title: DP Mnase-Seq

data_processing:
For the SOLiD 4 System, high-quality reads were matched to individual samples based on the barcode tag and using default parameters in SOLiD Experimental Tracking Software (SETS) v4.0.1. For SOLiD 5500xl, basecalls were performed using 5500 Series Genetic Analyzers Instrument Control Software v1.2.
Alignment of reads to the mm9 genome was conducted using  BFast 0.7.0 for SOLiD sequencing runs, according to manufacturers instructions. Only reads with a unique best scoring alignment were retained. Clonal artifacts were filtered out retaining the longer reads.
Aligned reads were processed using a previously described in-house ChIP-Seq analysis pipeline (Koch, Fenouil et al 2011).
Tags were then elongated to 146bp and converted to wig format using a binning window of 50bp. Replicate tracks were subsequently merged by addition. To account for differences in tag counts between DN and DP experiments, tag count normalization was performed by scaling DP datasets to DN tag counts. Visual inspection of invariant targets (e.g. Eβ for Ets1, β-actin for Pol II, H3K4me1/2, Mnase, the Hoxa locus for H3K27me3) allowed further fine tuning and scaling of DP tag-counts to reflect potential differences in signal to noise ratios between DN and DP experiments.
Inverse peak detection was carried out with CoCAS using inversed data (with 0s replaced by 0.01) averaged into 50bp windows and converted to general feature format (GFF). Thresholds were 7.5 x SD + mean for the main window and 5 x SD + mean for the extension window. Artifacts were detected and removed by performing peak detection in CoCAS (using 2 X SD + mean and SD + mean as main and extension window thresholds, respectively) in reads originating from the Input treatment. Peaks were annotated to the nearest TSS, except in the case of intragenic peaks which were assigned to the surrounding gene. Peaks outside of [-5kb; +5kb] around known TSSs (refSeq, miRNA, rRNA, scRNA, snRNA, snoRNA and tRNA) were considered to be distal, while those falling within [-5kb; +5kb] around known TSSs were considered proximal. Distal peaks within a gene body were considered intragenic and those outside of gene bodies were considered intergenic.
Genome_build: mm9
Supplementary_files_format_and_content: Fragments were extended using an R pipeline described in Koch, Fenouil, Gut et al. 2011. Fixed-step 50bp wig files were generated using an R pipeline described in Koch, Fenouil, Gut et al. 2011. Peaks were called using CoCAS

extract_protocol:
Phenol-chroloform
For MNase-Seq, 2x10e7 thymocytes were permeabilized in 50µl 150mM sucrose, 80mM KCl, 5mM K2HPO4, 5mM MgCl2, 0.5mM CaCl2, 35mM HEPES pH 7.4, 0.2% NP-40 for one minute at 37°C then treated with 10U MNase for 30 minutes at room temperature in 500µl 150mM sucrose, 50mM Tris pH8, 50mM NaCl, 2mM CaCl2. Digestions were stopped by adding 1.45ml lysis buffer for 10 minutes at 4°C. 200µl aliquots were subsequently treated with equal amounts of TE buffer and 0.2μg/ml RNAse A, 0.2µg/ml proteinase K for 2 hours each at 37°C and 55°C, respectively. DNA was purified via phenol-chloroform extraction and subsequently eluted in 50µl water using QiaQuick PCR purification columns. Following gel size-selection of mononucleosomal fragment sizes, libraries were been prepared according to the Life Technologies protocol, SOLiD ChIP-seq kit guide (A12066), using 15 PCR cycles. The quality of the libraries was checked with the Bioanalyser DNA High sensitivity. Sequencing was carried out on a SOLiD 4 sequencer at TAGC, Marseille, France.

value: 5-6 weeks

value: WT

tag: cell type

value: primary CD4+ CD8+ DP thymocytes


title: Rag2 -/- Mnase-Seq

status: Public on Apr 01 2014

type: SRA

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

country: Germany

institute: University Medical Center Freiburg

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: primary Rag2 -/- thymocytes

growth_protocol: Thymuses were extracted from 5-6-week-old Rag2-/- knockout as well as C57BL/6 wild type mice and stored in RPMI medium. Cohorts of litter mates were used as biological replicates. To recover thymocytes, thymuses were subsequently passed twice through a 70µm Falcon cell strainer and stored in PBS. Cells were crosslinked 10 min in 10% formaldehyde followed by 5 min quenching in 250 mM glycine. DP cells were subsequently sorted via AutoMACS using, in turn, α-CD8-PE antibody conjugated to α-PE beads, and α-CD4 beads (Miltenyi). FACS profiles and cell purities were obtained for Rag2-/- and DP thymocytes via CD44-APC, CD25-FITC and CD8-PE, CD4-FITC staining, respectively

tag: strain

tag: age

tag: genotype/variation

value: primary Rag2 -/- thymocytes

tag: cells used


title: Twin29-1_FAIREseq

city: Choongchung-Buk-do

first: Hyo-Jeong

last: Ban

address: OHTAC, Yeonje-ree 643, Osong-eup, Chungwon-Koon

department: bioinformatics

country: South Korea

institute: KCDC

description: FAIRE-seq

data_processing:
Raw data processing was carried out by means of Illumina data pipeline (ELAND and CASAVA). To identify the peaks of the reads, we ran Zinba with the default parameters. Meta-peaks were generated by merging the 72 FAIRE peak regions by using BEDTools.
Genome_build: hg19
Supplementary_files_format_and_content: bed

organism: Homo sapiens

source_name: blood

extract_protocol:
Cells were cross-linked by treating formaldehyde 1% for 5 min at room temperature followed by addition of 125mM glycine for 5 min and spinning at 3600g for 5 min. Pellets were washed three times with phosphate buffered saline and quickly frozen in liquid nitrogen. Subsequently, pellets were resuspended by adding 1ml lysis buffer (1% Triton X-100, 140 mM NaCl, 50mM HEPES-KOH at pH7.5, 0.1% Sodium Deoxycholate, 1 mM EDTA buffer) and disrupted by five cycles of 1-min vortexing and 2-min resting using glass beads (Sigma). Afterward, samples were sonicated for 60 rounds of 30 sec ON and 60 sec OFF using Bioruptor sonicator (Diagenode) and debris was cleared by centrifugation at 13000g for 10 min at 4°C. Finally, nucleosome-depleted DNA was extracted with phenol-chloroform followed by ethanol precipitation and RNase A (100 μg/ml) treatment.
After ensuring that the majority of DNA fragments were in the 100–350 bp range, 50-bp single-end Illumina HiSeq2000 sequencing was performed.

tag: twin pairing

value: MZ twin pair 29 sibling 1

tag: tissue

value: blood


title: Twin30-1_FAIREseq

description: FAIRE-seq

value: MZ twin pair 30 sibling 1


title: Twin29-2_FAIREseq

description: FAIRE-seq

value: MZ twin pair 29 sibling 2


title: Twin28-2_FAIREseq

description: FAIRE-seq

value: MZ twin pair 28 sibling 2


title: Twin27-1_FAIREseq

description: FAIRE-seq

value: MZ twin pair 27 sibling 1


title: Twin27-2_FAIREseq

description: FAIRE-seq

value: MZ twin pair 27 sibling 2


title: Twin28-1_FAIREseq

description: FAIRE-seq

value: MZ twin pair 28 sibling 1


title: Twin26-1_FAIREseq

description: FAIRE-seq

value: MZ twin pair 26 sibling 1


title: Twin35-2_FAIREseq

description: FAIRE-seq

value: MZ twin pair 35 sibling 2


title: Twin26-2_FAIREseq

description: FAIRE-seq

value: MZ twin pair 26 sibling 2


title: tofu-1(tm6424) capped small RNA

city: Shenzhen

first: Wee Siong Sho

last: Goh

state: Guangdong

address: Shenzhen Bay Laboratory, No. 5, Kelian Road, Goh Lab, A1819, Guangming District

department: Institute of Molecular Physiology

country: China

institute: Shenzhen Bay Laboratory

description: Sample 34

library_source: transcriptomic

data_processing:
library strategy: Small RNA cloning and capped small RNA cloning
Basecalling with Illumina Real Time Analysis
Sequenced reads longer than 15nt were trimmed for adaptor sequences, clipped of any 3' adaptor sequences, and mapped to ce6 genome using bowtie 0.12.8 with parameters -v 0 -k 10 -m 10.
Mapped reads were annotated by virtue of overlap with (in decreaseing priority) 21U-RNA loci, miRNA loci, genic regions, repeat regions.
Small RNA reads were quantified as raw small RNA read count per million non-structural mapped RNA reads.
Genome_build: ce6
Supplementary_files_format_and_content: tab-delimited text of small RNA reads that map to 21U-RNA loci with read counts (normalized to total mapped unstructured RNA reads)

molecule: total RNA

organism: Caenorhabditis elegans

source_name: tofu-1(tm6424) capped small RNA

growth_protocol: Staged N2 or N2-based mutant L1s were grown on NGM plates for 3 days at 20oC. Staged VT1012 L1s were grown in S Basal buffer (with 100µg/ml ampicilin and 4mM IPTG) for 4 days at 20oC.

extract_protocol:
Staged 12-36hr adults were harvested and washed with M9 buffer until supernatant was clear. Worms were homogenized in trizol reagent, subjected to 3 cycles of freezing in liquid nitrogen and thawing at room temperature before RNA extraction by phase separation and isopropanol precipitation.
Small RNA libraries: 20µg of total RNA was size selected on a 15% denaturing polyacrylamide (dPAA) gel to obtain 19-30nt RNA species. The resultant RNA was ligated at its 3’end to the Illumina RA3 using NEB truncated T4 RNA ligase 2 at 20OC for 2 hours. Ligated products were size selected on a 15% dPAA before being ligated at its 5’end to RA5 using Ambion T4 RNA ligase at 20OC for 2 hours. Ligated products were size selected on a 15% dPAA before being reverse transcribed with RTP and superscript III reverse transcriptase. Resultant cDNAs were amplified using RP1 forward primer and indexed reverse primers using NEB Phusion PCR mastermix. Amplified libraries were gel purified on a 2% low-melting agarose gel and sequenced using the Illumina Hi-seq platform. Capped small RNA libraries: Protocol is the same as that of small RNA library generation with 2 differences. First, 19-30nt size-selected RNA was de-phosphorylated at the 5’end with NEB CIP at 37oC for 1 hour before 3’ ligation. Second, 3’ ligated RNA was treated with Epicenter TAP to convert all 5’ RNA caps into 5’ monophosphates before 5’ ligation. RA3: /5rApp/TGGAATTCTCGGGTGCCAAGG/3ddC/ (ddC: dideoxyC, rN: ribonucleotide, p: phosphate). RA5: rGrUrUrCrArGrArGrUrUrCrUrArCrArGrUrCrCrGrArCrGrArUrC. RTP: GCCTTGGCACCCGAGAATTCCA. RP1: AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGA. RPI: CAAGCAGAAGACGGCATACGAGATIIIIIIGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA (IIIIII: 6-mer Illumina index sequence).

tag: strain background

value: tofu-1(tm6424) mutation

value: 3 days post L1 release

tag: growth medium type

value: Solid NGM plate

tag: clipping sequence

value: TGGAATTCTCGGGTGCCAAGGC

tag: molecule subtype

value: Capped small RNA


title: Twin25-1_FAIREseq

description: FAIRE-seq

value: MZ twin pair 25 sibling 1


title: Twin33-2_FAIREseq

description: FAIRE-seq

value: MZ twin pair 33 sibling 2


title: Twin25-2_FAIREseq

description: FAIRE-seq

value: MZ twin pair 25 sibling 2

value: blood


title: Twin31-2_FAIREseq

description: FAIRE-seq

value: MZ twin pair 31 sibling 2


title: Twin24-1_FAIREseq

description: FAIRE-seq

value: MZ twin pair 24 sibling 1


title: Twin23-1_FAIREseq

description: FAIRE-seq

value: MZ twin pair 23 sibling 1


title: tofu-4(tm6157) capped small RNA

description: Sample 30

data_processing:
Basecalling with Illumina Real Time Analysis
Sequenced reads longer than 15nt were trimmed for adaptor sequences, clipped of any 3' adaptor sequences, and mapped to ce6 genome using bowtie 0.12.8 with parameters -v 0 -k 10 -m 10.
Mapped reads were annotated by virtue of overlap with (in decreaseing priority) 21U-RNA loci, miRNA loci, genic regions, repeat regions.
Small RNA reads were quantified as raw small RNA read count per million non-structural mapped RNA reads.
Genome_build: ce6
Supplementary_files_format_and_content: tab-delimited text of small RNA reads that map to 21U-RNA loci with read counts (normalized to total mapped unstructured RNA reads)

source_name: tofu-4(tm6157) capped small RNA

extract_protocol:
Staged 12-36hr adults were harvested and washed with M9 buffer until supernatant was clear. Worms were homogenized in trizol reagent, subjected to 3 cycles of freezing in liquid nitrogen and thawing at room temperature before RNA extraction by phase separation and isopropanol precipitation.
Small RNA libraries: 20µg of total RNA was size selected on a 15% denaturing polyacrylamide (dPAA) gel to obtain 19-30nt RNA species. The resultant RNA was ligated at its 3’end to the Illumina RA3 using NEB truncated T4 RNA ligase 2 at 20OC for 2 hours. Ligated products were size selected on a 15% dPAA before being ligated at its 5’end to RA5 using Ambion T4 RNA ligase at 20OC for 2 hours. Ligated products were size selected on a 15% dPAA before being reverse transcribed with RTP and superscript III reverse transcriptase. Resultant cDNAs were amplified using RP1 forward primer and indexed reverse primers using NEB Phusion PCR mastermix. Amplified libraries were gel purified on a 2% low-melting agarose gel and sequenced using the Illumina Hi-seq platform. Capped small RNA libraries: Protocol is the same as that of small RNA library generation with 2 differences. First, 19-30nt size-selected RNA was de-phosphorylated at the 5’end with NEB CIP at 37oC for 1 hour before 3’ ligation. Second, 3’ ligated RNA was treated with Epicenter TAP to convert all 5’ RNA caps into 5’ monophosphates before 5’ ligation. RA3: /5rApp/TGGAATTCTCGGGTGCCAAGG/3ddC/ (ddC: dideoxyC, rN: ribonucleotide, p: phosphate). RA5: rGrUrUrCrArGrArGrUrUrCrUrArCrArGrUrCrCrGrArCrGrArUrC. RTP: GCCTTGGCACCCGAGAATTCCA. RP1: AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGA. RPI: CAAGCAGAAGACGGCATACGAGATIIIIIIGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA (IIIIII: 6-mer Illumina index sequence).
Small RNA cloning and capped small RNA cloning

value: tofu-4(tm6157)  mutation in N2 background


title: Twin23-2_FAIREseq

description: FAIRE-seq

value: MZ twin pair 23 sibling 2


title: tofu-1(tm6424) total small RNA

description: Sample 33

source_name: tofu-1(tm6424) total small RNA

value: Small RNA


title: tofu-3/ulp-5(tm3071) capped small RNA

description: Sample 29

source_name: tofu-3/ulp-5(tm3071) capped small RNA

value: tofu-3/ulp-5(tm3071) mutation in N2 background


title: Twin24-2_FAIREseq

description: FAIRE-seq

value: MZ twin pair 24 sibling 2


title: Twin22-1_FAIREseq

description: FAIRE-seq

value: MZ twin pair 22 sibling 1


title: tofu-3/ulp-5(tm3063) capped small RNA

description: Sample 27

source_name: tofu-3/ulp-5(tm3063) capped small RNA

value: tofu-3/ulp-5(tm3063) mutation in N2 background

value: 3 days post L1 release


title: tofu-2(tm6145) capped small RNA

description: Sample 26

source_name: tofu-2(tm6145) capped small RNA

value: tofu-2(tm6145) mutation in N2 background

value: Solid NGM plate

value: TGGAATTCTCGGGTGCCAAGGC


title: Twin22-2_FAIREseq

description: FAIRE-seq

value: MZ twin pair 22 sibling 2


title: Twin21-2_FAIREseq

description: FAIRE-seq

value: MZ twin pair 21 sibling 2


title: tofu-3/ulp-5(tm3068) capped small RNA

description: Sample 28

source_name: tofu-3/ulp-5(tm3068) capped small RNA

value: tofu-3/ulp-5(tm3068) mutation in N2 background

value: Capped small RNA


title: N2 capped small RNA

description: Sample 24

source_name: N2 capped small RNA

value: wild type


title: prg-1(tm872) capped small RNA

description: Sample 25

source_name: prg-1(tm872) capped small RNA

value: prg-1(tm872) mutation in N2 background


title: tofu-7 RNAi capped small RNA

description: Sample 23

source_name: tofu-7 RNAi capped small RNA

value: tofu-7 RNAi  in rrf-3 null background

value: 4 days post L1 release

value: Liquid S-basal media


title: Twin20-2_FAIREseq

description: FAIRE-seq

value: MZ twin pair 20 sibling 2

value: blood


title: Twin21-1_FAIREseq

description: FAIRE-seq

value: MZ twin pair 21 sibling 1


title: Twin20-1_FAIREseq

description: FAIRE-seq

value: MZ twin pair 20 sibling 1


title: tofu-4 RNAi capped small RNA

description: Sample 20

source_name: tofu-4 RNAi capped small RNA

value: tofu-4 RNAi in rrf-3 null background


title: tofu-5 RNAi capped small RNA

description: Sample 21

source_name: tofu-5 RNAi capped small RNA

value: tofu-5 RNAi in rrf-3 null background


title: Twin19-1_FAIREseq

description: FAIRE-seq

value: MZ twin pair 19 sibling 1


title: tofu-6/mel-47 RNAi capped small RNA

description: Sample 22

source_name: tofu-6/mel-47 RNAi capped small RNA

value: tofu-6/mel-47 RNAi in rrf-3 null background

value: TGGAATTCTCGGGTGCCAAGGC


title: Twin18-1_FAIREseq

description: FAIRE-seq

value: MZ twin pair 18 sibling 1


title: Twin18-2_FAIREseq

description: FAIRE-seq

value: MZ twin pair 18 sibling 2


title: Twin19-2_FAIREseq

description: FAIRE-seq

value: MZ twin pair 19 sibling 2


title: tofu-2 RNAi capped small RNA

description: Sample 19

source_name: tofu-2 RNAi capped small RNA

value: tofu-2 RNAi in rrf-3 null background

value: Capped small RNA


title: gfp RNAi capped small RNA

description: Sample 17

source_name: gfp RNAi capped small RNA

value: gfp RNAi  in rrf-3 null background


title: tofu-1 RNAi capped small RNA rep1

description: Sample 18

source_name: tofu-1 RNAi capped small RNA

value: tofu-1 RNAi in rrf-3 null background

value: 4 days post L1 release


title: Twin17-2_FAIREseq

description: FAIRE-seq

source_name: blood

value: MZ twin pair 17 sibling 2


title: Twin17-1_FAIREseq

description: FAIRE-seq

value: MZ twin pair 17 sibling 1

value: blood


title: Empty vector RNAi capped small RNA rep1

description: Sample 16

source_name: Empty vector RNAi capped small RNA

value: Empty vector RNAi in rrf-3 null background

value: Liquid S-basal media


title: Twin16-2_FAIREseq

description: FAIRE-seq

value: MZ twin pair 16 sibling 2


title: Twin16-1_FAIREseq

description: FAIRE-seq

value: MZ twin pair 16 sibling 1


title: tofu-3/ulp-5(tm3071) total small RNA

description: Sample 14

source_name: tofu-3/ulp-5(tm3071) total small RNA

value: tofu-3/ulp-5(tm3071) mutation in N2 background

value: 3 days post L1 release

value: Solid NGM plate

value: Small RNA


title: tofu-4(tm6157) total small RNA

description: Sample 15

source_name: tofu-4(tm6157) total small RNA

value: tofu-4(tm6157)  mutation in N2 background

value: TGGAATTCTCGGGTGCCAAGGC


title: tofu-3/ulp-5(tm3068) total small RNA

description: Sample 13

source_name: tofu-3/ulp-5(tm3068) total small RNA

value: tofu-3/ulp-5(tm3068) mutation in N2 background


title: tofu-3/ulp-5(tm3063) total small RNA

description: Sample 12

source_name: tofu-3/ulp-5(tm3063) total small RNA

value: tofu-3/ulp-5(tm3063) mutation in N2 background


title: Twin15-2_FAIREseq

description: FAIRE-seq

value: MZ twin pair 15 sibling 2


title: Twin15-1_FAIREseq

description: FAIRE-seq

value: MZ twin pair 15 sibling 1


title: Twin14-1_FAIREseq

description: FAIRE-seq

value: MZ twin pair 14 sibling 1


title: tofu-2(tm6145) total small RNA

description: Sample 11

source_name: tofu-2(tm6145) total small RNA

value: tofu-2(tm6145) mutation in N2 background


title: prg-1(tm872) total small RNA

description: Sample 10

source_name: prg-1(tm872) total small RNA

value: prg-1(tm872) mutation in N2 background


title: N2 total small RNA

description: Sample 9

source_name: N2 total small RNA

value: wild type


title: Twin13-2_FAIREseq

description: FAIRE-seq

value: MZ twin pair 13 sibling 2

value: blood


title: tofu-7 RNAi total small RNA

description: Sample 8

source_name: tofu-7 RNAi total small RNA

value: tofu-7 RNAi  in rrf-3 null background

value: 4 days post L1 release

value: Liquid S-basal media


title: Twin13-1_FAIREseq

description: FAIRE-seq

value: MZ twin pair 13 sibling 1


title: Twin11-2_FAIREseq

description: FAIRE-seq

value: MZ twin pair 11 sibling 2


title: Twin12-1_FAIREseq

description: FAIRE-seq

value: MZ twin pair 12 sibling 1


title: tofu-5 RNAi total small RNA

description: Sample 6

source_name: tofu-5 RNAi total small RNA

value: tofu-5 RNAi in rrf-3 null background

value: TGGAATTCTCGGGTGCCAAGGC

value: Small RNA


title: tofu-4 RNAi total small RNA

description: Sample 5

source_name: tofu-4 RNAi total small RNA

value: tofu-4 RNAi in rrf-3 null background


title: Twin12-2_FAIREseq

description: FAIRE-seq

value: MZ twin pair 12 sibling 2


title: Twin11-1_FAIREseq

description: FAIRE-seq

value: MZ twin pair 11 sibling 1


title: Twin10-2_FAIREseq

description: FAIRE-seq

value: MZ twin pair 10 sibling 2


title: tofu-1 RNAi total small RNA

description: Sample 3

source_name: tofu-1 RNAi total small RNA

value: tofu-1 RNAi in rrf-3 null background


title: tofu-2 RNAi total small RNA

description: Sample 4

source_name: tofu-2 RNAi total small RNA

value: tofu-2 RNAi in rrf-3 null background


title: gfp RNAi total small RNA

description: Sample 2

source_name: gfp RNAi total small RNA

value: gfp RNAi  in rrf-3 null background


title: Twin10-1_FAIREseq

description: FAIRE-seq

value: MZ twin pair 10 sibling 1

value: blood


title: Empty vector RNAi total small RNA

description: Sample 1

source_name: Empty vector RNAi total small RNA

value: Empty vector RNAi in rrf-3 null background

value: 4 days post L1 release


title: Twin14-2_FAIREseq

description: FAIRE-seq

value: MZ twin pair 14 sibling 2


title: Twin9-1_FAIREseq

description: FAIRE-seq

value: MZ twin pair 9 sibling 1


title: Twin8-1_FAIREseq

description: FAIRE-seq

value: MZ twin pair 8 sibling 1


title: Twin7-1_FAIREseq

description: FAIRE-seq

value: MZ twin pair 7 sibling 1


title: Twin7-2_FAIREseq

description: FAIRE-seq

value: MZ twin pair 7 sibling 2


title: tofu-6/mel-47 RNAi total small RNA

description: Sample 7

source_name: tofu-6/mel-47 RNAi total small RNA

value: tofu-6/mel-47 RNAi

value: Liquid S-basal media

value: TGGAATTCTCGGGTGCCAAGGC

value: Small RNA


title: Twin3-2_FAIREseq

description: FAIRE-seq

source_name: blood

value: MZ twin pair 3 sibling 2


title: Twin4-2_FAIREseq

description: FAIRE-seq

value: MZ twin pair 4 sibling 4


title: Twin5-2_FAIREseq

description: FAIRE-seq

value: MZ twin pair 5 sibling 4


title: Twin2-2_FAIREseq

description: FAIRE-seq

value: MZ twin pair 2 sibling 2


title: Twin8-2_FAIREseq

description: FAIRE-seq

value: MZ twin pair 8 sibling 2


title: Twin3-1_FAIREseq

description: FAIRE-seq

value: MZ twin pair 3 sibling 1

value: blood


title: Twin1-2_FAIREseq

description: FAIRE-seq

value: MZ twin pair 1 sibling 2


title: Twin1-1_FAIREseq

description: FAIRE-seq

value: MZ twin pair 1 sibling 1


title: Twin5-1_FAIREseq

description: FAIRE-seq

value: MZ twin pair 5 sibling 3


title: late_9_11

city: St. Louis

first: Maureen

middle: J

last: Donlin

state: MO

address: 1100 South Grand

department: Biochemistry and Molecular Biology

country: USA

institute: Saint Louis University School of Medicine

description: senescent BJ human foreskin fibroblasts

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequence reads were trimmed of adaptor sequences, low-quality reads and then aligned to Hg19 human genome (hg19) using TopHat version 2.0.6 using Bowtie2 version 2.0.6
Transcripts were generated using Cufflinks version 2.02
Transcripts were converted to read counts using ht-counts
Differentially expressed transcripts were identified using EdgeR
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: BJ foreskin fibroblasts

extract_protocol:
Total RNA was isolated using TRI Reagent (Life Technologies) and the RiboPure RNA isolation kit (Life Technologies).  Ribosomal RNA was removed by poly-A selection on oligo-dT beads.
Single-end libraries were generated using Illumina TruSeq RNA Sample Preparation Kit v2

treatment_protocol: Fibroblasts were treated iwth 10 uM SB203580 (Millipore) for 48 hours, replenished daily

value: BJ foreskin fibroblasts

tag: develpmental stage

value: senescent

tag: treatment


title: late_sb_9_24

description: senescent BJ human foreskin fibroblasts treated with p38MAPK inhibitor, SB203580 (Millipore)

value: 48 hours with p38-MAPK inhibitor SB203580 (Millipore)


title: late_sb_9_11


title: young_9_11

description: youngBJ human foreskin fibroblasts

value: young


title: Twin9-2_FAIREseq

description: FAIRE-seq

value: MZ twin pair 9 sibling 2


title: young_9_24

description: youngBJ human foreskin fibroblasts


title: mcf710m0h1

city: Ann Arbor

first: Mats

last: Ljungman

state: Michigan

address: NCRC, B520 Room 1346 2800 Plymouth Rd.

institute: University of Michigan

description: molecule: bru-labeled RNA

data_processing:
library strategy: BruSeq
Illumina Casava v1.8.2 software used for basecalling.
Reads were mapped to the Human ribosomal DNA complete repeating unit (U13369.1) using bowtie v.0.12.8 and parameters -n 3 -k 1 -m 1
Reads that did not map to the ribosomal DNA were mapped to the hg19 genome using TopHat v1.4.1 and parameters –min-isoform-fraction 0, --max-multihits 1, --no-closure-search, --no-coverage-search, --bowtie-n, --initial-read-mismatches 3
A coverage determination was then made for every base in the genome using Bedtools v.2.16.2 such that a base covered by one read was recorded as having a coverage of 1/read_length
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
RNA Pol II elongation rate was measured in the DRB treatment samples (Bru labeling immediately after DRB wash-out) using a 3 state Hidden Markov Model. The analysis region was divided into 250 base pairs long bins, and the expression rate in these bins was used to determine the total elongation observed during the labeling time.
Genome_build: hg19
Supplementary_files_format_and_content: The columns of the abundance measurement files(*genes.txt) indicate: (1) chromosome; (2) start; (3) end; (4) name; (5) score; (6) strand; (7) gene length; (8) feature type – exon, intron, etc; (9) number of introns and exons; (10) feautre length; (11) hits count; (12) density – count/length; (13) RPKM - count/(length/1E3)/(mapped read count/1E6)
Supplementary_files_format_and_content: The columns of the elongation rate measurements (*elongation_rates.txt)  indicate: (1) chromosome; (2) start of the analysis region; (3) end of the analysis region; (4) ENSEMBL transcript ID; (5) score; (6) strand; (7) ENSEMBL gene ID; (8) gene symbol; (9) ENSEMBL gene biotype; (10) elongation rate meausred in bp/min; (11) nascent gene expression for the analysis region in the relevant control sample measured in RPKM

growth_protocol: Human fibroblasts (HF1, TM and CS-B) were grown in MEM supplemented with 10% FBS, L-glutamine, vitamin mix and antibiotics. K562 human leukemia cells were grown in IMDM supplemented with 10% FBS supplemented with penicillin and streptomycin. MCF-7 human breast cancer cells were grown in high-glucose RPMI supplemented with 10% FBS.

extract_protocol:
Total RNA was isolated by using TRIzol reagent (Invitrogen), and Bru-labeled RNA was isolated from the total RNA by incubation with anti-BrdU antibodies (BD Biosciences) conjugated to magnetic beads (Dynabeads, Goat anti-Mouse IgG; Invitrogen) under gentle agitation at room temperature for 1 h. For more detail, see Paulsen et. al 2013
Bru-labeled RNA was mixed with first strand buffer and random primers and fragmented by heating at 85 ̊C for 10 minutes. The first strand cDNA was then  synthesized, in the presence of Actinomycin D to result in strand specific reads (only applicable to certain samples as indicated in sample table above). After purifying the first strand cDNA using AMPure RNAclean beads (Beckman Coulter), the second strand cDNA was synthesized. The resulting cDNA was purified with AMPure XP beads, after which the Illumina TruSeq RNA Sample Prep Kit was used to repair the cDNA ends, adenylate and ligate adaptors to the cDNA. The samples were then run on a 3% agarose gel and size-selected by excising gel slices in the 300bp region. These gel slices were purified using the QIAEX II Gel Extraction Kit (Qiagen) and then the Illumina TruSeq Kit PCR reagents were used to enrich the DNA fragments. After a final purification using AMPure XP beads, the quality and concentration of the DNA libraries were determined using an Agilent Bioanalyzer.

treatment_protocol: In the DRB treated samples, the drug 5,6-dichloro-1-bold beta-D-ribofuranosylbenzimidazole (DRB, Sigma) is added to the media to a final concentration of 100 μM and cells are incubated for a determined period of time at 37 ̊C. After the incubation with DRB, the cells were washed with PBS twice and nascent RNA was labeled in conditioned media containing 2 mM bromouridine (Bru) (Aldrich) for 10 min at 37°C. The cells were then directly lysed in TRIzol reagent (Invitrogen). K562 cells were grown in suspension so these cells were quickly spun down before being lysed in TRIzol. In the samples nfDRB0m1 and csbDRB0m1, the labeling with Bru is carried out in the presence of DRB.

tag: drb exposure time

value: 0 minutes

tag: bromouridine labeling start

tag: bromouridine labeling time

value: 10 minutes

tag: treatment group

value: Control

tag: exogenous dna


title: Twin4-1_FAIREseq

description: FAIRE-seq

value: MZ twin pair 4 sibling 3


title: K562DRB10m1

description: molecule: bru-labeled RNA

tag: cell type

value: 60 minutes

value: Immediately after washout

value: DRB exposure


title: tmemptyDRB10m1

description: molecule: bru-labeled RNA

source_name: Fibroblast (TM)

value: Fibroblast (TM)

value: empty vector


title: Twin6-1_FAIREseq

description: FAIRE-seq

value: MZ twin pair 6 sibling 1

value: blood


title: mcf7DRB10m1

description: molecule: bru-labeled RNA


title: Twin6-2_FAIREseq

description: FAIRE-seq

value: MZ twin pair 6 sibling 2


title: K56210m0h1

description: molecule: bru-labeled RNA


title: tmempty0h1

description: molecule: bru-labeled RNA

value: 30 minutes


title: csbDRB20m1

description: molecule: bru-labeled RNA

source_name: Cockayne syndrome group B fibroblasts

value: Cockayne syndrome group B fibroblasts

value: 10 minutes after washout


title: csbDRB10m1

description: molecule: bru-labeled RNA


title: csbDRB0m1

description: molecule: bru-labeled RNA

value: 10 minutes prior to washout


title: csb10m0h1

description: molecule: bru-labeled RNA


title: Twin2-1_FAIREseq

description: FAIRE-seq

value: MZ twin pair 2 sibling 1


title: nfDRB20m1

description: molecule: bru-labeled RNA

source_name: Foreskin fibroblasts (HF1)

value: Foreskin fibroblasts (HF1)


title: nfDRB0m1

description: molecule: bru-labeled RNA

value: 10 minutes


title: nfDRB10m1

description: molecule: bru-labeled RNA


title: nf_0h_3b

description:
GSM1062446
molecule: bru-labeled RNA

value: 0 minutes

value: Control


title: nf_0h_3a

description:
GSM1062445
molecule: bru-labeled RNA


title: late_9_24

description: senescent BJ human foreskin fibroblasts

value: BJ foreskin fibroblasts

value: senescent


title: PHF6 ChIP-seq in Jurkat

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description: Chromatin IP against PHF6 in Jurkat

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.

source_name: T-ALL cell line

growth_protocol: Human Jurkat cells were purchased from the American Type Culture Collection (ATCC), Manassas, VA. Cells were maintained under typical conditions in RPMI media with 10% Bovine Calf Serum. For location analysis, cells were grown to a density of 1 million per ml and 99% viability prior to cross-linked with formaldehyde for 20 min.

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

tag: chip antibody

tag: antibody catalog number

value: Bethyl A301-451A

value: Jurkat


title: H2AX_wtINO80_ChIPseq

city: Daejeon

first: Jungmin

last: Seo

address: #211, BVC, KRIBB, Eoung-dong, Yuseong-gu

department: Bioinformatics Research Institute

data_processing:
Basecalls performed using CASAVA version 1.8.2.
Sequence reads were obtained and mapped to the hg19 human genome using the Illumina Genome Analyzer Pipeline.
All reads uniquely mapped to the gnome with two or fewer mismatches were retained and extended to the library fragment size (200 bp) to create the BED files.
Genome_build: hg19
Supplementary_files_format_and_content: BED files

source_name: HeLa cells transfected with empty vector

growth_protocol: CD4+ T cells were isolated from human PBMC and maintain in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS). Hela-S3 cells were grown in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) and purmomycin.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
DNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: CD4+ T cells were incubated with IL-2, either alone or alongside anti-CD3 and anti-CD28 antibodies.

value: HeLa-S3 cells


title: SRCAP_IL2aCD3aCD28_ChIPseq

source_name: CD4+ T cells activated by IL-2+aCD3+aCD28

value: CD4+ T cells

value: SRCAP (Abcam, ab99408, lot GR58857-1)


title: Pol2_siINO80_ChIPseq

source_name: HeLa cells transfected with INO80 siRNA

value: RNA polymerase II (Abcam, ab5408, lot GR258-5)


title: H2AX_siINO80_ChIPseq


title: γ-H2AX_IL2aCD3aCD28_ChIPseq

value: gamma H2A.X (Abcam, ab2893, lot GR43146-1)


title: H2AZ_IL2aCD3aCD28_ChIPseq


title: H2AX_IL2aCD3aCD28_ChIPseq


title: INO80_IL2aCD3aCD28_ChIPseq


title: X7/C24 rep3

city: Lisbon

first: Andreia

middle: Jesus

last: Amaral

state: Estremadura

address: Camp Grande

department: Gene Expression and Bioinformatics Unit

country: Portugal

institute: Center for Biosystems, Integrative and Functional Genomics

description: Dms 16

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence
Supplementary_files_format_and_content: fly genes and their abundance

organism: Drosophila melanogaster

source_name: Central Nervous System

extract_protocol:
Approximately 200 central nervous system (CNS) were dissected from late third instar larvae in order to generate one biological replicate of the corresponding genotype in ice cold PBS. Dissected CNS samples were quickly frozen in TriPure Isolation Reagent (Roche Diagnostics GmbH, Mannheim, Germany). After, each ~200 CNS samples were pooled and crude total RNA for each sample was extracted using TriPure Isolation Reagent (Roche Diagnostics GmbH Roche Applied Science, Mannheim, Germany). The crude RNA extract was treated with rDNase set (Macherey-Nagel, Duren, Germany) to digest contaminated DNA and was, subsequently, cleaned-up with NucleoSpinRNA Clean-up XS kit (Macherey-Nagel, Duren, Germany) to remove impurities. The purified total RNA was quantified using spectrophotometry (NanoDrop; Thermo Scientific, DE, USA) and microfluidic analyzer, Agilent RNA 6000 Nano kit (Agilent Technologies, Waldbronn, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: SmnX7/elavGAL4-C24 or X7/C26

value: Central Nervous System

tag: developmental stage

value: third instar larvae


title: C24 rep7

description: Dms 13

tag: tissue


title: H2AZ_IL2_ChIPseq

source_name: CD4+ T cells activated by IL-2


title: C24 rep6

description: Dms 12


title: X7/C24 rep4

description: Dms 17

value: SmnX7/elavGAL4-C24 or X7/C27


title: X7/C24 rep1

description: Dms 14

value: SmnX7/elavGAL4-C24 or X7/C24


title: H2AX_IL2_ChIPseq


title: Pol2_IL2_ChIPseq


title: WT rep6

description: Dms 6

value: elavGAL4 or WT


title: C24 rep1

description: Dms 7


title: C24 rep3

description: Dms 9


title: C24 rep4

description: Dms 10


title: X7/C24 rep2

description: Dms 15

value: SmnX7/elavGAL4-C24 or X7/C25


title: WT rep4

description: Dms 4


title: C24 rep5

description: Dms 11


title: C24 rep2

description: Dms 8


title: WT rep5

description: Dms 5


title: WT rep1

description: Dms 1


title: Pol2_IL2aCD3aCD28_ChIPseq


title: WT rep2

description: Dms 2


title: Input control G

city: Regensburg

first: Michael

last: Rehli

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

department: Internal Med III

institute: University Hospital Regensburg

description: Input control

data_processing:
Sequence tags were mapped to the human reference sequence (GRCh27/hg19) using Bowtie1 and only uniquely mapped tags were used for downstream analyses. Parameters:  -q --best -m 1
Genome_build: hg19
Supplementary_files_format_and_content: alignment files produced with bowtie

source_name: Input control

growth_protocol: cells were isolated according to: Hoffmann P, Eder R, Boeld TJ, et al. Only the CD45RA(+) subpopulation of CD4(+)CD25(high) T cells gives rise to homogeneous regulatory T-cell lines upon in vitro expansion. Blood. 2006;108:4260-4267; cell populations were expanded according to: Hoffmann P, Eder R, Kunz-Schughart LA, Andreesen R, Edinger M. Large-scale in vitro expansion of polyclonal human CD4(+)CD25(high) regulatory T cells. Blood. 2004;104:895-903.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
DNA from chromatin immunoprecipitation was adapter-ligated and PCR amplified using NEBNext DNA Sample Prep Reagent Set1 (NEB E6000L) and Adapter Oligo Mix and PCR primers from Illumina following the manufacturer’s protocol. Barcoded Libraries were generated with the Bioo Nextflex barcoding materials. ChIP fragments were sequenced for 36 or 50 cycles on Illumina Genome Analyzers I, II, HiScanSQ or HiSeq 1000 according to the manufacturer’s instructions.

tag: donor

value: G

value: Input control

value: no antibody


title: ETS1_TregRA+ G

description: Chromatin IP against ETS1

source_name: CD4+CD25+CD45RA+ expanded naive regulatory T cells

value: ETS1 (Santa Cruz sc-350x)

tag: chip antibody manufacturer

value: Santa Cruz

tag: chip antibody catalog #


title: RUNX1_Tconv G

description: Chromatin IP against RUNX1

source_name: CD4+CD25- expanded conventional T cells

value: CD4+CD25- expanded conventional T cells

value: RUNX1 (abcam ab 23980)

value: abcam


title: ETS1_Tconv G

description: Chromatin IP against ETS1


title: Input control F

description: Input control

value: F


title: prde-1 TAP

city: London

first: Peter

last: Sarkies

address: Du Cane Road

department: MRC Clinical Sciences Centre

country: United Kingdom

institute: Imperial College London

data_processing:
Adapter trimming using Cutadapt v1
fastq to fasta conversion, selection for small RNAs of 15-30nt in length using custom Perl scripts using Perl v5.12.4
fasta collapsed using FastX toolkit fastx_collapser module
Supplementary_files_format_and_content: The .fasta files report seq_id_number of reads

source_name: Total RNA whole animal

growth_protocol: Animals were synchronized at L1 stage using hypochlorite treatment, followed by growth to young adult stage on NGM/HB101 using standard procedures.

extract_protocol:
Total RNA extracted using Trisure (BioLine) according to manufacturer's instructions
Illumina Truseq small RNA according to manufacturer's instructions

value: Young Adult

tag: genotype/variation

value: prde-1 mutant

value: TAP treated

value: whole animal


title: prg-1 5' dependent

value: prg-1 mutant

value: 5' polyphosphatase treated


title: prde-1_2 5' independent

value: 5' monophosphate only


title: prde-1_1 5'dependent


title: prde-1_1 5'independent


title: prg-1 TAP


title: N2 polyphosphatase

value: wild type


title: N2 5' dependent


title: N2 TAP


title: N2 5' independent


title: prg-1 5' independent


title: WT rep3

description: Dms 3

value: elavGAL4 or WT

value: Central Nervous System

value: third instar larvae


title: P16.6

city: Belfield

first: Paul

last: McGettigan

state: Co Dublin

address: Veterinary Sciences Centre, UCD

department: School of Agriculture, Food Science and Veterinary Medicine

country: Ireland

institute: University College Dublin

data_processing:
Image analysis and base calling was carried out using Illumina IPAR1.01 software
Alignment to bt4 genome was carried out with Illumina ELAND software
Read counts for each transcript was generated by Illumina CASAVA software
Genome_build: bt4
Supplementary_files_format_and_content: raw counts for each transcript for each sample

organism: Bos taurus

source_name: day 16 pregnant endometrium

growth_protocol: In brief, the estrus cycles of cross-bred beef heifers (predominantly Charolais and Limousin cross) were synchronized using a controlled internal drug release (CIDR) device (1.94 g pro- gesterone; InterAg, Hamilton, New Zealand) placed into the vagina for 8 days with intramuscular administration of a prostaglandin F2α analog (equivalent to 0.5 mg of PG, Estrumate; Shering-Plough Animal Health, Hertfordshire, UK) 3 days prior to CIDR removal. Only heifers detected in standing estrous were used (n = 54).

extract_protocol:
All reproductive tracts were processed <30 min post- slaughter, whereby the uterine horn ipsilateral to the CL was flushed with phosphate-buffered saline containing 5% fetal calf serum. In inseminated heifers, the presence of the conceptus was determined by examination under a stereomicroscope. Tissue was collected only from heifers from which a conceptus at the appropriate stage of development was recovered.  After being flushed, the uterine horn ipsilateral to the CL was opened longitudinally, and 300 mg strips of endometrium (predominantly inter- caruncular tissue) were immersed in 1:5 wt/vol of RNAlater. This tissue was transported back to the laboratory on ice, stored at 4°C for 24 h, removed from RNAlater, and stored at <80°C prior to RNA extrac- tion.
RNA libraries were prepared for sequencing using standard Illumina protocols for single read libraries.

treatment_protocol: Thirty-eight heifers were inseminated, and 16 were left as noninsemi- nated cyclic controls. Heifers were then randomly assigned to be slaughtered on day 13 or 16 of early pregnancy/estrous cycle corre- sponding to the initiation of conceptus elongation (day 13) and maternal recognition of pregnancy (day 16) in pregnant heifers, respectively.

tag: day

value: pregnant


title: P16.19


title: P16.1


title: P16.12rep2


title: P13.9

source_name: day 13 pregnant endometrium


title: P13.2


title: P13.14


title: P13.11


title: P13.20


title: C16.3

source_name: day 16 cyclic endometrium

value: cyclic


title: prde-1_2 5' dependent

tag: treatment


title: FOXP3_Tconv F

description: Chromatin IP against FOXP3

value: CD4+CD25- expanded conventional T cells

value: FOXP3 (Novus NB600-245)

value: Novus


title: C16.17


title: C16.7


title: C16.16


title: P16.4


title: C16.15


title: C13.8

source_name: day 13 cyclic endometrium


title: Rag2 -/- H3K36me3 ChIP-Seq biorep 2 techrep 2

description: Sample 17

data_processing:
For the Genome Analyzer II System, basecalls were performed using manufacturer’s instructions. For the SOLiD 4 System, high-quality reads were matched to individual samples based on the barcode tag and using default parameters in SOLiD Experimental Tracking Software (SETS) v4.0.1. For SOLiD 5500xl, basecalls were performed using 5500 Series Genetic Analyzers Instrument Control Software v1.2. For the HiSeq 2000 System, basecalls were performed using manufacturer's instructions (CASAVA).
Alignment of reads to the mm9 genome was conducted using CASAVA Eland and BFast 0.7.0 for Illumina and SOLiD sequencing runs, respectively, according to manufacturer’s instructions. Only reads with a unique best scoring alignment were retained. Clonal artifacts were filtered out retaining the longer reads.
Aligned reads were processed using a previously described in-house ChIP-Seq analysis pipeline (Koch, Fenouil et al 2011).  Using a stepwise tag size extension in 10bp increments, fragment size was estimated in silico for DN and DP ChIPs.
Tags were then elongated to the estimated mean fragment size and converted to wig format using a binning window of 50bp. Replicate tracks were subsequently merged by addition. To account for differences in tag counts between DN and DP experiments, tag count normalization was performed by scaling DP datasets to DN tag counts. Visual inspection of invariant targets (e.g. Eβ for Ets1, β-actin for Pol II, H3K4me1/2, Mnase, the Hoxa locus for H3K27me3) allowed further fine tuning and scaling of DP tag-counts to reflect potential differences in signal to noise ratios between DN and DP experiments.
Peak detection was carried out with CoCAS using averaged into 50bp windows and converted to general feature format (GFF). Thresholds were 7.5 x SD + mean for the main window and 5 x SD + mean for the extension window. Artifacts were detected and removed by performing peak detection in CoCAS (using 2 X SD + mean and SD + mean as main and extension window thresholds, respectively) in reads originating from the Input treatment. Peaks were annotated to the nearest TSS, except in the case of intragenic peaks which were assigned to the surrounding gene. Peaks outside of [-5kb; +5kb] around known TSSs (refSeq, miRNA, rRNA, scRNA, snRNA, snoRNA and tRNA) were considered to be distal, while those falling within [-5kb; +5kb] around known TSSs were considered proximal. Distal peaks within a gene body were considered intragenic and those outside of gene bodies were considered intergenic.
Genome_build: mm9
Supplementary_files_format_and_content: Fragments were extended using an R pipeline described in Koch, Fenouil, Gut et al. 2011. Fixed-step 50bp wig files were generated using an R pipeline described in Koch, Fenouil, Gut et al. 2011. Peaks were called using CoCAS

source_name: primary Rag2 -/- thymocytes

extract_protocol:
Phenol-chroloform
For ChIP-Seq, thymocytes were  aliquoted in crosslinked pellets of 5 107 cells and lysed by rotation for 10 min at 4°C in 2x 1.25ml LB1 (50mM Hepes pH 7.5, 140mM NaCl, 1mM EDTA, pH 8, 10% glycerol, 0.75% NP-40, 0.25% Triton X-100). Following centrifugation at 1,350g for 5 minutes at 4°C, nuclei were subsequently treated with 2x1.25ml LB2 (200mM NaCl, 1mM EDTA pH 8, 0.5mM EGTA pH 8, 10mM Tris pH 8) on a rotating wheel for 10 minutes at 4°C. Chromatin was resuspended in 1.5ml LB3 (1mM EDTA pH8, 0.5mM EGTA pH 8, 10mM Tris pH 8, 100mM, NaCl, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine) in 15ml polypropylene falcon tubes and then sonicated for 10 cycles (30 seconds on, 30 seconds off) at 40W using a VCX130 sonicator (VibraCell) down to an average size of about 250bp. 50µl aliquots were collected as Input controls. All buffers contained final concentrations of 1X protease inhibitors (Roche, France) as well as 0.2mM PMSF and 1μg /ml pepstatin. ChIPs were conducted using either α-rabbit (Ets1) or protein-G (all other ChIPs) DynaBeads (Invitrogen).Antibody and bead mixes were washed three times with 1ml BSA blocking buffer (0.5% BSA in 1x DPBS), incubated and rotated overnight at 4°C, and subsequently washed another three times  with 1ml BSA blocking buffer. Immunoprecipitation was carried out overnight in 750µl LB3 at 4°C on a rotating wheel. Samples were then washed 8 times in 1ml RIPA buffer (50mM Hepes pH 7.6, 500mM LiCl, 1mM EDTA pH 8, 1% NP-40, 0.7% Na-Deoxycholate) and once in 1ml TE buffer with 50mM NaCL. Two 15-min and 10-min subsequent elutions were carried out in a waterbath at 65°C, vortexing every other minute, for a final volume of 100µl. 100µl 1X elution buffer (50mM Tris pH 8, 10mM EDTA pH 8, 1% SDS) was added to eluates which were reverse-crosslinked overnight in a 65°C waterbath. Equal volumes of TE buffer (100µl) were added to samples as well as 0.2μg/ml RNAse A and placed at 37°C for 2 hours, followed by proteinase K treatment at 0.2μg/ml at 55°C. DNA purification was carried out via phenol-chloroform extraction followed by elution using QiaQuick PCR purification kits. (QiaGen) Samples were pooled per replicate then SpeedVac-ed down to 30µl. DNA quantification of eluates was obtained using Bioanalyzer High Sensitivity chips (Agilent). Library preparation was carried out as per manufacturer’s instructions (Illumina) using 10ng material. Samples were subsequently size-selected via gel migration and extraction, with average cut sizes at about 230 bp for DN and 250 bp for DP, including adapters.  Sequencing was performed using either Genome Analyzer II (Illumina) or SOLiD 5500xl sequencers (Applied Biosystems), whereby samples were sequenced at the CNAG, Barcelona, Spain and TAGC, Marseille, France, respectively. For SOLiD 5500xl sequencing, ChIP-seq libraries were been prepared according to the Life Technologies protocol, SOLiD ChIP-seq kit guide (A12066), using 15 PCR cycles. The quality of the libraries was checked with the BioAnalyzer DNA High sensitivity and by Q-PCR.

tag: strain

tag: age

value: 5-6 weeks

tag: cells used

tag: antibody

value: Abcam (ab9050)

tag: antibody quantity

value: 2 µg

tag: magnetic beads

value: Protein G dynabeads

tag: bead volume

tag: estimated fragment size


title: C13.10


title: C13.18


title: 104

city: Shanghai

first: Han

last: Xiao

address: 300 Fenglin Rd

department: National Key Laboratory of Plant Molecular Genetics

institute: Shanghai Institutes for Biological Sciences

description: p35S:HA-SlZFP2 line 104

data_processing:
Reads were mapped to tomato genome using Tophat program v.1.3.2 (Trapnell et al. 2009). Then the transcripts were assembled using cufflinks based on transcripts predicted in SL2.40 assembly from SGN (Trapnell et al. 2010). In total, the numbers of fragments (one or both of the paired-end reads) mapped were 13,560,517 (90.4%) for 103, 13,778,522 (91.9%) for 104, 13,592,147 (90.6%) for 103N, and 13,834,382 (92.2%) for 104N. The expression values of the transcripts were calculated in fragments per kilobase of transcript per million mapped reads (FPKM) (Mortazavi et al. 2008).
Genome_build: Tomato genome assembly SL2.40 from SGN (Sol Genomics Network: solgenomics.net) corresponding to 'Solyc2.40' from S.lycopersicum at http://www.ncbi.nlm.nih.gov/assembly/GCF_000188115.1/
Supplementary_files_format_and_content: expression values of the transcripts calculated in FPKM

organism: Solanum pimpinellifolium

source_name: transgenic_shoot tips

growth_protocol: Tomato plants including the transgenic lines were grown in phytotron under the condition of temperature at 20-25 °C and humidity of 70-80%, illuminated for 16 hours daily by light of 150 mE·m–2·s–1 from metal halide and high pressure sodium lamps. Plants were fertilized weekly with all-purpose fertilizer and watered as needed.

extract_protocol:
Total RNA was extracted by Trizol reagent (InvitroGen) from shoot tips including one small visible leaf were collected from one and half month old plants.
Paired-end sequencing libraries were created and sequenced on Illumina Hiseq2000 platform

tag: strain background

value: p35S:HA-SlZFP2 Transgenic

value: overexpresion of HA-SlZFP2

value: 45-days old plants

value: Shoot tips with one visible leaf


title: Rag2 -/- H3K36me3 ChIP-Seq biorep 1

description: Sample 15


title: C13.13


title: 103N

description: Nontransgenic sibling from line 103

source_name: nontransgenic_shoot tips

value: wild type (nontransgenic sibling)


title: 104N

description: Nontransgenic sibling from line 104


title: Rag2 -/- Ets1 ChIP-Seq biorep 2

description: Sample 2

value: Santa Cruz (sc-350x)

value: 20 µg

value: Sheep anti-rabbit IgG dynabeads


title: Rag2 -/- Ets1 ChIP-Seq biorep 1

description: Sample 1


title: P16.12rep1

value: pregnant


title: Rag2 -/- H3K4me1 ChIP-Seq biorep 2

description: Sample 6

value: Abcam (ab8895)


title: Rag2 -/- H3K36me3 ChIP-Seq biorep 2 techrep 1

description: Sample 16


title: Rag2 -/- short RNA-Seq

description:
Sample 1
Strand-specific RNA-Seq. Libraries were run on an Illumina GAII sequencer.

data_processing:
Pre-processing and pipeline Samples were sequenced on an Illumina Genome Analyzer II. We obtained the raw sequences and detected and removed the adapter sequences using the MIRO pipeline (http://seq.crg.es/main/bin/view/Home/MiroPipeline). The obtained reads were aligned against the mouse genome using the GEM aligner (http://gemlibrary.sourceforge.net). Only unambiguously aligned tags were used for further analysis.
Tags from technical replicates were merged. Coverage of tags was computed using bedtools genomecov and converted to wig format using a binning window of 50bp.
Genome_build: mm9
Supplementary_files_format_and_content: WIGfs_DN_TSSRNA_el0_bins50_ArtefactParam_NA.wig.gz: fixed-step wiggle file representing short RNA-Seq tag densities on both strands every 50bp
Supplementary_files_format_and_content: WIGfs_DN_TSSRNA_reverse_el0_bins50_ArtefactParam_NA.wig.gz: fixed-step wiggle file representing short RNA-Seq tag densities the minus strand every 50bp
Supplementary_files_format_and_content: WIGfs_DN_TSSRNA_forward_el0_bins50_ArtefactParam_NA.wig.gz: fixed-step wiggle file representing short RNA-Seq tag densities the plus strand every 50bp

growth_protocol: Thymuses were extracted from 5-6-week-old Rag2-/- knockout mice and stored in RPMI medium. Cohorts of litter mates were used as biological replicates. To recover thymocytes, thymuses were subsequently passed twice through a 70µm Falcon cell strainer and stored in PBS. Cells were crosslinked 10 min in 10% formaldehyde followed by 5 min quenching in 250 mM glycine. DP cells were subsequently sorted via AutoMACS using, in turn, α-CD8-PE antibody conjugated to α-PE beads, and α-CD4 beads (Miltenyi). FACS profiles and cell purities were obtained for Rag2-/- and DP thymocytes via CD44-APC, CD25-FITC and CD8-PE, CD4-FITC staining, respectively

extract_protocol:
Trizol
Illumina Small RNA Rev. B protocol with some minor modifications (see below) to yield directional short RNAseq profiling.
For short RNA-Seq, total RNA was extracted using TRIzol (Invitrogen, USA) according to the manufacturer’s instructions with some modifications to ensure higher recovery rates of small RNAs. In brief, Rag2-/- thymocytes were divided into 1x107 aliquots and 1ml of TRIzol was added. Cells were lysed with vigorous vortexing and pipetting. Homogenized samples were incubated at room temperature for 5 minutes and 0.2ml of chloroform was added. Samples were vigorously shaken and incubated at room temperature for an additional 5 minutes. Phase separation was carried out by centrifugation at 4°C and 12,000g in a tabletop centrifuge for 15 minutes. The aqueous phase was transferred to fresh tubes and 1.5 volumes (approximately 1ml) of isopropanol together with 10μg of linear acrylamide (Ambion, USA) were added. Samples were vortexed and incubated at room temperature for 15 minutes. The precipitated RNA was pelleted by centrifugation at 4°C and 12,000g in a tabletop centrifuge for 20 minutes. Pellets were washed with 80% ethanol, vortexed and centrifuged at 4°C and 7,500g in a tabletop centrifuge for 10 minutes. Pellets were allowed to air dry and resuspended in nuclease-free water (Ambion, USA). DNA was digested using the rigorous Turbo DNase (Ambion, USA) treatment as per manufacturer’s instructions. RNA quantity was measured on a Nanodrop 1000 and the quality was verified using RNA Nano chips on a 2100 Bioanalyzer (Agilent, USA).Small RNAs were purified from a 10% denaturing urea polyacrylamide gel, essentially as described in the Illumina Small RNA Rev. B protocol with some minor modifications. Approximately 10μg of total RNA was run at 200V for 1 hour, until the blue front reached the bottom of the gel. We used 21G needles to puncture holes into the bottom of two 0.5ml and placed them into 2ml eppendorf tubes. RNA corresponding to 15nt - 70nt was cut from the gel, diagonally cut in half and separately transferred into the 0.5ml tubes. The gel was crushed into the 2ml tubes by a two minute centrifugation at 14,000rpm. For gel elution by soaking, 0.4ml of 0.3M NaCl was added to each tube, before a 4 hour rotation at room temperature. After removal of gel particles using 0.22μm cellulose acetate filters, 10μg of linear acrylamide (Ambion, USA) and 2.5 volumes (approximately 1ml) of ice-cold absolute ethanol were added. After 30-minute incubation at -80°C, the eluted RNA was precipitated by centrifugation at 4°C and maximum speed for 45 minutes. The pellet was washed with 1ml of room temperature 80% ethanol and resuspended in 5.7μl of water. This PAGE purification step was repeated after both the 5’ and 3’ adapter ligations, which were carried out according to the protocol. The resulting cDNA was purified with the QIAquick Gel Extraction kit (Qiagen, Germany) using the DNA cleanup protocol modification in order to retain DNA fragments as low as 70bp. The DNA was quantified using a Nanodrop 1000 (Thermo Scientific, France) and verified using DNA High Sensitivity 2100 Bioanalyzer chips (Agilent, USA). The library was clustered and sequenced using 76 cycles on a Genome Analyzer II (Illumina, USA) at the CNAG, Barcelona, Spain, according to manufacturer’s instructions.

tag: cell type

value: primary Rag2 -/- thymocytes


title: C13.5

value: cyclic


title: 103

description: p35S:HA-SlZFP2 line 103

tag: tissue


title: Input control D

description: Input control

tag: donor

value: D

value: Input control

tag: chip antibody

value: no antibody


title: Celf1heart_72h_A3278

city: Gainesville

first: Eric

middle: T

last: Wang

state: FL

address: 2033 Mowry Rd

institute: University of Florida

data_processing:
Reads were aligned to the mm9 mouse genome and splice junctions using tophat/bowtie.
RPKM values were computed by counting the number of reads mapping to constitutive exons.
Genome_build: mm9
Supplementary_files_format_and_content: RPKM values in matrix format (Entrez IDs as gene identifiers).

molecule: polyA RNA

source_name: heart (ventricle)

extract_protocol:
Mice between 20 and 22 weeks old were fed 2 g/kg doxycycline to induce Celf1 expression in heart.  All food was removed from cages 2-3 hours prior to addition of dox food.  At the indicated time point, the mouse was sacrificed, and the heart was dissected.  Blood was removed by washing with PBS.  The atria were removed, and small portion of the apex was removed.  The remaining ventricle tissue was frozen in liquid nitrogen. Total RNA from the ventricle tissue was prepared by lysis in guanidium isothiocyanate, followed by phenol/chloroform extraction, and prepared for RNA sequencing.
Poly(A)+ RNA was selected by oligo-dT magnetic beads, and prepared for paired end RNA sequencing using Illumina paired end sequencing primers.

value: 2 g/kg dox

tag: time point

value: 72 hours


title: Celf1heart_24h_A3277

value: 24 hours


title: Celf1heart_24h_A3262


title: Celf1heart_72h_A3281


title: Celf1heart_7dy_A3345

value: 7 days


title: Celf1heart_7dy_A3283


title: Celf1heart_72h_A3264


title: Input control C

description: Input control

value: C


title: Celf1heart_12h_A3276

value: 12 hours


title: H3K4me1_TconvRA- D

description: Chromatin IP against H3K4me1

source_name: CD4+CD25-CD45RA- expanded memory conventional T cells

value: H3K4me1 (abcam ab 8895)

tag: chip antibody manufacturer

value: abcam

tag: chip antibody catalog #


title: Celf1heart_7dy_A3269

tag: treatment


title: H3K4me1_TconvRA- C

description: Chromatin IP against H3K4me1

value: CD4+CD25-CD45RA- expanded memory conventional T cells


title: Rag2 -/- H3K4me1 ChIP-Seq biorep 1

description: Sample 5

tag: strain

value: 5-6 weeks

tag: genotype/variation

value: 2 µg

value: Protein G dynabeads


title: Sample 39c

city: Baltimore

first: Sean

last: Daugherty

state: Maryland

address: 801 W. Baltimore St.

department: Institute for Genome Sciences

institute: University of Maryland School of Medicine

description: Ehrlichia chaffeensis West Paces strain-infected Ixodes tick cells

data_processing:
Base calls were performed using the bulit in Illumina basecaller.
Sequenced reads were mapped to the Canis lupus familiaris and Ixodes scapularis genomes using TopHat v. 1.4 and to the Ehrlichia chaffeensis genomes using Bowtie v. 0.12.9
RPKM values were calculated for the genes present in the Canis lupus familiaris, Ixodes scapularis and Ehrlicha chaffeensis genomes.
Genome_build: Canis lupus familiaris v. 3.1.71, Ixodes scapularius v. 1.20
Supplementary_files_format_and_content: Tab-delimted files report RPKM values.

organism: Ehrlichia chaffeensis str. West Paces

source_name: Ehrlichia (West Paces) in Ixodes tick cell line ISE6

growth_protocol: All Ehrlichia strains were cultured in DH82 canine cells (37°C 5%CO2 in DMEM medium supplemented with 2% L-Glutamine and 10% FBS), or ISE6 tick cells (34°C in L15C300 medium). No antibiotics were used.

extract_protocol:
Total RNA were extracted from E. chaffeensis-infected DH82 or ISE6 cells using RNeasy (Qiagen) with on-column DNase and bacterial mRNA were enriched by removing host and bacterial rRNA with Ribozero kits and subtracting polyA-RNA with Dynabeads.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: ehrlichia strain

value: West Paces

tag: host cell

value: Ixodes scapularis

tag: infectivity

tag: assayed molecule

value: mRNA


title: Celf1heart_24h_A3254


title: Celf1heart_12h_A3252


title: Sample 39b


title: H3K4me1_TregRA- D

description: Chromatin IP against H3K4me1

source_name: CD4+CD25+CD45RA- expanded memory regulatory T cells

value: D


title: Celf1heart_12h_A3258


title: Sample 39a


title: Celf1heart_ctl_A3280

value: MHCrtTA


title: Sample 29c

description: Ehrlichia chaffeensis West Paces strain-infected DH82 cells

source_name: Ehrlichia (West Paces) in canine cell line DH82

value: Canis lupus familiaris


title: H3K27ac_TconvRA- D

description: Chromatin IP against H3K27ac

value: H3K27ac (abcam ab 4729)


title: Celf1heart_ctl_A3259

value: 2 g/kg dox

value: 72 hours


title: Sample 29b


title: Celf1heart_ctl_A3250


title: H3K27ac_TconvRA- C

description: Chromatin IP against H3K27ac

value: C


title: Sample 29a


title: H3K27ac_TregRA- D

description: Chromatin IP against H3K27ac

value: CD4+CD25+CD45RA- expanded memory regulatory T cells


title: RMWT_227

city: Houston

first: deqiang

last: sun

state: TX

address: 2121 W Holcombe Blvd

institute: Texas A&M University

data_processing: Reads are mapped to genome using ELAND. Reads that are uniquely mapped and have no more than 2 mismatches are selected for future analysis. MACS is used to call peaks with p value 1e-10.

extract_protocol: Genomic DNA were extracted from the cells and fragmented via nebulization. The fragmented DNA was end polished and ligated with Illumina methylated PE adaptors followed by Chip treatments of RxRa and Pol II respectively. Sizes between 200 bp (including the adaptors) were selected and sequenced with the Illumina Genome Analyzer II.

tag: tissue type

value: liver

value: wildtype

tag: gender

value: male

tag: antibody

value: RXRa (D-20)

tag: antibody manufacturer

value: Santa Cruz Biotechnology

tag: antibody catalog number


title: PMWT_227

value: Pol II (8WG16)


title: Input

description: Input

source_name: Input

value: none, input


title: H3K4me1_TconvRA+ C

description: Chromatin IP against H3K4me1

source_name: CD4+CD25-CD45RA+ expanded naive conventional T cells

tag: donor

tag: cell type

value: H3K4me1 (abcam ab 8895)

value: abcam


title: Sample 18c

value: West Paces

value: Ixodes scapularis

value: total RNA


title: Sample 18a


title: RMWT_315


title: Sample 9c

value: Canis lupus familiaris


title: Sample 18b


title: H3K4me1_TregRA+ D

description: Chromatin IP against H3K4me1

source_name: CD4+CD25+CD45RA+ expanded naive regulatory T cells

value: D

tag: chip antibody


title: H3K27ac_TregRA- C

description: Chromatin IP against H3K27ac

value: H3K27ac (abcam ab 4729)

tag: chip antibody manufacturer


title: Sample 9b


title: H3K4me1_TregRA+ C

description: Chromatin IP against H3K4me1

value: C

value: CD4+CD25+CD45RA+ expanded naive regulatory T cells

tag: chip antibody catalog #


title: Sample 9a


title: PMWT_315

value: liver


title: H3K27ac_TconvRA+ D

description: Chromatin IP against H3K27ac

value: CD4+CD25-CD45RA+ expanded naive conventional T cells


title: PFWT_235

value: wildtype

value: female


title: RFWT_234

value: RXRa (D-20)

value: Santa Cruz Biotechnology


title: Sample 32c

description: Ehrlichia chaffeensis Arkansas strain-infected Ixodes tick cells

organism: Ehrlichia chaffeensis str. Arkansas

source_name: Ehrlichia (Arkansas) in Ixodes tick cell line ISE6

value: Arkansas

value: mRNA


title: H3K27ac_TconvRA+ C

description: Chromatin IP against H3K27ac

value: abcam


title: Sample 32b


title: PFWT_234

value: Pol II (8WG16)


title: H3K27ac_TregRA+ D

description: Chromatin IP against H3K27ac


title: H3K4me1_TconvRA+ D

description: Chromatin IP against H3K4me1

value: H3K4me1 (abcam ab 8895)


title: Sample 32a

value: Ixodes scapularis


title: RMKO_314

value: male


title: H3K27ac_TregRA+ C

description: Chromatin IP against H3K27ac


title: H3K4me1_TregRA- C

description: Chromatin IP against H3K4me1

value: CD4+CD25+CD45RA- expanded memory regulatory T cells


title: Sample 22c

description: Ehrlichia chaffeensis Arkansas strain-infected DH82 cells

source_name: Ehrlichia (Arkansas) in canine cell line DH82

value: Canis lupus familiaris


title: ETS1_TregRA+ A

description: Chromatin IP against ETS1

value: A

value: ETS1 (Santa Cruz sc-350x)

value: Santa Cruz


title: RFWT_235

value: liver


title: PMKO_225


title: PMKO_314


title: FOXP3_TregRA+ A

description: Chromatin IP against FOXP3

value: CD4+CD25+CD45RA+ expanded naive regulatory T cells

value: FOXP3 (Novus NB600-245)

value: Novus


title: RMKO_225

value: RXRa (D-20)

value: Santa Cruz Biotechnology


title: Input control B

description: Input control

source_name: Input control

value: B

value: Input control

value: no antibody


title: Input control A

description: Input control


title: Sample 22a

value: Arkansas

value: mRNA


title: RFKO_233

value: female


title: Sample 11b

value: Ixodes scapularis

value: total RNA


title: STAT5_Tconv B

description: Chromatin IP against STAT5

source_name: CD4+CD25- expanded conventional T cells

value: CD4+CD25- expanded conventional T cells

value: STAT5 (Santa Cruz sc-836x)


title: Sample 11a


title: RFKO_232


title: PFKO_233

value: Pol II (8WG16)


title: PFKO_232

value: liver


title: STAT5_TregRA+ A

description: Chromatin IP against STAT5

value: A

value: CD4+CD25+CD45RA+ expanded naive regulatory T cells

value: Santa Cruz


title: Sample 2a

value: Canis lupus familiaris


title: Sample 2b


title: Actively Growing Vascular Cambium

status: Public on Mar 31 2014

city: Beijing

first: Jinxing

last: Lin

address: No.20 Nanxincun, Xiangshan

institute: Institute of botany

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, then mapped to transcriptome using SOAPaligner/soap2 with and mismatches of only 1 bp were considered
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi et al., Nucleic Acids Research, 2008. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: C. lanceolata transcriptome
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Cunninghamia lanceolata

source_name: actively growing vascular cambium

growth_protocol: ~16 years old, 15 m tall, 12 cm in diameter) growing under natural conditions

extract_protocol: After extracting the total RNA from dormant, reactivating and actively growing vascular cambium of C.  lanceolata using tangential cryosections, mRNA of eukaryotes is enriched by using the oligo(dT) magnetic beads and mRNA of prokaryotes  is enriched just by removing rRNAs from the total RNA. Adding the  fragmentation buffer, the mRNA is interrupted to short fragments  (about 200 bp), then the first strand cDNA is synthesized by random  hexamer-primer using the mRNA fragments as templates. Buffer, dNTPs,  RNase H and DNA polymerase I are added to sythesize the second strand. The double strand cDNA is purified with QiaQuick PCR extraction kit and washed with EB buffer for end repair and single nucleotide A  (adenine) addition. Finally, sequencing adaptors are ligated to the fragments. The required fragments is purified by agrose gel electrophoresis and enriched by PCR amplification. The library products are ready for sequencing analysis via Illumina HiSeq 2000.

tag: tissue

value: vascular cambium

tag: Stage

value: active

tag: age

value: 16 years old


title: Dormant Growing  Vascular Cambium

source_name: dormant growing  vascular cambium

value: dormant


title: Reactivating Growing  Vascular Cambium

source_name: reactivating growing  vascular cambium

value: reactivating growing


title: Sample 22b

tag: ehrlichia strain

value: Arkansas

value: mRNA


title: Sample 11c

tag: host cell

value: Ixodes scapularis


title: R008_45gl

city: Padova

first: Stefano

last: Campanaro

address: Via Ugo Bassi 58/b

department: Biology

country: Italy

institute: University of Padua

description: vineyard strain (wild type) R008

data_processing:
SOLiD reads were aligned using PASS software; only those uniquely aligned on the genome were considered
The number of reads aliged on each gene for each strain and sample was determined using a self-written perl script and an input file for DEGseq was generated
Differentially expressed genes were determined using DEGseq software 2.11.1
Genome_build: Saccharomyces cerevisiae sacCer2.61
Supplementary_files_format_and_content: tab-delimited text file includes the RKPM value for each strain and sample normalized considering S288c sample at middle exponential phase (6 g/l of CO2 produced) as a reference and considering the total number of reads aligned for each experiment

organism: Saccharomyces cerevisiae

source_name: Yeast culture

growth_protocol: Yeast cultures were grown in 100 ml YPD medium at 25 °C in agitation for 18 hours. Each culture have been centrifuged and the pellet was resuspended into the volume of synthetic must MS300 required to obtain an OD600 of 0.5 of the 1:10 diluted solution (5x10^6 cells/ml). 100 ml of this pre-inoculum have been added to 900 ml of MS300, a synthetic medium that mimics the composition of a white wine must. Fermentation was performed at 25°C in 1 l bioreactors (Multifors, Infors HT) monitoring the temperature, the pH, and the CO2 flux in a range of 1-20 ml/min (red-y mod. GSM-A95A-BN00). Yeast cells were collected at two different steps of the fermentation curve: at the beginning of the process, when the CO2 produced by the cells was 6 g/l (middle exponential growth phase), and in the middle of fermentation, at 45 g/l (early stationary phase).

extract_protocol: For total RNA extraction we used the "PureLink  RNA Mini Kit" (life technologies). Starting from 10 μgs of total RNA, 18S and 26S rRNAs were removed using the RiboMinusTM Transcriptome Isolation Kit (Invitrogen). RNA molecules were decapped with the TAP enzyme (Wako Chemicals) resuspending the samples of purified total RNA into 12 μl of water and adding the 5X TAP buffer plus 10 U of TAP enzyme and incubating the reaction at 37°C for 40 minutes. Genomic DNA was removed using the DNA-free™ kit from Applied Biosystems. The RNA was used to prepare the libraries using the SOLiD 4 Whole Transcriptome Analysis Kit protocol.

tag: strain

tag: carbon dioxide produced before cell collection [g/l]


title: P301_45gl

description: vineyard strain (wild type) P301


title: P301_6gl

description: vineyard strain (wild type) P301


title: P283_6gl

description: vineyard strain (wild type) P238


title: R008_6gl

description: vineyard strain (wild type) R008


title: R103_6gl

description: vineyard strain (wild type) R103


title: Sample 2c

tag: infectivity

tag: assayed molecule

value: total RNA


title: EC1118_6gl

description: enological strain EC1118


title: EC1118_45gl

description: enological strain EC1118


title: hybrid_FP2

city: Los Angeles

first: Frank

middle: Wolfgang

last: Albert

state: CA

address: 695 Charles E. Young Drive South

department: Human Genetics

institute: UCLA

description: ribosomal footprints

data_processing:
Bases were called using Bustard
Sequences were adaptor-trimmed and the first base removed
Trimmed reads were aligned to the yeast genome using bwa
alignments were filtered to allow only unique alignment positions
reads were counted, either within ORFs (using the htseq-count script) or at SNP alleles. For the later, only reads that matched the BY or RM allele perfectly (without mismatches) were considered further
for statistical analyses, counts were downscaled to the smallest library size
Genome_build: sacCer3
Supplementary_files_format_and_content: we provide txt files with the raw counts at SNP alleles for all samples. For the hybrid data, there are two columns, one for the BY and one for the RM allele. For parental data, there is only one column with counts for the given strain. For parental samples, we also provide txt files with the number of counts for all reads mapping to a given ORF.

source_name: exponentially growing culture

growth_protocol: yeast were grown in YNB media and extracted from mid-log growth cultures

extract_protocol: procedues were as described in Ingolia et al., 2009

treatment_protocol: mRNA samples were flash-frozen, ribosomal footprint samples were treated with cycloheximide to block translation

value: BY/RM


title: hybrid_FP1

description: ribosomal footprints


title: RM_mRNA

description: mRNA

value: RM


title: BY_FP

description: ribosomal footprints

value: BY


title: RM_FP

description: ribosomal footprints


title: R103_45gl

description: vineyard strain (wild type) R103


title: BY_mRNA

description: mRNA


title: Human_AS_13

first: Liu

last: He

address: 320 Yue Yang Road

institute: PICB

data_processing:
Illumina Casava1.7 software used for basecalling, and only the ones passing illumina quality controls were retained.
Reads were mapped onto correponding reference genomes (hg19, panTro3) by Tophat-1.4.1, with parameters: -a 8 -m 2 no-coverage-search microexon-search segment-mismatches 3 segment-length 25.
We made a reciprocal lift-over between chimpanzee and human (Ensembl annotation v. 69, coding exons only), and used only exons that could be lift-overed to calculate RPKMs for each gene.
Then quantile normalization was applied, and each gene was z-transformed.
Genome_build: hg19, panTro3
Supplementary_files_format_and_content: tab-delimited text files including expression measurements for each gene from each sample.

source_name: Prefrontal Cortex

extract_protocol:
Total RNA was isolated using Trizol reagent (Cat. No. 15596-026, Invitrogen). The libraries were constructed from the isolated total RNA according to the "TruSeq RNA Sample Preparation Kit" protocol (www.illumina.com) without modification. As the protocol includes the procedure of enrichment for the mRNA, an additional polyA selection was not necessary.
RNA libraries were prepared for sequencing using Illumina TruSeq protocols

value: Prefrontal Cortex

tag: organism

value: human


title: Human_AF_12


title: Human_EU_14


title: Human_EU_11


title: Human_AS_10


title: 35S>>amiRSlDCL3-2

city: Bet Dagan

first: Tzahi

last: Arazi

state: ISRAEL

address: Institute of Plant Sciences, ARO the Volcani Center

department: Institute of Plant Sciences

country: Israel

institute: ARO - Volcani Center

description: Sample 4

data_processing:
The Cache ASsisted Hash Search with Xor logic (CASHX) Pipeline (release 2.3)  was used to parse and map the small sequences to the tomato genome SGN release version SL2.40
Reads in the size range of 18-26 nts and perfectly matched to the tomato genome were retained.
The small RNA CASHX database was annotated with the Repeats Master version 5.0 (ftp://ftp.solgenomics.net/tomato_genome/repeats/), Plant snoRNAs Database (version 1.2; http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home), SILVA rRNA database (http://www.arb-silva.de/), miRbase (release 19)http://www.mirbase.org/) ;
After annotation, only “clean” reads not matching tRNAs, rRNAs, snRNA and SnoRNA were used for further analysis.
Genome_build: tomato genome (SGN release version SL2.40; http://solgenomics.net/organism/Solanum_lycopersicum/genome)
Supplementary_files_format_and_content: Tab delimited values (txt) files include RPM values for each Sample

organism: Solanum lycopersicum

growth_protocol: growth chamber with a 16 h light period and 8 h dark period 24 °C

extract_protocol:
Tri-reagent extraction
Total RNA samples were used to construct small RNA libraries using the TruSeq small RNA kit as described by the manufacturer (Illumina, San Diego, CA, USA).

tag: cultivar

tag: genotype/variation

value: SlDCL3 silenced (35S>>amiRSlDCL3)

value: 14 days after sowing

value: Seedlings shoots


title: hybrid_mRNA2

description: mRNA


title: Human_AS_9


title: 35S>>amiRSlDCL3-1

description: Sample 3


title: hybrid_mRNA1

description: mRNA


title: S288c_6gl

description: laboratory strain S288c


title: P283_45gl

description: vineyard strain (wild type) P238


title: BP-53 CTC

city: Boston

first: Ben

middle: S.

last: Wittner

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

data_processing:
Helicos Digital Gene Expression pipeline. Pubmed ID 19581875
Genome_build: mm9
Supplementary_files_format_and_content: matrix of aligned read counts, rownames are UCSC knownGene transcript IDs or gene symbols and are specified in GEO GPL14759, column names are sample IDs.

source_name: blood enriched for circulating tumor cells

extract_protocol:
Blood samples were collected from mice with high tumor burden following tamoxifen injection. Blood from each mouse was split and processed through the CTC-chips functionalized with anti-CSPG4/MCAM antibody and control IgGs, respectively. Matched primary (from the tamoxifen injection site) and metastatic (from upper or lower back) tumors were harvested from the same mouse and immediately flash-frozen in liquid nitrogen. RNA extraction and single molecular sequencing was described previously in PMID: 22763454)
Qiagen RNeasy MinElute kit followed by Helicos single molecule sequencing: Pubmed ID 18388294, 20133332

tag: strain background

value: BRAF(CA/+)/PTEN(flox/flox)

tag: induced with

value: tamoxifen (focal subcutaneous injection)


title: S288c_45gl

description: laboratory strain S288c


title: 35S:LhG4-2 (control)

description: Sample 2

value: control (35S:LhG4)


title: Human_AF_8


title: 35S:LhG4-1 (control)

description: Sample 1


title: Human_AS_7


title: Human_AF_6


title: Human_AS_5


title: BP-55 IgG

source_name: blood

value: blood


title: Human_EU_4


title: BP-55 CTC

value: blood enriched for circulating tumor cells


title: BP-73 CTC


title: Chimpanzee_6

organism: Pan troglodytes

value: chimpanzee


title: BP-73 IgG


title: Human_EU_3


title: Chimpanzee_5


title: Human_AF_2


title: Chimpanzee_4


title: Chimpanzee_3


title: Chimpanzee_2


title: BP-53 mets

source_name: melanoma metastases

value: melanoma metastases


title: BP-55 mets


title: Chimpanzee_1


title: BP-58 mets


title: BP-73 mets


title: BP-72 IgG


title: BP-53 IgG


title: Spo11_5h_IP

city: Suita

first: Masaru

last: Ito

state: Osaka

address: Yamadaoka 3-2

country: Japan

institute: Osaka University

description: Used baseline: WCE at 5h after meiotic induction (SPO11-FLAG cells)

data_processing:
Sequence reads were filtered and end-trimmed using FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). The reads containing tag sequences were removed using tagdust (Lassmann et al. 2009).
The resulting reads were mapped to the S. cerevisiae genome (sacCer2 and SK1) using bowtie with default settings, except for the option “–n 3” (Langmead et al. 2009).
To calculate DNA enrichment (IP/input), the chromosomes were divided into 10-bp bins. Counting of reads in each bin and normalization were performed using parse2wig with the options “-binsize 10 -F3 47 -flen 150” (Nakato et al. 2013). The values of DNA enrichment of each bin were calculated as the average within a 600 bp window.
Peak calling was performed using drompa (Nakato et al. 2013) with the options “-sw 300 -binsize 10 -ipm 1 -divide -ethre 1.2”.
Genome_build: sacCer2 (Rec8 and Spo11) and SK1 (Rec8 and Gal4BD-Spo11)
Supplementary_files_format_and_content: bedGraph files. Scores represent DNA enrichment (IP/input).

source_name: Spo11-FLAG ChIP at 5h after meiotic induction

growth_protocol: Cells were grown on a YPD plate for 2 days at 30ºC. The cells were grown to a density of 4.0x10e7 cells/ml at 30ºC in presporulation medium (SPS; 0.5% yeast extract, 1% peptone, 0.17% yeast nitrogen base w/o amino acid and ammonium sulfate, 1% potassium acetate, 0.5% ammonium sulfate, usual level of amino acids, 50 mM potassium phthalate, and antifoam, pH 5.5). The cells were suspended in sporulation medium (SPM; 1% potasium acetate, 1/5 levels of amino acids, and polypropylene glycol) to a density of 2x10e7 cells/ml, and incubated at 30ºC for sporulation.

extract_protocol:
The cells were disrupted using Multi-Beads Shocker (YASUI KIKAI, Osaka) with 0.5-mm zirconia beads. Cell lysates were sonicated to obtain average 300 bp of genomic DNA fragments. Whole cell extracts (WCEs) were subjected to immunoprecipitation with anti-FLAG antibody (Wako) coupled to Dynabeads protein A (Invitrogen). A small amount of WCEs was used as input sample. The chromatin immunoprecipitated sample and input sample were incubated overnight at 65ºC, incubated for 2 hours at 50ºC with proteinase K, and DNA was purified using QIAquick Spin Purification Kit (QIAGEN).
Before library preparation, IP DNA and input DNA were fragmented to 150 bp using the covaris model S220. Multiplexed DNA library preparation was performed with the NEBNext ChIP-Seq library prep master mix set for Illumina (P/N E6240S, NEB) and the NEBNext multiplex oligos for Illumina (P/N E7335S, NEB). After 15 cycles of PCR amplification, about 275 bp libraries were obtained. The libraries were sequenced on the MiSeq with the MiSeq Reagent Kit v2 (50-cycles).

treatment_protocol: The cells were fixed in 1% formaldehyde for 10 min at room temperature and then treated with 125 mM glycine for 5 min at room temperature. The cells were washed with ice-cold TBS twice, freezed with liquid nitrogen, and stored at -80ºC.

tag: culture

value: 5h after transfer to sporulation medium (SPM)


title: BP-55 primary

source_name: primary melanoma tumor

value: primary melanoma tumor


title: BP-72 mets


title: Spo11_3h_IP

description: Used baseline: WCE at 3h after meiotic induction (SPO11-FLAG cells)

source_name: Spo11-FLAG ChIP at 3h after meiotic induction

value: 3h after transfer to sporulation medium (SPM)


title: input_4h

description: Baseline of ChIP sample at 4h after meiotic induction

source_name: WCE at 4h after meiotic induction (RED1-FLAG cells)

value: 4h after transfer to sporulation medium (SPM)


title: Gal4BDSpo11_0h_IP

description: Used baseline: WCE at 0h after meiotic induction (GAL4BD-SPO11-FLAG cells)

source_name: Gal4BD-Spo11-FLAG ChIP at 0h after meiotic induction

value: 0h after transfer to sporulation medium (SPM)


title: BP-58 primary


title: input_3h

description: Baseline of ChIP sample at 3h after meiotic induction

source_name: WCE at 3h after meiotic induction (SPO11-FLAG cells)


title: Human_EU_1

value: Prefrontal Cortex


title: BP-72 primary


title: input_5h

description: Baseline of ChIP sample at 5h after meiotic induction

source_name: WCE at 5h after meiotic induction (SPO11-FLAG cells)


title: input_0h

description: Baseline of ChIP sample at 0h after meiotic induction

source_name: WCE at 0h after meiotic induction (GAL4BD-SPO11-FLAG cells)


title: BP skin

source_name: skin

value: BP

value: wild type

value: skin


title: BP-73 primary


title: Spo11_4h_IP

description: Used baseline: WCE at 4h after meiotic induction (RED1-FLAG cells)

source_name: Spo11-FLAG ChIP at 4h after meiotic induction


title: BP-72 CTC


title: Rec8_GAL4BDSPO11_4h_IP

source_name: Rec8-FLAG ChIP in GAL4BD-SPO11 cells at 4h after meiotic induction


title: Rec8_4h_IP

source_name: Rec8-FLAG ChIP at 4h after meiotic induction


title: BP-53 primary


title: tongue_infected_Candida_day5.rep1

status: Public on Mar 30 2014

first: Amol

middle: Carl

last: Shetty

address: 670 W. Baltimore Street, Floor 3

institute: University of Maryland Baltimore

data_processing:
Base calls were performed using the built-in Illumina basecaller
Sequenced reads were trimmed for adaptor sequence, and then mapped to Mouse (GRCm38.70 + NT_096355 + NT_095534) whole genome reference using TopHat v1.4.0 and/or C. albicans SC5314 using Bowtie v0.12.9
Reads Per Kilobase of gene per Million mapped reads (RPKM) were calculated for each sample.
Differential expression of genes were computed between infected and uninfected samples
Genome_build: M.musculus (GRCm38.70 + NT_096355 + NT_095534), C. albicans (sc5314)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

organism:
Candida albicans
Mus musculus

source_name: Tongue

growth_protocol: C. albicans cells were either injected into the tail vein of a mouse or swabbed onto the tongue of a anesthetized mouse.

extract_protocol:
RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit (Cat#74104)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: mouse strain

value: BALB/c

tag: candida strain background

tag: strain genotype/variation

value: Tongue

tag: timepoint

value: infected -Day5


title: tongue_infected_Candida_day5.rep2

tag: tissue


title: 8h-OKF6.control-Candida.WO1.rep2

description:
SRX124614
55_8h_c_w

data_processing:
Base calls were performed using the built-in Illumina basecaller
Sequenced reads were trimmed for adaptor sequence, and then mapped to Human GRCh38 whole genome reference and/or C. albicans SC5314 or WO1 reference using TopHat v1.4.0
Reads Per Kilobase of gene per Million mapped reads (RPKM) were calculated for each sample.
Differential expression of genes were computed between infected and uninfected samples
Genome_build: H. sapiens (GRCh38), C. albicans (sc5314; GCF_000182965.2), C. albicans (wo1; GCA_000149445.2)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

organism: Candida albicans

source_name: mock infected

growth_protocol: C. albicans cells were used to infect HUVEC cells or OKF6-TERT2 cells in tissue culture media for the indicated amount of time at 37 degrees celcius. The negative control samples were the host or C. albicans cells alone in tissue culture media for the indicated amount of time.

extract_protocol:
RNA extractions were performed using RiboPure RNA Purification Kit, yeast (Life Technologies, AM1926) following manufacturer's protocols
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: candida strain

tag: infected human culture

value: none (C. albicans cells alone in tissue culture media)

tag: time point

value: 8 hours


title: 5h-OKF6.control-Candida.WO1.rep2

description:
SRX124511
52_5h_c_w

value: 5 hours


title: tongue_infected_Candida_day3.rep2

value: infected -Day3


title: tongue_infected_Candida_day3.rep1


title: 90m-OKF6.control-Candida.WO1.rep2

description:
SRX124509
50_90m_c_w

value: 90 minutes


title: tongue_infected_Candida_day2.rep2

value: infected -Day2


title: 8h-HUVEC.control-Candida.WO1.rep2

description:
SRX124507
48_8h_c_w


title: tongue_infected_Candida_day2.rep1


title: tongue_infected_Candida_day1.rep1

value: infected- Day1


title: 5h-HUVEC.control-Candida.WO1.rep2

description:
SRX124504
45_5h_c_w


title: tongue_infected_Candida_day1.rep2


title: 90m-HUVEC.control-Candida.WO1.rep2

description:
SRX124502
43_90m_c_w


title: 8h-HUVEC.control-Candida.SC5314.rep2

description:
SRX123788
34_8h_c


title: 90m-OKF6.control-Candida.SC5314.rep2

description:
SRX123790
36_90m_c


title: kidney_infected_rim101∆_Candida_24h.rep1

source_name: Kidney

value: Kidney

value: 24 Hours


title: 90m-HUVEC.control-Candida.SC5314.rep2

description:
SRX123789
29_90m_c


title: kidney_infected_rim101∆_Candida_24h.rep2


title: 5h-OKF6.control-Candida.SC5314.rep2

description:
SRX123792
38_5h_c


title: kidney_infected_Candida_48h.rep2

value: 48 Hours


title: kidney_infected_ahr1∆_Candida_24h.rep1


title: 8h-OKF6.control-Candida.SC5314.rep2

description:
SRX124478
41_8h_c


title: kidney_infected_orf19.4342∆_Candida_24h.rep2


title: 5h-HUVEC.control-Candida.SC5314.rep2

description:
SRX123784
31_5h_c


title: 5h-OKF6.control-Candida.WO1.rep1

description:
SRX123589
24_5h_c_w


title: kidney_infected_ahr1∆_Candida_24h.rep2


title: kidney_infected_orf19.4342∆_Candida_24h.rep1


title: 8h-OKF6.control-Candida.WO1.rep1

description:
SRX123781
27_8h_c_w


title: kidney_infected_Candida_48h.rep1


title: 90m-OKF6.control-Candida.WO1.rep1

description:
SRX123587
22_90m_c_w


title: kidney_infected_Candida_24h.rep2


title: kidney_infected_Candida_24h.rep1


title: 8h-HUVEC.control-Candida.WO1.rep1

description:
SRX123585
20_8h_c_w


title: kidney_infected_Candida_12h.rep2

value: 12 Hours


title: 5h-HUVEC.control-Candida.WO1.rep1

description:
SRX123582
17_5h_c_w


title: 90m-HUVEC.control-Candida.WO1.rep1

description:
SRX123453
15_90m_c_w


title: 8h-OKF6.control-Candida.SC5314.rep1

description:
SRX123450
13_8h_c


title: kidney_infected_Candida_6h.rep2

value: 6 Hours


title: 8h-HUVEC.control-Candida.SC5314.rep1

description:
SRX123448
11_8h_c


title: kidney_infected_Candida_6h.rep1

value: wild type


title: 5h-OKF6.control-Candida.SC5314.rep1

description:
SRX124667
8_5h_c


title: 5h-HUVEC.control-Candida.SC5314.rep1

description:
SRX124664
5_5h_c


title: 8h-OKF6.infected-Candida.WO1.rep2

description:
SRX124615
56_8h_co_w

organism:
Candida albicans
Homo sapiens

source_name: okf6 infected


title: 5h-OKF6.infected-Candida.WO1.rep2

description:
SRX124513
53_5h_co_w


title: 8h-HUVEC.infected-Candida.WO1.rep2

description:
SRX124508
49_8h_ch_w

source_name: huvec infected

value: HUVEC


title: 90m-OKF6.infected-Candida.WO1.rep2

description:
SRX124510
51_90m_co_w


title: 90m-OKF6.control-Candida.SC5314.rep1

description:
SRX124621
3_90m_c


title: 90m-HUVEC.infected-Candida.WO1.rep2

description:
SRX124503
44_90m_ch_w


title: 90m-HUVEC.control-Candida.SC5314.rep1

description:
SRX124620
1_90m_c


title: 8h-HUVEC.infected-Candida.SC5314.rep2

description:
SRX123787
35_8h_ch


title: uninfected_tongue_day5.rep2

value: BALB/c

value: uninfected- Day5


title: uninfected_tongue_day5.rep1

value: Tongue


title: 90m-OKF6.infected-Candida.SC5314.rep2

description:
SRX123791
37_90m_co


title: 90m-HUVEC.infected-Candida.SC5314.rep2

description:
SRX123783
30_90m_ch


title: 5h-HUVEC.infected-Candida.WO1.rep2

description:
SRX124505
46_5h_ch_w


title: 5h-HUVEC.infected-Candida.SC5314.rep2

description:
SRX123785
32_5h_ch


title: uninfected_tongue_day3.rep1

value: uninfected- Day3


title: uninfected_tongue_day2.rep2

value: uninfected- Day2


title: 90m-OKF6.infected-Candida.WO1.rep1

description:
SRX123588
23_90m_oc_w


title: uninfected_tongue_day2.rep1


title: kidney_infected_Candida_12h.rep1


title: 8h-HUVEC.infected-Candida.WO1.rep1

description:
SRX123586
21_8h_hc_w

value: 8 hours


title: uninfected_tongue_day1.rep2

value: uninfected- Day1


title: 5h-HUVEC.infected-Candida.WO1.rep1

description:
SRX123583
18_5h_hc_w

value: 5 hours


title: 5h-OKF6.infected-Candida.SC5314.rep2

description:
SRX123793
39_5h_co


title: 8h-OKF6.infected-Candida.SC5314.rep2

description:
SRX124501
42_8h_co


title: uninfected_kidney.rep1

value: 0 (uninfected)


title: 8h-OKF6.infected-Candida.WO1.rep1

description:
SRX123782
28_8h_oc_w


title: 8h-OKF6.infected-Candida.SC5314.rep1

description:
SRX123451
14_8h_oc


title: uninfected_tongue_day3.rep2


title: 8h-HUVEC.infected-Candida.SC5314.rep1

description:
SRX123449
12_8h_hc


title: 90m-OKF6.infected-Candida.SC5314.rep1

description:
SRX124660
4_90m_oc

value: 90 minutes


title: 5h-HUVEC.infected-Candida.SC5314.rep1

description:
SRX124665
6_5h_hc


title: 5h-OKF6.infected-Candida.SC5314.rep1

description:
SRX124668
9_5h_oc


title: chr11-1 chr17-1

city: shanghai

first: yijing

last: zhang

address: 2005 Songhu Road

department: Biochemistry

institute: Fudan University

description: iswi seedling

data_processing:
Illumina Casava1.8.2 software used for basecalling.
The beginning 8 bases with irregular GC content and the ending 5 bases with low sequencing quality were removed based on FastQC result
Trimmed reads were mapped to TAIR10 genome assembly using BOWTIE2 with default settings
Reads with low mapping quality (MAPQ < 20) were removed;only one copy of read was kept for duplicated reads
Each read was shifted 75 bp from 5’ to 3’ end.
Nucleosome positions were identified using the Template Filter software
Genome_build: TAIR10
Supplementary_files_format_and_content: wig file was generated with binsize = 100, step_size = 5, span = 5

organism: Arabidopsis thaliana

source_name: AtISWI mutant

growth_protocol: 16 h light, 8 h dark, 21-22°C

extract_protocol:
For nuclear extraction, two-week-old Arabidopsis seedlings without roots were ground to ﬁne powder in liquid nitrogen and resuspended in the lysis buffer (50 mM HEPES pH7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 10% glycerol, 10 mM β-mercaptoethanol and Protease Inhibitor Cocktail, Roche). After lysis for about half an hour, the lysis mixture were filtered through 40 μm cell strainer (BD). The filtered plant extracts were centrifuged for 20 min at 3,200 g to obtain the nuclei pellet. Isolated nuclei were washed each time with HBB buffer (25 mM Tris-Cl pH 7.6, 0.44 M sucrose, 10 mM MgCl2, 0.1% Triton-X and 10 mM β-mercaptoethanol) and HBC buffer (25 mM Tris-Cl pH 7.6, 25 mM Tris-Cl pH 7.6, 440 mM sucrose, 10 mM MgCl2, 0.1% Triton-X, 10 mM β-mercaptoethanol and 20% glycerol). The nuclei were resuspended with 100 μl HBC buffer and flashed frozen in liquid nitrogen.
(1) Perform End Repair. Prepare the following reaction mix: 85 μl of Eluted DNA and 5 μl of Enzyme mixture. Incubate in the thermal cycler for 30 minutes at 20 °C. Purify production with qiaquick or minelute. (2) Add “A” Bases to the 3' End of the DNA Fragments. Prepare the following reaction mix: 32 μl of DNA sample, 5 μl of NEBbuffer2, 10 μl of 1 mM dATP, 3 μl of Klenow exo (3’ to 5’ exo minus). The total volume should be 50 μl. Incubate for 30 minutes at 37 °C. Purify production with qiaquick or minelute. (3) Ligate Adapters to DNA Fragments. Prepare the following reaction mix: 37 μl of DNA sample + H2O, 5 μl of DNA ligase buffer, 3 μl of Adapter oligo mix, 5 μl of DNA ligase. The total volume should be 50 μl. Incubate for 60 minutes at 16 °C. Use a QIAGEN Qiaquick Kit (QIAGEN, part # 28104) to purify the DNA. (4) Enrich the Adapter-Modified DNA Fragments by PCR. Prepare the following PCR reaction mix: 36.5 μl of DNA sample + H2O, 10 μl of 5× Phusion buffer, 0.5 μl of Phusion*DNA polymerase, 1.25 μl of PCR primer, 1.25 μl of PCR primer 2.1, total 0.5 μl of 100 mM dNTP. The total volume should be 50 μl. Amplify using the following PCR protocol: 1 min at 98 °C, [10 seconds at 98 °C, 30 seconds at 60 °C, 30 seconds at 72 °C] for N cycles (dependent on the initial amount of DNA), 5 minutes at 72 °C, hold at 4 °C. Use a QIAGEN Qiaquick Kit (QIAGEN, part # 28104) to purify the DNA. Library construction was performed by Genergy Biotechnology (Shanghai) Co. LTD.

tag: cultivar/ecotype

value: AtISWI mutant

value: seedling


title: uninfected_kidney.rep2

value: Kidney


title: 5h-OKF6.infected-Candida.WO1.rep1

description:
SRX123779
25_5h_oc_w


title: 24hr-hRSV-infected

description:
intrument models: Illumina Hiseq 2000 and Illumina Genome Analyzer II
infected sample

data_processing:
Base calls were performed using the built-in Illumina basecaller
Sequenced reads were trimmed for adaptor sequence, and then mapped to Human GRCh37 whole genome reference using TopHat v1.4.0 and/or human respiratory syncytial virus (hRSV, AF035006) reference using Bowtie v0.12.9
Reads Per Kilobase of gene per Million mapped reads (RPKM) were calculated for each sample.
Differential expression of genes were computed between infected and uninfected samples
Genome_build: H. sapiens(GRCh37), hRSV(AF035006)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

organism:
Homo sapiens
human respiratory syncytial virus

source_name: human lung epithelial cell

growth_protocol: A549 cells infected with hRSV

extract_protocol:
Ambion miRVANA kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: cells collected by trypsinization; immediately put in Ambion reagent; stored at -80

tag: cell line


title: uninfected_tongue_day1.rep1

organism: Mus musculus


title: 16hr-hRSV-infected


title: 5h-OKF6.uninfected.sc.rep2

description:
SRX124473
40_5h_o

organism: Homo sapiens

source_name: okf6 uninfected

value: none (uninfected)


title: Col-0

description: WT seedling

source_name: WT

value: WT


title: 5h-HUVEC.uninfected.sc.rep2

description:
SRX123786
33_5h_h

source_name: huvec uninfected


title: 12hr-hRSV-infected


title: 5h-HUVEC.uninfected.wo.rep2

description:
SRX124506
47_5h_h_w


title: 5h-OKF6.uninfected.wo.rep2

description:
SRX124613
54_5h_o_w


title: 5h-OKF6.uninfected.wo.rep1

description:
SRX123780
26_5h_o_w


title: 90m-HUVEC.infected-Candida.SC5314.rep1

description:
SRX124619
2_90m_hc