title: GRO-seq nos-GAL4->white

data_processing:
Library strategy: GRO-Seq
NOTE: in the GRO-seq libraries 5'-end of all sequences starts with "T" and it should be trimmed before data processing.
Reads were aligned to consensus drosphila transposon sequences (v9.4.1 available from flybase.org) using bowtie2 (version 2.0.0-beta7) and the following parameters: -p2 -k 10 -N1
Reads were separately aligned to the dm3 genome using bowtie2 and the same parameters
For RNAseq and GROseq libraries, differential expression was performed with DESeq (release 1.10.1) with the following parameters: method='pooled',sharingMode="maximum",fitType="local"
Genome_build: dm3

molecule: nuclear RNA

source_name: GRO-seq nos-GAL4->white

extract_protocol:
GRO-seq: nuclei from about 100 ovaries were used for a run-on reaction
GRO-seq libraries were constructed as described in Core et al. 2008
The detailed methods described in the Rozhkov et al. 2013


title: GRO-seq nos-GAL4->piwi

status: Public on Feb 09 2013

type: SRA

city: Cold Spring Harbor

first: Nikolay

middle: V

last: Rozhkov

email: nik.rozhkov@gmail.com, rozhkov@cshl.edu

state: NY

address: 1 Bungtown Rd.

country: USA

institute: CSHL

library_source: transcriptomic

organism: Drosophila melanogaster

source_name: GRO-seq nos-GAL4->piwi

growth_protocol: flies were kept at 25 degrees

treatment_protocol: ovaries were dissected on ice

tag: tissue

value: ovaries

tag: age

value: 3-5 days


title: Liver Low androstenone rep 5

city: Bonn

first: Sudeeep

last: Sahadevan

state: NRW

address: Endenicher Allee 15

department: Institute of Animal Science

country: Germany

institute: University of Bonn

description: Sample B5

data_processing:
Base calling performed using Illumina Casava 1.7
The raw reads were trimmed for adapter sequences and mapped to sscrofa9 refseq and mRNA sequences and sscrofa9 whole genome using bwa using the default parameteres.
Raw read counts were calculated from the annotated files using samtools using default parameters for sscrofa9 refseq and mrna mapppings using the default parameters.
Genome_build: Sscrofa9 (NCBI)
Supplementary_files_format_and_content: tab limited text file include raw read count for each sample

molecule: total RNA

organism: Sus scrofa

source_name: Liver Low androstenone

extract_protocol:
Testis and liver were frozen in liquid nitrogen immediately after slaughter and stored at -80°C until used for RNA extraction. RNA was harvested using RNeasy Mini Kit according to manufacturer’s recommendations (Qiagen).
Full-length cDNA was obtained from 1 μg of RNA, with the SMART cDNA Library Construction Kit (Clontech, USA), according to the manufacturer's instructions. Libraries of amplified RNA for each sample were prepared following the Illumina mRNA-Seq protocol.
The library preparations were sequenced on an Illumina HiSeq 2000 as single-reads to 100 bp using 1 lane per sample on the same flow-cell (first sequencing run) at GATC Biotech AG (Konstanz, Germany).

tag: breed

value: Duroc x F2 cross. F2 was created by crossing F1 animals (Leicoma x German Landrace). Large White pig

value: liver

value: 116 day old


title: Liver Low androstenone rep 4

description: Sample B4


title: GRO-seq Tj-GAL4->white

source_name: GRO-seq Tj-GAL4->white


title: GRO-seq Tj-GAL4->piwi

source_name: GRO-seq Tj-GAL4->piwi


title: Liver Low androstenone rep 3

description: Sample B3


title: Liver Low androstenone rep 2

description: Sample B2


title: RNA-seq nos-GAL4->white

data_processing:
Reads were aligned to consensus drosphila transposon sequences (v9.4.1 available from flybase.org) using bowtie2 (version 2.0.0-beta7) and the following parameters: -p2 -k 10 -N1
Reads were separately aligned to the dm3 genome using bowtie2 and the same parameters
For RNAseq libraries, genomic alignments to dm3 were performed with tophat (v2.0.5) using the following parameters: --segment-length 18 -p 10 --library-type fr-firststrand
For RNAseq and GROseq libraries, differential expression was performed with DESeq (release 1.10.1) with the following parameters: method='pooled',sharingMode="maximum",fitType="local"
Genome_build: dm3

source_name: RNA-seq nos-GAL4->white

extract_protocol:
RNA-seq: libraries were constructed from 150ng of total RNA using Encore Complete RNA-seq kit (NuGen)
RNA-seq - using Encore Complete RNA-seq kit (NuGen)
The detailed methods described in the Rozhkov et al. 2013


title: Testis High androstenone rep 1

description: Sample A6

source_name: Testis High androstenone

value: testis


title: KO_Rep1

city: Oxford

first: Supat

last: Thongjuea

address: Headington

department: MRC Molecular Haematology Unit

country: United Kingdom

institute: The Weatherall Institute of Molecular Medicine

data_processing:
36 bp raw reads were mapped against NCBI build 37.1 of the mouse genome with ELAND (Illumina).
Uniquely mapped reads were extended to 200 bp and then transformed into the genome-wide reads density (coverage) with the ShortRead Bioconductor package. The coverage from ChIP and IgG control was visualized on a mirror of the UCSC genome browser.
MACS, CCAT,  and in-house developed software (unpublished) were used to detect Ldb1 binding peaks.
Identified binding peaks from all software were combined to get the consensus regions. Negative binomial distribution was performed to assign p-value to each consensus region.
Raw reads were mapped with Bowtie10 to mouse NCBI m37 Ensembl transcripts. Count number of reads for each transcript and reads per kb of a transcript per million mapped reads (RPKMs) were calculated and assigned to each transcript.
The longest transcript was chosen as a representative gene for downstream analysis and the highest expression level from alternative transcripts was assigned to the representative gene.
Read counts per representative genes were subjected to DESeq Bioconductor package11 for statistical testing of differentially expressed genes and p-values were adjusted with Benjamini and Hochberg (BH).
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited identified number of read counts per Ensembl transcript for each sample (count table generated for DESeq pipeline)

organism: Mus musculus

source_name: hemangioblast  equivalent cells

growth_protocol: Ldb1+/+ and Ldb1-/- ES cells were grown in suspension at 10.000 cells/ml on nonadherent dishes in IMDM medium (without Leukemia Inhibitory Factor (LIF)) with 15% FCS, 1% P/S, 1% L-glutamine (Gibco, Cat.25030-08), 0.05μg/ml transferrin (Roche, Cat.652-202), 0.05μg/ml ascorbic acid (Sigma, Cat.A-4544), 3μl/ml monothioglycerol (Sigma, Cat.M-6145) for day 4 EBs and 1.8μl/ml for day 6 and day 8 EBs. 5% protein free hybridoma medium II (Gibco, Cat.12040-077) was added for day 6 and day 8 EBs

extract_protocol: RNA-Seq library was prepared according to the Illumina protocol (www.illumina.com).

tag: cell-type

value: Ldb1-/- from Flk1+ cells

tag: genotype


title: KO_Rep4


title: KO_Rep3


title: WT_Rep2

value: Ldb1+/+ from Flk1+ cells


title: Testis Low androstenone rep 3

description: Sample A3

source_name: Testis Low androstenone


title: Testis High androstenone rep 3

description: Sample A8


title: Testis Low androstenone rep 2

description: Sample A2


title: Testis Low androstenone rep 1

description: Sample A1


title: KO_Rep2


title: Ldb1_Flk1+_BL-CFCs_ChIPSeq

library_source: genomic

data_processing:
36 bp raw reads were mapped against NCBI build 37.1 of the mouse genome with ELAND (Illumina).
Uniquely mapped reads were extended to 200 bp and then transformed into the genome-wide reads density (coverage) with the ShortRead Bioconductor package. The coverage from ChIP and IgG control was visualized on a mirror of the UCSC genome browser.
MACS, CCAT,  and in-house developed software (unpublished) were used to detect Ldb1 binding peaks.
Identified binding peaks from all software were combined to get the consensus regions. Negative binomial distribution was performed to assign p-value to each consensus region.
Raw reads were mapped with Bowtie10 to mouse NCBI m37 Ensembl transcripts. Count number of reads for each transcript and reads per kb of a transcript per million mapped reads (RPKMs) were calculated and assigned to each transcript.
The longest transcript was chosen as a representative gene for downstream analysis and the highest expression level from alternative transcripts was assigned to the representative gene.
Read counts per representative genes were subjected to DESeq Bioconductor package11 for statistical testing of differentially expressed genes and p-values were adjusted with Benjamini and Hochberg (BH).
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited identified peaks text files.

molecule: genomic DNA

extract_protocol: ChIP-Seq library was prepared according to the Illumina protocol (www.illumina.com).

value: Flk1+ BL-CFCs isolated from day 4 embryoid bodies

tag: chip antibody

value: anti-Ldb1 antibody N-18, Santa Cruz®


title: Testis High androstenone rep 5

description: Sample A10


title: Testis High androstenone rep 4

description: Sample A9


title: Testis Low androstenone rep 5

description: Sample A5


title: Ldb1_Flk1+_BL-CFCs_Control_ChIPSeq


title: WT_Rep1


title: V5-MBD2-HeLa_ChIP-Seq

status: Public on Feb 08 2013

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

institute: Justus-Liebig-University Giessen

description: V5-ChIP-Seq using extracts from HeLa cells transfected with V5-MBD2 vector

data_processing:
Quality control of FASTQ files was done using FastQC.
Removal of low quality reads was done using fastx_toolkit-0.06
Reads were aligned to a pre-compiled index of the mouse hg19 genome using Bowtie (options: -k 1 -m 1) 0.12.5.
Duplicate reads were removed with Samtools' rmdup function.
Samtools was used to convert aligned reads to BAM format.
PeakRanger1.15 was used to call peaks at default settings (p-value < 10E-04, FDR < 5E-02) where the Input sample was used as control.
Genome_build: hg19
Supplementary_files_format_and_content: WIG files were produced using Macs 1.4 at 10bp resolution
Supplementary_files_format_and_content: Aligned reads were converted to BED format using BedTools.

organism: Homo sapiens

source_name: HeLa

growth_protocol: HeLa cells were cultured at 37°C with 5% CO2 in DMEM media

extract_protocol: HeLa cells transiently expressing V5-MBD2b, V5-MBD3 or V5 were cross-linked with formaldehyde and sonicated. Sonicated chromatin was pre-cleared and incubated with V5-Agarose overnight at 4°C. After reversing the crosslinks, DNA was treated with Proteinase K and RNAse A. DNA was recovered by using illustra GFX PCR DNA and gel Band Purification Kit (GE HealthCare). The isolated DNA was sequenced using the Illumina sequencing platform (single read library 36bp length) using NEBs ChIP library preparetion kit.

treatment_protocol: HeLa cells were transfected with either 1 µg V5-MBD2b, V5-MBD3 or V5-construct using TurboFect (Fermentas) as transfection reagent and incubated for 48h

tag: cell type

value: HeLa

tag: transfected construct

tag: antibody vendor/catalog#

value: Sigma Aldrich:021M4839


title: wtsP2_wing_RNAseq_REP2

status: Public on Feb 07 2013

city: Chicago

first: Kevin

middle: P.

last: White

state: IL

address: 900 E. 57th STR. 10th FL.

department: Institute for Genomics and Systems Biology

institute: University of Chicago

description: wtsP2 wing disc RNA-seq, replicate 2

data_processing:
RNA-seq was performed using the SOLiD 5500xl platform, with Exact Call Chemistry (Applied Biosystems). Mapping of SOLiD sequencing reads to the Drosophila genome (Drosophila_melanogaster.BDGP5.68) was performed using Lifescope v2.5 under default conditions
RPKM values were derived using Avadis NGS
For differential expression analysis, HTSeq was used to count the number of reads falling in gene structures (Flybase 5.34) under "intersection-nonempty" model (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html). DEseq was applied to calculate the normalized read counts under both conditions
Genome_build: dm3
Supplementary_files_format_and_content: txt files containing gene read counts and RPKM values; data matrix of DEseq-based expression values for comparison of wtsP2 versus WT is also provided

source_name: Wing imaginal disc RNA

growth_protocol: Wandering 3rd instar larvae were manually removed from Drosophila culture. Larvae were inverted in PBS to expose imaginal discs. Imaginal discs dissected off before RNA extraction.

extract_protocol: RNA was isolated and prepared for sequencing using SOLiD Total RNA-seq kit

tag: strain

value: yw

tag: developmental stage

value: Wing imaginal disc


title: V5-HeLa_ChIP-Seq_control

description: V5-ChIP-Seq using extracts from HeLa cells transfected with empty V5-vector


title: HCF1 ChIP-Seq

city: Bruxelles

first: Matthieu

last: Defrance

address: CP614 route de Lennik 808

country: Belgium

institute: Université Libre de Bruxelles

data_processing:
ChIP-Seq reads were aligned to the mm9 & h18 genomes using BWA  0.5.9
peaks were called using MACS v1.4
Genome_build: mm9 & hg18
Supplementary_files_format_and_content: wig files were generated using MACS

growth_protocol: H293T cells were cultured in DMEM + serum at 37°C / 5% CO2.

extract_protocol: ChIP experiments were performed according to the Transcription ChIP kit (Diagenode) protocol and sonication was performed with a bioruptor (Diagenode).  Sonicated protein-DNA complexes were isolated with antibody or HaloLink resin (Promega).The library preparation was performed using ChIP-Seq DNA sample prep kit (Illumina). Briefly, 10ng of qPCR verified ChIPed DNA was subjected to 5’ and 3’ protruding ends repair. Non-templated adenines were added to the 3’ ends of the blunted DNA fragments.  DNA fragments were then size selected with a 2% agarose gel electrophoresis in order to remove all unligated adapters and to sequence 300bp fragments. 18 cycles of PCR were done to amplify the library. DNA was quantified by fluorometry using the Qubit 2.0 and its integrity was assessed with 2100 bioanalyzer (Agilent). 3 pM DNA library spiked with 1% PhiX viral DNA was clustered on cBot (Illumina), and then sequenced on HiScanSQ module (Illumina).

tag: cell line


title: Testis Low androstenone rep 4

description: Sample A4


title: wtsP2_wing_RNAseq_REP1

description: wtsP2 wing disc RNA-seq, replicate 1


title: V5-MBD3-HeLa_ChIP-Seq

description: V5-ChIP-Seq using extracts from HeLa cells transfected with V5-MBD3 vector


title: WT_wing_RNAseq_REP2

description: wild type wing disc RNA-seq, replicate 2

value: wildtype


title: WT_wing_RNAseq_REP1

description: wild type wing disc RNA-seq, replicate 1


title: WT_Rep3


title: WT_Rep4


title: Testis High androstenone rep 2

description: Sample A7


title: Liver Low androstenone rep 1

description: Sample B1


title: O-GlcNAc ChIP-Seq

value: O-GlcNAc

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #

tag: chip antibody lot#


title: HT-TET2 ChIP-Seq

description: The HT-TET2 refers as "HaloTag-TET2" fusion protein that was overexpressed in H293T cells. Chromatin isolation of those proteins was performed with HaloResin (Promega).

source_name: H293T_HT TET2

tag: genotype/variation

value: HT-TET2 overexpression


title: HT-OGT ChIP-Seq

description: The HT-OGT refers as "HaloTag-OGT" fusion protein that was overexpressed in H293T cells. Chromatin isolation of those proteins was performed with HaloResin (Promega).

source_name: H293T_HT OGT

value: HT-OGT overexpression


title: H293T_H3K4me3 RNAi TET2

source_name: H293T_TET2 kd_H3K4me3

value: TET2 knockdown (RNAi TET2)


title: H3K4me3 ChIP-Seq

value: wild type


title: Bone marrow_H3K4me3 ChIP-Seq

source_name: Bone Marrow_H3K4me3

value: Bone Marrow


title: Bone marrow_Tet2 ChIP-Seq

source_name: Bone Marrow_Tet2

value: Santa Cruz


title: H3K4me3 ChIP-Seq Tet2 Ko

source_name: Bone Marrow Tet2 Ko


title: crh6 mutant Hi-C

city: Los Angeles

first: Shawn

middle: J.

last: Cokus

state: CA

address: UCLA, 3000 Terasaki Life Sciences Building, 610 Charles Young Drive East

institute: UCLA

data_processing:
Sequencing reads were mapped to the TAIR8 A. thaliana reference genome using Bowtie 1 to obtain all zero-mismatch hits of ends independently and keeping only unique paired end reads.    Paired reads with ends aligning to the same HindIII fragment were discarded.
Reads were assigned to genomic bins of 50 kb or 200 kb, according to the center of their corresponding restriction fragment.  HindIII fragments which  overlapped regions of poor reference genome quality were excluded from the  analysis. Genomic 1-D bins (rows and columns) in which > 50% of the sequence  length was excluded by these filters were treated as missing data.  The binned interaction maps were then corrected for systematic biases by equalizing the total coverage (1D sum across the matrix) of every bin in the genome using 50 iterations of a normalization procedure previously described (PMID: 22341456).   Genomic bins with a total 1-D coverage more than 3 standard deviations greater or less than the mean were excluded.
Genome_build: tair8
Supplementary_files_format_and_content: IntMatrix files: Contains a matrix of normalized interaction frequencies for every pair of 50 kb or 200 kb bins in the genome.  Bin names and genomic coordinates are listed in row and column headers and then iteratively corrected interaction frequencies are listed in each pair of row and column.

organism: Arabidopsis thaliana

source_name: Floral tissue

extract_protocol:
Hi-C was carried out essentially as described previously (Lieberman-Aiden et al., 2009), with the exception that plant nuclei were prepared following a previously  published Arabidopsis ChIP protocol (PMID: 17337630)
The ligation products were fragmented by Covaris sonication to an average size of 200 bp and then the ideal size for Illumina sequencing (100-300 bp) was selected by Ampure fractionation.  The DNA ends were prepared for Illumina sequencing adapter ligation by repairing the DNA ends and adding an ‘A’ to each end.  The biotinylated junctions were then pulled down using MyOne streptavidin beads.  Illumina paired end adapters were ligated onto the DNA ends and then the fragments were PCR amplified.  Samples were sequenced on an Illumina HiSeq 2000 instrument using the Paired End 50 bp module.

treatment_protocol: Two grams of 3-week-old seedling leaves were crosslinked with formaldehyde as previously described (PMID: 17337630)

tag: ecotype

value: Columbia

value: floral


title: WT Hi-C

tag: tissue

value: wild-type


title: Wing disc input, replicate2

description:
Wing disc input, replicate 2
NA
NA

data_processing:
The Raw images were first processed with the Casava 1.7.0.
Base-called sequences with confidence metrics were obtained using OLB-1.9.0.  All multiplexed samples were demultiplexed using Casava 1.7.0
The BWA program was used to align the sequence reads to the Drosophila melanogaster (v5.32) genome, allowing up to 2 edit distance in the seed region and 3 in the full read length. Tags that aligned to more than one  location were excluded from our analysis for both ChIP sample and the corresponding control sample (input chromatin). Only properly aligned reads with mapping quality more than 30 were kept.
Peaks were called using MACS (v2), on merged replicates, using bandwidth of 100 and a p-value cutoff of 1E-5
Genome_build: dm3
Supplementary_files_format_and_content: bedGraph files were generated using SPP from sorted bam file, which was generated by SAM/bowtie, under 100 bp step

source_name: Wing imaginal disc Input chromatin; Iso1 strain; no antibody

growth_protocol: Embryos were collected at 8-16 hours after egg laying. For wing discs, wandering 3rd instar larvae were manually removed from Drosophila culture. Larvae were inverted in PBS to expose imaginal discs. Imaginal discs dissected off before fixation.

extract_protocol: Chromatin lysates were clarified from homogenized and sonicated tissues; protein-DNA complexes were isolated with antibody.  DNA fragments recovered following chromatin IP prepared for Illumina sequencing using the Epicentre Nextera DNA Sample Prep Kit (Cat. # GA0911).  Briefly, up to 12.5 ng DNA was included in the high molecular weight (HMW) tagmentation reaction (5 minutes at 55 degrees Celsius). Tagmented DNA was purified using a Qiagen MinElute column. Addition of barcoded PCR-compatible sites and library enrichment were performed using 12 cycles of PCR. Amplified DNA was purified using the Qiagen MinElute PCR Purification Kit. Library fragments of approximately 225 bp were gel purified and captured on an Illumina flow cell for cluster generation. Libraries were sequenced on a HiSeq2000 according to the manufacturer’s protocol.

tag: antibody


title: Yki wing disc ChIP, replicate1

description:
Yki wing disc ChIP, replicate 1
Yki_wing.bedGraph
Yki_wing.bed

source_name: Wing imaginal disc ChIP; Iso1 strain; Yki antibody

value: anti-Yki


title: GAF wing disc ChIP, replicate2

description:
GAF wing disc ChIP, replicate 2
GAF_wing.bedGraph
GAF_wing.bed

source_name: Wing imaginal disc ChIP; Iso1 strain; GAF antibody

value: anti-Trl (antii-GAF)


title: GAF wing disc ChIP, replicate1

description:
GAF wing disc ChIP, replicate 1
GAF_wing.bedGraph
GAF_wing.bed


title: H3K4me3 embryo ChIP, replicate1

description:
H3K4me3 embryo ChIP, replicate 1
H3K4me3_E8-16.bedGraph
H3K4me3_E8-16.bed

source_name: 8-16hr embryo ChIP; Iso1 strain; H3K4me3 antibody

value: Embryo, 8-16hr

value: Whole embryo


title: Embryo input

description:
Embryo input
NA
NA

source_name: 8-16hr embryo Input chromatin; Iso1 strain; no antibody


title: Yki embryo ChIP, replicate2

description:
Yki embryo ChIP, replicate 2
Yki_E8-16.bedGraph
Yki_E8-16.bed

source_name: 8-16hr embryo ChIP; Iso1 strain; Yki antibody


title: Yki embryo ChIP, replicate1

description:
Yki embryo ChIP, replicate 1
Yki_E8-16.bedGraph
Yki_E8-16.bed


title: GAF embryo ChIP, replicate2

description:
GAF embryo ChIP, replicate 2
GAF_E8-16.bedGraph
GAF_E8-16.bed

source_name: 8-16hr embryo ChIP; Iso1 strain; GAF antibody


title: GAF embryo ChIP, replicate3

description:
GAF embryo ChIP, replicate 3
GAF_E8-16.bedGraph
GAF_E8-16.bed


title: GAF embryo ChIP, replicate1

description:
GAF embryo ChIP, replicate 1
GAF_E8-16.bedGraph
GAF_E8-16.bed


title: HT-TET3 ChIP-Seq

description: The HT-TET3 refers as "HaloTag-TET3" fusion protein that was overexpressed in H293T cells. Chromatin isolation of those proteins was performed with HaloResin (Promega).

source_name: H293T_HT TET3

value: HT-TET3 overexpression


title: H293T_H3K4me3 RNAi control

source_name: H293T_RNAi control_H3K4me3

value: control (RNAi control)


title: HeLa si-C23 3

city: Bellinzona

first: Luciano

last: Cascione

state: Ticino

address: Via Chiesa 5

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

description: 43_Hela_sic23_3_solid0379_20110818_FRAGBCKal5Fla6mirRNA_solid0379_20110818_FRAGBCKal5Fla6mirRNA_F3_43_Hela_sic23_3

data_processing:
Mapping of SOLiD reads was performed using both the small RNA pipeline (Life Technologies) and PASS (Campagna et al., 2009). The small RNA pipeline and PASS were used to extract counts and extensions of miRNA in small RNA reads, from 18 nucleotides in length.
Alignments with up to one mismatch has been recorded when matching to either miRNome (precursor sequences from miRBase) or human genome. Only reads with at least 3 sequenced copies per sample were inputted in the SQL database.
Raw digital expression values (read counts) were obtained by summing the number of reads that mapped to one of the reference databases
Genome_build: human genome hg19 or miRBase release 17.0
Supplementary_files_format_and_content: RPKM data

source_name: HeLa si-C23

growth_protocol: HeLa cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) with 10% FBS, L-glutamine, and antibiotics (Life Technologies; Invitrogen).

extract_protocol:
Total RNA was prepared using Trizol® (Invitrogen) and libraries for deep sequencing were prepared from 2 µg of total RNA. Specifically 2 µg of total RNA underwent size selection by Flashpage Fractionator (AM110226001 Life Technologies). RNA that was 40bp and under was then quality checked by RNA pico-chip from Agilent.
The Applied Biosystems Total RNA-Seq Kit (cat # 4445374) was used to produce a cDNA library by the following steps. 5’ and 3’ specific adapters undergo hybridization and ligation to the RNA. cDNA was produced by reverse transcription and then purified and size-selected on a gel. The gel slices containing the cDNA library were amplified by PCR with primers specific to the adapter sequences, and then purified and sized selected on a gel. Templated sequencing beads were produced via emulsion PCR with Applied Biosystems’ EZ Bead system. The templated sequencing beads were sequenced on an Applied Biosystems SOLiD 5500 system according to the manufacturer’s protocol (Life Technologies, Foster City).

treatment_protocol: Sub-confluent HeLa cells were transfected with Nucleolin shRNA (sc-29230-SH) or Control shRNA (sc-3314-SH) plasmids, and stably transfected clones were selected by using 1 µg/ml puromycin.

value: HeLa

value: cervical cancer cells

value: stably expressing double-strand (ds) interfering RNA against NCL (sh-NCL)

tag: molecule subtype

value: small RNA


title: Bone marrow_O-GlcNAc ChIP-Seq

source_name: Bone Marrow_OGlcNAc

value: O-GlcNAc

value: Abcam


title: HeLa si-C23 2

description: 42_Hela_sic23_2_solid0379_20110818_FRAGBCKal5Fla6mirRNA_solid0379_20110818_FRAGBCKal5Fla6mirRNA_F3_42_Hela_sic23_2


title: HeLa Sh-Scr 3

description: 40_Hela_ctr3_solid0379_20110818_FRAGBCKal5Fla6mirRNA_solid0379_20110818_FRAGBCKal5Fla6mirRNA_F3_40_Hela_ctr3

source_name: HeLa Sh-Scr

value: stably expressing double-strand (ds) interfering RNA against scrambled sequences (sh-Scr)


title: H3K4me3 ChIP-Seq Tet2 Wt

source_name: Bone Marrow Tet2 Wt


title: Panagrellus redivivus RNA-seq reads (2x75)

city: Minneapolis

first: Marissa

last: Macchietto

address: 117 Pleasant Street SE

department: Minnesota Supercomputing Institute

institute: University of Minnesota, Minneapolis

data_processing:
Paired sequence reads were split into individual files
Mapped RNA-seq reads to de novo assembled scaffolds using Tophat v. 1.4.0 and Bowtie v. 0.12.8 and used Augustus gene predictions to guide mapping(-G Tophat option).
Predicted gene expression levels from Tophat-mapped reads using Cufflinks v. 2.0.2 (used Cufflinks' novel isoform option: -g )
Cuffcompare (Cufflinks v. 2.0.2)

molecule: polyA RNA

organism: Panagrellus redivivus

source_name: whole organism

growth_protocol: We used the P. redivivus strain (PS2298/MT8872) {Sternberg and Horvitz, 1981} in our genomic and transcriptomic analysis. This strain was raised at 20oC using standard methods.

extract_protocol:
P. redivivus worms were grown on five to ten 10-cm nutrient agar containing E. coli OP50 plates until near starvation. They were washed and collected with M9 buffer and washed multiple times to remove any E. coli. After the last wash in M9, the worms were suspended in M9 for 15-30 minutes. The worms were then snap-frozen in liquid nitrogen in ~100-uL aliquots and stored at 80°C. Worms were thawed and refrozen two to three times to break the cuticle before extracting bulk RNA. Bulk RNA was extracted using the Qiagen RNeasy mini kit. Oligo(dT) selection was performed twice on Total RNA by using Dynal magnetic beads (Invitrogen) according to the manufacturer's protocol. After selection, a single 100-ng aliquot of mRNA was reserved for evaluation on the BioAnalyzer.
The RNA-seq mixed-stage, poly(A)-selected library was created from 10 ug of total RNA using a standard unstranded protocol {Mortazavi et al., 2008, Mortazavi et al., 2010}. The mRNA was first fragmented by addition of 5x fragmentation buffer (200 mM Tris acetate, pH 8.2, 500 mM potassium acetate and 150 mM magnesium acetate) and heating at 94 °C for 2 min 30 s in a thermocycler and was then transferred to ice and run over a Sephadex-G50 column (USA Scientific) to remove the fragmentation ions. The reason for using random priming rather than dT priming is that the latter typically produces a bias in the product that favors 3' end representation. The extension issues do not affect all transcripts identically, and the cDNA population that results for each RNA species is a complex function of its specific properties as a substrate for reverse transcription and the overall transcript length. We used 3ug random hexamers, added to prime first-strand reverse transcription according to the manufacturer's protocol (Invitrogen cDNA synthesis kit). After the first strand was synthesized, a custom second-strand synthesis buffer (Illumina) was added, and dNTPs, RNase H and Escherichia coli polymerase I were added to nick translate the second-strand synthesis for 2.5 h at 16 °C. The reaction was then cleaned up on a QiaQuick PCR column (Qiagen) and eluted in 30  l EB buffer (Qiagen). Libraries were quantified using Qubit fluorometer (Invitrogen) and size distributions were verified using Agilent Bioanalyzer and the High Sensitivity DNA Kit. Libraries were sequenced on Illumina Genome Analyzer IIx sequencer in paired-end mode with the read length of 76 nt.

value: Mixed stage


title: HeLa Sh-Scr 2

description: 39_Hela_ctr2_solid0379_20110818_FRAGBCKal5Fla6mirRNA_solid0379_20110818_FRAGBCKal5Fla6mirRNA_F3_39_Hela_ctr2


title: Wing disc input, replicate1

description:
Wing disc input, replicate 1
NA
NA

value: Wing imaginal disc


title: HeLa Sh-Scr 1

description: 38_Hela_ctr1_solid0379_20110818_FRAGBCKal5Fla6mirRNA_solid0379_20110818_FRAGBCKal5Fla6mirRNA_F3_38_Hela_ctr1


title: H3K4me3 embryo ChIP, replicate2

description:
H3K4me3 embryo ChIP, replicate 2
H3K4me3_E8-16.bedGraph
H3K4me3_E8-16.bed


title: Yki embryo ChIP, replicate3

description:
Yki embryo ChIP, replicate 3
Yki_E8-16.bedGraph
Yki_E8-16.bed


title: NFIB_ChIPSeq_replicate2

city: New York

first: Chiung-Ying

last: Chang

address: 1230 York Avenue

institute: Rockefeller University

description: Chromatin IP against NFIB

data_processing:
Reads aligned to mm9 using bowtie (v.0.12.5) with no more than 2 mismatches at 36bp; only uniquely aligning reads were used.
wig files created from resulting bam files using IGVTools count command with 100bp extension
Genome_build: mm9
Supplementary_files_format_and_content: wig file with uniquely aligning reads

growth_protocol: HFSCs were purifed by FACS from the backskins of mice

extract_protocol:
Sorted cells were crosslinked by addition of 1/10th volume of fresh 11% formaldehyde solution. Before ChIP, cells were resuspended, lysed, and sonicated to solubilize and shear crosslinked DNAs. The resulting whole-cell extract was incubated 5 mg of NFIB antibody. After ChIP, samples were washed with low salt, high salt, LiCl, and Tris-EDTA buffer. Bound complexes were eluted and crosslinking was reversed.
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 25 cycles and library fragments of 150-300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: gender

value: female

tag: age

value: Mouse back skin

value: Hair follicle stem cells (HfSCs)

tag: sorting markers

value: integrin α6 and CD34

value: NFIB

value: Active Motif

tag: chip antibody lot #


title: input DNA_replicate1

description: input DNA

source_name: HfSCs_input DNA

tag: cell type

tag: chip antibody


title: NFIB_ChIPSeq_replicate1

description: Chromatin IP against NFIB

tag: strain


title: S2-mock

status: Public on Feb 06 2013

city: Strasbourg Cedex

first: Jean-Luc

last: Imler

address: 2, Allée Konrad Roentgen

department: IBMC

country: France

institute: CNRS

description: non infected Drosophila S2 cells

data_processing:
Software: preProcessing-v1.3.sh
Removal of low complexity reads (Dustmasker)
Removal of 3' adapter (FASTX_Toolkit) - Removal of size markers (19/24nt)
Size selection of remaining reads [15-32nt] - Final quality analysis - Retrieving of all filtered out reads
Sequenced reads were then mapped to IIV6 whole genome using bowtie v0.12.7 with parameters -n 1 -l 33
Genome_build: IIV6 genome on NCBI: NC_003038
Supplementary_files_format_and_content: _count tab-delimited text files include Read Number (colum 2) for each Read Size (column 1)
Supplementary_files_format_and_content: IIV6 alignment tab-delimited text files include Read Number (colum 2) for each first nucleotide Position (column 1)

organism: Invertebrate iridescent virus 6

source_name: Drosophila S2 cells

growth_protocol: S2 cells were grown in Schneider’s medium (Biowest) supplemented with 10% fetal calf serum, Glutamax (Invitrogen), Penicillin/Streptomycin (100x mix, 10 mg/mL/ 10000 U, Invitrogen) at 25°C. Adult flies were mainteined on standard cornmeal–agar medium at 25°C.

extract_protocol:
Total RNA from infected flies was isolated using Trizol Reagent RT bromoanisole solution (MRC), according to the manufacturer’s instructions.
The small RNA library of S2 cells and whole flies were constructed as described (Pfeffer, S. 2007. Identification of virally encoded microRNAs. Methods Enzymol 427:51-63).

treatment_protocol: For S2 cells, IIV6 is infected with MOI=0.01 for 5 days at 25°C. For adult flies, IIV6 (5000 PFU/fly) was injected and maintained at 22°C for 10 days.

tag: infection

value: mock


title: yw-IIV6

description: IIV6 infected Drosophila adult flies

source_name: Adult flies

value: whole organism

value: yw

value: Invertebrate iridescent virus 6


title: S2-IIV6

description: IIV6 infected Drosophila S2 cells

tag: cell line


title: EGFP_2

city: Basel

first: Tobias

last: Kockmann

address: Mattenstr. 26

department: D-BSSE

institute: ETHZ

data_processing:
tophat -p 13 -o tophat_alignment_BSSE-DSU-1902 -G Drosophila_melanogaster.BDGP5.25.64.cor.gtf --no-novel-juncs --no-novel-indels --no-coverage-search --no-closure-search --no-convert-bam /usr/local/paro/el5/bowtie/indexes/dm3_BDGPRelease5 BSSE-DSU-1902_CGATGTA_L007_R1_001.fastq.gz
htseq-count -q -s no ./tophat_alignment_BSSE-DSU-1902/accepted_hits.sam Drosophila_melanogaster.BDGP5.25.64.cor.gtf > 1902.counts
Genome_build:   Release 5
Supplementary_files_format_and_content: htseq-count

source_name: S2-DRSC CELLS

growth_protocol: S2-DRSC cells were grown in Schneider's Drosophila medium incl. 10% FCS at 25 degree celsius.

extract_protocol:
RNA extraction from S2-DRSC cells was done using Trizol reagent according to manufacturer’s instruction for adherent cells (Invitrogen).
Illumina TruSeq

treatment_protocol: RNAi was carried out according to standard bathing protocols in 6-well plate format (Drosophila RNAi Screening Center, Harvard Medical School) by adding 15 µg of dsRNA to each well before platting S2-DRSC cells in serum free Schneider’s medium and starving cells for 30 min.

tag: RNAi

value: EGFP

tag: replicate


title: FSH-L_2

value: FSH-L


title: FSH-L_1


title: Positive Sample 2 SL16145

city: Cambridge

first: Mackenzie

middle: W.

last: Amoroso

state: MA

address: 52 Oxford St.

institute: Harvard University

data_processing:
The RNA samples sequenced on an Illumina HiSeq instrument at the HudsonAlpha Institute of Biotechnology.
The reads were aligned to the reference transcriptome as well as a library of exon junctions using Bowtie
Data was analyzed using Expression Plot using a P value of 0.0001 and a 2 fold change threshold
Gene ontology was performed using DAVID with enrichment sets from Expression Plot.

source_name: Human Stem Derived Motor Neurons GFP high

growth_protocol: human stem cell line HUES 3 Hb9::GFP was differentiated as described in Amoroso et al with SHH or  SAG + PUR (S+P). Total cultures at day 21 were collected, dissociated into single cells, and FACS-purified based on the presence or lack of GFP expression. Both fractions were collected at the same time into different tubes.

extract_protocol:
Trizol extraction of total RNA
NuGEN RNA kit for genomic sample amplification

treatment_protocol: Positive Sample 1: SHH-derived, day 21 GFP-high FACS purified motor neurons  Positive Sample 2: S+P-derived, day 21 GFP-high FACS purified motor neurons  Negative: S+P condition, day 21 no GFP FACS purified motor neurons

value: HUES 3Hb9::GFP

tag: day of collection

value: Day 21 GFP high

tag: treatment

value: S+P derived

value: FACS-purified motor neurons


title: Negative Sample 1 SL16148

source_name: Human Stem Derived Motor Neurons no GFP

value: Day 21 no GFP


title: EGFP_1


title: Positive Sample 1 SL16147

value: SHH derived


title: HeLa si-C23 1

description: 41_Hela_sic23_1_solid0379_20110818_FRAGBCKal5Fla6mirRNA_solid0379_20110818_FRAGBCKal5Fla6mirRNA_F3_41_Hela_sic23_1

value: HeLa

value: cervical cancer cells

tag: genotype/variation

value: stably expressing double-strand (ds) interfering RNA against NCL (sh-NCL)

value: small RNA


title: FSH-S+L_1


title: FSH-S+L_2


title: input DNA_replicate2

description: input DNA

value: female

tag: tissue

value: Mouse back skin

value: Hair follicle stem cells (HfSCs)

value: integrin α6 and CD34


title: Dm S2-DRSC FSH-S+L ChIP-seq

data_processing:
Quality filtered reads were aligned to the Drosophila reference genome (BDGP Release 5) using Bowtie 0.12.7 and the following parameters: -n 2 -m 20 -k 1 --best (Langmead et al. 2009). Merging and indexing of alignments was done using SAMtools 0.1.9 (Li et al. 2009). Read coverage profiles and regions showing significantly enriched read coverage (peaks) were calculated using MACS 1.4.0 with the following parameters: band width=300, model fold=10 to 30, p-value cut-off=1x10^5 (Zhang et al. 2008). Alignments of sequenced input chromatin were used a control files during peak calling. Coverage profiles were calculated from shifted and extended reads according to the fitted MACS model.
BDGP Release 5

source_name: S2-DRSC cells

growth_protocol: S2-DRSC cells (DGRC lot 181A1) were grown at 25°C in Schneider's Drosophila medium (Invitrogen) supplemented with 10% heat-inactivated fetal bovine serum (HyClone Cat No.: SH30070.03, Lot No. ASK30724).

extract_protocol: Chromatin fixation and immunoprecipitation were performed essentially as described in DOI 10.1006/meth.1996.0407. In short,  1x10^9 cells were fixed in 200 ml medium with 1% formaldehyde for 10 min at room temperature. Cross-linked cells were sonicated to produce chromatin fragments of an average size of 200-400 bp. Soluble chromatin was separated from insoluble material by centrifugation. The supernatant containing chromatin of 2.5 x 10^7 cells was taken for immunoprecipitation. ASH1 bound chromatin was enriched using ASH1-N and ASH1-C polyclonal rabbit antibodies (kind gift from Frank Sauer, Riverside). Polyclonal rabbit antibodies for FSH were a gift from Igor Dawid, Laboratory of Molecular Genetics, PGD, NICHD. The antibody ID173 was raised against protein 4.1 (recognizes FSH-L only) and ID166 was raised against the N-terminal, common part of FSH-S and FSH-L, protein 1.2. The cDNAs used for the expression of both antigenes have been described in Digan ME et al. 1986. Libraries were prepared from ~10 ng of precipitated DNA using ChIP-seq DNA Sample Prep. Kit according to manufacturer’s instructions (Illumina, Cat# IP-102-1001). After adapter ligation library fragments of ~250 bp were excised from an agarose gel. The size selected DNA was PCR-amplified with Illumina primers for 18 (ChIP-seq) cycles, purified and loaded on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer IIx following the manufacturer's protocols.

value: S2-DRSC cells

value: FSH-S and FSH-L

tag: chip antibody source


title: Dm S2-DRSC FSH-S ChIP-seq

value: FSH-S

value: Igor Dawid, Laboratory of Molecular Genetics, PGD, NICHD


title: JQ1_20h_RNAseq

data_processing:
Reads were aligned to the Drosophila genome release BDGP5 using the splice junction aware aligner TopHat (http://tophat.cbcb.umd.edu/) and standard parameters. Reads uniquely mapping to Drosophila gene sets (Ensembl release 64) were counted using the htseq-count script (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html#count). Gene sets in GTF format were obtained from http://www.ensembl.org/info/data/ftp/index.html.
Genome Build:
1739.counts: BDGP5

source_name: S2-DRSC cells, JQ1, 20h

growth_protocol: S2-DRSC cells were grown in Schneider's medium incl. 10% FCS.

extract_protocol: Total RNA was extracted using standard Trizol protocols for adherent cells. 4 microg of total RNA served as the starting material to construct the libraries using the TruSeq RNA Sample Prep Kit (Illumina) according to the manufacturer's instructions.

treatment_protocol: Cells were treated either with JQ1 or DMSO by adding the compound to the growth medium for the indicated time periods.

tag: treatment duration

value: 20 hrs


title: JQ1_4h_RNAseq

data_processing:
Reads were aligned to the Drosophila genome release BDGP5 using the splice junction aware aligner TopHat (http://tophat.cbcb.umd.edu/) and standard parameters. Reads uniquely mapping to Drosophila gene sets (Ensembl release 64) were counted using the htseq-count script (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html#count). Gene sets in GTF format were obtained from http://www.ensembl.org/info/data/ftp/index.html.
Genome Build:
1738.counts: BDGP5

source_name: S2-DRSC cells, JQ1, 4h

value: 4 hrs


title: DMSO_20h_RNAseq

data_processing:
Reads were aligned to the Drosophila genome release BDGP5 using the splice junction aware aligner TopHat (http://tophat.cbcb.umd.edu/) and standard parameters. Reads uniquely mapping to Drosophila gene sets (Ensembl release 64) were counted using the htseq-count script (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html#count). Gene sets in GTF format were obtained from http://www.ensembl.org/info/data/ftp/index.html.
Genome Build:
1734.counts: BDGP5

source_name: S2-DRSC cells, DMSO, 20h

value: DMSO


title: JQ1_1h_RNAseq

data_processing:
Reads were aligned to the Drosophila genome release BDGP5 using the splice junction aware aligner TopHat (http://tophat.cbcb.umd.edu/) and standard parameters. Reads uniquely mapping to Drosophila gene sets (Ensembl release 64) were counted using the htseq-count script (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html#count). Gene sets in GTF format were obtained from http://www.ensembl.org/info/data/ftp/index.html.
Genome Build:
1735.counts: BDGP5

source_name: S2-DRSC cells, JQ1, 1h

value: 1 hr


title: JQ1_2h_RNAseq

data_processing:
Reads were aligned to the Drosophila genome release BDGP5 using the splice junction aware aligner TopHat (http://tophat.cbcb.umd.edu/) and standard parameters. Reads uniquely mapping to Drosophila gene sets (Ensembl release 64) were counted using the htseq-count script (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html#count). Gene sets in GTF format were obtained from http://www.ensembl.org/info/data/ftp/index.html.
Genome Build:
1736.counts: BDGP5

source_name: S2-DRSC cells, JQ1, 2h

value: 2 hrs


title: BtAdV-8h

city: Wuhan

first: Lijun

last: Wu

address: 44, Xiao hongshan street

country: China

institute: wuhan institute of virology

description: sample 3

data_processing:
Sequenced reads were generated from BtAdV infected bat cell as 49-mers using the standard Illumina GA pipeline (version 1.6).
Clean reads were mapped to both  BtAdV-TJM reference genome and M. davidii reference genome using SOAPaligner/soap2 with no more than three nucleotide mismatches allowed
RPKM method was used to  clustered BtAdV gene transcription profiles
Genome_build: BtAdV genome genebank accession no.GU226970
Supplementary_files_format_and_content: SESoap.txt alignment fiiles and RPKM of BtAdV 30 genes (RPKM_genes.txt)

organism: Myotis davidii

source_name: bat kidney cells_BtAdV-8h

growth_protocol: Cells were cultured in 3.3 cm well plate for 18 h at 37°C and maintained in RPMI 1640 medium supplemented with 15% FBS

extract_protocol:
total RNA is extracted by RNeasy Mini Kit
The mRNA was fragmented by addition of 5×fragmentation buffer after enrichment using the oligo(dT) magnetic beads. First strand cDNA was synthesized using random hexamer-primer and reverse transcriptase (Invitrogen). The second-strand cDNA was synthesized using RNase H (Invitrogen) and DNA polymerase I (New England BioLabs). The double stranded cDNA was purified by QiaQuick PCR extraction kit (Qiagen) and end repair and adenine addition were performed before the ligation of sequencing adaptors. The required fragments were purified by agrose gel electrophoresis and enriched by PCR amplification. The library products were sequenced via Illumina HiSeqTM 2000.

value: bat kidney cell

tag: infected with

value: bat adenovirus

tag: time point


title: BtAdV-18h

description: sample 5

source_name: bat kidney cells_BtAdV-18h


title: BtAdV-12h

description: sample 4

source_name: bat kidney cells_BtAdV-12h


title: Dm S2-DRSC ASH1C ChIP-seq

value: Frank Sauer, Riverside


title: Dcr2[R416X]-IIV6

description: IIV6 infected Drosophila adult Dcr2 mutant flies

value: whole organism

value: Invertebrate iridescent virus 6


title: Dm S2-DRSC ASH1N ChIP-seq


title: BtAdV-6h

description: sample 2

source_name: bat kidney cells_BtAdV-6h


title: RP Dex

status: Public on Feb 05 2013

city: Helsinki

first: Olli

middle: A.

last: Jänne

department: Inst. of Biomedicine/Physiology

country: Finland

institute: University of Helsinki

description: Chromatin IP against RNA Pol II in cells treated with 100 nM Dex

data_processing:
Alignment: Sequence reads were obtained and mapped to the human (Feb, 2009) genomes using the Illumina Genome Analyzer Pipeline (ELAND) or BOWTIE. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 400 bp to create summary windows.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/) and overlapping peaks present in both biological replicates at a 2% FDR cutoff are used for further downstream analysis.
Genome_build: hg19
Supplementary_files_format_and_content: aligned files are in BED and wig format

source_name: LNCaP-1F5 cells

growth_protocol: LNCaP-1F5 and VCaP cells were cultured in RPMI-1640 medium containing 10% fetal bovine serum (FBS), 2 mM L-glutamine, and 10 mM HEPES supplemented with antibiotics (penicillin and streptomycin).

extract_protocol: Lysates were clarified from sonicated nuclei and DNA-protein complexes were isolated with respective antibodies. Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Cells were treated with vehicle, 100 nM DHT, 1000 nM CPA, 1000 nM RU486, 1000 nM Bica or 100 nM DEX for 2 hours followed by Chromatin Immunoprecipitation. For combination experiments 100 nM DHT and 100 nM Dex were given concomittantly. CHIP antibodies: AR (Sahu et al. 2011), rat GR (Widen et al., Sahu et al. 2011), Human GR (BuGR2, Millipore and Mab-010-050, Diagenode), RNA Pol II (sc-899x, Santa Cruz), rabbit IgG (sc-2027, Santa Cruz) and mouse IgG (sc-2025, Santa Cruz).

value: Prostate epithelial cells derived from metastatic prostate carcinoma, genetically engineered to express rat glucocorticoid receptor (Cleutjens et al., 1997).

tag: passages

value: LNCaP-1F5 cells

value: 100 nM DEX

value: RNA Pol II (sc-899x, SantaCruz)

tag: chip antibody manufacturer

value: Santa Cruz

tag: chip antibody catalog #


title: DMSO_1h_RNAseq

data_processing:
Reads were aligned to the Drosophila genome release BDGP5 using the splice junction aware aligner TopHat (http://tophat.cbcb.umd.edu/) and standard parameters. Reads uniquely mapping to Drosophila gene sets (Ensembl release 64) were counted using the htseq-count script (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html#count). Gene sets in GTF format were obtained from http://www.ensembl.org/info/data/ftp/index.html.
Genome Build:
1733.counts: BDGP5

source_name: S2-DRSC cells, DMSO, 1h


title: RP DHT

description: Chromatin IP against RNA Pol II in cells treated with 100 nM DHT

tag: cell type

value: 100 nM DHT

tag: chip antibody


title: BtAdV-0h

description: sample 1

source_name: bat kidney cells_BtAdV-0h


title: AR Bica

description: Chromatin IP against AR in cells treated with 1000 nM Bica

value: 1000 nM Bica

value: AR (Kang et al. 2004; Sahu et al. 2011)


title: AR RU486 rep 2

description: Chromatin IP against AR in cells treated with 1000 nM RU486


title: AR Vehicle

description: Chromatin IP against AR in cells treated with vehicle

value: Vehicle


title: AR CPA rep2

description: Chromatin IP against AR in cells treated with 1000 nM CPA

value: 1000 nM CPA


title: AR RU486 rep1


title: AR CPA rep1


title: H3K4me2 ChIP-Seq in Cdx2 KO mouse villus cells

city: Piscataway

first: Michael

middle: P

last: Verzi

state: NJ

address: 145 Bevier Road

department: Genetics

institute: Rutgers, the State University of New Jersey

description: chromatin IP against H3K4me2 in Cdx2KO mouse villus cells

data_processing:
H3K4me2_villus_Cdx2KO_NPS_pe-5.txt; genome build: mm9
ChIP-Seq: ELAND mapping (mm9) + MACS.

growth_protocol: for ChIP-seq experiments, Villus epithelium were isolated by incubating dissected jejunm tissues with 15mm EDTA and then mechanical disruption with gentle vortexing. Villi were collected atop a 70 um filter while smaller crypts and fragments of epithelium went through. Villi were then fixed in 1% Formaldehyde for 15 minutes at 4 degrees and allowed to warm to room temperature for 35 minutes before processing chromatin for ChIP. Genomic DNA was extracted by reverse crosslinking overnight in 1%SDS 0.1M NaHCO3 buffer and collected on PCR purification columns (Qiagen). For MNase preps, villi were collected in the same fashion but not fixed and instead treated with MNase. Both approaches have been described previously by the same contributors (PMID #s: 21402776 and 21074721)

extract_protocol: Libraries were constructed from pooled ChIP experiments totaling 10-20ng of DNA using Illumina's recommended protocol

value: Mouse villus

tag: antibody

value: Millipore 07-030, lots DAM1570816 and DAM1724042

tag: type

value: ChIP DNA

tag: strain

value: 129xC57BL6 mixed background


title: H3K4me2 ChIP-Seq in Cdx2-Hnf4a D KO mouse villus cells

description: chromatin IP against H3K4me2 in Cdx2-Cdx1 D KO mouse villus cells

data_processing:
H3K4me2_villus_Cdx1Cdx2DKO_NPS_pe-5.txt; genome build: mm9
ChIP-Seq: ELAND mapping (mm9) + MACS.

value: Millipore 07-030, lots DAM1570816 and DAM1724043


title: H3K4me2 ChIP-Seq in Hnf4a KO mouse villus cells

description: chromatin IP against H3K4me2 in Hnf4aKO mouse villus cells

data_processing:
H3K4me2_villus_Hnf4aKO_NPS.txt; genome build: mm9
ChIP-Seq: ELAND mapping (mm9) + MACS.


title: Hnf4a ChIP-Seq in WT mouse villus cells

description: chromatin IP against Hnf4a in WT mouse villus cells

data_processing:
Hnf4a_villus_WT_pe-5_peaks.bed; genome build: mm9
ChIP-Seq: ELAND mapping (mm9) + MACS.

source_name: Hnf4a ChIP-Seq in WT mouse villus cells

value: HNF4α c-19 (Santa Cruz 6556, lot c1810)


title: Mouse villus cell input DNA

description: sonicated input DNA fragments

data_processing: ChIP-Seq: ELAND mapping (mm9) + MACS.

source_name: Mouse villus cell input DNA

value: input DNA


title: Hnf4a ChIP-Seq in Cdx2 KO mouse villus cells

description: chromatin IP against Hnf4a in Cdx2 KO mouse villus cells

data_processing:
Hnf4a_villus_Cdx2KO_pe-5_peaks.bed; genome build: mm9
ChIP-Seq: ELAND mapping (mm9) + MACS.


title: H3K4me2 ChIP-Seq in WT mouse villus cells

description: chromatin IP against H3K4me2 in WT mouse villus cells

data_processing:
H3K4me2_villus_WT_NPS_pe-5.txt; genome build: mm9
ChIP-Seq: ELAND mapping (mm9) + MACS.


title: CDX2 ChIP-Seq in Hnf4a KO mouse villus cells

description: chromatin IP against Cdx2 in Hnf4a KO mouse villus cells

data_processing:
Cdx2_villus_Hnf4aKO_pe-5_peaks.bed; genome build: mm9
ChIP-Seq: ELAND mapping (mm9) + MACS.


title: GR Dex 2011

description: Chromatin IP against GR in cells treated with 100 nM Dex

value: Prostate epithelial cells derived from metastatic prostate carcinoma, genetically engineered to express rat glucocorticoid receptor (Cleutjens et al., 1997).

tag: cell line

value: 100 nM Dex

value: GR (Widen et al. 2000)


title: H3K4me2 ChIP-Seq in Cdx2-Cdx1 DKO mouse villus cells

description: chromatin IP against H3K4me2 in Cdx2-Hnf4a D KO mouse villus cells

data_processing:
H3K4me2_villus_Cdx2Hnf4aDKO_NPS_pe-5.txt; genome build: mm9
ChIP-Seq: ELAND mapping (mm9) + MACS.

source_name: H3K4me2 ChIP-Seq in Cdx2-Hnf4a D KO mouse villus cells


title: AR DHT 2011

description: Chromatin IP against AR in cells treated with 100 nM DHT

value: LNCaP-1F5 cells


title: GR Dex

source_name: VCaP

value: Prostate epithelial cells derived from vertebral bone metastasis from patient with hormone refractory cancer.

value: VCaP

value: 100 nM DEX

value: GR (BuGr2, Millipore and Mab-010-050, Diagenode)

value: Millipore and Diagenode

value: BuGr2 and Mab-010-50


title: CDX2 ChIP-Seq in WT mouse villus cells

description: chromatin IP against Cdx2 in WT mouse villus cells

data_processing:
Cdx2_villus_WT_pe-5_peaks.bed; genome build: mm9
ChIP-Seq: ELAND mapping (mm9) + MACS.

source_name: CDX2 ChIP-Seq in WT mouse villus cells

value: Mouse villus


title: CDX2 ChIP-Seq in WT mouse villus cells-2

data_processing:
Cdx2_villus_WT-2_pe-5_peaks.bed; genome build: mm9
ChIP-Seq: ELAND mapping (mm9) + MACS.


title: GR DHT+Dex 2011

description: Chromatin IP against GR in cells treated with 100 nM DHT+Dex

value: 100 nM DHT+Dex


title: VCaP mIgG

description: Chromatin IP against mouse IgG

value: mIgG (sc-2025, Santa Cruz)

value: Santa Cruz


title: VCaP rIgG

description: Chromatin IP against rabbit IgG

value: 100 nM DHT

value: rIgG (sc-2027, SantaCruz)


title: AR DHT rep2

value: AR (Kang et al. 2004; Sahu et al. 2011)


title: GR Dex rep1

value: Prostate epithelial cells derived from metastatic prostate carcinoma, genetically engineered to express rat glucocorticoid receptor (Cleutjens et al., 1997).


title: AR DHT+Dex 2011

description: Chromatin IP against AR in cells treated with 100 nM DHT+Dex


title: HT-Control ChIP-Seq

data_processing:
ChIP-Seq reads were aligned to the mm9 & h18 genomes using BWA  0.5.9
peaks were called using MACS v1.4
Genome_build: mm9 & hg18
Supplementary_files_format_and_content: wig files were generated using MACS

source_name: H293T_HT Control

value: HT control


title: mIgG

description: Chromatin IP against mouse IgG


title: AR DHT rep1


title: Snyder_DPL-1_GFP_L1v2_rep2_Input_CATT

status: Public on Feb 04 2013

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

description: input DNA

data_processing: Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS220

organism: Caenorhabditis elegans

extract_protocol:
Worms are grown on peptone-enriched plates seeded with E. coli (HB101) and maintained according to standard protocol. Briefly, starved and synchronized L1s are first obtained, and then plated on peptone-enriched plates with HB101, which serves as a food source. Worms are grown at 20ºC to the desired developmental stage before harvesting. Since growth rates are frequently strain-specific, we use developmental milestones to determine developmental stages. Worms at the designed developmental stage are immediately crosslinked with 2% formaldehyde, quenched with 100 mM Tris buffer, washed with M9 buffer, and then stored at -80 as packed pellets.
The current ChIP Protocol is modified from Ercan et al., Nature Genetics 39: 403-408 (2007). Worm samples are lysed and solubilized by sonication in the presence of protease inhibitors and non-ionic detergents. The cellular debris is removed by centrifugation and the supernatant containing any formaldehyde crosslinked chromatin is saved for preparing input DNA and collecting immunocomplexes. 10% (or 50 ul) of the above supernatant from each sample is saved as input sample (control). Input sample (also known as whole cell extract) represents the total genomic DNA and is processed later (treated with RNAase A, proteinase K and reverse crosslink steps) along with the ChIPed samples to isolate genomic DNA (input DNA). The remaining supernatant is incubated with affinity-purified anti-GFP antibodies and Protein G-sepharose beads to collect the immunocomplexes containing a targeted transcription factor that is C-terminally tagged with GFP and its genomic binding fragments. Alternatively, the 8WG16 mouse monoclonal antibodies and Protein A-sepharose beads are used to collect the immunocomplexes containing RNA polymerase II. After extensive washing, any immunocomplexes are eluted and the protein-DNA crosslinks are reversed. The degree of sonication is assessed by running a small aliquot of DNA on a 2% agarose gel. Quantitative PCR is used to check if the ChIPed sample contains any of the targeted transcription factor's known genomic binding sites.
DNA fragments recovered following chromatin IP are size selected using gel electrophoresis.  The DNA is then prepared for deep sequencing using the protocols and reagents provided by Illumina.  This involves rendering the ends blunt, followed by the addition of single deoxy adenylate residues on each end.  The fragments are ligated to Illumina's propietary adapters and amplified.  After a final gel purification step the DNA is loaded into a flow cell for sequencing.

value: OP105(official name :OP105 genotype :unc119(ed3);wgIs105(dpl-1::TY1 EGFP FLAG;unc119) outcross :0 mutagen :None tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for bombardment transformation of an unc-119(ed3) strain.  The DPL-1::EGFP fusion protein has broad expression pattern description :but silence in germline cells.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the DPL-1 transcription factor. made_by :Bob Waterston's lab from UW )

tag: developmental stage

value: fed L1

tag: genotype

tag: Sex

value: Hermaphrodite


title: Snyder_DPL-1_GFP_L1v2_rep1_GFP_GTAT

description: ChIP DNA; Antibody information listed below: official name: Anti-eGFP; target name: eGFP; host: Goat; antigen: Full-length EGFP; clonal: Polyclonal; purified: Affinity; company: Lab; catalog: Hyman Goat anti-GFP; reference: PMID: 18391959; short description: A Bacterially expressed full-length EGFP protein tagged with 6xHis was used to raise a goat antisera and the resulting antibodies were affinity-purified.

data_processing: Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS220


title: Snyder_DPL-1_GFP_L1v2_rep2_GTP_CATT


title: Snyder_DPL-1_GFP_L1v2_rep1_Input_GTAT

description: input DNA


title: Snyder_Pges-1_HPL-2_YL416_L1_rep2_GFP_ACGT

data_processing: Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS220

value: YL416(official name :YL416 genotype :unc-119(ed3) III; vrIs64[pGES-1::HPL-2::GFP FLAG:HPL-2 3'-UTR genotype :unc-119 (+)] outcross :0 mutagen :None tags :GFP::3xFlag description :The HPL-2::GFP fusion protein is driven by the ges-1 promoter and is expressed in the intestine. made_by :Michelle Kudron in Reinke lab )


title: Snyder_Pges-1_LIN-35_YL398_L1_rep2_GFP_GTAT

value: YL398(official name :YL398 genotype :unc-119(ed3) III; vrIs55[pGES-1::LIN-35::GFP FLAG:LIN-35 3'-UTR genotype :unc-119 (+)] outcross :0 mutagen :None tags :GFP::3xFlag description :The LIN-35::GFP fusion protein is driven by the ges-1 promoter and is expressed in the intestine. made_by :Michelle Kudron in Reinke lab )


title: Snyder_Pges-1_HPL-2_YL416_L1_rep2_Input_ACGT

description: input DNA

value: unc-119(ed3) III; vrIs64[pGES-1::HPL-2::GFP FLAG:HPL-2 3'-UTR


title: Snyder_Pges-1_HPL-2_YL416_L1_rep1_Input_ACGT

description: input DNA


title: Snyder_SPTF-1_GFP_L1_rep1_GFP_GTAT

value: OP196(official name :OP196 genotype :unc119(ed3);wgIs196(sptf1::TY1 EGFP FLAG C;unc119) outcross :3 transgene :sptf-1 tags :Bombard tag :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The SPTF-1::EGFP fusion protein is expressed in the correct sptf-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the SPTF-1 transcription factor. made_by :S Kim )

tag: transgene


title: Snyder_LIN-35_GFP_yA_rep2_GFP_TGCT

value: YL402(official name :YL402 genotype :unc-119(ed3) III; vrIs56[pPIE-1::LIN-35::GFP FLAG:LIN-35 3'-UTR genotype :unc-119 (+)] outcross :0 mutagen :None tags :GFP::3xFlag description :The LIN-35::GFP fusion protein is driven by the pie-1 promoter. made_by :Michelle Kudron in Reinke lab )

value: Young adult


title: Snyder_SPTF-1_GFP_L1_rep2_GFP_CATT

value: unc119(ed3);wgIs196(sptf1::TY1 EGFP FLAG C;unc119)


title: Snyder_LIN-35_GFP_yA_rep1_Input_TGCT

description: input DNA

value: unc-119(ed3) III; vrIs56[pPIE-1::LIN-35::GFP FLAG:LIN-35 3'-UTR


title: Snyder_NHR-116_GFP_L4_rep2_Input_TGCT

description: input DNA

value: OP226(official name :OP226 genotype :unc119(ed3);wgIs226(nhr-116::TY1 EGFP FLAG;unc119) outcross :3 transgene :nhr-116 tags :Bombard tag :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The NHR-116::EGFP fusion protein is expressed in the correct nhr-116 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-116 transcription factor. made_by :M Sarov )


title: Snyder_Pges-1_LIN-35_YL398_L1_rep1_GFP_GTAT

value: unc-119(ed3) III; vrIs55[pGES-1::LIN-35::GFP FLAG:LIN-35 3'-UTR


title: Snyder_Pges-1_LIN-35_YL398_L1_rep1_Input_GTAT

description: input DNA


title: Snyder_Pges-1_LIN-35_YL398_L1_rep2_Input_CATT

description: input DNA


title: Snyder_NHR-116_GFP_L4_rep1_GFP_ACGT


title: Snyder_SPTF-1_GFP_L1_rep2_Input_CATT

description: input DNA


title: Snyder_NHR-116_GFP_L4_rep2_GFP_TGCT


title: Snyder_LIN-35_GFP_yA_rep1_GFP_TGCT


title: Snyder_LIN-35_GFP_yA_rep2_Input_TGCT

description: input DNA


title: Snyder_NHR-116_GFP_L4_rep1_Input_ACGT

description: input DNA


title: Snyder_NHR-77_GFP_L1_rep2_GFP_TGCT

value: OP353(official name :OP353 genotype :unc119(ed3);wgIs353(nhr-77::TY1 EGFP FLAG;unc119) outcross :3 transgene :nhr-77 tags :Bombard tag :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The NHR-77::EGFP fusion protein is expressed in the correct nhr-77 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-77 transcription factor. made_by :R Waterston )


title: Snyder_SPTF-1_GFP_L1_rep1_Input_GTAT

description: input DNA


title: Snyder_NHR-77_GFP_L1_rep1_Input_GTAT

description: input DNA


title: Snyder_ZK377.2_GFP_L4_rep2_Input_TGCT

description: input DNA

value: OP355(official name :OP355 genotype :unc-119(ed3) III; wgIs355(ZK377.2::TY1 EGFP FLAG; unc-119(+)) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Dresden using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The sax-3::EGFP fusion protein is expressed in the correct sax-3 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the sax-3 transcription factor. The sax-3 gene is encoded by the ZK377.2 CDS. made_by :R Waterston )


title: Snyder_NHR-77_GFP_L1_rep2_Input_CATT

description: input DNA


title: Snyder_ZK377.2_GFP_L4_rep1_Input_ACGT

description: input DNA


title: Snyder_Pges-1_HPL-2_YL416_L1_rep1_GFP_ACGT


title: Snyder_ZK377.2_GFP_L4_rep2_GFP_TGCT


title: Snyder_ZK377.2_GFP_L3_rep1_Input_GTAT

description: input DNA


title: Snyder_ZK377.2_GFP_L1_rep2_GFP_CATT


title: Snyder_ZK377.2_GFP_L1_rep1_GFP_GTAT


title: Snyder_LIN-15B_GFP_L1_rep2_GFP_CATT

value: OP184(official name :OP184 genotype :unc119(ed3);wgIs184(lin-15B::TY1 EGFP FLAG;unc119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The LIN-15B::EGFP fusion protein is expressed in the correct lin-15B spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the LIN-15B transcription factor. made_by :S Kim )


title: Snyder_LIN-15B_GFP_L1_rep2_Input_GTAT

description: input DNA


title: Snyder_ZK377.2_GFP_L1_rep2_Input_CATT

description: input DNA


title: Snyder_LIN-15B_GFP_L1_rep1_GFP_GTAT


title: Snyder_LIN-15B_GFP_L1_rep1_Input_CATT

description: input DNA


title: Snyder_R02D3.7_GFP_L3_rep1_GFP_CATT

value: OP218(official name :OP218 genotype :unc-119(ed3); wgIs218(R02D3.7:TY1 EGFP FLAG; unc-119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The R02D3.7::EGFP fusion protein is expressed in the correct R02D3.7 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the RO2D3.7 transcription factor. made_by :Mihail Sarov )


title: Snyder_R02D3.7_GFP_L3_rep1_Input_ACGT

description: input DNA


title: Snyder_R02D3.7_GFP_L3_rep2_GFP_ACGT


title: Snyder_ALY-2_GFP_L2_rep2_CATT

value: OP217(official name :OP217 genotype :unc-119(ed3); wgIs217(aly-2:TY1 EGFP FLAG; unc-119(+)) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Dresden using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The ALY-2::EGFP fusion protein is expressed in the correct aly-2 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ALY-2 transcription factor. made_by :Mihail Sarov )


title: Snyder_ALY-2_Input_L2_rep2_CATT

description: input DNA

value: unc-119(ed3); wgIs217(aly-2:TY1 EGFP FLAG; unc-119(+))


title: Snyder_ALY-2_Input_L2_rep1_GTAT

description: input DNA

value: Hermaphrodite


title: Snyder_NHR-77_GFP_L1_rep1_GFP_ACGT

value: fed L1


title: Snyder_ZK377.2_GFP_L3_rep2_Input_CATT

description: input DNA


title: Snyder_ZK377.2_GFP_L1_rep1_Input_GTAT

description: input DNA


title: Snyder_ALY-2_GFP_L2_rep1_GTAT


title: Snyder_F45C12.2_Input_L2_rep2_TGCT

description: input DNA

value: OP212(official name :OP212 genotype :unc119(ed3);wgIs212(F45C12.2:TY1 EGFP FLAG;unc119) outcross :3 transgene :F45C12.2 tags :Bombard tag :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The F45C12.2::EGFP fusion protein is expressed in the correct F45C12.2 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the F45C12.2 transcription factor. made_by :Mihail Sarov )


title: Snyder_F45C12.2_GFP_L2_rep2_TGCT


title: Snyder_R02D3.7_GFP_L3_rep2_Input_TGCT

description: input DNA


title: Snyder_F45C12.2_Input_L2_rep1_ACGT

description: input DNA


title: Snyder_ZK377.2_GFP_L4_rep1_GFP_ACGT


title: Snyder_ZK377.2_GFP_L3_rep2_GFP_TGCT


title: Snyder_C16A3.4_GFP_L1_rep2_CATT

value: OP345(official name :OP345 genotype :unc119(ed3);wgIs345(C16A3.4::TY1 EGFP FLAG;unc119) outcross :0 mutagen :None tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for bombardment transformation of an unc-119(ed3) strain.  The C16A3.4::EGFP fusion protein has broad expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the C16A3.4 transcription factor. made_by :Bob Waterston's lab from UW )


title: Snyder_ZK377.2_GFP_L3_rep1_GFP_ACGT


title: Snyder_C16A3.4_GFP_L1_rep1_GTAT


title: Snyder_C16A3.4_Input_L1_rep1_GTAT

description: input DNA


title: Snyder_C16A3.4_Input_L1_rep2_CATT

description: input DNA


title: Snyder_DPL-1_Input_L4_rep2_ACGT

description: input DNA

value: OP105(official name :OP105 genotype :unc119(ed3);wgIs105(dpl-1::TY1 EGFP FLAG;unc119) outcross :0 mutagen :None tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for bombardment transformation of an unc-119(ed3) strain.  The DPL-1::EGFP fusion protein has broad expression pattern description :but silence in germline cells.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the DPL-1 transcription factor. made_by :Bob Waterston's lab from UW )


title: Snyder_DPL-1_Input_L4_rep1_GTAT

description: input DNA


title: Snyder_AHA-1_Input_L4_rep1

description: input DNA

data_processing: Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS180

value: OP124(official name :OP124 genotype :unc-119(ed3); wgIs124(aha-1::TY1 EGFP FLAG;unc-119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The AHA-1::EGFP fusion protein is expressed in the correct aha-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the AHA-1 transcription factor. made_by :R. Waterston and S. Kim )


title: Snyder_AHA-1_GFP_L4_rep1

data_processing: Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS180

value: unc-119(ed3); wgIs124(aha-1::TY1 EGFP FLAG;unc-119)


title: Snyder_F45C12.2_GFP_L2_rep1_ACGT


title: Snyder_AHA-1_GFP_L4_rep2


title: Wnt3a

city: South San Francisco

first: Jinfeng

last: Liu

address: 1 DNA Way, MS93

department: Bioinformatics and Computational Biology

institute: Genentech Inc.

data_processing:
Illumina Casava1.7 software used for basecalling.
The RNA-seq reads were first aligned to ribosomal RNA sequences to remove potential ribosomal reads. The remaining reads were aligned to the human reference genome (NCBI Build 37) using GSNAP, allowing maximum of 5 mismatches per 75bp sequencing end.
To quantify the gene expression level, the number of reads mapped to the exons of each RefSeq gene was calculated, and the corresponding RPKM value (reads mapping to the genome per kilobase of transcript per million reads sequenced) was also derived.
For clustering and correlation analysis, variance-stablized expression values were derived using DEseq
Genome_build: hg19 (NCBI Build 37)

source_name: PA1 cell

growth_protocol: PA-1 cells were grown in 50:50 high-glucose DMEM and Ham's F12 with 10% FBS.

extract_protocol:
RNA was extracted with a Qiagen RNeasy kit following the standard protocol provided by the vendor.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: PA-1 cells were transfected with 8ug of pCDNA3.1 vector, RIPK1, RIPK2, RIPK3, RIPK4 for 48h, or were treated with 200ng Wnt3a for 16h.

tag: transfection

value: PA1 cell


title: RIPK1


title: Vector

value: Vector


title: RIPK3


title: RIPK4


title: RIPK2


title: NT_WT_RNAseq_rep2

city: Philadelphia

first: Robert

middle: Babak

last: Faryabi

state: Pennsylvania

address: Room 553 BRB II/III, 421 Curie Boulevard

department: Pathology

institute: University of Pennsylvania

data_processing:
Illumina Casava1.7.0 or 1.8.0 software used for basecalling.
RNA-Seq sequenced reads were mapped to mm9 using Tophat v2.0.6. Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using exons of each transcript annotated by BioConductor's GenomicFeatures 1.10.1.
Genome_build: mm9

source_name: Splenic B Cells

growth_protocol: CD43- resting B cells were isolated from mouse spleens by negative selection with magnetic beads (Miltenyi Biotech). Following isolation, resting B cells were stimulated with LPS (25 mcg/ml, Sigma) and IL-4 (5 ng/ml, Sigma) for 28 hrs.

extract_protocol: Total RNA was isolated using TRIzol (Ambion) following manufacturer's protocol. RNA was washed, purified  using RNeasy kit (Qiagen), and measured for quality. RNA was then prepared for sequencing using the TruSeq RNA sample prep kit  (Illumina).  Four libraries were sequenced on one lane of HiSeq 2000.

value: In vitro activated B Cells

value: wildtype

tag: growth duration

value: 28 hr

tag: treatment protocol

value: 0 mM hydroxyurea for 6 hrs


title: HU_WT_RNAseq_rep1

data_processing:
Illumina Casava1.7.0 or 1.8.0 software used for basecalling.
Genome_build: mm9
RNA-Seq sequenced reads were mapped to mm9 using Tophat v2.0.6. Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using exons of each transcript annotated by BioConductor's GenomicFeatures 1.10.1.

value: 10 mM hydroxyurea for 6 hrs


title: NT_WT_RNAseq_rep1


title: NT_53BP1mm_Smc5

data_processing:
Illumina Casava1.7.0 or 1.8.0 software used for basecalling.
Sequenced reads were trimmed, and masked for low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.8 determined uniquely aligned reads with at most 2 mismatches.
SICER with parameters: e-value, 100, gap size 600 (200) for RPA and γ−H2AX  (BRCA1 and SMC5) is used to find enriched bins over Poisson distribution. Then the enrichment of bins passing the first criterion was examined relative to whole-cell extract control based on FDR of 1x10-5. Subsequently, the identified enriched windows that were less than 5 kbp apart were merged to delineate islands.
Genome_build: mm9

growth_protocol: CD43- resting B cells were isolated from mouse spleens by negative selection with magnetic beads (Miltenyi Biotech). Following isolation, resting B cells were stimulated with LPS (25 mcg/ml, Sigma) and IL-4 (5 ng/ml, Sigma) for 72 hrs.

extract_protocol: Cells were fixed with 1% paraformaldehyde followed by quenching with 0.125 glycine and sonication. Chromatin fragments were then immunoprecipitated with the antibodies shown in the sample characteristics following protocols described in the manuscript. Immunoprecipitates were processed following Illumina’s protocol and sequenced on a Genome Analyzer IIx.

tag: ChIP

value: 53BP1 KO

value: 72 hr

value: Calbiochem, DR1030


title: HU_WT_RNAseq_rep2


title: Snyder_DPL-1_GFP_L4_rep2_ACGT

value: Hermaphrodite


title: NT_53BP1pp_Smc5


title: NT_53BP1pp_Brca1

value: mouse monoclonal raised against mouse BRCA1 (160-300 amino acids)


title: NT_53BP1mm_Brca1


title: wild type offspring of wild type mother

first: Miklos

last: Toth

address: 1300 York Ave. Room W-506

department: Department of Pharmacology

institute: Weill Cornell Medical College

description: Bisulfite treated, MspI digestion

data_processing:
RRBS data was received as FASTQ files from the core facility and converted to Goby compact read files (http://goby.campagnelab.org). Alignments were performed using GobyWeb (http://gobyweb.campagnelab.org) and the LAST aligner (parameters: -d 108 -e 120 –s 150) (http://last.cbrc.jp/) against the mm9 mouse reference genome.
Genome Build:
DPXSSHK-miklos-rrbs-Sample_5ht1a_wtwt-all.bedGraph: mm9

source_name: ventral dentate granule cell

extract_protocol: Protocol was performed as described in (Ref 1).  Briefly, 50ng of DNA was digested with MspI restriction enzyme.  This was followed by end repair and ligation of paired end illumina sequencing adaptors fully methylated at all cytosines.  Size selection for library sizes of 150-400 bp was perfomed followed by a single round of bisulfite treatment using the EZ DNA Methylation Kit (Zymo Research). PCR amplification using Illumina PCR PE1.0 and 2.0 was followed by product isolation using AMPure XP beads per manufacturer’s recommended protocol (Agencort). Quality control was performed using quantitation on a Qubit 2.0 fluorometer (Invitrogen) and library visualization using a Quant-iT dsDNA HS Assay Kit for (Agilent 2100 Bioanalyzer). The amplified libraries were sequenced using a 50bp single end read run on a HiSeq2000 per manufacturer’s recommended protocol. Image capture, analysis and base calling was performed using Illumina’s CASAVA 1.7.   References:  1 Altuna Akalin and Francine E. Garrett-Bakelman, Matthias Kormaksson, Jennifer Busuttil, Lu Zhang, Irina Khrebtukova, Peter JM Valk, Bob Löwenberg, Ruud Delwel, Hugo F Fernandez, Elisabeth Paietta, Martin S Tallman, Gary P. Schroth, Christopher E. Mason, Ari Melnick and Maria E. Figueroa. Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in Acute Myeloid Leukemia. Under review.

value: Swiss Webster

tag: tissue

value: hippocampus

tag: genotype/variation

value: wild type offspring of wild type mother


title: 5HT1A knock-out offspring of heterozygote mother

description: Bisulfite treated, MspI digestion

data_processing:
RRBS data was received as FASTQ files from the core facility and converted to Goby compact read files (http://goby.campagnelab.org). Alignments were performed using GobyWeb (http://gobyweb.campagnelab.org) and the LAST aligner (parameters: -d 108 -e 120 –s 150) (http://last.cbrc.jp/) against the mm9 mouse reference genome.
Genome Build:
PPOBQDA-miklos-rrbs-Sample_5ht1a_koh-all.bedGraph: mm9


title: NT_WT_DHS

extract_protocol: DNAse treated DNA was extracted and amplified according to Sekimata et al., Immunity, 31, 551-564, 2009. Library was sequenced on a Genome Analyzer IIx.

value: DHS


title: 5HT1A knock-out offspring of knock-out mother

description: Bisulfite treated, MspI digestion

data_processing:
RRBS data was received as FASTQ files from the core facility and converted to Goby compact read files (http://goby.campagnelab.org). Alignments were performed using GobyWeb (http://gobyweb.campagnelab.org) and the LAST aligner (parameters: -d 108 -e 120 –s 150) (http://last.cbrc.jp/) against the mm9 mouse reference genome.
Genome Build:
GYACOIP-miklos-rrbs-Sample_5ht1a_koko-all.bedGraph: mm9


title: wild type offspring of heterozygote mother

description: Bisulfite treated, MspI digestion

data_processing:
RRBS data was received as FASTQ files from the core facility and converted to Goby compact read files (http://goby.campagnelab.org). Alignments were performed using GobyWeb (http://gobyweb.campagnelab.org) and the LAST aligner (parameters: -d 108 -e 120 –s 150) (http://last.cbrc.jp/) against the mm9 mouse reference genome.
Genome Build:
PLKIQUC-miklos-rrbs-Sample_5ht1a_wth-all.bedGraph: mm9


title: HU_WT_Brdu_rep2

growth_protocol: CD43- resting B cells were isolated from mouse spleens by negative selection with magnetic beads (Miltenyi Biotech). Following isolation, resting B cells were stimulated with LPS (25 mcg/ml, Sigma) and IL-4 (5 ng/ml, Sigma) in media containing 10 mcM BrdU for 28 hrs.

extract_protocol: Illumina sequencing libraries were constructed from the random-primed BrdU-DNA material according to standard procedures according to Hansen et al. PNAS, 107, 139-144, 2010. Each library was sequenced on a Genome Analyzer IIx.

value: Brdu

value: GE Healthcare, RPN-202 and BD Biosciences, 347580


title: Snyder_AHA-1_Input_L4_rep2

description: input DNA

value: OP124(official name :OP124 genotype :unc-119(ed3); wgIs124(aha-1::TY1 EGFP FLAG;unc-119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The AHA-1::EGFP fusion protein is expressed in the correct aha-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the AHA-1 transcription factor. made_by :R. Waterston and S. Kim )


title: NT_WT_Brca1

value: In vitro activated B Cells


title: NT_WT_Smc5

value: wildtype


title: NT_53BP1pp_RPA

value: RPA

value: Calbiochem, RPA34-20


title: HU_WT_Smc5_rep1

value: 28 hr

value: 10 mM hydroxyurea for 6 hrs


title: NT_WT_RPA

value: 0 mM hydroxyurea for 6 hrs


title: HU_WT_Brdu_rep1


title: HU_WT_Smc5_rep2

value: Calbiochem, DR1030


title: HU_WT_Brca1_rep1


title: HU_WT_RPA_rep1


title: HU_WT_RPA_rep2


title: HU_WT_gH2AX_rep1

extract_protocol: Cells were fixed with 1% paraformaldehyde followed by quenching with 0.125 glycine and sonication. Debris was removed by centrifugation and the supernatant diluted 10-fold in immunoprecipitation buffer, protease inhibitors (EDTA-free, Roche), and phosphatase inhibitors (Cocktail II, Sigma) and incubated with antibodies overnight. The next morning, chromatin fragments were then immunoprecipitated with the antibodies shown in the sample characteristics following protocols described in the manuscript. Immunoprecipitates were processed following Illumina’s protocol and sequenced on a Genome Analyzer IIx.

value: Millipore, 05-636


title: HU_WT_Brca1_rep2

value: mouse monoclonal raised against mouse BRCA1 (160-300 amino acids)


title: HU_WT_gH2AX_rep2


title: Col-0 6-week-old leaf tissues

city: Paris

first: Emmanuelle

last: Lastrucci

address: 46 rue d'Ulm

institute: Institut de Biologie de l’Ecole Normale Supérieure

data_processing:
map to Arabidopsis genome TAIR9
keep fully matched sequences
count the number of times a sRNA mapped to the genome
create a fasta file with unique sRNA sequences
Vmatch for aligning sRNA sequences and Python for counting
Genome_build: TAIR9
Supplementary_files_format_and_content: fasta sRNA sequences

source_name: Adult leaves

growth_protocol: The plants used in this study were grown at 21-23 °C with a 8h photoperiod. The plants were first grown on plates containing Murashige and Skoog medium (Duchefa), 0.5% sucrose and 0.8% agar and then transferred to soil at 10 day-post-germination (dpg).

extract_protocol: The small RNA libraries have been prepared with the Small RNA v1.5 kit according to the manufacturer ("illumina") instructions, with the following exceptions: the size selection was done on 15-45nt fragments, the 3' adapter have been replaced by the Universal miRNA cloning linker (NEB) and the PCR  primer have been replaced by Fasteris primers in order to add index during the amplification step.

tag: ecotype

tag: age

value: 6 weeks

value: leaves


data_processing:
Fastq reads were converted to Goby compact-read files (http://goby.campagnelab.org). Alignments were perfomred with GobyWeb (http://gobyweb.campagnelab.org) and the bwa aligner.  Alignment parameters allowed for 2 mismatches over the length of a read and unique alignments.
Genome Build:
UVPUVKT-5HT1A-KO-KOKO-s5-all.wig: NCBI37.55

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA, USA).  RNA concentration was measured using NanoDrop ND-1000 (Thermo Scientific, Wilmington, DE, USA).  Following isolation total RNA integrity was checked using Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA, USA).  RNA was purified using magnetic beads and fragmented using divalent cations at high temperature.  cDNA library construction was carried out following the Illumina recommended sample preparation guide (Document 10004898 Rev. D) (Illumina, San Diego, CA, USA).  Briefly, the cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers.  Then RNaseH removed a strand of mRNA and a replacement strand synthesized to generate double-strand cDNA.  The overhangs resulting from fragmentation were converted into blunt ends using T4 DNA polymerase and E. coli DNA polymerase I Klenow fragment.  An ‘A’ base was added to the 3' end of the blunt phosphorylated DNA fragments, using the polymerase activity of Klenow fragment (3' to 5' exo minus).  Adapters were ligated to the DNA fragments, and the ligation products purified on a 2% TAE agarose gel.  Size selection for 200bp ±25bp fragments was carried out.  The Adapter-cDNA Fragments were amplified for 15 cycles of PCR.  The library was validated by checking the size, purity, and concentration of the library constructs on an Invitrogen Qubit Fluorometer using Quant-IT dsDNA HS Assay Kit and Agilent Technologies 2100 Bioanalyzer using High Sensitivity DNA Kit.  The libraries were sequenced on the Illumina GAIIx (one sample per lane) using a single end protocol for 42 cycles.

value: Swiss Webster

value: hippocampus

value: 5HT1A knock-out offspring of knock-out mother


title: wild type offspring of wild type mother

data_processing:
Fastq reads were converted to Goby compact-read files (http://goby.campagnelab.org). Alignments were perfomred with GobyWeb (http://gobyweb.campagnelab.org) and the bwa aligner.  Alignment parameters allowed for 2 mismatches over the length of a read and unique alignments.
Genome Build:
FGHSUFU-5HT1A-KO-WTWT-s5-all.wig: NCBI37.55

value: wild type offspring of wild type mother


title: Racing_heart

status: Public on Feb 03 2013

city: Shenzhen

first: tan

last: hao

state: Guangdong

address: Building No.11,Beishan Industrial Zone,Yantian District

department: Department of Science & Technology

institute: BGI-Shenzhen

data_processing:
Using the rock pigeon genome as reference, sequenced reads were aligned onto the corresponding reference using TopHat v1.0.12 with default parameters except  -p 4 -r 20 --mate-std-dev 10 -m 2 -I 100000 --solexa1.3-quals
Genome_build: BioProject PRJNA167554
WGS/SRA: SRA052637

organism: Columba livia

source_name: Racing heart

extract_protocol: For RNA-seq, poly-A+ RNA was isolated with 30 oligo-dT-coupled beads from 20 μg total RNA of each sample. First strand cDNA synthesis was performed with random hexamers and Superscript II reverse transcriptase (Invitrogen). The second strand was synthesized with E. coli DNA PolI (Invitrogen). Double stranded cDNA was purified with Qiaquick PCR purification kit (Qiagen), and sheared with a nebulizer (Invitrogen) to 100-500 bp fragments. After end repair and addition of a 3’ dA overhang the cDNA was ligated to Illumina PE adapter oligo mix, and size selected to 200±20 bp fragments by gel purification. After 15 cycles of PCR amplification the libraries were sequenced using Illumina HiSeq 2000 and the paired-end sequencing module.

tag: breed

value: Racing

value: heart


data_processing:
Fastq reads were converted to Goby compact-read files (http://goby.campagnelab.org). Alignments were perfomred with GobyWeb (http://gobyweb.campagnelab.org) and the bwa aligner.  Alignment parameters allowed for 2 mismatches over the length of a read and unique alignments.
Genome Build:
ZQPDKUJ-5HT1A-KO-WTHet-s7-all.wig: NCBI37.55

value: wild type offspring of heterozygote mother


title: Danish_Tumbler_liver

source_name: Danish Tumbler liver

value: Danish Tumbler

value: liver


data_processing:
Fastq reads were converted to Goby compact-read files (http://goby.campagnelab.org). Alignments were perfomred with GobyWeb (http://gobyweb.campagnelab.org) and the bwa aligner.  Alignment parameters allowed for 2 mismatches over the length of a read and unique alignments.
Genome Build:
HPMHHYJ-5HT1A-KO-KOHet-s8-all.wig: NCBI37.55

value: 5HT1A knock-out offspring of heterozygote mother


title: Racing_liver

source_name: Racing liver


title: Oriental_Frill_liver

source_name: Oriental Frill liver

value: Oriental Frill


title: Wild type total RNA-seq

city: New Haven

state: CT

address: 10 Amistad st

institute: Yale University

data_processing:
TotalWT_mapped.txt; genome build: UCSC dm3
We removed the linker from the sequences by using in-house program. And sequences that perfectly match the Drosophila melanogaster release 5 genome (excluding Uextra) were collected by bowtie-0.10.0.

source_name: ovary

growth_protocol: All Drosophila melanogaster strains were reared between 18 and 25 0C on yeast/molasses agar medium. The Piwi null strain used, piwi1, has been previously described (Lin and Spradling, 1997)

extract_protocol: RNA with low weight was isolated from the adult ovaries of wild type and mutant flies, using miRNA isolation kit (Ambion). Small RNAs ranging in size below 2.5S rRNA was gel purified, and small RNA libraries were prepared using small RNA sample prep kit (Illumina) according to the alternative v1.5 protocol. The clones were sequenced using Genome Analyzer II.

value: ovary

value: wild type

tag: antibody


title: Mutant IP RNA-seq

data_processing:
IPMT_mapped.txt; genome build: UCSC dm3
We removed the linker from the sequences by using in-house program. And sequences that perfectly match the Drosophila melanogaster release 5 genome (excluding Uextra) were collected by bowtie-0.10.0.

value: Piwi null (piwi1)

value: mouse anti_Myc [Cell Signaling, 9B11, cat no. 2276]


title: Danish_Tumbler_heart

source_name: Danish Tumbler heart


title: Wild type IP RNA-seq

data_processing:
IPWT_mapped.txt; genome build: UCSC dm3
We removed the linker from the sequences by using in-house program. And sequences that perfectly match the Drosophila melanogaster release 5 genome (excluding Uextra) were collected by bowtie-0.10.0.


title: Blastocyst 4

city: Davis

first: James

middle: Lee

last: Chitwood

address: 1 Shields Avenue

department: Animal Science

institute: University of California, Davis

data_processing:
Filtering for quality by Galaxy FastQC
RNA-Seq analysis using CLC Genomics Workbench Ver. 4.7
Genome_build: Btau 4.0, Btau4.2 and UMD3.1
Supplementary_files_format_and_content: Ensembl Gene ID and RPKM

organism: Bos taurus

source_name: Ovary

growth_protocol: 24 hour maturation following follicular aspiration of oocyte; IVF; and then culture in KSOM+BSA for 7 days

extract_protocol:
Arcturus Picopure (RNA)
Nugen Ovation V1 (cDNA) followed by Nugen Encore (Library)

value: blastocyst


title: Blastocyst 3


title: NT_53BP1mm_RPA

value: RPA

tag: cell type

value: In vitro activated B Cells

value: 53BP1 KO

value: 72 hr

tag: chip antibody

value: Calbiochem, RPA34-20

value: 0 mM hydroxyurea for 6 hrs


title: Blastocyst 2


title: Blastocyst 1


title: Blastocyst 5