title: small_RNAs_leaves

city: University Park

first: Michael

middle: J

last: Axtell

state: PA

address: 280 Mueller Lab

institute: Pennsylvania State University

description: Coded adapters appear on 3' end of reads in the raw data.  Linker one = CTGTAGGCACCATCAAT and corresponds to this sample.  Linker three = TTTAACCGCGAATTCCAG and corresponds to a small RNA sample from another specimen which will be described elsewhere.  The processed data only includes linker one (the Arabidopsis lyrata library for this study).

data_processing: The A. lyrata data (this sample) and the other library embedded within the raw data was computationally identified by parsing the 3' adapter sequences.  Reads between 19 and 26 nts in length were retained for analysis (this submission).  Only linker 1 data (from A. lyrata) is included in the processed data.

organism: Arabidopsis lyrata

source_name: rosette leaves

growth_protocol: Plants were grown for ~8 weeks at 22C in long-day conditions.

extract_protocol: Total RNA was isolated using Tri-reagent.  A small RNA library was generated for the Illumina Genome Analyzer using sequential adapter ligations with a barcoded 3' adapter.  2 libraries (one from A. lyrata and another from a different experiment to be described elsewhere) with different barcodes were mixed and sequenced in one lane of an Illumina GA.  Raw data provided is the original FASTQ file, containing data for both barcoded libraries performed during this run.

treatment_protocol: None.

value: rosette leaves

value: 8 weeks


title: NA18523_argonne

status: Public on Feb 28 2010

type: SRA

city: Chicago

first: Joseph

last: Pickrell

state: IL

country: USA

institute: University of Chicago

description: RNA-Seq

library_source: transcriptomic

data_processing: Mapped using MAQ v. 0.6.8

molecule: total RNA

organism: Homo sapiens

source_name: lymphoblastoid cell line

growth_protocol: 37o in RPMI

extract_protocol: Total RNA from HapMap Yoruba lymphoblastoid cell lines was extracted using an RNeasy Mini Kit (Qiagen) and assessed using an Agilent Bioanalyzer. mRNA was then isolated with Dyna1 oligo-dT beads (Invitrogen) from 10 micrograms of total RNA. The mRNA was randomly fragmented using the RNA fragmentation kit from Ambion. First-strand cDNA synthesis was performed using random primers and SuperScriptII reverse-transcriptase (Invitrogen). This was followed by second-strand cDNA synthesis using DNA Polymerase I and RNaseH (Invitrogen).  The short cDNA fragments from each sample were prepared into a library for Illumina sequencing. Briefly, the Illumina adaptor was ligated to the ends of the double-stranded cDNA fragments and a 200 bp size-selection of the final product was performed by gel-excision, following the Illumina-recommended protocol. 200 bp cDNA template molecules with the adaptor attached were enriched by PCR to create the final library.

tag: cell line


title: Rice_dcl3

status: Public on Mar 12 2010

city: Beijing

first: Yijun

last: Qi

address: No.7 Science Park Road,Zhongguancun Life Science Park

country: China

institute: National Institute of Biological Sciences, Beijing

data_processing: The adaptor sequences in Illumina 1G sequencing reads were removed by using ‘‘vectorstrip’’ in the EMBOSS package. The small RNA reads with length of 19–27 nt were mapped to the genome using Blast. small RNAs with match to transgenic inverted-repeat or without perfect match to the genome were removed.

organism: Oryza sativa

source_name: dcl3a-17 seedling

growth_protocol: Rice plants were gorwn in growth chambers with 12-h light/dark cycles, 28 oC during the day and 23 oC during the night.

extract_protocol: Small RNAs were ligated to a 3' adaptor and a 5' acceptor sequentially, and then RT-PCR amplified using a pair of Illumina cloning primers and then provided for Illumina sequencing.

treatment_protocol: RNAs were extracted from total extract and immunopurified AGO4 complexes by Trizol reagents. Bigger RNAs were removed by PEG precipitation, and enriched small RNAs were seperated on 15% PAGE/7M Urea gel, and small RNA within the range of 18-28 nt were purified from the gel.

tag: protein complex

value: total extract


title: Rice_AGO4a

source_name: Wild type seedling


title: NA19159_argonne

description: RNA-Seq


title: NA18486_argonne

description: RNA-Seq


title: NA19204_argonne

description: RNA-Seq


title: NA19116_argonne

description: RNA-Seq


title: NA18871_argonne

description: RNA-Seq


title: NA19093_argonne

description: RNA-Seq


title: NA18498_argonne

description: RNA-Seq


title: NA19172_argonne

description: RNA-Seq


title: Rice_dcl1

source_name: DCL1IR-2 seedling


title: Rice_AGO4b


title: Rice_AGO16


title: NA19171_2_yale

description: RNA-Seq


title: NA18516_argonne

description: RNA-Seq


title: NA18504_argonne

description: RNA-Seq


title: NA18517_2_argonne

description: RNA-Seq


title: NA19099_argonne

description: RNA-Seq


title: NA18517_argonne

description: RNA-Seq


title: NA19203_argonne

description: RNA-Seq


title: NA19130_argonne

description: RNA-Seq


title: NA19101_argonne

description: RNA-Seq


title: NA18486_yale

description: RNA-Seq


title: NA19159_yale

description: RNA-Seq


title: NA18871_yale

description: RNA-Seq


title: NA18510_yale

description: RNA-Seq


title: NA19128_argonne

description: RNA-Seq


title: NA18516_2_argonne

description: RNA-Seq


title: NA19114_argonne

description: RNA-Seq


title: NA19225_argonne

description: RNA-Seq


title: NA18504_2_argonne

description: RNA-Seq


title: NA18507_argonne

description: RNA-Seq


title: NA19160_argonne

description: RNA-Seq


title: NA19138_argonne

description: RNA-Seq


title: NA18519_argonne

description: RNA-Seq


title: booting panicle RNA-Seq data rep12

status: Public on Mar 01 2010

city: Shenzhen

first: Guangwu

last: Guo

state: Guangdong Province

address: Main Building,Beishan Industrial Zone, Yantian District

department: Bioinformatics center

institute: Beijing Genomics Institute at Shenzhen

description:
sample for paired-end library with insert size of 178 bp which generates 75 bp paired-end reads
processed_data_file_type: alignment

data_processing: After removing reads containing sequencing adapters and reads of low quality (reads containing Ns >5), we aligned paired-end reads to the Indica genome using SOAP 1 allowing up to 2 mismatches. Reads failed to be mapped were progressively trimmed off 1 base from the 3'-end and mapped to genome again until a match was found. Meanwhile, we set insert of paired reads was 1~10 kilo bases allowing to span introns with varied sizes on genome.

molecule: polyA RNA

source_name: booting panicle

extract_protocol:
mRNA was purified from total RNA with oligo-dT magnetic beads and cDNA was synthesized with random primer priming.The double stranded cDNA was fragmented and subjected to high throughput Illumina sequencing in which 75 bp of sequence was determined from the both of fragment ends with insert size of 200 ±50 bp
Total RNA was isolated with TRIzol (Invitrogen) from each sample according to the manufacturer’s instructions and stored at -80℃. At the beginning of all below experiments, total RNA was treated for 30 minutes at 37℃ with RNase-free DNase I (New England Biolabs, NEB) to remove residual DNA.

tag: tissue

value: panicle at booting stage

tag: cultivar

value: Oryza sativa L. ssp. indica cv. 9311


title: NA18508_argonne

description: RNA-Seq


title: NA18505_argonne

description: RNA-Seq


title: NA19160_2_yale

description: RNA-Seq


title: NA19127_argonne

description: RNA-Seq


title: NA19160_yale

description: RNA-Seq


title: NA18502_argonne

description: RNA-Seq


title: NA19140_argonne

description: RNA-Seq


title: NA18517_2_yale

description: RNA-Seq


title: NA19116_yale

description: RNA-Seq


title: NA18498_yale

description: RNA-Seq


title: NA19101_yale

description: RNA-Seq


title: NA19204_yale

description: RNA-Seq


title: NA19203_yale

description: RNA-Seq


title: NA19099_yale

description: RNA-Seq


title: NA18853_argonne

description: RNA-Seq


title: NA18913_argonne

description: RNA-Seq


title: Rice_total_wildtype


title: NA18916_argonne

description: RNA-Seq


title: NA19222_argonne

description: RNA-Seq


title: NA18858_argonne

description: RNA-Seq


title: NA18862_argonne

description: RNA-Seq


title: SPR

city: Ploen

first: Bettina

last: Harr

address: August-Thienemannstrasse 2

country: Germany

institute: Max-Planck-Institute for Evolutionary Biology

description:
sample 19 (SPR.1_1), paired with sample 20
sample 20 (SPR.1_2), paired with sample 19
sample 21 (SPR.2_1), paired with sample 22
sample 22 (SPR.2_2), paired with sample 21

data_processing:
Library preparation and deep sequencing using a Genome Analyzer II (Illumina, San Diego, CA) was performed by the National Center for Genome Resources (Santa Fe, NM) following paired-end sequencing and mRNA sequencing protocols from Illumina.
FASTQ files were generated using the Illumina pipeline version 1.0. The program Tophat/Bowtie was used to align the reads to the mouse reference genome [Ensembl Build NCBIM37.50 (mm9, NCBI Build 37)]. The outfiles (in .sam format) were then filtered for reads that matched uniquely in the genome and in the expected "paired-end" fashion.

organism: Mus spretus

source_name: adult testis

growth_protocol: adult mice were sacrifieced at an age of 6-8 weeks

extract_protocol:
Library construction protocol: Paired-end
We extracted RNA from flash-frozen testis tissue using TRIZOL (Invitrogen, Carlsbad, CA), and isolated mRNA from total RNA using the μMACS mRNA isolation kit (Miltenyi Biotec, Bergisch Gladbach, Germany). Sample integrity of total RNA and mRNA were verified using the RNA 6000 Nano chip kit on an Agilent Technologies 2100 Bioanalyzer (Waldbronn, Germany).
We synthesized cDNA from mRNA using Superscript III reverse transcriptase (Invitrogen) and a 10:1 primer mixture of random dodecamers and oligo(dT)18. The insert size was 200 bp.

tag: strain

value: spr


title: DOM2

description:
sample 9 (DOM2.1_1), paired with sample 10
sample 10 (DOM2.1_2), paired with sample 9
sample 11 (DOM2.2_1), paired with sample 12
sample 12 (DOM2.2_2), paired with sample 11

organism: Mus musculus domesticus


title: NA19257_argonne

description: RNA-Seq


title: NA18861_argonne

description: RNA-Seq


title: DOM1

description:
sample 5 (DOM1.1_1), paired with sample 6
sample 6 (DOM1.1_2), paired with sample 5
sample 7 (DOM1.2_1), paired with sample 8
sample 8 (DOM1.2_2), paired with sample 7


title: NA19192_argonne

description: RNA-Seq


title: NA19190_argonne

description: RNA-Seq


title: NA18498_2_argonne

description: RNA-Seq


title: NA19108_argonne

description: RNA-Seq


title: NA18520_argonne

description: RNA-Seq


title: NA18516_2_yale

description: RNA-Seq


title: NA19131_argonne

description: RNA-Seq


title: NA19193_yale

description: RNA-Seq


title: NA18504_2_yale

description: RNA-Seq


title: NA19127_yale

description: RNA-Seq


title: NA18502_yale

description: RNA-Seq


title: NA18519_yale

description: RNA-Seq


title: NA19138_yale

description: RNA-Seq


title: NA19140_yale

description: RNA-Seq


title: NA18522_yale

description: RNA-Seq


title: NA18505_yale

description: RNA-Seq


title: NA19114_yale

description: RNA-Seq


title: NA18516_yale

description: RNA-Seq


title: NA18508_yale

description: RNA-Seq


title: NA19093_yale

description: RNA-Seq


title: NA19172_yale

description: RNA-Seq


title: NA18504_yale

description: RNA-Seq


title: NA18517_yale

description: RNA-Seq


title: NA18511_argonne

description: RNA-Seq


title: NA19200_yale

description: RNA-Seq


title: NA19102_yale

description: RNA-Seq


title: NA18507_yale

description: RNA-Seq


title: NA19239_yale

description: RNA-Seq


title: NA19128_yale

description: RNA-Seq


title: NA19238_yale

description: RNA-Seq


title: NA18912_yale

description: RNA-Seq


title: NA19130_yale

description: RNA-Seq


title: NA18916_yale

description: RNA-Seq


title: NA19192_yale

description: RNA-Seq


title: NA19225_yale

description: RNA-Seq


title: NA18870_yale

description: RNA-Seq


title: NA18913_yale

description: RNA-Seq


title: NA19131_yale

description: RNA-Seq


title: NA18501_yale

description: RNA-Seq


title: NA18856_yale

description: RNA-Seq


title: NA19143_yale

description: RNA-Seq


title: NA18853_yale

description: RNA-Seq


title: NA18862_yale

description: RNA-Seq


title: NA19143_argonne

description: RNA-Seq


title: NA19190_yale

description: RNA-Seq


title: NA19257_yale

description: RNA-Seq


title: NA19209_argonne

description: RNA-Seq


title: NA19119_yale

description: RNA-Seq


title: NA19171_yale

description: RNA-Seq


title: NA18499_argonne

description: RNA-Seq


title: NA19152_argonne

description: RNA-Seq


title: NA19147_argonne

description: RNA-Seq


title: NA19137_argonne

description: RNA-Seq


title: NA19147_yale

description: RNA-Seq


title: NA19222_yale

description: RNA-Seq


title: NA18909_argonne

description: RNA-Seq


title: NA19153_argonne

description: RNA-Seq


title: NA18861_yale

description: RNA-Seq


title: NA19210_argonne

description: RNA-Seq


title: NA19201_argonne

description: RNA-Seq


title: NA19144_argonne

description: RNA-Seq


title: NA19238_argonne

description: RNA-Seq


title: NA19239_argonne

description: RNA-Seq


title: NA18520_yale

description: RNA-Seq


title: NA18499_yale

description: RNA-Seq


title: NA19098_argonne

description: RNA-Seq


title: NA18498_2_yale

description: RNA-Seq


title: NA18909_yale

description: RNA-Seq


title: NA19201_yale

description: RNA-Seq


title: NA19209_yale

description: RNA-Seq


title: NA19144_yale

description: RNA-Seq


title: NA19098_yale

description: RNA-Seq


title: NA19152_yale

description: RNA-Seq


title: NA19153_yale

description: RNA-Seq


title: NA19210_yale

description: RNA-Seq


title: NA18511_yale

description: RNA-Seq


title: NA18522_argonne

description: RNA-Seq


title: IP_Ago2-myc-MUT_miR-294_sample5B

status: Public on Feb 27 2010

city: Cambridge

first: Sophie

middle: Alexandra

last: Hanina

state: Cambridgeshire

address: Tennis Court Road

department: Gurdon Institute

country: United Kingdom

institute: University of Cambridge

description: RNA-IP against anti-myc

data_processing: Cfasta processed files generated by ABI gene expression pipeline. Details can be found in the Supplementary materials from the paper: mRNA-Seq whole-transcriptome analysis of a single cell.Tang F, Barbacioru C, Wang Y, Nordman E, Lee C, Xu N, Wang X, Bodeau J, Tuch BB, Siddiqui A, Lao K, Surani MA., Nat Methods. 2009 May;6(5):377-82.

organism: Mus musculus

source_name: Dicer1-null ES cells

growth_protocol: Feeder-free ES cells were cultured in ES cell media consisting of (15% v/v) FCS and 2000U/ml LIF

extract_protocol: Total RNA and RNA isolated from RNA-IP of Ago2-myc were extracted using Trizol. Whole transcriptome amplification by RT-PCR

treatment_protocol: whole cell lysis

tag: variable

value: miRNA transfected:miR-294             Ago2-myc:catalytically-inactive (MUT)

tag: cell type

value: Embryonic stem cell


title: INPUT_Ago2-myc_cel-239b_sample4A

description: INPUT

value: miRNA transfected:cel-239b control              Ago2-myc:wild-type (WT)


title: INPUT_Ago2-myc-MUT_miR-294_sample5A

description: INPUT


title: IP_Ago2-myc_cel-239b_sample3B

description: RNA-IP against anti-myc

value: miRNA transfected:cel-239b control             Ago2-myc:wild-type (WT)


title: INPUT_Ago2-myc_cel-239b_sample3A

description: INPUT


title: IP_Ago2-myc-MUT_miR-294_sample2B

description: RNA-IP against anti-myc

value: miRNA transfected:miR-294              Ago2-myc:catalytically-inactive (MUT)


title: INPUT_Ago2-myc-MUT_miR-294_sample2A

description: INPUT


title: NA19108_yale

description: RNA-Seq


title: INPUT_Ago2-myc_miR-294_sample1A

description: INPUT

value: miRNA transfected:miR-294              Ago2-myc:wild-type (WT)


title: IP_Ago2-myc_cel-239b_sample4B

description: RNA-IP against anti-myc


title: ergo1_input_TAP_seq_prb_s4

status: Public on Feb 25 2010

city: Worcester

first: Craig

last: Mello

state: MA

address: 368 Plantatoin Street, Suite AS5-2047

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

description: TAP cloning method, as described in Distinct Argonaute-mediated 22G-RNA pathways direct genome surveillance in the C. elegans germline [of the biogenesis and diversity of 22G-RNAs and suggest additional regulatory functions for small RNAs [PMID: 19800275].

data_processing: Small RNA sequences longer than 17 nt were mapped to the Caenorhabditis elegans genome (WS192, www.wormbase.org). Sequences that matched tRNA or rRNA sequences were then removed. Only full-length perfect matches were allowed. siRNA-targeted loci were defined as a region containing at least 25 reads per million matching reads. Relative abundance at each locus was determined by calculating (22G-RNAs in mutant(or)IP)/(22G-RNAs in wt+22G-RNAs in mutant(or)IP ).

organism: Caenorhabditis elegans

source_name: embryos

growth_protocol: Animals were grown at 20 C for approximately 60-70h.

extract_protocol: Small RNA amplicons were prepared as described in Distinct Argonaute-Mediated 22G-RNA Pathways Direct Genome Surveillance in the C. elegans Germline.  Mol Cell. , 2009 Oct 2 [PMID: 19800275]

tag: developmental stage

value: embryo


title: rrf3_CIPPNK_seq_prb_s6

description: CIPPNK cloning method, as described in Distinct Argonaute-mediated 22G-RNA pathways direct genome surveillance in the C. elegans germline [of the biogenesis and diversity of 22G-RNAs and suggest additional regulatory functions for small RNAs [PMID: 19800275].

source_name: gravid adult worms

value: adult


title: WT_TAP_seq_prb_s5

value: Wild type N2


title: rrf1_CIPPNK_seq_prb_s4


title: IP_Ago2-myc_miR-294_sample1B

description: RNA-IP against anti-myc

value: miRNA transfected:miR-294               Ago2-myc:wild-type (WT)


title: ergo1_CIPPNK_seq_prb_s3


title: ergo1_IP_TAP_seq_prb_s5


title: beta_TAP_seq_prb_s3

tag: protocol

value: RNA sample treated with beta elimination


title: beta_TAP_seq_prb_s4


title: normal_tissue_patient_33

city: Foster City

first: Brian

last: Tuch

state: CA

address: 850 Lincoln Center Dr.

institute: Life Technologies

data_processing: AB WT Pipeline. The reads were aligned to the human hg18 (NCBI Build 36) genome. Alignments are provided in MAX format. A MAX specification file is available on the Series GSE20116 record.

source_name: Oral cavity normal tissue

growth_protocol: Surgically excised human tissue.

extract_protocol: SOLiD whole transcriptome (WT) protocol with total RNA extracted using Qiagen RNAeasy Mini Kit. Total RNA was depleted of 18S and 28S rRNA using GLOBINclear.

value: oral cavity normal tissue

tag: patient


title: tumor_tissue_patient_8

source_name: Oral squamous cell carcinoma

value: oral squamous cell carcinoma


title: tumor_tissue_patient_51


title: normal_tissue_patient_51


title: tumor_tissue_patient_33


title: small RNAs_wild type (fog-2)_adult males_part1

status: Public on Feb 24 2010

description: 18 to 26 nt small RNAs from wild type males

data_processing: Small RNA sequences bigger than 17 nt were mapped to the Caenorhabditis elegans genome (WS192, www.wormbase.org). Sequences that matched tRNA or rRNA sequences were then removed. Only full-length complete matches were allowed. siRNA-targeted loci were defined as a region containing at least 25 reads per million matching reads. Relative abundance at each locus was determined by calculating (22G-RNAs in mutant(or)IP)/(22G-RNAs in wt+22G-RNAs in mutant(or)IP ).

source_name: wild type adult males

growth_protocol: For male isolation animals were grown at 20 C for approximately 60h and males were seperated from females to achieve greater than 95% male populations.  For spermatid isolations fem-3 worms were grown at 25oC for ~45-50hrs and spermatids were extracted.

extract_protocol: Library construction protocol: RNA was extracted from ~200,000 adult worms or from ~200ul isolated spermatids, from alg-3(tm1155);alg-4(ok1041);fog-2(q71), fog-2(q71) male samples and fem-3(q20) purified spermatids. RNA was eluted by extraction with TRI Reagent (MRC Reagents, Inc). RNA was extracted as described in the manufacturer's protocol. Small RNAs from the immunopercipitated complex, and wild type input, were resolved in a 15% polyacrylamide 7M Urea Gel, along with 20 picomoles of RNA standard (18- and 26-nt) in separate lanes. Ethidium Bromide staining was used to visualize the RNA standards. A gel fragment was excised from the sample lanes in the migration range between the two standards. RNA was eluted from the gel fragment in (0.3M NaCl-TE pH7.5) solution overnight and ethanol-precipitated using 20mg of glycogen as the carrier. Gel purified RNA was incubated with 0.05 Unit/µl Tobacco Acid Pyrophosphatase (Epicenter Biotechnologies) in 10µl reaction buffer containing 1 Unit/µl SUPERase Inhibitor (Ambion) for 1h at 37°C. After phenol extraction, the RNA was ethanol precipitated. The gel purified RNA and 1µM of each standard were incubated with 20µM of 3'-end linker, 1 Unit of SuperRNaseIN, 10% DMSO and 3 Units T4 RNA ligase (Takara) in 10µl ligation buffer (50mM Tris-Cl pH7.5, 10mM MgCl2, 6mg/mL BSA, 10mM DTT). The 3' ligated products were gel purified and the RNAs were incubated in the presence of 30µM of 5' adapter oligonucleotide, 1 Unit SuperRNaseIN (Ambion) and 1.5 Units of T4 RNA ligase in ligation buffer (50mM Tris-HCI (pH7.5), 10mM MgCI2, 10mM DTT, 1mM ATP and 10% Dimethyl sulfoxide). The ligated products were gel purified as described above and reverse transcribed in a standard 50µl reaction (SuperScript III, Invitrogen). The cDNA was amplified by PCR and purified in a 10% acrylamide gel. PCR products generated for all the samples were sequenced on a Solexa sequencing platform (Illumina, Inc.).

value: Wild type, fog-2(q71)


title: small RNAs_wild type (fog-2)_adult males_part2


title: small RNAs_spermatids_fem-3(q20)

description: 18 to 26 nt small RNAs from isolated spermatids

source_name: ferm-3(q20) spermatids


title: small RNAs_alg-3(tm1155);alg-4(ok1041);fog-2(q71) and fog-2(q71)_adult males

description: 18 to 26 nt small RNAs from alg-3/4 males

source_name: Argonaute CSR-1 immunopercipitate

tag: antibody


title: dis3-54,D171N

status: Public on Feb 23 2010

city: Munich

first: Mario

last: Halic

address: Feodor-Lynenstr. 25

department: Department of Biochemistry

institute: Gene Center, University of Munich

description: small RNA profiling (by high-throughput sequencing) in wild type S. pombe cells and in 12 mutant cells

data_processing:
Alignment: Sequence reads were obtained and mapped to the S. pombe (20080716) genome using the Maq and Novoalign. All reads mapping with two or fewer mismatches were retained.

Processed data files:
1. Aligned file is MAQ output data format.
Each line consists of read name, chromosome, position, strand, insert size from the outer coordinates of a pair, paired flag, mapping quality, single-end mapping quality, alternative mapping quality, number of mismatches of the best hit, sum of qualities of mismatched bases of the best hit, number of 0-mismatch hits of the first 24bp, number of 1-mismatch hits of the first 24bp on the reference, length of the read, read sequence and its quality.
More information is available at http://maq.sourceforge.net/maq-manpage.shtml
2. Peak file can be loaded in IGV browser (http://www.broad.mit.edu/igv).
Each line consists of chromosome, start position, end position, and the peak value.

organism: Schizosaccharomyces pombe

source_name: mutant S. pombe

growth_protocol: S. pombe cells were grown on minimal media (EMMC -leu).

extract_protocol: siRNAs associated with Ago1 were purified by Flag purification from cells expressing Flag-Ago1 from a pREP1 plasmid (Buker et al., 2007). siRNAs were then recovered by phenol-chloroform extraction and ethanol precipitation and 18-30nt small RNAs were PAGE purified. Gel-purified Ago1-associated RNAs were incubated with 2μM pre-adenylated 3’-adaptor oligonucleotide (miRNA Cloning Linker-1 from IDT, AppCTGTAGGCACCATCAAT/ddC/), 1 U/μL RNAsin (Promega), 1 U/μL T4 ligase (Takara) in 10 μL ligation buffer without ATP at 20°C for 2h minutes. The 3´-ligation reaction was purified on a 17% gel. For the 5’-ligation, 3´-ligated products were incubated with 2 pmol 5’ adaptor oligonucleotide (GUU CAG AGU UCU ACA GUC CGA CGA UC), 1 U/μL RNAsin (Promega), 0.06 μg/μL BSA ,1 U/μL T4 ligase (Promega) in 10μL ligation buffer at 20°C for 2 hours. The ligated reaction was gel purified and used for first strand cDNA synthesis with RT oligo (ATT GAT GGT GCC TAC AG) for 1h at 44°C in 1x first strand buffer, 10mM DTT, 0.2 mM dNTP, 1 U/μL RNAsin (Promega) and Superscript III. cDNA was amplified using PCR with Illumina P5 (AAT GAT ACG GCG ACC ACC GAC AGG TTC AGA GTT CTA CAG TCC GAC GAT C) and Illumina P7 (CAA GCA GAA GAC GGC ATA CGA ATT GAT GGT GCC TAC AG ) oligos for 10-15 cycles and gel purified.

tag: mutant description

value: mutation in 3'-5' exoribonuclease subunit Dis3


title: dcr1Δdis3-54,D171N

value: deletion of Dicer and mutation in 3'-5' exoribonuclease subunit Dis3


title: chp1Δ

value: deletion of chromodomain protein Chp1


title: normal_tissue_patient_8


title: arb2Δ

value: deletion of argonaute binding protein 2


title: swi6Δ

value: deletion of HP1 protein Swi6


title: arb1Δ

value: deletion of argonaute binding protein 1


title: clr4Δ

value: deletion of histone H3 methyltransferase Clr4


title: cid12Δ + nmt1-rdp1+

value: cid12Δ + nmt1-rdp1+

value: Cid12 deletion strain overexpressing Rdp1


title: rdp1Δ

value: deletion of RNA-directed RNA polymerase Rdp1


title: wild type

source_name: wildtype S. pombe

value: wild type


title: flg22

first: Jianmin

last: Zhou

address: # Science Park road,Zhongguancun Life Science Park,Beijing

description: Small RNAs were prepared from Arabidopsis AGO1 complexes, ligated to a 3' adaptor and a 5' acceptor sequentially, and then RT-PCR amplified. PCR products were reamplified using a pair of solexa cloning primers and then provided for sequencing.

data_processing: The adaptor sequences were removed using “vectorstrip” in EMBOSS package. The sRNA reads with length of 19-27 nt were mapped to the Arabidopsis nuclear, chloroplast and mitochondrial genomes (http://www.arabidopsis.org/). The sRNAs with perfect genomic matches are used for further analysis

molecule: other

organism: Arabidopsis thaliana

source_name: 5-6 week old Arabidopsis leaves

growth_protocol: Arabidopsis were grown in a growth room maintained at 23℃ and 70% relative humidity with a 10/14 hr day/night light

extract_protocol: Small RNAs were extracted from immunopurified AGO1 complexes using Trizol reagent,ligated to a 3' adaptor and a 5' acceptor sequentially, and then RT-PCR amplified. PCR products were reamplified using a pair of solexa cloning primers and then provided for sequencing.The small RNA reads with length of 19-27 nt were mapped to the Arabidopsis nuclear, chloroplast and mitochondrial genomes (http://www.arabidopsis.org/). The small RNAs with perfect genomic matches were used for further analysis. Annotation of small RNAs was performed using the following databases: TAIR7 annotations for coding sequences and non-coding RNAs (rRNAs, tRNAs, snoRNAs, snRNAs), and sequences from the intergenic regions (ftp://ftp.arabidopsis.org/Sequences/blast_datasets/TAIR7_blastsets/), Repbase (http://www.girinst.org) for transposons and repeats, ASRP for tasiRNA annotations (http://asrp.cgrb.oregonstate.edu/), and miRBase for miRNA annotations (http://microrna.sanger.ac.uk/sequences/).

treatment_protocol: 5-6 week old Arabidopsis leaves were infiltrated with 2 μM flg22 or H2O and harvested 1 hr later. Small RNAs were prepared from Arabidopsis AGO1complexes which immunoprecipitated with anti-AGO1 antibody..

tag: age

value: 5-6 weeks

value: leaves


title: wild type + ago1D580A

value: wild type + ago1D580A

value: wild type strain expressing ago1D580 mutant


title: D_sec

status: Public on Feb 20 2010

city: Farmington

first: Brenton

middle: R

last: Graveley

state: CT

address: 400 Farmington Avenue

department: Genetics and Genome Sciences

institute: University of Connecticut Health Center

description: Oligo-dT selected, double stranded cDNA, Paired-end sequencing

data_processing: Reads were aligned to the reference assemblies either individually (D_sec and D_mel) or to both genomes (D_mel_x_D_sec and D_mel_+_D_sec).  For Hybrid and Mixed-Parental datasets, allele-specific read assignment was performed by comparing the alignment results for each genome. Sequence reads were aligned to the dm3 and droSec1 assemblies of the D. melanogaster and D. sechellia databases (available at UCSC genome browser downloads).  For the Hybrid and Mixed_Control samples, reads were aligned to both genomes, and alignments were compared to identify reads that map to only one species (species-specific).  Alignment positions were subsequently converted to dm3 coordinates using the UCSC liftover tool.

organism: Drosophila sechellia

source_name: Drosophila sechellia

growth_protocol: Cornmeal / molasses

extract_protocol: Total RNA was prepared using Trizol (Invitrogen). Oligo-dT beads (Dynal, Invitrogen) were used to enrich for polyadenylated RNAs.  Ambion fragmentation reagent was used to fragment poly-A+ RNA, which was subsequently reverse transcribed using random primers and SuperScript II RT (Invitrogen).  Library preparation was performed using the Illumina paired-end genomic DNA library preparation kit as described by the manufacturer.

value: whole fly

tag: library strategy

value: Paired-End RNA-seq

tag: library source

value: RNA

tag: library selection

value: RT and size selection


title: Infected_peach

city: Sherbrooke

first: Jean-Pierre

last: Perreault

state: Québec

address: 3001, 12ième avenue Nord

department: Biochimie

country: Canada

institute: Université de Sherbrooke

description: small RNAs from 18-30 nucleotides fraction

data_processing:
Two lanes were obtained for each library:
Infected library raw files: Inf_lane1.fastq, Inf_lane2.fastq
Healthy library raw files: Hea_lane3.fastq, Hea_lane4.fastq.
Raw data (unfiltered sequence reads) were transformed using different perl scripts. Briefly, raw data from both sets were trimmed of the 3’ adapter (TCGTATGCCGTCTTCTGCTTGT). The search was for the seven first nucleotides (TCGTATG), allowing for one mismatch only. Reads that did not contain the 3’ adapter, those shorter than 16 nt, and those with ambiguous nucleotides were discarded. Finally, resulting sequences from two lanes were combined into one processed file and transformed in fasta format.
Single resulting processed file per sample:
Infected_processed.fa AND Healthy_processed.fa.
Example of an entry in a processed .fa file:
>Infected_1_145026_21
TCGGACCAGGCTTCATTCCCC
The first number: 1 (arbitrarily given name to the reads)
The second number: 145026 (number of times this reads is found in the library)
The third number: 21 (length of the reads)

organism: Prunus persica

source_name: leaf tree, peach latent mosaic viroid infected

growth_protocol: Infected and healthy trees are grown on the west coast of Canada (Sidney, British Columbia)

extract_protocol: For each library (healthy and PLMVd-infected) 10 micrograms of total RNA was size fractionated on a 15% denaturing polyacrylamide gel and the 18-30 nt fraction excised from the gel. Following elution of the RNA, 5’ and 3’ adapters were added to the RNA species using the Digital Gene Expression for Small RNA Sample Prep Kit (Illumina Part#1003801 Rev.B). After reverse transcription, the samples were PCR amplified, purified on 10% polyacrylamide gels and then eluted according to the manufacturer’s protocol.

value: Siberian C

tag: infection

value: peach latent mosaic viroid (PLMVd)


title: H2O


title: Healthy_nectarine

organism: Prunus persica var. nucipersica

source_name: leaf tree


title: cid12Δ

value: deletion of nucleotidyltransferase Cid12


title: dcr1Δ

value: deletion of Dicer


title: D_mel_+_D_sec

data_processing:
For BED files:  Reads were aligned to the reference assemblies either individually (D_sec and D_mel) or to both genomes (D_mel_x_D_sec and D_mel_+_D_sec). For Hybrid and Mixed-Parental datasets, allele-specific read assignment was performed by comparing the alignment results for each genome. Sequence reads were aligned to the dm3 and droSec1 assemblies of the D. melanogaster and D. sechellia databases (available at UCSC genome browser downloads). For the Hybrid and Mixed_Control samples, reads were aligned to both genomes, and alignments were compared to identify reads that map to only one species (species-specific). Alignment positions were subsequently converted to dm3 coordinates using the UCSC liftover tool.
For GFF files:  For comparison to other data, reads were trimmed to include only the first 37 nts. Sequence reads were aligned to the dm3 and droSec1 assemblies of the D. melanogaster and D. sechellia databases (available at UCSC genome browser downloads). Allele-specific read assignment was performed by comparing the alignment results for each genome. For the Hybrid and Mixed_Control samples, reads were aligned to both genomes, and alignments were compared to identify reads that map to only one species (species-specific). Alignment positions were subsequently converted to dm3 coordinates using the UCSC liftover tool. Pairs of reads in which each read mapped to the same (cis) or opposite (trans) species were identified and GFF files were prepared (processed data files). GFF files are provided for pairs of reads mapping to any chromosome (*all_chr.GFF.gz) and for pairs mapping to the same chromosome within 100,000 bp of each other (*same_chr.GFF.gz). **Note that the *all_chr.GFF files will not be browser viewable as many pairs contain reads which map to different chromosomes.

organism:
Drosophila melanogaster
Drosophila sechellia

source_name: Drosophila melanogaster and Drosophila sechellia Mixed RNA

extract_protocol: Total RNA was prepared using Trizol (Invitrogen). Oligo-dT beads (Dynal, Invitrogen) were used to enrich for polyadenylated RNAs. Ambion fragmentation reagent was used to fragment poly-A+ RNA, which was subsequently reverse transcribed using random primers and SuperScript II RT (Invitrogen). Library preparation was performed using the Illumina paired-end genomic DNA library preparation kit as described by the manufacturer. Insert size for these libraries is ~350 bp +/- 20 bp.

value: D.melanogaster strain 14021-0231.36 and D. sechellia strain 14021-0248.25

tag: sex

value: Female

value: Adult (0-2d post eclosion)


title: D_mel

organism: Drosophila melanogaster

source_name: Drosophila melanogaster


title: BN-Lx_adult_male_whole_liver, replicate 2

status: Public on Feb 17 2010

city: Utrecht

first: Sam

last: Linsen

address: Uppsalalaan 8

department: Genome Biology

country: Netherlands

institute: Hubrecht Institute

description: Bn-Lx Liver replicate 2

data_processing:
miRNAs: All reads were submitted to the miRIntess small RNA analysis pipeline (InteRNA Genomics B.V., Bilthoven, The Netherlands). This pipeline provided us with known miRNA reads and predicted miRNA reads with different levels of confidence. For instance, reads mapping to known miRNAs, but derived from the other arm, or from the opposite strand, were annotated with high confidence if they represented expected Dicer products and the pre-miRNA would form a stable hairpin. Homologous miRNAs were accordingly annotated. Similar rules applied to reads derived from yet unknown miRNAs, but the number of total reads should match at least 50 before these were assigned highly confident. Only low-confident novel miRNAs were excluded from the analysis, since predictions that fall into this category were indistinguishable from predictions performed on hairpins that had been randomly selected from genomic sequence (data not shown). Simultaneously the reads with a perfectly matching linker sequence were collected. The pre-miRNAs annotated by the mirIntess pipeline, except the category of low confident novel ones, were used to re-map the linker-trimmed reads, to obtain only perfectly mapping miRNA reads. For the fine mapping of the small RNA reads we used the pre-miRNA hairpins that were identified by the miRIntess pipeline. Trimming of the sequencing linker was performed on the sequencing reads. Reads were subsequently remapped using SHRiMP (http://compbio.cs.toronto.edu/shrimp/) with the following settings (-h 50% -v 50% -s 1110111). Because this software package can natively map ABI colorspace reads, it has a higher sensitivity than the BLAST algorithm used in the miRIntess pipline.
piRNA clusters: We mapped reads to annotated repeats (LTRs and LINE elements) and counted the amount of possible reverse complementary interactions, for lengths from 1 to 30 nt. We also performed this analysis for a randomized set of 30-mers derived from the same repeat sequence.
After filtering out reads that are aligned to miRNAs, sn(o)RNAs, small cytoplasmic RNAs, rRNA genes or known coding genes, we found 271,382 unique start positions on the positive strand and 309,051 unique start positions on the negative strand. We have observed that distribution of these reads is non-random in the genome, i.e. clustered in certain locations. To rule out effects of clonality or cloning bias we only considered unique start positions. Regions that contain within a 2 kb window more than 20 unique start positions on the same strand are selected as the core of a piRNA cluster. From these piRNA core regions the start and end of the cluster is extended up- and downstream when a read is found on the same strand within 1 kb. This is continued until a read is found more than 1 kb from either start or end of the cluster.

organism: Rattus norvegicus

extract_protocol: Small RNA Expression Kit by Ambion

treatment_protocol: frozen in liquid nitrogen, total RNA isolation by mirvana kit (Ambion),

value: BN-Lx

value: liver


title: BN-Lx_adult_male_whole_liver, replicate 3

description: Bn-Lx Liver replicate 3


title: SHR_adult_male_whole_liver, replicate 3

description: SHR Liver replicate 3

value: SHR


title: SHR_adult_male_whole_spleen

description: SHR Spleen

value: spleen


title: D_mel_x_D_sec

organism: Drosophila melanogaster x Drosophila sechellia

source_name: Drosophila melanogaster and Drosophila sechellia F1 hybrid

value: D.melanogaster strain 14021-0231.36 crossed to D. sechellia strain 14021-0248.25


title: SHR_adult_male_whole_heart

description: SHR Heart

value: heart


title: BN-Lx_adult_male_whole_spleen

description: Bn-Lx Spleen


title: SHR_adult_male_whole_liver

description: SHR Liver


title: BN-Lx_adult_male_whole_heart

description: BN-Lx Heart


title: SHR_adult_male_whole_brain

description: SHR Brain

value: brain


title: SHR_adult_male_whole_liver, replicate 2

description: SHR Liver replicate 2


title: BN-Lx_adult_male_whole_testis

description: BN-Lx Testis

value: testis


title: BN-Lx_adult_male_whole_liver

description: Bn-Lx Liver


title: BN-Lx_adult_male_whole_brain

description: BN-Lx Brain


title: BN-Lx_adult_male_whole_kidney

description: BN-Lx Kidney

value: kidney


title: Wild-type

status: Public on Feb 16 2010

city: Basel

first: Dimos

last: Gaidatzis

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute

description: Schizosaccharomyces pombe small RNA library from total RNA isolations, barcode 5' AAAC, 3' TCGTATGCCGTCTTCTGCTTG

data_processing: All samples were barcoded at the 3'end of the 5'adapter using a hamming distance two code with a 3' cytosine (AAAC,ACCC,AGGC,ATTC,CACC,CCGC,CGTC,CTAC,GAGC,GCTC,GGAC,GTCC,TATC,TCAC,TGCC,TTGC) and sequenced (with other samples) in one lane of an Illumina GA2 instrument. Individual reads were assigned to their sample based on the first 4 nucleotides containing the barcode. The 3' adapter was removed by aligning it to the read allowing one or two mismatches in prefix alignments of at least 7 or 10 bases respectively. Low complexity reads were filtered out based on their dinucleotide entropy (removing <1% of the reads). All the reads that were shorter than 14 nucleotides were removed.

source_name: wt

extract_protocol: Total RNA was isolated from cells harvested at OD600=0.5 using the hot phenol method (Leeds, 1991) and subjected to size fractionation using RNeasy Midi columns (QIAGEN) as previously described (Buhler, 2006). 17-30nt small RNAs were PAGE purified and were cloned based upon the preactivated, adenylated linkering method described previously (Lau, 2001) using a mutant T4 RNA ligase (Rnl21-249) (Ho, 2004). Bar coded linkers suitable for Solexa sequencing were used for multiplexing and sequencing using an Illumina Genome Analyzer 2 (GA2).


title: dcr1Delta

description: Schizosaccharomyces pombe small RNA library from total RNA isolations, barcode 5' ACCC, 3' TCGTATGCCGTCTTCTGCTTG


title: postnatal (day 30)

city: Ya'an

first: Mingzhou

last: Li

state: Sichuan

address: No.46  Xinkang Road

department: College of Animal Science and Technology

institute: Sichuan Agricultural University

description:
Mixture of 60 normal tissues
Three female and three male were pooled.

data_processing: Sequ-seqs were processed using the Pipeline software from the Genome Analyzer GA-1 instrument (Illumina Inc.) at first, then were subject to a series of data filtration steps to obtain "mappable sequences", which are sequences satisfy the following criteria from the statistics of miRBbase 13.0: (1) not sequencing adapters; (2) containing no more than 80% A, C, G, or T; (3) containing no more than two N (undermined bases); (4) containing no stretches of A7, C8, G6, or T7; (5) been observed more than two times; (6) being longer than 14 nts and shorter than 27 nts; and (7) not originating from mRNA, rRNA, tRNA, snRNA, snoRNA and repetitive sequence elements. Further data analysis of the "mappable sequences" mainly used ACGT101-miR, our own development software for discovering miRNAs from next-generation sequencing (NGS) data (to be published separately), based on the databases of pig genome (Sscrofa9, April 2009) & EST sequences and mammalian konwn miRNA genes in miRBase 13.0 (March 2009).

organism: Sus scrofa

source_name: at day 30

extract_protocol: Ten sample sets used in this experiment that cover six prenatal (entire 114 days of pregnancy) and four postnatal (180 days after birth) developmental stages of Rongchang pigs (a Chinese indigenous breed). Six sows were artificially inseminated with semen from purebred sires and one sow was sacrificed at each of the six prenatal stages (i.e. 30, 45, 60, 75, 90 and 105 days post conception) to obtain three male and three female fetuses. The 30 and 45 days fetuses samples were simply homogenized; other prenatal samples were a mixture of whole body tissues without bones. For four postnatal samples (i.e. birth, 30, 120 and 180 days) the mixture samples were from 60 tissues at equal amounts for each type of tissue. The mixture samples from individual three female and three male fetuses or pigs were kept separately. The low molecular weight RNA was extracted using mirVana miRNA Isolation Kit (Ambion Life Technologies) according to the manufacturer’s protocol. RNA samples were prepared as follows: for each developmental stage, equal quantities (10 µg) of small RNA isolated from six individuals, three female and three male were pooled. Approximately 60 µg of small RNA representing each developmental stage was used for library preparation for sequencing. In brief, the sequencing was performed as follows: small RNA fraction between 18 and 30 nt was isolated by polyacrylamide gel electrophoresis (PAGE), and ligated with proprietary adaptors (Illumina Inc.). The short RNAs were converted to cDNA by RT-PCR and the cDNA was sequenced on the Genome Analyzer GA-I (Illumina Inc.) following the Illumina protocol.

value: postnatal (day 30)


title: SHR_adult_male_whole_testis

description: SHR Testis


title: siMRG15

status: Public on Feb 10 2010

city: Toronto

first: Qun

last: Pan

address: 160 College St.

institute: University of Toronto

description: RNA-Seq performed on polyadenylated RNA

data_processing: The sequence reads were aligned to human genomic sequence (NCBI Genome Assembly Build #36) using Bowtie (Langmead et al., Genome Biol. 2009 10).

source_name: hMSC cells depleted of MRG15 using specific siRNA

extract_protocol: polyA+ RNA isolated from hMSC cells transfected with control and targeting siRNAs

value: hMSC cells


title: siSETD2

description: RNA-Seq performed on polyadenylated RNA

source_name: hMSC cells depleted of SETD2 using specific siRNA


title: siPTB

description: RNA-Seq performed on polyadenylated RNA

source_name: hMSC cells depleted of PTB using specific siRNA


title: PCL2_ChIPSeq

status: Public on Feb 05 2010

first: William

middle: L

last: Stanford

state: Ontario

address: 164 College St

department: IBBME

description: Chromatin IP against PCL2

library_source: genomic

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse (UCSC July 2007) genomes (Johnson et al., 2007). Settings for enrichment analysis: maxSpacing=500; minHits=20; minPeakHits=6;
Peaks: Peak detection was performed as described in Johnson et al., Science, 2007.

molecule: genomic DNA

source_name: Undifferentiated mouse embryonic stem cells

growth_protocol: R1 ESCs were cultured at 37°C and 5% CO2, on a layer of mitomycin-treated embryonic fibroblasts (MEFs) in ESC media consisting of Dulbecco modified eagle serum (DMEM) supplemented with 15% FBS (North Bio, Lot SF30408), 0.1 mM nonessential amino acids, 1 mM sodium pyruvate, 2 mM L-glutamine (all from Gibco), 1000 U/mL leukemia inhibitory factor (LIF) (ESGRO, from Chemicon, batch 11061065) and 100µM b-mercaptoethanol (Sigma).

extract_protocol: R1 ESCs were pelleted and lysed in a series of three lysis buffers. Material was sonicated on ice using a Beckman sonicator at a setting of 6.5, 6 pulses of 10 seconds ON, 30 seconds OFF. This was repeated until DNA was reduced to approximately 1kb lengths. Equal volumes of sonicated DNA was used for IP and control. 10 ug of anti-MTF2 antibody (Genway 18-003-42503) was combined with sonicated DNA and incubated O/N. Pre-blocked protein A/G beads (Sigma) were used to immobilize DNA-antibody complexes. Beads were washed in RIPA buffer, collected, resuspended in elution buffer and DNA-antibody complexes were eluted at 65ºC for 15 minutes. Cross-links were reversed by incubating the supernatant at 65ºC O/N. Cellular protein was digested by incubation with proteinase K at 55ºC and DNA was purified using a Qiagen PCR purification kit. DNA was supplied to The Centre for Applied Genomics (TCAG) for highthroughput sequencing.

tag: chip antibody

value: PCL2 (MTF2)


title: IMR90hTert_Input

status: Public on Feb 11 2010

city: Lausanne

first: Nicolo

last: Riggi

state: VD

address: Bugnon 25

department: Département de Pathologie Expérimentale

institute: CHUV

description: High-throughput sequencing of control input DNA (collected after the crosslinking and sonication steps)

data_processing:
Alignment : The sequenced tags were mapped onto the unmasked genome build hg18 using the fetchGWI software and allowing 1000 repeats on the genome. The tags mapping more than once onto the genome were then attributed a weight corresponding to the number of times the tag was sequenced divided by the number of genomic matches . The files with these weighted repeated tags as well as the unique tags were then used for peak detection
Peak detection : peaks were determined with the sissrs software (www.rajajothi.com/sissrs/). Peaks common to the control input material and the ChIP material, as well as peaks mapping in satellite and micro-satellite repeats and peaks mapping in 18 and 28S rRNA sequences, were eliminated from the analysis. This first analysis resulted in the identification of peaks.  The obtained peaks were then quantified using the protocol described in the paper describing this dataset

growth_protocol: The chromatin immunoprecipitations (ChIPs) were performed with exponentially growing IMR90HTert cells, which are diploid fibroblast-like cells established from fetal female lung tissue and transfected with the gene coding for human Telomerase reverse Transcriptase.

extract_protocol: At least 10 ng was used to prepare sequencing libraries with the Illumina ChIP-Seq Sample Preparation Kit according to the protocol supplied with the reagents. Aliquots of the sequencing libraries were then loaded into Genome Analyzer flow cells and sequenced with the Genome Analyzer II (Illumina) using the 36 Cycle Sequencing Kit v2 (Catalog number FC-204-2036). As controls, aliquots of the input DNA (collected after the crosslinking and sonication steps) were also subjected to ultra high throughput sequencing.

treatment_protocol: MR90HTert cells were cross-linked for seven minutes in 1% formaldehyde.  Following cell and nuclear lysis as described, extracted chromatin was sonicated to an average size of 200-600 base pairs and used for immunoprecipitations.  The sonicated chromatin was mixed with various antibodies and incubated on a rotating wheel overnight at 4˚C.  Immunoprecipitated material was recovered by addition of 10 µl of protein A agarose beads (pre-blocked with 10µg/ml of BSA and salmon sperm DNA) and incubation for 1 h at room temperature on a rotating wheel.  The beads were then washed with dialysis and wash buffer {O'Geen, 2006 #64}.  De-crosslinking, RNase A and proteinase K treatments, and DNA purification were conducted as described {O'Geen, 2006 #64}.


title: IMR90hTert_Bdp1

description:
Chromatin IP against Bdp1, followed by high-througput sequencing
IMR90hTert_Bdp1_run19_lane_5
IMR90hTert_Bdp1_run19_lane_6
IMR90hTert_Bdp1_run21_lane_1


title: IMR90hTert_SNAP45

description:
MR90HTert stable cell line expressing the human SNAP45 fused to the Tobacco etch virus (TEV), the Flag epitope, and the biotin acceptor domain (BAD) growing DMEM, 10% FBS, and 0,1% of non essential amino acids, were cross-linked for 7 min by addition of 1% of Formaldehyde (Sigma, Cat. No. F-1635). Crosslinking was stopped by addition of glycine to a final concentration of 0.125 M, followed by 5-min incubation at room temperature. Fixed cells were washed twice with cold PBS and harvested in cold PBS containing protease inhibitors. Cells were pelleted by centrifugation, suspended in 1mL of Cell lysis buffer (5mM Pipes at pH 8.0, 0.5% NP40, 85mM KCl, 1mM DTT and protease inhibitors (sigma N° 8340)), and incubated for 10 min on ice. Cells were then pelleted by centrifugation, resuspended in 200 µL of Nuclear lysis buffer (50mM Tris-Cl pH 8.0, 10mM EDTA, 1% SDS, 1mM PMSF, 1mM DTT and protease inhibitors) and incubated for 30min at room temperature. Nuclear extraction was diluted 1:5 with salty buffer (250mM NaCl, 25mM Hepes pH 7.9, 2mM DTT, 0,5 mM PMSF). DNA was disrupted by sonication, yielding genomic DNA fragments  of a size of 200–600 bp. Crude chromatin was cleared by centrifugation at 16’000xg for 20 minutes. 500µl of cleared chromatin was next incubated overnight with 30µl of Dynabeads M280-streptavidin (Invitrogen N° 112.05D). Beads were then washed twice with SDS buffer (20mM Hepes pH 7.9, 200mM NaCl, 0.5mM EDTA, 10% glycerol 1mM DTT, 10.5mM PMSF, 2% SDS) followed by two washes with IP wash buffer (100mM Tris at pH 8.0, 500mM LiCl, 1% NP-40, 1% deoxycholic acid), and two washes with TEV-buffer (20mM Hepes pH 7.9, 200mM NaCl, 0.5mM EDTA, 10% glycerol 1mM DTT, 0.5mM PMSF).  Samples were then resuspended in 100µl TEV-buffer containing 1unit of TEV enzyme; incubated for 3 hours at room temperature. Beads were concentrate with a magnet and supernatant was collected as first elution. 100µl of TEV-buffer was added to beads and supernatant was pooled with the first elution, then 2µl of DNase-free RNase-A (10mg/ml) was added and samples were decrosslinked by an overnight incubation at 65 °C. Proteinase K and 5X Proteinase K buffer (50mM Tris at pH 7.5, 25mM EDTA, 1.25% SDS) were then added to the samples and incubate at 37°C for 2 hours. DNA from the samples was purified using Gene PCR cleanup columns (Sigma, NA-1020). Purified DNA was recovered in 50µl of elution buffer.
IMR90hTert_SNAP45_run41_lane_2_175-225
IMR90hTert_SNAP45_run41_lane_3_225-275


title: IMR90hTert_RPC4

description:
Chromatin IP against RPC4, followed by high-througput sequencing
IMR90hTert_RPC4_run13_lane_5
IMR90hTert_RPC4_run14_lane_1


title: IMR90hTert_Brf1

description:
Chromatin IP against Brf1, followed by high-througput sequencing
IMR90hTert_Brf1_run27_lane_5
IMR90hTert_Brf1_run27_lane_6


title: leukemia cell line K-562 (K-562-3)

status: Public on Feb 04 2010

first: Michael

last: Berger

address: 7 Cambridge Center

department: Cancer Program

institute: The Broad Instititute

description:
fragment lengths for the paired-end library, as determined by aligning to a reference transcriptome: 327 +/- 53
raw file name: BI.PE.080918_SL-XAN_0001_FC30C3WAAXX.080921_SL-XAN_0003_FC30C3WAAXX.8.srf
processed data file build: hg18
processed data file type: alignment (bam)
SRA Study Accession: SRP000931
SRA Run Accession: SRR018269
SRA Experiment Accession: SRX006135

data_processing: Reads were independently aligned to a single reference file consisting of all human transcripts in Ensembl build 52 and the human genome (hg18). Alignments were performed using the Burrows-Wheeler Alignment Tool (BWA), allowing up to 4 mismatches with the reference (Li and Durbin 2009). Reads aligning to the transcriptome were mapped to their genomic coordinates, and alignments were considered unique if all placements to the reference arise from a single genomic locus. 68% of reads mapped to the references with no more than 4 mismatches (81% of these corresponded to annotated genes in Ensembl). Read pairs were considered informative if both reads independently aligned uniquely. Duplicate read pairs (originating from a single original template molecule) were removed to leave a single read pair per fragment. Alignments are represented in standard SAM/BAM format (http://samtools.sourceforge.net/).

source_name: leukemia cell line K-562

growth_protocol: cell lines and short-term cultures were grown as described in Lin et al, Cancer Research (2008), 68:664-673

extract_protocol: For each sample, we removed DNA (Turbo DNA-free treatment, Ambion) and isolated polyA+ RNA from 25 mg total RNA. We synthesized cDNA from 65 to 101 ng polyA+ RNA, with a peak length of ~1500 bases using the SuperScript Double-Stranded cDNA Synthesis kit (Invitrogen), SuperScript III Reverse Transcriptase (Invitrogen), and 10 ng random hexamer primers (Invitrogen). Primer annealing was done at room temperature for 10 min followed by 1 h at 55°C for first strand synthesis and 2 h at 16°C for second strand synthesis. Following second strand synthesis and cDNA clean-up, each cDNA library was sheared by sonication with 4 alternating cycles between “high intensity” (30 s; duty cycle, 5%; intensity, 5%; cycles per burst, 200) and “low intensity” (5 s; duty cycle, 1%; intensity, 1%; cycles per burst, 200) in the Frequency Sweeping mode (Covaris S2 machine). Paired-end adapters for Illumina sequencing were added following Illumina protocols, except that 5 times less adapter mix was ligated to the cDNAs. PCR primers were removed by using 1.8x volume of Agencourt AMPure PCR Purification kit (Agencourt Bioscience Corporation). cDNA libraries were prepared with a fragment length range of 400-600 base pairs.

treatment_protocol: cells were grown under standard conditions (no treatment)

tag: disease state

value: leukemia

tag: leukemia type

value: cell line K-562

tag: passages


title: leukemia cell line K-562 (K-562-4)

description:
fragment lengths for the paired-end library, as determined by aligning to a reference transcriptome: 428 +/- 105
raw file name: BI.PE.080918_SL-XAN_0001_FC30C3WAAXX.080921_SL-XAN_0003_FC30C3WAAXX.7.srf
processed data file build: hg18
processed data file type: alignment (bam)
SRA Study Accession: SRP000931
SRA Run Accession: SRR018268
SRA Experiment Accession: SRX006134


title: prenatal, fetus at day 30

description:
Mixture of entire fetus
Three female and three male were pooled.

source_name: E30d (fetus at day 30)

value: prenatal, fetus at day 30


title: melanoma short-term culture M990802

description:
fragment lengths for the paired-end library, as determined by aligning to a reference transcriptome: 369 +/- 113
raw file name: BI.PE.080828_SL-XAN_0002_FC30BV1AAXX.080831_SL-XAN_0004_30BV1AAXX.6.srf
processed data file build: hg18
processed data file type: alignment (bam)
SRA Study Accession: SRP000931
SRA Run Accession: SRR018260
SRA Experiment Accession: SRX006126

source_name: melanoma short-term culture M990802

value: melanoma

tag: melanoma type

value: patient-derived short-term culture M990802


title: melanoma short-term culture M990514

description:
fragment lengths for the paired-end library, as determined by aligning to a reference transcriptome: 377 +/- 114
raw file name: BI.PE.080828_SL-XAN_0002_FC30BV1AAXX.080831_SL-XAN_0004_30BV1AAXX.3.srf
processed data file build: hg18
processed data file type: alignment (bam)
SRA Study Accession: SRP000931
SRA Run Accession: SRR018258
SRA Experiment Accession: SRX006124

source_name: melanoma short-term culture M990514

value: patient-derived short-term culture M990514


title: melanoma short-term culture M980928

description:
fragment lengths for the paired-end library, as determined by aligning to a reference transcriptome: 401 +/- 105
raw file name: BI.PE.080828_SL-XAN_0002_FC30BV1AAXX.080831_SL-XAN_0004_30BV1AAXX.2.srf
processed data file build: hg18
processed data file type: alignment (bam)
SRA Study Accession: SRP000931
SRA Run Accession: SRR018257
SRA Experiment Accession: SRX006123

source_name: melanoma short-term culture M980928

value: patient-derived short-term culture M980928


title: melanoma short-term culture M980409

description:
fragment lengths for the paired-end library, as determined by aligning to a reference transcriptome: 357 +/- 114
raw file name: BI.PE.080828_SL-XAN_0002_FC30BV1AAXX.080831_SL-XAN_0004_30BV1AAXX.7.srf
processed data file build: hg18
processed data file type: alignment (bam)
SRA Study Accession: SRP000931
SRA Run Accession: SRR018261
SRA Experiment Accession: SRX006127

source_name: melanoma short-term culture M980409

value: patient-derived short-term culture M980409


title: melanoma short-term culture M000216

description:
fragment lengths for the paired-end library, as determined by aligning to a reference transcriptome: 396 +/- 100
raw file name: BI.PE.080828_SL-XAN_0002_FC30BV1AAXX.080831_SL-XAN_0004_30BV1AAXX.5.srf
processed data file build: hg18
processed data file type: alignment (bam)
SRA Study Accession: SRP000931
SRA Run Accession: SRR018259
SRA Experiment Accession: SRX006125

source_name: melanoma short-term culture M000216

value: patient-derived short-term culture M000216


title: postnatal (day 120)

source_name: at day 120

value: postnatal (day 120)


title: melanoma short-term culture M000921

description:
fragment lengths for the paired-end library, as determined by aligning to a reference transcriptome: 432 +/- 96
raw file name: BI.PE.080918_SL-XAN_0001_FC30C3WAAXX.080921_SL-XAN_0003_FC30C3WAAXX.6.srf
processed data file build: hg18
processed data file type: alignment (bam)
SRA Study Accession: SRP000931
SRA Run Accession: SRR018267
SRA Experiment Accession: SRX006133

source_name: melanoma short-term culture M000921

value: patient-derived short-term culture M000921


title: melanoma short-term culture M010403

description:
fragment lengths for the paired-end library, as determined by aligning to a reference transcriptome: 404 +/-117
raw file name: BI.PE.080918_SL-XAN_0001_FC30C3WAAXX.080921_SL-XAN_0003_FC30C3WAAXX.3.srf
processed data file build: hg18
processed data file type: alignment (bam)
SRA Study Accession: SRP000931
SRA Run Accession: SRR018265
SRA Experiment Accession: SRX006131

source_name: melanoma short-term culture M010403

value: patient-derived short-term culture M010403


title: melanoma cell line MeWo (replicate 2)

description:
fragment lengths for the paired-end library, as determined by aligning to a reference transcriptome: 414 +/- 91
raw file name: BI.PE.080918_SL-XAN_0001_FC30C3WAAXX.080921_SL-XAN_0003_FC30C3WAAXX.2.srf
processed data file build: hg18
processed data file type: alignment (bam)
SRA Study Accession: SRP000931
SRA Run Accession: SRR018264
SRA Experiment Accession: SRX006130

source_name: melanoma cell line MeWo

value: cell line MeWo


title: melanoma short-term culture M970109

description:
fragment lengths for the paired-end library, as determined by aligning to a reference transcriptome: 383 +/- 109
raw file name: BI.PE.080828_SL-XAN_0002_FC30BV1AAXX.080831_SL-XAN_0004_30BV1AAXX.8.srf
processed data file build: hg18
processed data file type: alignment (bam)
SRA Study Accession: SRP000931
SRA Run Accession: SRR018262
SRA Experiment Accession: SRX006128

source_name: melanoma short-term culture M970109

value: patient-derived short-term culture M970109


title: melanoma cell line 501 Mel

description:
fragment lengths for the paired-end library, as determined by aligning to a reference transcriptome: 375 +/- 123
raw file name: BI.PE.080918_SL-XAN_0001_FC30C3WAAXX.080921_SL-XAN_0003_FC30C3WAAXX.5.srf
processed data file build: hg18
processed data file type: alignment (bam)
SRA Study Accession: SRP000931
SRA Run Accession: SRR018266
SRA Experiment Accession: SRX006132

source_name: melanoma cell line 501 Mel

value: cell line 501Mel


title: prenatal, fetus at day 105

description:
Mixture of all tissues, only discard the bones
Three female and three male were pooled.

source_name: E105d (fetus at day 105)

value: prenatal, fetus at day 105


title: postnatal (day 180)

description:
Mixture of 60 normal tissues
Three female and three male were pooled.

source_name: at day 180

value: postnatal (day 180)


title: melanoma cell line MeWo (replicate 1)

description:
fragment lengths for the paired-end library, as determined by aligning to a reference transcriptome: 414 +/- 91
raw file name: BI.PE.080918_SL-XAN_0001_FC30C3WAAXX.080921_SL-XAN_0003_FC30C3WAAXX.1.srf
processed data file build: hg18
processed data file type: alignment (bam)
SRA Study Accession: SRP000931
SRA Run Accession: SRR018263
SRA Experiment Accession: SRX006129


title: prenatal, fetus at day 45

source_name: E45d  (fetus at day 45)

value: prenatal, fetus at day 45


title: melanoma cell line MeWo

description:
fragment lengths for the paired-end library, as determined by aligning to a reference transcriptome: 418 +/- 91
raw file name: BI.PE.080828_SL-XAN_0002_FC30BV1AAXX.080831_SL-XAN_0004_30BV1AAXX.1.srf
processed data file build: hg18
processed data file type: alignment (bam)
SRA Study Accession: SRP000931
SRA Run Accession: SRR018256
SRA Experiment Accession: SRX006122


title: siControl

description: RNA-Seq performed on polyadenylated RNA

source_name: hMSC cells mock-depleted using a control siRNA

tag: cell type

value: hMSC cells


title: Liquid culture control RNA-Seq

status: Public on Feb 02 2010

description: sample for paired-end library with insert size of 500 bp which generates 44 bp paired-end reads

data_processing: Alignment:   After removing reads containing sequencing adapters and reads of low quality (reads containing Ns >5), we aligned paired-end reads to the  Aspergillus oryzae genome using SOAP 2 allowing up to 2 mismatches. Reads failed to be mapped were progressively trimmed off 1 base from the 3'-end and mapped to genome again until a match was found. Meanwhile, we set insert of paired reads was 1~5 kilo bases allowing to span introns with varied sizes on genome.

organism: Aspergillus oryzae

source_name: cell in liquid culture

growth_protocol: Aspergillus oryzae RIB40 was got from NITE Biological Resource Center (NBRC) in Japan. The CD medium used has been modified, composed of 0.3% NaNO3, 0.2% KCl, 0.05% MgSO4·7H2O, 0.001% FeSO4·7H2O, 0.1% K2HPO4, 2.0% glucose, pH5.5.

extract_protocol: mRNA was purified from total RNA with oligo-dT magnetic beads and cDNA was synthesized with random primer priming.The double stranded cDNA was fragmented and subjected to high throughput Illumina sequencing in which 44 bp of sequence was determined from the both of fragment ends with insert size of 500 ±25 bp

treatment_protocol: 107 spores were inoculated into 30 mL CD medium in 100 mL flask, and were cultivated at 30 oC at 200 rpm until the mid-logarithmic phase (40 h).

tag: strain


title: Solid culture ER stress RNA-seq

source_name: cell under ER stress in solid culture

treatment_protocol: the mycelia together with the cellophane, was transferred to the surface of 2 cm-thick filter paper soaked with 20 mL CD medium which contained 20 mmol/L dithiothreitol (DTT) for induce treatment


title: Solid culture control RNA-Seq

source_name: cell in solid culture

treatment_protocol: 107 spores were distributed over the CD medium-agar plate which was covered by a layer of cellophane, and were cultivated at 30 oC until the mid-logarithmic phase (40 h)


title: Islet_FAIRE-seq 2

status: Public on Jan 31 2010

city: San Diego

first: Kyle

middle: Jeffrie

last: Gaulton

address: 9500 Gilman Drive

department: Pediatrics

institute: UCSD

description: FAIRE-seq

data_processing:
Alignment: reads were mapped to the human genome (hg18) using MAQ and filtered using a MAQ quality score of 30
Peaks:  areas of enrichment were called using Fseq at three enrichment thresholds (liberal, moderate, stringent)

organism: Homo sapiens

source_name: pancreatic islet cells

extract_protocol: FAIRE

tag: tissue

value: Purified pancreatic islets


title: postnatal (birth day)

source_name: Birth

tag: developmental stage

value: postnatal (birth day)


title: MCF7_E2_ER

status: Public on Feb 01 2010

first: Jindan

last: Yu

address: 303 E. Superior St.

department: Medicine - Hem/Onc

institute: Northwestern University

description: Chromatin IP against ER

data_processing:
Alignment: Sequence reads were obtained and mapped to the human (hg18; March, 2006) 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 250 bp to create summary windows.

Peaks: Peak detection was performed with the Hpeak algorithm (http://www.sph.umich.edu/csg/qin/HPeak/). The single Peak file 'MCF7_E2-ethl.hpeak.out' comparing E2 and ethl-treated (control) samples is attached to the Series record.

Please see readme files attached to the Series record for additional information about data files.

growth_protocol: MCF7 cells were grown to 50% confluence in RPMI + 10% FBS, changed to the starving medium (RPMI with 5% FCS) for 3 days, prior to treatment by ethanol (ethl) or 10nM beta-estradiol (E2).

extract_protocol: 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 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Hormone-starved cells were treated with 1% ethanol (ethl) or 10nM beta-estraidiol for 45 min.

tag: cell line

value: estrogen-responsive breast cancer

tag: antibody

value: Estrogen Receptor (ER)

tag: treatment variable

value: hormone starved for 3 days, treated with 10 nM β-estradiol for 45 minutes


title: Enrich3_35

first: Michal

last: Mokry

address: Lundlaan 6

institute: Wilhelmina Children's Hospital, University Medical Center Utrecht

description: The SNP supplementary files have 384 known positions

data_processing: Sequencing reads were mapped against the reference genome (hg18 assembly, NCBI build 36) using the Maq package, which allows mapping in SOLiD color space corresponding to dinucleotide encoding of the sequenced DNA with following settings: number of maximum mismatches that can always be found -n 3, threshold on the sum of mismatching base qualities -e 150. Raw variant positions were called by the Maq package and filtered using custom scripts (available upon request). For stringent SNP calling we used the following filtering settings: 1) positions with lower than 20x and higher than 5000x coverage were excluded, 2) each of non-reference alleles had to be supported by at least 3 independent reads (as determined by different read start positions) separately on positive and negative strand with quality > 10, 3) the non-reference allele should account for at least 20% of the reads covering the polymorphic position, and 4) the ratio between + and – strand reads should be between 1/9 and 9. Positions that passed these filtering settings were considered as SNPs. A SNP was qualified as homozygous when the fraction of non-reference alleles was above 95% and heterozygous when the fraction of non-reference alleles was between 20% and 95%.

source_name: blood

extract_protocol: DNA was fragmented for 6 minutes using a Covaris S2 sonicator (6 x 16 mm AFA fiber Tube, duty cycle: 20%, intensity: 5, cycles/burst: 200, frequency sweeping). After fragmentation, fragments were blunt-ended and phosphorylated at the 5' end using End-it Kit (Epicentre) according to the manufacturer’s instructions, followed by ligation of double-stranded short adapters (adapter 1: pre-annealed duplex of 5'-CTA TGG GCA GTC GGT GAT-3'  and 5'-ATC ACC GAC TGC CCA TAG TTT-3' and adapter 2:  pre-annealed duplex of 5'-CGC CTT GGC CGT ACA GCA G-3' and 5'-GCT GTA CGG CCA AGG CG-3'; all oligo’s were acquired through Integrated DNA Technologies (Coralville, IA) and pre-annealing was done by mixing complementary oligonucleotides at 500 µM concentration and running on thermocycler with the following program: 95˚C for 3 min, 80˚C for 3 min, 70˚C for 3 min, 60˚C for 3 min, 50˚C for 3 min, 40˚C for 3 min and 4˚C hold). Ligation was performed using Quick ligation kit (New England Biolabs) with 1 µg of fragmented DNA, 750 nM adaptor 1 and adaptor 2, 150 µl of 2x Quick ligation buffer, and 5 µl Quick Ligase in a total volume of 300 µl. Samples were purified on Ampure beads (Agencourt) and run on a native 6% polyacrylamide gel. Fragments ranging from 150 to 175 bp were excised; the piece of gel containing fragments was shredded and dispersed into 400 µl of Platinum PCR Supermix with 750 nM of both amplification PCR primers ( provide sequence of amplification primers), 2.5 U of Pfu DNA polymerase (Stratagene) and 5 U Taq DNA polymerase (Bioline). Before ligation-mediated amplification, the PCR sample was incubated at 72˚C for 20 minutes in PCR mix to let the DNA diffuse from the gel and to perform nick translation on non-ligated 3'-ends. After 8 cycles of amplification, the library DNA was purified on Ampure beads and the quality was checked on a gel for the proper size range and the absence of adapter dimers and heterodimers. This library served as a stock for all subsequent hybridization experiments.

value: blood


title: Islet_FAIRE-seq 1

description: FAIRE-seq


title: Enrich1_50

description: The SNP supplementary files have 384 known positions. The SNP_1_50_all file has all SNPs.


title: Enrich2_35


title: Islet_FAIRE-seq 3

description: FAIRE-seq


title: Enrich1_35


title: Anterior silkgland_primary results

city: Beibei

first: Qingyou

last: Xia

state: Chongqing

address: Tiansheng Road

department: College of Biotechnology

institute: Southwest University

description: all information for the raw data and processed files, including the names and descriptions, can be found in the READEME file.

data_processing: 0. Run Solexa pipeline [*fq];   1. Remove low qulity reads strictly;   2. Trim 3' adaptor sequence;   3. Remove 5' adaptor contaminants;   4. Plot data distribution;   5. Remove too small and polyA [small.txt, clean.txt].

organism: Bombyx mori

source_name: anterior silk glands

growth_protocol: Domesticated silkworm (Bombyx mori) strain DaZao, was reared at 25°C on a natural diet of clean mulberry leaves.

extract_protocol: Silk glands and whole bodies of day-3 fifth instar larvae were collected for RNA isolation. Following purification, total RNA samples were immediately preserved in ethanol and stored at -80℃ until further use. For deep sequencing, the total RNA samples were prepared as follows: total RNA of each sample was size-fractionated on a 15% PAGE gel, and a 16–30 nt fraction collected. The 5′ RNA adapter (5’-GUUCAGAGUUCUACAGUCCGACGAUC-3’) was ligated to the RNA pool with T4 RNA ligase. Ligated RNA was size-fractionated on a 15% agarose gel, and a 40–60 nt fraction excised. The 3′RNA adapter (5’-pUCGUAUGCCGUCUUCUGCUUGidT-3’; p, phosphate; idT, inverted deoxythymidine) was subsequently ligated to precipitated RNA using T4 RNA ligase. Ligated RNA was size-fractionated on a 10% agarose gel, and the 70-90 nt fraction (total RNA + adaptors) excised. Small RNAs ligated with adaptors were subjected to RT-PCR (Superscript II reverse transcriptase, 15 cycles of amplification) to produce sequencing libraries. PCR products were purified and total RNA libraries sequenced using Solexa, a massively parallel sequencing technology.

treatment_protocol: Silk glands were manually dissected from day-3 fifth larvae in 0.9% NaCl, rinsed with DEPC-treated water, and promptly immersed in liquid nitrogen.

value: anterior silk glands

value: from 5th-instar day-3 larvae


title: Whole body_primary results

source_name: whole silkworm body (whole body)

value: whole silkworm body

value: of 5th-instar day-3 larvae


title: MCF7_ethl_ER

city: Chicago

description: Chromatin IP against ER

data_processing:
Alignment: Sequence reads were obtained and mapped to the human (hg18; March, 2006) 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 250 bp to create summary windows.

Peaks: Peak detection was performed with the Hpeak algorithm (http://www.sph.umich.edu/csg/qin/HPeak/). The single Peak file 'MCF7_E2-ethl.hpeak.out' comparing E2 and ethl-treated (control) samplesis attached to the Series record.

Please see readme files attached to the Series record for additional information about data files.

value: hormone starved for 3 days, treated with 1% ethanol for 45 minutes


title: Posterior silkgland_primary results

source_name: posterior silk glands

tag: wtissue

value: posterior silk glands


title: SHR_adult_male_whole_kidney

description: SHR Kidney

value: SHR

value: kidney


title: prenatal, fetus at day 90

source_name: E90d (fetus at day 90)

value: prenatal, fetus at day 90


title: dcr1DeltaC33

description: Schizosaccharomyces pombe small RNA library from total RNA isolations, barcode 5' AGGC, 3' TCGTATGCCGTCTTCTGCTTG


title: shJarid2_Suz12_ChIPseq

status: Public on Jan 27 2010

city: Milano

first: Diego

last: Pasini

address: Via Adamello, 16

department: Experimental Oncology

country: Italy

institute: European Institute of Oncology

description: Chromatin IP against Suz12

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse (July, 2007) genomes using the Illumina Genome Analyzer Pipeline version 1.4 alowing up to 2 mismatches in the first 32 bases of the read. Only reads that align uniquely are reported.
Peaks: Peak detection was performed with CisGenome software (http://www.biostat.jhsph.edu/~hji/cisgenome/) as described in Hongkai et al. (2008) Nature Biotechnology, 26: 1293-1300.

source_name: Embyonic stem cells

growth_protocol: ES cells were infected with lentivirus expressing a Neomycin resistant construct expressing either control (SCR) and Jarid2 specific shRNA, cells were selected with 0.5mg/ml of G418 and cultured for two weeks under selection prior collection of samples for ChIPseq analyses.

extract_protocol: ChIP analyses were performed as described in Pasini et al. (2008). Genes Dev 22, 1345-1355. DNA from 3 independent ChIP experiments was pooled and prepared for sequencing with the Illumina ChIPSeq Sample Prep kit (IP-102-1001). DNA libraries were quantified using a fluorometer (Fluoroscan, Ascent) and diluted to 5-10 pM. Diluted libraries were used directly for cluster generation and sequencing analysis using the Genome Analyzer II (Illumina) following the protocol of the manufacturer. Basecalling and mapping of the 36 bp sequences were done using Illumina's analysis Pipeline v1.4 allowing up to two mismatches in the first 32 bases of a read against mouse genomes July 2007 release (mm9).

value: Embyonic stem cells

tag: genome/variation

value: Infected with Jarid2 shRNA expression lentivirus


title: shSCR_Jarid2_ChIPseq

description: Chromatin IP against Jarid2

value: Infected with SCR shRNA expression lentivirus


title: WT_fetus_bisulfite

status: Public on Jan 26 2010

city: Los Angeles

first: matteo

last: Pellegrini

address: 621 Charles Young Drive South

department: MCD Biology

institute: UCLA

description: Bisulfite conversion of unmethylated cytosines

data_processing:
Illumina Genome Analyzer 300 tiles/lane (samples 1..4, 6..8), Illumina Genome Analyzer 330 tiles/lane (sample 5), Illumina Genome Analyzer II 100 tiles/lane (samples 9..12)
Illumina_native (_sig2, _seq, _prb): samples 1..8 are by Solexa pipeline 0.2.2.4/OS X, 36 physical cycles all given to Solexa pipeline, autocalibration from all tiles and cycles of lane 4 on same flow cell which was one of two genomic libraries (#1 for samples 1..4/6/8, #2 for samples 5/7) with high representation of A/C/G/T; samples 9..12 are by Solexa pipeline 1.3rc5/Linux, 55 physical cycles all given to Solexa pipeline, autocalibration from all tiles and cycles of Phi-X library on lane 4 of same flow cell.
BSseq--chrStrandCoord-observeMethOrUnme processing was similar to a previous study (Cokus et al., Nature 451, 215-219) with some adjustments; briefly: (1) GMM (sig2V9) fits were made to _sig2 files and movies manually inspected; (2) PWM-based probabilistic alignment (CokusAlignment) was performed (cycles 10..36 for samples 1/2/6/8, cycles 6..32 for samples 3..5/7, cycles 6..55 for samples 9..12) against reference genome UCSC mm9 (chr1..19, X, Y; no rnd or chrU or chrM, except samples 9..12 included chrM from NCBI gi 34538597) with per-read FW/RC probability scoring priors derived from cycles 1..5 of _prb files; (3) only reads aligning to exactly one genomic 27-mer (samples 1..8) or 50-mer (samples 9..12) that is BS-unique were retained; (4) non-conversion filtering was performed; and (5) data from cycles 15..31 (samples 1/2/6/8), cycles 11..27 (samples 3..5/7), and cycles 20..46 (samples 9..12) was gathered.

source_name: Fetus

extract_protocol: Genomic DNA extracted from mouse tissues were treated with sodium bisulfite and then used to generate Illumina/Solexa sequencing libraries as described previously (Cokus et al., Nature 451, 215-219), except that fewer cycles of PCR amplification were used (15 cycles instead of 18 cycles). For PGC samples, due to the limited sources of tissue, the input DNA amount for libraries had to be reduced to as low as 150 ng. Therefore, the enzymatic reaction steps used for library construction (including reagents and adapters for PCR) were scaled down to accommodate the reduced input amount. On the other hand, more DNA template (in volume) was used in each PCR reaction and more duplicate PCR reactions were performed in parallel in order to obtain equivalent amounts of product as for the other libraries.

tag: genotype

value: wild type

value: Fetus


title: Aid_placenta_bisulfite

source_name: Placenta

value: aid -/-

value: Placenta


title: Np95_ES_cell_bisulfite

source_name: Embryonic stem cells

value: Embyonic stem cell


title: WT_placenta_bisulfite


title: Aid_fetus_bisulfite


title: shSCR_Suz12_ChIPseq

description: Chromatin IP against Suz12


title: WT_ES_cell_bisulfite


title: Aid_sperm_bisulfite

source_name: Sperm

value: Sperm


title: WT_sperm_bisulfite


title: WPP_INPUT_3

first: Kevin

middle: P.

last: White

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

department: Institute for Genomics and Systems Biology

institute: University of Chicago

data_processing: Reads were aligned to the flybase BDGPv5 reference genome using the Illumina Genome Analyzer Pipeline Software.  Signal files were generated with the R package SPP.  Peaks were called with MACS (parameters: --format=ELAND --gsize=120000000 --tsize=36 --bw=250 --mfold=2 --pvalue=1e-3).

growth_protocol: 1. y; bw cn sp flies are cultivated in standard fly food covered with yeast powder. 2. Flies are removed from the bottles after 24 hours and eggs are allowed to grow at 25 C for several days until they reach the desired growth stage. 3. Larvae and Pupae are collected from the side of the bottles using a brush. They are rinsed with EWB and cross-linked in 1.8% formaldehyde at room temperature for 15 min.

extract_protocol: Drosophila whole animals (embryos, larvae, pupae or adults) are crushed in presence of 1.8% of formaldehyde for 15 minutes with the help of a douncer. After washing, the material is sonicated for 15 minutes to solubilize the chromatin. After centrifugation, the supernatant containing soluble chromatin is collected for IPs. Specific antibodies are added to the chromatin extract while one aliquot will be treated for DNA extraction corresponding to the reference samples. ChIP are carried overnight at room temperature. Protein A Sepharose beads are used to pull down the chromatin bound antibodies. After washes and finally elution, the DNA corresponding to the IPed material is extracted and purified. The DNA is directly used for Solexa library preparation.

treatment_protocol: No Treatment

tag: development stage

tag: reference

value: input


title: WPP30-33_INPUT_3


title: w3L_INPUT_3


title: WPP_INPUT_1


title: WPP(EcR-GFP)_ChIPSeq_1, 2 and 3

description:
WPP_EcRGFP_ChIPSeq_1, 2 and 3
corresponding input record(s): GSM499658, GSM499659 and GSM499660

source_name: WPP_EcRGFP_ChIPSeq_1, 2 and 3

growth_protocol: 1.  y w, VK33 flies are cultivated in standard fly food covered with yeast powder. 2. Flies are removed from the bottles after 24 hours and eggs are allowed to grow at 25 C for several days until they reach the desired growth stage. 3. Larvae and Pupae are collected from the side of the bottles using a brush. They are rinsed with EWB and cross-linked in 1.8% formaldehyde at room temperature for 15 min.

value: goat anti GFP

tag: test

value: ChIP


title: w3L_INPUT_1


title: w3L_7T(cad-GFP)_ChIPSeq_1, 2 and 3

description:
w3L_7TGFP_ChIPSeq_1, 2 and 3
corresponding input record(s): GSM499662, GSM499663 and GSM499664

source_name: w3L_7TGFP_ChIPSeq_1, 2 and 3

growth_protocol: 1. y w, VK33 flies are cultivated in standard fly food covered with yeast powder. 2. Flies are removed from the bottles after 24 hours and eggs are allowed to grow at 25 C for several days until they reach the desired growth stage. 3. Larvae and Pupae are collected from the side of the bottles using a brush. They are rinsed with EWB and cross-linked in 1.8% formaldehyde at room temperature for 15 min.


title: w3L_INPUT_2


title: WPP_INPUT_2


title: S2_CTCF200_INPUT_1

growth_protocol: 1. S2 cells are cultivated in Schneider medium according to the recommendations from the Drosophila Genome Ressource Center (DGRC). 2. 1 plate is used for 2 IPs. When cells reach confluence, formaldehyde is added to the plate.

extract_protocol: Drosophila cells are cross-linked by the addition of 1.8% of formaldehyde directly in the plate for 15 minutes. The plates are gently rocked every 2 minutes. The cross-linking reaction is quenched by the addition of glycine in the medium for 5 minutes. The cells are then scraped from the plates and pelleted down. After washing, the material is sonicated for 15 minutes to solubilize the chromatin. After centrifugation, the supernatant containing soluble chromatin is collected for IPs. Specific antibodies are added to the chromatin extract while one aliquot will be treated for DNA extraction corresponding to the reference samples. ChIP are carried overnight at room temperature. Protein A Sepharose beads are used to pull down the chromatin bound antibodies. After washes and finally elution, the DNA corresponding to the IPed material is extracted and purified. The DNA is directly used for Solexa library preparation.


title: WPP30-33_EcRGFP_ChIPSeq_1, 2 and 3

description:
WPP30-33_EcRGFP_ChIPSeq_1, 2 and 3
corresponding input record(s): GSM499654, GSM499655 and GSM499656

source_name: WPP30-33_EcRGFP_ChIPSeq_1, 2 and 3

growth_protocol: 1. y w, VK33  flies are cultivated in standard fly food covered with yeast powder. 2. Flies are removed from the bottles after 24 hours and eggs are allowed to grow at 25 C for several days until they reach the desired growth stage. 3. Larvae and Pupae are collected from the side of the bottles using a brush. They are rinsed with EWB and cross-linked in 1.8% formaldehyde at room temperature for 15 min.


title: S2_CTCF500_INPUT_1


title: WPP30-33_INPUT_2


title: S2_CTCF200_ChIPSeq_1 and 2

description:
S2_CTCF200_ChIPSeq_1 and 2
corresponding input record(s): GSM499650

source_name: S2_CTCF200_ChIPSeq_1 and 2

value: CTCF


title: E4-8h_7T_INPUT_1

growth_protocol: 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder. 2. For a 0-4 hours egg laying for example, new plates are added after a 2hours pre-egglaying and flies are allowed to lay eggs for 4 hours. 3. Embryos are collected using a filter mesh and a brush. They are rinsed with EWB and cross-linked in 1.8% formaldehyde at room temperature for 15 min.


title: WPP30-33_INPUT_1


title: prenatal, fetus at day 60

source_name: E60d (fetus at day 60)

value: prenatal, fetus at day 60


title: E0-4h_7T_INPUT_1


title: E4-8h-7T(cad-GFP)-ChIPSeq_1

description:
E4-8h_7T_ChIPSeq_1
corresponding input record(s): GSM499648

growth_protocol: 1. y w, VK33 flies are cultivated in cages with apple juice agar plates covered with yeast powder. 2. For a 0-4 hours egg laying for example, new plates are added after a 2hours pre-egglaying and flies are allowed to lay eggs for 4 hours. 3. Embryos are collected using a filter mesh and a brush. They are rinsed with EWB and cross-linked in 1.8% formaldehyde at room temperature for 15 min.


title: E0-4h_7T_INPUT_2


title: S2_CTCF500_ChIPSeq_1 and 2

description:
S2_CTCF500_ChIPSeq_1 and 2
corresponding input record(s): GSM499652

source_name: S2_CTCF500_ChIPSeq_1 and 2


title: E0-12_HDAC-501_ChIPSeq_1 and 2

description:
E0-12_HDAC-501_ChIPSeq_1 and 2
corresponding input record(s): GSM499634

source_name: E0-12_HDAC-501_ChIPSeq_1 and 2


title: E0-12_HDAC-499_ChIPSeq_1 and 2

description:
E0-12_HDAC-499_ChIPSeq_1 and 2
corresponding input record(s): GSM499634

source_name: E0-12_HDAC-499_ChIPSeq_1 and 2


title: E0-4h_7T_ChIPSeq_1 and 2

description:
E0-4h_7T_ChIPSeq_1 and 2
corresponding input record(s): GSM499645 and GSM499646

source_name: E0-4h_7T_ChIPSeq_1 and 2

value: Caudal


title: E0-12_HDAC-500_ChIPSeq_1 and 2

description:
E0-12_HDAC-500_ChIPSeq_1 and 2
corresponding input record(s): GSM499634

source_name: E0-12_HDAC-500_ChIPSeq_1 and 2


title: E0-12_HDAC-495_ChIPSeq_1 and 2

description:
E0-12_HDAC-495_ChIPSeq_1 and 2
corresponding input record(s): GSM499634

source_name: E0-12_HDAC-495_ChIPSeq_1 and 2


title: E0-12_HDAC-494_ChIPSeq_1 and 2

description:
E0-12_HDAC-494_ChIPSeq_1 and 2
corresponding input record(s): GSM499634

source_name: E0-12_HDAC-494_ChIPSeq_1 and 2


title: E0-12_HDAC-497_ChIPSeq_1 and 2

description:
E0-12_HDAC-497_ChIPSeq_1 amd 2
corresponding input record(s): GSM499634

source_name: E0-12_HDAC-497_ChIPSeq_1 amd 2


title: E0-12_HDAC-[492..501]_INPUT_1


title: E0-12_HDAC-493_ChIPSeq_1 and 2

description:
E0-12_HDAC-493_ChIPSeq_1 and 2
corresponding input record(s): GSM499634

source_name: E0-12_HDAC-493_ChIPSeq_1 and 2


title: 21d-Female-7T(cad-GFP)-ChIPSeq_1

description:
A-Female_7T_ChIPSeq_1
corresponding input record(s): GSM499632

value: Adult-Female


title: Aid_male_PGC_bisulfite

source_name: Male primordial germ cells

value: Male primordial germ cell


title: E0-12_HDAC-496_ChIPSeq_1 and 2

description:
E0-12_HDAC-496_ChIPSeq_1 and 2
corresponding input record(s): GSM499634

source_name: E0-12_HDAC-496_ChIPSeq_1 and 2


title: Aid_female_PGC_bisulfite

description: Bisulfite conversion of unmethylated cytosines

source_name: Female primordial germ cells

value: Female primordial germ cell


title: E0-12_HDAC-492_ChIPSeq_1 and 2

description:
E0-12_HDAC-492_ChIPSeq_1 and 2
corresponding input record(s): GSM499634

source_name: E0-12_HDAC-492_ChIPSeq_1 and 2


title: WT_male_PGC_bisulfite


title: Liquid culture ER stress RNA-Seq

city: Shenzhen

first: Guangwu

last: Guo

address: Main Building,Beishan Industrial Zone, Yantian District

department: Bioinformatics center

institute: Beijing Genomics Institute at Shenzhen

description: sample for paired-end library with insert size of 500 bp which generates 44 bp paired-end reads

source_name: cell under ER stress in liquid culture

treatment_protocol: For induce treatment, DTT was added to the culture at a final concentration of 20 mmol/L.


title: A-Female_7T_INPUT_1


title: WT_female_PGC_bisulfite


title: shJarid2_Jarid2_ChIPseq

description: Chromatin IP against Jarid2

source_name: Embyonic stem cells

value: Embyonic stem cells

value: Infected with Jarid2 shRNA expression lentivirus


title: prenatal, fetus at day 75

description:
Mixture of all tissues, only discard the bones
Three female and three male were pooled.

source_name: E75d (fetus at day 75)

value: prenatal, fetus at day 75


title: Head_Dpseud_Female

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

description: Deposited sequence data are high quality sequence reads that passed default parameters of the Illumina quality filter. Data were generated using Genome Analyzer I and II and various versions of the GA pipeline, see readme file on GSE19989 for details

data_processing: Reads that passed default parameters of the Illumina quality filter were mapped with Bowtie 0.10.0. The reference sequence used to built an index for mapping was flybase r2.4 for D. pseudoobscura. Reference index was created using the bowtie-build function with default parameters. Reads were then mapped using -v 2 -m 1 in Bowtie v. 0.10.0.

organism: Drosophila pseudoobscura

source_name: head tissue

growth_protocol: D. pseudoobscura (Drosophila Species Stock Center (DSSC) 14011-0121.94) were grown at 22°C, 60% relative humidity in standard plastic vials containing banana-opuntia media. All media was purchased from the Tucson Stock Center, Tucson, Arizona (recipes: http://flyfood.arl.arizona.edu/). There were no lights inside of incubators and room lighting (standard fluorescent bulbs) was on at all times. Newly eclosed flies of both females and males were housed together in vials at normal density (60-100 flies) and aged for 7 days. On day 7, flies were anesthetized with CO2 and then females and males were sorted and placed into separate vials. Flies in same sex vials were aged an additional 24 hours then flash frozen on dry ice in 50 ml Falcon tubes and stored at -80°C until dissection.

extract_protocol:
Fly heads were immersed in 250 µl of TRIzol and thoroughly homogenized using a 1.5 ml RNAase free pestle (Kimble-Chase, Vineland, New Jersey) fitted to a Pellet Pestle Motor (Sigma-Aldrich, St. Louis, Missouri). After initial homogenization, 550 µl of TRIzol was added and the solution was further homogenized by hand. Chloroform (160 µl) was added to the homogenate and then the sample was centrifuged at 12,000 g for 15 minutes at 4°C. The aqueous layer was removed, precipitated with isopropyl alcohol and glycogen (8 µg), then centrifuged for 10 minutes at 4°C to pellet the RNA. The supernatant was removed and the RNA pellet was washed with fresh 75% ethanol. The pellet was dried briefly and then dissolved in 50 µl DEPC treated H2O. mRNA was enriched from total RNA by poly A+ selection using a QIAGEN Oligotex mRNA kit (Valencia, California) following manufacture instructions. mRNA was eluted from small spin columns twice with hot 30 µl buffer OEB. mRNA quality and quantity was determined by Bioanalyzer (Agilent, Santa Clara, California) and 260/280 ratio from Nanodrop ND-1000 UV spectrophotometer.
We fragmented mRNA using alkaline hydrolysis. First, 9 µl of 100 ng of mRNA and 1 µl of 10X fragmentation buffer (Ambion, Austin, Texas.) was incubated at 70°C 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 µl 3 M NaOAC (pH 5.2), 2 µl glycogen (5 µg/µl , Ambion, Austin, Texas), and 30 µl 100% EtOH and then incubated for 30 minutes at -80 °C. Fragmented RNA was pelleted at 14000 rpm with a microcentrifuge at 4°C. The pellet was washed with 70% EtOH, air dried and resuspended with 10.5 µl RNase free H2O. Fragmented mRNA was reverse transcribed to create cDNA. One microliter of random hexamer primers (3µg/µl, Invitrogen, Carlsbad, California) was placed with 10.5 µl of fragmented mRNA, then samples were incubated at 65°C for 5 minutes and placed on ice. Four microliters 5X first strand buffer, 2 µl 100 mM DTT, 1 µl dNTP, and 0.5 µl RNaseOUT were added to the mRNA and samples were incubated at 25°C for 2 minutes. One microliter of SuperScript II (200 U/µl, Invitrogen, Carlsbad, California) was added and samples were incubated under the following conditions: 25°C-10 minutes, 42°C-50 minutes, 70°C-15 minutes. Samples were then placed on ice. Second strand cDNA was synthesized by adding 61µl H2O to the first strand mix, 10 µl 10X second strand buffer (500 mM Tris-HCl pH 7.8, 50 mM MgCl2, 10 mM DTT), and 3 µl dNTP (10 mM), mixed, incubated on ice for 5 minutes, then 1 µl RNaseH (2U/µl, Invitrogen, Carlsbad, California) and 5 µl DNA Pol I (10 U/µl, Invitrogen, Carlsbad, California) were added. Samples were incubated at 16°C for 2.5 hours and DNA products purified using a QIAquick spin column and following manufacture directions and eluted with 30 µl. cDNA fragment libraries were prepared for sequencing. The ends of cDNA fragments were repaired using 30 µl of DNA, 45 µl H2O, 10 µl T4 DNA ligase buffer with 10 mM ATP, 4 µl dNTP mix (10 mM), 5 µl T4 DNA polymerase (3 U/µl), 1 µl Klenow DNA polymerase (5U/µl), and 5 µl T4 PNK(10 U/µl). Samples were incubated for 30 minutes at 20°C, purified with QIAquick PCR spin columns, and eluted with 32 µl of Buffer EB. A single "A" base was added to the ends of cDNA by using 5 µl Klenow buffer, 10 µl dATP (1 mM) and 3 µl Klenow 3' to 5' exonuclease (5 U/µl). Samples were incubated at 37°C for 30 minutes, purified with a QIAquick MiniElute column, and eluted with 19µl of EB solution. Adaptor oligonucleotdies were ligated to A overhang fragments as follows. Overhang fragments were combined with 25 µl DNA ligase buffer, 1 µl adaptor olio mix, and 5 µl DNA ligase (1U/µl). Samples were incubated at room temperature for 15 minutes, purified with a QIAquick MiniElute column, and eluted with 10 µl 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 µl buffer EB. Purified cDNA was amplified in a 50 µl reaction using 25 µl Phusion Mix (Phusion polymerase, dNTPs, and buffer), 1 µl primer 1.1, 1 µl primer 2.1, and 23 µl template along with the following cycling conditions: initial denaturation 98°C-30 sec, cycle denaturation 98°C-10 sec, anneal 65°C-30 sec, and extend 72°C -30 sec with 15X cycles and a final extension of 72°C for 5 minutes followed by a hold at 4°C. The amplified product was purified using a QIAquick column and eluted with 30 µl buffer EB.

treatment_protocol: Frozen whole flies were placed on 10.8 x 10.8 cm ceramic plates frozen on dry ice. Forceps were used to dissect 400-500 heads/sex for subsequent RNA extraction.

tag: source

value: Drosophila Species Stock Center (DSSC) 14011-0121.94. Line MV2-25 Baylor sequencing strain (Richards et al. 2005. Comparative genome sequencing of Drosophila pseudoobscura:chromosomal, gene, and cis-element evolution. Genome Res. 15:1-18). Wild-type genotype. Collected from Anderson, Mesa Verde, Colorado in 1996. Unknown inbred generations.

value: head

tag: gender

value: female


title: HA-Nr5a2_ChIPseq

status: Public on Jan 22 2010

city: Singapore

first: Mikael

last: Huss

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

description: Anti-HA ChIP was performed to enriched for the binding sites of HA-tagged Nr5a2 in ES cells

data_processing: The raw images have been processed using the Solexa Pipeline and mapped to the reference genome (NCBI Build 36, mm8) using Eland software with maximal 2 mis-matches.

source_name: embryonic stem cells

growth_protocol: E14 mouse ES cells, cultured under feeder-free conditions were maintained in Dulbecco's Modified Eagle-Medium (DMEM, GIBCO), with 15 % heat-inactivated ES qualified fetal bovine serum (FBS, GIBCO), 0.055 mM beta-mercaptoethanol (GIBCO), 2mM L-glutamine, 0.1 mM MEM non-essential amino acid, 5,000 units/ml penicillin/streptomycin and 1,000 units/ml of LIF (Chemicon). Control shRNA and Eset shRNA knockdown samples were obtained by transfecting ES cells with the respective shRNAs using lipofectamine-2000(invitrogen). The transfected ES cells were maintained in the ES medium with 0.8ug/ml puromycin.

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. ChIP-enriched DNA from multiple ChIP experiments was pooled and quantified using PicoGreen dsDNA quantitation kit (Invitrogen). The ChIP-enriched DNA was processed for Solexa sequencing using ChIP-Seq Sample Prep Kit (Illumina).

treatment_protocol: The ES cells were fixed in 1 % formaldehyde for 10 minutes at room temperature. The formaldehyde was quenched using 0.1 M glycine before harvest for extract preparation.

value: embryonic stem cells

tag: dev stage

value: anti-HA