title: 00000-37C.CO2.90m-2-12.13.11-03.12.12-152

description: wildtype in 37°C + CO2 for 90mins


title: 03902-37C.CO2.90m-3-12.13.11-03.12.12-156

status: Public on Jan 14 2015

type: SRA

city: Saint Louis

first: Ezekiel

middle: John

last: Maier

state: MO

address: 4444 Forest Park Ave

department: Computer Science

country: USA

institute: Washington University

description: RDS2(CNAG_03902)Δ in 37°C + CO2 for 90mins

library_source: transcriptomic

data_processing:
Sequenced reads were aligned to the C. neoformans H99 reference sequence (v2) using TopHat version 2.0.4 and Bowtie version 0.12.8
Reads that aligned uniquely to the reference sequence were considered for gene expression quantification with Cufflinks version 2.0.2. Gene boundaries were defined using the current C. neoformans genome annotation provided by the Broad institute. Gene expression was normalized using the Cufflinks provided option for quartile normalization.
After gene expression quantification, samples not passing the following quality control filters were removed from consideration. The expression of the deleted gene in mutant expression profiles was required to be less than 10% of its expression in WT. The mean and median expression of the deleted genes were 0.7% and 0% of the WT levels respectively. The low levels of expression that remained for some samples were likely the result of errors in the sequencing process itself, either due to contamination between samples or a low level of error in matching barcodes for multiplexed samples to reads. Wild-type samples were required to express the resistance marker at less than 10% of its median level in all mutant expression profiles. In addition, to maximize the power to detect differentially expressed genes, a quality control filter was established to ensure that replicate expression profiles were in agreement. Specifically, within a replicate set the median of all gene coefficients of variation (CoV), defined as the standard deviation of gene expression over mean gene expression, was required to be less than or equal to 0.2. Any replicate set which did not pass this CoV filter was not used for differential expression analysis, and the mutant expression profiles were remade. However, replicate sets were rescued if the median CoV could be lowered below 0.2 by removing an outlier expression profile replicate.
Differential expression analysis comparing matched mutant and wild type expression profile replicate sets was performed with Cuffdiff using a 5% false discovery rate. If multiple replicate sets of a mutant passed the quality control standards, only the replicate set with the lowest CoV was used for differential expression analysis.
Genome_build: C. neoformans H99 reference sequence (Cryptococcus neoformans var. grubii H99 Sequencing Project)
Supplementary_files_format_and_content: cuff: Gene expression was quantified processing tophat produced bam alignments with Cufflinks v0.9.3 with the current H99 annotation (v2) provided by the Broad institute's Fungal Genome initiative. Expression was normalized by applying the Cufflinks supplied quartile normalization routine.

molecule: total RNA

organism: Cryptococcus neoformans

source_name: cultured cells

growth_protocol: All strains were constructed in the C. neoformans KN99α background. Cells were cultured overnight in YPD to a density of 1-2 OD600.

extract_protocol:
For RNA isolation, the culture was treated with ice-cold stop solution (5% Tris-saturated phenol in ethanol) to prevent RNA degradation and then collected by centrifugation. The cells were suspended in TRIzol reagent (Life Technologies) and lysed by mechanical bead-beating at 4°C with 0.5-mm silica-zirconia beads (4 cycles of 3 min of beating followed by 2 min on ice). Following lysis, total RNA was extracted according to the manufacturer’s instructions. Residual DNA was removed from the RNA preparation with the TURBO DNA-free kit (Life Technologies).
Poly(A) RNA was selected from the total using the mRNA Catcher Plus Kit (Life Technologies) with an epMotion 5075 automated pipettor (Eppendorf). The poly(A) RNA was subsequently sheared by incubating in TURBO DNA-free buffer at 75°C for 10 minutes and purified with the QIAquick PCR Purification Kit (Qiagen). First strand cDNA synthesis was performed using random hexameric primers and SuperScript III Reverse Transcriptase, followed by treatment with E. coli DNA ligase, DNA polymerase I, and RNase H for second-strand synthesis, all using standard methods. The cDNA libraries were end-repaired with a Quick Blunting kit and A-tailed using Klenow exo- with dATP (New England Biolabs). Illumina adapters were ligated to the cDNA and fragments ranging from 150-250 bp in size were selected using gel electrophoresis. The libraries were enriched and indexed in a 10-cycle PCR using Phusion Hot Start II High-Fidelity DNA (Fermentas), purified, and pooled in equimolar ratios for multiplex sequencing on an Illumina HiSeq 2500 at the Genome Technology Access Center.

treatment_protocol: Cells were transfered to grow for 90 minutes in either capsule-inducing (DMEM, 37 °C, 5% CO2) or capsule non-inducing (DMEM, 30 °C, room air) conditions prior to isolation of total RNA.

tag: strain

tag: genotype

tag: condition description

value: capsule-inducing

tag: condition

tag: replicate

tag: induction date

tag: library date

tag: sample id


title: 04345-37C.CO2.90m-3-12.13.11-03.12.12-159

description: ARO8001(CNAG_04345)Δ in 37°C + CO2 for 90mins


title: 07924-37C.CO2.90m-3-12.14.11-02.13.12-147

description: MCM1(CNAG_07924)Δ in 37°C + CO2 for 90mins


title: 04345-37C.CO2.90m-1-12.13.11-03.12.12-157


title: 00000-37C.CO2.90m-3-12.13.11-03.12.12-153

description: wildtype in 37°C + CO2 for 90mins

value: wildtype


title: 03902-37C.CO2.90m-2-12.13.11-03.12.12-155


title: 00000-37C.CO2.90m-1-12.13.11-03.12.12-151

description: wildtype in 37°C + CO2 for 90mins


title: 03902-37C.CO2.90m-1-12.13.11-03.12.12-154


title: 00883-37C.CO2.90m-2-12.14.11-02.13.12-149

description: ECM2201(CNAG_00883)Δ in 37°C + CO2 for 90mins


title: 04345-37C.CO2.90m-2-12.13.11-03.12.12-158


title: 00000-37C.CO2.90m-3-12.14.11-02.13.12-144

description: wildtype in 37°C + CO2 for 90mins


title: 07924-37C.CO2.90m-2-12.14.11-02.13.12-146


title: 00000-37C.CO2.90m-1-12.14.11-02.13.12-142

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-2-12.09.11-03.19.12-167

description: wildtype in 37°C + CO2 for 90mins


title: 01626-37C.CO2.90m-3-12.15.11-02.13.12-138

description: ADA2(CNAG_01626)Δ in 37°C + CO2 for 90mins


title: 04864-37C.CO2.90m-1-12.15.11-02.13.12-139

description: CIR1(CNAG_04864)Δ in 37°C + CO2 for 90mins


title: 04864-37C.CO2.90m-2-12.15.11-02.13.12-140


title: 01626-37C.CO2.90m-2-12.15.11-02.13.12-137


title: 04864-37C.CO2.90m-3-12.15.11-02.13.12-141


title: 00000-37C.CO2.90m-2-12.15.11-02.13.12-134

description: wildtype in 37°C + CO2 for 90mins


title: 00883-37C.CO2.90m-1-12.14.11-02.13.12-148


title: 00000-37C.CO2.90m-3-12.15.11-02.13.12-135

description: wildtype in 37°C + CO2 for 90mins


title: 01626-37C.CO2.90m-1-12.15.11-02.13.12-136


title: 00000-37C.CO2.90m-2-09.27.11-02.13.12-132

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-1-12.15.11-02.13.12-133

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-1-09.27.11-02.13.12-131

description: wildtype in 37°C + CO2 for 90mins


title: 05431-37C.CO2.90m-3-12.07.11-01.30.12-127

description: RIM101(CNAG_05431)Δ in 37°C + CO2 for 90mins


title: 00440-37C.CO2.90m-3-12.07.11-01.30.12-130

description: SSN801(CNAG_00440)Δ in 37°C + CO2 for 90mins


title: 05431-37C.CO2.90m-2-12.07.11-01.30.12-126


title: 07924-37C.CO2.90m-1-12.14.11-02.13.12-145


title: 00000-37C.CO2.90m-2-12.14.11-02.13.12-143

description: wildtype in 37°C + CO2 for 90mins


title: 05222-37C.CO2.90m-3-12.06.11-01.30.12-122

description: NRG1(CNAG_05222)Δ in 37°C + CO2 for 90mins


title: 05222-37C.CO2.90m-1-12.06.11-01.30.12-120


title: 00000-37C.CO2.90m-2-12.06.11-01.30.12-115

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-2-12.07.11-01.30.12-123

description: wildtype in 37°C + CO2 for 90mins


title: 01551-37C.CO2.90m-3-12.06.11-01.30.12-119

description: GAT201(CNAG_01551)Δ in 37°C + CO2 for 90mins


title: 00871-37C.CO2.90m-1-12.08.11-01.23.12-111

description: CLR3(CNAG_00871)Δ in 37°C + CO2 for 90mins


title: 00871-37C.CO2.90m-3-12.08.11-01.23.12-113


title: 06276-37C.CO2.90m-3-12.08.11-01.23.12-110

description: CEP3(CNAG_06276)Δ in 37°C + CO2 for 90mins


title: 06276-37C.CO2.90m-1-12.08.11-01.23.12-108


title: 00000-37C.CO2.90m-1-12.06.11-01.30.12-114

description: wildtype in 37°C + CO2 for 90mins


title: 06276-37C.CO2.90m-2-12.08.11-01.23.12-109


title: 00440-37C.CO2.90m-1-12.07.11-01.30.12-128


title: 00000-37C.CO2.90m-1-12.08.11-01.23.12-105

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-3-12.08.11-01.23.12-107

description: wildtype in 37°C + CO2 for 90mins


title: 04908-37C.CO2.90m-3-12.09.11-01.23.12-101

description: CLR4(CNAG_04908)Δ in 37°C + CO2 for 90mins


title: 04908-37C.CO2.90m-1-12.09.11-01.23.12-99


title: 04093-37C.CO2.90m-2-12.09.11-01.23.12-103

description: YRM103(CNAG_04093)Δ in 37°C + CO2 for 90mins


title: 04908-37C.CO2.90m-2-12.09.11-01.23.12-100


title: 01551-37C.CO2.90m-2-12.06.11-01.30.12-118


title: 04093-37C.CO2.90m-3-12.09.11-01.23.12-104


title: 04093-37C.CO2.90m-1-12.09.11-01.23.12-102


title: 00000-37C.CO2.90m-3-12.07.11-01.30.12-124

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-3-12.09.11-01.23.12-98

description: wildtype in 37°C + CO2 for 90mins


title: 00570-37C.CO2.90m-3-12.12.11-01.03.12-92

description: PKR1(CNAG_00570)Δ in 37°C + CO2 for 90mins


title: 01523-37C.CO2.90m-2-12.12.11-01.03.12-94

description: HOG1(CNAG_01523)Δ in 37°C + CO2 for 90mins


title: 01523-37C.CO2.90m-1-12.12.11-01.03.12-93


title: 00570-37C.CO2.90m-2-12.12.11-01.03.12-91


title: 00871-37C.CO2.90m-2-12.08.11-01.23.12-112


title: 00000-37C.CO2.90m-2-12.12.11-01.03.12-88

description: wildtype in 37°C + CO2 for 90mins


title: 04345-37C.CO2.90m-3-12.13.11-01.03.12-86


title: 00000-37C.CO2.90m-2-12.08.11-01.23.12-106

description: wildtype in 37°C + CO2 for 90mins


title: 04345-37C.CO2.90m-2-12.13.11-01.03.12-85


title: 03902-37C.CO2.90m-3-12.13.11-01.03.12-83


title: 00570-37C.CO2.90m-1-12.12.11-01.03.12-90


title: 03902-37C.CO2.90m-2-12.13.11-01.03.12-82


title: 00000-37C.CO2.90m-1-12.12.11-01.03.12-87

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-2-12.13.11-01.03.12-79

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-2-10.04.11-10.25.11-77

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-1-09.27.11-10.19.11-76

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-2-09.27.11-10.19.11-69

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-1-10.07.11-10.25.11-68

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-2-12.09.11-01.23.12-97

description: wildtype in 37°C + CO2 for 90mins


title: 01523-37C.CO2.90m-3-12.12.11-01.03.12-95


title: 00000-37C.CO2.90m-2-10.04.11-10.19.11-66

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-3-10.07.11-10.25.11-65

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-3-10.04.11-10.19.11-63

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-1-10.04.11-10.25.11-67

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-3-09.27.11-10.19.11-60

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-1-10.04.11-10.19.11-58

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-2-10.07.11-10.25.11-55

description: wildtype in 37°C + CO2 for 90mins


title: 04864-37C.CO2.90m-2-03.05.11-03.10.11-53


title: 04345-37C.CO2.90m-1-12.13.11-01.03.12-84


title: 04864-37C.CO2.90m-1-03.05.11-03.10.11-51


title: 01626-37C.CO2.90m-2-03.05.11-03.10.11-49


title: 00000-37C.CO2.90m-2-03.05.11-03.10.11-45

description: wildtype in 37°C + CO2 for 90mins


title: 01626-37C.CO2.90m-1-03.05.11-03.10.11-47


title: 00000-37C.CO2.90m-1-01.30.11-02.05.11-40

description: wildtype in 37°C + CO2 for 90mins


title: 00440-37C.CO2.90m-2-01.30.11-02.05.11-37


title: 00000-37C.CO2.90m-1-03.05.11-03.10.11-43

description: wildtype in 37°C + CO2 for 90mins


title: 00440-37C.CO2.90m-1-01.30.11-02.05.11-36


title: 00000-37C.CO2.90m-3-12.13.11-01.03.12-80

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-3-10.04.11-10.25.11-72

description: wildtype in 37°C + CO2 for 90mins


title: 04369-37C.CO2.90m-2-01.30.11-02.05.11-32

description: CNAG_04369Δ in 37°C + CO2 for 90mins


title: 05431-37C.CO2.90m-1-01.30.11-02.05.11-34


title: 04369-37C.CO2.90m-1-01.30.11-02.05.11-30

description: CNAG_04369Δ in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-1-04.15.10-04.20.10-28

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-1-04.14.10-04.18.10-26

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-2-04.15.10-04.20.10-24

description: wildtype in 37°C + CO2 for 90mins


title: 05222-37C.CO2.90m-2-04.15.10-04.20.10-23


title: 05222-37C.CO2.90m-1-04.15.10-04.20.10-22


title: 00000-37C.CO2.90m-2-01.30.11-02.05.11-41

description: wildtype in 37°C + CO2 for 90mins


title: 01626-37C.CO2.90m-2-04.14.10-04.18.10-11


title: 04864-37C.CO2.90m-1-04.15.10-04.20.10-20


title: 00000-37C.CO2.90m-2-04.14.10-04.18.10-14

description: wildtype in 37°C + CO2 for 90mins


title: 01551-37C.CO2.90m-1-04.14.10-04.18.10-12


title: 01551-37C.CO2.90m-2-04.14.10-04.18.10-13


title: 00000-37C.CO2.90m-1-05.25.10-06.01.10-2

description: wildtype in 37°C + CO2 for 90mins


title: DNMT3 A/A

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

library_source: genomic

data_processing:
Data were mapped to the Mus musculus reference genome version 10
MethylC-Seq analysis were performed as described in Schmtiz et al. Epigenome-wide inheritance of DNA methylation variants in a recombinant inbred population. Genome Research (2013).
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text file
Supplementary_files_format_and_content: column 1 = chr = chromosome\  column 2 = pos = coordinate for the cytosine position on the chromosome\  column 3 = strand = + or - strand\  column 4 = mc_class = context of the cytosine and the two following bases from the same strand\  column 5 = mc_count = number of reads supporting a methylated cytosine\  column 6 = total = total number of reads at that position\  column 7 = methylated = cytosine is considered methylated if there is a 1 or unmethylated if there is a 0}

molecule: genomic DNA

organism: Mus musculus

source_name: DNMT3 A/A

extract_protocol: Genomic DNA (gDNA) was purified from FACS-purified prospermatogonia using QIAmp DNA Micro Kit (Qiagen, Valencia, CA), according to the manufacturer’s instructions. MethylC-Seq libraries were constructed according to Schmitz, R.J. et al. Transgenerational epigenetic instability is a source of novel methylation variants. Science 334, 369-73 (2011).

tag: genotype/variation

value: DNMT3 A/A


title: Nrg1 tagged capsule inducing input replicate 1

description: ChIP-seq input control: Nrg1 tagged capsule inducing

data_processing:
Sequenced reads were aligned to the C. neoformans H99 reference sequence (v2) using Bowtie version 0.12.8
Peak calling was performed with MACS (v1.4.0) by comparing tagged IP reads as the treatment sample and input, mock, and untagged IP reads as the control samples.
For NRG1 analysis, tagged IP treatment replicates 2 & 3 were compared with the untagged wildtype IP control. Any gene falling completely or partially within 1,000 bp on either side of a peak’s summit was considered ChIP positive for that IP-control pair. Only genes that were ChIP-positive for both IP-control pairs were considered NRG1 bound. For Usv101, ChIP-positive genes were called separately for cells grown in capsule-inducing and non-inducing conditions. In each condition, the tagged IP treatment was compared the tagged input and mock controls, and the untagged wildtype IP control. Any gene falling completely or partially within 1,000 bp on either side of a peak’s summit was considered ChIP positive for that IP-control pair. Only genes that were ChIP-positive for all three IP-control pairs were considered USV101 bound.
Genome_build: C. neoformans H99 reference sequence (Cryptococcus neoformans var. grubii H99 Sequencing Project)
Supplementary_files_format_and_content: bed (peaks): Peak calling was performed with MACS (v1.4.0). Each line a peaks bed file gives the coordinates and score (-10log10(pval)) of a MACS identified peak.

growth_protocol: Wild-type and HA-tagged strains were cultured overnight in YPD to a density of 1-2 OD600.

extract_protocol:
The cells were fixed with formaldehyde, lysed by mechanical bead-beating, and the cell debris was  removed by centrifugation. The supernatant fraction, containing isolated chromatin, was sheared by sonication, cleared again by centrifugation, and an aliquot was reserved as ‘input’. The remaining material was incubated with rabbit IgG anti-HA antibody (Abcam) tethered to protein A sepharose (‘IP’) or sepharose alone (‘mock’) overnight at 4°C. The beads were then washed, incubated at 65°C to reverse DNA-DNA and DNA-protein crosslinks, and the DNA recovered by phenol/chloroform/isoamyl alcohol (25:24:1) extraction, ethanol precipitation, and resuspension in nuclease-free water.
ChIP-DNA for for all samples was end-repaired with Klenow DNA Polymerase and the DNA was purified with AMPure XP System beads (Beckman Coulter Genomics) and modified with A-tails using Klenow exo- before ligation to adapters to incorporate 7-base index sequences using T4 DNA ligase (Enzymatics). Adapter addition was confirmed on an Agilent 2100 bioanalyzer, and the DNA was PCR-amplified and then gel purified to remove adapter dimers and select sizes optimal for high-throughput sequencing (150 to 300 bp). Samples were submitted to the Washington University Genome Technology Access Center for library preparation and multiplex sequencing.

treatment_protocol: Cells were transfered to grow for 90 minutes in either capsule-inducing (DMEM, 37 °C, 5% CO2) or capsule non-inducing (YPD, 30 °C) conditions

tag: chip antibody

value: 37°C + CO2 for 90mins


title: Wild type

source_name: Wild type

value: WT


title: Nrg1 tagged capsule inducing ip replicate 1

description: ChIP-seq IP: Nrg1 tagged capsule inducing

value: rabbit IgG anti-HA antibody


title: 00440-37C.CO2.90m-3-12.07.11-03.26.12-200


title: wt exp2

city: Buffalo

first: Steven

last: Pruitt

state: NY

address: Elm & Carlton Streets

department: Molecular & Cellular Biology

institute: Roswell Park Cancer Institute

description: Illumina HiSeq 2000

data_processing:
Illumina Casava1.8.2 software was used for basecalling.
Sequenced reads were mapped to mm9 whole genome using bwa-0.6.2 with default parameters
MACS-1.4.2 was used to generate wiggle files
Genome_build: mm9
Supplementary_files_format_and_content: wiggle file

source_name: wt

extract_protocol:
IntegenX PrepX DNA ChIP kit
Nascent strand capture and release

value: wild type

tag: cell type

value: MEF


title: Nrg1 tagged capsule inducing ip replicate 2


title: Nrg1 tagged capsule inducing input replicate 3


title: wt exp1

description: Illumina HiSeq 2000

extract_protocol:
NEBNext ChIP Seq Library prep kit
Nascent strand capture and release


title: Nrg1 tagged capsule inducing ip replicate 3


title: Wildtype capsule inducing input Nrg1 Control

description: ChIP-seq input control: wildtype capsule inducing


title: Wildtype capsule inducing ip Nrg1 Control

description: ChIP-seq IP control: wildtype capsule inducing


title: Mcm2 deficient exp2

description: Illumina HiSeq 2000

source_name: Mcm2 deficient

value: Mcm2 null


title: set2_YPD_2

city: Solna

first: Vicent

last: Pelechano

address: Nobels väg 16

department: MTC

country: Sweden

institute: ScilifeLab - Karolinska Institutet

data_processing:
Base-calling was done during processing of sequencing data with the illumina pipeline casava v1.8.2
Reads were mapped to S. cerevisiae genome (SGD R64-1-1) using the Novoalign software with default settings
Reads with multiple alignments and/or carrying soft-clipped bases on the 5’ end or on more than 10% of the total read length were excluded from downstream analysis
Genome_build: R64-1-1 (sacCer3)
Supplementary_files_format_and_content: chromosome - start - stop - count; we have obtained single base pair resolution and, to avoid any ambiguity have opted for the use of the same start and stop coordinates that represent the boundaries of an interval of 1bp.

organism: Saccharomyces cerevisiae

source_name: ∆set2::kanMX4, BY4741 background

growth_protocol: S. cerevisiae strains were grown to mid-log phase (OD~1) in YPD (1% yeast extract, 2% peptone, 1% glucose) at 30ºC

extract_protocol:
Total RNA was isolated by a standard hot phenol method and treated with RNase-free DNaseI using Turbo DNA-free kit (Ambion)
10 µg of DNA-free total RNA was desphosphorylated by treatment with Calf Intestinal Alkaline Phosphatase, phenol purified and incubated with Tobacco Acid Pyrophosphatase. Sample was phenol purified and ligated overnight using T4 RNA ligase 1 (NEB) to a DNA/RNA oligo containing a random 8N molecular barcode (CTTTCCCTACACGACGCTCTTCCGATrCrUrNrNrNrNrNrNrNrN). Ligated total RNA was poly(A) purified, and reverse transcribed using random hexamers. Second strand was generated by 1 cycle PCR using oligo Biotin-TATAGCGGCCGCAATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT. Double stranded cDNA was bound to Streptavidin beads, washed, end repaired, dA added and ligated to barcoded P7 linkers as described for the 3’T-fill protocol (PMID: 23295673). The PCR product was size-selected using double Ampure XP size and libraries with an average size of 308bp were submitted for Illumina 50bp paired-end sequencing.


title: Mcm2 deficient exp1

description: Illumina HiSeq 2000


title: 01626-37C.CO2.90m-1-04.14.10-04.18.10-10


title: set2_YPD_1


title: TT-04 CCR6+CXCR3+CCR4–

status: Public on Jan 13 2015

city: Bellinzona

first: Mathilde

last: Foglierini

address: Via Vincenzo Vela 6

country: Switzerland

institute: Institute for Research in Biomedicine

description:
CFSE labeled T cells were incubated with autologous monocytes and indicated antigen, CFSE low blasts were sorted at d6 based and gDNA was obtained
library strategy: DNA-seq

data_processing:
TCRbeta immunosequencing was performed by Adaptive Biotechnologies (Seattle, WA). Briefly, input DNA was amplified in a two-step multiplex PCR in which the first PCR amplified the CDR3 region of T cell genomes and the second PCR added adaptor sequences compatible with Illumina(R) Next Generation Sequencing (NGS) platform. Sequencing was performed using Illumina's NGS platform and processing of raw data, including filtering, clustering and V/J segment identification was performed using Adaptive's immunoSEQ Analyzer software pipeline (Carlson et. al., Nature Communications, 2014).
Supplementary_files_format_and_content: DNA TCR sequences with reads number

organism: Homo sapiens

source_name: blood

growth_protocol: Human memory T cells were sorted from peripheral blood according to the expression of the indicated chemokine receptors,CFSE-labeled, co-cultured for 6 days with autologous monocytes in the presence of heat killed C. albicans, M. tuberculosis, or tetanus toxoid. After 6 days proliferating cells were sorted based on CFSE dilution and DNA extracted for TCR sequencing.

extract_protocol:
Pellets from T proliferating T cells were obtained and snap-frozen. DNA was extracted from pellets using commercial extraction kit.
Library were prepared according to Illumina protocol (by Adaptive Biotechnologies Corp.)

value: CD45RA-CD4+ T lymphocytes

tag: markers used for sorting

tag: specificity

value: Tetanus toxoid


title: TT-04 CXCR3+CCR4–CCR6–


title: by_YPD_1

source_name: Mat a; his3^1leu2^0 ura3^0 met15^0


title: TT-04 CCR4+CXCR3–CCR6–


title: TT-03 CCR4+CXCR3–CCR6–


title: TT-03 CCR6+CCR4+CXCR3–


title: TT-03 CXCR3+CCR4–CCR6–


title: TT-04 CCR6+CCR4+CXCR3–


title: TT-02 CXCR3+CCR4–CCR6–


title: Nrg1 tagged capsule inducing input replicate 2


title: TT-03 CCR6+CXCR3+CCR4–


title: by_YPD_2


title: TT-02 CCR6+CXCR3+CCR4–


title: TT-02 CCR6+CCR4+CXCR3–


title: TT-02 CCR4+CXCR3–CCR6–


title: 04864-37C.CO2.90m-2-04.15.10-04.20.10-21


title: TT-01 CCR6+CXCR3+CCR4–


title: TT-01 CXCR3+CCR4–CCR6–


title: TT-01 CCR6+CCR4+CXCR3–


title: MT-02 CCR6+CXCR3-CCR4+

value: M. tuberculosis


title: MT-01 CCR6+CXCR3-CCR4+


title: MT-01 CCR6+CXCR3+CCR4+


title: MT-02 CCR6+CXCR3+CCR4-


title: TT-01 CCR4+CXCR3–CCR6–


title: MT-02 CCR6+CXCR3+CCR4+


title: MT-01 CCR6+CXCR3+CCR4-


title: CA-05 CXCR3+CCR4–CCR6–

value: C. albicans


title: CA-05 CCR4+CXCR3–CCR6–


title: CA-04 CCR6+CXCR3+CCR4–


title: CA-05 CCR6+CCR4+CXCR3–


title: CA-04 CXCR3+CCR4–CCR6–


title: CA-04 CCR6+CCR4+CXCR3–


title: CA-05 CCR6+CXCR3+CCR4–


title: CA-04 CCR4+CXCR3–CCR6–


title: CA-03 CCR6+CCR4+CXCR3–


title: CA-03 CCR6+CXCR3+CCR4–


title: CA-03 CXCR3+CCR4–CCR6–


title: T1080_UV1

city: Cologne

first: Ales

last: Pecinka

address: Carl von Linne Weg 10

country: Germany

institute: Max Planck Institute for Plant Breeding Research

description: Sample 21

data_processing:
read quality control (FastQC)
low quality read trimming / adapter clipping (FASTX tools)
mapping to Arabidopsis TAIR9 for T1080 and C24 and to TAIR10 for Ba-1, Lip-0, Mh-0 and Got-7 (TopHat)
retrieving number of reads per gene coordinates (qualimap)
Genome_build: TAIR9 / TAIR10
Supplementary_files_format_and_content: EXCEL file, readcounts per gene for each of the libraries

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: plants were grown for 14 days on soil at long day conditions (day: 16 h, 6 am to 10 pm, light intensity ~150 µmol m-2 s-1, 22° C; night: 8 h, no light, 18° C) and 50% relative humidity.

extract_protocol:
Whole seedlings were flash frozen and RNA was extracted using the RNeasy Mini Kit (Qiagen) with additional on column DNAse I (Roche) digest
RNA libraries were prepared for sequencing using RNA TruSeq kit (Illumina) using standard protocol

treatment_protocol: UV treatments were carried out using four Philips TL40 W/12RS SLV UV fluorescent tubes  (fluence rate at 312 nm: 4.35 W/m² at the plant level) without filtering and dimming. After treatment plants were kept under standard growth conditions for 3 hours until tissue was harvested.

tag: background

tag: tissue

value: seedling

tag: treatment

value: UV


title: T1080_UV2

description: Sample 22


title: T1080_mock

description: Sample 20

value: mock


title: Mh0_UV2

description: Sample 19


title: Mh0_UV1

description: Sample 18


title: Mh0_mock2

description: Sample 17


title: CA-02 CCR6+CXCR3+CCR4–


title: CA-02 CXCR3+CCR4–CCR6–


title: Mh0_mock1

description: Sample 16


title: Lip0_UV1

description: Sample 14


title: Lip0_UV2

description: Sample 15


title: Lip0_mock1

description: Sample 12


title: Lip0_mock2

description: Sample 13


title: CA-01 CXCR3+CCR4–CCR6–


title: CA-02 CCR4+CXCR3–CCR6–


title: CA-01 CCR6+CXCR3+CCR4–


title: Got7_UV

description: Sample 11


title: Got7_mock1

description: Sample 9


title: C24_UV1

description: Sample 7


title: C24_mock1

description: Sample 5


title: C24_UV2

description: Sample 8


title: CA-03 CCR4+CXCR3–CCR6–


title: Got7_mock2

description: Sample 10


title: CA-01 CCR6+CCR4+CXCR3–


title: C24_mock2

description: Sample 6


title: CA-01 CCR4+CXCR3–CCR6–


title: Ba1_mock2

description: Sample 2


title: Ba1_UV2

description: Sample 4


title: Ba1_mock1

description: Sample 1


title: CA-02 CCR6+CCR4+CXCR3–


title: WT_M2

city: Madrid

first: Manuel

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

data_processing:
Illumina RTA software v 1.13.48.0
Illumina2bam v:0.03
SamToFastq.jar v1.86
Reads were pre-processed with Cutadapt 1.2.1, To remove TruSeq adapters.
Resulting reads were mapped on the mouse transcriptome (Ensembl gene-build GRCm38.v70) using RSEM v1.2.3.
Data were normalized using TMM with the Bioconductor package EdgeR
Differential expression were tested using GLM with the Bioconductor package EdgeR
Genome_build: GRCm38.v70
Supplementary_files_format_and_content: matrix_table.xls file contains ENSEMBL gene Ids and TMM-Normalized counts per million for each sample.

extract_protocol:
Twelve 17-weeks post induction per genotype were killed by cervical decapitation and heart (left ventricle) tissues were dissected and immediately frozen in liquid nitrogen. Total RNA was extracted with QIAzol Lysis Reagent and then purified on RNeasy spin columns (Qiagen). RNA integrity (RNA Integrity Score ≥ 7.9) and quantity were determined on the Agilent 2100 Bioanalyzer. RNA samples from different animals were mixed in equal proportion at four samples per pool, and three pools per genotype were analyzed in the Illumina Genome Analyzer IIx.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: αMHCTM-Cretg/+

value: heart


title: Bmi1KO_M1


title: Bmi1KO_M6


title: Bmi1KO_M3


title: WT_M5


title: WT2

city: Mainz

first: Tobias

last: Bopp

address: Langenbeckstrasse 1

department: Institute for Immunology

institute: University Medical Center Mainz

description: Treg isolated from tracheal lymphnodes

data_processing:
Illumina CASAVA 1.8.2 software were used for basecalling
Sequence reads were trimmed for adapter sequence on the Miseq-system and further processed using the software CLC genomics workbench (6.5; using CLC's default settings for RNA-Seq analysis). Reads were aligned to mm9 genome.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated employing CLC Genomics Workbench (6.5)
Genome_build: mm9

source_name: CD4+Foxp3+ regulatory T cell (tLN)

extract_protocol:
CD4+FoxP3+ regulatory T cells were isolated from spleen and tracheal lymphnodes (tLN)  using a FACS Aria II (BD) and total RNA was isolated using Trizol (Sample 1 and 2) or RNeasy micro kit (Qiagen; sample 3 and 4). TruSeq RNA Sample Prep Kit V2 was used for the construction of sequencing libraries from samples 1 and 2. For library constructions of samples 3 and 4 SMARTer PCR cDNA synthesis Kit V1 (Takara CLontech) followed by Nextera XT library prep kit (Illumina) was used.
RNA libraries were prepared for sequencing using standard Illumina TruSeq RNAv2 protocol (Sample 1 und sample 2) and standard Nextera XT protocol (sample 3 and sample 4). Barcode sample 1: Illumina adapter 6, barcode sample 2: Illumina adapter 12, barcode sample 3: N701/S502, barcode sample 4: N702/S503.

value: CD4+FoxP3+ regulatory T cell


title: Csnk2b-deficient1

description: Treg isolated from spleen

source_name: CD4+Foxp3+ regulatory T cell (Spleen)


title: Csnk2b-deficient 2

description: Treg isolated from tracheal lymphnodes


title: WT1

description: Treg isolated from spleen


title: WxP_H3K4me3_Input_sample_2

city: Bar Harbor

first: Christopher

middle: Lee

last: Baker

state: ME

address: 600 Main Street

department: Research

institute: The Jackson Laboratory

data_processing:
Basecalls performed using CASAVA version 1.8
For initial peak calling using MACS reads were mapped to mm9 in all samples. For haplotype analysis using the EMASE method individual diploid genomes were created for MACS intervals using available SNPs (Sanger) using the software package Seqnature (Munger, S.C. et al. Genetics. 2014)
For peak calling using MACS reads were mapped with BWA (v0.5.10) with default settings. For mapping to individual diploid genomes (haplotype analysis) reads were mapped with bowtie (v0.2.8) with the following settings: -S --best -a --strata -m 5 -v 3.
Genome_build: mm9
Supplementary_files_format_and_content: Files with .xls extension are standard MACS v1.4.2 output in tab-delimited format and contain argument settings and column headers. Peaks were called with p = e-5. For H3K4me3 duplicate reads were retained. Files labeled EMASE are tab-delimited tables with haplotype ratios for F1 hybrid hotspots. EMASE files have the following column format: chr, start, stop, # of reads mapped to haplotype 1, # of reads mapped to haplotype 2, total mapped reads, fraction of haplotype 1.

source_name: spermatocytes

growth_protocol: For Mnase ChIP-seq germ cells were enriched from male mice at 12 days post-partum (dpp). For PRDM9 ChIP-seq whole tubules were collected and homogenized from male mice at 12 dpp. For detailed protocol see publication

extract_protocol:
Nuclei were isolated from cells using hypotonic lysis. Chromatin was fragmented either by Mnase digestion or sonication (PRDM9 ChIP). After high speed spin soluble chromatin was removed and used for ChIP
Libraries were prepared for sequencing using Bioo Scientific's NEXTflex ChIP-Seq Kit (protocol version V11.11) without size selection. Amplification of the libraries was done using 14-18 cycles of PCR.

value: spermatocyte

tag: age

value: 12 days post-partum

value: WSBxPWD F1 Hybrid


title: BxC_PRDM9_ChIP

description:
BxC_P9_e-5_peaks.xls
EMASE_BxC_P9_haplotype.txt

source_name: testis

value: testis

tag: strain

value: B6xCAST F1 Hybrid


title: CxB_H3K4me3_Input_sample_2

value: CASTxB6 F1 Hybrid


title: CxB_H3K4me3_Input_sample_1


title: BxC_PRDM9_Input


title: BxC_H3K4me3_Input_sample_2


title: PWD_H3K4me3_Input_sample_2

value: PWD/PhJ


title: BxC_H3K4me3_Input_sample_1


title: Ba1_UV1

description: Sample 3


title: WSB_H3K4me3_Input_sample_2

value: WSB/EiJ


title: WSB_H3K4me3_Input_sample_1


title: WT_M4

tag: genotype


title: WxP_H3K4me3_ChIP_sample_2

description:
H3K4me3_WxP_merge_e-5_peaks.xls
EMASE_WxP_H3K4me3_merge_haplotype.txt


title: CxB_H3K4me3_ChIP_sample_2

description:
H3K4me3_CxB_merge_e-5_peaks.xls
EMASE_CxB_H3K4me3_merge_haplotype.txt


title: CAST_H3K4me3_Input_sample_2

value: CAST/EiJ


title: WxP_H3K4me3_ChIP_sample_1


title: CxB_H3K4me3_ChIP_sample_1


title: BxC_H3K4me3_ChIP_sample_2

description:
H3K4me3_BxC_merge_e-5_peaks.xls
EMASE_BxC_H3K4me3_merge_haplotype.txt


title: BxC_H3K4me3_ChIP_sample_1


title: PWD_H3K4me3_ChIP_sample_1


title: WSB_H3K4me3_ChIP_sample_1


title: CAST_H3K4me3_ChIP_sample_1


title: CAST_H3K4me3_ChIP_sample_2


title: WxP_H3K4me3_Input_sample_1


title: RepC_2i

city: Madison

first: Rupa

last: Sridharan

state: WI

address: 330 N. Orchard Street

department: Department of Regenerative Biology

institute: University of Wisconsin

data_processing:
Low quality reads were removed ( <30) and High quality reads were trimmed and adapters clipped using FASTX-Toolkit
Processed reads were aligned to the mm9 genome using bowtie
Expression level was determined by RSEM 1.2.4 with forward probability of 0.5
Genome_build: mm9
Supplementary_files_format_and_content: txt file containing gene expression values in FPKM, TPM, and expected counts

source_name: partially reprogrammed iPSC line, 48 hour treatment with 2i

growth_protocol: pre-iPSC were grown and maintianed in standard mouse embryonic stem cell media in DMEM 15% FBS supplemented with non-essential amino acids, glutamine, pen-strep and b-mercatoethanol, on irradiated feeders

extract_protocol:
RNA was extracted using the Qiagen RNA-easy minikit
Library was constructed by Illumina TruSeq RNA Sample Preparation Kit following Illumina's protocol

treatment_protocol: pre-iPSC were treated in ESC media with DMSO or AA at 50ug/ml or 2i at 1uM MEK inhibitor and 3uM GSK inhibitor, or a combination of AA and 2i, in the absence of the feeder layer.

value: partially reprogrammed iPSC


title: RepC_AA2i

source_name: partially reprogrammed iPSC line, 48 hour treatment with AA+2i


title: PWD_H3K4me3_ChIP_sample_2


title: PWD_H3K4me3_Input_sample_1


title: RepB_DMSO

source_name: partially reprogrammed iPSC line, 48 hour treatment with DMSO


title: RepB_AA2i


title: RepB_AA

source_name: partially reprogrammed iPSC line, 48 hour treatment with AA


title: RepC_AA


title: RepB_2i


title: RepA_2i


title: RepC_DMSO


title: RepA_AA


title: CAST_H3K4me3_Input_sample_1


title: RepA_DMSO


title: S1

status: Public on Jan 12 2015

city: College Park

first: Bhanu Prakash

last: Telugu

state: MD

address: 2121 ANSC Lab

department: Animal and Avian Sciences

institute: University of Maryland

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence (trimmomatic v0.32), then mapped to mus musculus whole genome using tophat v2.0.9 and bowtie v2.1.0
Reads were quantified using the cufflinks (v.2.2.1) and cuffdiff packages. RPKM values per gene feature can be found the the processed data table. Defult parameters were used.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delmited RPKM counts for each sample and gene in mm9 bulid.

source_name: Gfra1+ spermatogonial stem cells

growth_protocol: Stem cells were cultured in mouse embryonic stem cell medium supplemented with LIF and DOX

extract_protocol:
Total RNA was extracted with miRNeasy Minikit. Ribosomal RNA was depleted using Ribozero kit
libraries generated by TruSeq® Stranded mRNA kit (Illumina)
Clustered and sequenced was using TruSeq PE Cluster Kit v3

treatment_protocol: Primary spermatogonial stem cells were obtained using Magnetic assisted cell sorting for Gfra1 antibody.

value: primary spermatogonial stem cells

tag: passage


title: A2

source_name: SSC derived IPSC

value: iPSC from SSC


title: WSB_H3K4me3_ChIP_sample_2


title: S3


title: S2


title: D3

source_name: Fibroblast derived iPSC

value: iPSC from somatic cells


title: A3


title: D2


title: A1


title: iPS sRNA

city: Pasadena

first: Diane

middle: E

last: Trout

state: CA

address: 1200 E California Blvd M/C 156-29

department: Biology

institute: California Institute of Technology

description: small RNA

data_processing:
Reads were trimmed to 50-mers and mapped against the mm9 version and the set of splice junctions from the ENSEMBL63 annotation of the mouse genome using TopHat 1.2.1. Expression level were quantified using Cufflinks 2.0.0
Genome_build: mm9
Supplementary_files_format_and_content: fastq files and fpkm values

source_name: iPS cell

growth_protocol: cells were grown in standard ES cell medium on irradiated feeder cells

extract_protocol:
cell lysates were used for cDNA synthesis or RNA extraction using TRI reagent
libraries were prepared according to Illumina protocols for Ultra Low Input RNA

treatment_protocol: cells were treated with doxycycline to induce OSKM transgenes

value: iPS cell

value: Sample 13965

tag: technology used

value: small RNA seq


title: iPS KD1

description: bulk

value: Sample 13707

value: bulk RNA-seq


title: iPS

description: bulk

value: Sample 13706


title: iPS KD2

description: bulk

value: Sample 13710


title: TTF

description: bulk

source_name: tail tip fibroblast

value: tail tip fibroblast

value: Sample 13702


title: iPS 2i 6

description: single-cell

value: Sample 13990

value: single-cell RNA-seq


title: iPS 2i 3

description: single-cell

value: Sample 13987


title: ES

description: bulk

source_name: ES cell

value: 129 x castaneus

value: ES cell

value: Sample 13696


title: iPS 2i 4

description: single-cell

value: Sample 13988


title: iPS 2i 2

description: single-cell

value: Sample 13986


title: iPS 2i 7

description: single-cell

value: iPS cell

value: Sample 13991


title: mES 6

description: single-cell

value: Sample 13092


title: RepA_AA2i

value: partially reprogrammed iPSC


title: mES 3

description: single-cell

value: Sample 13089


title: iPS 2i 1

description: single-cell

value: Sample 13985


title: mES 4

description: single-cell

value: Sample 13090


title: D1

value: iPSC from somatic cells


title: mES 2

description: single-cell

value: Sample 13088


title: Wk2 4

description: single-cell

source_name: reprogramming cell

value: reprogramming cell

value: Sample 12933


title: mES 1

description: single-cell

value: Sample 13087

value: single-cell RNA-seq


title: Wk2 2

description: single-cell

value: Sample 12931


title: TTF 3

description: single-cell

value: tail tip fibroblast

value: Sample 12928


title: Wk2 1

description: single-cell

value: Sample 12930


title: TTF 4

description: single-cell

value: Sample 12929


title: TTF 2

description: single-cell

value: Sample 12927


title: Wk2 3

description: single-cell

value: Sample 12932


title: iPS 2i 8

description: single-cell

value: iPS cell

value: Sample 13992


title: iPS 2i 5

description: single-cell

value: Sample 13989


title: TTF 1

description: single-cell

value: Sample 12926


title: fES 8

description: single-cell

value: 129 x castaneus

value: ES cell

value: Sample 12925


title: fES 7

description: single-cell

value: Sample 12924


title: fES 6

description: single-cell

value: Sample 12923


title: fES 4

description: single-cell

value: Sample 12921

value: single-cell RNA-seq


title: fES 2

description: single-cell

value: Sample 12919


title: fES 5

description: single-cell

value: Sample 12922


title: fES 3

description: single-cell

value: Sample 12920


title: mES 5

description: single-cell

value: Sample 13091


title: fES 1

description: single-cell

value: Sample 12918


title: iPS 9

description: single-cell

value: Sample 12610


title: iPS 10

description: single-cell

value: iPS cell

value: Sample 12613


title: iPS 7

description: single-cell

value: Sample 12608


title: iPS 8

description: single-cell

value: Sample 12609


title: iPS 6

description: single-cell

value: Sample 12607


title: iPS 1

description: single-cell

value: Sample 12600


title: iPS 4

description: single-cell

value: Sample 12605


title: iPS 3

description: single-cell

value: Sample 12602


title: iPS 5

description: single-cell

value: Sample 12606


title: iPS 2

description: single-cell

value: Sample 12601


title: MixInfert A2

city: Santa Barbara

first: Delany

last: Rodriguez

address: Biological Science Building  RM1201 University of California Santa Barbara

department: Molecular Cellular and Developmental Biology

institute: University of California Santa Barbara

data_processing:
For sequencing libraries were diluted to 16 pM then applied to a V3 flowcell using the Illumina cBot according to manufacturer’s instructions.   Sequencing was carried out on the Hi-Seq 2000 using HSCS v 1.5.15.1.  Image analysis and basecalling were carried out using RTA 1.13.48.0, and deconvolution and fastq file production were performed with CASAVA 1.8.2.
Sequenced reads were trimmed for adaptor sequenceusing FastQC
Mapped to EST database "Bot_asmb assembly (04.05.2011, A. Gracey)" using bowtie v0.12.7
The number of reads mapping to each EST were obtained with Sam2Counts (Samtools version 0.1.18)
Fragments per kilobase per million (FPKM) were calculated using RSEM 1.2.3 for each paired-end library for each genotype at each stage of the blastogenic cycle for both infertile and fertile colonies.
Differential expression analysis was performed with DESeq 1.10.1
Supplementary_files_format_and_content: tab-delimited text files
Genome_build: http://octopus.obs-vlfr.fr/public/botryllus/blast_botryllus.php  (Note: use EST: *Bot_asmb assembly (04.05.2011, A. Gracey)*)

organism: Botryllus schlosseri

source_name: Whole colony

growth_protocol: Botryllus schlosseri raised in the lab

extract_protocol:
Total RNA was extracted with Nucleo Spin RNA II kit from MN
The standard protocol for library construction began with 1 ug of total RNA.  Since the protocol utilized was based on polyA capture, RNA was visualized on a BIoRad Experion to insure RNA Quality Index values were greater than 8.  For library construction the illumina TruSeq v2 mRNA kit was utilized.  The protocol was followed according to manufacturer’s instructions except the final number of PCR cycles was 12 and not 15.  Following construction, libraries were visualized by Bioanalyzer (Agilent) using the High Sensitivity Chip and quantified for pooling and sequencing using Kapa Biosystems qPCR quantitation kit according to manufacturer’s instructions.

tag: group

value: Infertile

tag: Stage

value: Stage A2


title: MixInfert B1

value: Stage B1


title: MixInfert A1

value: Stage A1


title: MixInfert C2

value: Stage C2


title: MixInfert B2

value: Stage B2


title: MixInfert D

value: Stage D


title: Infert802 C1

value: Stage C1


title: Infert802 B2


title: Infert802 C2


title: Infert802 B1


title: Infert802 D


title: Infert001 D


title: Infert802 A1


title: Infert001 C2


title: Infert001 B1


title: Infert001 B2


title: Infert001 C1


title: MixFert D

value: Hermaprhodite


title: MixFert B2


title: Infert001 A2


title: MixFert C1


title: MixFert B1


title: Infert001 A1


title: MixFert A1


title: MixFert C2


title: MixInfert C1


title: MixFert A2


title: Fert801 D


title: Fert841 A2


title: Fert841 B1


title: Fert801 C2


title: Fert841 C2


title: Fert801 B2


title: iPS 31

data_processing: Reads were trimmed to 50-mers and mapped against the mm9 version and the set of splice junctions from the ENSEMBL63 annotation of the mouse genome using TopHat 1.2.1. Expression level were quantified using Cufflinks 2.0.0

extract_protocol:
cell lysates were used for cDNA synthesis or RNA extraction
libraries were prepared according to Illumina protocols for Ultra Low Input RNA

value: iPS cell

tag: technology

value: single-cell


title: Fert841 B2


title: Fert841 C1


title: Infert802 A2


title: Fert801 C1


title: iPS 29


title: iPS 30


title: Fert841 A1


title: Fert801 B1


title: iPS 28


title: Fert841 D


title: iPS 26


title: Fert801 A1


title: Fert801 A2


title: iPS 25


title: iPS 24


title: iPS 23


title: iPS 21


title: mec1 R 1h from Exp B

city: Syracuse

first: Wenyi

last: Feng

address: 750 East Adams Street

department: Biochemistry and Molecular Biology

institute: SUNY Upstate Medical University

description:
Library Strategy: Break-Seq
Sample name: EH052313I
Processed using two-sample analysis in MACS: EH052313I against EH052313G

data_processing:
Sequence alignment was performed with Bowtie2 for files associated with sample AB052313F and with BWA version 0.6.2 for all other samples, using default parameters.
Peak calling was performed by MACS version 1.4.1, either as a one-sample or a two-sample analysis, using default parameters.
See description whether MACS was used as a one-sample or two-sample analysis and which samples were used in two-sample analyses.
Genome_build: SacCer3
Supplementary_files_format_and_content: Raw sequence data files are in the fastq format.  Processed MACS files are in BED format.

source_name: Saccharomyces cerevisiae_mec1_R

growth_protocol: Yeast cells were grown to approx. 5x10E6 cells/ml before alpha factor treatment in YPD medium.

extract_protocol:
Agarose plugs containing yeast cells for spheroplasting were prepared as described (Van Brabant et al., 2001 Mol Cell 7, 705-713).
Approximately 10E6 yeast cells from each sample were washed in 50 mM EDTA and embedded in 0.5% Incert low melting agarose (Lonza) in 50 mM EDTA, then cast in a 100-μl mold (BioRad) to solidify.  The plugs were then processed for cell lysis and protein removal as previously described (Feng et al. 2011).  Each processed agarose plug was incubated twice in 5 ml of TE 0.1 buffer (10 mM Tris-HCl, 0.1 mM EDTA, pH 8.0) for 15 min at room temperature, then incubated twice in 5 ml of 1X End-Repair reaction buffer (33 mM Tris-acetate, pH 7.8, 66 mM potassium acetate, 10 mM magnesium acetate, and 0.5 mM dithiothreitol) for 30 min at room temperature.  Each plug was then mixed with 50 μl of labeling mix (1X End-Repair buffer, 100 μM each of dTTP, dCTP, and dGTP, 84 μM dATP, 16 μM Biotin-14-dATP (Invitrogen), 1 mM ATP, and 3 μl End-It enzyme mix (Epicentre)) and incubated at 25°C for 1.5 h.  The plug was washed twice with 5 ml TE 0.1 buffer at room temperature for 15 min.  The agarose was digested by β-agarase (New England Biolabs) according to manufacturer’s recommendation.  The released genomic DNA was brought to a final volume of 250-300 μl in TE 0.1 buffer and sonicated in a Bioruptor to achieve an average size of smaller than 500 bp.  The fragmented DNA was purified by a Qiagen PCR Cleanup Kit, followed by End-Repair (with unmodified dNTPs) and A-tailing using standard Illumina DNA library construction conditions.   The A-tailed DNA was then brought to a volume of 100 μl with EB buffer (Qiagen) for binding with M270 Dynabeads (Life technologies).  For each DNA sample, 50 μl of bead suspension was first immobilized on a magnet and washed three times each with 100 μl of 1X Binding and Washing buffer (B&W buffer, 5 mM Tris-HCl, pH 7.5, 0.5 mM EDTA, pH 8.0, and 1 M NaCl), followed by resuspension in 100 μl of 2X B&W buffer.  The 100-μl DNA sample was then mixed with the beads and incubated at room temperature for 30 min with agitation.  The DNA-bound beads were washed twice each with 100 μl of 1X B&W buffer, then washed twice each with 100 μl of EB buffer.  The washed beads were then resuspended in ligation reaction mix containing 3 μM each of Adapter 1 and Adapter 2 and incubated at room temperature overnight with agitation.   The beads were washed twice each with 200 μl of 1X B&W buffer and twice each with 200 μl of EB and the associated DNA was then amplified by PCR using multiplexed PE PCR primers using standard procedures recommended by Illumina.  The PCR products were purified by AmPure beads to remove free adapters according to manufacturer’s recommendations and the resulting DNA was subjected to 50-bp or 100-bp paired-end sequencing on the Illumina Hi-Seq platform.

treatment_protocol: Alpha factor was used at 3 micromolar and hydroxyurea was used at 200 mM.  At the time of sampling, cells were treated with 0.1% sodium azide.

tag: time point

value: R 1h

tag: experiment group

value: Exp B


title: Wk2 15

source_name: transitional cell

value: transitional cell


title: mec1 HU 1h from Exp A

description:
Library Strategy: Break-Seq
Sample name: EH040213H
Processed using one-sample analysis in MACS: EH040213H

source_name: Saccharomyces cerevisiae_mec1_HU

value: HU 1h

value: Exp A


title: mec1 G1 from Exp A digested with BamHI

description:
Library Strategy: Break-Seq
Sample name: AB052313F
Processed using one-sample analysis in MACS: AB052313F

source_name: Saccharomyces cerevisiae_mec1_G1_bamH1


title: mec1 R 1h from Exp A

description:
Library Strategy: Break-Seq
Sample name: EH040213G
Processed using two-sample analysis in MACS: EH040213G againt EH040213H


title: mec1 HU 1h from Exp B

description:
Library Strategy: Break-Seq
Sample name: EH052313G
Processed using one-sample analysis in MACS: EH052313G


title: ES 21

value: ES cell


title: ES 20


title: ES 18


title: ES 16


title: ES 15


title: ES 19


title: iPS 27


title: TTF 12

value: tail tip fibroblast


title: MEC1 (WT) R 1h from Exp C

description:
Library Strategy: Break-Seq
Sample name: EH052313C
Processed using two-sample analysis in MACS: EH052313C against EH052313A

source_name: Saccharomyces cerevisiae_wt_R

value: WFA72 (MEC1)

value: Exp C


title: TTF 13


title: MEC1 (WT) HU 1h from Exp C

description:
Library Strategy: Break-Seq
Sample name: EH052313A
Processed using one-sample analysis in MACS: EH052313A

source_name: Saccharomyces cerevisiae_wt_HU


title: TTF 10


title: TTF 6


title: TTF 7


title: TTF 11


title: TTF 9


title: iPS 20


title: iPS 18


title: iPS 16


title: iPS 15


title: A73-R60_S8_L001

data_processing:
Sequence mapping by BWA
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using SeqMonk quantification pipeline.
Pair-wise comparisons between samples were performed to identify those mRNA features with significant differences (p<0.05) between samples.  The  RPKM quantification results for all samples as well as the pair-wise comparison results can both be found in the supplemental information of the manuscript.
Genome_build: SacCer3
Supplementary_files_format_and_content: Text file with RPKM values can be found on the series record.

source_name: Saccharomyces cerevisiae_mec1_R60

growth_protocol: Log phase cells were synchronized by alpha factor in G1 and released into S phase in the presence of 200 mM HU for 1h. Cells were then filtered to remove HU and allowed to recover in fresh media without HU for 30 and 60 min.

extract_protocol:
Total RNA was isolated based on standard "hot phenol" isolation protocol.
The Illumina TruSeq Stranded mRNA Sample Preparation Kit was used to prepare the mRNA libraries according to the manufacturer’s recommendations.


title: iPS 22


title: TTF 14


title: iPS 13


title: A73-HU_S6_L001


title: iPS 17


title: iPS 14


title: ES 17


title: A73-R30_S7_L001

source_name: Saccharomyces cerevisiae_mec1_R30


title: iPS 11


title: A73-G1_S5_L001

source_name: Saccharomyces cerevisiae_mec1_G1


title: TTF 8


title: Wk2 13


title: Wk2 14


title: A72-R60_S4_L001

source_name: Saccharomyces cerevisiae_wildtype_R60

value: wildtype


title: TTF 5


title: Wk2 12


title: A72-R30_S3_L001

source_name: Saccharomyces cerevisiae_wildtype_R30


title: Wk2 10


title: iPS 19


title: A72-HU_S2_L001

source_name: Saccharomyces cerevisiae_wildtype_HU


title: MEC1 (WT) G1 from Control Exp

description:
Labeled DNA double strand breaks
Processed_data file= MACS two sample analysis: AMc111214WT_HU_to_G1_peaks.bed
Library Strategy: Break-Seq

data_processing:
Sequence mapping by BWA
Genome_build: SacCer3
Peak calling by MACS, either as a one-sample or a two-sample analysis
Supplementary_files_format_and_content: Processed MACS files are in BED format.

source_name: MEC1 (WT) G1 from Control Exp

value: Control experiment


title: Wk2 11


title: Wk2 9


title: MEC1 (WT) HU 1h from Control Exp mock labeling

description:
Mock Labeled (without biotinylated dNTP mix) DNA double strand breaks
Processed_data file= MACS two sample analysis: AMc111214WT_HU_to_minusBiotin_peaks.bed
Library Strategy: Break-Seq


title: mec1 G1 from Control Exp

description:
Labeled DNA double strand breaks
Processed_data file= MACS two sample analysis: AMc111214mec1_HU_to_G1_peaks.bed
Library Strategy: Break-Seq

source_name: mec1 G1 from Control Exp


title: iPS 12

source_name: iPS cell


title: Wk2 6


title: Wk2 7


title: mec1 HU 1h from Control Exp

description:
Labeled DNA double strand breaks
Processed_data file= MACS one sample analysis: AMc111214mec1_HU_peaks.bed
Library Strategy: Break-Seq

source_name: mec1 HU 1h from Control Exp


title: Wk2 5


title: mec1 HU 1h from Control Exp mock labeling

description:
Mock Labeled (without biotinylated dNTP mix) DNA double strand breaks
Processed_data file= MACS two sample analysis: AMc111214mec1_HU_to_minusBiotin_peaks.bed
Library Strategy: Break-Seq


title: (Negative Control for SVP-ChIPSeq) 35S:GFP rep2

status: Public on Jan 11 2015

first: Julieta

last: Mateos

address: Carl-von-Linné-Weg 10

department: Department of Plant Developmental Biology

data_processing:
We followed recommended guidelines in the analysis of ChIP-seq data for quality control, read mapping, normalization, peak-calling, assessment of reproducibility among biological replicates, and post-processing of peaks (Bailey et al., PLoS Computational Biology 2013, DOI: 10.1371/journal.pcbi.1003326).
Basecalls were performed using CASAVA version 1.8.
Low-quality reads in the raw data (fastq files) were filtered out using Parallel-QC 1.0 (Zhou et al., PLoS ONE 2013). Low-quality reads were defined as those not having Phred quality scores ≥ 13 in the bases called.
Reads kept were aligned to the Arabidopsis thaliana genome (TAIR10, http://www.arabidopsis.org/) using Bowtie (Langmead et al., Genome Biology 2009) version 2.0.2, under default mode parameters.
Peak calling was done in each biological replicate separately using MACS version 2 (Feng et al., Nature Protocols 2012) with a p-value cutoff 1e-3, followed by an Irreproducible Discovery Rate (IDR) analysis (Li et al., Annals of Applied Statatistics 2011). Using the code provided in https://sites.google.com/site/anshulkundaje/projects/idr, a conservative estimate number of peaks for each experiment was selected as the maximum number of reproducible peaks for IDR ≤ 0.05 found at any pair-wise comparison between biological replicates.
We further post-processed the peaks using shape analysis implemented in the Bioconductor package NarrowPeaks v1.4.0 (http://www.bioconductor.org/). Only MACS peaks confirmed also by NarrowPeaks are reported. Duplicated reads were not considered during peak calling in order to achieve a better specificity (Bailey et al., PLoS Computational Biology 2013).
Target genes for genomic regions of interest were retrieved using the function 'distance2Genes' in the Bioconductor package CSAR (Muino et al., Plant Methods 2011) for genes annotated in TAIR10.
Genome_build: TAIR10
Supplementary_files_format_and_content: Comma-separated values .csv files containing peak definitions: chromosome, peak start, peak end, peak summit (0-based offset from peak start), fold enrichment, -log10(p-value), and genes with a peak summit in a region spanning from 3kb upstream to 1kb downstream the gene body.

source_name: Seedlings

growth_protocol: 2 weeks seedling grown in Long days photoperiod

extract_protocol: Ovation Ultralow DR Multiplex System

value: seedlings

tag: ecotype

value: Columbia-0 FRI

tag: chip antibody

value: anti-GFP (Ab290)


title: (Negative Control for FLC-ChIPSeq) svp-41 flc-3 FRI rep3

value: FLC antiserum


title: svp-41 FLC FRI rep3


title: (Negative Control for FLC-ChIPSeq) svp-41 flc-3 FRI rep1


title: svp-41 FLC FRI rep2


title: (Negative Control for FLC-ChIPSeq) svp-41 flc-3 FRI rep2


title: (Negative Control for SVP-ChIPSeq) 35S:GFP rep3


title: SVP FLC FRI rep3


title: svp-41 FLC FRI rep1


title: SVP FLC FRI rep2


title: A72-G1_S1_L001

source_name: Saccharomyces cerevisiae_wildtype_G1


title: SVP FLC FRI rep1


title: pSVP:SVP:GFP svp-41 flc-3 FRI rep3


title: pSVP:SVP:GFP svp-41 flc-3 FRI rep2


title: pSVP:SVP:GFP svp-41 flc-3 FRI rep1


title: pSVP:SVP:GFP svp-41 FLC FRI rep3


title: pSVP:SVP:GFP svp-41 FLC FRI rep1


title: Wk2 8

source_name: transitional cell

tag: cell type


title: pSVP:SVP:GFP svp-41 FLC FRI rep2


title: MEC1 (WT) HU 1h from Control Exp

description:
Labeled DNA double strand breaks
Processed_data file= MACS one sample analysis: AMc111214WT_HU_peaks.bed
Library Strategy: Break-Seq

source_name: MEC1 (WT) HU 1h from Control Exp


title: (Negative Control for SVP-ChIPSeq) 35S:GFP rep1


title: Stretch B

status: Public on Jan 09 2015

city: Seattle

first: Vishal

last: Nigam

state: WA

address: 1900 9th Ave

department: Pediatrics

institute: Seattle Childrens Research Institute

data_processing:
Bowtie2 was used to map the sequence tags to the GRCh37.p10 human genome build
edgeR algorithm in the Bioconducter suite was used to obtain expression levels and statistical significance
Genome_build: GRCh37.p10

source_name: Stretched AVIC

extract_protocol:
Total RNA was isolated using RNAeasy columns using the protocol that includes small RNAs
The Illumina TruSeq Small RNA protocol was used. 1 microgram of total RNA was used. After adapter ligation, the small RNAs were gel purified according the manufactuers protocol.

value: aortic valve interstitial cells

tag: condition

value: Stretch


title: Static control E

source_name: Static AVIC

value: Static


title: Stretch C


title: Static control C


title: Static control B


title: d3 Input

city: Boston

first: Johnny

middle: T

last: Kung

state: MA

address: 185 Cambridge St

department: Molecular Biology

institute: HHMI, Massachusetts General Hospital, Harvard Medical School

data_processing:
Base-calling was performed with Illumina real time analysis (RTA) basecaller v1.17.21.3
Adaptor sequences were trimmed from libraries with either Trim Galore! v0.3.3 (for CLIP-seq and RNA-seq; stringency 15 and allowed error rate 0.2) or Cutadapt v1.0 (for ChIP-seq; allowed error rate 0.2). PCR duplicates were removed by custom programs prior to alignment (exception CHIP D0 rep2 PCR duplicates were removed after alignment using SAMtools). To account for the M. mus (mus) / M. castaneus (cas) hybrid character of the ES cell lines, reads were first aligned to custom mus/129 and cas genomes, and then mapped back to the reference mm9 genome. RNA was aligned with Tophat (v2.0.8 or greater), while DNA was aligned using Novoalign (3.00.03). Post-processing of mm9 alignments was performed with custom C and Perl programs and bash shell scripts, SAMtools v0.1.18, and BEDtools v2.17.0. These included accounting, alignment file-type conversion, extracting and sorting uniquely/paired-end reads (SAMtools), and obtaining wig coverage files (DNA: BEDtools genomecov; RNA: SAMtools depth).
For CLIP-seq, uniquely aligned fragments from +UV and -UV libraries were scaled according to total number of fragments in each library (determined by SAMtools flagstat combining reads “with itself and mate mapped” and “singletons”). After subtracting -UV hits from +UV single nucleotide hit counts, peaks of CTCF enrichment were called using Piranha v1.2.0 based on a zero-truncated Poisson distribution and a p-value cutoff of 0.01.
To assemble RNA transcripts from RNA-seq data, Cufflinks (v2.1.1) was used on composite d0 and d3 alignments with upper-quartiles-norm normalization, and guided (-g) with mm9 Ensembl transcripts. The resulting transcripts were purged of entries with FPKM=0, converted to bed format, and merged using BEDtools merge with options –nms, -scores mean, -s.
ChIP-seq coverage of uniquely aligned neutral/cas/mus (comp) reads were obtained and normalized to input libraries using in-house software (smoothing parameters: window size 125 and step size 25). ChIP binding positions were identified by intersecting the results of the mirror tag correlation (MTC) and window tag density (WTD) peak-finding methods within the SPP program. Briefly, both IP and input data had local anomalies removed, then binding positions were identified using the find.binding.positions routine (FDR = 0.01; default method for WDT, and tag.lwcc for MTC, whs=detection.window.halfsize). Peak regions were extended using the add.broad.peak.regions function (window.size=102, z.thr=3). Finally these results were merged and intersected with MTC method to give a final high confidence peak list.
Allelic peak calling was performed to identify a peak as being on the active (cas) or inactive (mus) chromosome. Under the null hypothesis it was equally likely that a CLIP/ChIP region would be identified by tags of either cas or mus and thus was treated as if following a binomial distribution. p-values associated with cas or mus tag-id counts under a peak were determined from the q-value of the cumulative binomial distribution (p=0.5, N=3 or greater).
Genome_build: mm9
Supplementary_files_format_and_content: bed files containing location information (chromosome, coordinates, strand if for RNA) of each entry. For RNA-seq transcripts, 5th column of bed file is FPKM. For composite CLIP and ChIP peaks, 5th column is coverage. For allelic CLIP and ChIP peaks, 5th column is negative log of p-value, and last column is .

source_name: Embryonic stem cells

growth_protocol: d0 ES cells were cultured in the presence of LIF under adherent conditions. d3 ES cells were cultured without LIF under non-adherent conditions for 3 days.

extract_protocol:
CLIP-seq: Nuclei were isolated and lysed. Nuclear lysates were DNase-treated, then fragmented by sonication to an RNA size of 150-200 nt. Cleared lysates were incubated overnight with 15 uL of Anti-FLAG M2 Magnetic Beads. After stringent washing and DNase treatment, CLIP-tags on beads were radiolabelled with [γ-32P]ATP, run on Bis-Tris SDS-PAGE in MOPS buffer, and transferred to nitrocellulose membrane. Membrane fragments containing CLIP signal and corresponding positions on control lanes were excised, and RNA was eluted by proteinase K, followed by Trizol extraction and ethanol precipitation.
RNA-seq: Nuclear lysate was removed from CLIP protocol before sonication and treated with proteinase K and reprecipitated in the same way as CLIP RNA eluted from membrane. RNA was depleted of ribosomal RNA with RiboMinus Eukaryote System (Ambion A15026), treated with TURBO DNase, and cleaned up with RNeasy MinElute columns (Qiagen 74204). RNA was fragmented in Superscript III first strand synthesis buffer before first strand cDNA synthesis.
ChIP-seq: Cells were crosslinked with 1% formaldeyde for 10 min, then nuclei were isolated and lysed. Chromatin was sheared by sonication to a size of ~1-2kb. Cleared lysates were incubated overnight with CTCF antibodies, with 10% saved as input, then captured with Dynabeads Protein G. After stringent washes, ChIP DNA was eluted from beads, and together with input chromtain was reverse-crosslinked with proteinase K. DNA was purified by phenol/chloroform extraction and ethanol precipitation.
CLIP-seq: Library was constructed from CLIP RNA using the NEBNext Small RNA Library Prep set (New England Biolabs E7330), size-selected and cleaned up of primer/adaptor-dimers using Agencourt AMPure XP beads.
RNA-seq: Fragmented RNA was used for first strand cDNA synthesis with the addition of actinomycin D. Second strand cDNA synthesis was performed with NEBNext mRNA Second Strand Synthesis Module (E6111) in the presence of dUTP to preserve directionality. Double-stranded cDNA was then used to generate RNA-seq libraries using the NEBNext ChIP-Seq Library Prep Master Mix Set (E6240).
ChIP-seq: Library was constructed from ChIP DNA using the NEBNext ChIP-Seq Library Prep Master Mix Set.

value: 129S1/CastEiJ x 129S1

value: differentiating ES cell (day 3)

tag: Sex

value: female

tag: antibody


title: Stretch E


title: JY1-PA75

city: Dallas

first: Philipp

last: Scherer

state: TX

address: 5323 Harry Hines Boulevard

department: Touchstone Diabetes Center

institute: The University of Texas Southwestern Medical Center

description: islets pooled from 4 mice

data_processing:
Base-calling software: Illumina Casava 1.8.2.
Samtool was used to remove mapped reads with phred score <10.
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality and unspecific reads.
Picard was used to mark duplicates.
Filtered reads were mapped to mm9 whole genome with TopHat.
Cufflinks was used to assemble transcripts, and cuffmerge was used to generate the final transcriptome assembly.
Cuffdiff was used to calculate the differential expression results, presented as fragments per kilobase of exon per million fragments mapped (FPKM) values.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include cuffdiff-normalized FPKM values for each sample. There are three columns: Gene symbol, FPKM values of sample JY1-PA75, and FPKM values of sample JY1-d89.

source_name: Pancreatic islets of Langerhans

growth_protocol: Mice were bred and maintained on a 12-hr dark/light cycle, with ad libitum access to water and regular chow diet. Mice were subjected to dimerizer treatment at the age of 8 weeks.

extract_protocol:
Mice were euthanized by cervical dislocation following isoflurane anesthesia, and pancreatic islets were isolated as previously described (Ye et al., 2010b). Immediately after euthanasia, the major duodenal papilla of the mouse was blocked with a micro bulldog clamp. Ice-cold digestion solution, i.e. Hank's Balanced Salt Solution (HBSS) with 0.1 g/L Liberase TL (Roche # 05401020001, Indianapolis, IN), 0.1 g/L DNase I (Roche # 10104159001), 2.5 mM HEPES, 8 mM glucose, 0.2% BSA, pH 7.2-7.4, was inject via the common bile duct into the pancreatic duct. The inflated pancreas was transferred into a scintillation vial with digestion solution on ice. Subsequently, the vial was incubated at 37°C water bath for 25 min, and shaken vigorously to disperse the pancreas. The digested content was resuspended with ice-cold HBSS and settled on ice for 2-5 min, and supernatant was removed without disturbing the precipitate. The wash was repeated until the supernatant became clear, and the content was transferred into a 6-cm Petri dish with ice-cold HBSS plus 2.5 mM HEPES, 8 mM glucose, 0.2% BSA, pH 7.2-7.4. Under a dissection microscope, islets of Langerhans were picked with a 200-μL pipette to new dishes until free of exocrine pancreas content. The freshly isolated islets were either frozen immediately in liquid nitrogen followed by -80°C storage. Total RNA was purified from isolated pancreatic islets with RNeasy Mini Kit (Qiagen #74106) plus on-column DNase digestion.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Mice were subjected to 6 daily intraperitoneal injections of the dimerizer AP20187 at the dose of 0.5 μg/g body weight/day.

value: FVB

tag: tissue

value: regenerating pancreatic islets

value: P-Adn+/+


title: Stretch D


title: transcriptomic profile of atpip1;2-1 Arabidopsis thaliana mutant leaf

status: Public on Jan 10 2015

city: Darmstadt

first: Marlies

last: Heckwolf

address: Schnittspahnstraße 10

institute: Technische Universität Darmstadt

data_processing:
Sequencing reads were aligned to the Arabidopsis TAIR9 reference genome using BLAT (Kent, 2002). The resulting mapping file was parsed using an in-house pearl script kindly provided by A. Weber, Düsseldorf, Germany (Brautigam et al., 2008). This procedure ensured that only the mapping hit with the best match to the corresponding read was retained. Differentially expressed genes were identified by applying a Poisson statistics and a Bonferroni correction (Audic and Claverie, 1997).
Genome Build:
atpip1:2-1_counts.txt: TAIR9
atpip1:2-1.fas: TAIR9

source_name: leaf, atpip1;2-1 mutant

growth_protocol: plants were grown on soil under standard greenhouse conditions with a 12-h photoperiod (24°C day/20°C night), 60% relative humidity, a photon flux density at plant level of about 70 to 80 µmol m-2 s-1 and at an ambient CO2 concentration of 370 µmol mol-1

extract_protocol: Total RNA was isolated from leaf samples of 10 individual plants (3 weeks old) using RNeasy Plant Mini Kit (Qiagen, Hilden Germany) according to the manufacturer’s manual. Subsequently, 3’ UTR cDNA libraries were constructed by GATC–Biotech (Konstanz, Germany). Libraries were sequenced using the Genome Analyzer II. After quality control, raw reads were obtained from GATC–Biotech (Konstanz, Germany).

value: Columbia, NASC ID N519794

tag: organ

value: leaf

tag: developmental stage

value: 3 weeks old

tag: genotype/variation

value: atpip1;2-1 mutant


title: Stretch F


title: Stretch A


title: Static control F


title: transcriptomic profile of Arabidopsis thaliana wildtype leaf

data_processing:
Sequencing reads were aligned to the Arabidopsis TAIR9 reference genome using BLAT (Kent, 2002). The resulting mapping file was parsed using an in-house pearl script kindly provided by A. Weber, Düsseldorf, Germany (Brautigam et al., 2008). This procedure ensured that only the mapping hit with the best match to the corresponding read was retained. Differentially expressed genes were identified by applying a Poisson statistics and a Bonferroni correction (Audic and Claverie, 1997).
Genome Build:
wildtype_counts.txt: TAIR9
wildtype.fas: TAIR9

source_name: leaf, wildtype

value: Columbia, NASC ID N60000

value: wildtype


title: Static control D


title: d3 ChIP

tag: strain

value: CTCF (Cell Signaling 2899)


title: d3 CLIP rep2 [mUV]

value: CAST/Ei x 129/Sv/Jae

tag: treatment

value: without UV irradiation

value: Anti-Flag M2 (Sigma-Aldrich A2220)


title: d0 Input

value: undifferentiated ES cell (day 0)


title: d0 Input rep2

value: 129S1/CastEiJ x 129S1

value: undifferentiating ES cell (day 0)


title: d3 CLIP rep1 [pUV]

value: differentiating ES cell (day 3)

value: female

value: with UV irradiation


title: d0 CLIP rep1 [mUV]


title: d3 CLIP rep2 [pUV]


title: d0 ChIP rep2


title: d3 CLIP rep1 [mUV]


title: d0 CLIP rep2 [mUV]


title: d0 ChIP


title: Static control A

value: aortic valve interstitial cells

value: Static


title: JY1-d89

description: islets pooled from 4 mice

value: FVB

value: regenerating pancreatic islets

tag: genotype

value: P-AdnTg/+


title: d0 CLIP rep2 [pUV]


title: d0 CLIP rep1 [pUV]


title: RNASeq_IFN

city: Pamplona

first: Victor

last: Segura

state: Navarra

address: Avda. Pío XII, 55

department: Unit of Proteomics, Genomics and Bioinformatics

institute: FIMA

description: Gene expression analysis of HuH7 cells treated with IFN

data_processing:
Illumina Casava1.7 software used for basecalling.
The processing of reads included elimination of contaminant adaptar substrings with Scythe and quality-based trimming using Sickle. The alignment of reads to the human genome (hg19) was performed using Tophat2 mapper.
The transcript assembly  and quantification using FPKM of transcripts was carried out using Cufflinks2.
Annotation of the gene locus obtained was performed using Cuffmerge with Gencode v19 as reference.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample using cufflinks and GENCODE v19

growth_protocol: HuH7 cells were incubated at 37 degress in 5% CO2 environment with DMEM media plus antibiotics and 10% FCS

extract_protocol:
RNA was isolated with TRIZOL (SIGMA)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HuH7 cells were treated with 10000 units/ml of IFN a2 and RNA was isolated 3 days post-treatment

tag: cell line

value: Human liver (hepato cellular carcinoma) cells

tag: treated with

value: 10000 units/ml of IFN

value: 3 days post-treatment


title: m27_3

city: Poznan

first: Michał

last: Szcześniak

address: Uniwersytetu Poznanskiego 6

department: Institute of Human Biology and Evolution

country: Poland

institute: Adam Mickiewicz University

data_processing:
adapter removal using Perl script.
quality filtering using fastx_quality_filter (fastx-toolkit) with the following parameters: -Q33 -q 20 -p 100
removal of sequence redundancy with fastx_collapser from fastx-toolkit
mapping reads to apple genome with Bowtie; parameters: -v 0 -a -m 20
processing the mapping results with Python script to obtain miRNA candidates. The procedure was as follows.
Based on genomic coordinates of mapped reads, the genomic sequences comprising of the putative miRNA itself as well as 250 bases upstream and downstream were extracted. A putative miRNA was required to have RPM > 2 and length between 19 and 22 bases. The latter parameter is justified by the fact that in plants 23-25 nt long reads contain only a small fraction of miRNAs, which are hugely outnumbered by other classes of small regulatory RNAs, like ca-siRNAs. For extracted genomic fragments secondary structure was predicted using hybrid-ss-min from UNAFold package (Markham and Zuker, 2008) with default settings. We kept only those structures, where 1) there were no more than five mismatches and two bulges between mature miRNA candidate and the opposite hairpin arm, 2) mature miRNA candidate was entirely found in one hairpin arm. At this step the hairpin was cut out from a longer sequence if needed and it was required that the hairpin was at least 40 bases long. Next, we made sure that there is a miRNA-like profile of reads mapped to the hairpin. To this point we kept only the hairpins where i) mature miRNA was represented by the most abundant read in at least one library, ii) mature miRNA abundance constituted at least 20% of total read counts in at least one library, and iii) the total count of reads starting at mature miRNA 5’ end was the maximal one in at least one library. The sequences that bore 60% or more low-complexity regions were identified using Dustmasker from BLAST package (Camacho et al., 2009) and discarded. The settings were default except for '-level' set from 20 to 15. Finally, we performed BLAST search against proteins from UniProtKB/Swiss-Prot and non-coding RNAs other than miRNAs from RFAM and removed candidates that produced the E-value of 1e-20 (proteins) or 1e-10 (RNAs).
Genome_build: Malus x domestica v1.0
Supplementary_files_format_and_content: tab-delimited text file with the following fields: mature miRNA sequence and expression values in twelve small RNA deep-sequencing libraries (in reads per million): b9_1, b9_2, b9_3, g30_1, g30_2, g30_3, m111_1, m111_2, m111_3, m27_1, m27_2, m27_3

organism: Malus domestica

source_name: shoot tip

growth_protocol: Plant material was purchased from Cameron Nursery (Eltopia, Washington).  ‘Crimson Gala’ scions were bench-grafted onto four distinct rootstocks: Malling 27 EMLA (M.27), Budagovsky 9 (B.9), Geneva 30 (G.30), and Malling Merton 111 EMLA (MM.111).  The trees were bench-grafted by the nursery, by splicing a two-bud, dormant shoot and planted at Rock Springs, PA in March 2005.

extract_protocol:
The samples (approximately 0.5 g each) included the meristem, stem and the leaves but not including the first fully expanded leaf. Shoot tips were flash-frozen in liquid nitrogen and stored at -80°C for later RNA isolation.  Samples were ground with a mortar and pestle chilled with liquid nitrogen. The frozen powder was mixed with extraction buffer (2% Cetyltrimethylammonium bromide, 2% polyvinylpyrolidone, 100 mMTris pH 8.0, 25 mMethylenediaminetetraacetic acid, 2 M NaCl, 0.5 g L-1 (w/v) spermidine, 2% ß-mercaptoethanol) and total RNA was isolated using 0.8 M LiCl and isopropanol (Sigma).  Total RNA concentration and purity were determined using NanoDrop (Thermo Fischer Scientific). Total RNA quality was determined on BioAnalyzer (Agilent).
Small RNA libraries were prepared using the Applied Biosystems (Life Technologies) Total RNA-Seq Kit according to the Small RNA Library Preparation protocol.

value: Actively-growing shoot tip tissue


title: RNASeq_Huh7

description: Gene expression analysis of HuH7 cells

value: none (control)

tag: time point


title: b9_3


title: d3 RNAseq

data_processing:
Base-calling was performed with Illumina real time analysis (RTA) basecaller v1.17.21.3
Adaptor sequences were trimmed from libraries with either Trim Galore! v0.3.3 (for CLIP-seq and RNA-seq; stringency 15 and allowed error rate 0.2) or Cutadapt v1.0 (for ChIP-seq; allowed error rate 0.2). PCR duplicates were removed by custom programs prior to alignment. To account for the M. mus (mus) / M. castaneus (cas) hybrid character of the ES cell lines, reads were first aligned to custom mus/129 and cas genomes, and then mapped back to the reference mm9 genome. RNA was aligned with Tophat (v2.0.8 or greater), while DNA was aligned using Novoalign (3.00.03). Post-processing of mm9 alignments was performed with custom C and Perl programs and bash shell scripts, SAMtools v0.1.18, and BEDtools v2.17.0. These included accounting, alignment file-type conversion, extracting and sorting uniquely/paired-end reads (SAMtools), and obtaining wig coverage files (DNA: BEDtools genomecov; RNA: SAMtools depth).
For CLIP-seq, uniquely aligned fragments from +UV and -UV libraries were scaled according to total number of uniquely aligned fragments in each library (determined by SAMtools flagstat combining reads “with itself and mate mapped” and “singletons”). After subtracting -UV hits from +UV single nucleotide hit counts, peaks of CTCF enrichment were called using Piranha v1.2.0 based on a zero-truncated Poisson distribution and a p-value cutoff of 0.01.
To assemble RNA transcripts from RNA-seq data, Cufflinks (v2.1.1) was used on composite d0 and d3 alignments with upper-quartiles-norm normalization, and guided (-g) with mm9 Ensembl transcripts. The resulting transcripts were purged of entries with FPKM=0, converted to bed format, and merged using BEDtools merge with options –nms, -scores mean, -s.
ChIP-seq coverage of uniquely aligned neutral/cas/mus (composite) reads were obtained and normalized to input libraries using in-house software (smoothing parameters: window size 125 and step size 25). ChIP binding positions were identified by intersecting the results of the mirror tag correlation (MTC) and window tag density (WTD) peak-finding methods within the SPP program. Briefly, both IP and input data had local anomalies removed, then binding positions were identified using the find.binding.positions routine (FDR = 0.01; default method for WDT, and tag.lwcc for MTC, whs=detection.window.halfsize). Peak regions were extended using the add.broad.peak.regions function (window.size=102, z.thr=3). Finally these results were merged and intersected to give a final high confidence peak list.
Allelic peak calling was performed to identify a peak as being on the active (cas) or inactive (mus) chromosome. Under the null hypothesis it was equally likely that a CLIP/ChIP region would be identified by tags of either cas or mus and thus was treated as if following a binomial distribution. p-values associated with cas or mus tag-id counts under a peak were determined from the q-value of the cumulative binomial distribution (P=0.5).
Genome_build: mm9
Supplementary_files_format_and_content: bed files containing location information (chromosome, coordinates, strand for RNA) of each entry. For RNA-seq transcripts, 5th column of bed file is FPKM. For composite CLIP and ChIP peaks, 5th column is coverage. For allelic CLIP and ChIP peaks, 5th column is negative log of p-value, and last column is allelic coverage.

extract_protocol:
RNA-seq: Nuclear lysate was removed from CLIP protocol before sonication and treated with proteinase K and reprecipitated in the same way as CLIP RNA eluted from membrane. RNA was depleted of ribosomal RNA with RiboMinus Eukaryote System (Ambion A15026), treated with TURBO DNase, and cleaned up with RNeasy MinElute columns (Qiagen 74204). RNA was fragmented in Superscript III first strand synthesis buffer before cDNA synthesis.
RNA-seq: Fragmented RNA was used for first strand cDNA synthesis with the addition of actinomycin D. Second strand cDNA synthesis was performed with NEBNext mRNA Second Strand Synthesis Module (E6111) in the presence of dUTP to preserve directionality. Double-stranded cDNA was then used to generate RNA-seq libraries using the NEBNext ChIP-Seq Library Prep Master Mix Set (E6240).

value: CAST/Ei x 129/Sv/Jae


title: d0 RNAseq

value: undifferentiated ES cell (day 0)


title: m111_3


title: m27_1


title: m27_2


title: g30_2


title: g30_3


title: m111_1


title: HHV6a miRNA sample

city: Cleveland

first: Eain

middle: Anthony

last: Murphy

state: OH

department: Molecular Genetics

institute: Cleveland Clinic Foundation

data_processing:
Basecalls performed using off-line basecaller (OLB) v.1.9.4
Basecalls were sorted using Casava software v 1.8.2
discarded sequences that matched human genome (version hg18)
discarded sequences that did not match the HHV-6A genome (Genbank # X83413.1)
parsed sequences that matched the HHV-6A genome with exact read lengths of 19-24nt.
Genome_build: kept reads that did NOT match hg18
Supplementary_files_format_and_content: Files are .txt files generated from perlscript algorithms identifying sequences with 100% match to refrence sequence with read lengths >18 and <23 identical matches.

source_name: Jjhan HHV-6a tranfected

growth_protocol: Jjhan cells were propagated in RPMI 1640 medium with 8% Fetal Bovine Serum (Sigma-Aldrich; St. Louis MO) and supplemented with 100 U/ml each of penicillin and streptomycin

extract_protocol:
Isolate Total RNA, size select for transcripts <30nt,
Illumina Small RNA Sample Preparation Kit Version 1.5 (Illumina; San Diego, CA)

treatment_protocol: HHV-6A-BAC DNA (5mg) and the HCMV pp71 expressing plasmid pCGN1-pp71 (1mg) were transfected into 3.0 X 106 Jjhan cells with transfection reagent “V” utilizing a Neucleofector (Lonza AG; Basel Switzerland) per the manufacturer’s protocols. After 5-7 days (d) the media was changed and supplemented with 20ng/mL tissue plasminogen activator (TPA) (Sigma) and 3mM Na-butyrate (Sigma) for 24 hours (h). Cells were washed 3X with 1X PBS to remove the TPA and Na-butyrate and co-cultured with an equal number of HSB2 cells that were pre-stimulated for 24 h with 2ng/ml IL-2 (Sigma) and 5ug/ml phytohemagglutinin (PHA) (Sigma). Fresh, pre-stimulated HSB2 cells were added every 4-6 d to allow accumulation of the virus by cell-to-cell spread.

value: Jjhan cells

tag: transfection

value: HHV-6A BAC


title: Tragopogon dubius

status: Public on Jan 08 2015

city: shanghai

first: Ming

middle: Ju

last: Lu

state: shanghai

address: 320 Yueyang Road, Xuhui Area, Shanghai, China

department: Partner Institute for Computational Biology, Shanghai Institutes for Biologic Sciences, CAS

country: China

institute: Shanghai Institutes for Biological Sciences, CAS

data_processing:
raw reads were mapping to CDS of Arabidopsis thanliana using Blat  version v. 34x12 with parameter [-t=dnax -q=dnax -repMatch=100 -trim
calculate RPM of gene for each samples
calingl consensus sequence and construct phylgenetic data matrix are using in-home perl program
extimate proper DNA mutation model using PartitionFinder version V1.1.1
infer phylogentic tree using Bayesian version 3.2.1 and RAxMLboth  apply applying GTR+GAMMA+I model
visual phylogentic tree using Figtree
Genome_build: Arabidopsis thaliana coding sequence, TAIR 10
Supplementary_files_format_and_content: tab-delimited text files include RPM values for 17 Flaveria sample

organism: Tragopogon dubius

source_name: Tragopogon dubius

growth_protocol: plant were grown in green house at the University of Toronto

extract_protocol:
This RNA isolation method is a multi-component method involving an initial extraction by hot acid phenol and then a purification and DNase treatment using the RNeasy Mini Kit by Qiagen
RNA libraries were prepared for sequencing using an in-house service by BGI using 20 µg total RNA and the standard Illumina protocol

treatment_protocol: Leaves of multiple plants were sampled to make up 0.1 to 1.0 grams of tissue. For mature leaves, the newest fully expanded leaf was chosen. For juvenile leaves, the leaves most recently starting to expand from the main stem were chosen (0.1 to 0.5 mm depending on species).

value: leaves

value: mature


title: g30_1


title: m111_2


title: Helenium autumnale

organism: Helenium autumnale

source_name: Helenium autumnale


title: b9_1


title: b9_2


title: F. kochiana mature

organism: Flaveria kochiana

source_name: F. kochiana mature


title: F. brownii mature

organism: Flaveria brownii

source_name: F. brownii mature


title: KC2 bio rep2

city: Chicago

first: zhike

last: lu

state: IL

address: 5801 South Ellis Avenue

department: department of chemistry

institute: University of Chicago

description: Photo-crosslinking-assisted-m6A-seq with anti-m6A antibody

data_processing:
Adapters were trimed by FASTX and also the first and last bases were removed because of the quality.
Then the reads were mapped onto the human genome (hg19) using bowtie with at most two mismatches allowed
PARalyzer was used for peak calling using default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: bed format, contains the m6A sites

source_name: HeLa cells

growth_protocol: HeLa cell was grown in Gibco DMEM media supplemented with 10% FBS and 1% pen-strep (Life Technologies).

extract_protocol:
Total RNA was extracted by TRIzol and mRNA was isolated by FastTrack MAG mRNA isolation kit.
Libraries were constructed by Illumina TruSeq Small RNA Sample Prep Kit.

treatment_protocol: 4-thiouridine was added to growth media to a final concentration of 200 mM and treated for 16 hrs.

value: Cervical cancer cells

tag: passages

tag: ip antibody

value: Anti-m6A antibody


title: F. trinervia juvenil

organism: Flaveria trinervia

source_name: F. trinervia juvenil

value: juvenile


title: F. brownii juvenil

source_name: F. brownii juvenil


title: F. trinervia mature

source_name: F. trinervia mature


title: F. pubescens mature

organism: Flaveria pubescens

source_name: F. pubescens mature


title: KC1 bio rep1

tag: cell type


title: F. pubescens juvenil

source_name: F. pubescens juvenil


title: F. sonorensis juvenil

organism: Flaveria sonorensis

source_name: F. sonorensis juvenil


title: F. pringlei mature

organism: Flaveria pringlei

source_name: F. pringlei mature


title: F. pringlei juvenil

source_name: F. pringlei juvenil


title: DARPA_98_CAAAAG_L006_R1

city: new york

first: Bojan

last: Losic

address: 1425 Madison Avenue

department: Genetics and Genomics

institute: ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI

data_processing:
Raw 100 bp cDNA reads were aligned to the Ensembl NCBIM37 mouse reference genome via the popular wrapper tophat (Trapnell et al., 2009), which uses bowtie1 (Langmead et al., 2009) and a spliced junction mapper to treat the problem of spliced gap alignment. Nearly default settings were used with the exception of disabling coverage-based junction detection, which artificially constricts candidate splice junctions to GT-AG (thus losing e.g. GCAG and ATAC) and is only useful for relatively short (<= 75 bp) reads.
Raw read count values were deduced from quantitation against the NCBIM37 annotation features using the package htseq with a strict intersection criterion (reads must be completely enclosed within genic feature, i.e. zero overhang), and these raw values in turn were normalized for median coverage across all samples on a genewise basis.
Based on the distribution of count values, the entire mode of low count values was deleted since it likely corresponds to mapping or other technical errors. The resulting data contain a total of 26,927 genes.
This expression dataset was then investigated for influences from potential covariates, including testing cohorts and process variables of RNA preparation and sequencing. The identification of covariates with significant effects was the same as described for phenotypic measurements. Animal cohorts, RNA preparation batches, and sequencing runs were subsequently identified as significant covariates, and expression data of all genes were then adjusted for these selected covariates by fitting them in a robust linear model and taking the intercept + residuals as the adjusted expression values. Additionally, principal components were extracted from the covariate-adjusted expression data, as they can capture additional unknown factors that influenced gene expression. The first few principal components that were not driven by genetic factors (i.e., did not yield QTL) were selected to further adjust expression data by fitting with a robust linear model. For this expression dataset, the first three principal components were used. Finally, adjusted expression data were inverse normal-transformed and were then for downstream analyses.
Genome_build: MGSCv37 (mm9, NCBIM37)
Supplementary_files_format_and_content: raw_count_matrix.txt file: Count quantitation, constructed as an N x M matrix, where N is the number of genes and M is the number of samples.
Supplementary_files_format_and_content: processed_normalized_expression_matrix.txt file: Normalized, covariate-adjusted, transformed count matrix, as described above.

source_name: striatum

extract_protocol:
RNA samples were extracted using TRIzol® reagent (Life Technologies, Grand Island, NY) from the striatum of a random subset of 100 F2 mice, and were then shipped to the Genomics Core Facility at the Icahn School of Medicine at Mount Sinai. Sample integrity was assessed using either an Agilent 2100 Bioanalyzer with the RNA 6000 Nano assay or an Agilent 2200 TapeStation with the R6K ScreenTape (Agilent, Santa Clara, CA). The average RIN values were above 9 for all processed total RNA samples.
The standard TruSeq RNA Sample Prep Kit v2 protocol (Illumina, San Diego, CA) was used to prepare the sequencing library. Briefly, the cDNA was synthesized from poly-A-selected and then fragmented total RNA using random hexamers, followed by end-repair and ligation with appropriate sequencing adaptors. The libraries were then subject to size selection and was purified using AMPure XP beads (Beckman Coulter, Brea, CA). Barcode bases (6 bp) were introduced at one end of the adaptors during PCR amplification steps. The size and concentration of the cDNA libraries was measured by Bioanalyzer and Qubit fluorometry (Life Technologies, Grand Island, NY) before sequencing. The cDNA libraries were sequenced on the Illumina HiSeq 2500 System with 100 nucleotide single-end reads, according to the standard manufacturer's protocol (Illumina, San Diego, CA).

tag: strain/background

value: striatum

tag: animal id


title: DARPA_97_ATTCCT_L006_R1


title: DARPA_96_ATGAGC_L005_R1


title: AB

city: Albi

first: Wafa

last: BOUZID

address: place de verdun

country: France

institute: centre universitaire JFC

data_processing:
Quality of reads generated by deep sequencing was checked within the ng6 environment using fastQC program (available at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and Burrows-Wheeler Aligner tool (BWA) to search for contamination
The transcriptome de novo assembly was performed using Velvet/Oases
The first step consisted of nine independent assemblies using different k-mers (k-mers for velveth: 25,31,37,43,49,55,61,65,69; parameters for velvetg: -read_trkg yes -min_contig_lgth 100 -cov_cutoff 4 and parameters for oases: -cov_cutoff 4)
The raw transcripts files were filtered to retain only 1% of transcripts per locus with a modified version of a Perl script developed at Brown University (https://sites.google.com/a/brown.edu/bioinformatics-in-biomed/velvet-and-oases-transcriptome)
Anti-sense chimeras accidentally produced during the assembly step were cut with a home-made script. Then, independent assemblies were pooled, and duplicate/similar transcripts build by close k-mers were removed by a cd-hit-est  step (parameters: -M 0 -d 0 -c 0.98) and merged by a TGICL  step (parameters: -l 60 -p 96 -s 100,000).
All input reads were mapped back to the set of transcripts using BWA
Genome_build: No refrence genome was used, the transcriptome de novo assembly was performed using Velvet/Oases
Supplementary_files_format_and_content: Count file with one column per sample and strand

organism: Tetramorium bicarinatum

source_name: Ant whole body

growth_protocol: Polygynous colonies of the species T. bicarinatum were maintained under homogeneous conditions  (a temperature of 25 –28 °C). They were reared in artificial  nests consisting of a plastic box  connected to a foraging arena. Ants were fed on mealworm  larvae and diluted honey twice a week.

extract_protocol:
Given the very limited amount of the total RNA extracted from the venom glands (7ng/µl), mRNA from this sample (sample G) was transcribed into cDNA and amplified using the Ovation RNA-Seq System V2 kit, especially applied to limited biological material (NuGEN Technologies Inc.). After cDNA fragmentation, end-repair and purification with the Agencourt® AMPure® XP kit (Agencourt Bioscience, Beckman Coulter, San Carlos, CA, USA), TruSeq sequencing adapters (Illumina) were ligated to the cDNA fragments. Finally, the library was PCR-amplified (14 cycles) to about 20-30 ng/μl using a high fidelity DNA polymerase. Total RNAs (tRNAs) from venom glands sample were isolated with RNeasy Micro Kit (Qiagen, France) including an on column DNase digestion whereas total RNAs from ant body carcasses were extracted using 400 µl of TRI reagent (Sigma) according to the manufacturer’s protocol. Illumina TruSeq RNA Sample Prep Kit was used for the construction of sequencing libraries.
For the total RNA sample from ant carcasses, poly(A) RNA was isolated and fragmented. First-strand cDNA synthesis was primed with an N6 randomized primer. Illumina TruSeq adapters were ligated to the 5' and 3' ends of the cDNA of both smaples. The cDNA was finally PCR amplified using a proof reading enzyme (Beckman genomics). For Illumina sequencing, the cDNA samples were fractionated on preparative agarose gels in the size range of 300 – 500 bp. PCR amplification were designed for TruSeq sequencing (using HiSeq2000 technology) according to the instructions of Illumina.

value: Ant whole body without abdomen


title: DARPA_93_GAGTGG_L005_R1


title: DARPA_95_ACTGAT_L005_R1


title: DARPA_94_GGTAGC_L005_R1


title: DARPA_87_GTAGAG_L004_R1


title: DARPA_88_GTCCGC_L004_R1


title: DARPA_89_GTGAAA_L004_R1


title: DARPA_86_CCGTCC_L003_R1


title: VG

source_name: Venom gland

value: Venom gland tissue


title: DARPA_99_CAACTA_L006_R1


title: DARPA_92_CGTACG_L005_R1


title: DARPA_85_ATGTCA_L003_R1


title: DARPA_84_AGTTCC_L003_R1


title: DARPA_90_GTGGCC_L004_R1


title: DARPA_82_CTTGTA_L003_R1


title: DARPA_81_GGCTAC_L002_R1


title: DARPA_79_GATCAG_L002_R1


title: DARPA_80_TAGCTT_L002_R1


title: DARPA_83_AGTCAA_L003_R1


title: DARPA_78_ACTTGA_L006_R1


title: DARPA_77_CAGATC_L002_R1


title: DARPA_74_TGACCA_L001_R1


title: DARPA_73_TTAGGC_L001_R1


title: DARPA_75_ACAGTG_L001_R1


title: DARPA_100_CACCGG_L006_R1


title: DARPA_76_GCCAAT_L002_R1


title: DARPA_91_GTTTCG_L004_R1


title: DARPA_72_CGATGT_L001_R1


title: DARPA_70_CTCAGA_L008_R1


title: DARPA_69_CTATAC_L007_R1


title: DARPA_67_CGGAAT_L007_R1


title: DARPA_68_CTAGCT_L006_R1


title: DARPA_64_CATGGC_L006_R1


title: DARPA_65_CATTTT_L006_R1


title: DARPA_61_CACGAT_L005_R1


title: DARPA_58_CAAAAG_L005_R1


title: DARPA_60_CACCGG_L005_R1


title: DARPA_63_CAGGCG_L006_R1


title: DARPA_56_ATGAGC_L007_R1


title: DARPA_57_ATTCCT_L005_R1


title: DARPA_54_GGTAGC_L004_R1


title: DARPA_71_ATCACG_L001_R1


title: DARPA_55_ACTGAT_L008_R1


title: DARPA_51_GTTTCG_L004_R1


title: DARPA_53_GAGTGG_L004_R1


title: DARPA_50_GTGGCC_L004_R1


title: DARPA_52_CGTACG_L007_R1


title: DARPA_46_CCGTCC_L003_R1


title: DARPA_47_GTAGAG_L003_R1


title: DARPA_49_GTGAAA_L004_R1


title: DARPA_48_GTCCGC_L003_R1


title: DARPA_66_CCAACA_L008_R1


title: DARPA_45_ATGTCA_L003_R1


title: DARPA_43_AGTCAA_L002_R1


title: DARPA_42_CTTGTA_L007_R1


title: DARPA_62_CACTCA_L006_R1


title: DARPA_59_CAACTA_L005_R1


title: DARPA_41_GGCTAC_L008_R1


title: DARPA_33_TTAGGC_L001_R1


title: DARPA_34_TGACCA_L001_R1


title: DARPA_35_ACAGTG_L001_R1


title: DARPA_36_GCCAAT_L002_R1


title: DARPA_40_TAGCTT_L002_R1


title: DARPA_37_CAGATC_L002_R1


title: DARPA_38_ACTTGA_L008_R1


title: DARPA_32_CGATGT_L001_R1


title: DARPA_28_ACTTGA_L004_R1


title: DARPA_39_GATCAG_L002_R1


title: DARPA_29_GATCAG_L004_R1


title: DARPA_27_CAGATC_L004_R1


title: DARPA_30_TAGCTT_L004_R1


title: DARPA_26_GCCAAT_L004_R1


title: DARPA_23_TTAGGC_L003_R1


title: DARPA_22_CGATGT_L003_R1


title: DARPA_24_TGACCA_L003_R1


title: DARPA_21_ATCACG_L003_R1


title: DARPA_44_AGTTCC_L003_R1


title: DARPA_25_ACAGTG_L003_R1


title: DARPA_19_GTGAAA_L005_R1


title: DARPA_17_GTAGAG_L005_R1


title: DARPA_18_GTCCGC_L005_R1