title: 7Jvvs

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:
basecalled using Illumina software
aligned to bovine genome using Illumina ELAND software using bt4 genome and ensembl bovine annotation version 54
read counts for each sample were generated using Illumina CASAVA software
Reads per kilobase of exon per million mapped sequence reads (RPKM) was calculated.
Genome_build: Btau_4.0; Ensembl bovine genome annotation version 54
Supplementary_files_format_and_content: tab delimited text files give RPKM counts for each sample

organism: Bos taurus

source_name: day 7 blastocyst pool

growth_protocol: Synchronization of animals to collect in vivo-derived bovine embryos was carried out as previously described. Briefly, the estrous cycles of crossbred beef heifers (approximately 18 mo old, predominantly Charolais and Limousin cross; n 1⁄4 72) were synchronized using an 8-day Controlled Internal Drug Release (CIDR) device treatment (1.94 g progesterone; InterAg, Hamilton, New Zealand) with administration of a prostaglandin PGF2a analogue (Estrumate; Shering-Plough Animal Health; containing 0.5 mg cloprostenol) the day before CIDR removal to ensure complete regression of the corpus luteum. Animals were checked regularly, and only those heifers that came into standing estrus (Day 0) within a narrow window (36–48 h after CIDR removal) were used for the experiment. Based on our predicted embryo recovery rates at the different stages, heifers were assigned randomly to five experimental groups for embryo recovery on a specific day: group 1 (Day 7; n 1⁄4 9 animals), group 2 (Day 10; n 1⁄4 13), group 3 (Day 13; n 1⁄4 23), group 4 (Day 16; n 1⁄4 16), and group 5 (Day 19; n 1⁄4 15). In order to ensure sufficient numbers of blastocysts to work with on Day 7 and Day 10, the heifers assigned to those days were superovulated. Starting on Day 10 of the estrous cycle, heifers in groups 1 and 2 were superovulated with FSH given as twice-daily injections over 4 days, and luteolysis was induced with a second PG injection on Day 12, while heifers in groups 3, 4, and 5 were not superovulated. All heifers were kept under identical conditions and inseminated with semen from the same bull with proven fertility.

extract_protocol:
Day 7 and Day 10 blastocysts were pooled into groups of five, while individual conceptuses from Days 13, 16, and 19 were used for mRNA extraction. Polyadenylated mRNA was isolated from Day 7, Day 10, and Day 13 blastocysts/conceptuses by two rounds of selection using the Dynabeads mRNA DIRECT Kit (Invitrogen). However, for Day 16 and Day 19 conceptuses, initially total RNA was isolated using the TRIzol reagent (Invitrogen) per the manufacturer’s instructions. On-column DNase digestion and RNA cleanup was performed using an RNeasy Midi Kit (Qiagen) followed by two rounds of polyadenylated mRNA selection using Dynabeads mRNA DIRECT Kit (Invitrogen). Each developmental stage was represented by five biological replicates that were processed independently.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: In order to determine the precise temporal relationship between stages of conceptus development and transcript profiles, the key time points in development examined were Day 7 (blastocyst formation), Day 10 (posthatch- ing spherical conceptus), Day 13 (ovoid conceptus, initiation of elongation), Day 16 (filamentous conceptus, day of maternal recognition) and Day 19 (filamentous conceptus, initiation of implantation). Following slaughter on a given day, the reproductive tract of each heifer was recovered within 30 min of slaughter and placed on ice. Both uterine horns were flushed with 40 ml PBS supplemented with 3% fetal calf serum to recover the embryos. All embryos were washed in PBS and then immediately frozen at -80 degrees C with a minimum volume of PBS until processed for RNA extraction. Only morphologically intact blastocysts/conceptuses were selected and used.

tag: day

value: blastocyst

tag: superovulated

value: Yes

tag: pooled


title: 7Hvvs

status: Public on Apr 04 2014

type: SRA

library_source: transcriptomic

molecule: total RNA

tag: Stage


title: 5h input mRNA run 2

city: New Haven

first: Antonio

middle: J.

last: Giraldez

state: CT

address: 333 Cedar Street

department: Genetics

country: USA

institute: Yale University

data_processing:
Base calling was performed using CASAVA-1.8.2.
The Illumina TruSeq adaptor sequence was then trimmed from raw reads by aligning its sequence, requiring 100% match of the first five base-pairs and a minimum alignment score of 60 (Matches:5, Mismatches:-4, Gap opening:-7, Gap extension:-7). Trimmed reads were then depleted of rRNA, tRNA, snRNA, snoRNA, and misc_RNA from Ensembl and RepeatMasker annotations using strand-specific alignment performed with Bowtie2 v2.1.0 with default parameters.
Filtered reads were aligned strand-specific to the Zebrafish Zv9 genome assembly using Tophat v2.0.8 with default parameters and the exon-junction coordinates from Ensembl r70.
Using the spliced version of each transcript (ensembl r73, Pauli et al lincRNAs, Ulitsky et al lincRNAs) we defined all ORFs as stop codon to most distal in-frame AUG codon without an intervening stop. Read coverage and counts were calculated using 28 & 29nt reads. For position-related calculation of ORFScore and Frame1 coverage, we counted reads only with the +12 position within the interior of the ORF (defined as the region excluding the reads aligning to the start and stop(-1) codons). RPKM values were calculated using input mRNA per transcript, normalizing WITHIN but not between transcript sets (total reads mapping to ensembl r73 or either lincRNA set). ORFScore and coverage values were calculated as outlined in Bazzini et al, 2013. Sequencing data were combined for each timepoint.
Genome_build: Zv9/danRer7
Supplementary_files_format_and_content: allinfo_final_ORFs.txt :: orfID=unique ID of ORF; geneID; transcriptID; startLoc & stopLoc=1-based transcript coordinates of ORF; txCDSStart&txCDSEnd=start and end of annotated CDS; Source=transcript source; orfFrame=ORFScore; orfRate=# of reads in ORF; covF1Prop=proportion of in-frame positions with aligning read(s); tx_Input_RPKM=RPKM of transcript from input mRNA

molecule: polyA RNA

organism: Danio rerio

source_name: Whole embryos

growth_protocol: Embryos are incubated at 28C

extract_protocol:
For ribosome profiling, 50 wild type embryos for each condition were collected at a given stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction (ARTseq Ribosome Profiling Kit, RPHMR12126, Epicentre). For nuclease treatment, 3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28-29nt fragments were gel purified as previously described in (Bazzini et al., 2012) and cloned according to the manufacturers protocol (ARTseq Ribosome Profiling Kit, RPHMR12126, Epicentre). For RNA input, total RNA was isolated from 400 ul of the 800 ul of clarified extract before ART- seq Nuclease treatment. Poly-A selection was done according to manufacturer guide- lines (Dynabeads mRNA Purification Kit, Cat no.610.06), and RNA fragmented using the Artseq Ribosome Profiling Kit Mammalian protocol.
Both RPF and RNA input fragments were cloned according to the Artseq Ribosome Profiling Kit, Mammalian. The final PCR was carried out with an initial 15 second denaturation at 98 °C, followed by 9-12 cycles of 15 seconds at 98 °C, 5 seconds at 55 °C and extension at 72 °C for 10 s. Reactions were separated on a non-denaturing 8% polyacrylamide TBE gel and DNA fragments of the correct size were extracted and sequenced.

tag: strain

value: TUAB

tag: separation

value: column


title: 7Dvvs


title: 5h RPFs column replicate 2 run 3


title: 7Bvvs


title: 23vvs

source_name: day 19 implantation

value: implantation

value: No


title: 5h RPFs column replicate 1 run 3


title: 24vvs


title: 19vvs


title: 48h RPFs run 1


title: 24h RPFs run 1


title: 16vvs


title: 6vvs

source_name: day 16 maternal recognition of pregnancy

value: maternal recognition of pregnancy


title: 14vvs


title: 5vvs


title: 7vvs


title: 173vvs


title: 12h RPFs run 2


title: 12h RPFs run 1


title: 7Ivvs


title: 7Gvvs


title: 178vvs

source_name: day 13 elongated embryo pool

value: elongated embryo


title: 12h input mRNA run 1


title: 24h input mRNA run 1


title: 180vvs


title: 48h input mRNA run 1


title: 177vvs


title: 121vvs


title: 155vvs


title: 132vvs


title: 2h input mRNA run 1


title: 5h RPFs column replicate 2 run 2


title: 10Kvvs

source_name: day 10 hatched embryo pool

value: hatched embryo


title: 5h RPFs column replicate 1 run 2


title: 10Ivvs


title: 5h input mRNA run 1


title: 5h RPFs sucrose replicate 2

value: sucrose cushion


title: 10Hvvs


title: 10Gvvs


title: 10Fvvs


title: 5h RPFs sucrose replicate 1


title: 5h RPFs column replicate 2 run 1


title: 10Evvs


title: 10Cvvs


title: 5h RPFs column replicate 1 run 1


title: wt_40_2

status: Public on Apr 03 2014

city: Kansas City

first: Chris

middle: W

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

library_source: genomic

data_processing:
library strategy: DNA-seq; quantitative replication assays
CASAVA-1.8.2 used for base calling.
Sequence reads were aligned to sacCer3 using bowtie with the following parameters: -v 2 --best --strata -k 1 -m 1, which results in the reporting of unique matches.
Replication profiles for wt and mutant at 20 and 40 minutes after release from G1 arrest were generated by dividing the genome into bins of 1000 bases, counting how many reads map to each bin, normalizing the counts to reads per million, and then dividing the 20 and 40 minute data sets by the time 0 data set. This creates a set of ratios in log2 format between S-phase and G1. Loess smoothing is applied with a window span of 25, and degree of 2. For graphical display the final result is multiplied by 1.5 to reflect the expected ratio of DNA between S-phase and G1 cells midway through the replication cycle.
Genome_build: sacCer3; Saccharomyces cerevisiae S288c assembly from Saccharomyces Genome Database (GCA_000146055.2)
Supplementary_files_format_and_content: Tab-delimited text file with S/G1 ratios (20/0 and 40/0) of 1 kb bins across the genome for each replicate of wt and mutant in log2 format. The raw ratio and the ratio value after smoothing is applied are both present for each bin as indicated.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: wild type control_40 min

growth_protocol: Cultures were innoculated from overnights and grown to exponential phase in YPD media.

extract_protocol:
DNA was extracted using standard genomic DNA extraction methods for yeast consisting of vortexing cells with glass beads, followed by phenol-chloroform extraction and ethanol precipitation.
For each sample 8 ng of Genomic DNA was prepared for sequencing using the Nextera XT DNA Sample Preparation Kit from Illumina following the manufacturer’s instructions.

treatment_protocol: Exponentially growing cells were arrested in G1 phase by the addition of α-factor (1.5×10-8 M final) for 2 hrs. To release cells from α-factor arrest, cells were spun down and washed twice in media containing 0.1 mg/ml Protease (Sigma, P-6911).

tag: genotype/variation

value: wild type control

tag: time after release from g1 arrest (min)

tag: replicate


title: wt_40_1


title: wt_20_2

source_name: wild type control_20 min


title: wt_0_2

source_name: wild type control_0 min


title: wt_20_1


title: eco1_40_1

source_name: eco1 mutant_40 min

value: eco1-W216G mutant


title: eco1_0_2

source_name: eco1 mutant_0 min


title: wt_0_1


title: eco1_0_1


title: eco1_40_2


title: eco1_20_2

source_name: eco1 mutant_20 min


title: eco1_20_1


title: input_LSK

city: Aurora

first: Patricia

last: Ernst

state: CO

department: Pediatrics

institute: University of Colorado

data_processing:
Debarcoding of the multiplex runs was performed using Unix shell scripts.
Tags were mapped to the mouse genome (mm9) using bowtie v0.12.7 with parameters -v 2 -m 1 -S --best --strata
Peak identification was performed with MACS v1.3.7.1 using default parameters
bedgraph files were created using Homer (Heinz et al., 2010) using -auto parameter converted into bigwig (bedGraphToBigWig) and visualized on UCSC (Kent et al., 2002) genome browser as custom tracks
the ChIP-diff method (Xu et al., 2008) was used to identify DNA regions with significant histone modification enrichment. The method divides the whole genome into bins with equal size of 1kb and compares the tags (reads) between two samples (e.g. S1 versus S2) to calculate the posterior probabilities (P1, P2 and P0 with P1+P2+P3=1) of each bin to be S1-enriched, S2-eriched or non-differential between S1 and S2. S1-enriched bins are defined as those with 1.5-fold tag enrichment in S1 versus S2, and with a posterior probability P1>0.95. We applied ChIP-diff to compare Mll1∆/∆ with control to further categorize bins into Mll1∆/∆-enriched, control-enriched and non-differential bins. Finally, enriched bins in a sample within 1kb in distance were merged into regions to yield the enriched regions for that sample.
Genome_build: mm9
Supplementary_files_format_and_content: BIGWIG file with ChiP enrichment signal

organism: Mus musculus

source_name: sorted murine lin-/Sca-1/c-Kit in vitro cultured cells

growth_protocol: HSC medium (SFEM (StemCell Technology) plus 300 ng/mL rmSCF, 20 ng/mL rm IL-11, and 4 ng/mL rmFlt3L (R&D Systems)).

extract_protocol:
Cells in 96 wells were pooled and resuspended to 1 million/mL  in phosphate-buffered saline (PBS) containing 1% formaldehyde and incubated 10 minutes, followed by centrifugation and resuspension in 50 mM glycine/PBS, a 10 minute incubation, then a PBS incubation for 10 minutes. All steps were performed at room temperature at a cell density of 1 million/mL. Fixed cell pellets were either processed immediately or stored at -80°C.To shear the chromatin, the cell pellet was resuspended in lysis buffer (Tris pH 7.5, EDTA 1 mM, SDS 1%, 1X protease inhibitor complex, Roche) at 5x104 cells per 20 µL. Low-retention surface barrier tips were used for all steps (CLP Neptune). Sonication was performed for 10 cycles (30 seconds with 30 seconds rest) using a Bioruptor UCD-200 (Diagenode Inc.). Sonicated chromatin was centrifuged at 13,000 x g at 4°C for 5 minutes and the supernatant was diluted 10-fold with 2X RIPA buffer (20 mM Tris pH7.5, 2 mM EDTA, 2% Triton X-100, 0.1% SDS, 0.2% sodium deoxycholate, 200 mM NaCl). For each ChIP reaction 200µL diluted chromatin incubated with 1 µg antibody overnight at 4°C then 7.5 µL each of protein A and protein G Dynabeads (Invitrogen), previously washed in 1X RIPA buffer, were added to each immunoprecipitation and incubated for additional 2 hours at 4°C. The bead:protein complexes were washed three times with 200 µL 1X RIPA buffer and once with 200 µL TE (10mM Tris pH 7.5, 1mM EDTA). Genomic DNA was eluted from the ChIP and input samples for 3 hours at 65°C in 300 µL elution buffer (20 mM Tris pH 7.5, 5 mM EDTA, 50 mM NaCl, 1% SDS, 50 µg/mL proteinase K) using an Eppendorf Thermomixer at 1,000 rpm. Samples were phenol/chloroform extracted, ethanol precipitated with 10 µg each linear acrylamide and glycogen then centrifuged at 13,000xg for 20 minutes at 4°C. Pellets were air dried and resuspended in 15 µL TE containing 0.1 mM EDTA.
The library for sequencing was constructed using Ovation Ultralow DR Multiplex System 1-8 according to manufacturer's instructions (Nugen, San Carlos CA). Libraries were sequenced using HIseq-2000 (Illumina, San Diego, CA) to obtain 50 bp long reads. Half of the input or of the ChIP sample was used to prepare sequencing libraries with specific barcodes for individual ChIP sample according to the manufacturer’s instructions (Ovation Ultralow Library Systems, NuGEN). DNA concentration in each ChIP-library was measured using Qubit Fluorometer (Invitrogen) and 10 nM DNA from each library was used for running next-generation multiplexed sequencing using 50 bp single-end reads on a HiSeq-2000 instrument (Illumina).

treatment_protocol: LSK cells were incubated in HSC medium  supplemented with 300-400 nM 4-OHT (Sigma) to induce maximal deletion without harming cell viability. 4-OHT was washed out of the culture at 24 hours and cells were incubated an additional 24 hours.

value: C57Bl/6.SJL congenic

tag: cell type

value: LSK hematopoietic stem cells

tag: treatment

value: 4-OHT 48 hrs

tag: antibody/vendor/catalog#


title: 6.15_LSK_KO_H3K4me3


title: 6.15_LSK_control_H3K4me3


title: 6.3_LSK_KO_H3K27Ac


title: 6.3_LSK_control_H3K27Ac


title: 6.3_LSK_KO_H3K4me3


title: 6.3_LSK_control_H3K4me3


title: 6.15_LSK_KO_H3K4me1


title: 6.3_LSK_KO_H3K4me1


title: 6.15_LSK_control_H3K4me1


title: ChIP-Seq Analysis of PC in S2 cells, first replicate

city: Montpellier

first: Giacomo

last: Cavalli

address: IGH - CNRS, 141, rue de la Cardonille

country: France

institute: CNRS

data_processing:
Basecalling, CASAVA 1.8.2, Illumina
Alignment on dm3, CASAVA 1.8.2, Illumina
Quality measures with FastQC
Peak calling using MACS 1.4.2
Assignment to genes using Perl scripts
Genome_build: dm3
Supplementary_files_format_and_content: bed peak files

organism: Drosophila melanogaster

source_name: PC 1

extract_protocol:
Purified ChIP-DNA was prepared for sequencing on a HiSeq 2000 sequencer using Illumina standard protocol.
TruSeq ChIP Sample Preparation Kit

tag: chip antibody

value: Polycomb

tag: cell line


title: ChIP-Seq Analysis of Velo in S2 cells, first replicate

source_name: Velo 1

value: Velo


title: 6.3_LSK_control_H3K4me1


title: ChIP-Seq input in S2 cells

source_name: Input


title: ChIP-Seq Analysis of SUMO in S2 cells, second replicate

source_name: SUMO 2

value: SUMO


title: 214676_Face_4 RNA-seq

city: Heidelberg

first: Massimo

last: Petretich

address: Meyerhofstraße 1

department: Developmental biology

country: Germany

institute: EMBL

description: Sample 6_RNA-seq

data_processing:
The RNA- seq data was processed with the iRAP (45) (version 0.2.0) analysis pipeline (with default settings).
Readcounts for each gene were estimated with HTSeq-count
Data normalization and identification of significantly differentially expressed genes was performed using the DESeq method (version 1.10.1)
genome build: mm9
processed data files format and content: Text file with gene readcounts for all the 8 samples (biomaRt annotation)

source_name: facial mesenchyme

growth_protocol: Mouse facial mesenchyme: dissected from bronchial arch to forebrain boundary

extract_protocol:
RNA samples were processed using Tru-Seq RNA sample preparation guide (Illumina).
The eight samples were barcoded and run on the same flow cell of an Illumina HiSeq2000.

treatment_protocol: Embryonic faces from 4 del(8-17) homozygous and 4 wildtype littermates were dissected and treated as independent biological replicates. 72000 drosophila S2 cells were added to each tube as spikes to detect any global perturbation of mRNA levels.

tag: background strain

value: del(8-17) homozygous

tag: mother id

tag: embryonic stage


title: 214676_Face_6 RNA-seq

description: Sample 8_RNA-seq


title: 214676_Face_5 RNA-seq

description: Sample 7_RNA-seq

value: wt


title: ChIP-Seq Analysis of SUMO in S2 cells, first replicate

source_name: SUMO 1


title: 214676_Face_3 RNA-seq

description: Sample 5_RNA-seq


title: input (ChIP)

description: Sample 3_ChIP-seq

data_processing:
ChIP-seq reads were aligned to the reference genome mm9 with bowtie2 allowing for max 1 mismatch.
Duplicted reads and reads mapping multiple locations were removed. In the end bam files containing 10 - 20 e6 useful reads were subjected to MACS14 for peak calling with default parameters.
Tracks were made using genomeCoverageBed and wigToBigWig softwares.
genome build: mm9
processed data files format and content: .txt files report Base pair coverage was calculated and normalized to 1X ~11e6 reads, then the coverage was summed within bins of 50bp
processed data files format and content: .bed MACS14 Peak calling file. MACS was run with default parameters
processed data files format and content: .bw Tracks of the coverage file. (Not normalized to input)

extract_protocol:
Lysates were clarified from drbris of nuclei and DNA-wrapped histones were Immunoprecipitated with specific antibody.
Libraries were prepared with NEB Next ChIP-seq Sample Prep Master Mix Set I (Cat.No.E6240S, NEB) and NEB Next Multiplex Oligos for Illumina (Cat.No: E7335S, NEB)


title: 214676_Face_1 RNA-seq

description: Sample 3_RNA-seq


title: 214262_Face_2 RNA-seq

description: Sample 1_RNA-seq


title: 214676_Face_2 RNA-seq

description: Sample 4_RNA-seq


title: H3K4me1 ChiP-seq

description: Sample 2_ChIP-seq

value: anti-H3K4me1 antibody (Abcam, catalog# ab8895, lot# GR61294-1)


title: 214262_Face_4 RNA-seq

description: Sample 2_RNA-seq


title: ChIP-Seq Analysis of PC in S2 cells, second replicate

source_name: PC 2


title: ChIP-Seq Analysis of Velo in S2 cells, second replicate

source_name: Velo 2


title: TbNup92Δ_A RNAseq

city: Seattle

first: Alexander

last: Ratushny

state: WA

address: 307 Westlake Avenue North, Suite 500

institute: Seattle BioMed

description: Sample 1

data_processing:
Paired-end reads were mapped to the T. brucei 427 strain reference genome sequence using Burrows-Wheeler Aligner (Li and Durbin, 2010).
The mapped reads were further filtered by SAMtools (Li et al, 2009), allowing that the read is mapped in proper pair by a minimum 20 MAPQ (MAPing Quality).
After filtering, the paired-reads were aligned to annotated transcripts. Transcript abundances were calculated based on FPKM (Fragments Per Kilobase of transcript per Million mapped reads) (Trapnell et al, 2010).
All FPKMs of annotated transcripts were normalized by quantile normalization. Low FPKM values (less than the median of FPKM values for all annotated transcripts) were removed.
Transcripts that are annotated as rRNA/tRNA were excluded. The statistical significance for transcript level changes was calculated based on (FPKMtreat/FPKMwt) values against Null distribution using t-test.
Genome_build: http://tritrypdb.org/common/downloads/Current_Release/TbruceiLister427/gff/data/
Supplementary_files_format_and_content: The tab-delimited text file include FPKM values for each sample.

organism: Trypanosoma brucei

growth_protocol: PCF trypanosomes were cultured in SDM-79 media supplemented with 20% FCS, 100U/ml penicillin and 2mM glutamine. Cells were icubated at 27C

extract_protocol:
RNA was extracted and cDNA synthesised from two independent TbNup92Δ cell lines and the parental cell line. Sheared cDNA was sequenced by 76bp paired end Ilumina sequencing. Paired-end reads were mapped to the T. brucei 427 strain reference genome sequence using Burrows-Wheeler Aligner. The mapped reads were further filtered by SAMtools, allowing that the read is mapped in proper pair by a minimum 20 MAPQ (MAPing Quality). After filtering, the paired-reads were aligned to annotated transcripts. Transcript abundances were calculated based on FPKM (Fragments Per Kilobase of transcript per Million mapped reads). All FPKMs of annotated transcripts were [AR1] normalised by quantile normalisation. Low FPKM values (less than the median of FPKM values for all annotated transcripts) were removed. Transcripts that are annotated as rRNA or tRNA were excluded. To calculate the statistical significance for transcript level changes, the observed log-fold expression changes (FPKMtreat/FPKMwt), were tested against an empirical null distribution using t-test. The empirical null distribution of the log-fold changes were computed from all possible permutations of the samples.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: Procyclic


title: Parental RNAseq

description: Sample 3

source_name: Parental

value: wild type


title: KIKO 1h E2 PolII alpha ChIP-seq

city: Research Triangle Park

first: Sylvia

middle: C

last: Hewitt

state: NC

address: 111 Alexander Dr

department: RDBL

institute: NIEHS

data_processing:
Sequences (36 nucleotide reads) were aligned to the mouse genome (National Center for Biotechnology Information Build 37.1/mm9) using Eland (Illumina pipeline) software.
Duplicate mapped reads were removed with MarkDuplicates.jar from the Picard suite (v1.62).
ER alpha peak calls were made with Partek Genomics Suite (v 6.11.1101; Partek, Inc, St Louis, MO) using default parameters.
Called peaks were filtered to exclude peaks with Mann-Whitney P-value > 0.01.
Mapped reads were extended at their 3' end to a length equal to the estimated average fragment size for that library and then converted to aggregate coverage (bedGraph format) with BEDtools genomeCoverageBed.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph file per sample showing aggregate coverage of mapped extended reads; generated by BEDtools genomeCoverageBed.
Supplementary_files_format_and_content: Called ER alpha peaks (idnetified via Partek Genomic Suite) in BED format.

source_name: uterus

growth_protocol: mice were maintained on NIH-31 chow, standard light/dark cycle, 1-5 mice per cage

extract_protocol:
Uteri were submersed in PBS + 1% formaldehyde, cut into small (~1 mm3) pieces with a razor blade and incubated at room temperature for 15 minutes. Fixation was stopped by the addition of 0.125 M glycine (final). The tissue pieces were then treated with a TissueTearor (Biospec Products, Bartlesville, OK) and finally spun down and washed 2x in PBS. Chromatin was isolated from the sample by adding 5-10 ml lysis buffer containing PIPES, Igepal, PMSF and Protease Inhibitor Cocktail, followed by disruption with a Dounce homogenizer. Samples were pelleted by centrifugation and resuspended in buffer containing Na deoxycholate, SDS, and Triton X-100. Lysates were sonicated using a Misonix Sonicator 3000 (Misonix, Farmingdale, NY) equipped with a microtip in order to shear the DNA to an average length of 300-500 bp. Lysates were cleared by centrifugation and the chromatin suspensions were transferred to new tubes and stored at -80 C. To prepare Input DNA (genomic DNA), two aliquots of 10-25 µl each (approximately 1/50 of each chromatin preparation) were removed and treated with RNase for 1-2 h at 37 C, proteinase K for 3 h at 37 C, and 65 C heat for at least 6 h to overnight for de-crosslinking. DNAs were purified by phenol-chloroform extraction and ethanol precipitated. Pellets were resuspended in 1/5 TE. Resulting DNAs were quantified on a Nanodrop spectrophotometer (Thermo Scientific, Wilmington, DE). Extrapolation to the original chromatin volume allowed determination of the yield for each chromatin preparation, as measured by the DNA content.  Prior to use in ChIP, protein A agarose beads (Invitrogen Technologies, Carlsbad, CA) were preblocked using blocking proteins and nucleic acids for 3 h. For each ChIP reaction, an aliquot of chromatin (20-30 µg) was precleared with 30 µl preblocked protein A agarose beads for 1-2 h. ChIP reactions were set up using precleared chromatin and antibody to ERα (sc-542, Santa Cruz Inc, Santa Cruz CA) or PolII phospho Ser5 (ab5095, Abcam, Cambridge, MA) in a buffer containing Na deoxycholate and incubated overnight at 4 C. Preblocked protein A agarose beads were added and incubation at 4 C was continued for another 3 h. Agarose beads containing the immune complexes were washed two times each with a series of buffers consisting of the deoxycholate sonication buffer, high salt buffer, LiCl buffer, and TE buffer. An SDS-containing buffer was added to elute the immune complexes from the beads, and the eluates were subjected to RNase treatment at 37 C for 20 min and proteinase K treatment at 37 C for 3 h. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNAs were purified by phenol/chloroform extraction and ethanol precipitation. Quality of ERα ChIP enrichment was assayed by qPCR using primers against candidate EREs in the Igf1 and Stat5a promoters (9). Quality of PolII ChIP enrichment was assayed by qPCR using primers against region in Intron 1 of the housekeeping genes Actin B and  Gapdh. Input DNA was queried at the same sites in parallel.
ChIP DNA was amplified by following the Illumina ChIP-Seq DNA Sample Prep Kit (Illumina, Inc.  San Diego, California)  protocol. In brief, DNA ends were polished and 5’-phosphorylated using T4 DNA polymerase, Klenow polymerase and T4 polynucleotide kinase. After addition of 3’-A to the ends using Klenow fragment (3’-5’ exo minus), Illumina genomic adapters were ligated and the sample was size fractionated (200-250 bp) on a 2% agarose gel. After a final PCR amplification step (18 cycles, Phusion polymerase, New England Bioloabs, Ipswich, MA), the resulting DNA libraries were quantified and tested by qPCR at the same specific genomic regions as the original ChIP DNA to assess quality of the amplification reactions. DNA libraries were sequenced on a Genome Analyzer II (Illumina).

treatment_protocol: mice were ovariectomized and injected intraperitoneally 10-14 days later with saline vehicle or estradiol (250 ng/mouse). Uterine tissue was collected one hour later

tag: tissue

value: uterus

value: estradiol (250 ng/mouse)

tag: antibody

tag: background mouse strain


title: KIKO V PolII alpha ChIP-seq

value: saline vehicle

value: PolII phospho Ser5 (ab5095, Abcam, Cambridge, MA)


title: Kaleso_CBSV

city: Chatham Maritime

first: sophie

last: BOUVAINE

state: kent

address: Central Avenue

country: United Kingdom

institute: Natural resources Institute

data_processing:
Sequenced reads were trimmed for adaptor sequence, and quality filitered
mapped to the genome Cassava 4.1 using BWA aligner
Genome_build: Cassava4.1 from www.phytozyme.net
Supplementary_files_format_and_content: each tab-delimited text files include gene id and  RPKM values

organism: Manihot esculenta

source_name: Cassava cv Kaleso leaf tissue

growth_protocol: Plant grown for 14 months

extract_protocol:
Total RNAS were extracted using  CTAB methods and concentrated using Rneasy mini-elute kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: CBSV was graft inoculate on two month old plants

tag: infection

value: CBSV infected

tag: cultivar

value: Kaleso

value: leaf


title: Albert_CBSV

source_name: Cassava cv Albert leaf tissue

value: Albert


title: KIKO V ER alpha ChIP-seq

value: ERα (sc-542, Santa Cruz Inc, Santa Cruz CA)


title: KIKO 1h E2 ER alpha ChIP-seq


title: 97.5_S15

status: Public on Apr 02 2014

city: Lausanne

first: Gergana

last: Bounova

state: VD

address: Quartier Sorge, bâtiment Génopode

department: Center for Integrative Genomics

country: Switzerland

institute: University of Lausanne

description: Mouse + Human spike

data_processing:
The sequencing data was mapped to both the mouse (mm9) and the human (hg19) genomes using the Illumina embedded mapper: ELAND.
Reads mapping to mouse and human were separated for further analysis. Tags mapping to both genomes were discarded.
Mouse counts were assigned to a list of 671 PolIII loci, with a redundancy cutoff of 50. The genes were extended with 150 bp upstream and downstream.
Human counts were assigned to a list of 702 PolIII loci, with the same redundancy cutoff. The genes were extended with 150 bp upstream and downstream.
For PolII the same procedure was followed, except that counts were assigned to a loci list of 11217 mouse TSS, and 22572 human TSS, centered in a region of 500 bp.
Genome_build: mm9, hg19
Supplementary_files_format_and_content: Tab-separated values. Every line contains four fields: chromosome, start position, end position and counts.

source_name: Mouse Liver

extract_protocol:
Mouse livers : livers were perfused with 5 ml of PBS through the spleen, immediately homogenized in PBS containing 1% formaldehyde, and then processed as described in (Ripperger and Schibler 2006).
Aliquots of sonicated chromatin were mixed with different antibodies and incubated overnight at 4˚C on a rotating wheel. Immunoprecipitated material was recovered by addition of 25 µl of protein A agarose beads (pre-blocked with 10 µg/ml of BSA and 10 µg/ml of salmon sperm DNA) and incubation for 3 h at 4°C on a rotating wheel. The beads were washed with dialysis and wash buffer (O’Green et al., 2006). De-crosslinking, RNase A treatment, proteinase K treatment, and DNA purification were performed as described in (O’Green et al., 2006).Ten ng of immunopurified chromatin as well as input DNA was used to prepare sequencing libraries with the ChIP-Seq Sample Preparation Kit (Illumina; San Diego, California, USA; Cat. No IP-102-1001) according to the protocol supplied by the manufacturer

tag: strain

tag: sample

value: mouse:97.5%; human spiked DNA (HeLa): 2.5%

value: HeLa

tag: age

value: post natal 12 weeks

value: anti-POLR3D (mouse and human) CS681 Ab,  raised against peptide CSPDFESLLDHKHR {Chong et al 2001}


title: RPB2_95

description: Mouse + Human spike

value: mouse:95%; human spiked DNA (HeLa): 5%

value: anti-POLR2B (mouse and humans), Santa Cruz Cat N. SC-67318 (H-201)


title: 97.5_S5

description: Mouse + Human spike


title: 97.5_P1

description: Mouse + Human spike


title: 97.5_S10

description: Mouse + Human spike


title: H3K27ac ChIP-seq

description: Sample 1_ChIP-seq

tag: genotype/variation

value: wt

value: anti-H3K27ac antibody (Abcam, catalog# ab4729, lot# GR7675-1)


title: Input 95

description: Mouse + Human spike


title: 90_R1

description: Mouse + Human spike

value: mouse:90%; human spiked DNA (HeLa): 10%


title: 95_R1

description: Mouse + Human spike


title: Ikaros ChIP sample

city: Illkirch

first: Susan

last: Chan

address: 1, rue Laurent Fries

institute: IGBMC

data_processing:
Illumina pipeline v1.3 to v1.6 are used for basecalling.
Sequence reads were mapped to reference genome mm9/NCBI37 using GERALD. Only 2 mismatch reads were kept for further analysis.
Genome_build: mm9
Supplementary_files_format_and_content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b)

source_name: T29 Ik1-ER cells treated with 4OHT

extract_protocol: ChIP-seq libraries were prepared using ChIP-Seq Sample Prep Kit (#IP-102-1001, Illumina) following the manufacturer's protocol with some modifications. Briefly, 10 ng of ChIP enriched DNA or control DNA were end repaired using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK. A single ‘A’ nucleotide was added to the 3’ ends of the blunt DNA fragments with a Klenow fragment (3' to 5'exo minus). The ends of the DNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR (30 sec at 98°C; [10 sec at 98°C, 30 sec at 65°C, 30 sec at 72°C] x 14 cycles; 5 min at 72°C) and then purified using Agencourt AMPure XP beads (#A63881, Beckman). DNA library size selection was performed by excising the 250-350 bp fragments from a 2% agarose gel followed by purification using a QIAquick Gel Extraction Kit (#28906, Qiagen).

treatment_protocol: T29-IKER cells were treated with 4OHT (100 nM) for 24h.

tag: cell type

value: T29 Ik1-ER cells treated with 4OHT

value: mixed C57Bl/6/129sv

value: in house anti-Ikaros rabbit polyclonal antibody ; lot:A3


title: input for Ikaros ChIP


title: BG3_STARRseq_rep1

city: Vienna

first: J. Omar

last: Yanez-Cuna

address: Dr. Bohr-Gasse 7

country: Austria

institute: Research Institute of Molecular Pathology

description:
polyA+ RNA
PCR amplified cDNA (STARR-seq transcript)

data_processing:
STARR-Seq:
Reads were mapped to the dm3 genome using bowtie (bowtie -p 12 -f -X 2000 -v 3 -m 1 --best --strata --quiet INDEX -1 reads_1.fa -2 reads_2.fa) excluding chrU, chrUextra, and chrM. For all subsequently analysis we used only reads collapsed on chromosome, start, end, strand (fragments). Significantly enriched regions (peaks) were called with an in-house pipeline using read density profiles of cDNA and input and an hypergeometric test to assign a p-value to each peak. Enrichment values were corrected within a 95% confidence interval taking into account the number of independent fragments at a single peak summit position.
Genome_build: dm3
Supplementary_files_format_and_content: All processed data files are in plain text. For STARR-seq we report for each peak the chromosome, the summit position, the enrichment over input (log2-scale) at the summit, and the p-value.

source_name: BG3 cells

extract_protocol: STARR-Seq: Genomic DNA (source: embryos of the sequenced strain: y; cn bw sp) was isolated, sheared and size selected (~500bp). Following the instructions of NEBNext® DNA Library Prep Reagent Set for Illumina® (NEB; cat. no. E6000L), Illumina Multiplexing Adapters (Illumina Inc; cat. no. PE-400-1001) were ligated and homology arms for In-Fusion® recombination were added by PCR, followed by recombination into the STARR-seq vector (pGL3-Promotor backbone (Promega; cat. no. E1751) with the sequence between BglII and FseI replaced with the following sequence, containing a Drosophila Synthetic Core Promoter (DSCP) (1), an ORF (sgGFP, Qbiogene, Inc), a ccdB suicide gene flanked by homology arms (used for cloning the genomic enhancer candidates during library generation), and the pGL3’s SV40 late polyA-signal.). The In-Fusion® reactions were transformed (MegaX DH10B; Invitrogen), grown in liquid culture and plasmids were isolated.

value: BG3 cells

tag: experimental procedure

value: STARR-Seq


title: STARRseq_input_lib5.2

description:
plasmid DNA (containing genomic DNA fragments)
PCR amplified Plasmid library, used for BG3 STARR-seq

source_name: whole genome library (in STARR-seq vector)

tag: genotype

value: y; cn bw sp - sequenced strain (Adams et al. 2000)


title: BG3_STARRseq_rep2

tag: cell line


title: TbNup92Δ_B RNAseq

description: Sample 2

value: Procyclic


title: 97.5_R1

description: Mouse + Human spike


title: RPB2_90

description: Mouse + Human spike


title: Albert_healthy

value: non infected

value: Albert

value: leaf


title: Kalesos_healthy

value: Kaleso


title: input sample for RBPJ ChIP experiment 1

source_name: T29 cells

value: T29 cells

tag: chip antibody


title: E16.5, biological replicate 1, single cells, transcriptome 15

status: Public on Apr 08 2014

city: Stanford CA

first: Barbara

last: Treutlein

state: CA

address: 318 Campus Drive

department: Bioengineering

institute: Stanford University

data_processing:
CASAVA 1.8.2 was used to separate out the data for each single cell using unique barcode combinations from the Nextera XT preparation and to generate *.fastq files.
adapter sequences were removed using cutadapt-1.2.1
trimming by base quality was performed and low complexity reads were removed using prinseq-lite-0.20.3
paired reads were aligned against mm10 using bowtie2-2.1.0 and tophat-2.0.8
Fragments Per Kilobase of transcript Per Million mapped reads (FPKM) values were computed using cufflinks-2.0.2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: distal lung epithelium

growth_protocol: Mice were housed in filtered cages and all experiments were performed in accordance with approved IACUC protocols. Timed-pregnant C57BL/6J females (JAX) were used for all embryonic time points reported with gestation age verified by crown-rump length prior to use.  For adult mice, a transgenic-labeling approach was employed. Mice were bred to be homozygous for a knock-in allele into Sftpc encoding for a reverse tetracycline transactivator (SftpC-Cre-ERT2-rtTA) and heterozygous for an inserted transgene, which drives the expression of a GFP tagged human histone 1 in a tetracycline-dependent manner (tetO-HIST1H2BJ/GFP).

extract_protocol:
Cells were loaded into the Fluidigm C1 microfluidic platform, where single cells were captured. Lysis of single cells, reverse-transcription of mRNA into cDNA as well as preamplification of cDNA occured within the microfluidic device using reagents provided by Fluidigm as well as the SMARTer Ultra Low RNA kit for Illumina (Clontech). External RNA spike-in transcripts (ERCC spike-in Mix, Ambion) were added to all single cell lysis reactions. As a bulk control, cDNA was prepared from approximately 200 cells in a PCR tube using the same protocol and reagents as used for the single cells. In addition, one "no cell control" was prepared using reagents without any cell input in a PCR tube.
Libraries were prepared using Illumina Nextera XT kit per illumina's protocols.

treatment_protocol: To obtain AT2 cells from the adult lung, an adult mouse whose genome contained a tetracycline-responsive, nuclear reporter only transcribed in cells transcribing Sftpc (Sftpc-Cre-ERT2-rtta-/- tetO-HIST1H2BJ-GFP+/-) was injected with 2 mg of doxycycline (Sigma) and used 3 days afterwards. Pregnant and non-pregnant adult mice were euthanized by CO2 administration. For embryonic samples (E14.5, 16.5, and 18.5), embryonic lungs were isolated and either a single embryonic lung was used or 5-7 sibling lungs were pooled. For the adult experiment, the pulmonary vasculature was cleared and lungs were gently inflated with digestion buffer prior to isolation and mincing of the lung. All tissue was digested at 37C for 45 min using Elastase and DNase I, triturated and subsequently filtered using 100µm and 40µm strainers to obrtain a single cell suspension. Embryonic lung epithelial cells were purified by magnetic-assisted cell sorting using CD45 depletion followed by EpCAM enrichment. Transgenically labeled adult AT2 cells were purified by fluorescence-assisted cell sorting.

value: lung

value: Embryonic day 16.5

value: wild type


title: RBPJ ChIP sample 2

value: T6719; Institute of Immunology, Kyoto ; lot:901119


title: Strepatvidin ChIP-seq of Beko cells expressing Biotinylated ICN1

data_processing:
Illumina pipeline version >1.8.0 used for basecalling.
Sequence reads were mapped to reference genome mm9/NCBI37 using Bowtie.
Genome_build: mm9
Supplementary_files_format_and_content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b)

source_name: Beko-bioNIC cells

value: Beko-bioNIC cells

value: TCRb KO

value: Streptavidin Dynalbeads (Invitrogen)


title: mdx_young_tsa

first: Iros

last: Barozzi

address: Borschkegasse 8a

institute: Medical University Vienna

data_processing:
Library strategy: NA-Seq
Reads quality filtered according to the Illumina pipeline
Paired-end short reads were aligned onto the mm9 release of the murine genome using Bowtie v0.12.7 (PMID: 19261174). Only unique alignments were retained, allowing up to two mismatches compared to the reference genome. Since NlaIII recognize CATG sequences, 4 bp at the 5’ ends of the reads were trimmed prior to alignment. Bowtie was run with the following parameters: -v 2 -m 1 -X 800 -5 4. Pairs showing a valid alignment were then retained if and only if they were showing a CATG site at one of the two ends in the reference genome. All samples were downsized to the sequencing depth of the smallest one (old mdx mice, TSA treated) by randomly pick the same number of aligned fragments.
Nuclease-accessible regions (NAS) in each sample were identified using a genomic window of 1 kbp sliding 100 bp along the entire murine genome. Every window was scored for statistical significance using the theoretical pattern of NlaIII recognition sites as control. A Chi-squared test was performed using the number of fragments within and outside the window, as well as the number of NlaIII recognition sites within and outside the window. All the windows showing more digested fragments than expected with a p-value equal or lower than 1e-5 were retained. All overlapping windows were then merged, and the statistics recalculated. The pipeline is implemented in C++ and statistics are performed using the GNU Scientific Libraries (GSL, http://www.gnu.org/software/gsl/).
Using the same pipeline, TSA samples were compared to their age-matched untreated samples. TSA-induced regions were defined as regions showing significantly more digested fragments (p-value <= 1e-5) in TSA-treated than untreated and more than expected by the theoretical pattern of NlaIII recognition sites. In a similar way, TSA-repressed regions were defined as regions showing significantly more digested fragments in control samples than TSA-treated sample and more than expected by the theoretical pattern of NlaIII recognition sites.
Genome_build: mm9 (NCBI Build 37)
Supplementary_files_format_and_content: bed files

source_name: Fibro/adipogenic progenitors (FAPs) from hind limb muscles

growth_protocol: C57BL6 mdx mice were purchased from the Jackson Laboratories.

extract_protocol:
Fibro/adipogenic progenitors (FAPs) cells were isolated as Ter119-/CD45-/CD31-/α7integrin-/Sca-1+ cells. Hind limb muscles were minced and digested in HBSS (Gibco) containing 2 μg/mL Collagenase A (Roche), 2.4 U/mL Dispase I (Roche), 10 ng/mL DNase I (Roche), 0.4 mM CaCl2 and 5mM MgCl2 for 90 min at 37°C. Cells were stained with primary antibodies (10 ng/mL) CD31-eFluor450 (eBioscience), CD45-eFluor450 (eBioscience), TER-119-eFluor450 (eBioscience), Sca-1-FITC (eBioscience) and α7integrin-APC for 30 min on ice. Cells were finally washed and resuspended in HBSS containing 0.2% (w/v) BSA and 1% (v/v) Penicillin-Streptomycin. Flow cytometry analysis and cell sorting were performed on a DAKO-Cytomation MoFlo High Speed Sorter.
The library for NA-seq was prepared as described in Gargiulo et al. (PMID: 19289091) with some modifications. 1e6 FAPs freshly isolated by FACS, were washed twice with ice‐cold PBS, and centrifuged for 5 min at 500g at 40°C. Cells were resuspended in 1 ml ice-cold homogenization buffer (10 mM Tris-Cl pH 7.4, 15 mM NaCl, 60 mM KCl, 5%sucrose, 1 mM EDTA, 0.1 mM EGTA, 0.1% NP-40, 0.15 mM spermine, 0.5mM spermidine, 1 mM DTT, 0.5 mM PMSF). The homogenate was transferred to a fresh tube and 400 μl of a sucrose "pad" solution (10 mM Tris‐Cl pH 7.4, 15 mM NaCl, 60 mM KCl, 10% sucrose, 1 mM EDTA, 0.1 mM EGTA, 0.15 mM spermine, 0.5 mM spermidine, 1 mM DTT, 0.5 mM PMSF) was added to the homogenate to form a layer underneath it. The nuclei were pelleted at 140g at 4°C for 20 min and gently resuspended in 100 μl of ice-cold reaction buffer (10 mM HEPES pH 7.5, 25 mM KCl, 5 mM MgCl2, 5% glycerol, 0.15 mM spermine, 0.5 mM spermidine, 1 mM DTT, 0.5 mM PMSF), incubated at 37°C for 1 min, and then treated with 1/10th v/v of NlaIII or HpaII (NEB, 50'000 units/ml) for 5 min. at 37°C. The reaction was stopped by adding 0.5M EDTA to reach a final concentration of 25mM. After purification the second enzymatic digestion was perfomed using Sau3aI (20 U) for 2h at 37°C and again purified. Libraries for sequencing on HiSeq2000 were prepared according to the Illumina standard protocol.

treatment_protocol: Animals at the specified age were treated for 15 days with daily i.p. injections of Trichostatin A, TSA (0.5 mg/Kg/day; Sigma), dissolved in saline solution, or saline alone as control (Ctrl).

value: C57BL/6 mdx

value: FAPs

tag: treatment

value: TSA


title: control streptavidin ChIP-seq of BirA expressing Beko cells

source_name: Beko-bio cells

value: Beko-bio cells


title: RBPJ ChIP sample 1

value: mixed C57Bl/6/129sv


title: mdx_old_tsa


title: Stationary culture

city: Barcelona

first: BERNARDO

last: BELLO ORTI

state: Barcelona

address: Bellaterra

department: Bacteriology

country: Spain

institute: CReSA

data_processing:
A customised version of the count-based differential expression analysis method was carried out. Briefly, reads quality control was performed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/), and reads were then mapped to H. parasuis F9 genome using the recommended Torrent Mapping Alignment Program (TMAP) (https://github.com/iontorrent/TMAP) v3.4.1 with map2 setting. Alignments were inspected using SAMtools and Integrative Genomics Viewer (IGV).
HTSeq v0.5.4p3 (https://pypi.python.org/pypi/HTSeq) was used for feature counting with intersection-nonempty setting and discarding non-protein coding CDS. Differentially expressed genes (DEGs) were identified with edgeR R package with a 5% P-value cut-off, using an assigned dispersion value of 0.04.
Genome_build: Haemophilus parasuis F9; Genbank accession JHQI00000000
Supplementary_files_format_and_content: tab-delimited text files include counts for each gene

organism: Glaesserella parasuis

source_name: in vitro culture_stationary

growth_protocol: For comparison, F9 was also grown in a shaker until the culture reached stationary phase and was processed for RNA extraction.

extract_protocol:
Bacteria from all three samples were recovered by centrifugation and pellets were used for RNA extraction. The three bacterial samples were processed for RNA extraction as follows. Pellets were resuspended in 2% SDS 16 mM EDTA 10 mM TRIS (pH XX) and incubated for 5 min at 100 ºC. Afterwards, samples were processed by two hot acid phenol-chloroform extractions, followed by two chloroform/ isoamyl alcohol extractions. RNA was then precipitated with 0.6 volumes of isopropanol 0.1 volumes of 5M ammonium acetate and 1μL of glycogen. After centrifugation the pellet was washed with 70% ethanol, dried and resuspended in warmed RNase-free water. To ensure that contaminating bacterial DNA was eliminated from the samples, treatment with RNase-free DNase (Qiagen) was performed. In addition, ribosomal RNA was eliminated with the Ribo-Zero rRNA removal kit (Epicentre Biotechnologies, Madison, WI, USA) following manufacturer’s instructions. PCR reactions using primers specific for H. parasuis 16S rRNA gene were carried out to ensure that no bacterial DNA was left in the sample.
Libraries were generated using an Ion Torrent RNA-Seq v2 kit (Life Technologies), multiplexed and sequenced by an Ion Torrent PGM (Life Technologies) with an Ion 318 chip (Life technologies) at the Centre for Research in Agricultural Genomics (CRAG, Campus de Bellaterra-UAB, Spain).

tag: culture time


title: mdx_young_ctrl


title: Planktonic

source_name: in vitro culture_planktonic

growth_protocol: Planktonic and biofilm samples were obtained under static conditions. Bacteria were cultured in 6-well microtiter plates and after 36h, planktonic cultures were transferred to sterile tubes, while biofilm bacteria were collected by scrapping the surface of the wells with lysis buffer (2% SDS in PBS).


title: Biofilm

source_name: in vitro culture_biofilm


title: Sample 27b

status: Public on Apr 01 2014

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 St. Vincent strain-infected DH82 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. Saint Vincent

source_name: Ehrlichia (St. Vincent) in canine cell line DH82

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: St. Vincent

tag: host cell

value: Canis lupus familiaris

tag: infectivity

tag: assayed molecule

value: mRNA


title: Sample 37a

description: Ehrlichia chaffeensis St. Vincent strain-infected Ixodes tick cells

source_name: Ehrlichia (St. Vincent) in Ixodes tick cell line ISE6

value: Ixodes scapularis


title: Sample 27a


title: Sample 37b


title: Sample 27c


title: Sample 37c


title: Sample 16b

value: total RNA


title: Sample 16a


title: Sample 7b


title: Sample 16c


title: Sample 7a


title: Sample 21b

description: Canine Cell Line Uninfected Control

organism: Canis lupus familiaris

source_name: Canine cell line DH82


title: MEL BirA only cells

city: Memphis

first: Jian

last: Xu

state: Tennessee

address: 262 Danny Thomas Place, MS 345

department: Pathology

institute: St. Jude Children's Research Hospital

description:
ChIP-seq data
We used streptavidin-based ChIP and ChIP-seq. No antibody was used. The product information for Dynabeads MyOne Streptavidin T1 (Invitrogen, Cat.# 656.01, lot # 757581130).

data_processing:
Aligment: Sequence reads were obtained and mapped the mouse genome assembly mm9 (NCBI version 37) using Helisphere software with default parameters. Only the reads that were uniquely aligned to reference genome with read alignment score higher than 4.5 were retained for further analysis.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)

source_name: MEL cells expressing BirA alone

growth_protocol: MEL cells were maintained in DMEM supplemented with 10% FCS at 37oC incubator.

extract_protocol: 3-9 ng ChIP DNA was used in the direct polyA tailing step according to Helicos HeliScope standard procedure.

treatment_protocol: Cells were fixed in 1% formaldehyde for 5 min at room temperature.

value: Mouse erythroleukemia cells


title: Sample 21a

description: Canine Cell Line Uninfected Control


title: Input DNA

description:
Inupt data
We used streptavidin-based ChIP and ChIP-seq. No antibody was used. The product information for Dynabeads MyOne Streptavidin T1 (Invitrogen, Cat.# 656.01, lot # 757581130).

source_name: ChIP Input DNA


title: Sample 21c

description: Canine Cell Line Uninfected Control


title: mdx_old_ctrl


title: Sample 1c

description: Canine Cell Line Uninfected Control


title: Sample 1b

description: Canine Cell Line Uninfected Control


title: Sample 1a

description: Canine Cell Line Uninfected Control


title: MEL cells expressing FLAG-Biotin-tagged BCL11A

source_name: MEL cell clones expressing BirA and FLAG-Biotin-tagged BCL11A


title: Sample 40b

description: Ehrlichia sp. HF strain-infected Ixodes tick cells

organism: Ehrlichia japonica

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

value: HF


title: Sample 30c

description: Ehrlichia sp. HF strain-infected DH82 cells

source_name: Ehrlichia (HF) in canine cell line DH82


title: Sample 30a


title: Sample 40a


title: Sample 20c


title: Sample 31b

description: Tick Cell Line Uninfected Control

organism: Ixodes scapularis

source_name: Tick cell line ISE6


title: Sample 7c


title: Sample 31a

description: Tick Cell Line Uninfected Control


title: Sample 31c

description: Tick Cell Line Uninfected Control


title: Sample 20b


title: Sample 20a


title: Sample 19a


title: Sample 10c

description: Tick Cell Line Uninfected Control


title: Sample 10a

description: Tick Cell Line Uninfected Control


title: Sample 10b

description: Tick Cell Line Uninfected Control


title: Sample 38a

description: Ehrlichia chaffeensis Wakulla strain-infected Ixodes tick cells

organism: Ehrlichia chaffeensis str. Wakulla

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

value: Wakulla


title: Sample 28b

description: Ehrlichia chaffeensis Wakulla strain-infected DH82 cells

source_name: Ehrlichia (Wakulla) in canine cell line DH82


title: Sample 28c


title: Sample 40c


title: Sample 8c


title: Sample 17a


title: Sample 28a


title: Sample 38b


title: Sample 17b


title: Sample 17c


title: Sample 8a


title: Sample 8b


title: input sample for RBPJ ChIP experiment 2

source_name: T29 cells

value: T29 cells


title: Sample 30b


title: QM9414 Glucose 3

city: Campinas

first: Gabriela

middle: F

last: Persinoti

state: São Paulo

address: Rua Giuseppe Máximo Scalfaro, 10.000

department: Brazilian Biorenewables National Laboratory LNBR

country: Brazil

institute: Brazilian Center for Research in Energy and Materials CNPEM

description: Sample 9

data_processing:
Illumina HiseqTM 2000 technology was used to perform sequencing, resulting in 147 million and  187 million 100 bp paired-end reads for parental (QM9414) and mutant (Δxyr1) strains, respectively. Quality-filtered reads were mapped to the Trichoderma reesei 2.0 reference genome, available at JGI Genome Portal (http://genome.jgi-psf.org/Trire2/Trire2.home.html), using the TopHat2 v2.0.4  aligner (Kim et al, 2013), allowing two mismatches and only unique alignments. After alignment, Samtools version 0.1.19 (Li et al., 2009) was used to process the alignments files which were visualized using the Integrative Genomics Viewer (Thorvaldsdottir et al., 2012). HTSeq version 0.6.0. was used to count reads over Trichoderma reesei transcripts. Bioconductor DESeq2 package version 1.6.3  (Love et al, 2014) was employed to differential expression analysis, using two-fold change, i.e., log2 fold change ≥ 1 or ≤ -1 and adjusted p-value ≤ 0.05 as thresholds.
Genome_build:v2.0
Supplementary_files_format_and_content: Tab-delimited text files containing gene expression information expressed as normalized abundance counts and as log2 Fold change between indicated samples and the respective p-value calculated by DESeq2.

organism: Trichoderma reesei

source_name: mycelia

growth_protocol: Wild-type strain was grown in MEX medium at 28°C for 7-10 days for complete sporulation. For gene expression assays, a spore suspension containing approximately 107 cells mL-1 was inoculated into 200 mL of Mandels-Andreotti medium (Schmollet al. 2009) containing 1% (w/v) of cellulose, or 2% (w/v) of glucose, or 1 mM of sophorose, as the carbon source.

extract_protocol:
Total RNA was extracted using the TRIzol kit (Invitrogen) according to manufacture's instructions.
RNA-seq libraries were prepared for sequencing using Illumina TruSeq RNA Sample Prep Kit.

value: wild type

tag: tissue

value: mycelia

tag: carbon source

value: Glucose


title: Sample 19c


title: Sample 19b


title: QM9414 Glucose 1

description: Sample 7


title: QM9414 Glucose 2

description: Sample 8

data_processing:
Illumina Casava1.8.2 software used for base-calling.
The Illumina HiSeq 2000 system was used to sequence approximately 117 million 100 bp paired-end reads. These sequences were firstly quality-filtered and mapped to the Trichoderma reesei 2.0 reference genome available the JGI Genome Portal (http://genome.jgi-psf.org/Trire2/Trire2.home.html) using the Bowtie aligner version 0.12.8 (Li, Durbin, 2009), allowing two mismatches and only unique alignments.
After alignment, Samtools version 0.1.18 (Li et al., 2009) was used to process the alignments files which were visualized using the Integrative Genomics Viewer (Thorvaldsdottir et al., 2012).
Bioconductor DESeq package version 1.10.1 (Anders, Huber, 2010) was employed to differential expression analysis, using two-fold change, i.e., log2 fold change ≥ 1 or ≤ -1 and adjusted p-value ≤ 0.05 as thresholds.
Genome_build: v2.0
Supplementary_files_format_and_content: Tab-delimited text files containing gene expression information expressed as normalized abundance counts and as log2 Fold change between indicated samples and the respective p-value calculated by DESeq.


title: QM9414 Sophorose 3

description: Sample 6

value: Sophorose


title: QM9414 Cellulose 1

description: Sample 1

value: Cellulose


title: QM9414 Cellulose 2

description: Sample 2


title: QM9414 Sophorose 1

description: Sample 4


title: QM9414 Cellulose 3

description: Sample 3


title: MCF7 input rep2

first: Paul

middle: A

last: Wade

address: 111 TW Alexander Drive

department: Laboratory of Molecular Carcinogenesis

description:
Sample 6
processed data file: MCF7.input.bedGraph.gz

data_processing:
Basecalls performed using CASAVA version 1.7.0 (MCF7 GATA3 ChIP & input first replicates), version 1.8.0 (T47D GATA3 ChIP & input first replicates), or version 1.8.2 (all second replicates).
Filtered raw data to remove read with average base quality score <20.
Reads were mapped against hg19 reference genome (excluding haplotype chromosomes) with Bowtie 0.12.8 using the folowing parameters:  -m 1 -v 2.
Duplicate mapped reads per library were removed with MarkDuplicates.jar (Picard tools v1.62).
Replicates were combined with MergeSamFiles.jar (Picard tools v1.62).
Peak calls were performed with HOMER 'findPeaks' (v1.4) using the following parameters:  -style factor -tbp 0 -inputtbp 0 [all other parameters default]. Input sequence was used for background.
Mapped reads were extended at their 3' end to a length of 180 bases, then converted to aggregate coverage in bedGraph format by genomeCoverageBed (BEDtools v2.16.2).
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph file per sample showing aggregate coverage of mapped extended reads.
Supplementary_files_format_and_content: Called GATA3 peaks in BED format.

organism: Homo sapiens

source_name: MCF7 breast cancer cell line

growth_protocol: Breast cancer cell lines were cultured in DMEM/F-12 medium supplemented with 10% FBS at 37°C in 5% CO2

extract_protocol:
Cells were cross-linked, lysed and sonicated to generate 200 to 400 bp DNA fragments.  Immunoprecipitation was performed with GATA3 serum generated in rabbits using recombinant 6x histidine tag-fused GATA3 full-length wild-type protein.
ChIP DNA generated in 4-5 individual reactions was pooled to obtain 100ug. Libraries were constructed using TruSeq RNA Sample Preparation kit (Illumina, San Diego, CA, USA). The library was prepared following the manufacturer’s instructions, starting with the end repair step, and amplified with twelve PCR cycles.

tag: replicate

value: none (input)


title: QM9414 Sophorose 2

description: Sample 5


title: T47D GATA3 rep2

description:
Sample 7
processed data file: T47D.GATA3.bedGraph.gz
processed data file: T47D.GATA3.peaks.bed.gz

source_name: T47D breast cancer cell line

value: GATA3 serum (generated in rabbits using recombinant 6x histidine tag-fused GATA3 full-length wild-type protein)


title: T47D GATA3 rep1

description:
Sample 3
processed data file: T47D.GATA3.bedGraph.gz
processed data file: T47D.GATA3.peaks.bed.gz


title: MCF7 GATA3 rep1

description:
Sample 1
processed data file: MCF7.GATA3.bedGraph.gz
processed data file: MCF7.GATA3.peaks.bed.gz


title: MCF7 input rep1

description:
Sample 2
processed data file: MCF7.input.bedGraph.gz


title: PtrSND1-B1 (25h)-1

city: Raleigh

first: Vincent

middle: L

last: Chiang

address: 840 Main Campus Drive

department: Forestry and Environmental Resources

institute: North Carolina State University

data_processing:
Six libraries with different index numbers were pooled by mixing equal quantities of DNA from each library and applied as one lane for Illumina GAIIx sequencing
72-bp average read lengths were obtained.  After removing the 4-bp library sequence index sequences from each read, the remaining 68 bp were mapped to the reference P. trichocarpa genome release V2.2 (Phytozome V7.0, http://www.phytozome.com) using the program “TOPHAT”.
DEGs were identified using “edgeR” by comparing the relative transcript abundance for each gene between the PtrSND1-B1 and the sGFP (control) transfection at each incubation time point (7, 12, and 25 h).
Genome_build: P. trichocarpa genome release V2.2 (Phytozome V7.0, http://www.phytozome.com)
Supplementary_files_format_and_content: processed file with phytozome Populus trichocarpa gene model name and the read counts. The gene information provided in our processed data file correspond to Popgenie Transcript name.

organism: Populus trichocarpa

source_name: Stem differentiating xylem protoplast

growth_protocol: P. trichocarpa plants were maintained in greenhouse

extract_protocol:
stem defferentiating xylem protoplast isolation
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: PEG-mediated DNA transfection

value: Protoplast

tag: transfection time

value: 25 hours

tag: overexpressed gene


title: PtrSND1-B1 (25h)-2


title: PtrSND1-B1 (12h)-2

value: 12 hours


title: PtrSND1-B1 (12h)-3


title: PtrSND1-B1 (12h)-1


title: PtrSND1-B1 (7h)-3

value: 7 hours


title: wt-p53_ChIPseq

city: Bunkyo-ku

first: Nurmaa

last: Dashzeveg

state: Tokyo

address: 1-5-45 Yushima

department: Molecular Biology

country: Japan

institute: Tokyo Medical and Dental University

description: Whole cell lysates

data_processing:
Basecalls performed using Pipeline version 1.5.1
ChIP-seq reads were aligned to the hg18 genome assembly using Bowtie version 0.11.3 with the following configuration (-p24 -v2 -m1 --best --strata --all --sam-nohead --sam --max)
Peaks were called using Illumina ChIP Sequencing Module version 1.0 with the following settings:  Automatically Canculate regions and Peaks (on); Count Threshold (200); Peak Finder Window (21); Region-Finder Window (51); Region-Merging Threshold (100).
Genome_build: hg18
Supplementary_files_format_and_content: Wig files were generated using Takara original program (Please refer to the Takara. Co.LTD)

source_name: osteosarcoma cell line

extract_protocol: The cells were harvested and washed once in 1% of the chilled phosphate-buffered saline (PBS). 1-5x107 cells were centrifuged at 500 x g for 5 min at 4oC then incubated in 1% formaldehyde for 15 min at room temperature and washed with chilled PBS. After a further centrifugation, cell pellets were resuspended in SDS lysis buffer (50 mM of Tris/HCl, pH 8.0, containing 1 mM of DTT, 1 mM of PMSF, 1 mM of Na3VO4, 10µg/ml of aprotinin, 1 µg/ml of leupeptin, 1 µg/ml of pepstatin A, 1% (w/v) of SDS and 10 mM of EDTA) and lysates were sonicated to obtain DNA fragments that consist of 200-500 bp in length. Immunoprecipitation was performed with mouse monoclonal anti-p53 (Santa Cruz Biotechnology) for 2 h at 4oC on the rotation. Immuno-complexes were collected with 30 µl of Protein G-Sepharose beads (Invitrogen) for 1 h at 4oC on rotation. Beads were washed sequentially with 300 µl of washing buffer I (20 mM of Tris/HCl, pH 8.0, containing 500 mM of NaCl, 0.1% of SDS and 2 mM of EDTA), 300 µl of washing buffer II (10 mM of Tris/HCl, pH 8.0, containing 250 mM of LiCl, 1 mM of EDTA, and 1% of dyoxyholate), and with 300 µl of Tris/EDTA buffer twice. Precipitated chromatin complexes were eluted with 100 µl of elution buffer (10 mM of DTT, 1% of SDS and 0.1 M of NaHCO3) for 15 min on shaker. Cross-linking was reversed by adding NaCl, to a final concentration of 200 mM and incubated at 65oC overnight. Remaining proteins were digested with the extraction buffer (50 mM of Tris/HCl, pH 6.8, containing 10 mM of EDTA, and 40 µg/ml of proteinase K) for 1 h at 45oC. DNA was recovered phenol / chloroform / isoamyl alcohol (25 / 24 / 1) extraction and ethanol precipitaded. Recovered DNA was blunt-ended with T4 DNA polymerase (Takara) before cloning into pBluescript SK vector. Sequencing was performed by Takara BIO INC.


title: PtrSND1-B1 (25h)-3


title: Sample 38c

value: Ixodes scapularis

value: mRNA


title: PtrSND1-B1 (7h)-1


title: PtrSND1-B1 (7h)-2


title: GFP (25h)-3

value: sGFP (control)


title: GFP (12h)-3


title: GFP (25h)-2


title: GFP (25h)-1


title: GFP (12h)-2


title: T47D input rep2

description:
Sample 8
processed data file: T47D.input.bedGraph.gz


title: GFP (12h)-1


title: GFP (7h)-3


title: T47D input rep1

description:
Sample 4
processed data file: T47D.input.bedGraph.gz


title: GFP (7h)-2


title: GFP (7h)-1


title: MCF7 GATA3 rep2

description:
Sample 5
processed data file: MCF7.GATA3.bedGraph.gz
processed data file: MCF7.GATA3.peaks.bed.gz


title: MOCK

city: Shanghai

first: Jiao

last: Liu

address: 300 Fenglin Road

country: China

institute: Shanghai Institute of Plant Physiology & Ecology

data_processing:
To get the high quality tags that we used for analysis, we filtered the potentially erroneous tags (only one copy number, only adaptor sequences, or containing unknown sequences "N") to get the clean tags.
For mapping the clean tags to reference sequences, a database containing all possible CATG +17 bases length sequences was created using a large collection of cassava ESTs from TIGR (Manihot_esculenta_release_5, containing 5,189 assemblies, 10,214 singletons, released 1 June 2007), cassava ESTs from NCBI (80,631 ESTs, released 25 August 2010), 34,151 predicted cassava transcripts from Phytozome and a 35,400 full-length cDNA RIKEN library. The clean tag expression was normalized to TPM (transcripts per million clean tags).
Mapped genes were locally blasted against the NCBI non-redundant protein database using the blastx program in the blastall package (version 2.2.25), and the top hits were used for gene annotation. Mapped genes were further analyzed with Blast2go to get GO annotations.
Genome_build: cassava ESTs from TIGR and NCBI, predicted cassava transcripts from Phytozome and a 35,400 full-length cDNA RIKEN library.
Supplementary_files_format_and_content: *_TagCopyNumber.txt: Tag copy number and TPM value of each sample. Tab-delimited text format. Extraction of tags and tag counting were performed using the Illumina pipeline.

source_name: Control cassava leaves

growth_protocol: Cassava variety TMS30555 were planted in a greenhouse condition under 25±2ºC and 16 h/8 h photoperiod.

extract_protocol:
Samples from three independent replicates were pooled for RNA isolation and library construction. Control leaves were treated in parallel. Total RNA was isolated from the leaf mixture using the RNAprep pure Plant Kit (Tiangen Biotech; Beijing, China). Six micrograms of total RNA were used for sequencing tag preparation with Digital Gene Expression Sample Prep Kit (Illumina Inc; San Diego, CA, USA) according to the manufacturer's protocol.
Using Oligo (dT) magnetic bead, mRNA was purified from each of the two samples, then Oligo (dT) was used as primer to synthesize cDNA. The bead-bound cDNA was subsequently digested with restriction enzyme NlaIII, which recognizes and cuts off the CATG sites. The fragments apart from the 3' cDNA fragments connected to Oligo (dT) beads were washed away and the Illumina adaptor 1 was ligated to the 5' end of the bead-bound cDNA fragments. The junction of Illumina adaptor 1 and CATG site is the recognition site of MmeI, and this enyme could cut at 17bp downstream of the CATG site, and then produce tags with adaptor 1. After removing 3' fragments with magnetic beads precipitation, Illumina adaptor 2 was ligated to the 3' ends of tags, finally acquired tags with different adaptors of both ends formed a tag library. After 15 cycles of linear PCR amplification, 95 bp fragments were purified by 6% TBE PAGE Gel electrophoresis. After denaturation, the single-chain molecules were fixed onto the Illumina Sequencing Chip. Each molecule grew into a single-molecule cluster sequencing template through in situ amplification and was sequenced with the method of sequencing by synthesis (SBS).

treatment_protocol: A. tumefaciens strain LBA4404 containing the infectious clones of ACMV-NOg DNA-A and DNA-B were separately cultured on YEB plates supplemented with Streptomycin (100 mg/L), Rifampicin (25 mg/L) and Kanamycin (50 mg/L) at 28ºC for 48 hours. Then equal amounts of each culture were mixed together. One-month-old cassava plantlets with 5-6 leaves were needle-punctured 4-6 times with the mixed agrobacteria suspension at the tip of the shoot axis using a syringe needle (Ø 0.5 mm). Control samples were harvested from empty agrobacteria treated leaves incubated under the same conditions.

tag: cultivar

value: leaf

tag: age

value: 1 month

tag: virus infection

value: control


title: INF

source_name: ACMV-infected cassava leaves

value: African cassava mosaic virus


title: RUNX1_Tconv S030b

city: Regensburg

first: Michael

last: Rehli

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

department: Internal Med III

institute: University Hospital Regensburg

description: Chromatin IP against RUNX1

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: CD4+CD25- expanded conventional T cells

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

tag: cell type

value: CD4+CD25- expanded conventional T cells

value: RUNX1 (abcam ab 23980)

tag: chip antibody manufacturer

value: abcam

tag: chip antibody catalog #


title: H3K27ac_TregRA+ S030b

description: Chromatin IP against H3K27ac

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

tag: chip antibody

value: H3K27ac (abcam ab 4729)


title: FOXP3_Tconv S30b

description: Chromatin IP against FOXP3

value: FOXP3 (Novus NB600-245)

value: Novus


title: RUNX1_TregRA+ S030b

description: Chromatin IP against RUNX1

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


title: STAT5_Tconv S030b

description: Chromatin IP against STAT5

value: STAT5 (Santa Cruz sc-836x)

value: Santa Cruz


title: STAT5_TregRA+ S030b

description: Chromatin IP against STAT5


title: Input control S030b

description: Input control

source_name: Input control

value: Input control

value: no antibody


title: tofu-1 RNAi capped small RNA rep2

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

institute: Shenzhen Bay Laboratory

description: Sample 32

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)

organism: Caenorhabditis elegans

source_name: tofu-1 RNAi 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).
Small RNA cloning and capped small RNA cloning

tag: strain background

tag: genotype/variation

value: tofu-1 RNAi rrf-3 null background

value: 4 days post L1 release

tag: growth medium type

value: Liquid S-basal media

tag: clipping sequence

value: CTGTAGGCACCATCAATCGTATGCCGTCTTCTGCTTG

tag: molecule subtype

value: Capped small RNA


title: Rag2 -/- Runx1

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

institute: University Medical Center Freiburg

description: Sample 18

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

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

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

value: 5-6 weeks

tag: cells used

tag: antibody

value: Abcam (ab23980)

tag: antibody quantity

value: 10 µg

tag: magnetic beads

value: Protein G dynabeads

tag: bead volume

tag: estimated fragment size


title: ETS1_TregRA+ S030b

description: Chromatin IP against ETS1

tag: donor

value: ETS1 (Santa Cruz sc-350x)


title: ETS1_Tconv S030b

description: Chromatin IP against ETS1

tag: cell type

value: CD4+CD25- expanded conventional T cells


title: Worker brain

city: Canberra

first: Sylvain

last: Foret

state: ACT

address: Gould Building #116

department: Research School of Biology

country: Australia

institute: The Australian National University

description:
Sample 2
bisulfite converted DNA

data_processing:
Extraction of sequences was done using Illumina Pipeline v1.4 software
Basecalling was done using Illumina SCS v2.5 software
Reads were mapped using BSMAP-1.0240 with minor modifications
We only took into account bases of quality 20 or more, flanked by at least three perfectly matching bases of quality 15 or more
Genome_build: Amel_4.5
Supplementary_files_format_and_content: The process files contain the following columns: scaffold name, position, strand, neighboring sequence (from -2 to +2), type, number of methylated reads, number of unmethylated reads, p-value, adjusted p-value

organism: Apis mellifera

source_name: Brain

extract_protocol:
Material was prepared from 50 brains of age-matched 2.5 wk old queen and 8 d old workers
Illumina paired-end bisulfite sequencing preparation kit

tag: caste

value: worker

tag: Stage

value: adult

tag: age

value: 8 days


title: Empty vector RNAi capped small RNA rep2

description: Sample 31

source_name: Empty vector RNAi capped small RNA

tag: strain background

value: Empty vector RNAi rrf-3 null background


title: Queen brain

description:
Sample 1
bisulfite converted DNA

value: queen

value: 18 days


title: RNAseq_LEC_rep1

city: EMERYVILLE

first: ALEXANDRE

last: MERCIER

address: 5300 CHIRON WAY

department: INFECTIOUS DISEASES

institute: NOVARTIS INSTITUTES FOR BIOMEDICAL RESEARCH

data_processing:
Basecalls performed using CASAVA version 1.8
ChIPseq: reads were aligned to the hg19 genome assembly using Bowtie2 (v2.1.0, default parameters)
ChIPseq: peaks were called using MACS 1.4.2 using the default parameters except when otherwise specified (see Samples section)
RNAseq: reads were aligned to the hg19 genome assembly using TopHat2 (v2.0.8b, default parameters)
RNAseq: gene expression analysis was performed with the Cufflinks/Cuffdiff package v2.1.1 using default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: ChIPseq: peak calling output files from the MACS program (tab-delimited text format). Contain peak genomic location, tag abundance and peak score (p-value, FDR)
Supplementary_files_format_and_content: RNAseq: output files from Cufflinks and Cuffdiff (tab-delimited format) that include FPKM values, gene expression ratios (LEC219 vs LEC) and statistical analysis (scores) for all hg19-annotated genes

source_name: Dermal lymphatic endothelium

extract_protocol:
Total RNA was extracted from 1x10^7 cells using RNABee (AMSBIO cat. Cs-104B) following the manufacturer guidelines. Polyadenylated RNA was isolated from the total fraction using Oligotex mRNA kit (Qiagen cat. 70022). The resulting mRNA was partially fragmented by alkaline hydrolysis with sodium carbonate to ,150 nt segments on average, and then fragments between 40–100 nt were isolated from gel.
Libraries for RNA-seq were prepared using the Ribo-Zero magnetic and the ART-seq kits following the manufacturer recommendations (Epicentre, MRZH11124 and RPHMR12126).

treatment_protocol: When indicated, 1 µM doxycyclin (dox) and 500 µM phosphonoformic acid (PFA) were added to the culture medium for 72 hrs

value: Dermal lymphatic endothelial cells

tag: cell line

value: LEC


title: RNAseq_LEC_rep2


title: RNAseq_LEC219_rep1

tag: infection


title: RNAseq_LEC219_rep2


title: ChIPseq_input_iSLK219

description: Sequencing control

source_name: Kidney epithelium

extract_protocol:
1 x 10^7 cells were fixed with 1% formaldehyde 5 minutes prior to harvest. Nuclei preparations were done using the truChIP High Cell Chromatin Shearing Kit with SDS from Covaris and chromatin was sheared with a Covaris E220 Ultrasonicator. The average size of chromatin fragments was ~200 bp. Antibodies for ChIP were coupled to Dynabeads (Invitrogen) and incubated with chromatin extracts for 4 hours at 4C in cold RIPA buffer (10 mM Tris pH 8.0, 1 mM EDTA, 150 mM NaCl, 5% glycerol, 0.1% Na deoxycholate, 0.1% SDS, 1% Triton X-100, protease inhibitors (Complete Mini, Roche)). Antibodies used for ChIP: rat α-LANA (Advanced Biotechnologies, 13-210-100), α-H3K4me3 (Abcam, ab8580), α-H3K27me3 (Millipore, 07-449), α-H3K36me3 (Abcam, ab9050), and α-Pol II (Santa Cruz Biotechnology, sc-899 X). The immunoprecipitated chromatin was sequentially washed in high salt RIPA buffer (500 mM NaCl) and LiCl wash buffer (50 mM Tris pH 8.0, 1 mM EDTA, 250 mM LiCl, 1% NP-40, 0.5% Na deoxycholate). Chromatin crosslinks were reversed by incubating samples overnight at 65°C in the presence of proteinase K (200 µg/ml, Invitrogen). DNA was recovered using AMPure XP beads (Beckman Coulter, Inc).
Libraries were prepared according to Illumina's instructions (TruSeq ChIP Sample Prep Kit, part # 15034288)

value: Kidney epithelial cells


title: ChIPseq_H3K36me3_iSLK219

tag: chip antibody

value: H3K36me3 (Abcam, ab9050)


title: ChIPseq_H3K27me3_iSLK219

value: H3K27me3 (Millipore, 07-449)


title: FOXP3_TregRA+ S30b

description: Chromatin IP against FOXP3

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

value: FOXP3 (Novus NB600-245)

tag: chip antibody manufacturer

value: Novus

tag: chip antibody catalog #


title: ChIPseq_IgG_LEC219

description: ChIPseq peak calling control data set for sample #22,23

value: IgG (Millipore, pp64b)


title: ChIPseq_IgG_iSLK219

description: ChIPseq peak calling control data set for sample #20,21


title: ChIPseq_H3K4me3_LEC

value: H3K4me3 (Abcam, ab8580)


title: ChIPseq_H3K4me3_iSLK

value: iSLK


title: ChIPseq_LANA_BCBL1_rep2

source_name: Primary effusion lymphoma

value: Primary effusion lymphoma B cells

value: KSHV

value: LANA (Advanced Biotechnologies, 13-210-100)


title: ChIPseq_H3K4me3_iSLK219


title: H3K27ac_Tconv S030b

description: Chromatin IP against H3K27ac

value: CD4+CD25- expanded conventional T cells

value: H3K27ac (abcam ab 4729)

value: abcam


title: ChIPseq_LANA_BCBL1_rep1


title: ChIPseq_IgG_BCBL1

description: ChIPseq peak calling control data set for samples #18,19


title: ChIPseq_LANA_BJAB

description: ChIPseq peak calling control data set for sample #16

source_name: Human Burkitt lymphoma

value: Human Burkitt lymphoma B cells

value: BJAB


title: ChIPseq_LANA_BEC219

source_name: Dermal blood endothelium

value: Dermal blood endothelial cells


title: ChIPseq_LANA_LEC219_rep1

value: Dermal lymphatic endothelial cells


title: ChIPseq_LANA_LEC_rep1

description: ChIPseq peak calling control data set for sample #10

value: LEC


title: ChIPseq_LANA_LEC219_rep2


title: ChIPseq_LANA_BJAB219


title: ChIPseq_LANA_BEC

description: ChIPseq peak calling control data set for sample #14

value: BEC


title: ChIPseq_LANA_iSLK219_dox_rep2

value: Kidney epithelial cells


title: ChIPseq_LANA_LEC_rep2

description: ChIPseq peak calling control data set for sample #12


title: ChIPseq_LANA_iSLK219_dox_PFA_rep2


title: ChIPseq_LANA_iSLK219_dox_PFA_rep1


title: ChIPseq_H3K4me3_LEC219


title: ChIPseq_LANA_iSLK219_rep1


title: ChIPseq_LANA_iSLK_rep1

description: ChIPseq peak calling control data set for samples #2,3,4


title: Sample 36c

description: Ehrlichia chaffeensis Osceola strain-infected Ixodes tick cells

organism: Ehrlichia chaffeensis str. Osceola

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

tag: ehrlichia strain

value: Osceola

tag: host cell

value: Ixodes scapularis

tag: infectivity

tag: assayed molecule

value: mRNA


title: Sample 26b

description: Ehrlichia chaffeensis Osceola strain-infected DH82 cells

source_name: Ehrlichia (Osceola) in canine cell line DH82

value: Canis lupus familiaris


title: Sample 26a


title: Sample 36a


title: Sample 15b

value: total RNA


title: Sample 15a


title: Sample 26c


title: Sample 6b


title: Sample 6c


title: Sample 6a


title: Sample 35c

description: Ehrlichia chaffeensis Liberty strain-infected Ixodes tick cells

organism: Ehrlichia chaffeensis str. Liberty

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

value: Liberty


title: ChIPseq_LANA_iSLK219_rep2

value: LANA (Advanced Biotechnologies, 13-210-100)


title: Sample 25c

description: Ehrlichia chaffeensis Liberty strain-infected DH82 cells

source_name: Ehrlichia (Liberty) in canine cell line DH82


title: Sample 25a


title: Sample 14c


title: Sample 35b


title: Sample 25b


title: Sample 35a


title: Sample 14a


title: Sample 14b


title: ChIPseq_LANA_iSLK_rep2

description: ChIPseq peak calling control data set for samples #6,7,8

value: iSLK


title: ChIPseq_LANA_iSLK219_dox_rep1


title: Sample 15c


title: Sample 5b


title: Sample 34b

description: Ehrlichia chaffeensis Jax strain-infected Ixodes tick cells

organism: Ehrlichia chaffeensis str. Jax

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

value: Jax


title: Sample 34c


title: Sample 24b

description: Ehrlichia chaffeensis Jax strain-infected DH82 cells

source_name: Ehrlichia (Jax) in canine cell line DH82


title: Sample 24a


title: Sample 5a


title: Sample 13a


title: Sample 13c


title: Sample 13b


title: Sample 4b


title: Sample 4a


title: Sample 4c


title: Sample 33c

description: Ehrlichia chaffeensis Heartland strain-infected Ixodes tick cells

organism: Ehrlichia chaffeensis str. Heartland

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

value: Heartland


title: Sample 33b


title: Sample 33a


title: Sample 5c


title: Sample 23a

description: Ehrlichia chaffeensis Heartland strain-infected DH82 cells

source_name: Ehrlichia (Heartland) in canine cell line DH82


title: Sample 23c


title: Sample 12c


title: Sample 12a


title: Sample 3c


title: Sample 3b


title: Sample 12b


title: Sample 24c


title: Sample 34a


title: Sample 3a


title: Sample 36b


title: DP E47

description: Sample 20

organism: Mus musculus

source_name: primary CD4+ CD8+ DP thymocytes

tag: strain

value: 5-6 weeks

tag: genotype/variation

value: WT

tag: cells used

tag: antibody

value: Santa Cruz (SC-349X)

tag: antibody quantity

value: 10 µg

tag: magnetic beads

value: Protein G dynabeads

tag: bead volume


title: Twin31-1_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

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 31 sibling 1

tag: tissue

value: blood


title: Twin33-1_FAIREseq

description: FAIRE-seq

value: MZ twin pair 33 sibling 1


title: Twin32-2_FAIREseq

description: FAIRE-seq

value: MZ twin pair 32 sibling 2


title: Twin34-2_FAIREseq

description: FAIRE-seq

value: MZ twin pair 34 sibling 2


title: Twin34-1_FAIREseq

description: FAIRE-seq

value: MZ twin pair 34 sibling 1


title: Twin36-1_FAIREseq

description: FAIRE-seq

value: MZ twin pair 36 sibling 1


title: Twin36-2_FAIREseq

description: FAIRE-seq

value: MZ twin pair 36 sibling 2


title: Twin32-1_FAIREseq

description: FAIRE-seq

value: MZ twin pair 32 sibling 1


title: Twin35-1_FAIREseq

description: FAIRE-seq

value: MZ twin pair 35 sibling 1


title: Rag2 -/- Input

description: Sample 19

source_name: primary Rag2 -/- thymocytes

tag: age

tag: estimated fragment size


title: Twin30-2_FAIREseq

description: FAIRE-seq

value: MZ twin pair 30 sibling 2


title: Sample 23b

value: Heartland

value: Canis lupus familiaris

value: mRNA