title: Dsim_0251.199_Testes_and_Reproductive_Tract_Replicate_2

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

data_processing: Reads were either generated as 76 or 101 bp paired-end. However, all 101 bp reads were trimmed to 76 bp due to low quality on the 3' end. Trimmed 76 bp reads were used for subsequent analyses. Trimmed reads that passed the Illumina filter were mapped with Tophat 1.2.0. The species-specific reference sequence (FlyBase release 2 in the case of Drosophila pseudoobscura and FlyBase release 1 in the case of Drosophila simulans) was used to build a reference index for mapping. The reference index was created using the bowtie-build function (bowtie version 0.12.7) with default parameters and reads were mapped to this reference using the Tophat parameters -g 1 -F 0 -r 148 -i 42 -solexa1.3-quals.

organism: Drosophila simulans

source_name: Dissected Testes and Reproductive Tract

growth_protocol: Virgins were collected under CO2 anestesia and aged 5-8 days on standard cornmeal medium at 25 degrees C.

extract_protocol: Total RNA was extracted from a pool of 30 carcasses using Trizol (Invitrogen, Carlsbad, CA). mRNA was extracted using the QIAGEN Oligotex kit (Qiagen, Valencia, CA). Illumina library preparation was as follows. We fragmented mRNA using alkaline hydrolysis. First, 9 ul of 100 ng of mRNA and 1 ul of 10X fragmentation buffer (Ambion, Austin, Texas.) was incubated at 70C for 5 minutes to fragment mRNA. One microliter of Stop Buffer (Ambion, Austin, Texas) was added and samples were placed on ice. Fragments were precipitated with 1 ul 3 M NaOAC (pH 5.2), 2 ul glycogen (5 ug/ul , Ambion, Austin, Texas), and 30 ul 100% EtOH and then incubated for 30 minutes at -80 C. Fragmented RNA was pelleted at 14000 rpm with a microcentrifuge at 4C. The pellet was washed with 70% EtOH, air dried and resuspended with 10.5 ul RNase free H2O. Fragmented mRNA was reverse transcribed to create cDNA. One microliter of random hexamer primers (3ug/ul, Invitrogen, Carlsbad, California) was placed with 10.5 ul of fragmented mRNA, then samples were incubated at 65C for 5 minutes and placed on ice. Four microliters 5X first strand buffer, 2 ul 100 mM DTT, 1 ul dNTP, and 0.5 ul RNaseOUT were added to the mRNA and samples were incubated at 25C for 2 minutes. One microliter of SuperScript II (200 U/ul, Invitrogen, Carlsbad, California) was added and samples were incubated under the following conditions: 25C-10 minutes, 42C-50 minutes, 70C-15 minutes. Samples were then placed on ice. Second strand cDNA was synthesized by adding 61ul H2O to the first strand mix, 10 ul 10X second strand buffer (500 mM Tris-HCl pH 7.8, 50 mM MgCl2, 10 mM DTT), and 3 ul dNTP (10 mM), mixed, incubated on ice for 5 minutes, then 1 ul RNaseH (2U/ul, Invitrogen, Carlsbad, California) and 5 ul DNA Pol I (10 U/ul, Invitrogen, Carlsbad, California) were added. Samples were incubated at 16C for 2.5 hours and DNA products purified using a QIAquick spin column and following manufacture directions and eluted with 30 ul. cDNA fragment libraries were prepared for sequencing. The ends of cDNA fragments were repaired using 30 ul of DNA, 45 ul H2O, 10 ul T4 DNA ligase buffer with 10 mM ATP, 4 ul dNTP mix (10 mM), 5 ul T4 DNA polymerase (3 U/ul), 1 ul Klenow DNA polymerase (5U/ul), and 5 ul T4 PNK(10 U/ul). Samples were incubated for 30 minutes at 20C, purified with QIAquick PCR spin columns, and eluted with 32 ul of Buffer EB. A single 'A' base was added to the ends of cDNA by using 5 ul Klenow buffer, 10 ul dATP (1 mM) and 3 ul Klenow 3' to 5' exonuclease (5 U/ul). Samples were incubated at 37C for 30 minutes, purified with a QIAquick MiniElute column, and eluted with 19ul of EB solution. Paired-end adaptor oligonucleotdies were ligated to A overhang fragments as follows. Overhang fragments were combined with 25 ul DNA ligase buffer, 1 ul adaptor olio mix, and 5 ul DNA ligase (1U/ul). Samples were incubated at room temperature for 15 minutes, purified with a QIAquick MiniElute column, and eluted with 10 ul of buffer EB. cDNA templates were sized selected by gel purification then amplified by PCR using oligo-specific primers. Samples were loaded into a 2% agarose gel with 1X TAE buffer and run for 50 minutes with a 100 bp ladder. The gel was stained with ethidium bromide and bands were visualized under UV fluorescence. For each sample, a gel slice was cut at the 200 (+/- 25) bp region, purified with a QIAquick gel extraction kit, and eluted with 30 ul buffer EB. Purified cDNA was amplified in a 50 ul reaction using 25 ul Phusion Mix (Phusion polymerase, dNTPs, and buffer), 1 ul PE primer 1.1, 1 ul PE primer 2.1, and 23 ul template along with the following cycling conditions: initial denaturation 98C-30 sec, cycle denaturation 98C-10 sec, anneal 65C-30 sec, and extend 72C -30 sec with 15X cycles and a final extension of 72C for 5 minutes followed by a hold at 4C. The amplified product was purified using a QIAquick column and eluted with 30 ul buffer EB.

treatment_protocol: Aged flies were snap frozen on dry ice and immediately dissected of their gonads and associated reproductive tract in 1X PBS. The reproductive tracts and remaining carcasses were placed in 1.5 ml microfuge tubes containing 1X PBS and snap frozen on dry ice before being placed at -80 degrees C until RNA extraction.

value: Dissected Testes and Reproductive Tract

tag: developmental stage

value: Adult

value: 5-8 days post eclosion

tag: Sex

value: Male

tag: read length

value: 101 bp paired end


title: Dsim_0251.199_Testes_and_Reproductive_Tract_Replicate_1_2

status: Public on Aug 26 2011

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

tag: strain

tag: tissue

tag: age


title: Dsim_0251.199_Ovaries_and_Reproductive_Tract_Replicate_2

source_name: Dissected Ovaries and Reproductive Tract

value: Female

value: 75 bp paired end


title: Dsim_0251.199_Female_Carcass_min_Reproductive_Tract_Replicate_2

source_name: Carcass minus reproductive tract

value: Carcass minus reproductive tract


title: TDRD1WK3

status: Public on Aug 31 2011

city: Groningen

first: Eugene

last: Berezikov

address: Antonius Deusinglaan 1

department: European Research Institute for the Biology of Ageing

country: Netherlands

institute: University Medical Center Groningen

description: Small RNA sequence data

data_processing: 3' adapter sequences were trimmed and inserts longer than 18 nt were mapped to the D. rerio genome (Zv9).

organism: Danio rerio

source_name: 3 week old tdrd1 mutant gonads

extract_protocol: Tissue was homogenized in trizol and total RNA was isolated. RNAs ranging from 18-35 nucleotides were size selected from gel. For cDNA synthesis, the RNA molecules in the immunoprecipitated fraction were first poly A-tailed using poly(A)polymerase followed by ligation of synthetic RNA adapter to the 5' phosphate. First strand cDNA synthesis was then performed using an oligo(dT)-linker primer and M-MLVRNase H- reverse transcriptase. cDNA was PCR-amplified with adapter-specific primers and used in Illumina sequencing.

value: TL


title: Dsim_0251.199_Ovaries_and_Reproductive_Tract_Replicate_1

value: Dissected Ovaries and Reproductive Tract


title: ZiliIPTes

description: Small RNA sequence data (RIP-Seq)

source_name: RNA obtained from immunoprecipitation with Zili antibody

extract_protocol: Tissues in IP lysis buffer were sonicated for 2 minutes at 4 oC and centrifuged for 10 minutes at 16000 rpm at 4 oC. Supernatant was used for IP. One IP contains 30 Âµl Dynabeads (Invitrogen), 3 or 6 testes, and Zili antibody in a total volume of 500 Âµl.  RNA was then size selected (18-35 nucleotides) from gel. For cDNA synthesis, adaptors were ligated to the 3' and 5' ends of the RNAof the size-selected immunoprecipitated fraction. First strand cDNA synthesis was then performed using an oligo(dT)-linker primer and M-MLVRNase H- reverse transcriptase. cDNA was PCR-amplified with adapter-specific primers and used in Illumina sequencing.


title: WT3WK

description: Small RNA sequence data

source_name: 3 week old whole gonads


title: Dsim_0251.199_Male_Carcass_min_Reproductive_Tract_Replicate_2


title: Dsim_0251.199_Male_Carcass_min_Reproductive_Tract_Replicate_1


title: Dsim_0251.199_Female_Carcass_min_Reproductive_Tract_Replicate_1


title: Th2-Gata3-replicate [ChIP-Seq]

city: Memphis

middle: J

last: Abraham

state: TN

address: 262 Danny Thomas Blvd

department: Computational Biology

institute: St. Jude Children's Research Hospital

description: Gata3 ChIP-Seq

library_source: genomic

data_processing: Reads were aligned against genome build mm8 using ELAND. .bsites (bedgraph) files were created using MACS (Model-based Analysis for ChIP-Seq) version 1.4.0, with a p-value threshold of 1e-13 and no redundant reads used.

molecule: genomic DNA

organism: Mus musculus

source_name: T-helper 2 cells

growth_protocol: DN, DP, Naive CD4, nTreg and NKT cells are directly separatly from mice. CD8, Th1, Th2, Th17 and iTreg cells are cultured in specifc growth media.

extract_protocol: Following standard ChIP-seq protocol

tag: cell type

value: T-helper 2 cells (unstimulated)

tag: chip antibody

value: anti-Gata3 (558686, BD bioscience)


title: Th1-Gata3-KO-2 [RNA-seq]

description: RNA-seq

data_processing: Reads were aligned using the ELAND algorithm from Solexa. Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.

source_name: T-helper 1 cells w/ Gata3 knockout

growth_protocol: DP cells are separated from WT and GATA3-knockout mice respectively. Naïve CD4 cells are separated from Gata3fl/fl mice and then are infected with Retroviruses containing hCre-GFP-RV when the cells are diffentiated under Th1, Th2, Th17 and iTreg conditions, respectively.

extract_protocol: Standard RNA-seq protocol. Cells were lysed in the buffer containing PCR buffer, NP-40, DTT and Rnase Inhibiter and mRNAs were reverse-transcribed into cDNA using a poly(T) primer with anchor sequence (UP1) and unused primers are digested. Poly(A) tails are added to the first-strand cDNAs at the 3' end, and second-strand cDNAs are synthesized using poly(T) primers with another anchor sequence (UP2). Then cDNAs are evenly amplified by PCR using UP1 and UP2 primers, fragmented, and Illumina adaptors are ligated to the ends. After PCR amplification with Illumina primers, 200-300bp DNA fragments are purified for sequencing.

tag: genotype/variation

value: Gata3 knockout

value: T-helper 1 cells


title: Th17-WT-2 [RNA-seq]

description: RNA-seq

source_name: T-helper 17 cells

value: WT

value: T-helper 17 cells


title: Th1-WT-2 [RNA-seq]

description: RNA-seq

source_name: T-helper 1 cells


title: Th2-Gata3-KO-2 [RNA-seq]

description: RNA-seq

source_name: T-helper 2 cells w/ Gata3 knockout

value: T-helper 2 cells


title: DP-Gata3-replicate [ChIP-Seq]

description: Gata3 ChIP-Seq

source_name: Double positive cells

value: Double positive cells


title: Th2-WT-2 [RNA-seq]

description: RNA-seq


title: CD8-Gata3-KO-Gata3 [ChIP-Seq]

description: Gata3 ChIP-Seq in Gata3 KO cells

source_name: CD8 cells

value: C57BL/6 Gata3 KO

value: CD8 cells


title: USC_ChipSeq_NT2-D1_H3K27me3B_UCDavis

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

organism: Homo sapiens

tag: lab

value: USC

tag: lab description

value: Farnham - University of Southern California

tag: datatype

value: ChipSeq

tag: datatype description

value: ChIP-Seq

tag: cell

tag: cell organism

value: human

tag: cell description

value: malignant pluripotent embryonal carcinoma (Ntera2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID:6694356)

tag: cell karyotype

value: cancer

tag: cell lineage

value: inner cell mass

tag: cell sex

value: M

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: antibody

tag: antibody antibodydescription

value: rabbit monoclonal

tag: antibody targetdescription

value: Histone H3 (tri-methyl K27) marks repressed chromatin regions

tag: antibody vendorname

value: Cell Signaling

tag: antibody vendorid

tag: control

value: UCDavis

tag: control description

value: Input library was prepared at UC Davis.

tag: controlid

tag: replicate

tag: replicate description

value: tier 1


title: Th17-Gata3-KO-2 [RNA-seq]

description: RNA-seq

source_name: T-helper 17 cells w/ Gata3 knockout

tag: strain

tag: genotype/variation

value: Gata3 knockout

tag: cell type

value: T-helper 17 cells


title: DP-CD3hi-WT1 [RNA-seq]

description: RNA-seq

source_name: Double-positive CD3hi cells

value: WT

value: Double-positive CD3hi cells


title: DP-CD3lo-Gata3-KO2 [RNA-seq]

description: RNA-seq

source_name: Double-positive CD3lo cells w/ Gata3 knockout

value: Double-positive CD3lo cells


title: DP-CD3hi-WT2 [RNA-seq]

description: RNA-seq


title: DP-CD3lo-WT1 [RNA-seq]

description: RNA-seq

source_name: Double-positive CD3lo cells


title: DP-CD3lo-WT2 [RNA-seq]

description: RNA-seq


title: Itreg-WT-2 [RNA-seq]

description: RNA-seq

source_name: Inducible regulatory T cells

value: Inducible regulatory T cells


title: DP-CD3lo-Gata3-KO1 [RNA-seq]

description: RNA-seq


title: DP-CD3hi-Gata3-KO1 [RNA-seq]

description: RNA-seq

source_name: Double-positive CD3hi cells w/ Gata3 knockout


title: iTreg-Gata3-KO-2 [RNA-seq]

description: RNA-seq

source_name: Inducible regulatory T cells w/ Gata3 knockout


title: WTTESTIS

description: Small RNA sequence data

source_name: adult testis extract

value: TL


title: Th2-Ets1 [ChIP-Seq]

description: Ets1 ChIP-Seq

extract_protocol: Following standard ChIP-seq protocol. Chromatin from 1 × 107 cells was used for each ChIP experiment, which yielded approximately 100 ng of DNA. Antibodies against Ets1 were used. After reverse cross-linking and purification with Qiagen PCR purification kit, the ChIP DNA fragments were blunt-ended, ligated to the Solexa adaptors, and sequenced using the Illumina 1G Genome Analyzer.

value: T-helper 2 cells

tag: chip antibody

value: Ets1 (santa cruz, cat#sc111X, Lot#G1905)


title: Th2-Gata3-KO-H3K4me2 [Methyl-Seq]

description: Methyl-Seq

data_processing: Reads were aligned against genome build mm8 using ELAND

growth_protocol: DP cells are separated from WT and GATA3-knockout mice respectively.

extract_protocol: Following standard ChIP-seq protocol. Briefly, T cells were treated with MNase to generate approximately 80% mononucleosomes and 20% dinucleosomes. Chromatin from 1 × 107 cells was used for each ChIP experiment, which yielded approximately 100 ng of DNA. Antibodies against histone H3K4me3 (ab8580, Abcam) and H3K27me3 (07-449, Upstate) were used. After reverse cross-linking and purification with Qiagen PCR purification kit, the ChIP DNA fragments were blunt-ended, ligated to the Solexa adaptors, PCR amplified, and sequenced using the Illumina 1G Genome Analyzer.


title: ZiwiIPTes

description: Small RNA sequence data (RIP-Seq)

source_name: RNA obtained from immunoprecipitation with Ziwi antibody from zebrafish testis extract

extract_protocol: Tissues in IP lysis buffer were sonicated for 2 minutes at 4 oC and centrifuged for 10 minutes at 16000 rpm at 4 oC. Supernatant was used for IP. One IP contains 30 Âµl Dynabeads (Invitrogen), 3 or 6 testes, and Ziwi antibody in a total volume of 500 Âµl.  RNA was then size selected (18-35 nucleotides) from gel. For cDNA synthesis, adaptors were ligated to the 3' and 5' ends of the RNAof the size-selected immunoprecipitated fraction. First strand cDNA synthesis was then performed using an oligo(dT)-linker primer and M-MLVRNase H- reverse transcriptase. cDNA was PCR-amplified with adapter-specific primers and used in Illumina sequencing.


title: Th2-WT-H3K4me2 [Methyl-Seq]

description: Methyl-Seq


title: Dsim_0251.199_Testes_and_Reproductive_Tract_Replicate_1_1

source_name: Dissected Testes and Reproductive Tract

tag: tissue

value: Dissected Testes and Reproductive Tract

tag: developmental stage

value: Adult

tag: age

value: 5-8 days post eclosion

tag: Sex

value: Male

tag: read length

value: 101 bp paired end


title: USC_ChipSeq_PBMC_Input_UCDavis

source_name: PBMC

tag: lab

value: USC

tag: lab description

value: Farnham - University of Southern California

tag: datatype

value: ChipSeq

tag: datatype description

value: ChIP-Seq

tag: cell

value: PBMC

tag: cell organism

value: human

tag: cell description

value: Peripheral blood mononuclear cells

tag: cell lineage

value: mesoderm

tag: cell sex

value: M

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: antibody

value: Input

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

value: UCDavis


title: DP-CD3hi-Gata3-KO2 [RNA-seq]

description: RNA-seq

tag: strain

tag: genotype/variation

value: Gata3 knockout

tag: cell type

value: Double-positive CD3hi cells


title: Th2-Fli1 [ChIP-Seq]

description: Fli1 ChIP-Seq

source_name: T-helper 2 cells

extract_protocol: Following standard ChIP-seq protocol. Chromatin from 1 × 107 cells was used for each ChIP experiment, which yielded approximately 100 ng of DNA. Antibodies against Fli1 were used. After reverse cross-linking and purification with Qiagen PCR purification kit, the ChIP DNA fragments were blunt-ended, ligated to the Solexa adaptors, and sequenced using the Illumina 1G Genome Analyzer.

value: T-helper 2 cells

tag: chip antibody

value: Fli1 (santa cruz, cat#sc356X, Lot#L0407)


title: DP-WT-H3K27me3 [Methyl-Seq]

description: Methyl-Seq

value: WT

value: Double-positive cells


title: DP-WT-H3K4me1 [Methyl-Seq]

description: Methyl-Seq


title: CD8-Gata3-KO-Fli1 [ChIP-Seq]

description: Fli1 ChIP-Seq in Gata3 KO cells

value: C57BL/6 Gata3 KO

value: CD8 cells


title: DP-WT-H3K4me3 [Methyl-Seq]

description: Methyl-Seq


title: TDRD1IPlong

description: Small RNA sequence data (RIP-Seq)

source_name: RNA obtained from immunoprecipitation with Tdrd1 antibody from zebrafish testis extract

extract_protocol: Tissues in IP lysis buffer were sonicated for 2 minutes at 4 oC and centrifuged for 10 minutes at 16000 rpm at 4 oC. Supernatant was used for IP. One IP contains 30 Âµl Dynabeads (Invitrogen), 3 or 6 testes, and Tdrd1 antibody 1:100 in a total volume of 500 Âµl.  For cDNA synthesis, the RNA molecules in the immunoprecipitated fraction were first poly A-tailed using poly(A)polymerase followed by ligation of synthetic RNA adapter to the 5' phosphate. First strand cDNA synthesis was then performed using an oligo(dT)-linker primer and M-MLVRNase H- reverse transcriptase. cDNA was PCR-amplified with adapter-specific primers and used in Illumina sequencing.

value: TL


title: Th2-Gata3-KO-H3K27me3 [Methyl-Seq]

description: Methyl-Seq


title: CD8-Fli1 [ChIP-Seq]

description: Fli1 ChIP-Seq


title: kn_0_seedling_br1

status: Public on Aug 29 2011

city: Salt Lake City

first: Richard

middle: M

last: Clark

state: Utah

department: Department of Biology

institute: University of Utah

description:
r38_l3_kn_0_seedling_1
polyA RNA

data_processing: Technical replicates were mapped to TAIR9 gene models. Biological replicates were mapped to a mix of TAIR10 gene models and computationally predicted gene models. Data for all gene models in the annotations are given in the supplementary processed data files.

organism: Arabidopsis thaliana

source_name: 11-day-old seedling, Kn-0

growth_protocol: Arabidopsis seeds were stratified for 5 days at 4C. Plants were germinated on soil and grown for approximately 11 days under standard long day conditions, 16 hours light 8 hours dark, at 20C.

extract_protocol: Libraries were generated with methods adapted from the Illumina mRNA sample preparation protocol (cat. no 1004894 Rev.A).

tag: accession

tag: tissue

value: seedling

tag: age

value: 11 days

tag: replicate

value: biological replicate 1


title: Th17-Gata3 [ChIP-Seq]

description: Gata3 ChIP-Seq

source_name: T-helper 17 cells

growth_protocol: DN, DP, Naive CD4, nTreg and NKT cells are directly separated from mice. CD8, Th1, Th2, Th17 and iTreg cells are cultured in specifc growth media.

extract_protocol: Following standard ChIP-seq protocol. Chromatin from 1 × 107 cells was used for each ChIP experiment, which yielded approximately 100 ng of DNA. Antibodies against GATA3 (558686, BD bioscience) was used. After reverse cross-linking and purification with Qiagen PCR purification kit, the ChIP DNA fragments were blunt-ended, ligated to the Solexa adaptors, and sequenced using the Illumina 1G Genome Analyzer.

value: T-helper 17 cells

value: anti-Gata3 (558686, BD bioscience)


title: iTreg-Gata3-KO [RNA-seq]

description: RNA-seq of mRNA fraction

value: Inducible regulatory T cells


title: DP-Gata3-KO-H3K4me1 [Methyl-Seq]

description: Methyl-Seq

source_name: Double positive cells


title: Th1-Gata3 [ChIP-Seq]

description: Gata3 ChIP-Seq

source_name: T-helper 1 cells

value: T-helper 1 cells


title: iTreg-WT [RNA-seq]

description: RNA-seq of mRNA fraction


title: iTreg-Gata3 [ChIP-Seq]

description: Gata3 ChIP-Seq


title: DN-Gata3 [ChIP-Seq]

description: Gata3 ChIP-Seq

source_name: Double negative cells

value: Double negative cells


title: DP-Gata3-KO-H3K27me3 [Methyl-Seq]

description: Methyl-Seq

value: Gata3 knockout


title: NKT-Gata3 [ChIP-Seq]

description: Gata3 ChIP-Seq

source_name: Natural Killer T cells

value: Natural Killer T cells


title: DP-Gata3-KO-H3K4me3 [Methyl-Seq]

description: Methyl-Seq


title: CD4-Gata3 [ChIP-Seq]

description: Gata3 ChIP-Seq

source_name: Naïve CD4 cells

value: Naive CD4 cells


title: DP-Gata3 [ChIP-Seq]

description: Gata3 ChIP-Seq

value: Double positive cells


title: Th17-Gata3-KO [RNA-seq]

description: RNA-seq of mRNA fraction

source_name: T-helper 17 cells w/ Gata3 knockout


title: nTreg-Gata3 [ChIP-Seq]

description: Gata3 ChIP-Seq

source_name: Naïve regulatory T cells

value: Naive regulatory T cells


title: Th2-Gata3 [ChIP-Seq]

description: Gata3 ChIP-Seq

source_name: Unstimulated T-helper 2 cells

value: T-helper 2 cells (unstimulated)


title: CD8-Gata3 [ChIP-Seq]

description: Gata3 ChIP-Seq

source_name: CD8 cells


title: Th17-WT [RNA-seq]

description: RNA-seq of mRNA fraction

value: WT


title: Th2-Gata3-KO [RNA-seq]

description: RNA-seq of mRNA fraction

source_name: T-helper 2 cells w/ Gata3 knockout

value: T-helper 2 cells


title: Th2-WT [RNA-seq]

description: RNA-seq of mRNA fraction


title: Th1-WT [RNA-seq]

description: RNA-seq of mRNA fraction


title: Th1-Gata3-KO [RNA-seq]

description: RNA-seq of mRNA fraction

source_name: T-helper 1 cells w/ Gata3 knockout


title: Dpse_0121.94_Testes_and_Reproductive_Tract_Replicate_2

organism: Drosophila pseudoobscura

source_name: Dissected Testes and Reproductive Tract

extract_protocol: Total RNA was extracted from a pool of 60 dissected reproductive tracts using Trizol (Invitrogen, Carlsbad, CA). Libraries were were created using the standard TruSeq Low-Throughput RNA sample protocol (Part# 15008136 Rev. A, November 2010) (Illumina, San Diego, CA). The entire protocol was carried out in PCR tubes and all locations in the protocol where suggested incubation time was 2 or 5 minutes, 5 minutes was used. The sample showed an overabundance of primer-dimers when analyzed by BioAnalyzer (Agilent, Santa Clara, CA) after completion of the protocol, so it was run through 2 subsequent rounds of purification using Ampure XP beads (Beckman Coulter Genomics, Danvers, MA) and the following protocol: 54 ul of Ampure XP beads were added to the sample followed by pipetting up and down 10 times to mix. The sample was incubated at room temp for 5 mins before being placed on an Agencourt SPRIPlate 96 (Beckman Coulter Genomics, Danvers, MA) for 5 mins. The cleared solution was apirated and discarded before adding 200 ul of freshly prepared 70% EtOH and incubating for 30 seconds before removing EtOH (this EtOH was repeated for a total of 2 washes). The beads were allowed to dry for 5 mins on plate with open tubes before transfering them off of the Spriplate and adding 30 ul Tru-Seq resuspension buffer and pipetting up and down 10 times to mix. Finally the samples were placed on the Spriplate for 5 mins to elute the DNA, which was transfered to a new tube.

value: Dissected Testes and Reproductive Tract

tag: developmental stage

value: Adult

value: 5-8 days post eclosion

tag: Sex

value: Male

tag: read length

value: 75 bp paired end


title: Dpse_0121.94_Ovaries_and_Reproductive_Tract_Replicate_2

source_name: Dissected Ovaries and Reproductive Tract

value: Female


title: Dpse_0121.94_Ovaries_and_Reproductive_Tract_Replicate_1

value: Dissected Ovaries and Reproductive Tract


title: Dpse_0121.94_Female_Carcass_min_Reproductive_Tract_Replicate_2

source_name: Carcass minus reproductive tract

extract_protocol: Total RNA was extracted from a pool of 30 carcasses using Trizol (Invitrogen, Carlsbad, CA). Libraries were were created using the standard TruSeq Low-Throughput RNA sample protocol (Part# 15008136 Rev. A, November 2010) (Illumina, San Diego, CA). The entire protocol was carried out in PCR tubes and all locations in the protocol where suggested incubation time was 2 or 5 minutes, 5 minutes was used. The sample showed an overabundance of primer-dimers when analyzed by BioAnalyzer (Agilent, Santa Clara, CA) after completion of the protocol, so it was run through 2 subsequent rounds of purification using Ampure XP beads (Beckman Coulter Genomics, Danvers, MA) and the following protocol: 54 ul of Ampure XP beads were added to the sample followed by pipetting up and down 10 times to mix. The sample was incubated at room temp for 5 mins before being placed on an Agencourt SPRIPlate 96 (Beckman Coulter Genomics, Danvers, MA) for 5 mins. The cleared solution was apirated and discarded before adding 200 ul of freshly prepared 70% EtOH and incubating for 30 seconds before removing EtOH (this EtOH was repeated for a total of 2 washes). The beads were allowed to dry for 5 mins on plate with open tubes before transfering them off of the Spriplate and adding 30 ul Tru-Seq resuspension buffer and pipetting up and down 10 times to mix. Finally the samples were placed on the Spriplate for 5 mins to elute the DNA, which was transfered to a new tube.

value: Carcass minus reproductive tract


title: Dpse_0121.94_Male_Carcass_min_Reproductive_Tract_Replicate_1


title: Dpse_0121.94_Male_Carcass_min_Reproductive_Tract_Replicate_2


title: Dpse_0121.94_Female_Carcass_min_Reproductive_Tract_Replicate_1


title: WCE - BGO3

status: Public on Aug 24 2011

city: Cambridge

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description:
05082009_42750AAXX_B2
WCE sequence for BGO3 FF cells

data_processing:
Images analysis and base calling was done using the solexa pipeline.
Reads aligned to mouse NCBI build 36 (mm8 for mouse samples and hg18 for human) using BOWTIE.
For ChIP-Seq, sequences from all lanes were extended 200bp downstream (with respect to strand), and allocated into 25 bp bins. Reads from replicates were merged and genomic bins containing statistically significant ChIP-seq enrichment were identified by comparison to a Poissonian background model, using a p-value threshold of 10-9. Additionally, we used an empirical background model obtained from identical Solexa sequencing of DNA from whole cell extract (WCE) or IgG IP's from matched cell samples (>5X normalized enrichment across the entire region). WIG tracks show bins with at least 2 counts in the respective dataset (after replicate merging, where appropriate).

source_name: Embryonic stem cells

growth_protocol: hES cells were grown in mTESR media (Stem Cell Technologies) on plates coated with matrigel (BD Biosciences) in the absence of feeder cells.

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.

value: BGO3 (feeder free)

value: None (WCE)

tag: antibody vendor

tag: antibody catalog number


title: Smad3 - BGO3

description:
08142009_42J7HAAXX_B6
Chromatin IP against Smad3 in BG03 cells

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. 1x10^8 cells were sonicated at 21 watts for 20 second pulses for a total of 3 minutes. 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.

treatment_protocol: Cross-linking was performed with 1% formaldehyde

value: Abcam


title: H3K4me3neg_ChIPSeq

first: Bill

last: Wong

institute: Whitehead Institute

description: Chromatin IP against H3K4me3

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse mm9 (July 2007) genomes using the Illumina Genome Analyzer Pipeline. 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 using the Young Lab Analysis tool (described in PMID: 19884255)

source_name: fetal liver cells

growth_protocol: Primary fetal liver cells were isolated from E14.5 C57Bl6 pregnant mice and homogenized.  Using anti-Ter119 magnetic beads, the positive and negative fractions were separated for each samole (for each cell type listed above).  Fresh cells were fixed with 1% formaldehyde and then quenched with 2.5M glycine.

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3â end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: None, cells were isolated in-vivo and fixed immediately

value: fetal liver erythroid Ter119- cells

tag: passages

value: primary cells

tag: gender

value: female


title: H3K4me2neg_ChIPSeq

description: Chromatin IP against H3K4me2


title: H3K27me3neg_ChIPSeq

description: Chromatin IP against H3K27me3


title: H3K36me3neg_ChIPSeq

description: Chromatin IP against H3K36me3


title: RNAPolIIpos_ChIPSeq

description: Chromatin IP against RNA Pol II

value: fetal liver erythroid Ter119+ cells

value: RNA Pol II


title: H4K16Acpos_ChIPSeq

description: Chromatin IP against H4K16Ac


title: H3K27me3pos_ChIPSeq

description: Chromatin IP against H3K27me3


title: H3K9Acneg_ChIPSeq

description: Chromatin IP against H3K9Ac


title: H3K36me3pos_ChIPSeq

description: Chromatin IP against H3K36me3


title: Oct4 - BGO3

description:
05082009_42750AAXX_B3
Chromatin IP against Oct4 in BG03 cells off feeders

treatment_protocol: Cross-linked with 1% formaldehyde

value: Santa Cruz


title: Dpse_0121.94_Testes_and_Reproductive_Tract_Replicate_1

value: Dissected Testes and Reproductive Tract


title: RNAPolIIneg_ChIPSeq

description: Chromatin IP against RNA Pol II


title: H3K79me2pos_ChIPSeq

description: Chromatin IP against H3K79me2


title: cortex_F (mostly layer 6b)

city: Oxford

first: T

middle: Grant

last: Belgard

address: Le Gros Clark Building, South Parks Road

department: Department of Physiology, Anatomy and Genetics

country: United Kingdom

institute: University of Oxford

description: mostly layer 6b

data_processing:
Bam: Reads were processed with versions 1.4 and 1.6 of the Illumina pipeline.  The internal insert size and standard deviation was estimated for each library by empirically calculating the full width at half max (FWHM) for an internal insert size distribution constructed using uniquely mapping reads on the same chromosome from Illumina's Gerald pipeline.  The insert size was estimated to be the midpoint of the minimum and maximum insert sizes at half (or greater) the frequency of the most common insert size, and the standard deviation was calculated under a Gaussian assumption StdDev=FWHM/(2*sqrt(2ln2)).  Using this insert size and standard deviation, lanes were separately mapped with TopHat v1.0.13 to the mouse reference genome (mm9, downloaded from UCSC) plus all splice junctions from the UCSC Table Browser (cite) tables all_mrna (mouse mRNAs), intronEst (mouse spliced ESTs), and xenoMrna (mRNAs mapped from other species to mouse) with the following options: butterfly search, closure search, fill gaps, microexon search, min anchor length = 5, min isoform fraction = 0.0, max intron length = 500 kb.  In a second round of TopHat mapping (default options except min isoform fraction = 0.0), all novel junctions identified from any sample in the previous step were given to TopHat again (as raw junctions), so splice junctions could be measured across all samples in an unbiased manner.
Wig: WIG files created by parsing a pileup were normalized (such that scales were comparable across samples) as follows.  For normalization, uniquely mapping reads were first extracted from alignment files using a custom script and pysam.  Then, the number of unique (and uniquely mapping) reads overlapping (at least partially) each Ensembl (release 56) protein-coding gene model were quantified for each sample.  The exonic Ensembl models were further required to be >200 nt in size, as the experimental protocol selected against these, and as variations in expression levels might derive from the upstream experimental protocol.  Eliminating these 328 small gene models left 22533 Ensembl protein-coding gene models that were used in subsequent analyses.  Read counts were then normalized to adjusted read counts that were directly comparable across samples as a measure of relative expression.   For each gene model, the number of reads falling (at least partially) into that model was summed separately for each sample. Then, for each gene model in every sample, the ratio of (read counts in that model in the sample):(total number of read counts in that model across all samples) was calculated. The median ratio across all gene models was found for each sample.  Adjusted read counts were calculated for each sample by multiplying all read counts in that sample by (the minimum median ratio of all samples)/(median ratio of that sample).  These ratios were used to adjust WIG coverage densities to (often non-integral) normalized values.  These wigs represent uniquely mapping reads.
Expression: De novo transcript models were built for each sample using CuffLinks v0.8.3, providing the average insert sizes and standard deviations calculated previously and using default options.  Transcript models were combined across all samples using cuffcompare with default options, and comparing against a GTF of Ensembl gene models downloaded from Ensembl (release 57) and adapted to use the UCSC nomenclature.  Expression levels of the resultant unified cuffcompare transcript models were assessed in every sample using cufflinks in quantification-only mode with default settings.  Expression levels of all genes and transcripts in Ensembl (release 57) were quantified with cufflinks in quantification-only mode with default settings.  This is the tab-separated cufflinks output.
GTF: De novo transcript models were built for each sample using CuffLinks v0.8.3, providing the average insert sizes and standard deviations calculated previously and using default options.  Transcript models were combined across all samples using cuffcompare with default options, and comparing against a GTF of Ensembl gene models downloaded from Ensembl (release 57) and adapted to use the UCSC nomenclature.

molecule: polyA RNA

source_name: primary somatosensory cortex

extract_protocol: Total RNA >200 nt was extracted using the RNeasy Lipid Tissue Mini kit (QIAGEN), following the manufacturer's instructions and using the on-column DNase digest.  RNA quantity was assessed using a NanoDrop 1000 spectrophotometer (ThermoScientific), and RNA quality and integrity assessed using a BioAnalyzer (Agilent Laboratories).  Total RNA was prepared for paired-end deep sequencing on Illumina's Genome Analyzer II following the manufacturer's protocol.  Briefly, poly(A) RNA was enriched using Dynal oligo(dT) beads (Invitrogen).  This was fragmented using the RNA fragmentation kit (Ambion).  First- and second-strand cDNA was synthesized with random hexamer primers (Invitrogen) and SuperScript II (Invitrogen).  Ends were repaired using T4 DNA polymerase and Klenow DNA polymerase.  A single adenosine and Illumina adapters were ligated using Klenow 3'-to-5' exo-nuclease.  Following gel purification of cDNA templates, the library was enriched with 15 rounds of PCR before being added to the flow cell for paired-end sequencing (51 nt from either end, of which 50 nt was used in mapping; except for two libraries in sample F where 76 nt were sequenced from either end, using 75 in mapping).  Paired-end library average internal insert sizes (standard deviations) were as follows: A 164 (27); B1 239 (29); B2 193 (28); C 184 (21); D 208 (22); E 172 (24); F 184 (28); DC2 A 287 (31); DC2 B 290 (28); DC2 C 291 (28); DC2 D 269 (30); DC2 E 284 (31); DC2 F 279 (21); LC A 281 (40); LC B 275 (32); LC C 282 (41); LC D 267 (29); LC E 268 (38); LC F 272 (34).

value: primary somatosensory cortex

tag: number of pooled mice

value: male

tag: laminar sample (see publication)

value: F


title: cortex_E (mostly layer 6)

description: mostly layer 6

tag: strain

value: E


title: cortex_D (mostly layer 5)

description: mostly layer 5

value: D


title: cortex_B_rep2 (mostly layer 4)

description: mostly layer 4


title: Smad3 - Day 5 - Plus Myod1

description:
08042010_70703AAXX_B5
Chromatin IP against Smad3 (+ Myod1)

growth_protocol: Cells containing a tetracycline-repressible Myod1 were grown in standard ES cell media with the exception that penn/strep was replaced with 0.2 ug/ml doxycycline and 1.0 ug/ml puromycin.  For induction, cells were grown in the same media without doxycycline.  Induction of Myod was initiated 24 hours after cells were plated on gelatin on the second passage off MEFs.

treatment_protocol: Cells were grown in the absence of dox for 5 days.  Media was changed daily

value: MC1R(20):tetMyod1(14) embryonic stem cells


title: cortex_A (mostly layer 1-3)

description: mostly layers 1-3

value: A


title: MyoD_H2Flag - Day 5 - Plus Myod1

description:
08042010_70703AAXX_B6
Chromatin IP against Myod1 (+ Myod1)

value: MyoD

value: Sigma


title: H3K9Acpos_ChIPSeq

description: Chromatin IP against H3K9Ac


title: H3K79me2neg_ChIPSeq

description: Chromatin IP against H3K79me2


title: H3K4me2pos_ChIPSeq

description: Chromatin IP against H3K4me2


title: cortex_B_rep1 (mostly layer 4)

description: mostly layer 4


title: H3K4me3pos_ChIPSeq

description: Chromatin IP against H3K4me3


title: Smad3 - Day 5 - No Myod1

description:
06112010_62309AAXX_B1
Chromatin IP against Smad3 (- Myod1)

treatment_protocol: Cells were cultured in the presence of dox for 5 days.  Media was changed daily.

value: Abcam


title: IgG - Myotubes

description:
11132009_619PLAAXX_B1
Chromatin IP against IgG in c2c12 cells

source_name: myotubes

growth_protocol: C2C12 myoblasts were grown under typical C2C12 myoblast conditions.  Myotube formation was induced for 48 hours in 2% horse serum and 1x selenium, transferrin and insulin.

value: C2C12 cells

value: IgG


title: Smad3 - Pro-B cells

description:
02192010_614DKAAXX_B2
Chromatin IP against Smad3 in 38B9 cells

source_name: pro-B cell

growth_protocol: 38B9 (pro-B) cells were grown under typical conditions in RPMI media with 10% FCS.

treatment_protocol: Cells were treated with 5.0 ng/ml TGFβ for 1 hr.

value: 38B9 cells

tag: drug

value: TGFβ

tag: concentration

value: 5.0 ng/ml

tag: duration of treatment

value: 1 hr


title: Smad2/3 Activin - ESC

description:
06242008_2051JAAXX_B7
Chromatin IP against Smad2/3 in mouse ES cells

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.

tag: cell type

value: V6.5 embryonic stem cells

value: Activin

value: 10 ng/ml

tag: chip antibody

tag: antibody provider

value: D. Wotton UVA174


title: Smad3 - Pro-B cells (replicate)

description:
03272010_61HT6AAXX_B7
Chromatin IP against Smad3 in 38B9 cells

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. 1x10^8 cells were sonicated at 21 watts in 20 second pulses for 3 min of sonication time. Half of the cell lysate was used for immunoprecipitation. 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.

treatment_protocol: 38B9 cells were treated with 5.0 ng/ml of TGF-beta for 1 hour prior to cross-linking with 1% formaldehyde


title: Myod1 - Myotubes (replicate)

description:
03162010_folder61487AAXX_B3
Chromatin IP against MyoD in C2C12 cells

value: Santa Cruz


title: Smad3 - Myotubes

description:
07312009_42K4LAAXX_B3
Chromatin IP against Smad3 in C2C12 myotubes

value: 2.5 ng/ml

value: 2 hr


title: Smad3 - Day2 - No Myod1

description:
02172010_61484AAXX_B2
Chromatin IP against Smad3 (- Myod1)

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. Approximately 1x10^8 cells were sonicated at 21 watts in 20 second pulses for 3 mins of sonication time. 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.

treatment_protocol: Cells were grown for 48 hours in the presence of doxycycline to repress Myod. Cells were treated with 10 ng/ml activin for 1 hour prior to cross-linking with 1% formaldehyde. This was performed in parallel with cells grown in the absence of doxycycline to induce Myod.

value: MC1R(20):tetMyod1(14) embryonic stem cells


title: cortex_C (mostly layer 5)

description: mostly layer 5

tag: tissue

value: primary somatosensory cortex

value: male

tag: age

value: C


title: Smad3 - Myotubes (replicate)

description:
03162010_folder61487AAXX_B4
Chromatin IP against Smad3 in C2C12 myotubes

value: C2C12 cells

value: Abcam


title: Smad3 - Day 2 - Plus Myod1

description:
02172010_61484AAXX_B3
Chromatin IP against Smad3 (+ Myod1)

treatment_protocol: Cells were grown for 48 hours in the absence of doxycycline to induce Myod. Cells were treated with 10 ng/ml activin for 1 hour prior to cross-linking with 1% formaldehyde. This was performed in parallel with cells grown in the presence of doxycycline to repress Myod.


title: Myod1 - Myotubes

description:
07312009_42K4LAAXX_B1
Chromatin IP against MyoD in C2C12 cells

value: MyoD


title: PU.1 - Pro-B cells (replicate)

description:
03162010_folder61487AAXX_B2
Chromatin IP against Pu.1

value: 38B9 cells


title: Smad3 - ESC

description:
08082008_309DNAAXX_B2
Chromatin IP against Smad3

treatment_protocol: Normal culture conditions


title: PU.1 - Pro-B cells

description:
10272009_42YHBAAXX_B1
Chromatin IP against Pu.1


title: X. tropicalis_stage 10.5 Input

status: Public on Aug 23 2011

first: Se-Jin

last: Yoon

address: 300 Pasteur Drive, Alway M311

department: Genetics

institute: Stanford University

description: Input DNA

data_processing:
Alignment: Sequence reads were obtained and mapped to the Xenopus tropicalis genome (xenTro2; Aug 2005) using the Illumina Genome Analyzer Pipeline.
Peaks: Peaks were called using MACS 1.4 (Zhang et al. Model-based Analysis of ChIP-Seq (MACS). Genome Biol (2008) vol. 9 (9) pp. R137) with default settings (1.5e9 genome size, peak threshold p < 1e-5)

organism: Xenopus tropicalis

source_name: Input DNA

growth_protocol: Stage 10.5 in vivo embryos

extract_protocol: Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Catalog # FC-102-1001). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3â end. After adapter ligation DNA was PCR amplified with Illumina primers for 17 cycles and library fragments of 200~400 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 II following the manufacturer's protocols.

treatment_protocol: not applicable

value: embryo

tag: developmental stage

value: Stage 10.5 embryo


title: Smad3 Activin - ESC

description:
06242008_2051JAAXX_B8
Chromatin IP against Smad3 after Activin stimulation

treatment_protocol: Activin 10 ng/ml x 1hr

value: V6.5 embryonic stem cells

value: 1 hr


title: input_WCE_elav_rep1

status: Public on Aug 22 2011

city: Kansas City

first: Chris

middle: W

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

description:
manuscript descriptor: Neuron input (EAG wce)
input DNA

data_processing:
Image analysis and base calling were performed using the Illumina analysis pipeline.
BED files: Reads were aligned to UCSC dm3 using ELAND. Reads mapping with 2 or fewer mismatches were retained for further analysis. Reads from biological replicates or separate sequencing runs of individual libraries were combined and duplicate reads were removed leaving a unique set representing each sample type.
bedGraph files: Sequence coverage was calculated in R and bioconductor with the unique combined reads for each sample type by first by extending to 150 bases, and then calculating Reads Per Million (RPM) for 10 base intervals across the genome.

organism: Drosophila melanogaster

source_name: FACS isolated neuronal cells

growth_protocol: Stage 15-16 Drosophila melanogaster embryos were collected on apple juice/agar plates at 25C.

extract_protocol: DNA concentration was determined by Invitrogen Quant-iT PicoGreen assay (Invitrogen). For Illumina sequencing analysis, DNA libraries were generated from 10 ng input and 0.8 - 4.5 ng IP material, using the ChIP-Seq DNA Sample Prep Kit (Illumina) according to the manufacturer's specifications. Per the specified protocol, end-repair was performed with Klenow DNA polymerase to blunt the DNA ends. A single adenosine nucleotide was then added to the 3' end of each strand and Illumina adaptors were ligated to the ends with DNA ligase.  The samples underwent a 200 bp size selection using agarose gel electrophoresis and were amplified for 18 cycles via a polymerase chain reaction. Illumina libraries were then column (Qiagen) purified and concentrations were determined via Agilent Bioanalyzer analysis (Agilent Technologies). Cluster generation was performed on an Illumina cBOT and sequencing was performed on an Illumina GAIIx sequencer using v4 chemistries according to manufacturer's recommendations.

treatment_protocol: Embryos were dechorionated for 2 min in 50% bleach and rinsed well with embryo wash buffer (0.04% Triton X-100; 0.7% NaCl) and distilled water. Embryos were transferred to a 7 mL Dounce Homogenizer on ice containing 5 mL Schneider media supplemented with 3 mM EGTA and homogenized gently with the loose pestle for 8 - 10 strokes. Debris was pelleted in a 15 mL conical tube for 3 min at 50 x g and the supernatant decanted to a fresh conical tube. Cells were pelleted at 350 x g for 5 min, resuspended in 1.5 mL cold PBS (pH 7.4) and passed through a 70 um filter. All centrifugation steps were performed at 4ºC. Formaldehyde was added to dissociated cells in PBS to a final concentration of 1% and chromatin was cross-linked for 10 min at room temperature with rotation. Cross-linking was quenched by the addition of 120 ul 2.5 M glycine for 1 min at room temperature, and cells were pelleted by centrifugation at 350 x g for 5 min at 4ºC. Fixed cells were resuspended in 1 mL PBS (pH 7.4) and stored at 4oC for up to 7 days prior to FACS. Dissociated cells were sorted on a MoFlo high speed sorter (Beckman Coulter) for FACS of GFP positive cells. Gating was performed by first excluding sub-cellular debris from a plot of light scatter characteristics. Further gating on pulse width was performed to exclude undesired large particles, clusters of cells and small debris. Finally, GFP was plotted against yellow autofluorescence and single GFP positive cells were isolated for further analysis. GFP and autofluorescence were both excited with 488 nm laser light at 200 mW from a water-cooled argon ion laser (Coherent). GFP fluorescence was collected behind a 530/40 bandpass filter and autofluorescence behind a 580/30 filter on the FL1 and FL2 detectors, respectively. Single GFP positive cells were sorted into Buffer A2 (15 mM HEPEs [Na+], pH 7.5; 140 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 1% TritonX-100; 0.1% sodium deoxycholate; 0.1% SDS; 0.5% N-lauroylsarcosine; supplemented with Roche protease inhibitor tablet). Chromatin was pelleted by centrifugation at 15,000 x g for 30 min at 4ºC. 1 x 10^7 cell equivalent of FACS-isolated chromatin was resuspended in 300 uL Buffer A2 (15 mM HEPEs [Na+], pH 7.5; 140 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 1% TritonX-100; 0.1% sodium deoxycholate; 0.1% SDS; 0.5% N-lauroylsarcosine) and sonicated using a probe sonicator for 6 x 12 s at 30% amplitude with cooling in dry ice-ethanol bath between sonications. Insoluble debris was pelleted at 14,000 rpm for 10 min at 4oC and 275 uL soluble chromatin was used for immunoprecipitation analysis (IP). 25 uL of the soluble chromatin was retained as the input (WCE) sample. The following antibodies were used for ChIP: 1 ug anti-FLAG M2 antibody (mouse; F1804; Sigma), 2 ug anti-Pol II  antibody (mouse; 4H8; ab5408; Abcam; recognizes both phosphorylated and unphosphorylated forms of the CTD). 50 uL of pan-mouse IgG Dynabeads (Invitrogen) was added per 1 ug of antibody for 2 h at 4ºC. Beads were washed 5 x in RIPA Buffer (50 mM HEPEs [Na+], pH 7.5; 1 mM EDTA; 0.7% sodium deoxycholate; 1% NP-40; 0.5 M LiCl). DNA/protein complexes were eluted in TE Buffer containing 1% SDS and 250 mM NaCl 2 x 30 min at 65ºC. Cross-links were reversed at 65oC 6 h, DNA was treated with RNAse and proteinase K, and purified by phenol-chloroform extraction and ethanol precipitation.

tag: genotype

value: w; P{w+mC=UAS-ADA2B-HA1FLAG2}, P{w+mC=GAL4-elav.L}2/CyO; P{w+mC=UAS-mCD8::GFP.L}LL6

value: elav+ neuron cells

value: stage 15-16 embryos


title: input_WCE_notag_elav_rep1

description:
manuscript descriptor: Control WCE
input DNA

source_name: FACS isolated untagged neuronal cells

value: P{w+mW.hs=GawB}elavC155, P{w+mC=UAS-mCD8::GFP.L}LL4, P{ry+t7.2=hsFLP}1, w*


title: input_WCE_mef_rep1

description:
manuscript descriptor: Muscle input (MAG wce)
input DNA

source_name: FACS isolated muscle cells

value: w; P{w+mC=UAS-ADA2B-HA1FLAG2}; P{w+mC=UAS-mCD8::GFP.L}LL6, P{w+mC=Dmef2-GAL4}

value: mef2+ muscle cells


title: IP_notag_elav_rep1

description:
manuscript descriptor: Control IP
Chromatin IP with FLAG anibody in strain with no FLAG tag

value: FLAG

tag: vendor

value: Sigma

tag: catalog


title: Ada2b_IP_elav

description:
manuscript descriptor: SAGA Neuron (EAG)
Chromatin IP against FLAG tagged Ada2b
sample consists of two replicates


title: Ada2b_IP_mef

description:
manuscript descriptor: SAGA muscle (MAG)
Chromatin IP against FLAG tagged Ada2b
sample consists of two replicates


title: pol2_IP_mef

description:
manuscript descriptor: Pol II muscle (Pol II IP)
Chromatin IP against RNA polymerase II
sample consists of two replicates


title: IgG - Pro-B cells

description:
11102009_42YJEAXX_B7
Chromatin IP against IgG in 38b9 cells

value: IgG

tag: antibody vendor

value: Santa Cruz

tag: antibody catalog number


title: VZ-2-1

city: New Haven

first: Albert

middle: E.

last: Ayoub

state: CT

address: 333 Cedar St. SHM C317

department: Neurobiology

institute: Yale University

data_processing: mapping reads was performed using bowtie-0.12.3 and cufflinks-0.8.3

source_name: Ventricular zone, sample2

extract_protocol: standard Illumina mRNAseq library prep

tag: tissue origin

value: cerebral cortex

tag: embryonic zone

value: ventricular zone


title: VZ-2-2

tag: strain


title: SVZ-IZ-2-1

source_name: Subventricular and intermediate zone, sample2

value: subventricular and intermediate zone


title: SVZ-IZ-2-2


title: H4K16Acneg_ChIPSeq

description: Chromatin IP against H4K16Ac

value: fetal liver erythroid Ter119- cells

tag: passages

value: primary cells

tag: gender

value: female


title: VZ-1-2

source_name: Ventricular zone, sample1


title: VZ-1-1


title: CP-2-1

source_name: Cortical plate, sample2

value: cortical plate


title: SVZ-IZ-1-2

source_name: Subventricular and intermediate zone, sample1


title: SVZ-IZ-1-1


title: CP-1-1

source_name: Cortical plate, sample1


title: CP-1-2


title: X. tropicalis_stage 10.5 Smad2/3

description: Chromatin IP against Smad2/3

source_name: Chromatin IP against Smad2/3

value: embryo

value: Stage 10.5 embryo

value: Smad2/3, rabbit polyclonal

tag: chip antibody vendor

value: Santa Cruz Biotechnology, Inc

tag: chip antibody lot

tag: chip antibody catalog number


title: Nicotiana benthamiana-inoculated with TYLCCNV-21dpi

status: Public on Aug 21 2011

city: Hangzhou

first: Xiuling

last: Yang

state: Zhejiang Province

address: 268# Kaixuan Road

department: Institute of Biotechnology

country: China

institute: Zhejiang University

description: viral RNA

data_processing: The adapter sequences were trimmed from raw reads using a set of Perl Scripts and small RNAs between 16-27 nt in length were extracted. Only small RNA reads of sequences identical or complementary to TYLCCNV or TYLCCNB genomic sequences were recognized as V-sRNA or S-sRNA and those ranging between 20-24 nt in length were extracted for further analysis. The V-sRNA and S-sRNA reads were mapped to the TYLCCNV and TYLCCNB genome, respectively, using BLAST

organism: Tomato yellow leaf curl China virus

source_name: TYLCCNV infected leaves

growth_protocol: Plants were kept in an insect-free chamber at 25oC with a 16:8 h (light/dark)

extract_protocol: Total RNA was extracted using Trizol reagent and low molecular weight RNA fraction was enriched using NaCl and PEG8000. Libraries were constructed according to Illumina’s instructions. Briefly, 18-28 nt sRNAs were sequentially ligated to a 3' adapter and a 5' accepter. After each ligation step, sRNAs were purified using 15% denaturing PAGE. The final purified ligation products were reverse transcribed into cDNA using Superscript III reverse transcriptase (Invitrogen). The first strand cDNA was PCR amplified using Taq polymerase (Roche) and DNA amplicons from each library were purified Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: host

value: Nicotiana benthamiana

tag: inoculum

value: TYLCCNV

tag: time

value: three weeks post-inoculation

tag: inoculation method

value: Agrobacterium-mediated inoculation


title: Solanum lycopersicum-inoculated with TYLCCNV-21dpi

description: viral RNA

value: Solanum lycopersicum


title: Solanum lycopersicum-inoculated with TYLCCNV/TYLCCNB-21dpi

description: viral RNA

source_name: TYLCCNV and TYLCCNB co-infectedleaves

value: TYLCCNV and TYLCCNB


title: Nicotiana benthamiana-inoculated with TYLCCNV/mutated TYLCCNB-21dpi

description: viral RNA

source_name: TYLCCNV and mutant TYLCCNB infected leaves

value: TYLCCNV and mutant TYLCCNB


title: Nicotiana benthamiana-inoculated with TYLCCNV/TYLCCNB-21dpi

description: viral RNA

source_name: TYLCCNV and TYLCCNB infected leaves


title: Skin Normal 19

status: Public on Aug 19 2011

city: Saint Louis

first: Xiang

last: Zhou

address: Campus Box 1045, One Brookings Dr.

department: Computer Science and Engineering

institute: Washington University in St. Louis

data_processing: Each deep sequencing library was processed independently. Raw sequence reads were parsed to remove the 3'-adapters using an in-house program. Reads with length greater or equal to 17nt were retained. Unique sequences and their raw abundances were calculated after that.

source_name: Skin biopsy

growth_protocol: Punch skin biopsies were immediately immersed in RNAlater and stored at -80 degrees C prior to extraction

extract_protocol: Illumina Small RNA v1.5 sample preparation protocol

treatment_protocol: RNA extraction with miRNeasy kit (Qiagen PN217004) and on-column Dnase treatment (Qiagen PN79254)

tag: tissue

value: normal skin

tag: disease state

value: normal


title: Skin Normal 17


title: Skin Normal 20


title: Skin Normal 15


title: Skin Normal 12


title: Skin Normal 13


title: Skin Normal 16


title: Skin Normal 11


title: CP-2-2

value: cerebral cortex


title: Skin Normal 14


title: Skin Normal 7


title: Skin Normal 6


title: Skin Normal 4


title: Skin Normal 8


title: Skin Normal 10


title: Skin Normal 3


title: Skin Normal 2


title: Skin psoriasis uninvolved 24

source_name: Skin uninvolved psoriasis biopsy

value: skin psoriatic uninvolved

value: psoriasis


title: Skin psoriasis uninvolved 23


title: Skin Normal 1


title: Skin psoriasis uninvolved 22


title: Skin Normal 18


title: Skin psoriasis uninvolved 15


title: Skin psoriasis uninvolved 16


title: Skin psoriasis uninvolved 13


title: Skin psoriasis uninvolved 18


title: Skin psoriasis uninvolved 21


title: Skin psoriasis uninvolved 11


title: Skin Normal 9


title: Skin psoriasis uninvolved 8


title: Skin psoriasis uninvolved 12


title: Skin psoriasis uninvolved 14


title: Skin psoriasis uninvolved 10


title: Skin psoriasis uninvolved 19


title: Skin psoriasis uninvolved 6


title: Skin psoriasis uninvolved 5


title: Skin psoriasis uninvolved 4


title: Skin psoriasis uninvolved 2


title: Skin psoriasis uninvolved 3


title: Skin psoriasis involved 21

source_name: Skin psoriasis biopsy

value: skin psoriatic involved


title: Skin psoriasis uninvolved 7


title: Skin psoriasis involved 23


title: Skin psoriasis involved 20


title: Skin psoriasis involved 19


title: Skin psoriasis uninvolved 20


title: Skin psoriasis uninvolved 9


title: Skin psoriasis involved 18


title: Skin psoriasis involved 24


title: Skin psoriasis uninvolved 17


title: Skin psoriasis involved 16


title: Skin psoriasis involved 15


title: Skin psoriasis involved 13


title: Skin psoriasis involved 12


title: Skin psoriasis involved 10


title: Skin psoriasis involved 11


title: Skin psoriasis involved 22


title: Skin psoriasis involved 5


title: Skin psoriasis involved 8


title: Skin psoriasis involved 9


title: Skin psoriasis involved 7


title: Skin psoriasis involved 6


title: Skin psoriasis involved 4


title: Skin psoriasis involved 3


title: Skin psoriasis involved 2


title: Skin psoriasis involved 1


title: Skin Normal 5


title: RB-: total RNA (GTTC)

status: Public on Aug 18 2011

city: Würzburg

first: Marco

last: Albrecht

address: Am Hubland

department: Department of Microbiology

country: Germany

institute: University of Würzburg

description: total RNA

data_processing: Linkers, Barcodes and polyA tails were removed

organism: Chlamydia pneumoniae CWL029

source_name: Reticulate Bodies

growth_protocol: Intracellular growth in Hep2 cells

extract_protocol: As described in Berezikov et al (Nat Genet 38: 1375-1377) but without size fractionation

tag: sample type

value: total RNA

tag: life cycle form

value: Reticulate Bodies


title: RB+: RNA enriched for native 5' (TCAT)

description: enriched RNA

value: RNA enriched for native 5' ends


title: RB-: total RNA (AGTCAG)

description: total RNA


title: RB+: RNA enriched for native 5' (ATACTG)

description: enriched RNA


title: EB+: RNA enriched for native 5' (GTGA)

description: enriched RNA

source_name: Elementary Bodies

value: Elementary Bodies


title: Skin psoriasis involved 17


title: EB+: RNA enriched for native 5' (AGCGTA)

description: enriched RNA


title: HuR PAR-CLIP

city: Durham

first: Neelanjan

last: Mukherjee

state: NC

address: 101 Science Drive

department: Institute for Genome Sciences & Policy

institute: Duke University

description: HuR ribonucleoprotein complexes

data_processing: Mapping Reads: The reads from the HuR PAR-CLIP deep sequencing library was stripped of the 3â adapter sequence using the FASTX toolkit (http://hannonlab.cshl.edu/fastx_toolkit/).  Reads that were less than 13nt in length or contained an ambiguous nucleotide were discarded.  The remaining reads were aligned to the human genome (hg19), with up to 2 mismatches allowed, by the Bowtie algorithm (Langmead et al., 2009).  Mapped locations were only reported for those with the minimum number of observed mismatches for each read.  All T to C mismatches between the RNA fragment and the genome were subtracted from the mismatch count for each mapped location.  After subtraction only reads that mapped to a single genomic location at the minimum number of mismatches were used for further analysis.  The location that a read mapped, relative to a known transcript, was determined based on the ENSEMBL v57 database 1(Hubbard et al., 2007).  If a read mapped to a location representing multiple categories, it was reported to belong to the category based on the following order of preference: 3'UTR, coding sequence, 5'UTR, intron, non-coding RNA, intergenic. Defining HuR binding sites by PARalyzer: Overlapping reads were grouped together for further analysis. A group must have contained >=5 reads with conversions at two or more locations. Separate kernel density estimates were calculated across all positions based on read counts both with and without T to C conversions, as long as there was a minimum read depth of 5 at a position to ensure a robust density estimate. Clusters were defined as regions for which the conversion density was greater than the non-conversion density for at least 5 consecutive nucleotides, and extended until the group read depth fell below 5. Following filtering (see supplemental methods), clusters were scored by a cross-linking index (CLI) = log2(1+T to C conversion events for all reads within a cluster). PARalyzer is available at http://www.genome.duke.edu/labs/ohler/research/PARalyzer

source_name: HEK 293

growth_protocol: HEK293 T-REx Flp-In cells (Invitrogen) were grown in D-MEM high glucose with 10% (v/v) fetal bovine serum, 1% (v/v) 2 mM L-glutamine, 1% (v/v) 10,000 U/ml penicillin/10,000 ug/ml streptomycin, 100 ug/ml zeocin and 15 Âµg/ml blasticidin. Cell lines stably expressing FLAG/HA-tagged HuR was generated by co-transfection of pFRT/TO/FLAG/HA/HuR construct with pOG44 (Invitrogen). Cells were selected by exchanging zeocin with 100 ug/ml hygromycin. Expression of FLAG/HA-HuR was induced by addition of 250 ng/ml doxycycline 15 to 20 h before crosslinking.

extract_protocol: The pellets of cells crosslinked with UV 365 nm were resuspended in NP40 lysis buffer and incubated on ice for 10 min. The cell lysate was cleared by centrifugation at 13,000g. RNase T1 (Fermentas) was added to the cleared cell lysates and the reaction mixture was incubated at 22 C for 15 min and subsequently cooled for 5 min on ice before addition of antibody-conjugated magnetic beads. The recovered RNA was carried through a cDNA library preparation protocol originally described for cloning of small regulatory RNAs (Hafner et al., 2008). The first step, 3' adapter ligation, was carried out as described on a 20 ul scale using 10.5 ul of the recovered RNA. UV 365 nm crosslinked sample RNAs were processed using Solexa sequencing adapter sets. Depending on the amount of RNA recovered, 5'-adapter-3'-adapter products without inserts may be detected after amplification of the cDNA as additional PCR bands. In such case, the longer PCR product of expected size was excised from a 3% NuSieve low-melting point agarose gel, eluted from the gel pieces with the Illustra GFX-PCR purification kit (GE Healthcare) and Solexa sequenced.

treatment_protocol: For UV crosslinking, cells were washed once with ice-cold PBS while still attached to the plates. PBS was removed completely and cells were irradiated on ice with 365 nm UV light in a Stratalinker 2400 (Stratagene). Cells were scraped off with a rubber policeman in 1 ml PBS per plate and collected by centrifugation at 500ug for 5 min.

tag: crosslinker and crosslinking wavelength

tag: antibody

value: Flag M2

tag: immunoprecipitated protein

value: HuR, ELAVL1


title: Vector, C2C12, Flag-IP

status: Public on Aug 17 2011

description:
07242008_20A50AAXX_B2
Control chromatin IP using Flag antibody in C2C12 cells infected with empty vector.

data_processing:
Images analysis and base calling were done using the Solexa pipeline.

For all samples, reads were aligned to mouse genome build mm8 using ELAND.

All Flag-Msx1 aligned sequences were combined and extended 200bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Bins with at least 2 reads are shown.

source_name: C2C12 cells infected with empty vector, Flag ChIP

growth_protocol: C2C12 myoblast cells were maintained in DMEM supplemented with 10% fetal bovine serum in a humidified atmosphere with 5% CO2 at 37 degrees C. Cells were then infected with retrovirus containing an empty expression vector, cultured for two days, and then crosslinked for ChIP analysis.

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 anti-Flag antibody. 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.

treatment_protocol: One day prior to retroviral infection, C2C12 cells were seeded at a density of 2.5x10^5 cells/10 cm plate, and subsequently infected with virus-containing supernatant supplemented with 8 ug/ml polybrene for two consecutive days. Cells were then crosslinked with 1% formaldehyde for 10 minutes at room temperature, harvested, and washed with PBS, and cell pellets were flash frozen and stored at -80 degrees Celsius until processing for ChIP-Seq.

tag: cell line

tag: cell type

value: myoblast

tag: chip antibody

value: anti-Flag

tag: antibody vendor

value: Sigma

tag: antibody catalog number

tag: antibody lot number

tag: vector

value: Flag


title: seq-JL00001_DPY27_N2_L3_3

city: Chapel Hill

first: Tristan

last: De Buysscher

address: CB# 3280, Coker Hall

department: Biology

institute: University of North Carolina at Chapel Hill

description:
input control: GSM706166
Chromatin IP against DPY27. http://wiki.modencode.org/project/index.php/Worm_chromatin_immunoprecipitation:JL:IL2

data_processing:
BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). See the link @ http://bio-bwa.sourceforge.net/. It runs as DEFAULT for both bwa aln and bwa samse.
ChIP-Seq MACS Peak-calling:JL:1. Peak calls were determined by using Model-based Analysis of ChIP-Seq (MACS) software. MACS was supplied with the following parameters: tagSize = 25 mfold = 10,30 genomeSize = 90000000 bandwidth = 300 pvalue = 1e-5
Processed data file build: ce6

organism: Caenorhabditis elegans

source_name: whole body

growth_protocol: About 2-7 million of worms are bleached and then hatched in M9 for 24-42 hrs. About 100 embryos are seeded onto the plate to test for contamination and hatching efficiency. Remaining hatched L1 larvae are inoculated in a proper volume of liquid culture. Next day when larvae reach the L3 stage they are cleaned by M9 washes and sucrose gradient and collected by freezing in liquid nitrogen. Just before collection DIC pictures are taken and about 50ul of worms are stained for DAPI to assess the stage. http://wiki.modencode.org/project/index.php/Worm_L3_growth_and_harvest:JL:PK1

extract_protocol: Libraries were prepared according to Illumina's instructions for "Preparing Samples for ChIP Sequencing of DNA", with some variation. DNA was end-repaired using T4 DNA polymerase, Klenow DNA polymerase and T4 DNA polymerase.  A's were then added to the 3' ends of the fragments using Kelow fragment (3'  5' exo minus). Paired-end adapters were then ligated onto the ends of the fragments.  DNA library was size selected by gel purification, fragments of 250-500 bp were band isolated from an agarose gel. DNA was PCR amplified for 18 cycles. The Bioanalyzer was used to verify fragment purification and quantify DNA.

treatment_protocol: Worms are frozen, ground, and crosslinked for 10 minutes in 1% formaldehyde. Formaldehyde is quenched and cross-linked tissue washed, then resuspended in FA buffer and subjected to sonication in Bioruptor (14 pulses of 30 seconds with 1 minute rests in between). Extracts are then spun down and soluble fraction is stored for quality tests and future ChIP. http://wiki.modencode.org/project/index.php/Worm_L3_extraction:JL:PK1

value: whole body

tag: strain

tag: Stage

tag: chip antibody supplier

value: Covance


title: EB-: total RNA (GTAT)

description: total RNA


title: Flag-Msx1, C2C12, Flag-IP

description:
This Sample represents three Flag-Msx1 experiments.

Chromatin IP against Flag-Msx1 expressed in C2C12 cells.

07242008_20A50AAXX_B1
08132008_20A63AAXX_B4
08132008_20A63AAXX_B5

source_name: C2C12 cells expressing Flag-Msx1, Flag ChIP

growth_protocol: C2C12 myoblast cells were maintained in DMEM supplemented with 10% fetal bovine serum in a humidified atmosphere with 5% CO2 at 37 degrees C. Cells were then infected with retrovirus expressing a Flag-Msx1 construct, cultured for two days, and then crosslinked for ChIP analysis.


title: seq-JL00001_DPY27_N2_L3_2

description:
input control: GSM706165
Chromatin IP against DPY27. http://wiki.modencode.org/project/index.php/Worm_chromatin_immunoprecipitation:JL:IL2

tag: tissue


title: Skin psoriasis involved 14

tag: disease state


title: seq-AB9050_H3K36me3_N2_L3_7

description:
input control: GSM706166
Chromatin IP against H3K36me3. http://wiki.modencode.org/project/index.php/Worm_Chromatin_Immunoprecipitation:JL:PK1

value: Abcam

tag: chip antibody catalog#

tag: chip antibody lot#


title: seq-NA_N2_L3_1_E77 [input DNA]

description:
C. elegans N2 L3 input control

Input lanes for ChIP-seq analysis of elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus.

source_name: Control sample from L3 stage N2 worms, whole body


title: seq-AB9050_H3K36me3_N2_L3_1

description:
input control: GSM779423
Chromatin IP against H3K36me3. http://wiki.modencode.org/project/index.php/Worm_Chromatin_Immunoprecipitation:JL:PK1


title: small RNAs (18-29nt) from homozygotes of zuc mutants

status: Public on Aug 16 2011

city: Vienna

first: Julius

last: Brennecke

address: Dr. Bohrgasse 3

country: Austria

institute: IMBA

description: small RNAs (18-29nt) selected by PAGE

data_processing: raw reads start at their 5'end with the first base of the small RNA; at the 3' end, reads contain the 3' linker used for library generation (sequence: TCGTATGCCGTCTTCTGCTTG); this linker was trimmed bioinformatically and resulting reads matching the release5 genome sequence of D. melanogaster were the basis for the processed data file.

source_name: zuc mut

growth_protocol: flies were grown at 25 degrees on standard medium

extract_protocol: total RNA was isolated with Trizol, piRNAs were cloned as described in Brennecke et al. 2007.

tag: genotype

tag: stage

value: from 5-6 days old flies

value: ovary


title: small RNAs (18-29nt) from homozygotes of fs(1)yb mutants

description: small RNAs (18-29nt) selected by PAGE

source_name: fs(1)yb mut


title: small RNAs (18-29nt) from heterozygotes of zuc mutants

description: small RNAs (18-29nt) selected by PAGE

source_name: zuc het

value: zuc_hm27/Cyo or zuc_cd761/Cyo


title: small RNAs (18-29nt) from heterozygotes of fs(1)yb mutants

description: small RNAs (18-29nt) selected by PAGE

source_name: fs(1)yb het


title: EB-: total RNA (ACGTGC)

description: total RNA

tag: sample type

tag: life cycle form


title: small RNAs (18-29nt) from heterozygotes of CG4771-delta1

description: small RNAs (18-29nt) selected by PAGE

source_name: CG4771 het


title: VDR ChIP-seq calcitriol

city: Kuopio

first: Sami

last: Heikkinen

address: Yliopistonranta 1E

department: Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

description: Chromatin IP against VDR

data_processing:
Alignment: Sequence reads were obtained and mapped to the human genome (hg19) using Bowtie.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)

source_name: THP-1 cells

growth_protocol: Cells were grown in RPMI 1640 medium supplemented with 10% fetal calf serum, 2 mM L-glutamine, 0.1 mg/ml streptomycin and 100 U/ml penicillin, and kept at 37 °C in a humidified 95% air/ 5% CO2 incubator.

extract_protocol: Standard protocol as suggested by the manufacturer for ChIP-seq libraries as utilized at the EMBL Gene Core in Heidelberg, Germany.  Complete protocols (including antibody details) are supplied as a supplementary file on the Series record.

treatment_protocol: Prior to chromatin immunoprecipitation with indicated antibody, cells were grown overnight in phenol red-free medium supplemented with charcoal-stripped fetal bovine serum. Then, cells were treated for 40 min with 10 nM 1?,25(OH)2D3 (Sigma-Aldrich) or left untreated (unstimulated)

tag: cell line

tag: treatment

tag: antibody

value: VDR


title: small RNAs (18-29nt) from homozygotes of armi mutants

description: small RNAs (18-29nt) selected by PAGE

source_name: armi mut


title: IgG control

description: Chromatin IP against IgG

value: pooled

value: IgG


title: small RNAs (18-29nt) from heterozygotes of armi mutants

description: small RNAs (18-29nt) selected by PAGE

source_name: armi het


title: Vret Heterozygote

status: Public on Aug 15 2011

city: New York

first: Colin

middle: Dean

last: Malone

state: NY

address: NYUMC, Skirball Institute, 540 1st Ave, 4-10

department: Skirball Institute - Developmental Genetics

institute: NYU Medical Center

description: small RNA sequencing

data_processing: The 36nt long Illumina reads were stripped of the 3â linker (CTGTAGGCACCATCAATC) and the resulting small RNA sequences were mapped to the Release 5 genome excluding the Uextra portion. Only reads matching the fly genome 100% were used for further analysis. For annotation, we used Flybase for protein coding genes, UCSC for non-coding RNAs and transposons/repeats (repeat masker tracks) and the most recent miRNA catalog. To control for sequencing depth, small RNA counts were normalized to the same total number after subtracting those matching abundant cellular RNAs such as rRNAs and tRNAs. For the piRNA analysis, we selected small RNAs, which exceeded 22 nt in length and were not annotated as miRNA, tRNA, rRNA, snoRNA, snRNA or smRNA. SEQLEN = the small RNA sequence length, in nucleotides. MAPNUM = the number of times the small RNA matches the respective genome sequence. All small RNAs were converted into DNA for sequencing, therefore U's are represented as T's.

source_name: heterozygote (control)

growth_protocol: 25 degrees C

extract_protocol: Trizol

treatment_protocol: Trizol/Phenol Chloroform extractions

tag: genotype/variation

value: Vret Heterozygote

value: ovaries


title: Nelf-b_ChIPSeq

city: Boston

first: Jianlong

last: Sun

address: 1 Blackfan Street

department: Hematology/Oncology

institute: Boston Children's Hospital

description: Chromatin IP against Nelf-b

data_processing: Sequence aligns (35 bases) were extended in silico at their 3’ ends to a length of 110 bp, which is the average fragment length in the size-selected library.  To identify the density of fragments (extended tags) along the genome, the genome is divided into 32-nt bins and the number of fragments in each bin is determined.  This information is stored in a BAR (Binary Analysis Results)     The MACS peak finding algorithm (Genome Biol, R137) was used to identify Nelf-b intervals, which represent the locations of fragment density peaks.  A cut-off of p-value 1.00e-10 was applied and intervals presented in the Input sample were excluded. The identified Nelf-b intervals were compiled into BED file and further analyzed using Genpathway proprietary software that provides comprehensive information on genomic annotation, peak metrics, and sample comparisons for all peaks (intervals).     Gene association of Nelf-b interval was analyzed by the “GeneMargin” method of Genpathway.  The GeneMargin was set as a region 10,000 bp upstream and downstream of NCBI-annotated genes.  Any interval within the GeneMargin of a gene is counted as being associated with that gene.

source_name: mouse embryonic fibroblast

growth_protocol: MEFs were maintained in Dulbecco's modification of Eagle's medium supplemented with 10% fetal bovine serum.

extract_protocol: Cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine.  Chromatin was isolated by adding lysis buffer, followed by disruption with a Dounce homogenizer.  Lysates were sonicated and the DNA was sheared to an average length of 300-500 bp.  Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K, and heat for de-crosslinking, followed by ethanol precipitation.  Pellets were resuspended and the resulting DNA was quantified on a NanoDrop spectrophotometer.  Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield.     An aliquot of chromatin (60 g) was precleared with protein A agarose beads (Invitrogen).  Genomic DNA regions of interest were isolated using the polyclonal anti-mouse Nelf-b antibody.  After incubation at 4°C overnight, protein A-agarose beads were used to isolate the immune complexes.  Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment.  Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.     Quantitative PCR (qPCR) reactions were carried out in triplicate on specific genomic regions using SYBR Green Supermix (Bio-Rad).  The resulting signals were normalized for primer efficiency by carrying out qPCR for each primer pair using Input DNA.      ChIP and Input DNAs were prepared for amplification by converting overhangs into phosphorylated blunt ends and adding an adenine to the 3’ ends.  Illumina adaptors were added and the library was size-selected (175-225 bp) on an agarose gel. The adaptor-ligated libraries were amplified for 18 cycles. The resulting amplified DNAs were purified, quantified, and tested by qPCR at the same specific genomic regions as the original ChIP DNA to assess quality of the amplification reactions.  Amplified DNAs (DNA libraries) were sent to Illumina Sequencing Services for sequencing on a Genome Analyzer II.

treatment_protocol: Asynchronously growing cells were used for ChIP

tag: cell type

value: embryonic fibroblast derived from Nelf-b f/- embryo

tag: chip antibody

value: anti-Nelf-b (purified polyclonal)

value: mixed background of 129/SvJ, C57BL/6, and FVB


title: dSETDB1 Mutant

description: small RNA sequencing

source_name: dSETDB1 Mutant

tag: strain

value: egg1473/ Df(2R)Dll-Mp

value: dSETDB1 Mutant


title: Vret Mutant

description: small RNA sequencing

source_name: mutant

value: Vret Mutant


title: Nascent RNA sequencing of C2C12 cell

city: Chicago

first: Zhe

last: Ji

state: ILLINOIS

address: 303 E Superior St, Lurie 6-107

institute: Northwestern University

description:
GRO-seq C2C12 cell
instrument model: Illumina Genome Analyzer IIx
library strategy: Directional RNA-seq

data_processing: Reads were mapped to the mouse genome (mm9) using Bowtie allowing up to 3 mismatches. Unmapped reads were trimmed to the first 38 nt and mapped to the genome again by Bowtie allowing up to 3 mismatches.

source_name: C2C12 nascent RNA

growth_protocol: C2C12 cells grown to ~80% confluency in DMEM + 10% FBS

extract_protocol: After nuclear run on (with 5-Bromo-UTP), the reaction mix was treated with 50 U DNase I (Roche) at 37oC for 1 hr followed by incubation for 1 hr at 55oC with an equal volume of buffer S containing 20 mM Tris-HCl pH7.4, 2% SDS, 10 mM EDTA, 200 mg/ml Proteinase K (Roche). RNA was extracted by 2x phenol/chloroform followed by ethanol precipitation. Purified RNA was fragmented to ~100 nt by the RNA Fragmentation Reagents kit (Ambion) for 15 min at 70oC, and was subjected to immunoprecipitation with the anti-BrdU antibody (2 mg/reaction, Sigma) conjugated with protein G Sepharose (GE Healthcare). Immunoprecipitated RNA was extracted by phenol/chloroform and ethanol precipitation. The immunoprecipitation step was repeated twice (three rounds in total) to obtain pure nascent RNA. Purified nascent RNA was treated with shrimp alkaline phosphatase (Roche) at 1 U/reaction for 30 min at 37oC to remove the 3’ phosphate group from RNA, followed by addition of the 5’ phosphate with T4 kinase (NEB) at 10 U/reaction for 1 hr at 37oC. Treated RNA was purified and used to prepare a sequencing library using the Illumina Small RNA Sample Prep Kit (v1.5). Deep sequencing was carried out on an Illumina GA IIx Genome Analyzer.

value: C2C12 cells

tag: rip antibody

value: anti-BrdU antibody

tag: rip antibody vendor

value: Sigma


title: Input_ChIPSeq

description: Input DNA


title: Bam Mutant

description: small RNA sequencing

source_name: Bam Mutant (developmental control)

value: Bam Mutant

tag: tissue


title: S2 input DNA rep2

city: Bethesda

first: Ryan

last: Dale

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

institute: National Institutes of Health

description: We used antibody published in Kawamura Y, et al. (2008) Drosophila endogenous small RNAs bind to Argonaute 2 in somatic cells. Nature 453(7196):793-797. The monoclonal antibody is named 9D6

data_processing:
SAM files were created by mapping raw reads with Bowtie v0.12.5 to the euchromatic chromosomes of dm3 (chr2L, chr2R, chr3L, chr3R, chr4, chrX), allowing up to 2 mismatches per read and reporting only uniquely-mapping reads (-n2 -m1 -best -sam)
WIG files were created by running MACS v1.3.7.1 on the SAM files for input and IP for each cell type, using the default settings and specifying a tag size of 36bp and bandwidth of 150bp (-tsize=36 -bw=150)

source_name: S2 cells

growth_protocol: Shield and Sangs M3 Insect medium (Sigma) supplemented with 0.1% yeast extract, 0.25% bactopeptone, and 10% fetal bovine serum (HyClone)

extract_protocol: Illumina Genomic DNA Sample Preparation


title: VDR ChIP-seq unstimulated

description: Chromatin IP against VDR

value: unstimulated


title: Sleeping Beauty induced lymphoma (NlaIII sample 126)

status: Public on Aug 12 2011

city: Amsterdam

first: Jos

last: Jonkers

email: j.jonkers@nki.nl, m.koudijs@nki.nl

address: Plesmanlaan 121

department: Molecular Biology

institute: Netherlands Cancer Institute

description:
Barcode sequence: TCGATCACGT
NlaIII sample 126
Processed data file: Insertions_Nla.bed
Processed data file build: NCBI m37
Original raw file name: Pool15.NlaIII.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR

data_processing: Sequence reads are mapped to NCBI m37 using BLAT, sorted on barcode and processed using custom made algortihms as described in the associated manuscript. All scripts available on request. The export.txt files contain a summary of all unique integration sites. Per integration site 1 read ID is shown together with the cumulative number of sequence reads (depth), without specifying the individual read IDs per integrations site.

source_name: LYMPHOMA THYMUS

extract_protocol: Isolation of gDNA and ligation-mediated amplification of regions flanking retroviral insertions after endonucelase digestion or acoustic shearing of gDNA. Subsequently, barcoded  PCR products were pooled and sequenced on a 454 GS_FLX system according to the manufacturers protocol.

value: mixed C57Bl6/129S5SvEvBrd

tag: mouse id#

tag: transposon

value: Sleeping beauty


title: Sleeping Beauty induced lymphoma (NlaIII sample 127)

description:
Barcode sequence: TCGCACTAGT
NlaIII sample 127
Processed data file: Insertions_Nla.bed
Processed data file build: NCBI m37
Original raw file name: Pool15.NlaIII.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR

source_name: LEUKAEMIA SPLEEN


title: Th2-WT-H3K27me3 [Methyl-Seq]

city: Memphis

first: Brian

last: Abraham

address: 262 Danny Thomas Blvd

institute: St. Jude Children's Research Hospital

description: Methyl-Seq

data_processing: Reads were aligned against genome build mm8 using ELAND

source_name: T-helper 2 cells

growth_protocol: DP cells are separated from WT and GATA3-knockout mice respectively.

extract_protocol: Following standard ChIP-seq protocol. Briefly, T cells were treated with MNase to generate approximately 80% mononucleosomes and 20% dinucleosomes. Chromatin from 1 × 107 cells was used for each ChIP experiment, which yielded approximately 100 ng of DNA. Antibodies against histone H3K4me3 (ab8580, Abcam) and H3K27me3 (07-449, Upstate) were used. After reverse cross-linking and purification with Qiagen PCR purification kit, the ChIP DNA fragments were blunt-ended, ligated to the Solexa adaptors, PCR amplified, and sequenced using the Illumina 1G Genome Analyzer.

value: WT

value: T-helper 2 cells


title: S2 input DNA rep1

data_processing:
SAM files were created by mapping raw reads with Bowtie v0.12.5 to the euchromatic chromosomes of dm3 (chr2L, chr2R, chr3L, chr3R, chr4, chrX), allowing up to 2 mismatches per read and reporting only uniquely-mapping reads (-n2 -m1 -best -sam)
WIG files were created by running MACS v1.3.7.1 on the SAM files for input and IP for each cell type, using the default settings and specifying a tag size of 36bp and bandwidth of 150bp (-tsize=36 -bw=150)
BED files were created by selecting MACS-called peaks with FDR < 5%

value: S2 cell line


title: AGO2 S2 ChIP-seq rep1

description:
AGO2_S2_ChIP-seq
We used antibody published in Kawamura Y, et al. (2008) Drosophila endogenous small RNAs bind to Argonaute 2 in somatic cells. Nature 453(7196):793-797.  The monoclonal antibody is named 9D6.

value: anti-AGO2 mAb 9D6


title: S3 input DNA

source_name: S3 cells

value: S3 cell line


title: AGO2 S3 ChIP-seq

description:
AGO2_S3_ChIP-seq
We used antibody published in Kawamura Y, et al. (2008) Drosophila endogenous small RNAs bind to Argonaute 2 in somatic cells. Nature 453(7196):793-797.  The monoclonal antibody is named 9D6.


title: AGO2 Mueller S2 ChIP-seq rep2

description: We used the polyclonal rabbit antibody published in Meyer et al. (2006) [PMID:16934003]

value: antiAGO2 pAb Mueller [PMID:16934003]


title: Sleeping Beauty induced lymphoma (NlaIII sample 124)

description:
Barcode sequence: TCACGTACTA
NlaIII sample 124
Processed data file: Insertions_Nla.bed
Processed data file build: NCBI m37
Original raw file name: Pool15.NlaIII.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR

source_name: LYMPHOMA   SPLEEN


title: small RNAs (18-29nt) from homozygotes of CG4771-delta1

description: small RNAs (18-29nt) selected by PAGE

source_name: CG4771 mut

value: from 5-6 days old flies

value: ovary


title: Sleeping Beauty induced lymphoma (NlaIII sample 123)

description:
Barcode sequence: TCACGCGAGA
NlaIII sample 123
Processed data file: Insertions_Nla.bed
Processed data file build: NCBI m37
Original raw file name: Pool15.NlaIII.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR

source_name: LYMPHOMA SPLEEN


title: Sleeping Beauty induced lymphoma (NlaIII sample 121)

description:
Barcode sequence: TATAGACATC
NlaIII sample 121
Processed data file: Insertions_Nla.bed
Processed data file build: NCBI m37
Original raw file name: Pool15.NlaIII.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR


title: Sleeping Beauty induced lymphoma (NlaIII sample 125)

description:
Barcode sequence: TCATCGAGTC
NlaIII sample 125
Processed data file: Insertions_Nla.bed
Processed data file build: NCBI m37
Original raw file name: Pool15.NlaIII.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR

source_name: LYMPHOMA LIVER


title: Sleeping Beauty induced lymphoma (NlaIII sample 122)

description:
Barcode sequence: TATCTGATAG
NlaIII sample 122
Processed data file: Insertions_Nla.bed
Processed data file build: NCBI m37
Original raw file name: Pool15.NlaIII.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR


title: Sleeping Beauty induced lymphoma (NlaIII sample 120)

description:
Barcode sequence: TAGTGTAGAT
NlaIII sample 120
Processed data file: Insertions_Nla.bed
Processed data file build: NCBI m37
Original raw file name: Pool15.NlaIII.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR


title: Sleeping Beauty induced lymphoma (NlaIII sample 119)

description:
Barcode sequence: TAGTCGCATA
NlaIII sample 119
Processed data file: Insertions_Nla.bed
Processed data file build: NCBI m37
Original raw file name: Pool15.NlaIII.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR

source_name: LYMPHOMA  SPLEEN


title: Sleeping Beauty induced lymphoma (NlaIII sample 116)

description:
Barcode sequence: TAGAGACGAG
NlaIII sample 116
Processed data file: Insertions_Nla.bed
Processed data file build: NCBI m37
Original raw file name: Pool15.NlaIII.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR

source_name: LYMPHOMA LYMPH NODE


title: Sleeping Beauty induced lymphoma (NlaIII sample 115)

description:
Barcode sequence: TACGTCATCA
NlaIII sample 115
Processed data file: Insertions_Nla.bed
Processed data file build: NCBI m37
Original raw file name: Pool15.NlaIII.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR


title: Sleeping Beauty induced lymphoma (NlaIII sample 117)

description:
Barcode sequence: TAGCGCGCGC
NlaIII sample 117
Processed data file: Insertions_Nla.bed
Processed data file build: NCBI m37
Original raw file name: Pool15.NlaIII.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR


title: Sleeping Beauty induced lymphoma (NlaIII sample 118)

description:
Barcode sequence: TAGTATCAGC
NlaIII sample 118
Processed data file: Insertions_Nla.bed
Processed data file build: NCBI m37
Original raw file name: Pool15.NlaIII.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR


title: Sleeping Beauty induced lymphoma (NlaIII sample 112)

description:
Barcode sequence: TACACACACT
NlaIII sample 112
Processed data file: Insertions_Nla.bed
Processed data file build: NCBI m37
Original raw file name: Pool15.NlaIII.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR


title: Sleeping Beauty induced lymphoma (NlaIII sample 113)

description:
Barcode sequence: TACGAGTATG
NlaIII sample 113
Processed data file: Insertions_Nla.bed
Processed data file build: NCBI m37
Original raw file name: Pool15.NlaIII.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR


title: Sleeping Beauty induced lymphoma (NlaIII sample 110)

description:
Barcode sequence: CTACGACTGC
NlaIII sample 110
Processed data file: Insertions_Nla.bed
Processed data file build: NCBI m37
Original raw file name: Pool15.NlaIII.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR


title: Sleeping Beauty induced lymphoma (NlaIII sample 114)

description:
Barcode sequence: TACGCTGTCT
NlaIII sample 114
Processed data file: Insertions_Nla.bed
Processed data file build: NCBI m37
Original raw file name: Pool15.NlaIII.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR


title: Sleeping Beauty induced lymphoma (NlaIII sample 111)

description:
Barcode sequence: CTATAGCGTA
NlaIII sample 111
Processed data file: Insertions_Nla.bed
Processed data file build: NCBI m37
Original raw file name: Pool15.NlaIII.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR


title: Sleeping Beauty induced lymphoma (NlaIII sample 107)

description:
Barcode sequence: CATTGAAGCT
NlaIII sample 107
Processed data file: Insertions_Nla.bed
Processed data file build: NCBI m37
Original raw file name: Pool14.NlaIII.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR


title: Sleeping Beauty induced lymphoma (NlaIII sample 108)

description:
Barcode sequence: CTAAGAACGT
NlaIII sample 108
Processed data file: Insertions_Nla.bed
Processed data file build: NCBI m37
Original raw file name: Pool14.NlaIII.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR


title: Sleeping Beauty induced lymphoma (NlaIII sample 106)

description:
Barcode sequence: CAGGTAAGTC
NlaIII sample 106
Processed data file: Insertions_Nla.bed
Processed data file build: NCBI m37
Original raw file name: Pool14.NlaIII.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR


title: Sleeping Beauty induced lymphoma (NlaIII sample 105)

description:
Barcode sequence: ACTTGCCGAT
NlaIII sample 105
Processed data file: Insertions_Nla.bed
Processed data file build: NCBI m37
Original raw file name: Pool14.NlaIII.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR


title: Sleeping Beauty induced lymphoma (NlaIII sample 104)

description:
Barcode sequence: AGCCTCCAGT
NlaIII sample 104
Processed data file: Insertions_Nla.bed
Processed data file build: NCBI m37
Original raw file name: Pool14.NlaIII.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR

source_name: LEUKAEMIA  SPLEEN


title: Sleeping Beauty induced lymphoma (NlaIII sample 103)

description:
Barcode sequence: CGAATCCGAT
NlaIII sample 103
Processed data file: Insertions_Nla.bed
Processed data file build: NCBI m37
Original raw file name: Pool14.NlaIII.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR

source_name: LEUKAEMIASPLEEN


title: Sleeping Beauty induced lymphoma (NlaIII sample 102)

description:
Barcode sequence: CAGGTCCAGT
NlaIII sample 102
Processed data file: Insertions_Nla.bed
Processed data file build: NCBI m37
Original raw file name: Pool14.NlaIII.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR


title: Sleeping Beauty induced lymphoma (NlaIII sample 101)

description:
Barcode sequence: ATCCGAATCG
NlaIII sample 101
Processed data file: Insertions_Nla.bed
Processed data file build: NCBI m37
Original raw file name: Pool14.NlaIII.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR

source_name: LEUKAEMIA LIVER


title: Sleeping Beauty induced lymphoma (NlaIII sample 99)

description:
Barcode sequence: TGTACTACTC
NlaIII sample 99
Processed data file: Insertions_Nla.bed
Processed data file build: NCBI m37
Original raw file name: Pool14.NlaIII.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR


title: Sleeping Beauty induced lymphoma (NlaIII sample 96)

description:
Barcode sequence: TCTAGCGACT
NlaIII sample 96
Processed data file: Insertions_Nla.bed
Processed data file build: NCBI m37
Original raw file name: Pool13.NlaIII.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR


title: Sleeping Beauty induced lymphoma (NlaIII sample 98)

description:
Barcode sequence: TCTGACGTCA
NlaIII sample 98
Processed data file: Insertions_Nla.bed
Processed data file build: NCBI m37
Original raw file name: Pool14.NlaIII.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR