title: Empty Vector_RIP-Seq, rep7

status: Public on May 05 2012

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: RNA immunoprecipitation (RIP).

data_processing:
Library strategy: RIP-Seq
Base calling and demultiplexing was performed using CASAVA 1.8.
Alignments were performed using TopHat version 1.4.0 with the following parameters: -p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).
bedGraph files were generated from bam files using bedTools with the following parameters: genomeCoverageBed -bg -split
Genome_build: Dm3
Supplementary_files_format_and_content: Genome browser files are presented in bedGraph format.

organism: Drosophila melanogaster

source_name: Drosophila tissue culture cells, empty vector control

growth_protocol: Cells were cultured in Schneider's medium at 25˚C.

extract_protocol: Whole-cell lysates were prepared in lysis buffer (25 mM NaF, 1 mM Na3VO4, 50 mM Tris [pH 7.5], 1.5 mM MgCl2, 125 mM NaCl, 0.2% IGEPAL, 5% glycerol, Complete, and RNase Inhibitor). Each clarified lysate was bound overnight to 75 ml of crosslinked HA immunoaffinity resin (Sigma). Unbound proteins were washed off with lysis buffer followed by PBS, and then bound protein complexes were competitively eluted using synthetic HA peptide YPYDVPDYA (250 mg/ml) in PBS. RNA was extracted and a sequencing library prepared using the Illumina Tru-Seq mRNA Library preparation kits.

treatment_protocol: Open reading frames for the indicated proteins were inserted into pMK33-C-FLAG-HA acceptor vector. Each clone was transiently transfected into a culture of Drosophila S2R+ cells. Protein expression was induced with 0.35 mM CuSO4.

tag: orf encoding protein

tag: rip antibody

value: HA Immunoaffinity Resin (Sigma)


title: Empty Vector_RIP-Seq, rep6

type: SRA

country: USA

description: RNA immunoprecipitation (RIP).

library_source: transcriptomic

molecule: total RNA

tag: cell line


title: RBM4 PAR-CLIP

status: Public on May 06 2012

city: Ottawa

first: Jim

last: Uniacke

state: Ontario

address: 451 Smyth

country: Canada

institute: University of Ottawa

data_processing:
Library strategy: PAR-CLIP
Sequence reads were analyzed with CLC Genomics Workbench 4.7.1. Adapter sequences were trimmed, and sequence reads were mapped using Basic Local Alignment Search Tool against the human genomic transcript database downloaded from Genbank (human_rna). The match reward/mismatch penalty was set to (1/-2) to allow for mismatches caused by T to C mutations at crosslinking sites. Sequences below 20 nt were discarded, and only sequences with 1 error or none were retained. Non-uniquely mapping reads were discarded, and at least five reads per cluster were required to consider a target significant. The reference genome used was ncbi36.

organism: Homo sapiens

source_name: glioblastoma cells

growth_protocol: Cells were maintained in 5% FBS at 37 oC

extract_protocol:
The RNA was ligated to adapters and reverse transcribed using the High-capacity cDNA Reverse Transcription kit (Applied Biosystems). The RNA was hydrolyzed by adding 40 μL of 150 mM KOH/20 mM Tris Base and incubated for 10 min at 90 oC. The solution was neutralized by adding 150 mM HCl to a final pH between 7.0 and 9.5 to not inhibit the PCR. PCR was performed under standard conditions using a forward primer (5’AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA3’) and a reverse primer (5’ CAAGCAGAAGACGGCATACGA3’) in a total volume of 100 μL. Aliquots of 12 μL were removed every two cycles between cycle 22 and 30 to determine the minimal cycle number. PCR was performed using 10 μL of cDNA with minimal cycle number determined previously. Sample was loaded on a 2 % agarose gel and DNA was excised and extracted using Qiaquick gel extraction kit (Qiagen).
The antibodies used were: anti-RBM4 (Proteintech Group, Cat no. 11614-1-AP, batch #00006245), and for HIF-2a we used GFP-TRAP (Chromotek, Cat no. gta-20, lot #101126001A).
76-bp single read Illumina

treatment_protocol: 24 hours after plating, cells were incubated for another 14 h with 100 μM 4-thiouridine.

tag: cell type

value: U87MG glioblastoma

tag: par-clip


title: Empty Vector_RIP-Seq, rep5

description: RNA immunoprecipitation (RIP).


title: HIF2a PAR-CLIP


title: Empty Vector_RIP-Seq, rep3

description: RNA immunoprecipitation (RIP).


title: Snyder_CEH-26_Input_LE_rep1 extraction1_seq1 aliquote 1

status: Public on May 07 2012

city: Toronto

first: DCC

last: modENCODE

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

institute: Ontario Institute for Cancer Research

description: input DNA

library_source: genomic

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

molecule: genomic DNA

organism: Caenorhabditis elegans

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

tag: strain

value: OP500(official name :OP500 genotype :unc119(ed3);wgIs500(ceh-26::TY1 EGFP FLAG;unc119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Dresden using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The CEH-26::EGFP fusion protein is expressed in the correct ceh-26 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the CEH-26 transcription factor. made_by :R. Waterston )

tag: developmental stage

value: late embryo

tag: genotype

tag: Sex

value: Hermaphrodite


title: CG9998_RIP-Seq, rep2

description: RNA immunoprecipitation (RIP).

source_name: Drosophila tissue culture cells, CG9998


title: Empty Vector_RIP-Seq, rep2

description: RNA immunoprecipitation (RIP).


title: CG8749_RIP-Seq, rep1

description: RNA immunoprecipitation (RIP).

source_name: Drosophila tissue culture cells, CG8749


title: CG8636_RIP-Seq, rep2

description: RNA immunoprecipitation (RIP).

source_name: Drosophila tissue culture cells, CG8636


title: CG8749_RIP-Seq, rep2

description: RNA immunoprecipitation (RIP).


title: CG8636_RIP-Seq, rep1

description: RNA immunoprecipitation (RIP).


title: CG9998_RIP-Seq, rep1

description: RNA immunoprecipitation (RIP).


title: CG7437_RIP-Seq, rep2

description: RNA immunoprecipitation (RIP).

source_name: Drosophila tissue culture cells, CG7437


title: CG6987_RIP-Seq, rep2

description: RNA immunoprecipitation (RIP).

source_name: Drosophila tissue culture cells, CG6987


title: CG7437_RIP-Seq, rep1

description: RNA immunoprecipitation (RIP).


title: CG6987_RIP-Seq, rep1

description: RNA immunoprecipitation (RIP).


title: Empty Vector_RIP-Seq, rep4

description: RNA immunoprecipitation (RIP).


title: Empty Vector_RIP-Seq, rep1

description: RNA immunoprecipitation (RIP).


title: CG6841_RIP-Seq, rep2

description: RNA immunoprecipitation (RIP).

source_name: Drosophila tissue culture cells, CG6841


title: LDM

status: Public on May 16 2012

city: Ya'an

first: Mingzhou

last: Li

state: Sichuan

address: No.46  Xinkang Road

department: College of Animal Science and Technology

country: China

institute: Sichuan Agricultural University

description: Tissue from three females were pooled.

data_processing:
The reads that passed through a series of additional filters are called "mappable reads", which are sequences that satisfy the following criteria from the statistics of mammalian miRNAs in miRBbase 16.0: (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 not only A and C or G and T, (5) containing no stretches of A7, C8, G6, or T7; (6) being longer than 14 nt and shorter than 27 nt; (7) not containing more than nine repeats of any dimer, more than five repeats of any trimer, or more than four repeats of any tetramer; (8) been observed more than two times; and (9) not originating from porcine known classes of RNAs (i.e., mRNA in NCBI database; rRNA, tRNA, snRNA and snoRNA in Rfam database; and repetitive sequence elements in Repbase database). All identical reads were counted and combined into one kind.

The UCSC pig reference genome (~2.26 Gbp) (Sscrofa9.2; ftp://hgdownload.cse.ucsc.edu/goldenPath/susScr2/) was used for mapping using NCBI Local BLAST, which included several major steps:
(a) map the mappable reads to known porcine and other mammalian pre-miRNAs from miRBase 16.0 in order;
(b) map the mapped reads in step (a) to the pig genome to obtain their genomic locations and annotations;
(c) cluster the unmapped sequences in step (b) (which are mapped to miRBase sequences, but not to the pig genome) as potential novel miRNAs from the gaps of the genome; and
(d) hairpin RNA structures encompassing reads not-mapped to miRBase in step (a) were predicated from the adjacent 60 nt sequences in either direction using UNAFold complying with criteria from the statistics of mammalian pre-miRNAs in miRBbase 16.0. To avoid the reads being assigned to the ambiguous multiple positions in the pig genome, herein, only the reads longer than 18 nt in length been included.

organism: Sus scrofa

source_name: longissimus doris muscle

extract_protocol: Eight different adipose tissues, two phenotypically distinct skeletal muscles, and cardiac muscle of three female Landrace pigs (a leaner, Western breed) were used for small RNA sequencing. Total RNA was extracted using the mirVana miRNA isolation kit (Ambion) following the manufacturer's procedure. For each tissue, equal quantities (5ug) of small RNA isolated from three female Landrace pigs were pooled. Approximately 15 ug of small RNA representing each tissue was used for library preparation and sequencing. The small RNA fraction between 10-40 nt was isolated by polyacrylamide gel electrophoresis (PAGE) and ligated with proprietary adaptors (Illumina). The short RNAs were then converted to cDNA by RT-PCR and each small RNA library was sequenced individually using the Illumina Genome Analyzer II according to manufacturer instructions.

tag: breed

value: Landrace

tag: gender

value: female

value: adult

tag: age

value: 210 days

tag: tissue

value: skeletal muscle:longissimus doris muscle


title: CG6841_RIP-Seq, rep1

description: RNA immunoprecipitation (RIP).


title: CG5099_RIP-Seq, rep2

description: RNA immunoprecipitation (RIP).

source_name: Drosophila tissue culture cells, CG5099


title: CG6203_RIP-Seq, rep1

description: RNA immunoprecipitation (RIP).

source_name: Drosophila tissue culture cells, CG6203


title: CG6779_RIP-Seq, rep1

description: RNA immunoprecipitation (RIP).

source_name: Drosophila tissue culture cells, CG6779


title: CG6203_RIP-Seq, rep3

description: RNA immunoprecipitation (RIP).


title: CG6227_RIP-Seq, rep2

description: RNA immunoprecipitation (RIP).

source_name: Drosophila tissue culture cells, CG6227


title: CG6779_RIP-Seq, rep2

description: RNA immunoprecipitation (RIP).


title: CG5442_RIP-Seq, rep1

description: RNA immunoprecipitation (RIP).

source_name: Drosophila tissue culture cells, CG5442


title: CG4816_RIP-Seq, rep2

description: RNA immunoprecipitation (RIP).

source_name: Drosophila tissue culture cells, CG4816


title: CG6779_RIP-Seq, rep3

description: RNA immunoprecipitation (RIP).


title: CG5099_RIP-Seq, rep1

description: RNA immunoprecipitation (RIP).


title: CG6203_RIP-Seq, rep2

description: RNA immunoprecipitation (RIP).


title: CG4816_RIP-Seq, rep1

description: RNA immunoprecipitation (RIP).


title: CG4602_RIP-Seq, rep1

description: RNA immunoprecipitation (RIP).

source_name: Drosophila tissue culture cells, CG4602


title: CG42670_RIP-Seq, rep3

description: RNA immunoprecipitation (RIP).

source_name: Drosophila tissue culture cells, CG42670


title: CG4602_RIP-Seq, rep2

description: RNA immunoprecipitation (RIP).


title: CG42670_RIP-Seq, rep2

description: RNA immunoprecipitation (RIP).


title: CG4262_RIP-Seq, rep2

description: RNA immunoprecipitation (RIP).

source_name: Drosophila tissue culture cells, CG4262


title: CG6227_RIP-Seq, rep1

description: RNA immunoprecipitation (RIP).


title: CG4262_RIP-Seq, rep1

description: RNA immunoprecipitation (RIP).


title: CG17838_RIP-Seq, rep2

description: RNA immunoprecipitation (RIP).

source_name: Drosophila tissue culture cells, CG17838


title: CG17838_RIP-Seq, rep1

description: RNA immunoprecipitation (RIP).


title: CG17136_RIP-Seq, rep2

description: RNA immunoprecipitation (RIP).

source_name: Drosophila tissue culture cells, CG17136


title: CG3613_RIP-Seq, rep1

description: RNA immunoprecipitation (RIP).

source_name: Drosophila tissue culture cells, CG3613


title: CG16901_RIP-Seq, rep1

description: RNA immunoprecipitation (RIP).

source_name: Drosophila tissue culture cells, CG16901


title: CG16901_RIP-Seq, rep2

description: RNA immunoprecipitation (RIP).


title: CG17136_RIP-Seq, rep1

description: RNA immunoprecipitation (RIP).


title: CG31716_RIP-Seq, rep2

description: RNA immunoprecipitation (RIP).

source_name: Drosophila tissue culture cells, CG31716


title: CG16788_RIP-Seq, rep3

description: RNA immunoprecipitation (RIP).

source_name: Drosophila tissue culture cells, CG16788


title: CG3613_RIP-Seq, rep2

description: RNA immunoprecipitation (RIP).


title: CG16788_RIP-Seq, rep1

description: RNA immunoprecipitation (RIP).


title: CG16788_RIP-Seq, rep2

description: RNA immunoprecipitation (RIP).


title: CG5442_RIP-Seq, rep2

description: RNA immunoprecipitation (RIP).


title: CG16725_RIP-Seq, rep3

description: RNA immunoprecipitation (RIP).

source_name: Drosophila tissue culture cells, CG16725


title: CG16725_RIP-Seq, rep2

description: RNA immunoprecipitation (RIP).


title: DRG_sciatic nerve resection_14d

city: Nantong

first: xiaosong

last: gu

state: Jiangsu

address: 19 Qixiu Road

institute: Nantong University

description: Total RNAs extracted from a pool of 6 Sprague-Dawley (SD) rats. Gel-purified small RNAs sequenced using Illumina technology.

data_processing:
Raw data processing: Sequence reads were obtained by Illumina pipeline. Reads of low quality were removed and adaptor sequences were trimmed by our Perl scripts.
Alignment: Unique small RNA sequences were aligned against rattus norvegicus genome by SOAP, tolerating one mismatch.

organism: Rattus norvegicus

source_name: dorsal root ganglia (DRGs)

growth_protocol: Thirty Sprague-Dawley (SD) rats (180–220 g) were provided by the Experimental Animal Center of Nantong University and randomly divided into five groups (six per group) to undergo sciatic neurectomy.

extract_protocol: Dorsal root ganglia (DRGs) in 6 SD rats following sciatic nerve resection were pooled together, and total RNA was extracted from pooled samples by using Trizol Reagent (Invitrogen). Briefly, small RNA molecules ranging from 18 to 30 nt were gel-purified and ligated with a pair of Solexa adaptors to their 5' and 3' ends. Ligation products were purified; reverse transcribed and amplified using adaptor primers. The amplified products were gel-purified and sequenced on an Illumina Genome Analyzer.

treatment_protocol: All animal tests were carried out in accordance with “NIH Guidelines for the Care and Use of Laboratory Animals”. All rats were anesthetized by an injection of complex narcotics (10 mg/kg xylazine, 95 mg/kg ketamine, acepromazine 0.7 mg/kg), and the sciatic nerve was identified and lifted through an incision on the lateral aspect of the mid-thigh of the right hind limb. A 1 cm segment of the right sciatic nerve was excised, and the distal and proximal nerve stumps were separately inserted into nearby inter-muscular spaces to prevent nerve regeneration. After the surgical incisions were closed, animals were housed in temperature- and humidity-controlled cages, maintained under 12:12 h light-dark cycle, and were allowed free access to water and food. One group of rats was euthanized immediately and the other groups were euthanized on days 1, 4, 7, and 14, with surgery to obtain DRGs following euthanasia.

value: Sprague-Dawley (SD)

tag: weight

tag: protocol

value: sciatic nerve resection

tag: time post-surgery

value: dorsal root ganglia (DRGs)


title: CG31716_RIP-Seq, rep1

description: RNA immunoprecipitation (RIP).


title: CG16725_RIP-Seq, rep1

description: RNA immunoprecipitation (RIP).


title: CG1559_RIP-Seq, rep2

description: RNA immunoprecipitation (RIP).

source_name: Drosophila tissue culture cells, CG1559


title: DRG_sciatic nerve resection_1d


title: CG1559_RIP-Seq, rep1

description: RNA immunoprecipitation (RIP).


title: CG12749_RIP-Seq, rep2

description: RNA immunoprecipitation (RIP).

source_name: Drosophila tissue culture cells, CG12749


title: DRG_sciatic nerve resection_7d


title: CG12749_RIP-Seq, rep1

description: RNA immunoprecipitation (RIP).


title: S_sciatic nerve resection_1d

description: total RNAs extracted from a pool of proximal sciatic nerve of 6 Sprague-Dawley (SD) rats

data_processing:
Raw data processing: Sequence reads were obtained by Illumina pipeline. Reads of low quality were removed and adaptor sequence was trimmed by our Perl scripts.
Alignment: Unique small RNA sequences were aligned against rattus norvegicus genome by SOAP, tolerating one mismatch.

source_name: proximal sciatic nerve

extract_protocol: proximal sciatic nerve in 6 SD rats following sciatic nerve resection were pooled together, and total RNA was extracted from pooled samples by using Trizol Reagent (Invitrogen). Briefly, small RNA molecules ranging from 18 to 30 nt were gel-purified and ligated with a pair of Solexa adaptors to their 5' and 3' ends. Ligation products were purified; reverse transcribed and amplified using adaptor primers. The amplified products were gel-purified and sequenced on an Illumina Genome Analyzer.

treatment_protocol: All animal tests were carried out in accordance with “NIH Guidelines for the Care and Use of Laboratory Animals”. All rats were anesthetized by an injection of complex narcotics (10 mg/kg xylazine, 95 mg/kg ketamine, acepromazine 0.7 mg/kg), and the sciatic nerve was identified and lifted through an incision on the lateral aspect of the mid-thigh of the left hind limb. A 1 cm segment of sciatic nerve was then resected at the site just proximal to the division of tibial and common peroneal nerves. After the surgical incisions were closed, animals were housed in temperature- and humidity-controlled cages, maintained under 12:12 h light-dark cycle, and were allowed free access to water and food. One group of rats was euthanized immediately and the other groups were euthanized on days 1, 4, 7, and 14, with surgery to obtain proximal sciatic nerve following euthanasia.

value: Sprague-Dawley

value: proximal sciatic nerve


title: S_sciatic nerve resection_14d


title: CG12357_RIP-Seq, rep2

description: RNA immunoprecipitation (RIP).

source_name: Drosophila tissue culture cells, CG12357


title: Clutch2_Stage44-45

status: Public on May 04 2012

city: Stanford

first: Kin Fai

last: Au

address: James H. Clark Center, 1st Floor East, 318 Campus Drive,

department: Statistics

institute: Stanford

description: polyA-selected RNA

data_processing:
Bowtie was used for alignment.
TopHat and SpliceMap were used for splice junction detection.
Cufflinks and Rseq were used to generate abundance measurements.
Genome_build: XenTro3

organism: Xenopus tropicalis

source_name: embryo_stage 44-45

extract_protocol: The general Illumina mRNA-Seq library preparation workflow was followed with some modifications. First, polyA-containing RNAs were selected. The RNAs were then fragmented in 5X First-Strand Buffer (Invitrogen) at 85oC for 7-8 minutes. Random hexamers and SuperScript III (Invitrogen) were used to synthesize the first strand cDNA. Second strand cDNA synthesis was performed with dUTP in place of dTTP to mark the second strand. After end repair and addition of adenosine to the 3'ends, standard Illumina adapters were ligated. DNA fragments in the size range of 300 to 600bp were gel extracted and treated with UDG before each library was amplified using Phusion (Finnzymes).

value: Outbred

tag: clutch

value: stage 44-45

value: embryo


title: CG10203_RIP-Seq, rep1

description: RNA immunoprecipitation (RIP).

source_name: Drosophila tissue culture cells, CG10203

tag: orf encoding protein

value: HA Immunoaffinity Resin (Sigma)


title: CG10203_RIP-Seq, rep2

description: RNA immunoprecipitation (RIP).

tag: rip antibody


title: CG10279_RIP-Seq, rep2

description: RNA immunoprecipitation (RIP).

source_name: Drosophila tissue culture cells, CG10279

tag: cell line


title: CG10851_RIP-Seq, rep2

description: RNA immunoprecipitation (RIP).

source_name: Drosophila tissue culture cells, CG10851


title: CG12357_RIP-Seq, rep1

description: RNA immunoprecipitation (RIP).


title: CG10851_RIP-Seq, rep1

description: RNA immunoprecipitation (RIP).


title: DRG_sciatic nerve resection_0h


title: CG10128_RIP-Seq, rep2

description: RNA immunoprecipitation (RIP).

source_name: Drosophila tissue culture cells, CG10128


title: CG10279_RIP-Seq, rep1

description: RNA immunoprecipitation (RIP).


title: CG10128_RIP-Seq, rep1

description: RNA immunoprecipitation (RIP).


title: Clutch2_Stage41-42

description: polyA-selected RNA

source_name: embryo_stage 41-42

value: stage 41-42


title: S_sciatic nerve resection_4d


title: DRG_sciatic nerve resection_4d


title: Clutch2_Stage40

description: polyA-selected RNA

source_name: embryo_stage 40

value: stage 40


title: Clutch2_Stage33-34

description: polyA-selected RNA

source_name: embryo_stage 33-34

value: stage 33-34


title: Clutch2_Stage38-39

description: polyA-selected RNA

source_name: embryo_stage 38-39

value: stage 38-39


title: Clutch2_Stage31-32

description: polyA-selected RNA

source_name: embryo_stage 31-32

value: stage 31-32


title: Clutch2_Stage28

description: polyA-selected RNA

source_name: embryo_stage 28

value: stage 28


title: Clutch2_Stage24-26_Set1

description: polyA-selected RNA

source_name: embryo_stage 24-26

value: stage 24-26


title: Clutch2_Stage24-26_Set2

description: polyA-selected RNA


title: Clutch2_Stage20-21

description: polyA-selected RNA

source_name: embryo_stage 20-21

value: stage 20-21


title: Clutch2_Stage22-23

description: polyA-selected RNA

source_name: embryo_stage 22-23

value: stage 22-23


title: S_sciatic nerve resection_7d

value: sciatic nerve resection


title: Clutch2_Stage19

description: polyA-selected RNA

source_name: embryo_stage 19

value: stage 19


title: CG42670_RIP-Seq, rep1

description: RNA immunoprecipitation (RIP).

source_name: Drosophila tissue culture cells, CG42670


title: Clutch2_Stage13-14_Set1

description: polyA-selected RNA

source_name: embryo_stage 13-14

value: stage 13-14


title: Clutch2_Stage8

description: polyA-selected RNA

source_name: embryo_stage 8

value: stage 8


title: Clutch2_Stage10

description: polyA-selected RNA

source_name: embryo_stage 10

value: Outbred

value: stage 10


title: Clutch2_Stage13-14_Set2

description: polyA-selected RNA

value: embryo


title: Clutch2_Stage6

description: polyA-selected RNA

source_name: embryo_stage 6

value: stage 6


title: Clutch2_Stage11-12

description: polyA-selected RNA

source_name: embryo_stage 11-12

value: stage 11-12


title: Clutch2_Stage16-18

description: polyA-selected RNA

source_name: embryo_stage 16-18

value: stage 16-18


title: Clutch2_16cell

description: polyA-selected RNA


title: Clutch2_4cell

description: polyA-selected RNA


title: Clutch2_Stage9

description: polyA-selected RNA

source_name: embryo_stage 9

value: stage 9


title: Clutch2_8cell

description: polyA-selected RNA


title: Clutch1_Stage41-42

description: polyA-selected RNA

source_name: embryo_stage 41-42

value: stage 41-42


title: Clutch1_Stage40

description: polyA-selected RNA

source_name: embryo_stage 40

value: stage 40


title: Clutch1_Stage33-34

description: polyA-selected RNA

source_name: embryo_stage 33-34

value: stage 33-34


title: Clutch1_Stage24-26

description: polyA-selected RNA

value: stage 24-26


title: Clutch1_Stage31-32

description: polyA-selected RNA

source_name: embryo_stage 31-32

value: stage 31-32


title: Clutch1_Stage28

description: polyA-selected RNA

source_name: embryo_stage 28

value: stage 28


title: Clutch1_Stage22-23

description: polyA-selected RNA

value: stage 22-23


title: Clutch1_Stage20-21

description: polyA-selected RNA

value: stage 20-21


title: Clutch2_2cell

description: polyA-selected RNA


title: crh6-3 ChIP H3

status: Public on May 03 2012

city: Los Angeles

first: Shawn

middle: J.

last: Cokus

state: CA

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

institute: UCLA

description: Genomic DNA immunoprecipitated using H3 antibody.

data_processing:
ChIP-Seq PF-passing reads were aligned with Bowtie 0.12.7 to the TAIR8 chr1..5/C/M reference genome, allowing up to 2 and fewest mismatches in the first 28 cycles and up to 100 sum of per-base quality scores at all mismatches, retaining all hits except none if more than 100 hits ('-l 28 -n 2 --nomaqround -e 100 -y -a --best --strata --chunkmbs 1024 -m 100'), filtering to retain only hits with fewest mismatches per read, then retaining only reads with a single hit. Hits were extended in the 3' direction from 50-mers to 220-mers to reflect nominal insert size from library preparation.

Supplementary_files_format_and_content: Each processed file gives the number of 220-mer extended hits covering each genomic basepair (on either strand, unnormalized for variation in genomic mappability or depth of sequencing), presented as a single basepair resolution UCSC Genome Browser wiggle file in plain text format with UNIX-style line endings (single 'fixedStep start=1 step=1 span=1' header per chromosome in order chr1..5/C/M with exactly one non-negative integer entry associated to each reference chr1..5/C/M basepair).

Supplementary_files_format_and_content: Quality scores in _qseq files are Phred scale with +64 ASCII offset... non-multiplexed: 1 lane.

Genome_build: TAIR8

organism: Arabidopsis thaliana

source_name: leaf tissue, crh6-3, H3 ChIP

extract_protocol:
Immunoprecipitated formaldehyde-crosslinked leaf tissue.
Lee et al., Plant Cell 2007 (PMID 17337630).

value: crh6-3 (eco. Columbia)

value: leaf

tag: chip antibody

tag: antibody vendor

value: Abcam

tag: antibody catalog #

tag: antibody lot#


title: Col ChIP H3

source_name: leaf tissue, wild type, H3 ChIP

tag: genotype

value: wild type (eco. Columbia)


title: Col ChIP H3K9me2

description: Genomic DNA immunoprecipitated using H3K9me2 antibody.

source_name: leaf tissue, wild type H3K9me2 ChIP


title: crh6-3 ChIP H3K9me2

source_name: leaf tissue, crh6-3, H3K9me2 ChIP


title: crt1-4 ChIP H3

source_name: leaf tissue, crt1-4, H3 ChIP

value: crt1-4 (eco. Columbia)


title: Col bisulfite

description: Bisulfite-treated genomic DNA.

data_processing:
BS-Seq reads were mapped with BS seeker (Chen et al., 2010 BMC Bioinformatics (PMID 20416082)) to TAIR8 chr1..5/C/M, allowing up to 2 mismatches and retaining only uniquely-mapping reads. Only reference genome cytosines covered with at least 4 reads were considered for analysis.

Supplementary_files_format_and_content: Each processed file is tab-delimited plain text with five columns and UNIX-style line endings. Lines enumerate a subset of TAIR8 chr1..5 genomic cytosines (ordered by ascending column 1 chromosome number, breaking ties by ascending column 2 coordinate). Column 1 is chromosome (1..5). Column 2 is 1-based coordinate of the genomic cytosine (successive reference + strand bases are 1, 2, 3, ... and each - strand base is numbered by the + strand base with which it is paired). Column 3 is context (CG, CHG, or CHH) of the genomic cytosine. Column 4 is genomic strand (+ or -) of the genomic cytosine. Column 5 is the empirical observed fraction of 5'-methylation, calculated as (# read C) / (# read C + # read T).

Supplementary_files_format_and_content: Quality scores in _qseq files are Phred scale with +64 ASCII offset... non-multiplexed: 1 lane.

Genome_build: TAIR8

source_name: leaf tissue, wild type, bisulfite-treated genomic DNA

extract_protocol:
Genomic DNA isolated by phenol/chloroform and bisulfite treated.
Converted and fragmented genomic DNA library as described in Cokus et al., Nature 2008 (PMID 18278030), except directly with pre-methylated final adapters (see Feng et al., Methods Mol. Biol. 2011;733:223-38 (PMID 21431774) for further information).


title: Clutch1_Stage16-18

description: polyA-selected RNA

tag: strain

value: Outbred

tag: developmental stage

value: embryo


title: Clutch1_Stage11-12_Set1

description: polyA-selected RNA

value: stage 11-12


title: Clutch1_Stage19_Set1

description: polyA-selected RNA

source_name: embryo_stage 19

value: stage 19


title: Clutch1_Stage15

description: polyA-selected RNA

source_name: embryo_stage 15

value: stage 15


title: Clutch1_Stage19_Set2

description: polyA-selected RNA


title: Clutch1_Stage9

description: polyA-selected RNA

value: stage 9


title: crt1-3 crh6-1 mRNA EMS batch 2

description: Purified mRNAs.

data_processing:
mRNA-Seq reads were mapped with Bowtie (Langmead, et al. 2009 Genome Biol. (PMID 19261174)) to TAIR8 chr1..5, allowing up to 2 mismatches and retaining only uniquely-mapping reads.

Supplementary_files_format_and_content: Each processed file gives 10- or 20-basepair resolution signal normalized as mapped reads per genomic kilobasepair per million mapped reads in the form of a UCSC Genome Browser wiggle file in plain text format with UNIX-style line endings (single `fixedStep start=1 step=10/20 span=10/20' header per chromosome in order chr1..5; non-negative decimal values).

Supplementary_files_format_and_content: Quality scores in _qseq files are Phred scale with +64 ASCII offset... multiplexed: 1/8 lane.

Genome_build: TAIR8

source_name: leaf tissue, SDC::GFP crt1-3 crh6-1, mRNA

extract_protocol:
Isolated mRNAs from total RNA Trizol preparation.
Illumina TruSeq RNA.

value: SDC::GFP crt1-3 crh6-1 (eco. Columbia)


title: BPD smallRNAseq

city: Shanghai

first: xiaolin

last: wang

address: 180 Feng Lin Rd

institute: Zhongshan Hospital, Fudan University

description: patients with BPD

data_processing:
Basecalls performed using CASAVA version 1.4
The 50nt sequence tags from HiSeq sequencing will go through the data cleaning first, which includes getting rid of the low quality tags and several kinds of contaminants from the 50nt tags
Align small RNA tags to the human miRNA precursor/mature miRNA of corresponding species in miRBase17 using BLAST 2.2.25 ,with the following configurations:blastall -p blastn -F F -e 0.01
Normalize the expression of miRNA in two samples to get the expression of transcript per million (TPM).    Normalization formula: Normalized expression = Actual miRNA count/Total count of clean reads*1000000
Calculate fold-change and P-value from the normalized expression
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: peripheral blood mononuclear cells

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated with lymphocyte separation medium following the manufacturerâ€™s instruction (Sigama,USA).
Peripheral blood (5 ml) was drawn into EDTA tubes, transferred to the laboratory within 30 min for blood processing.
Total RNA was extracted by Trizol Reagent according to the instructions from the manufacturer (invitrogen, USA).
Small RNA library was prepared according to the prescribed procedure and standards of the Illumina Sample Preparation Protocol.In brief, total RNA was purified by electrophoretic separation on a 15% TBE-urea denaturing PAGE gel and small RNA regions corresponding to the 18-30 nucleotide bands in the marker lane were excised and recovered. The 18-30 nt small RNAs were 5' and 3' RNA adapter-ligated by T4 RNA ligase and at each step length validated and purified by urea PAGE gel electrophoretic separation. The adapter-ligated small RNA was subsequently transcribed into cDNA by SuperScript II Reverse Transcriptase (Invitrogen) and PCR amplified, using primers that anneal to the ends of the adapters. The amplified cDNA constructs, too, were purified and recovered.

tag: disease

tag: cell type

value: peripheral blood mononuclear cells


title: Healthy smallRNAseq

description: healthy subjects

value: healthy


title: PDAC smallRNAseq

description: patients with PC

value: pancreatic cancer


title: crh6-1 mRNA EMS batch 2

description: Purified mRNAs.

source_name: leaf tissue, SDC::GFP crh6-1, mRNA

value: SDC::GFP crh6-1 (eco. Columbia)

tag: tissue


title: crt1-4 ChIP H3K9me2

source_name: leaf tissue, crt1-4, H3K9me2 ChIP


title: crt1-4 bisulfite

description: Bisulfite-treated genomic DNA.

source_name: leaf tissue, crt1-4, bisulfite-treated genomic DNA


title: cmt3-11 crt1-3 mRNA EMS batch 2

description: Purified mRNAs.

source_name: leaf tissue, SDC::GFP cmt3-11 crt1-3, mRNA

value: SDC::GFP cmt3-11 crt1-3 (eco. Columbia)


title: crh6-3 bisulfite

description: Bisulfite-treated genomic DNA.

source_name: leaf tissue, crh6-3, bisulfite-treated genomic DNA

value: crh6-3 (eco. Columbia)


title: Clutch1_Stage10

description: polyA-selected RNA

source_name: embryo_stage 10

value: stage 10


title: cmt3-11 mRNA EMS batch 2

description: Purified mRNAs.

source_name: leaf tissue, SDC::GFP cmt3-11, mRNA

value: SDC::GFP cmt3-11 (eco. Columbia)

value: leaf


title: SDC::GFP mRNA EMS batch 2

description: Purified mRNAs.

source_name: leaf tissue, SDC::GFP wild type, mRNA

value: SDC::GFP wild type (eco. Columbia)


title: cmt3-11 mRNA EMS batch 1

description: Purified mRNAs.

data_processing:
mRNA-Seq reads were mapped with Bowtie (Langmead, et al. 2009 Genome Biol. (PMID 19261174)) to TAIR8 chr1..5, allowing up to 2 mismatches and retaining only uniquely-mapping reads.

Supplementary_files_format_and_content: Each processed file gives 10- or 20-basepair resolution signal normalized as mapped reads per genomic kilobasepair per million mapped reads in the form of a UCSC Genome Browser wiggle file in plain text format with UNIX-style line endings (single `fixedStep start=1 step=10/20 span=10/20' header per chromosome in order chr1..5; non-negative decimal values).

Supplementary_files_format_and_content: Quality scores in _qseq files are Phred scale with +64 ASCII offset... non-multiplexed: 1 lane.

Genome_build: TAIR8


title: cmt3-11 crt1-3 mRNA EMS batch 1

description: Purified mRNAs.


title: SDC::GFP mRNA EMS batch 1

description: Purified mRNAs.


title: Clutch1_Stage11-12_Set2

description: polyA-selected RNA

source_name: embryo_stage 11-12

value: Outbred


title: crh6-3 mRNA

description: Purified mRNAs.

source_name: leaf tissue, crh6-3, mRNA


title: crh6-3 small RNA

description: Purified 15-30nt small RNAs.

data_processing:
Small RNA reads were demultiplexed (perfect matches to each index were required) and then filtered for average QC score > 30. Adapter sequences (identified by at least a 13 nt perfect match) were trimmed and reads >15 nt in length after trimming were retained. Reads with no identifiable adapter were discarded. Reads were then mapped with Bowtie to TAIR8 chr1..5/C/M, allowing for 2 mismatches and retaining only uniquely-mapping reads.

Supplementary_files_format_and_content: Each processed file gives 50-basepair resolution small RNA counts normalized by total number of uniquely-mapping reads as a UCSC Genome Browser wiggle file in plain text format with UNIX-style line endings (single `fixedStep start=1 step=50 span=50' header per chromosome in order chr1..5; non-negative decimal values).

Supplementary_files_format_and_content: Quality scores in _qseq files are Phred scale with +64 ASCII offset... multiplexed: 1/3 lane.

Genome_build: TAIR8

source_name: floral tissue, crh6-3, small RNA

extract_protocol:
Isolated small RNAs from total RNA Trizol preparation.
Illumina TruSeq small RNA.

value: floral


title: S_sciatic nerve resection_0h

source_name: proximal sciatic nerve

value: Sprague-Dawley

tag: weight

value: sciatic nerve resection

value: proximal sciatic nerve


title: crt1-4 mRNA

description: Purified mRNAs.

source_name: leaf tissue, crt1-4, mRNA

value: crt1-4 (eco. Columbia)


title: crt1-4 small RNA

description: Purified 15-30nt small RNAs.

source_name: floral tissue, crt1-4, small RNA


title: Col small RNA

description: Purified 15-30nt small RNAs.

source_name: floral tissue, wild type, small RNA

value: wild type (eco. Columbia)


title: xrn2-1xrn4-6 replicate 1

city: La Jolla

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

description: biological replicate 1

source_name: 2-week-old xrn2-1xrn4-6 seedlings

growth_protocol: Plants (Arabidopsis thaliana ecotype Columbia) were grown in the plastic dishes containing LS agar (0.85%) medium supplemented with 1% sucrose for 2 weeks or on soil for 3 weeks under 16-h-light/8-h-dark.

extract_protocol: Total RNA was extracted from the plants using Trizol reagent (Invitrogen, Carlsbad, CA). Poly(A)+ fraction was separated from 80 μg of total RNA using Oligotex mRNA Mini Kit (Qiagen, Valencia, CA) and fragmented using Fragmentation Reagents (Applied Biosystems/Ambion, Austin, TX) at 70°C for 15 min. Fifty nanograms of the fragmented RNA was used to generate strand-specific RNA-Seq library according to the Directional mRNA-Seq Library Preparation Protocol (Illumina). RNA-Seq libraries were sequenced for 42 cycles using the Illumina Genome Analyser II (wild type and fry1-6) or for 50 cycles using the HiSeq 2000 (xrn3-3, xrn3-3xrn4-6, 3-week-old wild type and xrn2-1xrn3-3) according to manufacturer’s instruction. Image analysis and base calling were performed with the standard Illumina pipeline. Read sequences were aligned with the Tophat software to the TAIR9 reference genome (Trapnell et al. 2009).

tag: condition

value: grown on LS plate

tag: age

tag: ecotype

value: Columbia

tag: rna fraction

value: polyA RNA

tag: genotype/variation

value: xrn2-1xrn4-6 plants


title: Wild-type-3w replicate 1

description: biological replicate 1

data_processing: Read sequences were aligned with the Tophat software to the TAIR9 reference genome

source_name: 3-week-old wild type seedlings

value: grown on soil

value: wild type plants


title: fry1-6 replicate 3

description: biological replicate 3

source_name: 2-week-old fry1-6 seedlings

value: fry1-6 plants


title: crh6-1 mRNA EMS batch 1

description: Purified mRNAs.

source_name: leaf tissue, SDC::GFP crh6-1, mRNA

value: SDC::GFP crh6-1 (eco. Columbia)


title: Wild-type replicate 2

description: biological replicate 2

source_name: 2-week-old wild type seedlings


title: xrn2-1xrn3-3 replicate 2

description: biological replicate 2

source_name: 3-week-old xrn2-1xrn3-3 seedlings

value: xrn2-1xrn3-3 plants


title: Wild-type replicate 3

description: biological replicate 3


title: fry1-6 replicate 1

description: biological replicate 1


title: Wild-type replicate 1

description: biological replicate 1


title: xrn3-3xrn4-6 replicate 2

description: biological replicate 2

source_name: 2-week-old xrn3-3xrn4-6 seedlings

value: xrn3-3xrn4-6 plants


title: xrn2-1xrn3-3 replicate 1

description: biological replicate 1


title: Footprint for Torin1-treated wild-type MEFs Replicate 2

city: Cambridge

first: Carson

middle: C

last: Thoreen

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute

data_processing:
Illumina Pipeline version RTA 2.8.0 / OLB 1.8.0 / CASAVA 1.7.0 for image analysis and base calling.
Reads were aligned to the mm9 genome and Refseq transcript junctions using the bowtie short read analyzer, allowing for up to 2 mismatches in the 25 nt seed region.
Aligned reads were mapped to Refseq gene definitions and used to calculate RPKMs. Reads mapping to mutliple locations were assigned to transcripts according the relative distribution of reads mapping to unique locations.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimted text file: Accession, Gene symbol, RPKM

organism: Mus musculus

source_name: Cell culture

growth_protocol: Cells were grown in complete DMEM supplemented with 10% IFS.

extract_protocol: Following treatment, cells were lysed in a detergent-based buffer and lysates were cleared by centrifugation. For footprint library generation, supernatants were treated with RNase and then separated on sucrose gradients to isolate monosome fractions. RNA was extracted and processed for sequencing using an Illumina Genome Analyzer II. For generation of total mRNA libraries, PolyA+ RNA was isolated from cell lysates and randomly fragmented by partial alkaline hydrolysis. ~30 nt fragments were isolated and used for library preparation.

treatment_protocol: Cells were treated for 2 h with either vehicle (DMSO) or 250 nM Torin1. All samples were treated with 100 ug/ml cycloheximide 10 min prior to lysis.

tag: treatment

value: embryonic fibroblast

tag: genetic background


title: Footprint for vehicle-treated wild-type MEFs Replicate 2

value: Vehicle


title: mRNA-seq for Torin1-treated 4EBP1/2 KO MEFs Replicate 1


title: Footprint for Torin1-treated 4EBP1/2 KO MEFs Replicate 2


title: Footprint for vehicle-treated 4EBP1/2 KO MEFs Replicate 2


title: xrn3-3 replicate 1

description: biological replicate 1

source_name: 2-week-old xrn3-3 seedlings

value: xrn3-3 plants


title: mRNA-seq for vehicle-treated 4EBP1/2 KO MEFs Replicate 1


title: Wild-type-3w replicate 2

description: biological replicate 2


title: xrn3-3xrn4-6 replicate 1

description: biological replicate 1


title: xrn3-3 replicate 2

description: biological replicate 2


title: Footprint for Torin1-treated 4EBP1/2 KO MEFs Replicate 1


title: fry1-6 replicate 2

description: biological replicate 2


title: Footprint for vehicle-treated 4EBP1/2 KO MEFs Replicate 1


title: mRNA-seq for Torin1-treated wild-type MEFs Replicate 1


title: Col mRNA

description: Purified mRNAs.

source_name: leaf tissue, wild type, mRNA

value: leaf


title: mRNA-seq for vehicle-treated wild-type MEFs Replicate 1


title: Footprint for vehicle-treated wild-type MEFs Replicate 1


title: Footprint for Torin1-treated wild-type MEFs Replicate 1


title: Hydrogen peroxide, t=1h after treatment

first: Sabeeha

last: Merchant

state: California

address: 607 Charles E. Young Drive East

department: Department of Chemistry and Biochemistry

institute: University of California Los Angeles

description: Illumina's RNA-Seq whole transcriptome analysis

data_processing:
SMDP37HP1h.TS1.bowtie; genome build: Augustus 10.2 gene models - Chlamydomonas V4 genome assembly
SMDP37HP1h.TS2.bowtie; genome build: Augustus 10.2 gene models - Chlamydomonas V4 genome assembly
The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of biological replicates. Processed files correpond to the bowtie standar output format.

organism: Chlamydomonas reinhardtii

source_name: Chlamydomonas cultured cells

growth_protocol: Cells were grown photoheterotrophically in 1 L TAP medium to 2 x 106 cells/mL, at 24 °C, agitated at 180 rpm at a photon flux density of 90 μmol/m2/s provided by cool white fluorescent bulbs at 4100K and warm white fluorescent bulbs at 3000K used in the ratio of 2:1

extract_protocol: Total RNA samples prepared from C. reinhardtii strain 2137 grown photoheterotrophically in the presence of 1 mM H2O2 for 30 and 60 minutes were sequenced on GAIIx platform. cDNA libraries were made using the Illumina manufacturer’s protocol (poly-A purification plus random fragmentation) and sequenced as single 76-mers.

treatment_protocol: When cells reached 2 x 106 cells/mL, the t=0 sample was taken, and H2O2 added to 1 mM final concentration (from 1 M stock in H2O). Samples were subsequently taken at t=0.5h, t=1h, and t=2h.

tag: time

value: Hydrogen peroxide

tag: medium

value: TAP


title: xrn2-1xrn4-6 replicate 2

description: biological replicate 2


title: Hydrogen peroxide, t=0h after treatment

data_processing:
SMDP37HP0h.TS1.bowtie; genome build: Augustus 10.2 gene models - Chlamydomonas V4 genome assembly
SMDP37HP0h.TS2.bowtie; genome build: Augustus 10.2 gene models - Chlamydomonas V4 genome assembly
The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of biological replicates. Processed files correpond to the bowtie standar output format.


title: Δabvf19-8 #2

city: Honolulu

first: Yangrae

last: Cho

state: HI

address: 3190 Maile Way, St John 317

department: Plant and Environmental Protection Sciences

institute: University of Hawaii at Manoa

library_source: non-genomic

data_processing: The sequenced reads were mapped to the genome sequence of A. brassicicola (version 1; http://jgi.doe.gov/Abrassicicola) and the UniGene sequences of B. oleracea (Build #5; ftp://ftp.ncbi.nih.gov/repository/UniGene/Brassica_oleracea/) using the program Tophat 1.3.1 (Trapnell et al., 2009) and Bowtie 0.12.7 (Langmead et al., 2009).  Default settings were used, with these exceptions: the segment length was set at 20 nucleotides and the number of allowed segment mismatches was set at 1 nucleotide.  Additionally, intron length was designated as a minimum of 10 nucleotides and a maximum of 400 nucleotides.  The program Cuffdiff version 1.0.3 (which is part of Cufflinks, (Trapnell et al., 2010)) was used to identify reads overlapping with previously predicted genes.  The expression levels of each predicted gene were determined and normalized by the mapped Fragments Per Kilobase of exon model per Million (FPKM).  Differentially expressed genes between the wild type and the mutant were determined by comparing FPKM from three biological replicates for both the wild type and the mutant.  We also applied a cutoff of at least a two-fold change in expression value for differential expression.  The bias correction method was used while running Cuffdiff (Roberts et al., 2011).  Custom scripts were written in Python to analyze the data. Processed data linked as supplementary files on Series record.

organism: Brassica oleracea

source_name: mixture of pathogen and host

growth_protocol: All host plant, Brassica oleracea were grown under 14 hours light 10 hour dark cycle.  Both wild type and Δabvf19-8 mutant were grown on PDA plates for 7 days before conidium harvest

extract_protocol: Libaray was constructed with TruSeq (Illumina kit) without mRNA purification

treatment_protocol: Conidia were harvested and washed three times with water.  2000 conidia in 10ul water were inoculated.

tag: fungal pathogen

value: Alternaria brassicicola

tag: pathogen genotype/variation

tag: infected host plants

value: 7 weeks old Brassica oleracea

value: mixed tissues of plant leaves and fungal mycelia

tag: infection stage

value: 4 days post inoculation


title: Δabvf19-8 #3


title: wild type #2

value: wildtype


title: hMeDIP-Seq-induced

city: heidelberg

first: michael

middle: thomas

last: bocker

address: Im Neuenheimer Feld

country: Germany

institute: DKFZ Heidelberg

data_processing: All processing steps of the sequencing data were carried out using the short read analysis pipeline shore (Ossowski et al., 2008). Reads were trimmed by removing stretches of bases having a quality score <30 at the ends of the reads. The trimmed reads were mapped to the most recent human genome assembly hg19 using the mapping program bowtie (Langmead et al., 2009). After the mapping duplicate reads were removed and the position-wise coverage of the HOXA cluster by sequencing reads was determined.

source_name: NTera2 D1 cell line

growth_protocol: NT2 cells were maintained in Dulbecco's Modified Eagle Medium (D-MEM, with l-glutamine, 4500 mg/l d-glucose, without sodium pyruvat; Gibco) supplemented with 10% fetal bovine serum and 200 U/ml penicillin and 200 µg/ml streptomycin (all from Gibco) in a humidified atmosphere of 5% CO2 in air.

extract_protocol: Genomic DNA was purified from untreated and RA-treated NT2 cells as described (Mohn et al., 2009). Fifty micrograms of genomic DNA for each sample was sonicated to 300bp fragments using a Covaris S220 (Covaris, Massachusetts, USA) according to manufactures instructions (5 cycles, each 60s: 10%; intensity=5, dust=100). Sheared DNA was ethanol precipitated, washed with 70% ethanol, and dissolved in TE buffer (pH8.0). Illumina adapters were ligated before (h)MeDIP as described before (Xu et al., 2011). Briefly, End-It DNA End-repair kit (Epicentre, Madison, USA) was used for 1h incubation at RT on sheared DNA in 150 µl reaction volume consisting of 12 µg DNA diluted to 102 μl with ddH2O, 15μl of 10x End-it buffer, 15μl of 2.5 mM dNTP mix, 15μl of 10 mM ATP and 3μl of End-it enzyme. DNA was purified with QiaQuick PCR purification kit (Qiagen) and diluted to 122.5μl with ddH2O. Then 15μl of NEB buffer 2, 3.5μl of 10mM ATP and 9μl of 5U/μl Klenow exo- (NEB) were added. After incubating at 37°C for 50min, the “A” base added DNA was purified with QiaQuick PCR purification kit, diluted to 24μl with ddH2O, and mixed with 50μl of 2x NEB quick ligation buffer, 20 μl of barcoded Illumina adapter and 6μl of quick T4 DNA ligase (NEB). DNA was purified with QiaQuick PCR purification kit after incubating at RT for 20 min. Ligation efficiency was analyzed by PCR on 10ng of final ligated DNA with Illumina sequencing primers and ran on a 1% agarose. Five micrograms of adapter ligated DNA was used for (h)MeDIP as described above. Immunoprecipitated DNA was finally resolved in 20µl of water and all MeDIP samples were pooled to create the MeDIP and hMeDIP libraries, respectively. Both libraries were purified on a e-Gel (Invitrogen) and the 300bp bands (containing roughly 200bp fragments of adapter-ligated immunopurified DNA) were extracted. Then, libraries were amplified using Illumina-Enrichment Primers for 12 cycles and purified using Agencourt AMPure XP beads (Beckman Coulter, Brea, USA) according to manufactures instructions. DNA concentrations were measured using a Agilent High Sensitivity DNA Assay (Agilent Technologies, Santa Clara, USA) and 7 pico mol were used for cluster PCR and substantial 50bp single-end sequencing on a HiSeq 2000 (Illumina).

treatment_protocol: NT2 cells were induced to differentiate with 10 µM all-trans retinoic acid (Sigma). Medium containing RA was changed every 2 days.

tag: cell line

value: NTera2 D1 cell line

tag: developmental stage

value: differentiated


title: hMeDIP-Seq-uninduced

value: pluripotent


title: MeDIP-Seq-uninduced


title: Δabvf19-8 #1

tag: tissue


title: MDAH087_IgG_ChIP-Seq

city: Jackson

first: Luis

middle: A

last: Martinez

state: MS

address: 1500 North State St

department: Biochemistry

institute: University of Mississippi Medical Center

data_processing:
Sequencing reads were mapped to Hg18 genome using CLC genomics Workbench 4 software
Peak identification was determined using default settings using IgG as negative control
Processed data provided are unfiltered comprising of entire peak identification dataset
Genome_build: hg18
Supplementary_files_format_and_content: Tab-delimited txt file with genomic coordinates of identified peaks, FDR, number of reads (forward and reverse) per peak, normalized peak ratios, and p-value

source_name: MDAH087 fibroblast cell line

growth_protocol: MDAH087 cells were growth in DMEM + GlutaMax (Invitrogen) media until 80% confluency

extract_protocol: ChIP-Seq samples were prepped using ChIP-Seq DNA Prep Kit (Illumnia)

tag: cell type

value: Fibroblast cells from Li Fraumeni patient

tag: mutant p53

tag: antibody

value: IgG (N-20; Santa Cruz; sc-651)


title: MAC C/EBPbeta

status: Public on May 02 2012

city: Regensburg

first: Michael

last: Rehli

address: F.-J.-Strauss-Allee 11

department: Internal Med III

institute: University Hospital Regensburg

description: Chromatin IP against C/EBPbeta

data_processing: Sequence tags were mapped to the current human reference sequence (GRCh27/hg19) using Bowtie and only uniquely mapped tags were used for downstream analyses. Except for EGR2 where only one donor was used (sample 12) all other samples represent combined data from 2-3 donors. Tag counts were normalized to 1e7 specifically mapped tags. Local tag counts were GC-normalized to match the corresponding monocyte data sets using HOMER.

source_name: Monocyte-derived macrophage

growth_protocol: Peripheral blood monocytes were separated by leukapheresis of healthy donors, followed by density gradient centrifugation over Ficoll/Hypaque and subsequent counter current centrifugal elutriation in a J6M-E centrifuge. Monocytes were > 85% pure as determined by morphology and expression of CD14 antigen. To generate macrophages, isolated monocytes were cultured in endotoxin-free RPMI 1640 medium supplemented with vitamins, antibiotics, pyruvate, nonessential amino acids, 5 x 10-8 M beta-mercaptoethanol, 2% human pooled AB-group serum on teflon foils for up to 7 days.

extract_protocol: DNA from chromatin immunoprecipitation (10-50ng) was adapter-ligated and PCR amplified using Illumina kit Preparing samples for ChIP sequencing of DNA (IP-102-1001) following the manufacturerâs protocol. ChIP fragments were sequenced for 36 cycles on Illumina Genome Analyzers I or II according to the manufacturerâs instructions.

tag: chip antibody

value: C/EBPbeta

value: Monocyte-derived macrophage


title: MAC EGR2

description: Chromatin IP against EGR2


title: MAC EGR2 2

description: Chromatin IP against EGR2


title: MAC PU.1

description: Chromatin IP against PU.1


title: MAC H3K27ac

description: Chromatin IP against H3K27ac


title: MAC H2AZ

description: Chromatin IP against H2AZ


title: MAC H3K4me1

description: Chromatin IP against H3K4me1


title: MO C/EBPbeta

description: Chromatin IP against C/EBPbeta

source_name: Blood monocytes

value: Blood monocytes


title: Hydrogen peroxide, t=0.5h after treatment

data_processing:
SMDP37HP05hTS1.bowtie; genome build: Augustus 10.2 gene models - Chlamydomonas V4 genome assembly
SMDP37HP05hTS2.bowtie; genome build: Augustus 10.2 gene models - Chlamydomonas V4 genome assembly
The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of biological replicates. Processed files correpond to the bowtie standar output format.

tag: strain


title: IgG

description: Chromatin IP against IgG

source_name: Blood monocytes/macrophages

value: IgG

value: Blood monocytes/macrophages


title: MO H3K4me1

description: Chromatin IP against H3K4me1


title: MO PU.1

description: Chromatin IP against PU.1


title: MO H3K27ac

description: Chromatin IP against H3K27ac


title: wild type #1


title: wild type #3


title: MO H2AZ

description: Chromatin IP against H2AZ


title: RCA1 revertant replicate 2

city: Lausanne

first: Dominique

last: Sanglard

address: Rue Bugnon 48

country: Switzerland

institute: University of Lausanne and University Hospital Center

data_processing:
purity filtered reads were aligned to C. albicans genome using TopHat
number of read count per gene was normalized with HTseq
normalization and differential expression were analyzed with R Deseq package
Genome_build: assembly 21 s01-m02-r04
Supplementary_files_format_and_content: RAW.txt: full differential expression results
Supplementary_files_format_and_content: FC2_p0.05.txt: differential expression results, filtered on fold change > 2 and p value < 0.05

organism: Candida albicans

source_name: mid exponential growth-phase culture in YEPD

growth_protocol: C. albicans cells were grown in YEPD liquid medium until mid exponential growth phase

extract_protocol: Yeast cells were harvested, washed, and total RNAs were extracted following standard phenol/chloroform extraction and lithium cholride precipitation. Strand specific librairies were prepared from 2 µg of total RNA following Illumina instructions.

tag: genotype/variation

value: RCA1 revertant


title: RCA1 revertant replicate 1


title: RCA1 mutant, replicate 2

value: RCA1 mutant


title: MeDIP-Seq-induced


title: MDAH087_p53_ChIP-Seq


title: RCA1 mutant, replicate 1


title: wt_FM391_RNA-seq_rep1

city: Kansas CIty

first: Alexander

middle: (Garrett)

last: Garruss

state: Missouri

address: 1000 East 50th Street

institute: Stowers Institute for Medical Research

data_processing:
Base-calling: Casava 1.8
Alignment: Bowtie 0.12.7 -m 10 -v 2 for ChIP-seq; TopHat 1.3.1 -g 1 with Ensembl 63 GTF for RNA-seq
Genome_build: UCSC sacCer2
Supplementary_files_format_and_content: UCSC BED

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: Wild-type yeast (FM391)

growth_protocol: For RNA-seq, total RNAs were prepared from the exponentially growing wild-type and CHD1 deleted mutants to ~0.8 OD600nm using the hot phenol method.

extract_protocol: Harvested cells were broken with 65⁰C acidic phenol and the lysates were extracted by phenol/chloroform/isoamylalcohol three times. Total RNAs were prepared from these lysates by ethanol precipitation. The library was prepared using the Tru-seq mRNA kit (cat# FC-122-1001) from Illumina.

treatment_protocol: wild-type

value: Wild-type (FM391)


title: delta_chd1_RNA-seq_rep2

source_name: delta_Chd1 yeast (FM391,delta Chd1)

treatment_protocol: deletion of Chd1

value: delta_Chd1 (FM391,delta Chd1)


title: delta_chd1_K79me3

growth_protocol: Chromatin immunoprecipitations (ChIPs) were performed with cell lysates prepared from exponentially growing wild-type and CHD1 deleted strains to OD600nm of 1.0 and the cells were cross-linked by formaldehyde treatment.

extract_protocol: We followed the modified ChIP protocol described previously (Wood et al., 2005) and used anti-trimethylated H3K4 and H3K79 antibodies for immunoprecipitation.; anti-trimethylated H3K4 was developed by our lab; and the anti-trimethylated H3K79 antibody was purchased from Abcam (ab2621). 10 ng of DNA prepared from each ChIP was amplified using LMPCR and subjected to single read sequencing on a HiSeq2000 instrument.

value: anti-trimethylated H3K79 antibody (Abcam, ab2621)


title: delta_chd1_RNA-seq_rep1


title: delta_chd1_wce

value: N/A (whole cell extract)


title: wt_FM391_K4me3

value: anti-trimethylated H3K4 antibody (developed by our lab)


title: wt_FM391_K79me3


title: wt_FM391_RNA-seq_rep2


title: wt_FM391_wce


title: delta_chd1_K4me3


title: WCE_ChIP-seq

data_processing:
wce_chip.txt.bam.bed; genome build: hg19
For ChIP-seq analyses, enriched regions were determined by the ‘MACS’ (Zhang et al. 2008) peak-finding program, version 1.4.0rc2. Sequence reads for each ChIP-seq dataset and their associated whole-cell extract controls were used for the input and control file, respectively. The effective genome size was configured appropriately for the human dataset, and the p-value cutoff was set to 1.00e-05 or FDR < 1%, and a fold-change greater than five. All other MACS parameters were left default. Genes were called bound for ChIP-seq sample if an enriched peak region was found within 1kb of the transcription start site of any isoform of a gene from RefSeq (downloaded from UCSC Jan. 21, 2011).

source_name: Whole Cell Extract_ChIP-seq (input control)

growth_protocol: HEK293T cells were cultured in DMEM supplemented with 10% FBS.  Cells were maintained at 37 °C under 5% CO2

extract_protocol: Cells were cross-linked with 1% formaldehyde and incubated with gentle rotation for 10 min at room temperature; cross-linking was quenched by the addition of glycine. Fixed cells were sonicated in lysis buffer using Bioruptor (Diagenode). Sonicated lysates equivalent to 5×10^7 cells were used per immunoprecipitation according to the previously described protocol (Lee et al. 2006).  ChIP-seq libraries were prepared with Illumina's ChIP-seq sample prep kit.

value: human embryonic kidney cells


title: AFF4_ChIP-seq

data_processing:
aff4_chip.txt.bam.bed; genome build: hg19
aff4_chip_peaks.bed; genome build: hg19
For ChIP-seq analyses, enriched regions were determined by the ‘MACS’ (Zhang et al. 2008) peak-finding program, version 1.4.0rc2. Sequence reads for each ChIP-seq dataset and their associated whole-cell extract controls were used for the input and control file, respectively. The effective genome size was configured appropriately for the human dataset, and the p-value cutoff was set to 1.00e-05 or FDR < 1%, and a fold-change greater than five. All other MACS parameters were left default. Genes were called bound for ChIP-seq sample if an enriched peak region was found within 1kb of the transcription start site of any isoform of a gene from RefSeq (downloaded from UCSC Jan. 21, 2011).

extract_protocol: Cells were cross-linked with 1% formaldehyde and incubated with gentle rotation for 10 min at room temperature; cross-linking was quenched by the addition of glycine. Fixed cells were sonicated in lysis buffer using Bioruptor (Diagenode). Sonicated lysates equivalent to 5×10^7 cells were used per immunoprecipitation according to the previously described protocol (Lee et al. 2006).  ChIP-seq libraries were prepared with Illumina's ChIP-seq sample prep kit.  The AFF4 antibody used was characterized previously (Lin et al. 2010).

value: AFF4 antibody [Lin et al. 2010]


title: Pol2_ChIP-seq

data_processing:
pol2_chip.txt.bam.bed; genome build: hg19
Reads were aligned to UCSC hg19 using Bowtie v.0.12.7, allowing up to two mismatches and uniquely aligning reads only.

source_name: Human Embryonic Kidney Cell 293T

value: Pol II (N20)

tag: chip antibody vendor

value: Santa Cruz Biotechnology.

tag: chip antibody cat#


title: AFF3 shRNA rep 2  RNA-seq

data_processing:
3869-2.bam; genome build: hg19
RNA-seq analysis was done using TopHat v1.3.2 (Trapnell et al. 2009) and Bowtie v0.12.7. Human transcript annotations were from RefSeq (downloaded from UCSC on Jan 21, 2011). Differentially expressed genes after RNAi were called with a FDRadjusted p-value < 0.05 and MA plots were determined by Cufflinks v1.1.0 (Trapnell et al. 2010). Paired-end read fragment insert lengths were estimated at a mean of 205 with a standard deviation of 145. Four non-targeting RNAi samples were used as the control samples. Each RNAi sample was done with two replicates.

source_name: AFF3 shRNA RNA-seq

extract_protocol: Total RNA was prepared from the shRNA stable cell lines, and biological duplicate experiments were performed. Polyadenylated RNA was purified from total RNA and fragmented. Double-stranded cDNA from the RNA fragments were ligated to adapters and subjected to deep sequencing (Illumina GA IIx).

treatment_protocol: HEK293T cells were transfected with AFF2, AFF3, or AFF4 SMARTpool siRNA duplex (Dharmacon) using Lipofectamine (Invitrogen). AFF2 shRNA (V2THS_113929), AFF3 shRNA (V2THS_133851), and AFF4 shRNA (V2THS_197522) and constructs were purchased from Open Biosystems. Lentiviral particle preparation and infection were performed as previously described (Lin et al. 2010). Total RNA was extracted with the RNeasy kit from Qiagen and residual DNA was digested with RNase-free DNase I (Sigma) before re-purification by the RNeasy kit.

tag: transfected with

value: AFF3 SMARTpool siRNA duplex


title: AFF4 shRNA rep 1  RNA-seq

data_processing:
H4-1.bam; genome build: hg19
RNA-seq analysis was done using TopHat v1.3.2 (Trapnell et al. 2009) and Bowtie v0.12.7. Human transcript annotations were from RefSeq (downloaded from UCSC on Jan 21, 2011). Differentially expressed genes after RNAi were called with a FDRadjusted p-value < 0.05 and MA plots were determined by Cufflinks v1.1.0 (Trapnell et al. 2010). Paired-end read fragment insert lengths were estimated at a mean of 205 with a standard deviation of 145. Four non-targeting RNAi samples were used as the control samples. Each RNAi sample was done with two replicates.

source_name: AFF4 shRNA RNA-seq

value: AFF4 SMARTpool siRNA duplex


title: AFF3 shRNA rep 1  RNA-seq

data_processing:
3869-1.bam; genome build: hg19
RNA-seq analysis was done using TopHat v1.3.2 (Trapnell et al. 2009) and Bowtie v0.12.7. Human transcript annotations were from RefSeq (downloaded from UCSC on Jan 21, 2011). Differentially expressed genes after RNAi were called with a FDRadjusted p-value < 0.05 and MA plots were determined by Cufflinks v1.1.0 (Trapnell et al. 2010). Paired-end read fragment insert lengths were estimated at a mean of 205 with a standard deviation of 145. Four non-targeting RNAi samples were used as the control samples. Each RNAi sample was done with two replicates.


title: Non-targeting shRNA rep 2 RNA-seq

data_processing:
NT-2.bam; genome build: hg19
RNA-seq analysis was done using TopHat v1.3.2 (Trapnell et al. 2009) and Bowtie v0.12.7. Human transcript annotations were from RefSeq (downloaded from UCSC on Jan 21, 2011). Differentially expressed genes after RNAi were called with a FDRadjusted p-value < 0.05 and MA plots were determined by Cufflinks v1.1.0 (Trapnell et al. 2010). Paired-end read fragment insert lengths were estimated at a mean of 205 with a standard deviation of 145. Four non-targeting RNAi samples were used as the control samples. Each RNAi sample was done with two replicates.

source_name: Non-targeting shRNA RNA-seq


title: AFF2 shRNA rep 1  RNA-seq

data_processing:
2929-1.bam; genome build: hg19
RNA-seq analysis was done using TopHat v1.3.2 (Trapnell et al. 2009) and Bowtie v0.12.7. Human transcript annotations were from RefSeq (downloaded from UCSC on Jan 21, 2011). Differentially expressed genes after RNAi were called with a FDRadjusted p-value < 0.05 and MA plots were determined by Cufflinks v1.1.0 (Trapnell et al. 2010). Paired-end read fragment insert lengths were estimated at a mean of 205 with a standard deviation of 145. Four non-targeting RNAi samples were used as the control samples. Each RNAi sample was done with two replicates.

source_name: AFF2 shRNA RNA-seq

value: AFF2 SMARTpool siRNA duplex


title: Stat5aabb wild-type rep1 in P6

city: Cheonan

first: Keunsoo

last: Kang

state: Chungnam

address: Dandae-ro 119

department: Microbiology

country: South Korea

institute: Dankook University

data_processing:
Basecalls performed using the CASAVA software
Sequenced reads were aligned to the mm9 genome assembly using the TopHat program (Trapnell et al., Bioinformatics, 2009)
Fragment Per Kilobase of exon per million fragments mapped (FPKM) were calculated using a protocol (Mortazavi et al., Nat. Methods, 2008). In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files (P6 and L1) include FPKM values for each Sample

source_name: Mammary gland

growth_protocol: Animals were handled and housed in accordance with the guidelines of NIH and all experiments were approved by the Animal Care and Use Committee of NIDDK. By mating Stat5ab+/- mice (Cui et al., 2004) with Stat5a-/- mice (Liu et al., 1997) and Stat5b-/- mice (Udy et al., 1997), we generated mice carrying a null allele of the Stat5ab locus and one functional allele of either Stat5a (Stat5ab-/Stat5b-) or Stat5b (Stat5ab-/Stat5a-). Stat5abf/f mice (Cui et al., 2004) were mated with the MMTV-Cre transgenic mouse line A (Wagner et al., 1997) in order to generate Stat5abf/f;MMTV-Cre mice (Yamaji et al., 2009).

extract_protocol: Mammary tissues without lymph nodes from two mice of each genotype were collected, frozen in liquid nitrogen, and stored at -80 °C. Total RNA was extracted using TRIzol reagent, followed by a cleanup step using the RNeasy Plus Mini Kit (QIAGEN). Poly(A) RNA was purified twice from 1 mg total RNA and cDNA was synthesized using SuperScript II (Invitrogen) and TruSeq RNA Sample Preparation Kit (Illumina Inc., San Diego, CA), and sequenced using HiSeq 2000 (Illumina).

tag: sample tag

value: Mammary gland

value: Day 6 of pregnancy

tag: genotype

value: Wild-type


title: Stat5aabb wild-type rep3 in P6


title: Stat5aabb wild-type rep2 in P6


title: Non-targeting shRNA rep 1 RNA-seq

data_processing:
NT-1.bam; genome build: hg19
RNA-seq analysis was done using TopHat v1.3.2 (Trapnell et al. 2009) and Bowtie v0.12.7. Human transcript annotations were from RefSeq (downloaded from UCSC on Jan 21, 2011). Differentially expressed genes after RNAi were called with a FDRadjusted p-value < 0.05 and MA plots were determined by Cufflinks v1.1.0 (Trapnell et al. 2010). Paired-end read fragment insert lengths were estimated at a mean of 205 with a standard deviation of 145. Four non-targeting RNAi samples were used as the control samples. Each RNAi sample was done with two replicates.

growth_protocol: HEK293T cells were cultured in DMEM supplemented with 10% FBS.  Cells were maintained at 37 °C under 5% CO2.


title: AFF2 shRNA rep 2  RNA-seq

data_processing:
2929-2.bam; genome build: hg19
RNA-seq analysis was done using TopHat v1.3.2 (Trapnell et al. 2009) and Bowtie v0.12.7. Human transcript annotations were from RefSeq (downloaded from UCSC on Jan 21, 2011). Differentially expressed genes after RNAi were called with a FDRadjusted p-value < 0.05 and MA plots were determined by Cufflinks v1.1.0 (Trapnell et al. 2010). Paired-end read fragment insert lengths were estimated at a mean of 205 with a standard deviation of 145. Four non-targeting RNAi samples were used as the control samples. Each RNAi sample was done with two replicates.


title: Stat5a/b single allele rep3 in P6


title: Stat5a/b single allele rep2 in P6


title: Stat5a/b single allele rep1 in P6


title: Stat5bb double alleles rep3 in P6


title: Stat5bb double alleles rep1 in P6


title: Stat5a single allele rep1 in P6

value: Stat5a (Stat5abnull/Stat5b-)


title: Stat5a single allele rep3 in P6


title: Stat5a single allele rep2 in P6


title: Stat5bb double alleles rep2 in P6


title: Stat5-null rep3 in P6


title: Stat5b single allele rep2 in P6

value: Stat5b (Stat5abnull/Stat5a-)


title: Stat5b single allele rep1 in P6


title: Stat5aabb wild-type rep2 in L1

value: Day of parturition within less than 12 hours after delivery


title: Stat5-null rep1 in P6


title: Non-targeting shRNA rep 4 RNA-seq

data_processing:
NT-4.bam; genome build: hg19
RNA-seq analysis was done using TopHat v1.3.2 (Trapnell et al. 2009) and Bowtie v0.12.7. Human transcript annotations were from RefSeq (downloaded from UCSC on Jan 21, 2011). Differentially expressed genes after RNAi were called with a FDRadjusted p-value < 0.05 and MA plots were determined by Cufflinks v1.1.0 (Trapnell et al. 2010). Paired-end read fragment insert lengths were estimated at a mean of 205 with a standard deviation of 145. Four non-targeting RNAi samples were used as the control samples. Each RNAi sample was done with two replicates.


title: Non-targeting shRNA rep 3 RNA-seq

data_processing:
NT-3.bam; genome build: hg19
RNA-seq analysis was done using TopHat v1.3.2 (Trapnell et al. 2009) and Bowtie v0.12.7. Human transcript annotations were from RefSeq (downloaded from UCSC on Jan 21, 2011). Differentially expressed genes after RNAi were called with a FDRadjusted p-value < 0.05 and MA plots were determined by Cufflinks v1.1.0 (Trapnell et al. 2010). Paired-end read fragment insert lengths were estimated at a mean of 205 with a standard deviation of 145. Four non-targeting RNAi samples were used as the control samples. Each RNAi sample was done with two replicates.


title: Stat5a/b single allele rep1 in L1

value: AB


title: Stat5a/b single allele rep2 in L1


title: Stat5aabb wild-type rep1 in L1

value: WT


title: Stat5-null rep2 in P6


title: Stat5bb double alleles rep2 in L1


title: AFF4 shRNA rep 2  RNA-seq

data_processing:
H4-2.bam; genome build: hg19
RNA-seq analysis was done using TopHat v1.3.2 (Trapnell et al. 2009) and Bowtie v0.12.7. Human transcript annotations were from RefSeq (downloaded from UCSC on Jan 21, 2011). Differentially expressed genes after RNAi were called with a FDRadjusted p-value < 0.05 and MA plots were determined by Cufflinks v1.1.0 (Trapnell et al. 2010). Paired-end read fragment insert lengths were estimated at a mean of 205 with a standard deviation of 145. Four non-targeting RNAi samples were used as the control samples. Each RNAi sample was done with two replicates.


title: Stat5a single allele rep2 in L1


title: Stat5bb double alleles rep1 in L1

value: BB


title: Stat5a single allele rep1 in L1


title: Stat5b single allele rep1 in L1


title: Stat5b single allele rep2 in L1


title: Stat5-null rep1 in L1


title: Stat5b single allele rep3 in P6


title: Stat5-null rep2 in L1


title: Quail_HH20_BS1

city: Saint Louis

first: Kara

last: Powder

state: MO

address: 4566 Scott Ave

department: Genetics

institute: Washington University in St Louis

data_processing: Adapter sequences were trimmed from reads and total reads per sequence were calculated using a custom Perl script.  The resultant data were then uploaded to the miRAnalyzer program, version 1 (http://web.bioinformatics.cicbiogune.es/microRNA/miRanalyser.php).  Processed data are presented as reads per million total reads (PMMR).

organism: Coturnix japonica

source_name: frontonasal prominence neural crest cells

growth_protocol: Eggs were incubated at 37C until specified Hamburger-Hamilton developmental stage.  Frontonasal mesenchyme was dissected as previously described (PMID 20015954).

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) per manufacturer's instructions.  Adapters were ligated to mature miRNAs using the Illumina Small RNA Sample Prep Kit per manufacturers instructions (v1.5 sRNA 3â Adapter).  RNA species from 20-40bp were size selected using a 6% Novex TBE Page gel (Invitrogen)

tag: # embryos pooled

tag: species

value: quail


title: Chicken_HH25_BS2.2

description: biological replicate of Chicken_HH25_BS1; technical replicate of Chicken_HH25_BS2.1

organism: Gallus gallus

value: chicken


title: Quail_HH25_BS1


title: Duck_HH20_BS2

description: biological replicate of Duck_HH20_BS1

organism: Anas platyrhynchos

value: duck


title: Duck_HH25_BS2

description: biological replicate of Duck_HH25_BS1


title: Chicken_HH25_BS1


title: Duck_HH20_BS1


title: Duck_HH25_BS1


title: Chicken_HH20_BS2

description: biological replicate of Chicken_HH20_BS1


title: BMM_KO_1

status: Public on May 01 2012

city: Copenhagen

first: Johannes

middle: Eichler

last: Waage

address: Ole Maaløesvej 5

department: Biotech Research and Innovation Center

country: Denmark

institute: University Of Copenhagen

data_processing: Sequences were mapped to the mouse mm9 genome with TopHat (v.1.0.14) using standard parameters, except the "--max-intron" command line parameter was set to 30,000. No filtering was applied to the fastq reads. SAM and BEDGRAPH files were output as by the TopHat standard.

source_name: Bone Marrow-Derived Macrophages, UPF2 KO

extract_protocol:
Total RNA was harvested in Trizol (Invitrogen) from Upf2fl/fl;LysMCre and Upf2fl/fl-derived male BMMs, grown as previously described (Weischenfeldt et al., 2008). Briefly, bone marrow cells were grown in vitro in the presence of M-CSF-conditioned medium for seven days, giving essentially 100% pure macrophage population. Total RNA from liver was harvested in Trizol (Invitrogen) 21 days post-poly I:C injection from Upf2fl/fl;Mx1Cre and Upf2fl/fl control mice, previously transplanted with wild-type bone marrow cells (Thoren et al., 2010). We pooled 50 µg RNA from each of three age-matched males to get a total of 150µg RNA that was subjected to two rounds of mRNA purification by hybridizing to oligo(dT) beads (Dynabeads mRNA purification Kit, Invitrogen). The resulting mRNA (1µg) was then used as template to prepare cDNA. Double-stranded cDNA was essentially prepared as described by the manufacturer (Superscript Double-Stranded cDNA Synthesis Kit, Invitrogen), using 10µM random hexamers to prime first-strand synthesis. Finally, the ds cDNA was purified using QiaQuick PCR columns (Qiagen) followed by phenol:chloroform extraction. The quality of the cDNA was verified using a Bioanalyzer.

Illumina library preparation for cDNA sequencing was performed as described in the whole genome DNA library construction (DNA sample prep Kit, Illumina). As input, 1 ug cDNA in 50ul TE buffer was fragmented by nebulization with compressed nitrogen gas at 32psi for 9 minutes. Nebulization generated double-stranded DNA fragments with blunt ends or with 3’ or 5’ overhangs. The overhangs were converted to blunt ends by using T4 DNA polymerase and Klenow polymerase. Then, an “A” base was added to the ends of double-stranded DNA using Klenow exo- (3’ to 5’ exo minus). Next, the DNA adaptors (Illumina) with a single “T” base overhang at the 3’ end was ligated to the above products. The ligation products were purified on a 2% agarose gel, and a slice or stab of gel between 150 and 250bp were excised and purified (Qiagen Gel Extraction Kit). The adapter-modified DNA fragments were enriched by PCR with PCR primer 1.1 and 2.1 (Illumina). Separate 12-cycle reactions were used for sequencing. The concentration of the libraries was measured by absorbance at 260nm. Sequencing was performed on an Illumina Genome Analyzer II flowcell, generating 75 bp reads.

value: UPF2 knockout

value: bone marrow-derived macrophages

tag: gender

value: male


title: Stat5b single allele rep3 in L1


title: BMM_WT_1

source_name: Bone Marrow-Derived Macrophages, WT

value: wildtype


title: Liver_KO_1

source_name: Liver, UPF2 KO

value: liver


title: Liver_WT_1

source_name: Liver, WT


title: Dsim wildtype testis expression profiling

first: Sidi

last: Chen

department: Biology

institute: MIT

description: Trizol-chloroform-Qiagen

data_processing:
The sequences in fastq files were mapped back to whole genome sequences using Bowtie, allowing 2 mismatches; all the unmapped sequences were then mapped to all possbile exon-exon conjuction sequences as annotated by flybase using Bowtie, allowing 2 mismatches. The number of reads of a gene is then calculated as the total number of unique sequence read overlapping with annotated exonic regions of the gene and RPKM values are calculated as the number of reads per kilo base of annotated exon length per million total uniquely mapped reads.
Genome Build:
dsim_1_testis_RPKM_value.txt: droSim1

organism: Drosophila simulans

source_name: Dsim wildtype

growth_protocol: standard cornmeal

extract_protocol: standard Illumina single-end mRNA-seq library prep Kit

value: 1-7d adult

value: dissected testis


title: Dyak wildtype testis expression profiling

description: Trizol-chloroform-Qiagen

data_processing:
The sequences in fastq files were mapped back to whole genome sequences using Bowtie, allowing 2 mismatches; all the unmapped sequences were then mapped to all possbile exon-exon conjuction sequences as annotated by flybase using Bowtie, allowing 2 mismatches. The number of reads of a gene is then calculated as the total number of unique sequence read overlapping with annotated exonic regions of the gene and RPKM values are calculated as the number of reads per kilo base of annotated exon length per million total uniquely mapped reads.
Genome Build:
dyak_1_testis_RPKM_value.txt: droYak2

organism: Drosophila yakuba

source_name: Dyak wildtype


title: Caf40 knockdown testis expression profiling 1

description: Trizol-chloroform-Qiagen

data_processing:
The sequences in fastq files were mapped back to whole genome sequences using Bowtie, allowing 2 mismatches; all the unmapped sequences were then mapped to all possbile exon-exon conjuction sequences as annotated by flybase using Bowtie, allowing 2 mismatches. The number of reads of a gene is then calculated as the total number of unique sequence read overlapping with annotated exonic regions of the gene and RPKM values are calculated as the number of reads per kilo base of annotated exon length per million total uniquely mapped reads.
Genome Build:
nos_Caf40_RNAi_1_testis_RPKM_value.txt: dm3

organism: Drosophila melanogaster

source_name: Caf40 testis knockdown

value: Oregon-R


title: Caf40 knockdown testis expression profiling 2

description: Trizol-chloroform-Qiagen

data_processing:
The sequences in fastq files were mapped back to whole genome sequences using Bowtie, allowing 2 mismatches; all the unmapped sequences were then mapped to all possbile exon-exon conjuction sequences as annotated by flybase using Bowtie, allowing 2 mismatches. The number of reads of a gene is then calculated as the total number of unique sequence read overlapping with annotated exonic regions of the gene and RPKM values are calculated as the number of reads per kilo base of annotated exon length per million total uniquely mapped reads.
Genome Build:
nos_Caf40_RNAi_2_testis_RPKM_value.txt: dm3


title: wild-type(N2) irradiated by UVC 100J/m2

city: Beijing

first: Guifeng

last: Wei

state: Beijing

address: 15 Datun Road

institute: Institute of Biophysics, Chinese Academy of Sciences

description: is-ncRNA

data_processing:
The raw data were aligned to the C. elegans genome (WS190) using Bowtie with no more than 2 mismatches.
Transfrags from the mapped reads were merged, and then transfrags of low sequencing depth (<6 reads) or which overlapped with annotated regions (ncRNAs, exons and pseudogenes) and repeats were removed.
Genome_build: WS190 (ce6)
Supplementary_files_format_and_content: wig

source_name: wild-type(N2) irradiated by UVC 100J/m2

growth_protocol: 44 hours after L1s; clutured at 20 degree

extract_protocol: Intermediate-sized transcripts (70-500nt) were size-fractionated by excising the band region corresponding to the appropriate RNA standard markers from a 6% denaturing urea PAGE gel. After extracting from the gel, rRNAs were removed using MicrobExpress kits (Ambion) with specifically designed probes. The shorter fractions (70-200nt) were dephosphorylated with CIAP (Fermentas), ligated to a 3’-adaptor using T4 RNA ligase (Promega) and reverse-transcribed with a universal primer (3’RT), while the longer fractions (200-500nt) were directly reverse transcribed with a random primer. A double-stranded cDNA library was constructed with a SMARTTM cDNA Library Construction Kit (Clontech) and sequenced using standard Solexa sequencing.

value: L4 larvae

value: wild type

tag: treatment

value: UV irradiation(100J/m2)


title: NER-deficient strain

description: is-ncRNA

source_name: NER-deficient strains(xpa-1)

value: no UV irradiation


title: Dmel wildtype testis expression profiling 2

description: Trizol-chloroform-Qiagen

data_processing:
The sequences in fastq files were mapped back to whole genome sequences using Bowtie, allowing 2 mismatches; all the unmapped sequences were then mapped to all possbile exon-exon conjuction sequences as annotated by flybase using Bowtie, allowing 2 mismatches. The number of reads of a gene is then calculated as the total number of unique sequence read overlapping with annotated exonic regions of the gene and RPKM values are calculated as the number of reads per kilo base of annotated exon length per million total uniquely mapped reads.
Genome Build:
dmel_2_testis_RPKM_value.txt: dm3

source_name: Dmel wildtype

tag: developmental stage


title: wild-type(N2)

description: is-ncRNA


title: Zeus knockdown testis expression profiling 1

description: Trizol-chloroform-Qiagen

data_processing:
The sequences in fastq files were mapped back to whole genome sequences using Bowtie, allowing 2 mismatches; all the unmapped sequences were then mapped to all possbile exon-exon conjuction sequences as annotated by flybase using Bowtie, allowing 2 mismatches. The number of reads of a gene is then calculated as the total number of unique sequence read overlapping with annotated exonic regions of the gene and RPKM values are calculated as the number of reads per kilo base of annotated exon length per million total uniquely mapped reads.
Genome Build:
nos_zeus_RNAi_1_testis_RPKM_value.txt: dm3

source_name: Zeus testis knockdown

tag: tissue


title: Zeus knockdown testis expression profiling 2

description: Trizol-chloroform-Qiagen

data_processing:
The sequences in fastq files were mapped back to whole genome sequences using Bowtie, allowing 2 mismatches; all the unmapped sequences were then mapped to all possbile exon-exon conjuction sequences as annotated by flybase using Bowtie, allowing 2 mismatches. The number of reads of a gene is then calculated as the total number of unique sequence read overlapping with annotated exonic regions of the gene and RPKM values are calculated as the number of reads per kilo base of annotated exon length per million total uniquely mapped reads.
Genome Build:
nos_zeus_RNAi_2_testis_RPKM_value.txt: dm3


title: Normals_MBD_seq

city: shanghai

first: jian

last: yu

address: LN 2200/25, Xietu Road

department: The State-key Laboratory for Oncogenes and Relatead Genes

institute: Shanghai Cancer Institute

description: DNA methylation

data_processing: We used BWA align tools to map these reads to hg19 (UCSC) in the human genome. Then, the peaks (hypermethylated regions) were identified using MACS software, and the human CpG islands (CGIs) were download from the UCSC database.

organism: Homo sapiens

source_name: Equal amounts of DNA from two normals

growth_protocol: BCa cell lines T24 (ATCC code: HTB-4) and 5637 (ATCC code: HTB-9) were purchased from ATCC and cultured until they reached the log phase in L-DMEM medium containing 10% FBS at 37°C in a 5% CO2 humidified incubator. Cells were harvested by scraping, and cell pellets were rinsed twice with 1x PBS. Two normal bladder mucosal tissues (BM1 and BM2) were obtained from healthy organ donors.

extract_protocol:
The commercial MethylMiner™ Methylated DNA Enrichment Kit (Invitrogen Inc., Carlsbad, CA, USA was used in this study. For each group, 1.2 μg of mixed DNA was processed according to the manufacturer’s protocol. After a NaCl gradient elution, we collected the final two fractions of high methylated DNA, which corresponded to the salt concentrations of 1M and 2M NaCl. The spike DNA control supplied by the kit was used to confirm the accuracy of the assay. The recovered DNA (in the range of nanograms) was quantified by Qubit™ (Invitrogen), and then 12 cycles of PCR amplification was performed to obtain enough material (in the range of micrograms) for deep sequencing. Finally, 1 μg of the PCR product was applied to the GAII sequencer to generate 75 bp long reads. We used BWA align tools to map these reads to hg19 (UCSC) in the human genome [25]. Then, the peaks (hypermethylated regions) were identified using MACS software [26], and the human CpG islands (CGIs) were download from the UCSC database.
DNA preparation from frozen tissues and cell lines was performed using a conventional proteinase K/organic extraction method as previously described [23]. Equal amounts of DNA from 5637 and T24 were mixed to form the BCC group, and equal amounts of DNA from BM1 and BM2 were mixed to form the BM group. In 1.5-mL centrifuge tubes, 1.5 μg of mixed DNA samples (BCC or BM) in 500 μL TE buffer were sonicated to yield the desired size range (200 ~ 300 bp). End-repair, <A>adenosine base addition and adaptor ligation steps were performed as described previously [24].

tag: tissue type

value: bladder

tag: cell type

value: normal


title: Cancer_MBD_seq

description: DNA methylation

source_name: Equal amounts of DNA from 5637 and T24

treatment_protocol: DNA preparation from frozen tissues and cell lines was performed using a conventional proteinase K/organic extraction method as previously described [23]. Equal amounts of DNA from 5637 and T24 were mixed to form the BCC group, and equal amounts of DNA from BM1 and BM2 were mixed to form the BM group. In 1.5-mL centrifuge tubes, 1.5 μg of mixed DNA samples (BCC or BM) in 500 μL TE buffer were sonicated to yield the desired size range (200 ~ 300 bp). End-repair, <A>adenosine base addition and adaptor ligation steps were performed as described previously [24].

value: cancer


title: Chicken_HH20_BS1

value: chicken


title: Chicken_HH25_BS2.1

description: biological replicate of Chicken_HH25_BS1; technical replicate of Chicken_HH25_BS2.2


title: INNOCUA_WT_37C_NOTAP

city: Rehovot

first: Omri

last: Wurtzel

address: Hertzel

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

data_processing:
Sequencing reads were mapped as described previously (Wurtzel et al, 2010a; Wurtzel et al, 2010b) to the corresponding reference genome of each sub-sample (TAP+ and TAP-) separately (Genbank: NC_003210 and NC_003212 for L. monocytogenes and L. innocua, respectively). Briefly, sequencing reads of either 34 or 36 bases were mapped using BLASTN with e-value of 0.0001 and the “-F F” flag, requiring minimal alignment length of 28 nt, while allowing up to 4 mismatches. The alignment with the best score was considered as the correct mapping, and reads that were mapped at equal scoring to more than one position were discarded from further analysis. In cases where the read alignment did not begin in the first base of the read, read position was corrected to represent the genuine read beginning. The reads mappings were validated using Novoalign 2.0.5.22 as previously described (Avrani et al, 2011). To differentiate between reads initiating from TSSs versus RNA processing sites, a set of 5’ ends that most likely represented real TSSs (positive set) was defined and compared to a group of 5’ ends most likely represented processed sites (negative set). The positive set included genomic positions located upstream to previously defined transcriptional units (Toledo-Arana et al, 2009) (up to 50 nt), in which at least 10 reads were mapped (n=1,140). If multiple genomic positions were located in a distance of less than 10 bases, the position with the highest number of supporting reads was selected as the TSS. The negative set for TAP+:TAP- enrichment analysis was defined as genomic positions located at least 50 nt downstream to ORF beginnings, in which at least 10 reads were mapped (n=33,826).
Genome Build:
INNOCUA_WT_37C_NOTAP.align.txt: NC_003212

organism: Listeria innocua Clip11262

growth_protocol: Strains used in this study were Listeria monocytogenes EGD-e (BUG1600), its isogenic mutants ∆prfA (BUG2214) and ∆sigB (Mandin et al, 2007) and Listeria innocua (CIP107775 CLIP11262BUG499) (Glaser et al, 2001). Bacteria were grown overnight in BHI medium at 37°C with shaking at 200 rpm. Cultures were subsequently diluted 1/500 into 100ml BHI and grown at either 37°C or 30°C until mid-exponential phase (OD600=1.0) or stationary phase (OD600=3.0 for L. monocytogenes and OD600=2.5 for L. innocua). For conditions of low oxygen (hypoxia), cultures were jar-sealed with CampyGen sachet (Oxoid). At the appropriate OD600, bacteria were pelleted by centrifugation at 10,000 X G for five minutes, flash frozen in liquid nitrogen and stored at -80°C until RNA was to be extracted.

extract_protocol: Each RNA sample was divided into two sub-samples (hereby TAP+ and TAP-) containing 2.5 μg of rRNA-depleted RNA. The RNA of TAP+ sub-sample was incubated with 2 U of TAP (Epicentre) for 1.5 h at 37°C to generate 5’ monophosphate RNAs. The other sub-sample (TAP-) was not treated with TAP. cDNA sequencing libraries were prepared as previously described (Wurtzel et al, 2010b), with an addition of a unique 4-base index sequence to the 5’ RNA adapter used for each sub-sample (Supplementary Figure S1A). cDNA libraries of every two sub-samples were mixed in equal amounts, and sent to Illumina sequencing. The resulting sequences were sorted to the correct sub-sample by their index. The TAP+ sub-samples include both primary RNAs and processed RNAs, in contrast to TAP- sub-samples, which contain only processed RNAs.

treatment_protocol: Bacterial pellets were resuspended in 400 ul solution A (½ vol Glucose 20% + ½ vol Tris 25mM pH7.6 + EDTA 10mM) to which an additional 60ul of 0.5M EDTA was added.  RNA was subsequently extracted using TRIzol reagent (Invitrogen) as described previously (Toledo-Arana et al, 2009).  RNA integrity was verified via analysis of intact ribosomal RNA bands via the Experion Automated Electrophoresis system (Biorad). Removal of 16S and 23S rRNA from total RNA was performed using MicrobExpress™ Bacterial mRNA Purification Kit (Ambion) according to the manufacturer's protocol (He et al, 2010). RNA concentrations and quality were determined by using the 2100 Bioanalzyer (Agilent).

tag: organism reference

value: Listeria innocua CIP107775 (Genbank NC_003212)

tag: growth phase

value: mid-log

tag: growth temperature