me3 antibody


title: Animal3_Male_Adrenal_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal3_Male_Adrenal
US-1458835_BC2BUMACXX_US-1458835_GCCAAT_L003_R1_001

value: male

value: Adrenal


title: Animal10_Female_Ovary_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal10_Female_Ovary
US-1458928_BC2BUMACXX_US-1458928_CACGAT_L001_R1_001

value: Ovary


title: 6d_CT5


title: 6d_CT3


title: Animal2_Male_Duodenum_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal2_Male_Duodenum
US-1459914_AD1GBMACXX_US-1459914_ACTTGA_L002_R1_001

value: Duodenum


title: Animal4_Male_Cerebrum_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal4_Male_Cerebrum
US-1459937_AD2C4RACXX_US-1459937_GTGAAA_L005_R1_001


title: Animal4_Male_Medulla_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal4_Male_Medulla
US-1458869_AD1GBMACXX_US-1458869_CCAACA_L004_R1_001

value: Medulla


title: RNA polymerase II ChipSeq 1

description: anti-Polymerase II antibody from Millipore catalog # 05-623


title: SMAD1_ChIP_IWR1-treated

city: Minneapolis

first: Alessandro

last: Magli

state: MN

address: 2231 6th St SE

department: Medicine

institute: University of Minnesota

description: ChIP antibody: Smad1 (Cell Signaling Technology #9743)

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie2 version 2.1.0 available at the Galaxy platform usign default parameters (Type of alignment: end to end; Preset option: sensitive; Disallow gaps within n-position of read: 4; Strand directions: both).
Data were filtered to remove PCR duplicates using the SAM tool rmdup 1.0.1
Peak calling was performed using both MACS 1.0.1 (parameters: -s 51 -bw 300, -p 1e-05 -m 32) and QESEQ (parameters: -s 100 -c 15 -p 0.05)
Common peaks from MACS and QESEQ were identified using the Intersect Interval tool available at BED tool. (Overlaps on either strand; -wa; Minimum ovelap required: 0.5)
Genome_build: mm10
Supplementary_files_format_and_content: Peak calling outputs for DMSO- and IWR1-treated samples generated using MACS and QESEQ softwares. Common peaks between MACS and QESEQ in DMSO-treated sample from Intersect-BED tool. Bigwig files for visualization on IGV generated by converting the wig files obtained from MACS using the Galaxy tool Wig-to-BigWig.

source_name: day4 reaggregated Embryoid bodies

growth_protocol: GFP-Bry mES cells were pre-plated for 30 minutes to remove MEFs and then plated in hanging drops (100 cells/10μl drop) in EB differentiation medium, IMDM (Gibco) supplemented with 15% FBS (Gibco), 4.5 mM monothioglycerol (Sigma), 100 μg/ml ascorbic acid (Sigma), and 200 μg/ml iron-saturated transferrin (Sigma), in 150 mm Petri dishes. After 48 hours, EBs were collected and resuspended into 10 cm Petri dishes in 10ml of EB differentiation medium. These dishes were cultured on a slowly swirling table rotator (80 rpm). All cultures were maintained in a humidified 37°C, 5% CO2 incubator.

extract_protocol:
Briefly, D4 EBs were trypsin-treated at 37°C for 1 minute with gentle shacking and reaction was inhibited by adding 10%FBS/PBS. Single cells were washed once with PBS, resuspended in 10%FBS/PBS and supplemented with formaldehyde (final concentration 1%) for crosslinking of protein-DNA complexes (10 minutes at RT) followed by quenching with 1M glycine (0.125mM final). Cells were snap-frozen in liquid nitrogen and stored at -80°C if not processed immediately. Cell pellets were incubated in lysis buffer LB1 supplemented with protease inhibitors (50mM HEPES KOH pH7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton X-100 + Complete-mini - Roche) for 10 minutes at +4°C followed by incubation in buffer LB2 supplemented with protease inhibitors (10mM TRIS HCl pH 8, 200mM NaCl, 1mM EDTA, 0.5mM EGTA + Complete-mini - Roche) for 10 minutes at +4°C. Cell pellet was then resuspended in LB3 supplemented with protease inhibitors (10mM TRIS HCl pH 8, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Sodium Deoxycholate, 0.5% N-lauroylsarcosine + Complete-mini - Roche) and then sonicated with a Branson sonicator at 18% power for 1 minute with intervals of 10 sec ON-10 sec OFF. Each sample was subjected to 5-6 cycles of sonication to reach an average chromatin size of 300bp. After shearing, samples were centrifuged for 10 minutes at 16000g and snap frozen in liquid nitrogen if not processed immediately. For each ChIP, 20µg of chromatin (diluted to 400µl) were precleared for 4h at 4°C with 15µl of BSA-blocked Protein A-conjugated sepharose beads (GE healthcare) and then supplemented with 1/10 volume of 10% Triton X-100. Immunoprecipitation was performed by overnight incubation with normal rabbit IgG (8µg – Santa Cruz Biotechnology) or anti-Smad1 antibody (1:25 – Cell Signaling Technology #9743). Immune complexes were recovered by incubation with 15µl of BSA-blocked Protein A-conjugated sepharose beads for 4h at 4°C and then washed 5 times with RIPA wash buffer (50mM HEPES KOH pH7.5, 500mM LiCl, 1mM EDTA, 1% NP40, 0.25% Triton X-100, 0.7% Sodium Deoxycholate) and one time with TEN buffer (10mM TRIS HCl pH 8, 1mM EDTA, 50mM NaCl). Immunoprecipitated chromatin was recovered by incubating beads with 200µl of Elution buffer (50mM TRIS HCl pH 8, 10mM EDTA, 1% Sodium Dodecyl Sulfate) for 20 minutes at 65°C. Chromatin from IP and Input (equivalent to 1% of starting material) was reverse crosslinked overnight at 65°C, then diluted 1:1 with TE (10mM TRIS HCl pH 8, 1mM EDTA) supplemented with 4µl of RNaseA 20mg/ml and incubated for 2 hours at 37°C followed by Proteinase K treatment (4µl of 20mg/ml stock for each sample) for 30 minutes at 55°C. DNA was purified by Phenol-chloroform-isoamyl alcol extraction (twice) followed by chloroform extraction, then supplemented with 1/10 of volume of 3M Sodium Acetate pH 5 and 1.5µl of Glycogen and precipitated with 2 volumes of 100% Ethanol at -80°C for >1 hour. Followed 30 minutes centrifuge at 16000g, pellet were washed with 75% ethanol, air dried and dissolved in 45µl H2O.
Libraries were generated following a gel-free protocol using AMPure XP beads (Beckman Coulter) for all the purification and size selection steps. 10ng or less of DNA were end repaired using End-it DNA end repair (Epicentre), then A-tailed using Klenow Fragment (3'→5' exo-  NEB) followed by adapter-barcode ligation using T4 DNA ligase (Enzymatics). Illumina compatible adapter-barcodes were purchased from BIOO scientific. After ligation, DNAs were negatively size selected using 0.5x Ampure XP beads and unbound DNAs were positively size selected by adding 0.4x Ampure XP beads (this step allows for retention of DNA fragments ranging 200-500bp). Libraries were amplified using Phusion High Fidelity PCR master mix 2x (NEB) with a 16 cycles program. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

treatment_protocol: Embryoid bodies from day 3 cultures were trypsinized and reaggregated at 10^6 cells/ml in non-adherent petri dishes. Samples were treated with 10uM of IWR1 (WNT inhibitor) or DMSO (vehicle) and then reaggregated Embryoid Bodies were collected 24 hours later for analysis.

tag: cell type

value: GFP-Bry ES derived day4 reaggregated Embryoid Bodies

tag: differentiation stage

value: day4 cultures


title: Pancreas-anti-Ptf1aJEJ-J7

value: pancreas

value: PTF1A antiboby from JE Johnson


title: Animal8_Female_WholeBlood_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal8_Female_WholeBlood
US-1459892_AD2C4RACXX_US-1459892_CTTGTA_L005_R1_001

value: Sprague Dawley

value: 12-13 weeks


title: Animal2_Male_Muscle_Soleus_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal2_Male_Muscle_Soleus
US-1456443_AD2C4RACXX_US-1456443_ACTGAT_L006_R1_001

value: Muscle - Soleus


title: SMAD1_ChIP_DMSO-treated


title: Pancreas-inputDNA


title: Animal5_Male_Ileum_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal5_Male_Ileum
US-1458884_AD1GBMACXX_US-1458884_GGCTAC_L004_R1_001

value: Ileum


title: Pancreas-anti-Ptf1aRJM-S5


title: Animal2_Male_WholeBlood_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal2_Male_WholeBlood
US-1459961_AD2C4RACXX_US-1459961_CTATAC_L007_R1_001

value: WholeBlood


title: Animal8_Female_Ileum_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal8_Female_Ileum
US-1458914_BC2BUMACXX_US-1458914_GGTAGC_L007_R1_001

value: female


title: Input_IWR1-treated

description: ChIP antibody: none


title: Animal11_Female_Medulla_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal11_Female_Medulla
US-1458838_BC2BUMACXX_US-1458838_GTAGAG_L003_R1_001


title: 6d_cKO3


title: Animal10_Female_Muscle_Soleus_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal10_Female_Muscle_Soleus
US-1466201_AD1GBMACXX_US-1466201_GGTAGC_L006_R1_001


title: 6d_cKO1


title: RNA polymerase II ChipSeq 2


title: spermatocytes

city: rennes

first: Chunxiang

last: HAO

address: 263, ave du Général Leclerc

institute: Université de Rennes 1

data_processing:
About 35 millions tags were derived from anti-H3K4me3 ChIP and input. The resulting sequences were quality filtered with the Sickle program (Joshi NA 2011) with –q33 and mapped back to the mouse mm9/ Ensembl genome using Bowtie 1.0.0 with seed length 20. Only tags that passed the quality filter and mapped uniquely to the genome were used. ChIP enrichment was further verified using CHANCE (Diaz et al. 2012). The H3K4me3 mark peaks were identified using MACS 2.0.1 (Feng et al. 2012) wit corresponding input, shift-size window 73 bp, no model, with p-value threshold <10E−5.
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph file

source_name: spermatocytes

extract_protocol:
Germ cells were separated according  y (Bellve, 1979). Briefly,  8  twelve weeks old c57Bl/6J male mice were  perfused, and testes were dissected. Testes were digested with collagenase, trypsine  and DNAse. The cells were loaded into 2-4% gradient of BSA and allowed to sedimentate. The spermatocytes and spermatids fractions were collected. The purity was confirmed by staining with DAPI of the small fractions of cells. Cells were fixed with paraformaldehyde and used for ChIP-seq.
The libraries were prepared from 50 ng of ChiP and input material using the NEBNext Ultra DNA library Prep Kit for Illumina (NEB #E7370S).
massively parallel 50-bp sequencing in single end mode for ChIP-seq

value: Rabbit anti-H3K4me3 (07-473)


title: Animal6_Male_Kidney_Homogenate_re-extract_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal6_Male_Kidney_Homogenate_re-extract
US-1462931_BC2BUMACXX_US-1462931_CAGGCG_L005_R1_001

value: Kidney


title: Animal7_Female_Hippocampus_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal7_Female_Hippocampus
US-1454172_AD1GBMACXX_US-1454172_ATGTCA_L002_R1_001

value: Hippocampus


title: 6d_CT4


title: Animal11_Female_Jejunum_Homogenate_re-extract_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal11_Female_Jejunum_Homogenate_re-extract
US-1462922_AD2C4RACXX_US-1462922_GGCTAC_L001_R1_001

value: Jejunum


title: Animal3_Male_Brainstem_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal3_Male_Brainstem
US-1459943_AD1GBMACXX_US-1459943_GTGGCC_L002_R1_001

value: male

value: Brainstem


title: Animal3_Male_Medulla_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal3_Male_Medulla
US-1458847_BC2BUMACXX_US-1458847_GTAGAG_L007_R1_001

value: Medulla


title: 6d_CT2


title: Animal7_Female_Ovary_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal7_Female_Ovary
US-1458929_AD1GBMACXX_US-1458929_ACAGTG_L005_R1_001

value: Ovary


title: 6d_CT1


title: day 7 pp whole testis RNA_n2

city: Ithaca

first: Andrew

last: Grimson

state: NY

address: 445 Biotechnology Building

department: Molecular Biology & Genetics

institute: Cornell University

description:
processed data file: mRNA_genes_merged_counts.tx
Day7n2WT

data_processing:
RNA SEQ: Aligned each raw file to genome using BWA v0.7.8
RNA SEQ: Used HTSeq v0.6.1 to count reads aligning to .gtf file (annotation file)
RNA SEQ: Used edgeR v3.6.8 to assess fold change and differential expression
RNA SEQ annotation file: UCSC mm9 .gtf transcriptome file from: https://support.illumina.com/sequencing/sequencing_software/igenome.ilmn
Small RNA SEQ: Trimmed off adapters and filtered out low-quality reads (ones with too many N's, or which failed Illumina's Y/N overall quality metric) - custom python script.
Small RNA SEQ: Aligned reads to genome using Bowtie 0.12.7. Exact match.
Small RNA SEQ: Aligned reads to miRNA hairpin sequences from miRBase v21 using a custom script.
Small RNA SEQ: Collapsed all hairpin aligning reads by their seed sequence using a custom script; this results in raw counts per miRNA family
Small RNA SEQ: Used edgeR v3.6.8 to assess fold change and differential expression
Genome_build: RNA SEQ: UCSC mm9, used pre-built BWA indexes from https://support.illumina.com/sequencing/sequencing_software/igenome.ilmn
Genome_build: Small RNA SEQ: mm9 Bowtie Indices
Supplementary_files_format_and_content: RNA SEQ: HTSeq raw counts file for each sample for each gene in annotation file
Supplementary_files_format_and_content: Small RNA SEQ: Raw counts file for each sample for each miRNA seed family

source_name: day 7 pp whole testis RNA

growth_protocol: All mice were fed ad libitum with standard laboratory rodent chow, and were maintained under controlled conditions of light and temperature, according to the strict regulations outlined and approved by the Cornell Institutional Care and Use Committee (IACUC).   Whole testis were isolated from mice at day 1 postpartum (pp), day 3 pp, and day 7 pp. Spermatocytes were isolated from adult mice about 70-80 days after birth.

extract_protocol:
Illumina TruSeq RNA Seq
Testes from day 1 postpartum (pp), day 3 pp, day 7 pp, and adult (day 70-80 pp) were removed and decapsulated prior to RNA isolation using TRIzol (Life Technologies) from either whole tesits or enriched cells. Enrichment of specific spermatogenic cell types (leptotene/zygotene and pachytene) was achieved using the STA-PUT method based on separation by cell diameter/density at unit gravity (Bellvé, 1993). Purity of resulting fractions was determined by microscopy based on cell diameter and morphology. Pachytene cells were approximately 90% pure, with residual possible contamination from spermatocytes of slightly earlier or later developmental stages. Leptotene and zygotene cells were isolated in combination, and were >90% pure. Neither pachytene nor leptotene/zygotene fractions exhibited evidence of any contaminating somatic cells. RNA was used as the source material for mRNA sequencing and small RNA sequencing.
We sequenced both small RNA and RNA from wildtype whole testis or purified meiotic cells at different stages of spermatogenesis. Sequencing libraries were genereated as replicates, from two biological replicates per sample type.

treatment_protocol: Mice were wild type (C57BI/6J)

tag: genotype/variation

value: wild type

tag: replicate

value: day 7 pp

tag: tissue/cell type

value: whole testis

tag: molecule subtype

value: RNA


title: Animal10_Female_Jejunum_Homogenate_re-extract_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal10_Female_Jejunum_Homogenate_re-extract
US-1462920_AD1GBMACXX_US-1462920_ATCACG_L002_R1_001

value: Sprague Dawley

value: 12-13 weeks


title: Animal6_Male_Muscle_Biceps_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal6_Male_Muscle_Biceps
US-1460693_AD1GBMACXX_US-1460693_CAAAAG_L004_R1_001

value: Muscle - Biceps


title: Animal9_Female_Ovary_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal9_Female_Ovary
US-1458879_AD1GBMACXX_US-1458879_ACTTGA_L005_R1_001


title: Animal6_Male_Heart_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal6_Male_Heart
US-1466243_AD2C4RACXX_US-1466243_GTAGAG_L002_R1_001

value: Heart


title: Animal9_Female_Adrenal_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal9_Female_Adrenal
US-1458870_AD2C4RACXX_US-1458870_GTGGCC_L008_R1_001

value: female

value: Adrenal


title: Input_DMSO-treated

description: ChIP antibody: none

value: GFP-Bry ES derived day4 reaggregated Embryoid Bodies

value: day4 cultures


title: Animal8_Female_Muscle_Soleus_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal8_Female_Muscle_Soleus
US-1459955_AD1GBMACXX_US-1459955_TAATCG_L003_R1_001

value: Muscle - Soleus


title: Animal10_Female_Cortex_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal10_Female_Cortex
US-1456445_AD1GBMACXX_US-1456445_CTTGTA_L004_R1_001

value: Cortex


title: Animal9_Female_Cerebrum_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal9_Female_Cerebrum
US-1466207_AD1GBMACXX_US-1466207_CATGGC_L005_R1_001

value: Cerebrum


title: purified pachytene spermatocytes RNA_n2

description:
processed data file: mRNA_genes_merged_counts.tx
Pachn2WT

source_name: purified pachytene spermatocytes RNA

value: purified pachytene spermatocytes


title: Animal11_Female_Uterus_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal11_Female_Uterus
US-1466217_AD2C4RACXX_US-1466217_CTCAGA_L007_R1_001

value: Uterus


title: purified pachytene spermatocytes SMALL RNA_n2

description:
processed data file: miRNAfamily_merged_counts.txt
Pachn2

extract_protocol:
Illumina TruSeq Small RNA Seq
Testes from day 1 postpartum (pp), day 3 pp, day 7 pp, and adult (day 70-80 pp) were removed and decapsulated prior to RNA isolation using TRIzol (Life Technologies) from either whole tesits or enriched cells. Enrichment of specific spermatogenic cell types (leptotene/zygotene and pachytene) was achieved using the STA-PUT method based on separation by cell diameter/density at unit gravity (Bellvé, 1993). Purity of resulting fractions was determined by microscopy based on cell diameter and morphology. Pachytene cells were approximately 90% pure, with residual possible contamination from spermatocytes of slightly earlier or later developmental stages. Leptotene and zygotene cells were isolated in combination, and were >90% pure. Neither pachytene nor leptotene/zygotene fractions exhibited evidence of any contaminating somatic cells. RNA was used as the source material for mRNA sequencing and small RNA sequencing.
We sequenced both small RNA and RNA from wildtype whole testis or purified meiotic cells at different stages of spermatogenesis. Sequencing libraries were genereated as replicates, from two biological replicates per sample type.

value: wild type

value: small RNA


title: day 1 pp whole testis RNA_n1

description:
processed data file: mRNA_genes_merged_counts.tx
Day1n1WT

source_name: day 1 pp whole testis RNA

value: day 1 pp

value: whole testis


title: spermatids

source_name: spermatids

value: Rabbit anti-H3K4me3 (07-473)


title: day 3 pp whole testis RNA_n2

description:
processed data file: mRNA_genes_merged_counts.tx
Day3n2WT

source_name: day 3 pp whole testis RNA

value: day 3 pp

value: RNA


title: Animal4_Male_Ileum_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal4_Male_Ileum
US-1458916_AD1GBMACXX_US-1458916_ATGAGC_L002_R1_001

value: Sprague Dawley

value: 12-13 weeks

value: male

value: Ileum


title: day 7 pp whole testis RNA_n1

description:
processed data file: mRNA_genes_merged_counts.tx
Day7n1WT

value: day 7 pp


title: day 7 pp whole testis SMALL RNA_n2

description:
processed data file: miRNAfamily_merged_counts.txt
D7n2

source_name: day 7 pp whole testis SMALL RNA


title: Animal10_Female_Duodenum_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal10_Female_Duodenum
US-1456498_AD2C4RACXX_US-1456498_CAGATC_L007_R1_001

value: female

value: Duodenum


title: day 7 pp whole testis SMALL RNA_n1

description:
processed data file: miRNAfamily_merged_counts.txt
D7n1


title: Animal8_Female_Stomach_Non-Glandular_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal8_Female_Stomach_Non-Glandular
US-1466238_BC2BUMACXX_US-1466238_CACGAT_L004_R1_001


title: purified leptotene/zygotene spermatocytes SMALL RNA_n2

description:
processed data file: miRNAfamily_merged_counts.txt
LZn2


title: Animal9_Female_Brainstem_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal9_Female_Brainstem
US-1466199_AD2C4RACXX_US-1466199_CTAGCT_L003_R1_001

value: Brainstem


title: Animal9_Female_Muscle_Biceps_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal9_Female_Muscle_Biceps
US-1463122_BC2BUMACXX_US-1463122_GACGAC_L002_R1_001

value: Muscle - Biceps


title: Animal5_Male_Kidney_Homogenate_re-extract_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal5_Male_Kidney_Homogenate_re-extract
US-1462988_AD2C4RACXX_US-1462988_AGTCAA_L005_R1_001

value: Kidney


title: Animal7_Female_WholeBlood_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal7_Female_WholeBlood
US-1462736_BC2BUMACXX_US-1462736_CAACTA_L001_R1_001

value: WholeBlood


title: Animal8_Female_Medulla_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal8_Female_Medulla
US-1458885_AD1GBMACXX_US-1458885_AGTTCC_L003_R1_001

value: Medulla


title: Liver, L85

city: East Lansing

first: Rance

last: Nault

state: United States

address: 1355 Bogue St. B403

department: Department of Pharmacology and Toxicology

institute: Michigan State University

description: Mice dosed every 4 days for 92 days

data_processing:
FASTQC v0.11.2 was used for quality control
FASTX v0.0.14 and Cutadapt 1.4.1 was used for adaptor removal and removal of low-complexity reads
TopHat v1.4.1 was used for alignment
SAMTools v0.1.19 was used for file conversion
HTSeq v0.6.1 was used to count feature aligned reads
DESeq was used to transform counts
Transformed counts were normalized using a semi-parametric approach (Eckel et al., 2004) and analyzed using an empirical Bayes method (Eckel et al., 2005).
Genome_build: GRCm38 release 74
Supplementary_files_format_and_content: Tab-delimited text files represent the number of aligned reads to each gene

source_name: Liver

extract_protocol:
Livers were homogenized in TRIzol (Invitrogen, Carlsbad, CA) using a mixer mill 300 tissue homogenizer (Retsch, Germany). Total RNA was isolated according to manufacturers instructions with an additional phenol:chloroform extraction and resuspended in RNA storage solution (Ambion Inc., Austin, TX). RNA was quantified and examined for purity and quality by nanodrop, Qubit, Bioanalyzer and visualization on a denaturing gel.
Libraries were were prepared using the Illumina TrueSeq RNA sample preparation kit according to manufacturers instructions. Library sizes were confirmed using Caliper GX and quantified by the Kapa biosystems qPCR according to manufacturers instructions

treatment_protocol: Female ovariectomized C57BL/6 mice were gavaged daily with sesame oil vehicle, 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 ug/kg TCDD every  4 days for 92 days.

tag: Sex

value: Female

tag: age (days)

tag: treatment

value: TCDD

tag: dose (ug/kg)

tag: duration (days)


title: Animal4_Male_Stomach_Glandular_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal4_Male_Stomach_Glandular
US-1460652_AD1GBMACXX_US-1460652_TACAGC_L005_R1_001

tag: strain

tag: animal id

tag: age

tag: tissue


title: Liver, L74

description: Mice dosed every 4 days for 92 days


title: Liver, L72

description: Mice dosed every 4 days for 92 days


title: Animal11_Female_Ovary_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal11_Female_Ovary
US-1454030_AD2C4RACXX_US-1454030_ACAGTG_L001_R1_001

tag: gender

value: Ovary

tag: rin


title: Liver, L81

description: Mice dosed every 4 days for 92 days


title: purified leptotene/zygotene spermatocytes RNA_n2

description:
processed data file: mRNA_genes_merged_counts.tx
LZn2WT

value: wild type


title: Animal7_Female_Muscle_Soleus_Homogenate_re-extract_Sequencing batch 4

description:
Sequencing batch 4 from sample Animal7_Female_Muscle_Soleus_Homogenate_re-extract
US-1466190_SEASDW062403C:145:D1GBMACXX:4

value: Muscle - Soleus


title: Animal3_Male_Duodenum_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal3_Male_Duodenum
US-1456465_AD1GBMACXX_US-1456465_CAACTA_L002_R1_001

value: Sprague Dawley


title: day 3 pp whole testis SMALL RNA_n2

description:
processed data file: miRNAfamily_merged_counts.txt
D3n2

source_name: day 3 pp whole testis SMALL RNA

value: day 3 pp

value: whole testis

value: small RNA


title: Animal8_Female_Cerebellum_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal8_Female_Cerebellum
US-1456472_BC2BUMACXX_US-1456472_CATGGC_L005_R1_001

value: 12-13 weeks

value: Cerebellum


title: day 1 pp whole testis RNA_n2

description:
processed data file: mRNA_genes_merged_counts.tx
Day1n2WT

value: day 1 pp

value: RNA


title: Animal5_Male_Testicle_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal5_Male_Testicle
US-1456484_AD1GBMACXX_US-1456484_CACGAT_L003_R1_001

value: male

value: Testicle


title: day 1 pp whole testis SMALL RNA_n2

description:
processed data file: miRNAfamily_merged_counts.txt
D1n2

source_name: day 1 pp whole testis SMALL RNA


title: Liver, L49

description: Mice dosed every 4 days for 92 days


title: Animal2_Male_Cortex_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal2_Male_Cortex
US-1456489_BC2BUMACXX_US-1456489_ATCACG_L005_R1_001

value: Cortex


title: Animal7_Female_Jejunum_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal7_Female_Jejunum
US-1458704_AD1GBMACXX_US-1458704_GATCAG_L002_R1_001

value: female

value: Jejunum


title: day 1 pp whole testis SMALL RNA_n1

description:
processed data file: miRNAfamily_merged_counts.txt
D1n1


title: Animal5_Male_Jejunum_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal5_Male_Jejunum
US-1458661_AD1GBMACXX_US-1458661_CACTCA_L003_R1_001


title: Liver, L87

description: Mice dosed every 4 days for 92 days

value: Female

value: TCDD


title: Liver, L76

description: Mice dosed every 4 days for 92 days


title: Animal2_Male_Testicle_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal2_Male_Testicle
US-1456514_AD2C4RACXX_US-1456514_GCCAAT_L007_R1_001


title: Animal2_Male_Stomach_Non-Glandular_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal2_Male_Stomach_Non-Glandular
US-1466221_AD1GBMACXX_US-1466221_CAGATC_L006_R1_001


title: Animal2_Male_Cerebellum_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal2_Male_Cerebellum
US-1456481_AD1GBMACXX_US-1456481_TAGCTT_L004_R1_001


title: Liver, L67

description: Mice dosed every 4 days for 92 days


title: Liver, L64

description: Mice dosed every 4 days for 92 days


title: Animal2_Male_Muscle_Biceps_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal2_Male_Muscle_Biceps
US-1466197_AD1GBMACXX_US-1466197_CGATGT_L004_R1_001

value: Muscle - Biceps


title: Liver, L58

description: Mice dosed every 4 days for 92 days


title: Liver, L54

description: Mice dosed every 4 days for 92 days


title: Liver, L53

description: Mice dosed every 4 days for 92 days


title: Liver, L70

description: Mice dosed every 4 days for 92 days


title: Animal2_Male_Kidney_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal2_Male_Kidney
US-1455468_AD2C4RACXX_US-1455468_CGATGT_L001_R1_001

value: Kidney


title: Liver, L43

description: Mice dosed every 4 days for 92 days


title: Animal2_Male_Liver_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal2_Male_Liver
US-1454084_AD1GBMACXX_US-1454084_AGTTCC_L005_R1_001

value: Sprague Dawley

value: Liver


title: Animal4_Male_Brainstem_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal4_Male_Brainstem
US-1459907_AD2C4RACXX_US-1459907_GTTTCG_L005_R1_001

value: Brainstem


title: Animal2_Male_Testicle_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal2_Male_Testicle
US-1456514_AD1GBMACXX_US-1456514_GCCAAT_L003_R1_001


title: Liver, L42

description: Mice dosed every 4 days for 92 days


title: Animal5_Male_Cerebrum_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal5_Male_Cerebrum
US-1458860_BC2BUMACXX_US-1458860_ACTTGA_L006_R1_001

value: Cerebrum


title: Liver, L12

description: Mice dosed every 4 days for 92 days


title: Liver, L2

description: Mice dosed every 4 days for 92 days

value: Vehicle


title: Animal6_Male_Stomach_Glandular_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal6_Male_Stomach_Glandular
US-1458850_AD1GBMACXX_US-1458850_GAGTGG_L005_R1_001

value: 12-13 weeks


title: Liver, L34

description: Mice dosed every 4 days for 92 days


title: Liver, L33

description: Mice dosed every 4 days for 92 days


title: Liver, L32

description: Mice dosed every 4 days for 92 days


title: F3_Liver_Atrazine_RNAseq_R1

data_processing:
The reads in FASTQ format were processed for quality control using the FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). For the analysis of differentially expressed genes, the quality-checked reads for each condition were processed using the TopHat version 2.0.12 package (Kim et al. 2013). The reads were mapped to the reference genome [Mus musculus Ensembl mm9 sequence], and the alignment files were generated as BAM files. These files were used as the input for Cufflinks, a complement method used to generate assembled transcripts for each condition; the abundance was evaluated using read data. The assembled transcripts were compared and annotated using Cuffmerge against the Ensembl (mm9) gene annotations (Trapnell et al. 2012). Mm9 gene annotation was used in this study for comparative analysis of previously published datasets. These assemblies are used in Cuffquant and Cuffnorm from the Cufflinks 2.2.1 package to calculate the expression levels. To identify transcripts differentially expressed between atrazine- and control-derived samples, we first selected the cases for which we obtained values greater than the 50th quantile of all values in at least one condition, and then we filtered transcripts which are more than a 2-fold different between atrazine and control -derived samples. Finally, we employed a statistical test implemented in the R package, Limma, with the false-discovery rate set at less than 5% (Ritchie et al. 2015). RNA-Seq data were visualized using the Integrated Genomics Viewer (version 2.3.36) (Thorvaldsdottir et al. 2013).
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph

growth_protocol: Eight-week-old adult CD1 mice were treated for at E6.5 to E15.5 with atrazine in oil at a concentration of 100 mg/l by gavage in oil or treated by oil vehicle in a control. The 12 weeks F1 male progeny was crossed with unrelated untreated 12- weeks old female and progeny of F2 were crossed again to receive F3 male progeny. Twelve weeks old F3 ATZ-derived or control-derived male mice were euthanized, and reproductive organs, liver and hypothalamus were dissected. At least five independent experiments were performed with at least six-to-ten animals in each group.

extract_protocol:
For RNA-seq 10 mkg of total RNA was used. Total RNA was extracted using Trizol reagent
A strand-specific library preparation protocol for RNA sequencing was performed using the sequencing technological platform at IGBMC, Strasbourg, France.
paired end, 100-bp sequencing stranded RNA-seq

treatment_protocol: Outbred pregnant CD1 mice were treated fromE6.5 to E15.5 by atrazine mixed in oil via force feeding, control animals were treated with vehicle (oil)

tag: generation

value: Atrazine


title: Animal5_Male_Muscle_Soleus_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal5_Male_Muscle_Soleus
US-1463138_AD1GBMACXX_US-1463138_CGGAAT_L005_R1_001

value: Muscle - Soleus


title: Animal6_Male_Stomach_Non-Glandular_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal6_Male_Stomach_Non-Glandular
US-1466200_AD2C4RACXX_US-1466200_GTTTCG_L008_R1_001

value: male


title: Animal8_Female_Cortex_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal8_Female_Cortex
US-1456510_AD1GBMACXX_US-1456510_CACCGG_L003_R1_001


title: Liver, L24

description: Mice dosed every 4 days for 92 days


title: Animal7_Female_Muscle_Soleus_Homogenate_re-extract_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal7_Female_Muscle_Soleus_Homogenate_re-extract
US-1466190_SEA055491C:302:H0HMMADXX:1


title: Animal4_Male_Heart_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal4_Male_Heart
US-1458684_BC2BUMACXX_US-1458684_CACCGG_L001_R1_001

value: Heart


title: F3_Liver_Control_RNAseq_R3

value: Control


title: Liver, L22

description: Mice dosed every 4 days for 92 days


title: Animal5_Male_Brainstem_Homogenate_re-extract_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal5_Male_Brainstem_Homogenate_re-extract
US-1466237_AD1GBMACXX_US-1466237_ACAGTG_L004_R1_001


title: Animal6_Male_Testicle_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal6_Male_Testicle
US-1456506_BC2BUMACXX_US-1456506_GCCAAT_L006_R1_001

value: Testicle


title: F3_Brain_Atrazine_RNAseq_R3

value: hypothalamus


title: Animal10_Female_Uterus_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal10_Female_Uterus
US-1456455_BC2BUMACXX_US-1456455_CCAACA_L008_R1_001

value: female

value: Uterus


title: Liver, L23

description: Mice dosed every 4 days for 92 days

value: Female

value: TCDD


title: Liver, L17

description: Mice dosed every 4 days for 92 days


title: Liver, L4

description: Mice dosed every 4 days for 92 days


title: Liver, L13

description: Mice dosed every 4 days for 92 days


title: Animal11_Female_Pancreas_Reextract_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal11_Female_Pancreas_Reextract
US-1459543_BC2BUMACXX_US-1459543_GTCCGC_L007_R1_001

value: Sprague Dawley

value: Pancreas


title: Animal5_Male_Pancreas_Reextract_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal5_Male_Pancreas_Reextract
US-1462435_BC2BUMACXX_US-1462435_CTATAC_L008_R1_001


title: F3_Liver_Atrazine_RNAseq_R2

value: Liver


title: Animal7_Female_Kidney_Homogenate_re-extract_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal7_Female_Kidney_Homogenate_re-extract
US-1462986_BC2BUMACXX_US-1462986_CTCAGA_L008_R1_001

value: Kidney


title: Animal4_Male_Testicle_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal4_Male_Testicle
US-1456459_AD2C4RACXX_US-1456459_GTTTCG_L002_R1_001


title: F3_Brain_Control_RNAseq_R2


title: F3_Brain_Control_RNAseq_R3


title: Animal2_Male_Pancreas_Reextract_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal2_Male_Pancreas_Reextract
US-1459548_AD1GBMACXX_US-1459548_CATTTT_L006_R1_001


title: Animal9_Female_Pancreas_Reextract_Sequencing batch 4

description:
Sequencing batch 4 from sample Animal9_Female_Pancreas_Reextract
US-1459554_SEA055491C:302:H0HMMADXX:2


title: Liver, L1

description: Mice dosed every 4 days for 92 days

value: Vehicle


title: Animal5_Male_Cortex_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal5_Male_Cortex
US-1456457_AD1GBMACXX_US-1456457_TTAGGC_L004_R1_001

value: 12-13 weeks

value: Cortex


title: F3_Liver_Control_RNAseq_R2


title: F3_Liver_Atrazine_RNAseq_R3

value: Atrazine


title: Animal8_Female_Liver_Homogenate_re-extract_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal8_Female_Liver_Homogenate_re-extract
US-1462945_AD1GBMACXX_US-1462945_ATTCCT_L004_R1_001


title: F3_Brain_Atrazine_RNAseq_R1


title: F3_Testis_Atrazine_RNAseq_R3

value: testis


title: F3_Brain_Atrazine_RNAseq_R2


title: Animal11_Female_Cerebrum_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal11_Female_Cerebrum
US-1459923_BC2BUMACXX_US-1459923_CAGATC_L003_R1_001

value: Cerebrum


title: F3_Testis_Atrazine_RNAseq_R2


title: F3_Liver_Control_RNAseq_R1

value: Control


title: F3_Testis_Atrazine_RNAseq_R1


title: Animal7_Female_Muscle_Soleus_Homogenate_re-extract_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal7_Female_Muscle_Soleus_Homogenate_re-extract
US-1466190_SEA062401C:142:C2BUMACXX:4

value: Muscle - Soleus


title: Animal11_Female_Kidney_Homogenate_re-extract_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal11_Female_Kidney_Homogenate_re-extract
US-1462979_BC2BUMACXX_US-1462979_CATGGC_L001_R1_001


title: F3_Testis_Control_RNAseq_R3


title: Animal10_Female_Brainstem_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal10_Female_Brainstem
US-1459933_BC2BUMACXX_US-1459933_GATCAG_L006_R1_001

value: Brainstem


title: Animal11_Female_Adrenal_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal11_Female_Adrenal
US-1458844_AD1GBMACXX_US-1458844_GAGTGG_L003_R1_001

value: female

value: Adrenal


title: Animal5_Male_Cerebellum_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal5_Male_Cerebellum
US-1459931_AD2C4RACXX_US-1459931_GACGAC_L007_R1_001

value: male

value: Cerebellum


title: F3_Testis_Control_RNAseq_R2


title: F3_Testis_Control_RNAseq_R1


title: Animal7_Female_Hippocampus_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal7_Female_Hippocampus
US-1454172_BC2BUMACXX_US-1454172_ATGTCA_L003_R1_001

value: Sprague Dawley

value: Hippocampus


title: Animal2_Male_Duodenum_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal2_Male_Duodenum
US-1459914_BC2BUMACXX_US-1459914_ACTTGA_L003_R1_001

value: Duodenum


title: Animal10_Female_Medulla_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal10_Female_Medulla
US-1458841_BC2BUMACXX_US-1458841_GAGTGG_L001_R1_001

value: Medulla


title: F3_Brain_Control_RNAseq_R1

value: hypothalamus


title: Animal8_Female_Cerebrum_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal8_Female_Cerebrum
US-1458895_AD1GBMACXX_US-1458895_ACTGAT_L002_R1_001

value: 12-13 weeks


title: F3_Testis_Control_Input_DNA

data_processing:
About 40 millions tags were derived from anti-H3K4me3 ChIP and input. The resulting sequences were quality filtered with the Sickle program (Joshi NA 2011) with –q33 and mapped back to the mouse mm9/ Ensembl genome using Bowtie 1.0.0 with seed length 20. Only tags that passed the quality filter and mapped uniquely to the genome were used. ChIP enrichment was further verified using CHANCE (Diaz et al. 2012). The H3K4me3 mark peaks were identified using MACS 2.0.1 (Feng et al. 2012) with two biological replicate samples, including corresponding input, shift-size window 73 bp, no model, with p-value threshold <10E−5. Peak regions determined by MACS were further divided into subpeak regions using PeakSplitter with default parameters (Salmon-Divon et al. 2010). Two biological replicates for each condition were analyzed independently. The set of peaks was verified at an irreproducible discovery rate (IDR) of 0.05 % (Li et al. 2011) to confirm that the biological replicates were sufficiently similar to be used in the analysis. The number of mapped reads was multiplied by a scale factor to normalize the total number of reads in different samples. To compare the H3K4me3 CHIP datasets of ATZ-treated and control samples, differential peak calling was performed using several steps. First, from all the peaks called above, we selected the peaks that were reproducible in both biological replicates in the same condition; second, we kept only peaks with average values above the 50th quantile; last, we selected the peaks with fold changes above 1.5 or 2 and FDR <10 %. Statistical significance was calculated using a Limma test (Ritchie et al. 2015). Annotation of significant differential peaks was performed by CEAS (Shin et al. 2009). The results were visualized in the Integrative genomics viewer IGV version 2.3.36 (Thorvaldsdottir et al. 2013).
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph

extract_protocol:
For ChIP seq protocol one testis from 12 weeks old males was used. Tissue was fixed with paraformaldehyde and sonicated to receive the average size of chromatin 500bp, histone DNA complexes were isolated with H3K4me3 antibody. The immunoprecipitated DNA was purified with Qiagen MinElute kit. For RNA-seq 10 mkg of total RNA was used. Total RNA was extracted using Trizol reagent
The libraries were prepared from 50 ng of ChiP and input material using the NEBNext Ultra DNA library Prep Kit for Illumina (NEB #E7370S).
massively parallel 50-bp sequencing in single end mode for

treatment_protocol: Outbred pregnant CD1 mice were treated from E6.5 to E15.5 by atrazine mixed in oil via force feeding, control animals were treated with vehicle (oil)

tag: chip antibody

value: control


title: F3_Testis_Atrazine_Input_DNA

value: atrazine


title: F3_Testis_Atrazine_H3K4me3_ChIPseq_R2

value: Rabbit anti-H3K4me3 (07-473)

value: testis


title: F3_Testis_Control_H3K4me3_ChIPseq_R2


title: F3_Testis_Control_H3K4me3_ChIPseq_R1


title: F1_Testis_Atrazine_H3K4me3_ChIPseq_R2


title: Animal7_Female_Cortex_Homogenate_re-extract_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal7_Female_Cortex_Homogenate_re-extract
US-1462958_AD1GBMACXX_US-1462958_TTAGGC_L006_R1_001

value: Cortex


title: 1005_Sequencing batch 2

description:
Sequencing batch 2 from sample 1005
US-1466230_AD1GBMACXX_US-1466230_GGCTAC_L006_R1_001

value: DRG


title: F1_Testis_Atrazine_H3K4me3_ChIPseq_R1


title: F3_Testis_Atrazine_H3K4me3_ChIPseq_R1


title: Animal8_Female_Jejunum_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal8_Female_Jejunum
US-1458710_AD1GBMACXX_US-1458710_CGATGT_L002_R1_001

value: Jejunum


title: Animal3_Male_Stomach_Glandular_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal3_Male_Stomach_Glandular
US-1456482_AD1GBMACXX_US-1456482_CGTACG_L005_R1_001


title: Animal10_Female_Cerebellum_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal10_Female_Cerebellum
US-1456494_AD2C4RACXX_US-1456494_AGTCAA_L001_R1_001

value: female


title: Animal6_Male_Liver_Homogenate_re-extract_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal6_Male_Liver_Homogenate_re-extract
US-1462929_AD2C4RACXX_US-1462929_TGACCA_L007_R1_001

value: Liver


title: Animal9_Female_Pancreas_Reextract_Sequencing batch 6

description:
Sequencing batch 6 from sample Animal9_Female_Pancreas_Reextract
US-1459554_SEA055491C:302:H0HMMADXX:1

value: Pancreas


title: F1_Testis_Control_H3K4me3_ChIPseq_R2


title: input DNA

city: Houston

first: Pawel

last: Stankiewicz

state: Texas

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

data_processing:
Sequence reads were mapped on to the mm10 genome using Bow-tie2. Percentage of uniquely mapped reads were 77.85%, 73.10%, and 73.10%, respectively, for the two biological replicates and input control samples
Peak calling procedure was performed using the Model-based Analysis of ChIP-Seq (MACS2) tool (Zhang et al. 2008)
The assessment of peak calling was done using IDR-score (Li et al. 2011).
The consensus FOXF1 binding motif was identified from the DNA sequences underlying the peaks, using the WebLogo tool (http://weblogo.berkeley.edu/logo.cgi).
Functional analysis of selected peak regions was performed using the GREAT tool (McLean et al. 2010) and classification of genes common to the ChIP-seq and microarray datasets was done using LungGENS (Du et al. 2015).
Genome_build: mm10
Supplementary_files_format_and_content: *.bed files were generated using MACS2 tool (Zhang et al. 2008)

source_name: Whole lung

extract_protocol:
Two biological replicates of pooled E18.5 lungs (n=3) were crosslinked with 37% formaldehyde to a final concentration of 1%. ChIP was performed using the SimpleChIP Enzymatic Chromatin IP Kit (Cell Signaling, 9005S). Micrococcal nuclease-digested chromatin was further sonicated using Diagenode Bioruptor with 20 pulses of 15s on and 15s off at high power to yield sheared chromatin. Ten micrograms of chromatin was used per immunoprecipitation with 7 µg of FOXF1 antibody.
The Rubicon ThruPlex DNA-Seq library preparation system was used to prepare ChIP-Seq libraries for sequencing on the Illumina HiSeq sequencing system.

value: lung

value: embryonic day 18.5


title: Foxf1 ChIP-seq biological replicate 2

value: FOXF1, R&D Biosystems, AF4798, Lot#B1508


title: Foxf1 ChIP-seq biological replicate 1


title: F1_Testis_Control_H3K4me3_ChIPseq_R1


title: Animal9_Female_Uterus_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal9_Female_Uterus
US-1456441_AD2C4RACXX_US-1456441_CGTACG_L005_R1_001

value: Sprague Dawley

value: Uterus


title: Animal5_Male_Adrenal_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal5_Male_Adrenal
US-1458862_AD1GBMACXX_US-1458862_ACTGAT_L006_R1_001

value: male

value: Adrenal


title: Animal10_Female_WholeBlood_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal10_Female_WholeBlood
US-1459934_AD2C4RACXX_US-1459934_TTAGGC_L001_R1_001

value: 12-13 weeks

value: WholeBlood


title: Animal7_Female_Ovary_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal7_Female_Ovary
US-1458929_BC2BUMACXX_US-1458929_ACAGTG_L006_R1_001

value: Ovary


title: Animal7_Female_Pancreas_Reextract_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal7_Female_Pancreas_Reextract
US-1459556_AD1GBMACXX_US-1459556_ATGAGC_L005_R1_001


title: P2 fraction, EE6 replicate

city: Richmond

first: Michael

last: Miles

state: VA

department: Pharmacology and Toxicology

institute: Virginia Commonwealth Univ.

data_processing:
Base calling and demultiplexing: CASAVA 1.8.2 (Illumina)
Read alignment was done by using Spliced Transcripts Alignment to a Reference (STAR), v2.3.0
Gene level abundance measurement: Cufflinks, ver. 2.1.1 with default parameters
Differential expression analysis: Cuffdiff, ver. 2.1.1 with default parameters
Genome_build: mm10/GRCm38 (Jan 2012) with DBA/2J polymorphisms annotated as per dbSNP
Supplementary_files_format_and_content: abundance measurements

source_name: brain, frontal pole

growth_protocol: DBA/2J male mice were obtained at 8 weeks of age and housed at 4/cage under standard animal care protocols.

extract_protocol:
On day 14 of the behavioral sensitization paradigm, mice were sacrificed by cervical dislocation 4 hours following i.p. injection. Immediately afterward, brains were removed and chilled for one minute in ice-cold 1x phosphate buffered saline. The frontal pole was dissected by making a cut rostral of the optic chiasm and then removing the olfactory bulbs. Excised tissue was stored in a tube on ice for less than 8 minutes before processing for synaptoneurosome isolation. Fresh tissue from 4 animals was pooled (approximately 0.45 g) and manually homogenized utilizing a 15 ml Potter-Elvehjem Safe-Grind® tissue grinder (#358009, Wheaton, Millville, NJ) and diluted 1:10 in synaptoneurosome homogenization buffer. The buffer consisted of 0.35 M nuclease free sucrose (CAS #57-50-1, Acros Organics, NJ), 10 mM HEPES (#15630-056, Life Technologies, Carlsbad, CA), and 1 mM EDTA (#AM9260G, Ambion, Carlsbad, CA), which was brought to a pH of 7.4 and filter sterilized. Immediately before use, 0.25 mM DTT (CAS #3483-12-3, Fisher Scientific, Waltham, MA), 30 U/mL RNase Out (#10777-019, Invitrogen, Carlsbad, CA), and protease inhibitor cocktail containing AEBSF, Aprotinin, Bestatin, E64, Leupeptin, and Pepstatin A (#1862209, Halt, Thermo Scientific, Rockford, IL), were added to buffer. Centrifugation of whole homogenate (WH) at 500 x g for 10 minutes at 4˚C removed nuclei and cellular debris, yielding pellet, P1 and supernatant, S1. The S1 fraction was passed through a series of nylon filters with successively decreasing pore sizes of 70, 35, and 10 µm (#03-70, #03-35, #03-10, SEFAR, Buffalo, NY). The filtrate was then diluted with 3 volumes of homogenization buffer, and centrifuged at 2000 x g for 15 minutes at 4˚C to yield the synaptoneurosome enriched pellet, P2, and supernatant, S2. Fractions were frozen on dry ice and then stored at -80˚C until further processing. Total RNA was isolated the using guanidine/phenol/chloroform method (#Cs-502, Stat-60, Tel-Test Inc., Friendswood, TX) and a Tekmar homogenizer as per the STAT-60 protocol. RNA concentration was determined by measuring absorbance at 260 nm and RNA quality was assessed by electrophoresis on an Experion Analyzer (Bio-Rad, Hercules, CA) and 260/280 absorbance ratios. All RNA samples had RNA quality indices (RQI) ≥ 7.6 and 260/280 ratios were between 1.97 and 2.06.
The preparation of cDNA libraries was conducted following standard protocols using TruSeq RNA Sample Preparation Kit (#RS-122-2001, Illumina, San Diego, CA). Briefly, mRNA was isolated from total RNA using poly-T oligo-attached magnetic beads. The mRNA was then fragmented in the presence of divalent cations at 94˚C. The fragmented RNA was converted into double stranded cDNA and ends polished using T4 and Klenow DNA polymerases, with an adenine base added to the 3’ ends followed by ligation of Illumina specific adaptors. The adaptor ligated DNA was amplified with 15 cycles of PCR and purified using QIAquick PCR Purification Kit (#28104, Qiagen, Venlo, Netherlands). Library insert size was determined using an Agilent Bioanalyzer. Library quantification was performed by qRT-PCR assay using KAPA Library Quant Kit (#KK4835, KAPA, Wilmington, MA). RNA-Seq libraries were analyzed using Illumina TruSeq Cluster V3 flow cells and TruSeq SBS Kit V3 (#FC-401-3001, Illumina, San Diego, CA), with six libraries of different indices pooled together in equal amounts loaded on to a single lane at a concentration of 13 pM and sequenced (2 x 100 paired end reads) on a Illumina HiSeq 2000. Sample EE6_P2 was removed from subsequent analyses due to exceedingly high duplication levels.

treatment_protocol: Mice were divided into three treatment groups (n = 16 each): saline-saline (SS), saline-EtOH (SE), and EtOH-EtOH (EE). Mice were acclimated to the behavioral room for 1 hour prior to the start of the experiment on testing days. All locomotor activity was measured immediately following i.p. injection with either saline or ethanol during 10 minute sessions in sound-attenuating locomotor chambers (Med Associates, model ENV-515, St. Albans, VT). The system is interfaced with Med Associates software that assesses activity using a set of 16 infrared beam sensors along the X-Y plane. Animals received two days of saline injections and placement in the testing apparatus for habituation to the experimental procedure. On test day 3, acute locomotor responses to i.p. saline (SS, SE) or 2.0 g/kg ethanol (EE) were measured. On conditioning days 4-13, animals received daily i.p. injections in their home cages of either saline (SS, SE) or 2.5 g/kg ethanol (EE). On the final testing day 14, the SS group received saline and the SE and EE groups received 2.0 g/kg ethanol and all groups were placed in subsequently monitored in activity chambers for 10 minutes.

tag: cell fraction

value: P2, synaptoneurosome

tag: treatement group

value: EE, ethanol-ethanol


title: Animal8_Female_Liver_Homogenate_re-extract_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal8_Female_Liver_Homogenate_re-extract
US-1462945_BC2BUMACXX_US-1462945_ATTCCT_L007_R1_001


title: P2 fraction, EE5 replicate


title: P2 fraction, EE4 replicate


title: Animal11_Female_Stomach_Non-Glandular_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal11_Female_Stomach_Non-Glandular
US-1466225_BC2BUMACXX_US-1466225_CGATGT_L005_R1_001


title: F1_Testis_Input_DNA

value: control

value: testis


title: Animal9_Female_Kidney_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal9_Female_Kidney
US-1455492_BC2BUMACXX_US-1455492_AGTCAA_L006_R1_001

value: female

value: Kidney


title: Animal5_Male_Hippocampus_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal5_Male_Hippocampus
US-1458648_AD1GBMACXX_US-1458648_TACAGC_L003_R1_001

value: Hippocampus


title: Animal7_Female_Stomach_Non-Glandular_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal7_Female_Stomach_Non-Glandular
US-1458858_AD2C4RACXX_US-1458858_GTGGCC_L002_R1_001


title: Animal8_Female_Pancreas_Reextract_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal8_Female_Pancreas_Reextract
US-1459539_AD1GBMACXX_US-1459539_CACCGG_L006_R1_001

value: Pancreas


title: Animal3_Male_Duodenum_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal3_Male_Duodenum
US-1456465_AD2C4RACXX_US-1456465_CAACTA_L006_R1_001

value: Duodenum


title: 1502_Sequencing batch 1

description:
Sequencing batch 1 from sample 1502
US-1463116_BC2BUMACXX_US-1463116_ACTGAT_L001_R1_001

value: DRG


title: Animal10_Female_Ileum_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal10_Female_Ileum
US-1458911_AD2C4RACXX_US-1458911_CTCAGA_L003_R1_001

value: Sprague Dawley

value: Ileum


title: S2 fraction, EE6 replicate

value: S2, cytosolic


title: Animal11_Female_Duodenum_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal11_Female_Duodenum
US-1454094_AD1GBMACXX_US-1454094_GCCAAT_L002_R1_001


title: P2 fraction, EE3 replicate


title: Animal3_Male_Cerebrum_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal3_Male_Cerebrum
US-1466228_AD1GBMACXX_US-1466228_GGTAGC_L004_R1_001

value: male

value: Cerebrum


title: S2 fraction, EE4 replicate


title: Animal11_Female_Cortex_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal11_Female_Cortex
US-1456479_BC2BUMACXX_US-1456479_GTGAAA_L004_R1_001

value: 12-13 weeks

value: Cortex


title: S2 fraction, EE5 replicate


title: S2 fraction, EE3 replicate


title: P2 fraction, SE5 replicate

value: P2, synaptoneurosome

value: SE, saline-ethanol


title: Animal2_Male_Kidney_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal2_Male_Kidney
US-1455468_AD1GBMACXX_US-1455468_CGATGT_L005_R1_001


title: S2 fraction, SE6 replicate


title: P2 fraction, SE4 replicate


title: P2 fraction, SE3 replicate


title: Animal4_Male_Heart_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal4_Male_Heart
US-1458684_AD1GBMACXX_US-1458684_CACCGG_L005_R1_001

value: Heart


title: Animal11_Female_Pancreas_Reextract_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal11_Female_Pancreas_Reextract
US-1459543_AD1GBMACXX_US-1459543_GTCCGC_L006_R1_001


title: S2 fraction, SE5 replicate


title: Animal4_Male_Pancreas_Reextract_Sequencing batch 6

description:
Sequencing batch 6 from sample Animal4_Male_Pancreas_Reextract
US-1462447_SEASDW062403C:145:D1GBMACXX:5


title: Animal4_Male_Pancreas_Reextract_Sequencing batch 4

description:
Sequencing batch 4 from sample Animal4_Male_Pancreas_Reextract
US-1462447_SEA055491C:302:H0HMMADXX:2


title: Animal5_Male_Cerebellum_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal5_Male_Cerebellum
US-1459931_AD1GBMACXX_US-1459931_GACGAC_L003_R1_001

value: Cerebellum


title: Animal10_Female_Hippocampus_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal10_Female_Hippocampus
US-1459960_AD1GBMACXX_US-1459960_CCAACA_L002_R1_001

value: female


title: S2 fraction, SE3 replicate


title: P2 fraction, SE6 replicate


title: P2 fraction, SS6 replicate

value: SS, saline-saline


title: 1004_Sequencing batch 1

description:
Sequencing batch 1 from sample 1004
US-1459915_AD2C4RACXX_US-1459915_GTAGAG_L005_R1_001


title: P2 fraction, SS5 replicate


title: S2 fraction, SS3 replicate


title: Animal9_Female_Liver_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal9_Female_Liver
US-1458635_AD1GBMACXX_US-1458635_GATCAG_L005_R1_001

value: Liver


title: S2 fraction, SS6 replicate


title: S2 fraction, SS4 replicate


title: P2 fraction, SS3 replicate


title: 1504_Sequencing batch 1

description:
Sequencing batch 1 from sample 1504
US-1466203_AD1GBMACXX_US-1466203_CATGGC_L004_R1_001


title: S2 fraction, SE4 replicate


title: Animal3_Male_Liver_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal3_Male_Liver
US-1454029_AD2C4RACXX_US-1454029_GACGAC_L003_R1_001


title: Animal10_Female_WholeBlood_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal10_Female_WholeBlood
US-1459934_AD1GBMACXX_US-1459934_TTAGGC_L003_R1_001

value: WholeBlood


title: Animal6_Male_Muscle_Biceps_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal6_Male_Muscle_Biceps
US-1460693_BC2BUMACXX_US-1460693_CAAAAG_L001_R1_001

value: Muscle - Biceps


title: shallow TABseq on a PyMT-induced breast tumor from a empty PRRL2-vector-overexpressing mouse 3

city: Heverlee

first: Bernard

last: thienpont

address: Herestraat 49

department: Vesalius Research Center

country: Belgium

institute: VIB

description: Sample 59

data_processing:
alignment was done using BisMark 0.13.1 (http://www.bioinformatics.babraham.ac.uk/projects/bismark/)
SeqMonk 0.29.0 was used to hydroxymethylation levels at 300kb sliding windows
Genome_build: Mm9
Supplementary_files_format_and_content: "TABseq hmC percentage in 300kb bins.txt" contains average 5hmC levels in 300kb bins for each sample

source_name: PyMT-induced breast tumor

growth_protocol: breast tumors were isolated, flash-frozen in liquid nitrogen and stored at -150 until further processing

extract_protocol:
Nucleic acids were subsequently extracted using the Wizard Genomic DNA Purification (Promega, Leiden, The Netherlands) kit according to instructions, with all buffers supplemented with DFO (200 µM), dissolved in 80 µL PBS-DFO with RNAse A (200 units, NEB, Ipswich, MA, USA), incubated for 10 minutes at 37°C. After proteinase K addition (200 units) and incubation for 30 minutes at 56°C, DNA was purified using the QIAQuick blood and tissue kit (all buffers supplemented with DFO), eluted in 100 µL of a 10 mM Tris, 1mM EDTA solution (pH 8) and stored at -80°C until further processing.
library preparations and TAB-conversion were as described by Yu and colleagues (Nat Protoc 2012), except that bisulfite conversion was done using the EZ DNA Methylation-Lightning Kit (ZYMO), and libraries were amplified using the KAPA Uracil+ 2x master mix.
tet-assisted-bisulfite-seq

treatment_protocol: Mice were either WT or Phd heterozygotes, or hydrodynamically injected with an empty or sFlk1-overexpression plasmid. Whereas the Phd2+/-genotype restores vascularisation and oxygenation levels in the tumor, the latter treatment renders tumors more hypoxic

value: FVB

tag: hydrodynamically injected plasmid

value: empty PRRL2

value: 12 weeks

tag: replicate

value: C


title: shallow TABseq on a PyMT-induced breast tumor from a sFlk1-overexpressing mouse 2

description: Sample 55

value: B


title: shallow TABseq on a PyMT-induced breast tumor from a sFlk1-overexpressing mouse 1

description: Sample 54

value: A


title: P2 fraction, SS4 replicate


title: Animal7_Female_Adrenal_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal7_Female_Adrenal
US-1458839_AD1GBMACXX_US-1458839_CAGATC_L005_R1_001

value: Sprague Dawley

value: 12-13 weeks

value: Adrenal


title: shallow TABseq on a PyMT-induced breast tumor from a empty PRRL2-vector-overexpressing mouse 1

description: Sample 57


title: shallow TABseq on a PyMT-induced breast tumor from a empty PRRL2-vector-overexpressing mouse 2

description: Sample 58


title: Animal7_Female_Cerebrum_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal7_Female_Cerebrum
US-1458873_AD1GBMACXX_US-1458873_CGTACG_L003_R1_001

value: Cerebrum


title: Animal11_Female_Ileum_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal11_Female_Ileum
US-1458887_AD2C4RACXX_US-1458887_GGTAGC_L002_R1_001

value: Ileum


title: Animal6_Male_Medulla_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal6_Male_Medulla
US-1458871_AD1GBMACXX_US-1458871_AGTTCC_L004_R1_001

value: male

value: Medulla


title: Animal3_Male_Hippocampus_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal3_Male_Hippocampus
US-1466189_AD2C4RACXX_US-1466189_ACTTGA_L007_R1_001

value: Hippocampus


title: Animal11_Female_Ileum_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal11_Female_Ileum
US-1458887_AD1GBMACXX_US-1458887_GGTAGC_L003_R1_001

value: female


title: shallow TABseq on a PyMT-induced breast tumor from a sFlk1-overexpressing mouse 3

description: Sample 56


title: shallow TABseq on a PyMT-induced breast tumor from a PHD2+/- mouse 3

description: Sample 52

value: FVB, Phd2+/-

value: 16 weeks


title: shallow TABseq on a PyMT-induced breast tumor from a PHD2+/- mouse 1

description: Sample 50


title: S2 fraction, SS5 replicate

value: S2, cytosolic

value: SS, saline-saline


title: shallow TABseq on a PyMT-induced breast tumor from a PHD2+/- mouse 4

description: Sample 53

value: D


title: Animal8_Female_Ovary_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal8_Female_Ovary
US-1458901_AD2C4RACXX_US-1458901_GTCCGC_L005_R1_001

value: Ovary


title: Animal9_Female_Pancreas_Reextract_Sequencing batch 3

description:
Sequencing batch 3 from sample Animal9_Female_Pancreas_Reextract
US-1459554_AD1GBMACXX_US-1459554_GTGGCC_L004_R1_001

value: Pancreas


title: Animal9_Female_Ileum_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal9_Female_Ileum
US-1458868_BC2BUMACXX_US-1458868_GGCTAC_L003_R1_001


title: shallow TABseq on a PyMT-induced breast tumor from a PHD2+/+ mouse 1

description: Sample 47

value: FVB

value: A


title: Animal8_Female_Stomach_Glandular_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal8_Female_Stomach_Glandular
US-1456493_AD1GBMACXX_US-1456493_TTAGGC_L005_R1_001

value: Sprague Dawley

value: 12-13 weeks


title: Animal3_Male_Stomach_Non-Glandular_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal3_Male_Stomach_Non-Glandular
US-1466235_AD1GBMACXX_US-1466235_CGTACG_L006_R1_001


title: shallow TABseq on a PyMT-induced breast tumor from a PHD2+/- mouse 2

description: Sample 51

value: B


title: Animal6_Male_Hippocampus_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal6_Male_Hippocampus
US-1454031_BC2BUMACXX_US-1454031_TTAGGC_L002_R1_001


title: Animal7_Female_Cerebrum_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal7_Female_Cerebrum
US-1458873_BC2BUMACXX_US-1458873_CGTACG_L007_R1_001

value: Cerebrum


title: Animal3_Male_Cerebellum_Sequencing batch 4

description:
Sequencing batch 4 from sample Animal3_Male_Cerebellum
US-1456436_SEA062401C:142:C2BUMACXX:6

value: male

value: Cerebellum


title: Animal4_Male_Pancreas_Reextract_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal4_Male_Pancreas_Reextract
US-1462447_SEA062401C:142:C2BUMACXX:6


title: Animal9_Female_Ileum_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal9_Female_Ileum
US-1458868_AD1GBMACXX_US-1458868_GGCTAC_L003_R1_001

value: Ileum


title: FemalePN_T3KO_2

city: Beijing

first: Xianlong

last: Li

address: 5, Yiheyuan Rd., Haidian District

department: Biodynamic Optical Imaging Center, College of Life Sciences

country: China

institute: Peking University

data_processing:
Base calling is performed by CASAVA_v1.8.2
Alignment is performed by Bismark v0.7.6
Convert alignment results to information of each base of reference sequence, using SAMTools mpileup v0.1.18 (r982:295)
Calculate modification p-value of each site using R (version 3.0.0) function dbinom().
Genome_build: mm9
Supplementary_files_format_and_content: wig files which records the genome coordinate and methylation level of each mapped CpG

source_name: maternally Tet3 KO female pronuclei

extract_protocol:
Approximately 100-130 pronuclei in each treatment were harvested, lysed in 5  μl lysis (20 mM Tris, 2 mM EDTA, 20 mM KCl, 0.3% Triton-X 100, 1 mg/ml QIAGEN protease) at 50°C for 3h. Protease was inactivated at 75°C for 30 min.
Genomic DNA from pronuclei was digested by 10 U TaqI (NEB) for 3 h at 65°C. Then the digested DNA was end-repaired and dA-tailed with exonuclease-deficient Klenow Fragment (Fermentas) in the presence of 40 μM dATP, 4 μM dGTP and 4 μM dCTP. Next the Illumina TruSeq adapters were ligated to the DNA fragments with concentrated T4 DNA ligase (Fermentas) overnight. After that, bisulfite conversion of the library was performed using MethylCode DNA Methylation Kit (Invitrogen). Then bisulfite-converted DNA was amplified by 20 cycles of PCR using PfuTurboCx polymerase (Agilent Technologies), and purified by AMPure XP beads (Beckman). Finally an extra round of PCR amplification was performed to increase the amount of DNA to about 500 ng with Phusion HF Master Mix (NEB), and the 200~500 bp DNA fragments were selected on a 12% polyacrylamide gel. The size distribution of the final library was analyzed by Fragment Analyzer (Advanced Analytical Technologies) and the libraries were sequenced on Illumina HiSeq 2000 or 2500.

treatment_protocol: One-cell zygotes were collected 7.5-8 hrs after ICSI. Their pronuclear stages were further determined based on microscope observation of the size of the two pronuclei and the distance between them. Zygotes [Tet3 mat∆/ +] deficient in maternal Tet3 were obtained using Zp3-Cre conditional knockout female mice as previously described. In experiments with the inhibition of pronuclear DNA replication, zygotes in culture after ICSI were incubated with 0.2 µg/ml of aphidicolin until the extraction of pronuclei.

value: female

tag: cell type

value: pronuclei


title: shallow TABseq on a PyMT-induced breast tumor from a PHD2+/+ mouse 3

description: Sample 49

value: 16 weeks

value: C


title: Animal4_Male_Cerebellum_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal4_Male_Cerebellum
US-1456451_AD1GBMACXX_US-1456451_CAGGCG_L003_R1_001


title: Animal5_Male_Muscle_Soleus_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal5_Male_Muscle_Soleus
US-1463138_AD2C4RACXX_US-1463138_CGGAAT_L003_R1_001

value: Muscle - Soleus


title: Animal11_Female_Cortex_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal11_Female_Cortex
US-1456479_AD1GBMACXX_US-1456479_GTGAAA_L004_R1_001

value: Cortex


title: Animal10_Female_Cerebrum_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal10_Female_Cerebrum
US-1458927_AD2C4RACXX_US-1458927_TAGCTT_L008_R1_001


title: Animal10_Female_Hippocampus_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal10_Female_Hippocampus
US-1459960_AD2C4RACXX_US-1459960_CCAACA_L006_R1_001

value: Hippocampus


title: Animal7_Female_Heart_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal7_Female_Heart
US-1458709_AD1GBMACXX_US-1458709_GTGGCC_L003_R1_001

value: Heart


title: Animal9_Female_Pancreas_Reextract_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal9_Female_Pancreas_Reextract
US-1459554_AD2C4RACXX_US-1459554_GTGGCC_L005_R1_001

value: Pancreas


title: Animal10_Female_Muscle_Biceps_Homogenate_re-extract_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal10_Female_Muscle_Biceps_Homogenate_re-extract
US-1466215_AD1GBMACXX_US-1466215_CACTCA_L004_R1_001

value: Muscle - Biceps


title: Animal3_Male_Pancreas_Reextract_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal3_Male_Pancreas_Reextract
US-1459546_AD1GBMACXX_US-1459546_GTAGAG_L006_R1_001

value: Sprague Dawley


title: Animal7_Female_Muscle_Soleus_Homogenate_re-extract_Sequencing batch 3

description:
Sequencing batch 3 from sample Animal7_Female_Muscle_Soleus_Homogenate_re-extract
US-1466190_BC2BUMACXX_US-1466190_CAACTA_L004_R1_001

value: 12-13 weeks


title: Animal10_Female_Adrenal_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal10_Female_Adrenal
US-1458877_AD2C4RACXX_US-1458877_ATGAGC_L006_R1_001

value: Adrenal


title: Animal9_Female_Cerebellum_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal9_Female_Cerebellum
US-1459958_AD2C4RACXX_US-1459958_CGGAAT_L006_R1_001


title: shallow TABseq on a PyMT-induced breast tumor from a PHD2+/+ mouse 2

description: Sample 48

value: FVB

value: B


title: 1002_Sequencing batch 2

description:
Sequencing batch 2 from sample 1002
US-1466214_BC2BUMACXX_US-1466214_CTATAC_L005_R1_001

value: male

value: DRG


title: Animal7_Female_Muscle_Biceps_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal7_Female_Muscle_Biceps
US-1459935_AD2C4RACXX_US-1459935_CAAAAG_L003_R1_001

value: female


title: Animal9_Female_Kidney_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal9_Female_Kidney
US-1455492_AD1GBMACXX_US-1455492_AGTCAA_L005_R1_001

value: Kidney


title: Animal2_Male_Stomach_Glandular_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal2_Male_Stomach_Glandular
US-1456450_AD2C4RACXX_US-1456450_CTTGTA_L001_R1_001


title: Animal9_Female_Pancreas_Reextract_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal9_Female_Pancreas_Reextract
US-1459554_SEASDW062403C:145:D1GBMACXX:4


title: Animal3_Male_Muscle_Biceps_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal3_Male_Muscle_Biceps
US-1456610_AD1GBMACXX_US-1456610_ATGTCA_L004_R1_001


title: Animal10_Female_Stomach_Non-Glandular_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal10_Female_Stomach_Non-Glandular
US-1466242_AD1GBMACXX_US-1466242_TACAGC_L006_R1_001


title: Animal5_Male_Duodenum_Homogenate_re-extract_Sequencing batch 6

description:
Sequencing batch 6 from sample Animal5_Male_Duodenum_Homogenate_re-extract
US-1462953_AD1GBMACXX_US-1462953_CAAAAG_L002_R1_001

value: Duodenum


title: Animal4_Male_Kidney_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal4_Male_Kidney
US-1458682_AD1GBMACXX_US-1458682_CTATAC_L004_R1_001


title: Animal10_Female_Pancreas_Reextract_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal10_Female_Pancreas_Reextract
US-1459542_AD2C4RACXX_US-1459542_TAATCG_L007_R1_001


title: Animal10_Female_Pancreas_Reextract_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal10_Female_Pancreas_Reextract
US-1459542_AD1GBMACXX_US-1459542_TAATCG_L006_R1_001


title: Animal2_Male_Medulla_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal2_Male_Medulla
US-1458843_AD1GBMACXX_US-1458843_ATTCCT_L003_R1_001

value: Medulla


title: Animal5_Male_Duodenum_Homogenate_re-extract_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal5_Male_Duodenum_Homogenate_re-extract
US-1462953_SEA055491C:302:H0HMMADXX:2


title: Animal9_Female_Hippocampus_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal9_Female_Hippocampus
US-1459925_AD1GBMACXX_US-1459925_ATTCCT_L002_R1_001


title: Animal10_Female_Ovary_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal10_Female_Ovary
US-1458928_AD1GBMACXX_US-1458928_CACGAT_L004_R1_001

value: Ovary


title: Animal5_Male_Cerebrum_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal5_Male_Cerebrum
US-1458860_AD1GBMACXX_US-1458860_ACTTGA_L003_R1_001

value: Cerebrum


title: Animal6_Male_Pancreas_Reextract_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal6_Male_Pancreas_Reextract
US-1462455_AD2C4RACXX_US-1462455_ACTTGA_L001_R1_001


title: Animal3_Male_Cerebellum_Sequencing batch 3

description:
Sequencing batch 3 from sample Animal3_Male_Cerebellum
US-1456436_SEA055491C:302:H0HMMADXX:2

value: Cerebellum


title: Animal4_Male_Hippocampus_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal4_Male_Hippocampus
US-1459916_AD1GBMACXX_US-1459916_CACGAT_L002_R1_001

value: Hippocampus


title: Animal7_Female_Brainstem_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal7_Female_Brainstem
US-1466205_BC2BUMACXX_US-1466205_AGTCAA_L003_R1_001

value: Brainstem


title: Animal3_Male_Stomach_Non-Glandular_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal3_Male_Stomach_Non-Glandular
US-1466235_BC2BUMACXX_US-1466235_CGTACG_L001_R1_001


title: Animal8_Female_Medulla_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal8_Female_Medulla
US-1458885_AD2C4RACXX_US-1458885_AGTTCC_L005_R1_001


title: Animal6_Male_Cerebrum_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal6_Male_Cerebrum
US-1459963_AD1GBMACXX_US-1459963_ATCACG_L003_R1_001


title: Animal8_Female_Stomach_Glandular_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal8_Female_Stomach_Glandular
US-1456493_AD2C4RACXX_US-1456493_TTAGGC_L007_R1_001


title: Animal2_Male_Adrenal_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal2_Male_Adrenal
US-1458853_AD1GBMACXX_US-1458853_GCCAAT_L005_R1_001


title: Animal3_Male_Cerebellum_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal3_Male_Cerebellum
US-1456436_SEA055491C:302:H0HMMADXX:1


title: Animal4_Male_Cerebellum_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal4_Male_Cerebellum
US-1456451_AD2C4RACXX_US-1456451_CAGGCG_L003_R1_001


title: Animal2_Male_Adrenal_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal2_Male_Adrenal
US-1458853_AD2C4RACXX_US-1458853_GCCAAT_L001_R1_001


title: Animal8_Female_Cortex_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal8_Female_Cortex
US-1456510_AD2C4RACXX_US-1456510_CACCGG_L003_R1_001

value: Cortex


title: Animal3_Male_Jejunum_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal3_Male_Jejunum
US-1458656_AD2C4RACXX_US-1458656_ACAGTG_L004_R1_001

value: Sprague Dawley

value: Jejunum


title: Animal4_Male_Testicle_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal4_Male_Testicle
US-1456459_AD1GBMACXX_US-1456459_GTTTCG_L004_R1_001

value: 12-13 weeks

value: Testicle


title: Animal6_Male_Duodenum_Homogenate_re-extract_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal6_Male_Duodenum_Homogenate_re-extract
US-1462960_BC2BUMACXX_US-1462960_ATGAGC_L001_R1_001


title: 1503_Sequencing batch 2

description:
Sequencing batch 2 from sample 1503
US-1463156_AD2C4RACXX_US-1463156_CAGATC_L001_R1_001


title: Animal10_Female_Stomach_Non-Glandular_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal10_Female_Stomach_Non-Glandular
US-1466242_BC2BUMACXX_US-1466242_TACAGC_L002_R1_001


title: Animal3_Male_Muscle_Biceps_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal3_Male_Muscle_Biceps
US-1456610_AD2C4RACXX_US-1456610_ATGTCA_L002_R1_001

value: Muscle - Biceps


title: Animal5_Male_Duodenum_Homogenate_re-extract_Sequencing batch 4

description:
Sequencing batch 4 from sample Animal5_Male_Duodenum_Homogenate_re-extract
US-1462953_SEASDW062403C:145:D1GBMACXX:2

value: male


title: Animal10_Female_Muscle_Biceps_Homogenate_re-extract_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal10_Female_Muscle_Biceps_Homogenate_re-extract
US-1466215_BC2BUMACXX_US-1466215_CACTCA_L008_R1_001


title: Animal9_Female_Medulla_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal9_Female_Medulla
US-1458872_AD2C4RACXX_US-1458872_CTAGCT_L007_R1_001


title: SWELL1 KO 3T3-F442A, rep 1

city: Boston

first: William

middle: James

last: Gibson

state: Massachusetts

address: 34 Fairfield St #1

institute: Harvard Medical School

description:
Gene expression data from the mouse adipocyte cell lines with SWELL1 knocked out by CRISPR/Cas9, biological replicate 1
Sample name: 11_D3_KO

data_processing:
Paired-end FASTQ files were aligned to the Mus_musculus_GRCm38_Ensembl reference genome with TopHat v8.7 on GenePattern.
Aligned BAMs were used as input to Cufflinks v2.02 for transcript quantification.
FPKM files from Cufflinks were converted to GCT files via the GenePattern module Fpkm_trackingToGct.
Differential expression analyses were computed by t-test in R.
Genome_build: Mus_musculus_GRCm38_Ensembl
Supplementary_files_format_and_content: gct file (gene expression quantification)

source_name: mouse SWELL1 KO 3T3-F442A, biological rep1

growth_protocol: Cells were cultured in RPMI+10% FBS

extract_protocol:
RNA was isolated with TRIZOL
Library preparation was performed by the University of Iowa genomics core facility

tag: cell line

value: mouse adipocyte cell line

tag: swell1 genotype

value: KO


title: SWELL1 KO 3T3-F442A, rep 3

description:
Gene expression data from the mouse adipocyte cell lines with SWELL1 knocked out by CRISPR/Cas9, biological replicate 3
Sample name: 13_D3_KO

source_name: mouse SWELL1 KO 3T3-F442A, biological rep3


title: 1003_Sequencing batch 2

description:
Sequencing batch 2 from sample 1003
US-1466240_BC2BUMACXX_US-1466240_CTCAGA_L002_R1_001

value: DRG


title: WT 3T3-F442A, rep 1

description:
Gene expression data from the mouse adipocyte cell lines with intact SWELL1, biological replicate 1
Sample name: 1_3T3

source_name: mouse WT 3T3-F442A, biological rep1

value: WT


title: Animal3_Male_Cerebrum_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal3_Male_Cerebrum
US-1466228_BC2BUMACXX_US-1466228_GGTAGC_L001_R1_001


title: Animal5_Male_WholeBlood_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal5_Male_WholeBlood
US-1459924_AD1GBMACXX_US-1459924_CATTTT_L003_R1_001

value: WholeBlood


title: Animal6_Male_WholeBlood_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal6_Male_WholeBlood
US-1459946_AD1GBMACXX_US-1459946_CAAAAG_L005_R1_001


title: Animal9_Female_Ovary_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal9_Female_Ovary
US-1458879_AD2C4RACXX_US-1458879_ACTTGA_L004_R1_001

value: female

value: Ovary


title: ES-WT-2i_RNA_rep3

city: Bethsda

first: Vittorio

last: Sartorelli

state: MD

address: 50 South Dr.

department: NIAMS

institute: NIH

data_processing:
Basecalls performed using CASAVA version 1.8.2
ChIP-seq reads were mapped to the mm9 genome assembly using Bowtie2 version 2.2.4 with the default configurations.
RNA-seq reads were mapped to the mm9 genome assembly using TopHat version 2.0.13 (Trapnell C, et.al 2009) with the default configurations.
peaks were called using SICER version 1.1 ( Zang et al, 2009) with the following setting: redundancy threshold (1), window size (200), fragment size (150), effective genome fraction (0.74), gap size (600),FDR (0.05) .
FPKM(RPKM) and differential expression analysis was done using Cufflink/Cuffdiff (Trapnell C, et.al 2009) with multi-reads correction and geometric normalization
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include peak values for each Sample;tab-delimited text files includes FPKM values for each Sample.

molecule: polyA RNA

source_name: ES cell line

growth_protocol: E14 wild type or mutant ES cells were maintained in ES medium ( high glucose-DMEM, 15% fetal bovine serum, 0.1 mM 2-mercaptoethanol, 1 mM sodium pyruvate, 2 mM glutamine, 0.1 mM nonessential amino acids, and 1000 U/ml mouse LIF), on tissue culture plates coated with 0.1% gelatin, in 6% CO2 at 37°C. Mouse skeletal muscle C2C12 cells  were  grown in high glucose- DMEM, 20% fetal bovine serum, 1x Penicillin/streptomycin.

extract_protocol:
For ChIPSeq, lysates were cleared from sonicated nuclei and used for immunoprecipitation. For RNASeq, RNA was extracted according to TRIzol protocol (invitrogen).
For ChIPSeq, cells were cross-linked in 1% formaldehyde and lysate to extract nuclei. The chromatin was sonicated to 250 bp fragments. Histone-DNA complexes were isolated with anti-H3K27me1 (Millipore #07-448), anti-H3K27me2 (Cell signaling #9728S), anti-H3K27me3 (Cell signaling #9733S), anti-H3K4me1 (Abcam #ab8899), anti-H3K27ac (Abcam #4729). 10ng of immuno-precipitated DNA fragments were used to prepare ChIP-seq libraries with the NEBNext RNA library prep kit (New England BioLabs) and Ovation SP Ultralow DR Multiplex system (Nugen) following the manufacturer’s protocol. For polyA RNA-Seq, Illumina protocol was followed.

treatment_protocol: For 24 hours differentiation, feeder-free ESC were plated at low density (1 x 106/10cm plate) for 24 hours in ES medium described above without LIF and serum. For EB culture, 1 x 106 feeder-free ESC were passaged onto 10 cm ultra low attachment culture dishes. Serum-cultured ESC were converted to ground state by culturing and passaging the cells in ESGRO-2i medium.

tag: developmental stage

value: Pluripotent ES cells


title: ES-WT-2i_RNA_rep2


title: 24h-diff-WT-serum_RNA_rep2

value: Pluripotent and 24h differentiated ES cells


title: SWELL1 KO 3T3-F442A, rep 2

description:
Gene expression data from the mouse adipocyte cell lines with SWELL1 knocked out by CRISPR/Cas9, biological replicate 2
Sample name: 12_D3_KO

source_name: mouse SWELL1 KO 3T3-F442A, biological rep2


title: WT 3T3-F442A, rep 3

description:
Gene expression data from the mouse adipocyte cell lines with intact SWELL1, biological replicate 3
Sample name: 3_3T3

source_name: mouse WT 3T3-F442A, biological rep3


title: ES-Y641F-2i_RNA_rep1


title: Animal6_Male_Kidney_Homogenate_re-extract_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal6_Male_Kidney_Homogenate_re-extract
US-1462931_AD1GBMACXX_US-1462931_CAGGCG_L006_R1_001

extract_protocol:
RNA was purified using the miRNAeasy protocol from Qiagen (Kit cat# 217004).
Library construction was performed according to Illumina’s TruSeq small RNA sample prep protocol (Cataloge # RS-200-0048) using a HiSeq2000.  Briefly, RNA was extracted from tissues using the miRNeasy protocol. Libraries were constructed using the Illumina TruSeq small RNA preparation guide which entails ligation of adapters on the 3' and 5' ends of the RNA molecules.  The libraries were quantitated using RiboGreen and were size selected through gel electrophoresis and libraries consistent with the size of miRNAs were gel purified.  Sequencing was performed with each sample receiving 4-5 million, 30bp, single-end reads. generated

value: Kidney


title: serum_2i_ES-Y641F


title: ES-Y641F-serum_RNA_rep3


title: WT 3T3-F442A, rep 2

description:
Gene expression data from the mouse adipocyte cell lines with intact SWELL1, biological replicate 2
Sample name: 2_3T3

source_name: mouse WT 3T3-F442A, biological rep2


title: ES-WT-serum_RNA_rep2


title: ES-Y641F-2i_RNA_rep2


title: ES-Y641F-2i_RNA_rep3


title: Animal6_Male_Cerebellum_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal6_Male_Cerebellum
US-1456495_AD1GBMACXX_US-1456495_GGTAGC_L005_R1_001

value: Cerebellum


title: ES-WT_ES-Y641F_24h-diff-wt


title: Animal6_Male_Stomach_Glandular_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal6_Male_Stomach_Glandular
US-1458850_AD2C4RACXX_US-1458850_GAGTGG_L002_R1_001

value: Sprague Dawley


title: 24h-diff-WT-serum_RNA_rep1


title: Animal10_Female_Adrenal_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal10_Female_Adrenal
US-1458877_AD1GBMACXX_US-1458877_ATGAGC_L006_R1_001

value: Adrenal


title: Animal4_Male_Jejunum_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal4_Male_Jejunum
US-1458698_AD2C4RACXX_US-1458698_CATTTT_L006_R1_001

value: 12-13 weeks

value: Jejunum


title: 24h-diff-WT-serum_RNA_rep3


title: ES-WT-2i_RNA_rep1


title: EB13-WT_EB13-Y641F

value: Day 13 embryoid bodies


title: ES-Y641F-serum_RNA_rep2


title: EB8-WT_EB8-Y641F

value: Day 8 embryoid bodies


title: ES-WT_H3K27me3_rep2

value: H3K27me3 (Cell signaling, 9733S, lot unknown)


title: Animal4_Male_Cortex_Homogenate_re-extract_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal4_Male_Cortex_Homogenate_re-extract
US-1462932_BC2BUMACXX_US-1462932_ATCACG_L002_R1_001

value: male

value: Cortex


title: ES-WT-serum_RNA_rep3


title: ES-Y641F_H3K27me3_rep1


title: Animal11_Female_Medulla_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal11_Female_Medulla
US-1458838_AD1GBMACXX_US-1458838_GTAGAG_L003_R1_001

value: Medulla


title: Animal4_Male_Adrenal_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal4_Male_Adrenal
US-1458848_AD1GBMACXX_US-1458848_GTGAAA_L006_R1_001


title: EB8-WT_H3K27me3


title: Animal9_Female_Uterus_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal9_Female_Uterus
US-1456441_AD1GBMACXX_US-1456441_CGTACG_L004_R1_001

value: Uterus


title: MB-C2C12_H3K27me2_rep2

source_name: C2C12 cell line

value: Myoblasts

value: H3K27me2 (Cell signaling, 9728S, lot unknown)


title: Animal4_Male_Liver_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal4_Male_Liver
US-1454077_AD1GBMACXX_US-1454077_CACCGG_L004_R1_001

value: Liver


title: Animal4_Male_Stomach_Non-Glandular_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal4_Male_Stomach_Non-Glandular
US-1466223_AD1GBMACXX_US-1466223_CACGAT_L006_R1_001


title: ES-WT_H3K27me2_rep2

value: Pluripotent ES cells


title: ES-WT_H3K27me2_rep1


title: 24h-diff-WT_H3K27me3_rep2

value: 24 hours differentiated ES cells


title: ES-Y641F_H3K27me2_rep1


title: 24h-diff-WT_H3K27me2_rep2


title: 24h-diff-WT_H3K27me2_rep1


title: ES-WT_H3K27me1_rep2

value: H3K27me1 (Millipore, 07-448, lot unknown)


title: 24h-diff-WT_H3K27me3_rep1


title: MB-C2C12_H3K27me2_rep1


title: ES-Y641F_H3K27me1_rep1


title: ES-Y641F_H3K27me2_rep2


title: 1503_Sequencing batch 1

description:
Sequencing batch 1 from sample 1503
US-1463156_AD1GBMACXX_US-1463156_CAGATC_L004_R1_001

value: Sprague Dawley

value: female

value: DRG


title: Animal5_Male_Stomach_Non-Glandular_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal5_Male_Stomach_Non-Glandular
US-1466229_AD2C4RACXX_US-1466229_GAGTGG_L005_R1_001

value: 12-13 weeks


title: 24h-diff-WT_H3K27me1_rep1


title: ES-WT_H3K27ac_rep2

value: H3K27ac (Abcam ab4729, lot unknown)


title: Animal6_Male_Liver_Homogenate_re-extract_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal6_Male_Liver_Homogenate_re-extract
US-1462929_AD1GBMACXX_US-1462929_TGACCA_L004_R1_001


title: ES-Y641F_H3K27ac_rep1


title: ES-Y641F_H3K27me1_rep2


title: 24h-diff-WT_H3K27me1_rep2


title: 1003_Sequencing batch 1

description:
Sequencing batch 1 from sample 1003
US-1466240_AD1GBMACXX_US-1466240_CTCAGA_L005_R1_001


title: Animal6_Male_Cortex_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal6_Male_Cortex
US-1456448_AD2C4RACXX_US-1456448_GTGAAA_L008_R1_001


title: 1505_Sequencing batch 2

description:
Sequencing batch 2 from sample 1505
US-1466236_AD2C4RACXX_US-1466236_CACTCA_L006_R1_001


title: ES-WT_H3K27ac_rep1


title: Animal7_Female_Uterus_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal7_Female_Uterus
US-1456454_BC2BUMACXX_US-1456454_TGACCA_L002_R1_001


title: 24h-diff-WT_H3K27ac_rep1


title: ES-Y641F_H3K27ac_rep2


title: ES-WT_H3K4me1

value: H3K4me1 (Abcam, ab8899, lot unknown)


title: Animal10_Female_Muscle_Soleus_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal10_Female_Muscle_Soleus
US-1466201_AD2C4RACXX_US-1466201_GGTAGC_L005_R1_001

value: Muscle - Soleus


title: ES-WT_Ezh2_rep2

value: Ezh2 (Cell signaling, 5246S, lot unknown)