title: PND_28_1

value: PND 28


title: Ribo_primerset2

status: Public on Apr 29 2013

type: SRA

city: la jolla

first: vipul

last: bhargava

state: California

address: 9500 gilman drive

country: USA

institute: ucsd

library_source: transcriptomic

data_processing:
Illumina Casava1.4 - SFM, SB, AA3, AA15, AA15_2,AA100,SFM_2
Illumina Casava1.7 - Ribo_primerset2, Ribo_primerset3
Illumina Casava1.8 - all rest of the samples
Sequence reads obtained from Illumina Genome Analyzer Iix were trimmed of first 2 and last 2 bases and mapped to mus musculus REFSEQ database using in-house mapping code allowing upto 2 mismatches
Sequence reads obtained from Illumina HiSEQ2000 were trimmed of first 14 bps (except for 10pg_TR2, 1pg_TR1 and 1pg_TR2) and next 32 bps were used for mapping with mus musculus REFSEQ database using in-house mapping code allowing upto 2 mismatches
Sequence reads obtained from Illumina HiSEQ2000 were trimmed of first 7 bps for 10pg_TR2, 1pg_TR1 and 1pg_TR2 and next 32 bps were used for mapping with mus musculus REFSEQ database using in-house mapping code allowing upto 2 mismatches
Genome_build: mus musculus REFSEQ database of RNA
Supplementary_files_format_and_content: tab-delimited text files include REFSEQ gene id and Unique Reads

molecule: total RNA

organism: Mus musculus

source_name: embryoid body

growth_protocol: Differentiating ESCs were grown in serum free conditions.

extract_protocol: Day 4 embroid bodies treated with either Activin A or SB-431542 compound were harvest and total RNA was extracted for each sample. Later mRNA was isolated from each sample and single stranded cDNA was prepared. Sequencing libraries were generated by using our DP-seq strategy which involved generation of the amplicon library from defined heptamer primers based amplification. Std. RNA-seq libraries were prepared as described by Mortazavi et al. (2008). SMARTseq libraries were prepared as described by Ramsköld et al. 2012. 13 cycles of uniform cDNA amplifications were performed and the amplified libraries were verified on high sensitivity Bioanalyzer.

treatment_protocol: At day2 of differentiation, embryoid bodies were dispersed and treated with either Activin A or SB-431542 compound for two days.

tag: tissue

value: embryo

tag: developmental stage

value: day 4 of differentiation

tag: treatment

value: addition of Activin A (3ng/mL), mRNA~500pg; Library prepared using Primer set2 for suppression of ribosomal transcript.


title: PND_7_2b

city: Jokioinen

first: Anu

last: Sironen

address: Myllytie 1

department: Biotechnology and Food Research

country: Finland

institute: Agrifood Research Finland

data_processing:
Sequence reads were obtained and mapped to the  Mus musculus (mm9) genome using SOLiD Lifescope v2.1 software with default settings.
Genome_build: mm9
Supplementary_files_format_and_content: .tab files report Counts and RPKM values.

source_name: testis

extract_protocol: Total RNA was extracted from the mouse testis at post natal days 7, 14, 17, 21 and 28 with RNeasy Midi kit (Qiagen). The libraries were constructed following the SOLiD™ Total RNA-Seq Kit's (Whole Transcriptome library) protocol, Applied Biosystems Part Number 4452437 Rev A, 01/2010

tag: time

value: PND 7

value: testis


title: PND_14_2

value: PND 14


title: PND_7_1b


title: SFM_2

value: control sample + spiked in Yeast transcripts


title: PND_7_2a


title: AA100

value: addition of Activin A (100ng/mL)


title: AA15_2

value: addition of Activin A (15ng/mL) technical replicate 2


title: PND_7_1a


title: H10

city: Atlanta

first: Yuhong

last: Fan

state: Georgia

address: IBB 2313, 315 Ferst Drive

department: School of Biology and the Petit Institute for Bioengineering and Bioscience

institute: Georgia Institute of Technology

library_source: genomic

data_processing:
Sequencing was performed with Illumina Genome Analyzer II and Illumina HiSeq 2000 systems. Raw sequence reads containing more than 30% of 'N' were removed and adaptor sequences were trimmed.
Clean sequences were aligned against mouse genome mm9 using Bowtie aligner software
IP-IN signals were calculated by subtraction of tag counts/100bp window/10 million mappable reads of ChIP-seq library (IP) by that of its corresponding input-seq library (IN) using GenPlay software.
aligned.bed files were generated from bowtie alignment. IP-IN.bed and IP-IN.wig files were obtained from Genplay software.
Genome_build: mm9
Supplementary_files_format_and_content: IP-IN.wig files

molecule: genomic DNA

source_name: Embryonic stem cells

growth_protocol: ESCs were cultured on mitotically inactivated mouse embryonic fibroblasts feeder layers in ESC media consisted of DMEM supplemented with 15% FBS, non-essential amino acids, β-mercaptoethanol, nucleotides and LIF.

extract_protocol:
Soluble chromatin lysates were extracted from sonicated nuclei and protein-DNA complexes were immunoprecipitated with antibody.
The libraries were prepared from 10 ng of immunoprecipiated DNA or input DNA using Illumina ChIP-seq Sample Preparation Kit and purified with a Qiagen DNA Isolation column.

tag: cell type

value: Embryonic stem cells

tag: strain

tag: passages

tag: epitope tagged protein

value: express FLAG-H10

tag: chip antibody

value: FLAG (Sigma, F3165)


title: H1d-Trans-2

value: FLAG-H1d Knock-in


title: H1d-Trans-1


title: AA15

value: addition of Activin A (15ng/mL) technical replicate 1


title: H3K9me3-3


title: H3K9me3-2


title: AA3

value: addition of Activin A (3ng/mL)


title: H3K9me3-1


title: SB

value: addition of SB-431542


title: H1c-2

value: Myc-H1c Knock-in

value: Myc (Cell Signaling, 2272)


title: H1c-1


title: H1d-4


title: SFM

value: embryo

value: day 4 of differentiation

value: control sample


title: H1d-3


title: H1d-1


title: PND_14_1

value: testis


title: Input-b


title: H3-ChIP  + calcipotriol +TGFb

city: La Jolla

first: Ruth

middle: T

last: Yu

state: CA

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

data_processing:
Alignment: Sequence reads were obtained using the Illumina Genome Analyzer Pipeline 1.7 and mapped to the human genome (hg18, NCBI Build 36.1) using Bowtie. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 200 bp to create summary windows.
Peaks: Peak detection was performed with the HOMER software suite (http://biowhat.ucsd.edu/homer/).
Genome_build: hg18
Supplementary_files_format_and_content: bowtie files are alignments made from fastq files with the Bowtie aligner; bedGraph files were generated on Homer and can be visualized on the UCSC genome browser; peak files were generated using Homer.

organism: Homo sapiens

source_name: human LX2 cells

growth_protocol: LX-2 cells were cultured as described by Xu, L., Hui, A.Y., Albanis, E., Arthur, M.J., O'Byrne, S.M., Blaner, W.S., Mukherjee, P., Friedman, S.L., and Eng, F.J. (2005). Human hepatic stellate cell lines, LX-1 and LX-2: new tools for analysis of hepatic fibrosis. Gut 54, 142-151.

extract_protocol: Standard Illumina DNA library construction

treatment_protocol: LX-2 cells were pretreated with 1,25(OH)2D3 (100nM) for 16 hours followed by incubation of 1,25(OH)2D3 (100nM) or TGFβ1 (1ng/ml) for another 4 hours.

value: human hepatic stellate cells

tag: cell line

value: 100nM calcipotriol + 1ng/ml TGFb

tag: chip antibody manufacturer

value: Abcam

tag: chip antibody catalog #


title: H1d-2


title: H3-ChIP  + calcipotriol

value: 100nM calcipotriol


title: VDR-ChIP + TGFb

value: VDR

value: 1ng/ml TGFb

value: Santa Cruz

tag: chip antibody lot #


title: SMARTseq_AA3_TR1

value: addition of Activin A (3ng/mL), mRNA amount 50pg; library prepared using SMARTseq protocol; Technical Replicate 1


title: SMARTseq_AA100_TR2

value: addition of Activin A (100ng/mL), mRNA amount 50pg; library prepared using SMARTseq protocol; Technical Replicate 2


title: Dpseq_AA100_TR1

value: addition of Activin A (100ng/mL), mRNA amount 50pg; library prepared using original (44) primer set; Technical Replicate 1


title: Dpseq_AA3

value: addition of Activin A (3ng/mL), mRNA amount 50pg; library prepared using original (44) primer set.


title: SMAD3-ChIP +  TGFb


title: SMARTseq_AA3_TR2

value: addition of Activin A (3ng/mL), mRNA amount 50pg; library prepared using SMARTseq protocol; Technical Replicate 2


title: SMAD3-ChIP + calcipotriol + TGFb


title: A100_std_RNASEQ

value: addition of Activin A (100ng/mL), mRNA=20ng;Standard RNA-seq


title: Ribo_primerset1

value: embryo

value: addition of Activin A (3ng/mL), mRNA~500pg; Library prepared using Primer set1 for suppression of ribosomal transcript.


title: PND_28_2

value: PND 28


title: 20ng_std_RNASEQ_TR2

value: day 4 of differentiation

value: addition of Activin A (3ng/mL), mRNA=20ng;Standard RNA-seq; Technical replicate 2


title: 20ng_std_RNASEQ_TR1

value: addition of Activin A (3ng/mL), mRNA=20ng; Standard RNA-seq; Technical replicate 1


title: 1pg_TR2

value: addition of Activin A (3ng/mL), mRNA amount 1pg; Technical replicate 2


title: VDR-ChIP + calcipotriol

value: human hepatic stellate cells

value: 100nM calcipotriol


title: VDR-ChIP + calcipotriol +TGFb

value: VDR

value: 100nM calcipotriol + 1ng/ml TGFb


title: 1pg_TR1

value: addition of Activin A (3ng/mL), mRNA amount 1pg; Technical replicate 1


title: input


title: PE_lib

value: addition of Activin A (3ng/mL), mRNA amount about 100pg; DP-seq paired end library; average insert length =150bp


title: 50pg_TR2

value: addition of Activin A (3ng/mL), mRNA amount 50pg; Technical replicate 2


title: VDR-ChIP

value: Santa Cruz


title: SMARTseq_AA100_TR1

value: addition of Activin A (100ng/mL), mRNA amount 50pg; library prepared using SMARTseq protocol; Technical Replicate 1


title: H3K27me3-2

value: Embryonic stem cells

value: H3K27me3 (Millipore, 07-449)


title: 10pg_TR1

value: embryo

value: addition of Activin A (3ng/mL), mRNA amount 10pg; Technical replicate 1


title: H3K27me3-1


title: 10pg_TR2

value: day 4 of differentiation

value: addition of Activin A (3ng/mL), mRNA amount 10pg; Technical replicate 2


title: 100pg_TR1

value: addition of Activin A (3ng/mL), mRNA amount 100pg; Technical replicate 1


title: Dpseq_AA100_TR2

value: addition of Activin A (100ng/mL), mRNA amount 50pg; library prepared using original (44) primer set; Technical Replicate 2


title: 1ng_TR2

value: addition of Activin A (3ng/mL), mRNA amount 1ng; Technical replicate 2


title: H3K4me3-2

value: H3K4me3 (Millipore, 07-473)


title: 100pg_TR2

value: addition of Activin A (3ng/mL), mRNA amount 100pg; Technical replicate 2


title: BM Gata1 ChIP-Seq

city: RTP

first: Raja

last: Jothi

state: NC

address: 111 TW Alexander Drive; A314

department: National Institute of Environmental Health Sciences

institute: National Institutes of Health

description: Chromatin IP against Gata1

data_processing:
Sequence reads were mapped to the mouse genome (mm8) using the Solexa Analysis Pipeline. The mapped reads for Ldb1, Scl/Tal1, and Gata1 samples were processed using the SISSRs peak-finder (Jothi et al, Nucl Acids Res 2008; PMID: 18684996) with control IgG reads as background and default parameters to identify genome-wide binding sites
Genome_build: mm8
Supplementary_files_format_and_content: BED files containign mapped reads; TEXT files containing the list of binding sites as defined by SISSRS [PMID: 18684996]

source_name: Total bone marrow

extract_protocol:
Freshly isolated bone marrow cells were crosslinked with formaldehyde and sonicated to generate chromatin fragment
Freshly isolated bone marrow cells were crosslinked with formaldehyde and sonicated to generate chromatin fragments, which were immunoprecipitated with Ldb1, Scl/Tal1, Gata1 or control IgG antibody. The DNA fragments were end-repaired and processed for sequencing on an Illumina Genome Analyzer using standard protocols.

value: bone marrow cells

value: Abcam


title: 10ng_TR2

value: addition of Activin A (3ng/mL), mRNA amount 10ng; Technical replicate 2


title: H3K4me3-1


title: Input-a


title: BM Control IgG ChIP-Seq

description: Chromatin IP against IgG

value: IgG


title: BM Ldb1 ChIP-Seq

description: Chromatin IP against Ldb1

value: Santa Cruz


title: BM Scl/Tal1 ChIP-Seq

description: Chromatin IP against Scl/Tal1


title: 10ng_TR1

value: addition of Activin A (3ng/mL), mRNA amount 10ng; Technical replicate 1


title: POU5F1_enzyme_replicate2_4C-Seq

status: Public on Apr 28 2013

city: Los Angeles

first: Fan

last: Gao

address: 1501 San Pablo St. ZNI 245

department: ZNI

institute: USC

data_processing:
Library strategy: 4C-Seq
For enzyme-based data, the sequencing reads with 5’ end aligned to the forward inverse PCR primer sequence were selected. The rest part of the selected reads (including HindIII sites) was mapped to the mm9 assembly using BWA to locate ligation sites in the genome. The mapped ligated HindIII sites were further matched to a reduced genome with the locations of all HindIII sites included.
A statistical model was built to identify interacting regions that exhibit a higher frequency of interactions with the bait than expected from random collision of the chromosomes.
Enriched interacting regions that overlap between replicate data were considered reproducible, and the identified 4C sites within the reproducible regions were further analyzed.
Genome_build: mm9
Supplementary_files_format_and_content: bed format with coordinates of distal interacting sites of Pou5f1 enhancer
Sequencing reads with the 5' end aligned to the forward PCR primer sequence were selected. The remaining part of the selected reads (including the HindIII sites) were mapped to the mm9 assembly using BWA to locate ligation sites in the genome. The mapped ligated HindIII sites were further matched to a reduced genome including locations of all HindIII sites. For statistical analysis, to define non-random long-range intrachromosomal interactions, we used a window size of 100 potential enzyme cutting sites and permutated the data 100 times to calculate FDR. To define interchromosomal interactions, we randomly permuted the data set 100 times with a window size of 500 to calculate FDR. The final processed bed file GSM1103986_Pou5f1_interact_domains2.bed.gz reported the genomic regions (windows) with FDR values no more than 0.05.

source_name: ES cells

growth_protocol: Mouse embryonic stem (ES) cell line E14 was grown in the culture dishes coated with 0.1% gelatin. A growth medium with Glasgow Minimum Essential Medium (GMEM) supplemented with 15% fetal bovine serum (FBS), 100 nM nonessential amino acids, 1% sodium pyruvate, 200 mM glutamate, 1% penicillin streptomycin, 50uM b-mercaptoethanol and 10 ng/mL LIF was replaced every 24 hours to support ES cell growth.

extract_protocol:
Triton X100 buffer (0.25% Triton X100, 10mM EDTA pH=8.0, 10mM Tris-HCl pH=8.0, 100mM NaCl, 1x protease inhibitor cocktail) to extract chromatins
For enzyme-based 4C library preparation, two rounds of enzyme digestions were carried out using HindIII and DpnII restriction enzymes respectively. The experimental procedure strictly followed a published protocol [PMID: 22609568].

treatment_protocol: 10 million cells were cross-linked with 1% fresh formaldehyde in the cell culture dishes

value: ES cells


title: POU5F1_enzyme_replicate1_4C-Seq

data_processing:
Library strategy: 4C-Seq
For enzyme-based data, the sequencing reads with 5’ end aligned to the forward inverse PCR primer sequence were selected. The rest part of the selected reads (including HindIII sites) was mapped to the mm9 assembly using BWA to locate ligation sites in the genome. The mapped ligated HindIII sites were further matched to a reduced genome with the locations of all HindIII sites included.
A statistical model was built to identify interacting regions that exhibit a higher frequency of interactions with the bait than expected from random collision of the chromosomes.
Enriched interacting regions that overlap between replicate data were considered reproducible, and the identified 4C sites within the reproducible regions were further analyzed.
Genome_build: mm9
Supplementary_files_format_and_content: bed format with coordinates of distal interacting sites of Pou5f1 enhancer
Sequencing reads with the 5' end aligned to the forward PCR primer sequence were selected. The remaining part of the selected reads (including the HindIII sites) were mapped to the mm9 assembly using BWA to locate ligation sites in the genome. The mapped ligated HindIII sites were further matched to a reduced genome including locations of all HindIII sites. For statistical analysis, to define non-random long-range intrachromosomal interactions, we used a window size of 100 potential enzyme cutting sites and permutated the data 100 times to calculate FDR. To define interchromosomal interactions, we randomly permuted the data set 100 times with a window size of 500 to calculate FDR. The final processed bed file GSM1103985_Pou5f1_interact_domains1.bed.gz reported the genomic regions (windows) with FDR values no more than 0.05.


title: POU5F1_sonication_replicate1_4C-Seq

data_processing:
For sonication-based data, BWA was employed with "samse" option for aligning two end-tags (20bp) separately to mm9 assembly. Alignment files for both ends were further merged using SAMtools, followed by a PERL script to select only uniquely aligned read pairs (BWA mapping score ≥1), where one end aligned to the bait region and the other end aligned to other regions. Finally, tags within a 100bp range were merged as a unique interacting site. Singlet interacting sites were considered as background noise and removed.
For enzyme-based data, the sequencing reads with 5’ end aligned to the forward inverse PCR primer sequence were selected. The rest part of the selected reads (including HindIII sites) was mapped to the mm9 assembly using BWA to locate ligation sites in the genome. The mapped ligated HindIII sites were further matched to a reduced genome with the locations of all HindIII sites included.
A statistical model was built to identify interacting regions that exhibit a higher frequency of interactions with the bait than expected from random collision of the chromosomes.
Enriched interacting regions that overlap between replicate data were considered reproducible, and the identified 4C sites within the reproducible regions were further analyzed.
Genome_build: mm9
Supplementary_files_format_and_content: bed format with coordinates of distal interacting sites of POU5F1 enhancer

extract_protocol:
Triton X100 buffer (0.25% Triton X100, 10mM EDTA pH=8.0, 10mM Tris-HCl pH=8.0, 100mM NaCl, 1x protease inhibitor cocktail) to extract chromatins
For sonication-based 4C library preparation, the isolated chromatin pellets were re-suspended in SDS lysis buffer (1% SDS, 5mM EDTA pH=8.0, 50mM Tris-HCl pH=8.0, 1x protease inhibitor cocktail) and sonicated to an average size of 500 bp. The diluted chromatin fragments were blunt-end repaired and ligated with T4 ligase for 24 hours at 4°C, followed by reverse crosslinking at 65°C for 20 hours with proteinase K. The purified DNA served as PCR template for 4C library construction. After nested PCR amplification for library construction, the purified PCR products (majority with size ranging from 500bp to 1kb) were further sonicated to small DNA fragments with an average size of 200 bp for sequencing.
For enzyme-based 4C library preparation, two rounds of enzyme digestions were carried out using HindIII and DpnII restriction enzymes respectively. The experimental procedure strictly followed a published protocol [PMID: 22609568].

tag: 4c protocol

value: sonication


title: POU5F1_sonication_replicate2_4C-Seq


title: 50pg_TR1

value: embryo

value: addition of Activin A (3ng/mL), mRNA amount 50pg; Technical replicate 1


title: Fine Sliced Embryo 7 slice 13

status: Public on Apr 27 2013

city: Stanford

first: Peter

middle: Acuña

last: Combs

address: Gilbert Rm 309, 371 Serra Mall

department: Biology

institute: Stanford University

description: 25um slice of D. melanogaster pooled with  S. cerevisiae Index Barcode 2

data_processing:
Bases were called using HiSeq Control Software v1.8 and Real Time Analysis v2.8.
Reads were aligned to concatenated D.melanogaster and carrier species reference genomes using Tophat v.2.0.6, tophat -p8 --no-novel-juncs --read-edit-dist 6 --report-secondary-alignments
Aligned reads were filtered using custom software (http://github.com/petercombs/EisenLab-Code/)
Only unambiguous D. melanogaster reads were used for FPKM estimation and differential expression calling using Cufflinks and Cuffdiff v2.0.2
Genome_build: FlyBase FB2012_05
Supplementary_files_format_and_content: genes.cuff: cuffdiff generated FPKM_tracking files for the combined replicates

organism: Drosophila melanogaster

source_name: Cryo-sliced embryo

growth_protocol: embryos were collected, fixed in methanol, imaged under a light microscope, and selected at various time points between stage 2 and late stage 5

extract_protocol:
25 um transverse sections of embryos were taken, then RNA was extracted in TRIzol.
Total RNA was pooled with total RNA from a yeast culture (S. cerevisiae or T. delbruckii). RNA libraries were prepared for sequencing using standard barcoded Illumina TruSeq protocols, scaling all reactions by half

treatment_protocol: Selected embryos were dyed with bromophenol blue, aligned, submerged in TFM, and flash-frozen in LN2.

value: Canton S

tag: sample type


title: Fine Sliced Embryo 7 slice 11

description: 25um slice of D. melanogaster pooled with  T. delbruckii Index Barcode 27


title: Fine Sliced Embryo 7 slice 10

description: 25um slice of D. melanogaster pooled with  T. delbruckii Index Barcode 25


title: Fine Sliced Embryo 7 slice 8

description: 25um slice of D. melanogaster pooled with  T. delbruckii Index Barcode 22


title: Fine Sliced Embryo 7 slice 9

description: 25um slice of D. melanogaster pooled with  T. delbruckii Index Barcode 23


title: 1ng_TR1

value: day 4 of differentiation

value: addition of Activin A (3ng/mL), mRNA amount 1ng; Technical replicate 1


title: Fine Sliced Embryo 7 slice 4

description: 25um slice of D. melanogaster pooled with  T. delbruckii Index Barcode 18


title: Fine Sliced Embryo 7 slice 3

description: 25um slice of D. melanogaster pooled with  T. delbruckii Index Barcode 16


title: Fine Sliced Embryo 7 slice 7

description: 25um slice of D. melanogaster pooled with  T. delbruckii Index Barcode 21


title: Fine Sliced Embryo 7 slice 2

description: 25um slice of D. melanogaster pooled with  T. delbruckii Index Barcode 15


title: Fine Sliced Embryo 7 slice 5

description: 25um slice of D. melanogaster pooled with  T. delbruckii Index Barcode 19


title: Fine Sliced Embryo 6 slice 10

description: 25um slice of D. melanogaster pooled with  T. delbruckii Index Barcode 10


title: Fine Sliced Embryo 7 slice 1

description: 25um slice of D. melanogaster pooled with  T. delbruckii Index Barcode 14


title: Fine Sliced Embryo 6 slice 9

description: 25um slice of D. melanogaster pooled with  T. delbruckii Index Barcode 9


title: Fine Sliced Embryo 6 slice 13

description: 25um slice of D. melanogaster pooled with  T. delbruckii Index Barcode 13


title: Fine Sliced Embryo 6 slice 12

description: 25um slice of D. melanogaster pooled with  T. delbruckii Index Barcode 12


title: Fine Sliced Embryo 6 slice 6

description: 25um slice of D. melanogaster pooled with  T. delbruckii Index Barcode 6


title: Fine Sliced Embryo 6 slice 8

description: 25um slice of D. melanogaster pooled with  T. delbruckii Index Barcode 8


title: Fine Sliced Embryo 6 slice 7

description: 25um slice of D. melanogaster pooled with  T. delbruckii Index Barcode 7


title: Fine Sliced Embryo 6 slice 4

description: 25um slice of D. melanogaster pooled with  T. delbruckii Index Barcode 4


title: Fine Sliced Embryo 6 slice 3

description: 25um slice of D. melanogaster pooled with  T. delbruckii Index Barcode 3


title: V6.5_H3K4me3_ChIP-Seq

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: mm8
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.

source_name: Chromatin IP against H3K4 (10^6)

growth_protocol: V6.5 (C57BL/6-129) murine ES cells were grown under typical ES conditions on irradiated mouse embryonic fibroblasts (MEFs). For location analysis, cells were grown for two passages off of MEFs, on gelatinized tissue-culture plates.

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

tag: antibody catalog number

value: Abcam AB8580

value: V6.5 embryonic stem cells


title: Fine Sliced Embryo 7 slice 12

description: 25um slice of D. melanogaster pooled with  S. cerevisiae Index Barcode 1


title: Fine Sliced Embryo 6 slice 2

description: 25um slice of D. melanogaster pooled with  T. delbruckii Index Barcode 2


title: Fine Sliced Embryo 6 slice 11

description: 25um slice of D. melanogaster pooled with  T. delbruckii Index Barcode 11


title: Fine Sliced Embryo 6 slice 5

description: 25um slice of D. melanogaster pooled with  T. delbruckii Index Barcode 5


title: Fine Sliced Embryo 6 slice 1

description: 25um slice of D. melanogaster pooled with  T. delbruckii Index Barcode 1


title: Fine Sliced Embryo 5 slice 8

description: 25um slice of D. melanogaster pooled with  S. cerevisiae Index Barcode 2


title: Fine Sliced Embryo 7 slice 6

description: 25um slice of D. melanogaster pooled with  T. delbruckii Index Barcode 20


title: Fine Sliced Embryo 5 slice 10

description: 25um slice of D. melanogaster pooled with  S. cerevisiae Index Barcode 4


title: Fine Sliced Embryo 5 slice 7

value: 25um slice of D. melanogaster pooled with  S. cerevisiae Index Barcode 1


title: Fine Sliced Embryo 5 slice 9

description: 25um slice of D. melanogaster pooled with  S. cerevisiae Index Barcode 3


title: Fine Sliced Embryo 4 slice 15

description: 25um slice of D. melanogaster pooled with  S. cerevisiae Index Barcode 19


title: Fine Sliced Embryo 5 slice 6

description: 25um slice of D. melanogaster pooled with  S. cerevisiae Index Barcode 27


title: Fine Sliced Embryo 5 slice 5

description: 25um slice of D. melanogaster pooled with  S. cerevisiae Index Barcode 25


title: Fine Sliced Embryo 5 slice 3

description: 25um slice of D. melanogaster pooled with  S. cerevisiae Index Barcode 22


title: Fine Sliced Embryo 5 slice 4

description: 25um slice of D. melanogaster pooled with  S. cerevisiae Index Barcode 23


title: Fine Sliced Embryo 5 slice 2

description: 25um slice of D. melanogaster pooled with  S. cerevisiae Index Barcode 21


title: Fine Sliced Embryo 4 slice 13

description: 25um slice of D. melanogaster pooled with  S. cerevisiae Index Barcode 16


title: Fine Sliced Embryo 4 slice 14

description: 25um slice of D. melanogaster pooled with  S. cerevisiae Index Barcode 18


title: Fine Sliced Embryo 5 slice 1

description: 25um slice of D. melanogaster pooled with  S. cerevisiae Index Barcode 20


title: Fine Sliced Embryo 4 slice 11

description: 25um slice of D. melanogaster pooled with  S. cerevisiae Index Barcode 14


title: Fine Sliced Embryo 4 slice 12

description: 25um slice of D. melanogaster pooled with  S. cerevisiae Index Barcode 15


title: Fine Sliced Embryo 4 slice 10

description: 25um slice of D. melanogaster pooled with  S. cerevisiae Index Barcode 13


title: Fine Sliced Embryo 3 slice 11

value: 25um slice of D. melanogaster pooled with  S. cerevisiae Index Barcode 15


title: Fine Sliced Embryo 3 slice 10

value: 25um slice of D. melanogaster pooled with  S. cerevisiae Index Barcode 14


title: Fine Sliced Embryo 4 slice 1

value: 25um slice of D. melanogaster pooled with  S. cerevisiae Index Barcode 4


title: Fine Sliced Embryo 4 slice 8

description: 25um slice of D. melanogaster pooled with  S. cerevisiae Index Barcode 11


title: Fine Sliced Embryo 4 slice 7

description: 25um slice of D. melanogaster pooled with  S. cerevisiae Index Barcode 10


title: Fine Sliced Embryo 4 slice 9

description: 25um slice of D. melanogaster pooled with  S. cerevisiae Index Barcode 12


title: Fine Sliced Embryo 4 slice 4

description: 25um slice of D. melanogaster pooled with  S. cerevisiae Index Barcode 7


title: Fine Sliced Embryo 3 slice 9

value: 25um slice of D. melanogaster pooled with  S. cerevisiae Index Barcode 13


title: Fine Sliced Embryo 4 slice 6

description: 25um slice of D. melanogaster pooled with  S. cerevisiae Index Barcode 9


title: Fine Sliced Embryo 4 slice 3

description: 25um slice of D. melanogaster pooled with  S. cerevisiae Index Barcode 6


title: Fine Sliced Embryo 4 slice 2

description: 25um slice of D. melanogaster pooled with  S. cerevisiae Index Barcode 5


title: Fine Sliced Embryo 4 slice 5

description: 25um slice of D. melanogaster pooled with  S. cerevisiae Index Barcode 8


title: Fine Sliced Embryo 3 slice 8

value: 25um slice of D. melanogaster pooled with  S. cerevisiae Index Barcode 12


title: Fine Sliced Embryo 3 slice 5

value: 25um slice of D. melanogaster pooled with  S. cerevisiae Index Barcode 9


title: Fine Sliced Embryo 3 slice 4

value: 25um slice of D. melanogaster pooled with  S. cerevisiae Index Barcode 8


title: Fine Sliced Embryo 3 slice 2

value: 25um slice of D. melanogaster pooled with  S. cerevisiae Index Barcode 6


title: Fine Sliced Embryo 3 slice 3

value: 25um slice of D. melanogaster pooled with  S. cerevisiae Index Barcode 7


title: Fine Sliced Embryo 3 slice 1

value: embryo

value: 25um slice of D. melanogaster pooled with  S. cerevisiae Index Barcode 5


title: Fine Sliced Embryo 3 slice 6

value: Canton S

value: 25um slice of D. melanogaster pooled with  S. cerevisiae Index Barcode 10


title: Fine Sliced Embryo 2 slice 9

value: 25um slice of D. melanogaster pooled with  S. cerevisiae Index Barcode 11


title: Fine Sliced Embryo 2 slice 10


title: Fine Sliced Embryo 2 slice 11


title: Fine Sliced Embryo 2 slice 8


title: Fine Sliced Embryo 2 slice 7


title: hom_CG5508_ovaries_RNAseq

city: Cold Spring Harbor

first: Vasily

last: Vagin

state: NY

address: 1 Bungtown Rd

institute: Cold Spring Harbor

data_processing:
first 8 nucleotides from 5'end  were trimmed and reverse-complemented before genomic mapping
DESeq was used according to (Anders and Huber 2010, Genome Biol 11: R106.) 28nt reads were mapped to the Drosophila melanogaster genome assembly.with TopHat (v1.4.1)
Custom Bowtie index (Bowtie v0.12.8) based on Drosophila annotated transcripts from Flybase release dmel-r5.43 for genes, transposable elements and a set of 20 piRNA clusters (Malone et al. 2009, Cell)
We calculated reads counts using bedtools (Quinlan and Hall 2010, Bioinformatics 26: 841-842) and identified significantly differentially expressed (p<0.10) candidates using DESeq v1.8.2 Anders and Huber 2010, Genome Biol 11: R106.)
We used a cutoff of at least 10 normalized reads per library and FDR<0.1 for deferentially expressed transcripts in the CG5508 mutant
Genome_build: Release 5 (dm3)
Supplementary_files_format_and_content: Results of DESeq analysis only for transcripts which are deferentially expressed between homozygous and heterozygous CG5508 mutant, files include fold change in raw counts normalized according to DESeq protocol (Anders and Huber 2010, Genome Biol 11:R106)  (up- (fold change<0) or down-regulated (fold change>0)) and p-values

source_name: ovaries

growth_protocol: Fly stocks were maintained at 25 ºC in standard conditions

extract_protocol:
total RNA
Transcriptome libraries were prepared according  (Armour et al. 2009, Nat Methods 6: 647-649) using not-so-random priming (NSR) for sequencing using standard Illumina protocols

value: ovaries

tag: age

value: 3-5 days old flies

value: homozygous z3-5967 (GC5508 mutant)


title: hom_CG5508_ovaries_smallRNA

description: 19-28 nt size fractionated RNA

data_processing:
clip 3' end adaptor GATCGGTACAGTTGCAGTAAGAGC, keep reads with min length 15nt
collapse reads
remove low-complexity reads and artifacts
map to genome
Genome_build: Release 5 (dm3)
Supplementary_files_format_and_content: tabular files with all mappers, their reads number and genomic annotation

extract_protocol:
total RNA was size selected (19-28nt)
libraries were prepared according (Malone et al. Cold Spring Harb Protoc. 2012 )

tag: tissue


title: het_CG5508_ovaries_RNAseq

value: heterozygous z3-5967 (GC5508 mutant)


title: het_CG5508_ovaries_smallRNA

description: 19-28 nt size fractionated RNA


title: Fine Sliced Embryo 2 slice 6

tag: developmental stage


title: Fine Sliced Embryo 3 slice 7


title: Fine Sliced Embryo 2 slice 3


title: Fine Sliced Embryo 2 slice 2

description: 25um slice of D. melanogaster pooled with  S. cerevisiae Index Barcode 4


title: Fine Sliced Embryo 2 slice 4


title: Fine Sliced Embryo 2 slice 5


title: V6.5_H3K27me3_ChIP-Seq

source_name: Chromatin IP against H3K27me3

value: Abcam AB6002

value: V6.5 embryonic stem cells


title: Fine Sliced Embryo 1 slice 12

description: 25um slice of D. melanogaster pooled with  S. cerevisiae Index Barcode 1


title: Fine Sliced Embryo 1 slice 14

description: 25um slice of D. melanogaster pooled with  S. cerevisiae Index Barcode 3


title: Fine Sliced Embryo 1 slice 11

description: 25um slice of D. melanogaster pooled with  S. cerevisiae Index Barcode 27


title: Fine Sliced Embryo 1 slice 10

description: 25um slice of D. melanogaster pooled with  S. cerevisiae Index Barcode 25


title: Fine Sliced Embryo 1 slice 8

description: 25um slice of D. melanogaster pooled with  S. cerevisiae Index Barcode 22


title: Fine Sliced Embryo 1 slice 7

description: 25um slice of D. melanogaster pooled with  S. cerevisiae Index Barcode 21


title: Fine Sliced Embryo 1 slice 6

description: 25um slice of D. melanogaster pooled with  S. cerevisiae Index Barcode 20


title: Fine Sliced Embryo 1 slice 5

description: 25um slice of D. melanogaster pooled with  S. cerevisiae Index Barcode 19


title: Fine Sliced Embryo 1 slice 4

description: 25um slice of D. melanogaster pooled with  S. cerevisiae Index Barcode 18


title: Fine Sliced Embryo 1 slice 9

description: 25um slice of D. melanogaster pooled with  S. cerevisiae Index Barcode 23


title: Fine Sliced Embryo 1 slice 2

description: 25um slice of D. melanogaster pooled with  S. cerevisiae Index Barcode 15


title: Fine Sliced Embryo 1 slice 3

description: 25um slice of D. melanogaster pooled with  S. cerevisiae Index Barcode 16


title: Fine Sliced Embryo 1 slice 1

description: 25um slice of D. melanogaster pooled with  S. cerevisiae Index Barcode 14


title: rpeh_143h_31_436

status: Public on Apr 26 2013

city: St. Louis

first: Charles

last: Higdon

state: Missouri

address: 4444 Forest Park Blvd.

department: Genetics

institute: Washington University

data_processing:
Align sequences using Novoalign to cDNA database
Calculate RPKMs from Novoalign output using Perl
Genome_build: Non-redundant database of 25,102 cDNAs generated by Higdon et al 2013, based on NCBI's RefSeq build from 8/29/2012, current RefSeq available at ftp://ftp.ncbi.nlm.nih.gov/refseq/D_rerio/mRNA_Prot/zebrafish.rna.fna.gz
Supplementary_files_format_and_content: Excell file containing RPKMs of each library

organism: Danio rerio

source_name: retinal pigmented epithelium

extract_protocol:
This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236.  Zebrafish were reared and bred according to standard protocols.  The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor  (mitfavc7).  This mutant facilitated the collection of RPE, as mitfa is not required for RPE development in zebrafish.  Melanocytes, iridophores, and RPE develop normally at 25°C in mitfavc7.  When held at 32°C, the neural crest-derived melanocytes do not develop, but RPE and iridophores develop normally.  All melanocyte and iridophore samples were incubated at 25°C prior to collection.  Fish were anesthetized with Tricaine, rinsed with Ca-, Mg- DPBS (Sigma, D8537), and immersed in 100mL TrypLE Express (Invitrogen, 12604039) per 1000 fish.  Fish were incubated at 37°C and shaken at 100rpm for 15-20 minutes, followed by trituration with a Pasteur pipette to remove eyes from larva.  After separation of eyes and larva, each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1-1.5 hr.  Dissociated cells were filtered through a 120uM screen into 50 mL tubes.  Remaining intact tissue was triturated 10-20 times, and again filtered through a 120uM screen into the dissociated cells.  Dissociated cells were pelleted in a swinging bucket rotor (Eppendorf 5810 R) at 500 relative centrifugal force (rcf) for 5 minutes at 4°C, then resuspended in 1mL cold isotonic Percoll (Sigma, P1644) by gentle pipetting.  Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll.  Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation.  Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum (FCS), and placed onto preformed Percoll density gradients.  Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10,000rcf for 15 minutes at 4°C in a fixed angle micro-centrifuge (Eppendorf 5415 R).  Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4°C.  Following centrifugation, overlying Percoll was aspirated, leaving the final 100µL containing the pigment cell pellet.  Cells were resuspended with 50µL of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500µL of cold DPBS with 2% FCS, and kept on ice until mRNA extraction or FACS.      FACS   We used the inherent properties of the pigmented cells to perform Fluorescence-Activated Cell Sorting (FACS).  Following resuspension in 500µL cold DPBS with 2% FCS, the enriched cell populations were screened through a 30uM cell filter (Partec, 04-0042-2316).  Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive (DD) frequency of 22390Hz.  Cells were illuminated using a 488 nm laser.  Cells were gated on two attributes to separate cells from each other and from cellular debris.  Cellular debris was detected using forward and side scatter, selecting against the smallest particles (~1µm or less).  Cells were sorted based on detection using 510-530nm and 575-595nm filters, corresponding to FL1 and FL2 in Figure 1D, respectively.  When excited by the 488 nm laser, the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant.  Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser, and cluster at the lower left of the FACS plot.  Cells were collected into ice-cold DPBS with 2% FCS and kept on ice until mRNA extraction.
Pigment cell cDNA library construction was as follows.  For mRNA extraction the Dynabeads® mRNA DIRECT Kit (Invitrogen) was used per manufacturer's instructions.  Following mRNA elution from the Dynabeads, first strand cDNA synthesis was performed using MMLV reverse transcriptase (Clontech) using an anchored polyT primer tailed with a universal primer sequence (See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview.)  A universal primer sequence was also added to the 3' end of the first strand by template switching, allowing for PCR-amplification of the resultant cDNA  [43,44].  Following PCR amplification using the high fidelity polymerase LA Taq (TaKaRa,  PCR cycle: 95C for 1 minute, followed by 20 cycles of 98C for 25 seconds, 60C for 1 minute, 68C for 20 minutes), cDNA was digested with AluI and RsaI restriction enzymes (NEB).  Blunt-end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end-repair step of Illumina library preparation.  Since this reduced representation strategy might miss short cDNAs that lack both restriction sites, we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers.  This allows for the inclusion of short cDNAs in our libraries.  Standard Illumina library preparations followed, performed by the Genome Technology Access Center (GTAC) at Washington University in St. Louis (http://gtac.wustl.edu).  In brief, a single A was added to the 3’ end of each strand, Y-adapters ligated, and library enrichment PCR performed, followed by gel extraction size-selection for fragments ranging from 200-400 base pairs in length.  Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45].  No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment.  Sequencing was performed on the GAIIX Illumina platform.

tag: hours post fertilization

tag: temperature


title: Fine Sliced Embryo 2 slice 1

value: 25um slice of D. melanogaster pooled with  S. cerevisiae Index Barcode 3


title: Fine Sliced Embryo 1 slice 13

description: 25um slice of D. melanogaster pooled with  S. cerevisiae Index Barcode 2


title: il_77h_49_440

source_name: iridophores


title: il_97h_42_440


title: rpeleye_77h_48_440


title: rpeh_86h_33_436


title: rpeh_86h_32_436


title: rpeh_86h_32_351


title: dm_116h_53

source_name: melanocytes


title: dm_97h_41_440


title: il_77h_38_351


title: il_77h_44_440


title: dm_77h_FM_351


title: rpeleye_77h_47_440


title: rpeh_143h_31_351


title: 3dpf_embryo_515s6

source_name: whole embryos


title: rpeh_86h_33_351


title: dm_77h_52_440


title: dm_77h_43_440


title: dm_77h_28_436


title: dm_77h_28_351


title: dm_77h_27_436


title: dm_77h_27_351


title: dm_77h_26_433


title: dm_77h_26_351


title: dm_77h_25_399s62


title: dm_77h_25_399s61


title: dm_77h_25_433


title: dm_77h_25_351


title: il_58h_50_440


title: dm_58h_45_440


title: dm_58h_23_351


title: 3dpf_embryo_318s5


title: dm_77h_28_399s62


title: dm_77h_28_399s61


title: PA-1 scramble

city: Shanghai

first: Ling-Ling

last: Chen

address: 320 Yue-Yang Road

country: China

institute: Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

description:
Poly(A)+ RNA.
This Sample represents 2 replicates.

data_processing:
Sequencing reads were obtained with Illumina HiSeq 2000.
All reads were uniquely aligned to the human hg19 genome by using Bowtie with up to 2 mismatches.
Genome_build: GRCh37
Supplementary_files_format_and_content: bigWig files were generated from the relevant bedGraph files according to the step-by-step protocol at http://genome.ucsc.edu/goldenPath/help/bigWig.html basically using the bedGraphToBigWig program. The bigWig format is for display of dense, continuous data that will be displayed in the Genome Browser as a graph. The resulting bigWig files are in an indexed binary format.

source_name: embryonal carcinoma PA-1 cells, scrambled ASO

growth_protocol: Embryonal carcinoma (EC) cell line PA-1 was cultured using standard protocols provided by ATCC.

extract_protocol: Total RNAs were prepared using Trizol Reagent. After treatment with DNase I, total RNAs were used for RNA-Seq libraries preparation with Illumina TruSeq RNA Sample Preparation Kits according to the manufacturer's instructions.

tag: cell type

value: embryonal carcinoma (EC) cells

tag: ploidy

value: diploid

tag: aso

value: scrambled


title: H_het_K27me3

city: Copenhagen

first: Sandra

middle: Ursula

last: Schmitz

address: Ole Maaløes Vej 5

country: Denmark

institute: Biotech Research and Innovation Centre

data_processing:
Basecalls performed using CASAVA version 1.8.2
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie version 0.12.7 with parameters: -p 20 -S -m 1 mm9 <FILE>.
SAM-files were converted to BAM using the “samtools view” command from “Samtools” version 0.1.18;
BAM-files were converted to BED-files using the “bamToBed” command from “bedtools” version 2.16.2
Genome_build: mm9
Supplementary_files_format_and_content: BED files (BED6)

source_name: E8.5 head

growth_protocol: In vivo, E8.5 embryos

extract_protocol:
Heads of E8.5 embryos were fixed in 1% formaldehyde, sonicated. 5 heads were used for each Chromatin IP. ChIP was done as described in Schmitz et al., EMBO, 2011
DNA libraries were prepared for sequencing using standard NEB protocols, using Illumina adaptors and indeces: NEBNext End Repair Module Protocol; NEBNext dA-Tailing Module Protocol; NEBNext Quick Ligation Module Protocol; Gel purification of Adaptor Ligated DNA; Amplifying Illumina libraries with standard primers; Purify DNA on magnetic beads (Beckman/Coulter, Agencourt, AMPure XP magnetic beads A63881) according to manufacturer´s protocol.

treatment_protocol: no treatment, Heterozygote versus knockout

tag: strain

tag: genotype/variation

value: Heterozygote

value: H3K27me3 (Cell Signaling, D18C8)

tag: body part

value: head


title: H_het_K4me3

tag: chip antibody

value: H3K4me3 (Cell Signaling, C42D8)


title: Small RNAs from ovaries of 3.9 strain

status: Public on Apr 25 2013

city: Moscow

first: Sergei

last: Ryazansky

address: Kurchatov sq., 2

department: Department of Molecular Genetics of Cell

country: Russia

institute: Institute of Molecular Genetics

data_processing:
The reads with clipped 3'-adapter were passed through length (>18 nt), quality (80% of nt should contain >=20 Phred score) and artefacts filters, and mapped by bowtie to dm3 genome assembly with requiring of perfect mathcing.
Genome_build: dm3
Supplementary_files_format_and_content: Tab-delimited files include the frequencies of clipped read occurrences in each library.

growth_protocol: Flies were grown according to standard protocols.

extract_protocol:
Total RNA was isolated by Trizol (Invitrogene) and size-fractioned by PAGE (19-29 nt)
Libraries of small RNAs 19-29 nt were constructed as previously described in (Muerdter et al. 2012)

tag: transgenic line

tag: background strain

value: wK


title: H_het_IgG

value: Rabbit IgG, sigma


title: Small RNAs from ovaries of 3.6 strain


title: H_KO_K27me3

value: Jarid1b knockout


title: Small RNAs from ovaries of wK strain

value: ovaries

value: none, wildtype


title: Small RNA from HeLa cell total RNA treated with siADAR1

city: Philadelphia

first: Kazuko

last: Nishikura

state: Pennsylvania

address: 3601 Spruce Street

department: Gene Expression & Regulation

institute: The Wistar Institute

data_processing:
The 3' adapter sequences (5'-TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC-3') were removed from the small RNA samples and length of >= 19 nucleotides were retained for our further study.
genome assembly: hg19

source_name: HeLa cell treated with siADAR1

extract_protocol: Illumina Library Preparation Protocol

treatment_protocol: Total RNA are extracted using miRNeasy (QIAGEN)

tag: cell line

value: HeLa

tag: transfection

tag: rna subtype

value: small RNA


title: Small RNAs from ovaries of 2.3 strain


title: Small RNAs from ovaries of 2.1 strain


title: Small RNAs from ovaries of 62.5.2 strain


title: Small RNAs from ovaries of 3.1 strain


title: Small RNA from HeLa cell total RNA treated with siLuc

source_name: HeLa cell treated with siLuc

value: siLuc


title: H_KO_K4me3

tag: age


title: Small RNAs from ovaries of 1.9 strain

tag: tissue


title: Small RNAs from ovaries of 2.6 strain


title: mRNAs from ADAR1 KO Embryo Day11.5

data_processing: The 3' adapter sequences (5'-TCGTATGCCGTCTTCTGCTTG-3') were removed from the small RNA samples and length of >= 17 nucleotides were retained for our further study. The RNA-seq samples were first mapped to the transcriptome generated by combining mRNA information from Refseq, UCSC, Ensembl, Vega and MGI. The unaligned reads then mapped directly to the mm9/NCBIM37 build. A maximum of 2 mismatches were allowed while mapping. A maximum of 10 multiple mapping was allowed while aligning to transcriptome but only unique alignment was considered while mapping directly to genome. We use Bowtie program for our alignment. Cufflinks program was used to estimate the expression of genes and transcripts.

source_name: ADAR1 KO Day11.5

treatment_protocol: Total RNA are extracted using TRIZOL.

value: Whole Embryo

tag: development stage

value: ADAR1 KO


title: PA-1 knockdown

source_name: embryonal carcinoma PA-1 cells, specific ASO

value: embryonal carcinoma (EC) cells

value: specific to PWS-associated sno-lncRNAs


title: Small RNAs from ADAR1 KO Mouse Embyro Day11.5


title: Small RNAs from ovaries of 67.2.1 strain


title: 3dpf_embryo_318s4

tag: hours post fertilization


title: mRNAs from WildType Embryo Day11.5

source_name: WildType Day11.5

value: wild type


title: Small RNAs from ovaries of 3.10 strain


title: Small RNAs from Mouse Embyro Day11.5


title: Small RNAs from Mouse Embyro Day11

source_name: WildType Day11


title: Small RNAs from ADAR1 KO Mouse Embyro Day11

source_name: ADAR1 KO Day11


title: Small RNAs from ovaries of 2.10 strain


title: BG3_Rad21RNAi_PROseq_Rep2

status: Public on Apr 24 2013

city: St Louis

first: Cheri

last: Schaaf

state: MO

address: 1100 South Grand Ave

department: Biochemistry & Molecular Biology

institute: Saint Louis University School of Medicine

data_processing:
Raw sequenced reads were trimmed for adaptor sequence using fastx_clipper of the FASTX-Toolkit.
The first 26 bases of each read were trimmed using fastx_trimmer of the FASTX-Toolkit, and sequence reads shorter than 16 bp were removed.
Reverse complementation of the sequence reads, which were the sense sequences of nascent RNA, were generated using fastx_reverse_complement of the FASTX-Toolkit.
Sequence reads were aligned to dm5.22 whole genome using bowtie allowing 2 mismatches and excluding any non-uniquely aligned reads.
Abundance measurements were generated in bedgraph format.
Genome_build: dm5.22
Supplementary_files_format_and_content: bedgraph files provide abundance measurements.

source_name: ML-DmBG3-c2 cells derived from larval central nervous system

growth_protocol: BG3 cells were cultured in Schneider's media with 10% FCS and 10 μg per ml insulin.

extract_protocol:
Nuclei Isolation: All steps were conducted at 4o unless indicated otherwise. 2.5 to 7.5 x 108 mock RNAi-treated control or RNAi-treated BG3 cells were collected by centrifugation (1000g for 5 min), suspended in 5 to 10 mL Phosphate Buffered Saline (PBS) pH 7.0, collected by centrifugation, suspended in 5 mL Buffer W [10 mM Tris-HCl pH 7.5,10 mM KCl, 150 mM sucrose 5 mM MgCl2, 0.5 mM CaCl2, 0.5 mM dithiothreitol (DTT)], and collected by centrifugation. The cells were suspended in 5 mL Buffer P (10mM Tris-HCl, pH 7.5, 10 mM KCl, 250 mM sucrose, 5 mM MgCl2, 1 mM EGTA, 0.05% Tween-20, 0.5 mM DTT), the suspension was adjusted to 0.14% NP-40, and then incubated on ice for 3 min. The nuclei were washed twice in 5 mL Buffer W, suspended in 1 mL Buffer W, and transferred to a siliconized 1.5 mL microcentrifuge tube. The nuclei were collected by centrifugation at 1000g for 5 min, suspended in 0.5 mL Buffer F (50 mM Tris-HCL pH 8.3, 40% glycerol, 5 mM MgCl2, 0.1 mM EDTA, 0.5 mM DTT), and counted using a hemacytometer. The nuclei were then suspended in Buffer F to concentration of 40 to 50 x 105 per microliter, distributed into 100 microliter aliquots in siliconized 1.5 mL tubes, snap frozen in liquid nitrogen, and stored at -80o.
Precision Run-On sequencing (PRO-seq): biotin-NTP nuclear run-on; RNA extraction; streptavidin affinity purification; base-hydrolysis; 3' RNA adaptor ligation; 5' end repair; 5' RNA adaptor ligation; reverse transcription; PCR amplification.

treatment_protocol: For RNAi, media was replaced with 1 ml of Express Five SFM (Invitrogen) with 1% FCS, (and 10 μg per ml insulin for BG3 cells), for 2 hours. 10 μg of dsRNA was added per well of a 6-well plate. Media was adjusted to 3 ml and 10% FCS with Schneider's media after 2 hrs of RNAi treatment. Cells were replated as needed. Templates for dsRNA synthesis were made by PCR from cDNA or genomic DNA templates using primers with T7 promoters. In most experiments, equal amounts of two dsRNAs against each target were used. Both individual dsRNAs knocked down the targets, but knockdown was generally more efficient with a mixture. Templates were designed to avoid off-target matches of ≥19 nucleotides using Drosophila RNAi Screening Center (http://www.flyrnai.org/) online tools. Cohesin RNAi-treated cells were screened for sister chromatid cohesion defects, and none were found, though a mild cell division delay occurred immediately following RNAi treatment.

tag: gender

value: male

tag: treatment

value: Rad21 RNAi-treated


title: BG3_Nipped-BRNAi_PROseq_Rep2

tag: cell type

value: Nipped-B RNAi-treated


title: Gfi1

first: Rebecca

middle: Louise

last: Hannah

address: Addenbrookes Hospital, Hills Road

department: Haematology

country: United Kingdom

institute: University of Cambridge

description:
Chromatin Immunoprecipitated genomic DNA
wildtype

data_processing:
Reads aligned to mm9 using Bowtie
bedGraphs created in-house
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph – read density profiles

source_name: MAST

growth_protocol: Bone marrow cells were collected from tibias and femurs of 3- to 5- month old adult mice. Cells were cultured in Iscove’s modified Dulbecco’s medium (IMDM) supplemented with 10% fetal bovine serum (Sigma), 1% penicillin/streptomycin (Sigma), 150 micromolar MTG (Sigma), 10% stem cell factor conditional media from BHK/MKL cells and 10ng/ml of recombinant mIL-3 (Peprotech). Cells were frequently transferred to new flasks to remove adherent cells and experiments were performed after 3 weeks, when cultures were homogenous. Homogeneity of culture was confirmed by presence of FcERI by FACS and toluidine blue staining of cytospins.

extract_protocol:
ChIP assays were performed as previously described (Wilson NK et al., 2010 Cell Stem Cell) using polyclonal antibodies against GATA2 (Santa Cruz, sc9008x) and GFI1 (Abcam, ab21061).
Each sample was amplified and sequenced Illumina's instructions.

value: Mast cell

tag: chip antibody manufacturer

value: Abcam

tag: chip antibody catalog #

tag: genetic background

value: B6CBA/F1 (a cross between a C57BL/6 and a CBA)


title: ACH3_MEF2_KO

city: Davis

first: Henriette

last: O'Geen

address: 1 Shields Avenue

institute: UC Davis

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse (mm9) genome using the bwa aligner (http://bio-bwa.sourceforge.net/).
Peaks: Peak detection was performed Solesearch (http://havoc.genomecenter.ucdavis.edu/cgi-bin/chipseq.cgi) using the input DNA as a control.
Genome Build:
libTMK4MEF2.bed: mm9
TMK4_MEF2_peaks.gff: mm9

growth_protocol: Frozen cells thawed at passage 5 and grown to passage 7 on 15 cm tissue culture treated plates in DMEM high glucose with L-glutamine and non-essential amino acids. Harvest at passage 7 yielded approximately 2 x 10^6 cells per line.

extract_protocol:
ChIP-seq: MEF cells were trypsinized, washed, then crosslinked with 1% formaldehyde for 10 minutes, and quenched with a final volume of 0.125M glycine. Cells were washed 3 times in cold PBS, flash-frozen, and stored at -80C.  Yield was approximately 2 x 10^6 cells per MEF line. Chromatin immunoprecipitation was performed exactly as described in O'Geen et al. 2011 (PMID: 21913086) with the following modifications: Nuclear pellet was flash frozen in liquid nitrogen after incubation in 100ul nuclear lysis buffer, and thawed on ice to aid disruption of nuclei before sonication. Chromatin was sonicated on a Diagenode Bioruptor in 1.5 ml Eppendorf tubes in a volume of 100 ul nuclear lysis buffer to a fragment size between 100-200 base pairs. ChIP assays were performed using H3K9Ac (Upstate # 06-942, lot number 31636) and H3K4Tm3 (Millipore # 04-475, lot number NG1680351) antibodies. Antibodies were collected with 20 ul magnetic protein G beads, and washed as described. After reversing the crosslinks, samples were purified and eluted in 2 x 10 ul elution buffer using the Qiagen MinElute PCR purification kit.
Libraries were prepared on the library automation system from IntegenX (Apollo324) using the PrepX™ DNA Library Kit.

tag: strain

tag: genotype/variation

value: wild-type

value: mouse embryonic fibroblasts (MEF)

tag: passages

value: passage 7, replicate 1

tag: chip-antibody


title: TMK4_MEF8_WT

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse (mm9) genome using the bwa aligner (http://bio-bwa.sourceforge.net/).
Peaks: Peak detection was performed Solesearch (http://havoc.genomecenter.ucdavis.edu/cgi-bin/chipseq.cgi) using the input DNA as a control.
Genome Build:
libACH3MEF8.bed: mm9
ACH3_MEF8_peaks.gff: mm9

value: homozygously constitutively null for H3f3b

value: passage 7, replicate 2


title: BG3_Nipped-BRNAi_PROseq_Rep1


title: TMK4_MEF2_KO

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse (mm9) genome using the bwa aligner (http://bio-bwa.sourceforge.net/).
Peaks: Peak detection was performed Solesearch (http://havoc.genomecenter.ucdavis.edu/cgi-bin/chipseq.cgi) using the input DNA as a control.
Genome Build:
libACH3MEF2.bed: mm9
ACH3_MEF2_peak.gff: mm9


title: ACH3_MEF3_WT

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse (mm9) genome using the bwa aligner (http://bio-bwa.sourceforge.net/).
Peaks: Peak detection was performed Solesearch (http://havoc.genomecenter.ucdavis.edu/cgi-bin/chipseq.cgi) using the input DNA as a control.
Genome Build:
libTMK4MEF3.bed: mm9
TMK4_MEF3_peaks.gff: mm9


title: BG3_Rad21RNAi_PROseq_Rep1


title: BG3_Mock_PROseq_Rep2

value: mock RNAi-treated


title: BG3_Mock_PROseq_Rep1


title: TMK4_MEF7_KO

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse (mm9) genome using the bwa aligner (http://bio-bwa.sourceforge.net/).
Peaks: Peak detection was performed Solesearch (http://havoc.genomecenter.ucdavis.edu/cgi-bin/chipseq.cgi) using the input DNA as a control.
Genome Build:
libACH3MEF7.bed: mm9
ACH3_MEF7_peaks.gff: mm9


title: TMK4_MEF3_WT

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse (mm9) genome using the bwa aligner (http://bio-bwa.sourceforge.net/).
Peaks: Peak detection was performed Solesearch (http://havoc.genomecenter.ucdavis.edu/cgi-bin/chipseq.cgi) using the input DNA as a control.
Genome Build:
libACH3MEF3.bed: mm9
ACH3_MEF3_peaks.gff: mm9


title: Egg

city: Hilo

first: Brian

last: Hall

state: Hawai'i

address: 64 NOWELO ST

institute: USDA PBARC

data_processing:
Transcriptome assembly using Trinity r2012_10_05 using all reads, in silico normalized to ~30x coverage
Alignment of concatenated reads to assembly using Bowtie 0.12.7
Abundance estimation on alignment file using RSEM 1.2.0
Filtering assembly based on RSEM TPM cutoff = 0.5, IsoPct cutoff = 5 and presence of likely coding region
Aligning individual samples to filtered assembly using Bowtie 0.12.7, abundance estimation with RSEM 1.2.0
Raw read count files from RSEM were TMM normalized and FPKM transformed to produce normailzed abundance measurements
Genome_build: n/a
Supplementary_files_format_and_content: Files are tab-separated text files containing either read or TMM normalized FPKM values for each developmental stage at a gene and isoform (transcript) level

organism: Bactrocera dorsalis

source_name: Egg

growth_protocol: Liquid Artificial Diet

extract_protocol:
Qiagen Rneasy Plus Mini Kit
Illumina TruSeq RNA Prep Kit

tag: life stage

value: Egg


title: Male

source_name: Male

value: Male


title: Larvae

source_name: Larvae

value: Larvae


title: Female

source_name: Female

value: Female


title: Pupae

source_name: Pupae

value: Pupae


title: Mated Female

source_name: Mated Female

value: Mated Female


title: Histone H3K27me3 ChIP-Seq of Fetal Intestine, Large; Histone.DS23306

status: Public on Apr 23 2013

city: Seattle

first: Northwest

last: REMC

state: WA

institute: University of Washington

description:
sample_term_id: UBERON_0000059
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K27me3 ChIP-Seq
Library name: Histone.DS23306
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.16243
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14913
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM1125768_UW.Fetal_Intestine_Large.H3K27me3.H-24595.Histone.DS23306.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS23306-Histone.DS23306.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Intestine Large H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on Fetal Intestine Large, Donor H-24595, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16832
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,865,452
FINDPEAKS_SCORE: 0.2259
FINDPEAKS_PERCENTILE: 86
HOTSPOT_SCORE: 0.3121
HOTSPOT_PERCENTILE: 82
IROC_SCORE: 0.9439
IROC_PERCENTILE: 74
POISSON_SCORE: 0.4619
POISSON_PERCENTILE: 84
MAXIMUM_REPLICATE_CORRELATION: 0.98

**********************************************************************

ANALYSIS FILE NAME: GSM1125768_UW.Fetal_Intestine_Large.H3K27me3.H-24595.Histone.DS23306.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS23306-Histone.DS23306.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Intestine Large H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from Fetal Intestine Large, Donor H-24595, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16928
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FIL H3K27me3 95 06
BROWSER_TRACK_DESCRIPTION: UW Fetal Intestine Large Histone H3K27me3 Donor H-24595 Library Histone.DS23306 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,865,452
FINDPEAKS_SCORE: 0.2259
FINDPEAKS_PERCENTILE: 86
HOTSPOT_SCORE: 0.3121
HOTSPOT_PERCENTILE: 82
IROC_SCORE: 0.9439
IROC_PERCENTILE: 74
POISSON_SCORE: 0.4619
POISSON_PERCENTILE: 84
MAXIMUM_REPLICATE_CORRELATION: 0.98

**********************************************************************

source_name: Fetal Intestine, Large primary tissue, day 108; Histone.DS23306

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample common name

value: Fetal Intestine, Large

tag: sra sample accession

tag: disease

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Primary Tissue

value: UW

value: fetal

value: day 108

value: Histone H3K27me3

value: Diagenode Bioruptor

value: 20-40 cycles of 0.5 minute on and 0.5 minute off

value: Millipore A/G agarose beads

value: 30ul A/G bead slurry

value: Millipore


title: Histone H3K36me3 ChIP-Seq of Fetal Intestine, Large; Histone.DS23307

description:
sample_term_id: UBERON_0000059
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K36me3 ChIP-Seq
Library name: Histone.DS23307
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.16240
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14913
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM1125769_UW.Fetal_Intestine_Large.H3K36me3.H-24595.Histone.DS23307.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS23307-Histone.DS23307.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Intestine Large H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on Fetal Intestine Large, Donor H-24595, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16845
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,404,697
FINDPEAKS_SCORE: 0.3832
FINDPEAKS_PERCENTILE: 78
HOTSPOT_SCORE: 0.3552
HOTSPOT_PERCENTILE: 78
IROC_SCORE: 0.9884
IROC_PERCENTILE: 71
POISSON_SCORE: 0.5937
POISSON_PERCENTILE: 81
MAXIMUM_REPLICATE_CORRELATION: 0.98

**********************************************************************

ANALYSIS FILE NAME: GSM1125769_UW.Fetal_Intestine_Large.H3K36me3.H-24595.Histone.DS23307.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS23307-Histone.DS23307.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Intestine Large H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from Fetal Intestine Large, Donor H-24595, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16941
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FIL H3K36me3 95 07
BROWSER_TRACK_DESCRIPTION: UW Fetal Intestine Large Histone H3K36me3 Donor H-24595 Library Histone.DS23307 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,404,697
FINDPEAKS_SCORE: 0.3832
FINDPEAKS_PERCENTILE: 78
HOTSPOT_SCORE: 0.3552
HOTSPOT_PERCENTILE: 78
IROC_SCORE: 0.9884
IROC_PERCENTILE: 71
POISSON_SCORE: 0.5937
POISSON_PERCENTILE: 81
MAXIMUM_REPLICATE_CORRELATION: 0.98

**********************************************************************

source_name: Fetal Intestine, Large primary tissue, day 108; Histone.DS23307

value: Male

value: Histone H3K36me3

value: Active Motif


title: MAV_TMC724_log

city: Berlin

first: Dmitriy

last: Ignatov

address: Charitéplatz 1

country: Germany

institute: Max Planck Unit for the Science of Pathogens

data_processing:
Basecalls were done with CASAVA version 1.4
Sequence reads were trimmed for adaptor sequences with custom perl script and mapped to Mycobacterium avium 104 genome (GenBank: CP000479.1) using Bowtie2. Mapping parameters: "bowtie2 -q --sensitive-local"
Transcriptional profile for visualization in Artemis genome browser was made with custom perl script. For each nucleotide of the genome the quantity of reads mapped to this nucleotide in forward and reverse orientation were counted. The file "profile_artemis.txt" represents these counts. The rows correspond to nucleotides of the M. avium 104 genome, the columns correspond to quantities of reads mapped to these nucleotides in forward and reverse orientation.
RPKM values for every gene of M. avium 104 genome, having homolog in M. avium TMC724 genome, were calculated with custom perl script. RPKM values were counted separately for reads mapped in sense and antisense orientation. A read was considered to be mapped to a gene, if at least one its nucleotide mapped within the gene borders.
Genome_build: Mycobacterium avium 104 (GenBank: CP000479.1)/ASM1498v1
Supplementary_files_format_and_content: "profile_artemis.txt". Tab-delimited text file: two columns and 5475491 lines. The file represents a transcriptional profile, which can be read with Artemis genome browser: after loading of Mycobacterium avium 104 genome (GenBank: CP000479.1), go to Graphs -> Add user plot -> select "profile_artemis.txt". The red line represents transcription from the forward strain of genome, the green line -from the reverse stand.
Supplementary_files_format_and_content: "RPKM.txt". Excel2010 file. The rows represent genes of M. avium 104 genome, which have homologs in M. avium TMC724 genome. Coordinates and directions of the genes are represented in columns 2-4. In the columns 5-6 RPKM values for sense and antisense orientation are represented.

organism: Mycobacterium avium

source_name: Bacterial cells grown in culture until mid-logarithmic growth phase

growth_protocol: Bacteria were grown at 37°C in Dubos broth with addition of 0.05% Tween 20 for approximately 2 weeks until logarithmic growth phase (OD600 ~ 0.6) was achieved.

extract_protocol:
Bacterial cells in Trizol were disrupted with Mini-Beadbeater-16 (Biospec products). RNA from disrupted cells was isolated according to conventional phenol-chloroform protocol and resuspended in mQ water. RNA integrity was verified by agarose gel electrophoresis. RNA was treated with Turbo DNase (Ambion) and purified on RNeasy columns (QIAGEN).
RNA was processed with MicrobExpress kit (Ambion) to remove 16S and 23S rRNA, and ethanol precipitated. The further procedures were performed according to "Directional mRNA-Seq Sample Preparation" guide issued by Illumina. RNA was sheared with RNA Fragmentation Reagents (Ambion) for 10 minutes, and ethanol precipitated. Fragmented RNA was dephosphorilated with Antarctic phosphatase (NEB) and 5' phosphate was added with T4 Polynucleotide Kinase (NEB). RNA was purified with RNeasy MinElute kit according to modified protocol from "Directional mRNA-Seq Sample Preparation" guide. Illumina 3' and 5' RNA adapters were ligated according to "TruSeq™ Small RNA Sample Preparation Guide". RNA was reverse transcribed and amplified for 11 cycles. PCR products were fractionated on PAGE and those with the lengths of cDNA inserts 25-75 nt were excized and eluted from the gel. These fragments were sequenced on Ilumina GAIIx.

treatment_protocol: Bacterial culture was rapidly chilled on ice and centrifuged at 3000g and 4⁰C for 15 minutes to pellet the mycobacteria. The liquid phase was discarded and the pellet was resuspended in Trizol reagent (1 ml Trizol per 100 ml of bacterial culture)


title: Histone H3K9me3 ChIP-Seq of Fetal Intestine, Large; Histone.DS22901

description:
sample_term_id: UBERON_0000059
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K9me3 ChIP-Seq
Library name: Histone.DS22901
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.16246
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14913
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM1125770_UW.Fetal_Intestine_Large.H3K9me3.H-24595.Histone.DS22901.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22901-Histone.DS22901-Histone.DS22901-Histone.DS22901.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Intestine Large H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 ChIP-Seq on Fetal Intestine Large, Donor H-24595, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16874
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,459,268
FINDPEAKS_SCORE: 0.1753
FINDPEAKS_PERCENTILE: 86
HOTSPOT_SCORE: 0.2399
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 0.8952
IROC_PERCENTILE: 76
POISSON_SCORE: 0.3655
POISSON_PERCENTILE: 82
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

ANALYSIS FILE NAME: GSM1125770_UW.Fetal_Intestine_Large.H3K9me3.H-24595.Histone.DS22901.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22901-Histone.DS22901-Histone.DS22901-Histone.DS22901.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Intestine Large H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 ChIP-Seq read mappings from Fetal Intestine Large, Donor H-24595, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16970
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FIL H3K9me3 95 01
BROWSER_TRACK_DESCRIPTION: UW Fetal Intestine Large Histone H3K9me3 Donor H-24595 Library Histone.DS22901 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,459,268
FINDPEAKS_SCORE: 0.1753
FINDPEAKS_PERCENTILE: 86
HOTSPOT_SCORE: 0.2399
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 0.8952
IROC_PERCENTILE: 76
POISSON_SCORE: 0.3655
POISSON_PERCENTILE: 82
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

source_name: Fetal Intestine, Large primary tissue, day 108; Histone.DS22901

value: Histone H3K9me3


title: Gata2

value: Mast cell

tag: chip antibody

value: Santa Cruz

value: B6CBA/F1 (a cross between a C57BL/6 and a CBA)


title: ACH3_MEF8_WT

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse (mm9) genome using the bwa aligner (http://bio-bwa.sourceforge.net/).
Peaks: Peak detection was performed Solesearch (http://havoc.genomecenter.ucdavis.edu/cgi-bin/chipseq.cgi) using the input DNA as a control.
Genome Build:
libTMK4MEF8.bed: mm9
TMK4_MEF8_peaks.gff: mm9

value: homozygously constitutively null for H3f3b

value: mouse embryonic fibroblasts (MEF)

value: passage 7, replicate 2


title: WT_Hippocampus-3_CLIP

first: Ranjan

last: Batra

address: 2880 Torrey Pines Scenic Drive

department: Cellular and Molecular Medicine

institute: University of California San Diego

data_processing:
Raw reads obtained from the Illumina pipeline include a 4 nt barcode (3 random positions and a G at the 4th position) at the 5end, followed by the actual CLIP tag of different sizes, and possibly part of the 3 adaptor sequence. They were filtered to remove low quality reads by requiring a minimum score of 20 in barcode positions and an average score of 20.
The filtered reads were then aligned to the mouse reference genome (mm9) by novoalign
Potential PCR duplicates, as judged from the starting position of genomic mapping and the barcode sequences, were removed to identify unique CLIP tags
Supplementary_files_format_and_content: BED

source_name: WT Hippocampus

growth_protocol: 3, 3month old WT mice were used.

extract_protocol:
Hippocampi were dissected from wild type mice (11-12 weeks), snap frozen in liquid nitrogen, ground to a fine powder, and crosslinked with UV-light in stratalinker 1800.
RNA-protein complexes were isolated from hippocampus and cDNA libraries were generated using RNA linkers and primers described for Ago CLIP (Chi et al.,2009).

treatment_protocol: Hippocampus dissected from WT female 3 mo old mice

tag: age

value: 3 mo

value: C57BL/6 and 129 SvlmJ mixed

tag: tissue

value: Hippocampus

value: WT

value: Female


title: WT_Hippocampus-2_CLIP

tag: gender


title: WT_Hippocampus-1_CLIP


title: ACH3_MEF7_KO

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse (mm9) genome using the bwa aligner (http://bio-bwa.sourceforge.net/).
Peaks: Peak detection was performed Solesearch (http://havoc.genomecenter.ucdavis.edu/cgi-bin/chipseq.cgi) using the input DNA as a control.
Genome Build:
libTMK4MEF7.bed: mm9
TMK4_MEF7_peaks.gff: mm9

value: wild-type


title: Mock ChIP 1

city: Lyon

first: Irene

last: Aksoy

address: 18 avenue du Doyen Lepine

country: France

institute: Stem Cell and Brain Research Institute

data_processing:
ChIP-Seq reads were aligned using the Eland software to NCBI build 37 (mm9) of the mouse genome.
The MACS program (version 1.4) was used to detect peaks of ChIP enrichment. It was run with the default settings using a tag size of 35 and band width 280.
For KH2 cells MACS was run by comparison to the Input DNA control, it was run separately for each ChIP replica and only those peaks were kept that were found in both replicas. The intersection was done by running windowBed with window size of 50. Intersecting peaks were additionally filtered by retaining only peaks with a p-value < 10-10.
Genome_build: mm9
Supplementary_files_format_and_content: bed format. Chrom, ChromStart, ChromEnd, Name and Score.

source_name: KH2 ES cells

growth_protocol: ES cells were grown with in standard media composed of  DMEM supplemented with ES qualified FBS and Leukemia Inhibitory Factor (LIF). F9 cells were grown in DMEM supplemented with 15% FBS.

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 10 min at room temperature, and formaldehyde was inactivated by the addition of 125 mM glycine. Chromatin from each cell line was sonicated to a length of around 250-500bp and immunoprecipitated using the following antibodies: V5 antibody (Invitrogen, R96025), Oct4 antibody (Santa Cruz, SC8628) and Sox17 antibody (R&D systems, AF1924) and sequenced using the SOLEXA platform.
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 (3' to 5' exo minus) and dATP. 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: ES cells were treated with doxycycline at 1µg/ml to induce the expression of either Sox2 or Sox17. F9 cells were treated with 1µM retinoic acid (RA) to induce their differentiation into primitive endoderm.

value: Embryonic stem cells

tag: developmental stage

value: Undifferentiated

tag: cell line

tag: chip antibody 1

tag: chip antibody manufacturer 1

tag: chip antibody catalog # 1

tag: chip antibody 2

tag: chip antibody manufacturer 2

tag: chip antibody catalog # 2


title: Pou5f1/Oct4_ES_Sox17EK-V5 B

tag: cell type

tag: treatment

value: Overexpress Sox17EK-V5 tagged

value: Invitrogen


title: Pou5f1/Oct4_ES_Sox17-V5 A

value: Overexpress Sox17-V5 tagged


title: Mock ChIP 2


title: Pou5f1/Oct4_ES_Sox17EK-V5 A


title: Sox17_ES ChIP-seq B

value: Overexpress Sox17_V5 tagged

value: R&D


title: Pou5f1/Oct4_ES_Sox2KE-V5 B

value: Overexpress Sox2KE-V5 tagged

value: Santa Cruz


title: Pou5f1/Oct4_ES_Sox2KE-V5 A


title: Sox17EK_ES ChIP-seq A


title: Sox2KE_ES ChIP-seq B


title: Sox17_F9+RA ChIP-seq

source_name: F9+RA cells

value: Embryonic carcinoma cell line

value: Differentiated into primitive endoderm-like cells

value: Treated with retinoic acid


title: Sox2KE_ES ChIP-seq A


title: Sox2_ES ChIP-seq_A

value: Overexpress Sox2-V5 tagged


title: Pou5f1/Oct4_F9+RA ChIP-seq


title: Pou5f1/Oct4_F9 ChIP-seq

source_name: F9 cells


title: Sox2_ES ChIP-seq_B


title: E3.75 ICM

data_processing:
Reads were aligned with ABI bioscope version 1. Reads were filtered for rRNA and tRNA sequences and then aligned to mouse mm9 genome.
Uniquely aligned read counts were used for RPKM calculation.
Genome_build: mm9
Supplementary_files_format_and_content: RPKM

source_name: blastycyst

extract_protocol:
PicoPure RNA isolation kit (KIT 0204) was used to extract RNA and RNA was eluted in 11ul of EB.
RNA was eluted in 11µl of elution buffer (EB). 5µl of the RNA solution was used for the reverse transcription / amplification by the Nugen Ovation RNA-Seq system (7100 - 08). The SOLiD fragment library construction kit (4443471) was used for the library construction from 1µg of amplified cDNA.

value: ICM

tag: genetic background

value: B6CBAF1 females crossed to CD-1 males


title: Mycobacterium smegmatis infected with mycobacteriophage Giles for 30min

city: Pittsburgh

first: Rebekah

middle: M

last: Dedrick

address: 4249 Fifth Ave

department: Biological Sciences

institute: University of Pittsburgh

data_processing:
Sequenced reads were masked for low-complexity or low-quality sequence, then mapped to mycobacteriophage Giles whole genome using bowtie v1.1.2
The SAM file was filtered for mapped reads only
SAM was converted to BAM using SAMtools
Pileup was generated from BAM using SAMtools
Genome_build: NC_009993.2
Supplementary_files_format_and_content: pileup

organism: Mycobacterium phage Giles

source_name: 30min post infection

growth_protocol: Mycobacterium smegmatis was grown as described previously (Morris P, Marinelli LJ, Jacobs-Sera D, Hendrix RW, & Hatfull GF. 2008. Genomic characterization of mycobacteriophage Giles: evidence for phage acquisition of host DNA by illegitimate recombination. J. Bacteriol. 190(6):2172-2182.)

extract_protocol:
RNA was extracted using Rneasy Mini Kit (Qiagen), rRNA was depleted using RiboZero (Epicentre)
Illumina TruSeq Kit

tag: time

value: 30 min post infection

tag: host

value: Mycobacterium smegmatis


title: E3.75 blastocyst

source_name: blastocyst

value: blastocyst


title: Mycobacterium smegmatis infected with mycobacteriophage Giles for 2.5hrs

source_name: 2.5hr post infection

value: 2.5 h post infection


title: Mycobacteirophage Giles lysogen in Mycobacterium smegmatis

source_name: Giles lysogen

value: N/A (lysogen)


title: Neisseria lactamica 020-06 WT plus TEX

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

data_processing:
Demultiplexing
FastQ quality trimming using FastX and a cut-off value of 20
Fastq to fasta conversion using FastX
Removal of polyA-tails from Fasta sequences
Size filtering: discarding reads shorter than 12 nt
Read mapping using segemehl version 0.9.4
Coverage calculation and normalization
Genome_build: NC_014752.1
Supplementary_files_format_and_content: Wiggle

organism: Neisseria lactamica 020-06

source_name: terminator exonuclease (TEX)

extract_protocol:
Frozen cell pellets from liquid cultures were lysed, and total RNA was extracted from the lysates using the hot-phenol method described previously (Blomberg et al., 1990). For depletion of processed transcripts, total RNA was freed of residual genomic DNA by DNase I treatment, and equal amounts of Neisseria RNA were incubated with Terminator 5’-phosphate-dependent exonuclease (TEX) (Epicentre) or in buffer alone as previously described (Sharma et al., 2010).
Libraries for Solexa sequencing (HiSeq) of cDNA were constructed by vertis Biotechnology AG, Germany (http://www.vertis-biotech.com/), as described previously for eukaryotic microRNA (Berezikov et al., 2006) but omitting the RNA size-fractionation step prior to cDNA synthesis.

tag: genotype

value: wild type

tag: strain


title: Neisseria lactamica 020-06 WT minus TEX

source_name: no treatment


title: Inflorescence_wt col_rep2

city: Milan

first: Giulio

last: Pavesi

address: Via Celoria 26

department: Biosciences

country: Italy

institute: Università di Milano

description:
Chromatin IP against GFP-SVP
processed data file: SVP_ChiPSeq_C_aligned.txt

data_processing: Reads were mapped to the unmasked Arabidopsis reference genome (TAIR8) using the seqmap software allowing at most two substitutions.Only uniquely mapped reads were retained. Reads were extended directionally to 300 nt. For each nucleotide position enrichment was tested using a negative binomial distribution model. Samples SVP_ChIPSeq_F1 and SVP_ChIPSeq_F2 were processed together to produce file SVP_ChiPSeq_F_aligned.txt. Samples SVP_ChIPSeq_L1 and SVP_ChIPSeq_L2 were processed together to produce file SVP_ChiPSeq_L_aligned.txt. Samples SVP_ChIPSeq_C1 and SVP_ChIPSeq_C2 were processed together to produce file SVP_ChiPSeq_C_aligned.txt.

organism: Arabidopsis thaliana

source_name: Inflorescence

growth_protocol: vegetative phase: pSVP::SVP-GFP svp-41 and wild-type seedlings grown for 2 weeks in Short Day (SD) conditions (8 h light/16 h dark); for the reproductive phase we used wild-type and pSVP::SVP-GFP svp-41 inflorescences grown for 2 weeks in SD conditions and then moved in (LD) conditions (16 h light/16 h dark). The inflorescences were collected at 2 weeks after bolting.

extract_protocol:
ChIP assays and genomic DNA extraction were performed as previously described in Dorca-Fornell et al. Plant J. 2011 Sep;67(6):1006-17 (PMID 21609362) with a minor modification in the sonication step. DNA samples were sonicated 6 times 30 seconds each with amplitude 30-40, with intervals of 1 minute (100-500 bp range fragments obtained). ChIP antibody used was the Living Colors  Full-Length A.v. Polyclonal Antibody from Clontech, Catalog number 632460, Lot 7090112.
Libraries for Solexa sequencing were performed following the instructions contained in the Illumina kit protocol

value: inflorescence meristem and flower from stages 1 to 11

tag: chip antibody

value: GFP:Living Colors_ full-length A.v. polyclonal antibody Clontech

tag: genotype/variation

value: wild type Col


title: Inflorescence_wt col_rep1

tag: developmental stage


title: Pou5f1/Oct4_ES_Sox2-V5 A

value: Embryonic stem cells

value: Undifferentiated

tag: cell line

value: Invitrogen


title: seedling_svp_SVP-GFP_rep2

description:
Chromatin IP against GFP-SVP
processed data file: SVP_ChiPSeq_L_aligned.txt

source_name: seedling

value: seedlings 2 weeks old

value: pSVP::SVP-GFP svp-41


title: Sox17_ES ChIP-seq A

value: Overexpress Sox17-V5 tagged

tag: chip antibody 1

value: R&D


title: Sox17EK_ES ChIP-seq B

value: Overexpress Sox17EK-V5 tagged

tag: chip antibody manufacturer 1


title: Inflorescence_svp_SVP-GFP_rep1

description:
Chromatin IP against GFP-SVP
processed data file: SVP_ChiPSeq_F_aligned.txt


title: seedling_svp_SVP-GFP_rep1


title: Pou5f1/Oct4_ES_Sox2-V5 B

value: Overexpress Sox2-V5 tagged

value: Santa Cruz

tag: chip antibody catalog # 1


title: Nr38 48h Arsen rep2

city: Jena

first: JenAge

last: Project

address: Beutenbergstr. 11

institute: Leibniz Institute for Age Research - Fritz Lipmann Institute

data_processing:
Illumina Casava software used for extraction of FASTQ files
FASTQ files were mapped using Bowtie vs. the C.elegans genome and a splice site data set created using UCSC's RefSeq annotation
Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor
Calculation of RPKM values for each transcript and gene from RefSeq annotation (see ce_Nr35-38_counts_rpkm.xls)
Genome_build: ce6\WBcel235
Supplementary_files_format_and_content: RPKM

organism: Caenorhabditis elegans

source_name: total RNA from whole animals

growth_protocol: Nematodes were grown and maintained on NGM agar plates according to standard protocol as described (Brenner et al. 1974)

extract_protocol:
RNA isolation was performed using a commercially available kit (Qiagen, Hilden, Germany, Rneasy Mini Kit) based on the phenol-chloroform extraction method according to the manufacturer’s instructions. Afterwards the RNA was quantified photometrically with a NanoDrop 1000 (PeqLab, Erlangen, Germany) and stored at −80°C until use.
For library preparation an amount of 5 μg of total RNA per sample was processed using Illumina’s mRNA-Seq sample prep kit (Illumina; San Diego; CA, USA) following the manufacturer’s instruction.

treatment_protocol: Treatment of C. elegans was carried out on NGM agar plates containing 100nM arsenite or the respective solvent control (H2O) and spotted with heat-inactivated OP50 E. coli. Thereby, agar plates were prepared from the same batch of NGM Agar, whereas treatment plates were supplemented with the arsenite and control plates with the corresponding solvent as described (Schmeisser et al. 2011).

value: Adult (48 hours after L4)

value: 100nM arsenite

tag: tissue

value: whole organism


title: Inflorescence_svp_SVP-GFP_rep2


title: Nr36 48h Arsen rep1


title: induced 1

city: Zurich

first: Ulrich

last: Omasits

address: Wolfgang Pauli-Str. 16

department: IMSB Institute of Molecular Systems Biology

country: Switzerland

institute: ETH Zurich

data_processing:
The sequenced reads were mapped using the BioScope 1.3.1 mapping pipeline (mapreads software using local alignment strategy).
SAM files were subsequently further processed to remove among all uniquely mapping reads those with an average mapping/read quality below 20, or more than two mismatches.
For the class of doubly mapped reads, we eliminated reads from duplicated 16S and 23S rRNA genes (accounting for >99%) and then filtered instances where, based on edit distance and map quality as selection criteria, one of the two mappings exhibited a better match with the reference genome sequence. This was repeated for triply mapped reads (including the 5S rRNA genes) and up to 4-7 mapped genome positions per read.
The count data summary for annotated B. henselae ORFs was generated using the HTSeq package, the quality of the reads was visually inspected with the HTSeq-qa program.
Transcript abundance was estimated via RPKM values. The number of mapped and filtered reads for each B. henselae protein-coding gene was divided by the length of the gene (in kilobases) and the number of mapped and filtered reads to all B. henselae protein-coding genes in the experiment (in million reads).
Differential transcript expression analysis was carried out with the R package DESeq (version 1.6.1).
Genome_build: B. henselae Houston-1 strain (NCBI RefSeq acc. NC_005956.1, slightly modified to include the bepD-gfpmut2 chromosomal reporter fusion, and retain the deleted batR-batS sequence)
Genome_build: ASM4670v1
Supplementary_files_format_and_content: Tab-delimited text file includes for each protein-coding gene reads and RPKM values per sample, as well as differential expression analysis for replicate 2.

organism: Bartonella henselae

source_name: bacterial colonies

growth_protocol: MQB307 was grown on Columbia agar plates containing 5% defibrinated sheep blood (CBA plates) supplemented with 30 mg/l kanamycin with (induced condition) or without (uninduced condition) 500 uM isopropyl β-D-thiogalactoside (IPTG) at 35°C and 5% CO2 for 60 h

extract_protocol:
RNA was isolated from bacterial cells using a modified hot-phenol extraction, followed by DNase I digestion, RNA cleanup (RNeasy Mini Kit, Qiagen). Integrity of total RNA was verified on an Agilent 2100 Bioanalyser using the RNA 6000 Nano LabChip kit (Agilent Technologies). The purified RNA was used directly for downstream application or stored at -70°C after precipitation with 2.5 volumes ethanol and 1/10 volume 3 M sodium acetate, pH 5.2.
The Whole Transcriptome library was produced using the Ribominus kit, Bacteria Module (Invitrogen PN 45-7014) and the SOLiD™ Total RNA-seq kit (Applied Biosystems p/n 4445374). Briefly, 5 μg of total RNA was depleted of rRNA and then fragmented using RNase III. Ligation of the adaptor mix and reverse transcription were performed following the manufacturer's protocol. cDNA libraries were size selected for fragments between 150 and 250 bp, amplified for 18 cycles of PCR using barcoded adaptor primers and purified with the PureLink PCR micro kit (Invitrogen PN K310050). Library size and concentrations were assessed on a Bioanalyzer (Agilent) and on a Qubit fluorometer (Invitrogen), respectively. The whole transcriptome library was used for emulsion-PCR based on a concentration of 0.5 pM. Sequencing beads from four barcoded libraries (2 biological replicates for the uninduced and induced condition, respectively) were pooled together and loaded on a full SOLiD™-4  slide (Applied Biosystems), according to manufacturer's instructions. SOLiD™ ToP Sequencing F3-Tag MM50 chemistry was used to produce 50 base sequencing reads.

value: 500 uM IPTG


title: induced 2


title: uninduced 1


title: Nr35 48h H20 rep1

value: control plate