title: P10.5 Miwi2 KO Replicate 1 RNA-seq

extract_protocol:
RNA was extracted from whole testes or cells using the RNeasy Micro Kit (Qiagen 74004). The material was quantified using a Nanodrop ND-1000 (Nanodrop) for RNA from whole testis or the Qubit RNA High Sensitivity Assay (Life Technologies) for RNA from sorted germ cells. RNA quality for material from whole testis was assessed by gel electrophoresis and visualization of the 28S and 18S rRNA bands.
RNA from whole testes was processed for sequencing using a TruSeq RNA Sample Preparation Kit v2 (Illumina) with 250ng - 2μg total RNA as starting material. Mutant and controls were always matched for starting RNA content. RNA from sorted germ cell was processed using the Ovation Human FFPE RNA-Seq Multiple kit (Nugen) using custom primers for depletion of murine rRNA provided by the manufacturer, using 10ng of total RNA. Each library was prepared using RNA from one individual mouse.

value: Miwi2 KO

value: TruSeq V2


title: P10.5 Miwi2 KO Replicate 2 RNA-seq

status: Public on Dec 12 2014

type: SRA

city: Dallas

first: Hume

last: Stroud

state: TX

address: 5323 Harry Hines Blvd

country: USA

institute: UT Southwestern

library_source: transcriptomic

data_processing:
RNA-seq.  For all analyses, reads were trimmed to 50bp and those mapping to ribosomal RNA (GenBank identifiers: 18S NR_003278.3; 28S NR_003279.1; 5S D14832.1; 5.8S K01367.1) by up to three mismatches were discarded.  Reads were then mapped to known mm9 gene and repeat annotations by allowing up to two mismatches and only retaining reads that mapped to one location. When reads did not map to the annotated genes and repeats, the reads were mapped to the mm9 genome. Number of reads mapping to genes and repeats were determined by using HTSeq (doi: 10.1101/002824) using default parameters. Expression values were calculated as reads per kilobase of exons per million mapping reads (RPKM). Differential gene and repeat expression was determined by using DESeq47 using default parameters.
smRNA-seq. Adapter sequences were removed prior to all analyses. For analyzing piRNA reads over genes and repeats misexpressed in Morc1 KO: Reads were mapped to the mm9 genome using Bowtie by not allowing any mismatches, and retaining reads that only mapped to one location in the genome.
ChIP-seq. Previously published ChIP-seq data28 was obtained from GSE38165 in Gene Expression Omnibus. Reads were mapped to the mm9 genome using Bowtie by allowing up to two mismatches, and only retaining reads that mapped to one location in the genome. Reads mapping to the same location were collapsed into one read. For all analyses, the data were normalized to total number of mapping reads in the library
Bisulfite-seq. Reads were split into 50bp reads prior to mapping. Reads were mapped to the mm9 genome as well as the lambda genome using BS seeker248 using default parameters. Methylation levels were determined by #C/(#C+#T).
Genome_build: mm9
Supplementary_files_format_and_content: RNA-seq. Column1: Ensembl ID; Column2: chromosome; Column3: strand; Column4: start of gene; Column5: end of gene; Column6: name; Column7: number of reads; Column8: RPKM.
Supplementary_files_format_and_content: smRNA-seq. Reads with adapter sequences trimmed.
Supplementary_files_format_and_content: Bisulfite-seq. Bigwig files of fractional methylation levels (#C/(#C+#T)) in CG and CH (H=A,T or C) sequence contexts.
Supplementary_files_format_and_content: ChIP-seq. Wig files. Coordinates, read density.

molecule: polyA RNA

organism: Mus musculus

source_name: P10.5 whole testis

tag: genotype/variation

tag: library type

tag: tissue

value: whole testis


title: P10.5 Miwi2 het Replicate 2 RNA-seq

value: Miwi2 het


title: L_D_H3T6ph

city: Toronto

first: Housheng

middle: Hansen

last: He

state: Ontario

address: 101 College Street, PMCRT 11-305

department: Medical Biophysics

country: Canada

institute: UNIVERSITY HEALTH NETWORK

library_source: genomic

data_processing:
Illumina Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v2.0.0 or tophat v2.0.4
MACS2 was used to call peaks and generate bigwiggle file, cuffdiff v2.0.1 was used to identify differentially expressed genes
Genome_build: hg19
Supplementary_files_format_and_content: Peaks files for ChIP-seq samples.
Supplementary_files_format_and_content: Abundance counts for RNA-seq samples.

molecule: genomic DNA

organism: Homo sapiens

source_name: Prostate cancer cell line LNCaP

growth_protocol: The prostate cancer cell line LNCaP and VCaP were obtained from the American Type Culture Collection. LNCaP cells were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS), 2mM glutamine, 100 U/mL penicillin and 100 mg/mL streptomycin. VCaP cells were maintained in DMEM medium supplemented with 10% fetal bovine serum (FBS), 2 mM glutamine, 100 U/mL penicillin, 100 mg/mL streptomycin.

extract_protocol:
LNCaP and VCaP cells were harvested by scraping from the plates.
Libraries were prepared according to Rubicon's instructions accompanying the ThruPLEX-FD kit (for ChIP-seq) or Illumina TruSeq RNA Sample Prep Kit v2 (for RNA-seq)

treatment_protocol: LNCaP and VCaP cells were starved in phenol-red-free medium supplemented with 10% charcoal stripped FBS for 3 days before hormone stimulation.

tag: cell type

value: LNCaP

tag: transfection

value: no treatment

tag: passage

tag: antibody

value: H3T6ph antibody (provided by Dr. Roland Schüle's lab)


title: P10.5 DNMT3L KO Replicate 3 RNA-seq

value: DNMT3L KO


title: P10.5 Miwi2 het Replicate 1 RNA-seq


title: P10.5 DNMT3L het Replicate 3 RNA-seq

value: DNMT3L het


title: P10.5 DNMT3L KO Replicate 1 RNA-seq


title: P10.5 DNMT3L het Replicate 1 RNA-seq


title: P10.5 DNMT3L wt Replicate 1 RNA-seq

value: DNMT3L WT


title: P10.5 DNMT3L KO Replicate 2 RNA-seq


title: P10.5 DNMT3L het Replicate 2 RNA-seq


title: P10.5 DNMT3L wt Replicate 2 RNA-seq


title: P14.5 Morc1 KO Replicate 1 RNA-seq

source_name: P14.5 whole testis

value: Morc1 KO


title: P14.5 Morc1 KO Replicate 2 RNA-seq


title: P14.5 Morc1 KO Replicate 3 RNA-seq


title: P14.5 Morc1 het Replicate 1 RNA-seq

value: Morc1 het


title: P14.5 Morc1 het Replicate 2 RNA-seq


title: E16.5 Morc1 het smRNA-seq

description: smRNA

molecule: total RNA

source_name: E16.5 whole testis

extract_protocol:
Total RNA was isolated from embryonic testes using Ribozol. Thirty μg total RNA was loaded on 12% urea-polyacrylamide (PAA) gel. The 19-30 nt fraction was excised and snap-frozen in liquid nitrogen in 400 μl 0.4M NaCl. RNA was eluted from the gel overnight at 16°C while shaken at 1,000 rpm  and then precipitated with 3 vol absolute ethanol. Pre-adenylated 3’ linker (/5`Phos/TGGAATTCTCGGGTGCCAAGGAACTC/3`ddC/; 5’DNA adenylation kit, NEB) was ligated to RNA over night at 4C using Truncated RNA Ligase 2 (NEB). Ligation reactions were loaded onto 10% urea-PAGE, the 45-56 nt fraction was excised and nucleic acids extracted as above. 5’ linker (rGrUrUrCrArGrArGrUrUrCrUrArCrArGrUrCrCrGrArCrGrArUrC) was ligated to the samples using RNA Ligase 1 (NEB) over night at 4C. Ligation reactions were loaded on 10% Urea-PAA gel, 72-83 nt fraction was excised and nucleic acids as above. Extracted samples were reverse-transcribed (primer sequence: GGAGTTCCTTGGCACCCGAGA) and library amplified by PCR using standard Illumina primers. Final libraries were excised from the agarose gel and sequenced.
 Since this is shaking, not centrifugation, we include rpm

value: In house smRNAseq method


title: P10.5 Morc1 KO Replicate 2 (testis) RNA-seq


title: P10.5 Morc1 KO Replicate 1 (testis) RNA-seq


title: P10.5 Morc1 het Replicate 2 (testis) RNA-seq


title: P10.5 Morc1 het Replicate 3 (testis) RNA-seq


title: P14.5 Morc1 het Replicate 3 RNA-seq


title: P10.5 Morc1 het Replicate 1 Preliminary RNA-seq


title: P10.5 Morc1 WT Replicate 1 RNA-seq

value: Morc1 WT


title: P10.5 Morc1 KO Replicate 3 RNA-seq

description: rRNA depleted

source_name: P10.5 sorted germ cells

value: Ovation Human FFPE w/murine rRNA depletion

value: sorted germ cells


title: P10.5 Morc1 KO Replicate 2 RNA-seq

description: rRNA depleted


title: P10.5 Morc1 KO Replicate 3 (testis) RNA-seq


title: P10.5 Morc1 WT Replicate 1 Preliminary RNA-seq


title: P10.5 Morc1 het Replicate 4 RNA-seq

description: rRNA depleted


title: P10.5 DNMT3L wt Replicate 3 RNA-seq


title: P10.5 Morc1 het Replicate 2 RNA-seq

description: rRNA depleted


title: P10.5 Morc1 het Replicate 1 RNA-seq

description: rRNA depleted


title: P2.5 Morc1 KO Replicate 2 RNA-seq

description: rRNA depleted

source_name: P2.5 sorted germ cells


title: P2.5 Morc1 het Replicate 2 RNA-seq

description: rRNA depleted


title: P2.5 Morc1 KO Replicate 1 RNA-seq

description: rRNA depleted


title: P2.5 Morc1 het Replicate 3 RNA-seq

description: rRNA depleted


title: E18.5 Morc1 KO Replicate 2 RNA-seq

description: rRNA depleted

source_name: E18.5 sorted germ cells


title: P2.5 Morc1 het Replicate 1 RNA-seq

description: rRNA depleted


title: PiDcl1_m

city: Uppsala

first: Anna

last: Åsman

address: PO Box 7080

department: Molecular Sciences

country: Sweden

institute: Swedish University of Agricultural Sciences (SLU)

data_processing:
Demultiplexing and conversion using CASAVA v1.8.2.
Adaptor trimming using cutadapt v2.2, only saving reads with adaptor match of at least 5 bp
Consensus reference sequences for P. infestans tRNA were constructed. Briefly, tRNA sequences for each codon were clustered using cd-hit, and a consensus sequence was obtained from the aligned sequences (tRNA_clusters.fa).
Reads were mapped to the tRNA reference sequence (bowtie v2.1.0, one mismatch in seed, seed length 18bp, report up to 10 matches)
The number of reads mapping to tRNA was asessed using bedtools v2.21.0.
Genome_build: P. infestans strain T30-4, http://www.broadinstitute.org
Supplementary_files_format_and_content: tRNA_read_counts.txt file shows the number of reads mapping to each tRNA.

organism: Phytophthora infestans

source_name: P. Infestans line PiDcl1 mycelium

extract_protocol:
Material from P. infestans mycelium and infected potato leaves were harvested and flash frozen in liquid nitrogen. Total RNA extraction was done with the mirVana™ miRNA Isolation Kit (Ambion), according to the manufacturer’s protocol.
RNA library preparation was done according to the Illumina small RNA sample preparation kit. RNA sequencing was done using the Illumina HiSeq 2500 platform.

tag: p. infestans strain

value: PiDcl1 knockdown (background 88069)


title: PiDcl1_72

source_name: P. infestans-inoculated potato leaf tissue

tag: host organism

value: Solanum tuberosum

tag: host potato cultivar

value: Désirée

tag: infection time point

value: 72 hours post inoculation


title: E18.5 Morc1 KO Replicate 1 RNA-seq

description: rRNA depleted


title: PiDcl1_48

value: 48 hours post inoculation


title: 88069_72

value: Isolate 88069


title: E18.5 Morc1 het Replicate 1 RNA-seq

description: rRNA depleted


title: E16.5 Morc1 KO Replicate 1 RNA-seq

description: rRNA depleted

source_name: E16.5 sorted germ cells


title: P10.5 Morc1 KO Replicate 1 RNA-seq

description: rRNA depleted


title: 88069_m

source_name: P. Infestans isolate 88069 mycelium


title: E16.5 Morc1 KO Replicate 2 RNA-seq

description: rRNA depleted


title: P10.5 Morc1 het Replicate 3 RNA-seq

description: rRNA depleted


title: PiDcl1_24

value: 24 hours post inoculation


title: 88069_24


title: E16.5 Morc1 het  Replicate 2 RNA-seq

description: rRNA depleted


title: E16.5 Morc1 het Replicate 1 RNA-seq

description: rRNA depleted


title: 88069_48


title: PDtr

status: Public on Dec 11 2014

city: Haifa

first: Itai

last: Yanai

address: Technion City

department: Biology

country: Israel

institute: Technion - Israel Institute of Technology

description: After an overnight incubation - more than 8 E cells are visible

data_processing:
Libraries were sequenced on the Illumina HiSeq2000 according to standard, paired-end sequencing, protocols. Primary analysis done in RTA 1.17.20,1.13.48
Conversion from BCL to FASTQ and deumltiplexing using CASAVA-1.8 (configureBclToFastq.pl--fastq-cluster-count 1234567890 --mismatches 0 --use-bases-mask Y15n,I6n,Y35n)
Filter and read trimming (minimum quality of 20, max 1 exception. trimming not required).
RNA-seq (Hashimshony, et a. 2012l) demultiplexing of second mate, using first mate barcode, allowing 1 mismatch in the 5 first letters of the barcode.
BWA mapping, version 0.6.1, against c. elegans genome WBCel215 (bwa aln -n 0.04 -o 1 -e -1 -d 16 -i 5 -k 2 -M 3 -O 11 -E 4)
Read counting with htseq-count version 0.5.3p1. Using a custom annotation,based on WS230 exon annotation (union of overlapping reads).
Genome_build: WBcel215
Supplementary_files_format_and_content: Expression matrix, transcripts per million - whole-embryo timecourse.  Meaned (Samples 1-56), 50 stages.
Supplementary_files_format_and_content: Expression matrix, transcripts per million - 5 lineages ,11 timepoints.  Meaned (Samples 57-184), 55 stages.
Supplementary_files_format_and_content: Expression matrix, read count. (Samples 1-184, unmeaned).
Supplementary_files_format_and_content: Expression matrix, read count. Spikeins (Samples 1-184, unmeaned)

organism: Caenorhabditis elegans

source_name: P blastomere tp 11

growth_protocol: The five lineages were cultured in a humid chamber in EGM.

extract_protocol:
Egg shells were removed from C. elegans embryos and the resulting blastomeres cultured. For the blastomere sampling, the egg shell and vitelline membrane were removed at the two cell stage, and the embryo separated to the AB and P1 blastomeres by pipetting. P1 was allowed to undergo one cell division and separated to EMS and P2, or two cell divisions before being separated to MS, E, C and P3 blastomeres. All lineages from a single embryo were frozen at the same time
The CEL-Seq protocol (Hashimshony, et al. 2012) was used to amplify and sequence both RNA from the whole embryos and the cultured blastomeres. CEL-seq multiplexing barocdes were used.

tag: experiment set

value: Blastomeres

tag: time

value: minutes passed the 2-cell stage:n.a.

tag: collection timing in reference to e lineage

tag: time - blastomeres

tag: germ layer

value: P


title: PD_(E8++)

description: 180 minutes after division of Eal, Ear, Epl and Epr to Eala, Ealp, Eara, Earp, Epla, Eplp, Epra and Eprp

source_name: P blastomere tp 10


title: PD_(E8+)

description: 90 minutes after division of Eal, Ear, Epl and Epr to Eala, Ealp, Eara, Earp, Epla, Eplp, Epra and Eprp

source_name: P blastomere tp 9


title: PD_(E8)_rep1

description: After division of Eal, Ear, Epl and Epr to Eala, Ealp, Eara, Earp, Epla, Eplp, Epra and Eprp

source_name: P blastomere tp 8

value: Blastomeres, developmental event

value: minutes passed the 2-cell stage:180


title: PD_(E8)_rep2


title: PD_(E4+)_rep3

description: 60 minutes after division of Ea and Ep to Eal,Ear,Epl and Epr

source_name: P blastomere tp 7

value: minutes passed the 2-cell stage:140


title: PD_(E4+)_rep1


title: PD_(E4+)_rep2


title: P4D_(E2+)_rep2

description: After division of MSa and MSp to MSaa, MSap, MSpa and MSpp

source_name: P blastomere tp 5

value: minutes passed the 2-cell stage:90


title: P4D_(E2+)_rep1


title: E18.5 Morc1 het Replicate 2 RNA-seq

description: rRNA depleted

value: Morc1 het


title: P4D_(E2)_rep2

description: After division of E to Ea and Ep

source_name: P blastomere tp 4

value: minutes passed the 2-cell stage:60


title: P3_(E)_rep3

description: After division of EMS to E and MS

source_name: P blastomere tp 3

value: Blastomere, developmental event

value: minutes passed the 2-cell stage:40

value: E


title: P3_(E)_rep2

description: After division of EMS to E and MS


title: P4D_(E2)_rep1

description: After division of E to Ea and Ep


title: P3_(E)_rep1

description: After division of EMS to E and MS


title: Ctr_rep2

source_name: C blastomere tp 11

value: C


title: Ctr_rep3


title: Ctr_rep1


title: C_(E8++)_rep2

source_name: C blastomere tp 10


title: C_(E8+)

source_name: C blastomere tp 9


title: C_(E8)_rep1

source_name: C blastomere tp 8


title: C_(E4+)_rep2

source_name: C blastomere tp 7


title: C_(E4+)_rep1


title: C_(E4)_rep2

description: After division of Ea and Ep to Eal, Ear, Epl and Epr

source_name: C blastomere tp 6

value: minutes passed the 2-cell stage:110


title: C_(E8)_rep2


title: C_(E8++)_rep1


title: PD_(E4)_rep2

source_name: P blastomere tp 6


title: C_(E2+)_rep2

source_name: C blastomere tp 5


title: C_(E4)_rep1


title: C_(E2)_rep3

description: After division of E to Ea and Ep

source_name: C blastomere tp 4


title: C_(E2)_rep2

description: After division of E to Ea and Ep


title: C_(E2+)_rep1


title: C_(E2)_rep1

description: After division of E to Ea and Ep


title: ABtr_rep3

source_name: AB blastomere tp 11

value: AB


title: C_(E)_rep1

description: After division of EMS to E and MS

source_name: C blastomere tp 3


title: ABtr_rep2


title: PD_(E4)_rep1


title: C_(E)_rep2

description: After division of EMS to E and MS


title: AB_(E8++)_rep2

source_name: AB blastomere tp 10


title: AB_(E8++)_rep3


title: ABtr_rep1


title: AB_(E8+)_rep3

source_name: AB blastomere tp 9


title: AB_(E8+)_rep2


title: AB_(E8+)_rep1


title: AB_(E8)_rep1

source_name: AB blastomere tp 8


title: AB_(E8)_rep3


title: AB_(E4+)_rep1

source_name: AB blastomere tp 7


title: AB_(E8)_rep2


title: AB_(E4)_rep3

source_name: AB blastomere tp 6


title: AB_(E4)_rep2


title: AB_(E4+)_rep2


title: AB_(E4)_rep1


title: C_(E)_rep3

description: After division of EMS to E and MS


title: AB_(E2+)_rep2

source_name: AB blastomere tp 5


title: AB_(E2+)_rep3


title: AB_(E2)_rep1

description: After division of E to Ea and Ep

source_name: AB blastomere tp 4


title: AB_(E2)_rep2

description: After division of E to Ea and Ep


title: AB_(E2+)_rep1


title: AB_(E)_rep3

description: After division of EMS to E and MS

source_name: AB blastomere tp 3


title: AB_(E)_rep2

description: After division of EMS to E and MS


title: AB_(E8++)_rep1


title: MStr_rep3

source_name: MS blastomere tp 11

value: MS


title: MStr_rep2


title: MStr_rep1


title: AB_(E)_rep1

description: After division of EMS to E and MS


title: MS16_(E8+)_rep1

source_name: MS blastomere tp 9


title: MS16_(E8+)_rep3


title: MS16_(E8++)

source_name: MS blastomere tp 10


title: MS16_(E8+)_rep2


title: MS8_(E4+)_rep3

source_name: MS blastomere tp 7


title: MS16_(E8)_rep3

source_name: MS blastomere tp 8


title: MS16_(E8)_rep1


title: MS16_(E8)_rep2


title: MS8_(E4+)_rep2


title: MS8_(E4+)_rep1


title: AB_(E2)_rep3

description: After division of E to Ea and Ep


title: MS4_(E4)_rep2

source_name: MS blastomere tp 6


title: MS4_(E4)_rep1


title: MS4_(E4)_rep3


title: MS4_(E2+)_rep2

source_name: MS blastomere tp 5


title: MS4_(E2+)_rep1


title: MS2_(E2)_rep1

description: After division of E to Ea and Ep

source_name: MS blastomere tp 4


title: MS_(E)_rep3

description: After division of EMS to E and MS

source_name: MS blastomere tp 3


title: MS2_(E2)_rep3

description: After division of E to Ea and Ep


title: MS_(E)_rep2

description: After division of EMS to E and MS


title: MS2_(E2)_rep2

description: After division of E to Ea and Ep


title: MS_(E)_rep1

description: After division of EMS to E and MS


title: Etr_rep2

source_name: E blastomere tp 11


title: E8+_rep3

source_name: E blastomere tp 9


title: Etr_rep1


title: E8_rep3

source_name: E blastomere tp 8


title: E8++

source_name: E blastomere tp 10


title: E8_rep2


title: E4+_rep3

source_name: E blastomere tp 7


title: E4+_rep2


title: MS4_(E2+)_rep3


title: E4_rep3

source_name: E blastomere tp 6


title: E8_rep1


title: E4_rep2


title: Etr_rep3


title: E2+_rep1

source_name: E blastomere tp 5


title: E2+_rep3


title: E4_rep1


title: E2_rep3

description: After division of E to Ea and Ep

source_name: E blastomere tp 4


title: E4+_rep1


title: E2+_rep2


title: E8+_rep2


title: E2_rep1

description: After division of E to Ea and Ep


title: E2_rep2

description: After division of E to Ea and Ep


title: E8+_rep1


title: E_rep3

description: After division of EMS to E and MS

source_name: E blastomere tp 3


title: P2_(EMS)_rep3

description: 4-cell embryo

source_name: P2 blastomere tp 2

value: minutes passed the 2-cell stage:20

value: P and C


title: E_rep1

description: After division of EMS to E and MS


title: E_rep2

description: After division of EMS to E and MS


title: AB_(EMS)_rep2

description: 4-cell embryo

source_name: AB blastomere tp 2

value: Blastomeres, developmental time


title: P2_(EMS)_rep2

description: 4-cell embryo


title: P10.5 Morc1 het bisuflite (4 replicates)

description: Bisulfite treated DNA

source_name: P10.5 sorted germ cells

extract_protocol:
DNA for bisulfite sequencing was extracted using the QiaAMP DNA Micro kit (Qiagen) and quantified using the Qubit dsDNA High Sensitivity Kit (Life Technologies).
Libraries were prepared using the Ovation Ultralow Methyl-Seq Library System (Nugen). 5ng – 25ng DNA was used as starting material. Matched mutant and control samples always contained identical quantities of DNA. Unmethylated Lambda phage DNA (NEB) was spiked in at 0.5% input DNA quantity to determine conversion efficiency, which was consistently >98%. Each library was prepared using DNA from one individual mouse.

value: Ovation Ultralow Methylseq

value: sorted germ cells


title: EMS_rep3

description: 4-cell embryo

source_name: EMS blastomere tp 2

value: E and MS


title: EMS_rep2

description: 4-cell embryo


title: P2_(EMS)_rep1

description: 4-cell embryo


title: AB_(EMS)_rep1

description: 4-cell embryo


title: EMS_rep1

description: 4-cell embryo


title: AB_(P1)_rep3

description: 4-cell embryo

source_name: AB blastomere tp 1


title: AB_(P1)_rep1

description: 2-cell embryo

value: minutes passed the 2-cell stage:0


title: P1_rep3

description: 2-cell embryo

source_name: P1 blastomere tp 1

value: P, C, E and MS


title: P1_rep2

description: 2-cell embryo


title: P1_rep1

description: 2-cell embryo

data_processing:
Libraries were sequenced on the Illumina HiSeq2000 according to standard, paired-end sequencing, protocols. Primary analysis done in RTA 1.17.20,1.13.48
Conversion from BCL to FASTQ and deumltiplexing using CASAVA-1.8 (configureBclToFastq.pl--fastq-cluster-count 1234567890 --mismatches 0 --use-bases-mask Y15n,I6n,Y35n)
Filter and read trimming (minimum quality of 20, max 1 exception. trimming not required).
CEL-Seq (Hashimshony, et a. 2012) demultiplexing of second mate, using first mate barcode, allowing 1 mismatch in the 5 first letters of the barcode.
BWA mapping, version 0.6.1, against c. elegans genome WBCel215 (bwa aln -n 0.04 -o 1 -e -1 -d 16 -i 5 -k 2 -M 3 -O 11 -E 4)
Read counting with htseq-count version 0.5.3p1. Using a custom annotation,based on WS230 exon annotation (union of overlapping reads).
Genome_build: WBcel215
Supplementary_files_format_and_content: Expression matrix, transcripts per million - whole-embryo timecourse.  Meaned (Samples 1-56), 50 stages.
Supplementary_files_format_and_content: Expression matrix, transcripts per million - 5 lineages ,11 timepoints.  Meaned (Samples 57-184), 55 stages.
Supplementary_files_format_and_content: Expression matrix, read count. (Samples 1-184, unmeaned).
Supplementary_files_format_and_content: Expression matrix, read count. Spikeins (Samples 1-184, unmeaned)


title: mpfc_810

description: 810 minutes past the 4-cell stage embryo

source_name: multicellular embryo tp 47

value: Whole embryo, 10min intervals

value: minutes passed the 2-cell stage:830


title: mpfc_830

description: 830 minutes past the 4-cell stage embryo

source_name: multicellular embryo tp 48

value: minutes passed the 2-cell stage:850


title: mpfc_700

description: 700 minutes past the 4-cell stage embryo

source_name: multicellular embryo tp 43

value: minutes passed the 2-cell stage:720


title: mpfc_750

description: 750 minutes past the 4-cell stage embryo

source_name: multicellular embryo tp 44

value: minutes passed the 2-cell stage:770


title: mpfc_800

description: 800 minutes past the 4-cell stage embryo

source_name: multicellular embryo tp 46

value: minutes passed the 2-cell stage:820


title: mpfc_760

description: 760 minutes past the 4-cell stage embryo

source_name: multicellular embryo tp 45

value: minutes passed the 2-cell stage:780


title: AB_(EMS)_rep3

description: 4-cell embryo

value: AB


title: mpfc_640

description: 640 minutes past the 4-cell stage embryo

source_name: multicellular embryo tp 42

value: minutes passed the 2-cell stage:660


title: mpfc_510

description: 510 minutes past the 4-cell stage embryo

source_name: multicellular embryo tp 38

value: minutes passed the 2-cell stage:530


title: mpfc_450

description: 450 minutes past the 4-cell stage embryo

source_name: multicellular embryo tp 36

value: minutes passed the 2-cell stage:470


title: mpfc_620

description: 620 minutes past the 4-cell stage embryo

source_name: multicellular embryo tp 40

value: minutes passed the 2-cell stage:640


title: mpfc_420

description: 420 minutes past the 4-cell stage embryo

source_name: multicellular embryo tp 34

value: minutes passed the 2-cell stage:440


title: mpfc_550

description: 550 minutes past the 4-cell stage embryo

source_name: multicellular embryo tp 39

value: minutes passed the 2-cell stage:570


title: mpfc_490

description: 490 minutes past the 4-cell stage embryo

source_name: multicellular embryo tp 37

value: minutes passed the 2-cell stage:510


title: mpfc_630

description: 630 minutes past the 4-cell stage embryo

source_name: multicellular embryo tp 41

value: minutes passed the 2-cell stage:650


title: mpfc_410_rep2

description: 410 minutes past the 4-cell stage embryo

source_name: multicellular embryo tp 33

value: minutes passed the 2-cell stage:430


title: mpfc_370

description: 370 minutes past the 4-cell stage embryo

source_name: multicellular embryo tp 29

value: Whole embryo, 10min intervals

value: minutes passed the 2-cell stage:390


title: mpfc_390

description: 390 minutes past the 4-cell stage embryo

source_name: multicellular embryo tp 31

value: minutes passed the 2-cell stage:410


title: mpfc_380_rep1

description: 380 minutes past the 4-cell stage embryo

source_name: multicellular embryo tp 30

value: minutes passed the 2-cell stage:400


title: mpfc_410_rep1


title: mpfc_400_rep1

description: 400 minutes past the 4-cell stage embryo

source_name: multicellular embryo tp 32

value: minutes passed the 2-cell stage:420


title: mpfc_430

description: 430 minutes past the 4-cell stage embryo

source_name: multicellular embryo tp 35

value: minutes passed the 2-cell stage:450


title: mpfc_350

description: 350 minutes past the 4-cell stage embryo

source_name: multicellular embryo tp 27

value: minutes passed the 2-cell stage:370


title: mpfc_400_rep2


title: AB_(P1)_rep2

description: 2-cell embryo

source_name: AB blastomere tp 1

value: Blastomere, developmental event

value: minutes passed the 2-cell stage:0

value: AB


title: mpfc_340_rep2

description: 340 minutes past the 4-cell stage embryo

source_name: multicellular embryo tp 26

value: minutes passed the 2-cell stage:360


title: mpfc_340_rep1


title: mpfc_330

description: 330 minutes past the 4-cell stage embryo

source_name: multicellular embryo tp 25

value: minutes passed the 2-cell stage:350


title: mpfc_360

description: 360 minutes past the 4-cell stage embryo

source_name: multicellular embryo tp 28

value: minutes passed the 2-cell stage:380


title: mpfc_320

description: 320 minutes past the 4-cell stage embryo

source_name: multicellular embryo tp 24

value: minutes passed the 2-cell stage:340


title: mpfc_300

description: 300 minutes past the 4-cell stage embryo

source_name: multicellular embryo tp 23

value: minutes passed the 2-cell stage:320


title: mpfc_290

description: 290 minutes past the 4-cell stage embryo

source_name: multicellular embryo tp 22

value: minutes passed the 2-cell stage:310


title: mpfc_280

description: 280 minutes past the 4-cell stage embryo

source_name: multicellular embryo tp 21

value: minutes passed the 2-cell stage:300


title: mpfc_270

description: 270 minutes past the 4-cell stage embryo

source_name: multicellular embryo tp 20

value: Whole embryo, 10min intervals

value: minutes passed the 2-cell stage:290


title: mpfc_230

description: 230 minutes past the 4-cell stage embryo

source_name: multicellular embryo tp 18

value: minutes passed the 2-cell stage:250


title: mpfc_210

description: 210 minutes past the 4-cell stage embryo

source_name: multicellular embryo tp 16

value: minutes passed the 2-cell stage:230


title: mpfc_220_rep2

description: 220 minutes past the 4-cell stage embryo

source_name: multicellular embryo tp 17

value: minutes passed the 2-cell stage:240


title: mpfc_190

description: 190 minutes past the 4-cell stage embryo

source_name: multicellular embryo tp 14

value: minutes passed the 2-cell stage:210


title: mpfc_200_rep2

description: 200 minutes past the 4-cell stage embryo

source_name: multicellular embryo tp 15

value: minutes passed the 2-cell stage:220


title: mpfc_180

description: 180 minutes past the 4-cell stage embryo

source_name: multicellular embryo tp 13

value: minutes passed the 2-cell stage:200


title: mpfc_220_rep1


title: mpfc_380_rep2

description: 380 minutes past the 4-cell stage embryo

source_name: multicellular embryo tp 30

value: minutes passed the 2-cell stage:400


title: mpfc_160

description: 160 minutes past the 4-cell stage embryo

source_name: multicellular embryo tp 11

value: minutes passed the 2-cell stage:180


title: mpfc_170

description: 170 minutes past the 4-cell stage embryo

source_name: multicellular embryo tp 12

value: minutes passed the 2-cell stage:190


title: mpfc_120

description: 120 minutes past the 4-cell stage embryo

source_name: multicellular embryo tp 8

value: minutes passed the 2-cell stage:140


title: mpfc_150

description: 150 minutes past the 4-cell stage embryo

source_name: multicellular embryo tp 10

value: minutes passed the 2-cell stage:170


title: mpfc_100

description: 100 minutes past the 4-cell stage embryo

source_name: multicellular embryo tp 7

value: minutes passed the 2-cell stage:120


title: mpfc_060

description: 60 minutes past the 4-cell stage embryo

source_name: multicellular embryo tp 5

value: minutes passed the 2-cell stage:80


title: mpfc_130

description: 130 minutes past the 4-cell stage embryo

source_name: multicellular embryo tp 9

value: minutes passed the 2-cell stage:150


title: mpfc_050

description: 50 minutes past the 4-cell stage embryo

source_name: multicellular embryo tp 4

value: minutes passed the 2-cell stage:70


title: mpfc_040

description: 40 minutes past the 4-cell stage embryo

source_name: multicellular embryo tp 3

value: Whole embryo, 10min intervals

value: minutes passed the 2-cell stage:60


title: mpfc_070

description: 70 minutes past the 4-cell stage embryo

source_name: multicellular embryo tp 6

value: minutes passed the 2-cell stage:90


title: mpfc_010

description: 10 minutes past the 4-cell stage embryo

data_processing:
Libraries were sequenced on the Illumina HiSeq2000 according to standard, paired-end sequencing, protocols. Primary analysis done in RTA 1.17.20,1.13.48
Conversion from BCL to FASTQ and deumltiplexing using CASAVA-1.8 (configureBclToFastq.pl--fastq-cluster-count 1234567890 --mismatches 0 --use-bases-mask Y15n,I6n,Y35n)
Filter and read trimming (minimum quality of 20, max 1 exception. trimming not required).
CEL-Seq (Hashimshony, et a. 2012l) demultiplexing of second mate, using first mate barcode, allowing 1 mismatch in the 5 first letters of the barcode.
BWA mapping, version 0.6.1, against c. elegans genome WBCel215 (bwa aln -n 0.04 -o 1 -e -1 -d 16 -i 5 -k 2 -M 3 -O 11 -E 4)
Read counting with htseq-count version 0.5.3p1. Using a custom annotation,based on WS230 exon annotation (union of overlapping reads).
Genome_build: WBcel215
Supplementary_files_format_and_content: Expression matrix, transcripts per million - whole-embryo timecourse.  Meaned (Samples 1-56), 50 stages.
Supplementary_files_format_and_content: Expression matrix, transcripts per million - 5 lineages ,11 timepoints.  Meaned (Samples 57-184), 55 stages.
Supplementary_files_format_and_content: Expression matrix, read count. (Samples 1-184, unmeaned).
Supplementary_files_format_and_content: Expression matrix, read count. Spikeins (Samples 1-184, unmeaned)

source_name: multicellular embryo tp 1

value: minutes passed the 2-cell stage:30


title: 1_cell

description: 1-cell embryo

source_name: 1-cell embryo

value: Whole embryo

value: minutes passed the 2-cell stage:n/a


title: mpfc_020

description: 20 minutes past the 4-cell stage embryo

source_name: multicellular embryo tp 2

value: minutes passed the 2-cell stage:40


title: FACS_Podocyte_RNAseq_replicate3

city: Boston

first: Peter

middle: J

last: Park

state: MA

address: 10 Shattuck St

department: Center for Biomedical Informatics

institute: Harvard Medical School

description:
Sample 9
Processed data file: FPKM.genes.podocytes.replicate3.txt

data_processing:
ChIP-seq analysis: Reads were mapped to mm9 using ELAND with a 25 bp seed and allowance of up to two mismatches.
ChIP-seq quality controls were carried out according to ENCODE guidelines.
ChIP-seq peaks were called using spp and IDR according to ENCODE guidelines (Landt et al. PMID 22955991) using an IDR threshold of 0.0025.
RNA-seq analysis: Reads were mapped to mm9 using TopHat (v2.0.10) with default parameters and no novel junction finding option (--no-novel-juncs).
For the estimation of the expression levels, FPKM values were estimated using Cufflinks2 (v2.1.1).
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: For ChIP-seq data, a bed file contains top 14,843 peaks passing the IDR threshold; Scores represent spp peak scores.
Supplementary_files_format_and_content: For RNA-seq data, tab-delimited text file contains FPKM values for each gene per each replicate.

source_name: Mouse glomerular podocytes

extract_protocol:
RNA-seq: Total RNA from primary podocytes was isolated as described in Boerries et al. (PMID: 23364521).
Libraries for sequencing were prepared using standard Illumina protocols.

tag: strain/background

value: Nphs2:Cre tg/wt; R26mTmG +/-

value: FACS-isolated glomerular podocytes

tag: age

value: 6 weeks


title: 36_MUT

city: Illkirch

first: Tao

last: YE

address: 1 rue Laurent Fries

country: France

institute: IGBMC (CNRS/INSERM/UDS)

data_processing:
Base calling : Image analysis and base calling were performed using RTA 1.17.20 and CASAVA 1.8.2
Alignment : Reads were mapped to mm9 assembly of mouse genome using Tophat v1.4.1
Quantification : Gene expression was quantified using HTSeq v0.5.3p9 and annotations from Ensembl release 67
Normalization : Data normalization was performed with DESeq2 v1.0.17 Bioconductor package
Genome_build: mm9
Supplementary_files_format_and_content: The processed data file is a tabulated text with the following columns : Ensembl gene id, Gene name and one column for each sample containing the normalized read counts

source_name: pancreatic islet

extract_protocol:
Islet RNA was extracted with Trizol reagent
Total cellular RNA from 6 samples, libraries of template molecules suitable for strand specific high throughput DNA sequencing were created using “TruSeq Stranded Total RNA with Ribo-Zero Gold Prep Kit” (Illumina). Briefly, starting with 1 µg of total RNA, the first step involved the removal of cytoplasmic and mitochondrial ribosomal RNA (rRNA) using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads. Following purification, the RNA was fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers, followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. The double stranded cDNA fragments were blunted 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 using a Klenow fragment (3' to 5'exo minus) enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification (30 sec at 98°C; [10 sec at 98°C, 30 sec at 60°C, 30 sec at 72°C] x 12 cycles; 5 min at 72°C). Then surplus PCR primers were removed by purification using AMPure XP beads (Agencourt Biosciences Corporation). Final cDNA libraries were checked for quality and quantified using 2100 Bioanalyzer (Agilent). The libraries were loaded in the flow cell at 8pM concentration and clusters were generated in the Cbot and sequenced in the Illumina Hiseq 2500 as single-end 50 base reads following Illumina's instructions

tag: Stage

value: adult

tag: genotype

value: Rfx6fl/fl; Ins1-CreERT2

tag: strain


title: HIC104

city: Houston

first: Suhas

last: Rao

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

data_processing:
library strategy: HiC-Seq
The paired end reads were aligned separately using BWA against the b37 human build or the mm9 mouse build
PCR duplicates, low mapping quality and unligated reads were removed using an in-house Hi-C analysis pipeline (see Rao, Huntley, et al)
Contact matrices were constructed at various resolutions and normalized using an in-house Hi-C analysis pipeline (see Rao, Huntley, et al)
loops were annotated using HiCCUPS (see Rao, Huntley, et al), domains were annotated using Arrowhead (see Rao, Huntley, et al), subcompartments were annotated using a Gaussian HMM (see Rao, Huntley, et al)
Genome_build: b37 (human), mm9 (mouse)
Supplementary_files_format_and_content: HiCCUPS_looplist.txt files contain loop calls generated via HiCCUPS; first three fields represent the locus participating in the loop closer to the p-end of the chromosome; fields 4-6 represent the locus participating in the loop closer to the q-end of the chromosome; field 7 represents the color used to display the feature in Juicebox (a Hi-C data visualization software, see www.aidenlab.org/juicebox); field 8 represents the observed number of counts at the loop; fields 9-12 represent the expected number of counts at the loop using four different expected models; fields 13-16 are the q-values over each of the expected values; field 17 is the number of enriched pixels that was clustered into a particular loop; field 18-19 are the centroid of the loop; field 20 is the radius of the loop
Supplementary_files_format_and_content: Arrowhead_domainlist.txt files contain domain calls generated via Arrowhead; first 6 fields represent the boundaries of the domain; field 7 represents the color used to display the feature in Juicebox (a Hi-C data visualization software, see www.aidenlab.org/juicebox); field 8 is the corner score for the domain (see Rao, Huntley, et al); fields 9-12 are the component scores used in the Arrowhead algorithm (see Rao, Huntley, et al)
Supplementary_files_format_and_content: the subcompartment bed file contains the coordinates of the 6 nuclear subcompartments identified in Rao, Huntley, et al.
Supplementary_files_format_and_content: HIC*_merged_nodups.txt files specify each Hi-C read pair (i.e., the mapping locations of each individual read pair).

source_name: B-lymphoblasts

growth_protocol: Cell lines were cultured according to manufacturer's instructions

extract_protocol:
Cells were crosslinked and then lysed with nuclei permeabilized but still intact. DNA was then restricted and the overhangs filled in incorporating a biotinylated base. Free ends were then ligated together in situ. Crosslinks were reversed, the DNA was sheared to 300-500bp and then biotinylated ligation junctions were recovered with streptavidin beads.
standard Illumina library construction protocol, Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 8-12 cycles and library fragments of 400-600 bp (insert plus adaptor and PCR primer sequences) were purified using SPRI beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the MiSeq/HiSeq2000/HiSeq2500 following the manufacturer's protocols

tag: cell line

tag: protocol

value: dilution Hi-C


title: HIC103


title: 81_MUT


title: 137_CTRL


title: 37_MUT


title: mpfc_200_rep1

source_name: multicellular embryo tp 15

value: minutes passed the 2-cell stage:220


title: 136_CTRL


title: 124_CTRL


title: M. marinum E11 5DPI [IL-13-08_Anita_39_CGATGT_L001_R1_001]

city: Leiden

first: Wouter

last: Veneman

state: Zuid-Holland

address: Einsteinweg 55

department: Institute Biology Leiden

country: Netherlands

institute: Leiden University

description: Wildtype; injected with M. marinum into the yolk at 2 hpf; RNA isolated at 5 days post injection. Biological replica 2

data_processing:
GeneTiles was used for quantification and visualization of the RNAseq data
Bowtie2 is used to align the reads in the fastq file to the genome (obtained from Ensemble). Bowtie2 generates SAM files that contain the reads together with the location on the genome.
Samtools is used to convert and compress the SAM files into a binary BAM file. Samtools is furthermore used to sort the reads in the BAM files based on the aligned read location in the genome, resulting in a sorted BAM file.
The BAM files is indexed to be able to quickly find the aligned reads based on a location in the genome, i.e. to be able to quickly search the BAM file. The index is a saved as a BAI file.
Using the available annotation from Ensemble we can search the BAM file for reads within a gene (using exon starting positions and lengths). This is done with a python script. The output of this script is a tab separated file (tsv) containing the read counts per gene.
We used DESeq, an R-script to perform statistical analysis. The DESeq script is used to normalise the reads per gene, based on (divided by) the total number of reads obtained per sample. Then variance and average of the measurement compared to the control can be expressed as a P-value, by calculating the dispersion per gene using DESeq. The size factors as well as the P-values are stored in ‘tsv’ files.
Using a script, all tsv files are combined into tsv files , e.g. per experiment, chromosome, per filtered results of most significant reads or highest ratio between measurement and control.
Genome_build: Zv9_toplevel
Supplementary_files_format_and_content: txt file containing read counts per gene

organism: Danio rerio

source_name: embryo 5 days post fertilization

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). Embryos were grown at 28,5°C in egg water (60µg/ml Instant Ocean sea salts).

extract_protocol:
Embryos for RNA isolation were snap frozen in liquid nitrogen and subsequently stored at -80°C. Embryos were homogenized in 1 ml of TRIZOL® Reagent (Invitrogen) and subsequently total RNA was extracted according to the manufacturer’s instructions. The RNA samples were incubated for 20 min at 37° with 10 units of DNaseI (Roche Applied Science) to remove residual genomic DNA prior to purification using the RNeasy MinElute Cleanup kit (Qiagen) according to the RNA clean up protocol. The integrity of the RNA was confirmed by Lab-on-chip analysis using the 2100 Bioanalyzer (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Zebrafish embryos were micro-injected into the yolk (64 cell stage) with M. marinum E11 mCherry bacteria suspended in PVP (Polyvinylpyrrolidone), or Non-injected as a control. At 5 days post injection 50 embryos per treatment group were snap-frozen in liquid nitrogen, and total RNA was isolated using TRIZOL reagent.

tag: infection

value: M. marinum E11 mCherry


title: M. marinum E11 5DPI [IL-13-08_Anita_38_ATTCCT_L002_R1_001]


title: M. marinum E11 5DPI [IL-13-08_Anita_27_ATCACG_L008_R1_001]


title: M. marinum E11 5DPI [IL-13-08_Anita_37_ACTGAT_L007_R1_001]


title: M. marinum E11 5DPI [IL-13-08_Anita_26_GTGAAA]

description: Wildtype; injected with M. marinum into the yolk at 2 hpf; RNA isolated at 5 days post injection. Biological replica 1


title: Non-injected 5 DPI [IL-13-08_Anita_6_GATCAG]

description: Wildtype: non-injected control; RNA isolated at 5 days post fertilization (=5DPI timepoint). Biological replica 2

value: control


title: 2_cell

description: 2-cell embryo

source_name: 2-cell embryo

value: minutes passed the 2-cell stage:0


title: Non-injected 5 DPI [IL-13-08_Anita_7_TAGCTT]

description: Wildtype: non-injected control; RNA isolated at 5 days post fertilization (=5DPI timepoint). Biological replica 3


title: Non-injected 5 DPI [IL-13-08_Anita_5_ACTTGA]

description: Wildtype: non-injected control; RNA isolated at 5 days post fertilization (=5DPI timepoint). Biological replica 1


title: HIC048_MiSeq

source_name: B-lymphoblastoids

value: in situ Hi-C


title: mpfc_260

description: 260 minutes past the 4-cell stage embryo

source_name: multicellular embryo tp 19

value: Whole embryo, 10min intervals

value: minutes passed the 2-cell stage:280


title: HIC042_MiSeq


title: HIC041_MiSeq


title: HIC199


title: HIC201


title: HIC200


title: HIC194


title: HIC196


title: HIC193


title: HIC195


title: HIC190


title: HIC191


title: HIC189


title: 8 weeks Unconventional prefoldin RPB5 interactor overexpression, replicate 1

city: Madrid

first: Nabil

last: Djouder

address: C/Melchor Fernandez Almagro, 3

country: Spain

institute: CNIO

description: Isolation of polyA+ RNA from total RNA.

data_processing:
Read files were quality-checked with FastQC.
Reads were aligned with the mouse genome (NCBI37/mm9) with TopHat-1.3.1 (using Bowtie 0.12.7 and Samtools 0.1.16), allowing 2 mismatches and 5 multihits.
Transcripts quantification and differential expression calculated with Cufflinks 1.3.0.
Transcripts annotations used were Mus musculus NCBIM37.65 from Ensembl.
Genome_build: MGSCv37
Supplementary_files_format_and_content: Tables were generated with Cufflinks 1.3.0 and contain transcripts abundance measured in FPKM values.

source_name: Liver, hURI expression, 8 weeks

growth_protocol: Bottom half of the right liver lobe was taken for each experiment.

extract_protocol:
Freshly taken liver tissues were snap frozen in liquid nitrogen, lysed in 1.5 ml of TRIZOL solution using precellys homogenizer at 25,000 rpm for 30 s. The mixture was mixed vigorously by vortexing. 0.4 volume of chloroform was added, homogenised by hand for 15 s and incubated at room temperature for 5 min. Then, a centrifugation step for 15 min at 12,000 speed was performed and the upper aqueous phase was transferred into a fresh Eppendorf tube containing 60% volume of Trizol. The upper phase was collected and a second chloroform extraction step was performed. Subsequently, RNA was precipitated by adding 0.8 volumes of 100% isopropanol to the aqueous phase, mixed and incubated at room temperature for 10 min. The RNA-isopropanol mixture was centrifugated for 13.000 rpm for 20 min and total RNA was precipitated. The supernatant was decanted and the pellet was washed with freshly prepared 80% ethanol.
1.5 µg of total RNA samples was used as provided by the user. RNA Integrity Numbers were 8.3 on average (range 7.5 to 9.2) when assayed by Lab-chip technology on an Agilent 2100 Bioanalyzer. PolyA+ RNA fraction was extracted and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq RNA Sample Preparation Guide" (Part # 15008136 Rev. A). Adapter-ligated library was completed by limited-cycle PCR with Illumina PE primers (10 cycles). The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation (TruSeq cluster generation kit v5) and sequenced on the Genome Analyzer IIx with SBS TruSeq v5 reagents by following manufacturer's protocols.

treatment_protocol: No treatments were done, except hURI ectopic expression since conception.

tag: tissue

value: liver (bottom half of right lobe)

tag: duration of huri expression

value: 8 weeks

tag: ectopic expression

value: hURI


title: 8 weeks Unconventional prefoldin RPB5 interactor overexpression, replicate 2

description: Isolation of polyA+ RNA from total RNA.


title: 8 weeks control, replicate 4

description: Isolation of polyA+ RNA from total RNA.

source_name: Liver, control, 8 weeks


title: HIC187


title: 8 weeks control, replicate 3

description: Isolation of polyA+ RNA from total RNA.


title: 8 weeks control, replicate 2

description: Isolation of polyA+ RNA from total RNA.


title: HIC198


title: HIC185


title: 8 weeks control, replicate 1

description: Isolation of polyA+ RNA from total RNA.


title: HIC192


title: 1 week Unconventional prefoldin RPB5 interactor overexpression, replicate 4

description: Isolation of polyA+ RNA from total RNA.

source_name: Liver, hURI expression, 1 week

value: 1 week


title: HIC197


title: HIC182


title: HIC180


title: HIC181


title: HIC179


title: HIC188


title: 1 week Unconventional prefoldin RPB5 interactor overexpression, replicate 3

description: Isolation of polyA+ RNA from total RNA.


title: HIC178


title: 1 week control, replicate 1

description: Isolation of polyA+ RNA from total RNA.

source_name: Liver, control, 1 week


title: 8 weeks Unconventional prefoldin RPB5 interactor overexpression, replicate 3

description: Isolation of polyA+ RNA from total RNA.


title: 1 week Unconventional prefoldin RPB5 interactor overexpression, replicate 1

description: Isolation of polyA+ RNA from total RNA.


title: 1 week Unconventional prefoldin RPB5 interactor overexpression, replicate 2

description: Isolation of polyA+ RNA from total RNA.


title: 1 week control, replicate 2

description: Isolation of polyA+ RNA from total RNA.


title: HIC177


title: 1 week control, replicate 3

description: Isolation of polyA+ RNA from total RNA.


title: HIC176


title: HIC080

source_name: Umbilical Vein Endothelial Cells

value: HUVEC (CC-2517)


title: HIC083


title: HIC184


title: HIC174


title: HIC173


title: HIC183


title: FACS_Podocyte_RNAseq_replicate2

description:
Sample 8
Ctrlinj2
Processed data file: FPKM.genes.podocytes.replicates1_2.txt

tag: genotype/variation

value: Nphs2:Cre tg/wt; R26mTmG +/-

value: FACS-isolated glomerular podocytes


title: HIC186


title: HIC172


title: HIC076

source_name: Near Haploid Myelogenous Leukemia


title: HIC068

source_name: Epidermal Keratinocytes


title: HIC171


title: HIC064

source_name: Mammary Epithelial Cells


title: FACS_Podocyte_RNAseq_replicate1

description:
Sample 7
Ctrlinj1
Processed data file: FPKM.genes.podocytes.replicates1_2.txt

value: 6 weeks


title: Input_DNA_replicate1

description:
Sample 4
Processed data file: spp.conservative.IP0_VS_Input0.bed

source_name: Mouse kidney cortex, input

extract_protocol:
ChIP-seq: Kidney cortex was dissected and crosslinked with formaldehyde. Chromatin was extracted, cleared and WT1-DNA complexes were enriched using a WT1 antibody (C-19; Santa Cruz, sc-192, Lot F1711).
Libraries for sequencing were prepared using standard Illumina protocols.

value: wildtype

value: kidney cortex

value: 3 weeks

tag: chip antibody


title: HIC169


title: HIC170


title: HIC168


title: Input_DNA_replicate2

description:
Sample 5
Processed data file: spp.conservative.IP0_VS_Input0.bed


title: Input_DNA_replicate3

description:
Sample 6
Processed data file: spp.conservative.IP0_VS_Input0.bed


title: WT1_ChIPseq_replicate1

description:
Sample 1
Processed data file: spp.conservative.IP0_VS_Input0.bed

source_name: Mouse kidney cortex, WT1 ChIP

value: WT1 (Santa Cruz, sc-192, Lot F1711)


title: HIC036

value: dilution Hi-C


title: WT1_ChIPseq_replicate3

description:
Sample 3
Processed data file: spp.conservative.IP0_VS_Input0.bed


title: HIC175


title: HIC165


title: HIC161


title: HIC162


title: HIC163


title: HIC166


title: HIC057

source_name: Lung Fibroblasts


title: HIC164


title: BlimpHet_GFPpos_Treg_19

city: Clayton

first: Wei

last: Shi

state: VIC

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology

country: Australia

institute: Monash University

data_processing:
Reads were mapped to mouse genome mm9 using the Subread aligner, with the minimum number of consensus reads set to two.
Mapped reads were assigned to mouse RefSeq genes using the featureCounts program and NCBI mouse annotation build 37.2.
Read counts were analyzed using Bioconductor software. Genes were filtered as not expressed if they had a total read count less than five.
Differential expression analysis was performed using generalized linear models functions of the edgeR package, with the negative binomial dispersion set to a common value of 0.02. A false discovery rate cut-off of 0.05 was applied.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include normalized log2-RPKM values for each sample

source_name: Blimp/GFP+ Treg (polyA)

extract_protocol:
RNA purification was performed following the manufacturer’s protocol using the RNAeasy Plus Mini Kit (Qiagen). Messenger RNA were obtained using the standard polyA approach or a single-cell approach (Tang et al, Nature, 2010,5:516-535)
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: tissue type

value: Spleens and lymph nodes

tag: cell type

value: Reguatory T cells

tag: cell population

value: Blimp/GFP+ Treg

tag: reporter

tag: mrna extraction

value: polyA


title: BlimpHet_GFPpos_Treg_4

source_name: Blimp/GFP+ Treg (single-cell)

value: Single-cell


title: HIC160

value: in situ Hi-C


title: HIC167


title: BlimpHet_GFPneg_Treg_20

source_name: Blimp/GFP- Treg (polyA)

value: Blimp/GFP- Treg


title: BlimpHet_GFPpos_Treg_1


title: BlimpHet_GFPneg_Treg_5

source_name: Blimp/GFP- Treg (single-cell)


title: BlimpHet_GFPneg_Treg_2


title: HIC159

source_name: B-lymphoblastoids


title: HIC158


title: WT1_ChIPseq_replicate2

description:
Sample 2
Processed data file: spp.conservative.IP0_VS_Input0.bed

tag: strain/background

tag: age


title: HIC082


title: HIC079


title: HIC156


title: HIC078


title: HIC157


title: HIC155


title: HIC081


title: HIC075


title: HIC154


title: HIC152


title: HIC151


title: HIC150


title: HIC073

source_name: Erythroleukemia


title: HIC071


title: HIC072


title: HIC149


title: HIC148

value: tethered in situ Hi-C


title: HIC067


title: HIC145


title: HIC144


title: HIC074


title: HIC146


title: HIC070


title: HIC153


title: HIC069


title: HIC066


title: HIC077


title: HIC065


title: vp64_myod.rep2

city: Durham

first: Charles

middle: A.

last: Gersbach

state: NC

address: 101 Science Dr

department: Biomedical Engineering

institute: Duke University

description: Sample name: AK02-6

data_processing:
Base-calling was performed on instrument using CASAVA software
Reads were aligned to the hg19 version of the human genome using bowtie version 0.12.9
Read counts were normalized and differential expression was called using Deseq (v. 1.10.1) by using a chi-squared test to compare fits to a model that contained donor and count (i.e. count ~ donor + condition) to a model that only contained donor information (i.e. count ~ donor).
P-values were converted to a False Discovery Rate using the method of Benjamini and Hochberg (1995)
Genome_build: RefSeq transcripts from hg19 with the mouse MyoD transcript (NM_010866) added
Supplementary_files_format_and_content: Counts of the number of reads aligned to each RefSeq transcript.

source_name: Cultured primary human dermal fibroblasts

growth_protocol: Primary human dermal fibroblasts (Catalog ID: GM03348) were obtained from Coriell Institute (Camden, New Jersey) and were maintained in DMEM supplemented with 10% FBS and 1% penicillin streptomycin at 37°C with 5% CO2.

extract_protocol:
The total cellular RNA from a confluent 15cm plate of human dermal fibroblasts was isolated using the RNeasy Plus RNA isolation kit (Qiagen). PolyA+ RNA was subsequently purified using oligo-dT beads (Invitrogen).
First strand cDNA was generated using SuperScript Vilo cDNA synthesis master mix (Invitrogen), and second strand cDNA was synthesized using E. coli DNA Polymerase I (New England Biolabs) with random hexamer primers. Double stranded cDNA was purified using 1.8X Agentcourt SPRI beads (Beckman Coulter). Double stranded cDNA was fragmented and sequencing adaptors added using Nextera transposase (Illumina) and indexed for sequencing by PCR as described previously. Samples were pooled in equimolar ratios and sequenced on an Illumina HiSeq 2000.

treatment_protocol: The transcriptional activation domain VP64 was genetically fused to the N-terminus of mouse wild-type (WT) MyoD via a short flexible serine glycine linker. The WT-MyoD or VP64-MyoD transcription factors were subcloned into a Tet-ON lentiviral vector. In this vector, each MyoD variant is co-expressed with dsRed-Express2, via a T2A ribosomal skipping peptide. Human dermal fibroblasts were transduced with the Tet-ON lentivirus by replacing the cell medium with viral supernatant supplemented with 4 μg/mL polybrene. Cells were then selected in 1 µg/ml puromycin to obtain a pure population of transduced cells. Selected cells were grown to confluence and MyoD transgene expression was induced by supplementing the medium with 3 µg/mL doxycycline. Cells were given fresh media supplemented with doxycycline every two days. Samples were harvested after ten days of expression.

value: Dermal Fibroblast from Coriell Institute (GM03348)

tag: replicate

tag: expressed gene

value: VP64 mouse MyoD fusion


title: HIC143

tag: cell line


title: wt_myod.rep2

description: Sample name: AK02-5

value: Wild type mouse MyoD


title: HIC062

tag: protocol


title: HIC063


title: vp64_myod.rep1

description: Sample name: AK02-3


title: untreated.rep2

description: Sample name: AK02-4


title: HIC141


title: HIC061


title: HIC142


title: HIC147


title: HIC060


title: untreated.rep1

description: Sample name: AK02-1


title: HIC138


title: HIC140


title: H3K79me3.shDOT1L

first: Yuanxin

last: Xi

address: 1400 Pressler St

department: Bioinformatics and Computational Biology

institute: The University of Texas MD Anderson Cancer Center

data_processing:
Basecalls performed by Illumina CASAVA 1.8.2
ChIP-seq reads were aligned to the hg18 genome using Bowtie version 0.12.7
Genome_build: hg18
Supplementary_files_format_and_content: ChIP-seq wig files were generated using MACS; Scores represent the ChIP-seq tag numbers

source_name: Hela cells

growth_protocol: Cells were maintained in DMEM with 10% FBS,  5% CO2, 37oC.

extract_protocol:
ChIP-seq were performed following the protocol: Using ChIP-seq technology to generate high-resolution profiles of histone modifications. O'Geen H, Echipare L, Farnham PJ. Methods Mol Biol. 2011;791:265-86. doi: 10.1007/978-1-61779-316-5_20.
Library was contracted by the MD Anderson DNA sequencing Core facility following standard protocol.

treatment_protocol: For stable cell selection, 10 ug/ml blasticidin was used for stable cells selection and 2ug/ml of puromycin was used for knockdown cells selection and subsequent cell maintenance

value: Hela Cells

tag: treatment

value: Abcam Ab2621


title: H3K9ac

value: 3Flag-AF9 stable

value: Abcam Ab4441


title: Input

value: WT


title: HIC139


title: wt_myod.rep1

description: Sample name: AK02-2


title: HIC059


title: HIC058


title: HIC137


title: HIC135

value: dilution Hi-C


title: H3K79me3.shAF9


title: HIC134


title: HIC136


title: HIC055


title: H3K79me3.shControl

value: shControl


title: HIC133


title: H3K79me3


title: HIC056


title: AF9

value: Sigma HPA001824


title: HIC054


title: HIC053


title: Flag_AF9

value: Sigma M2


title: HIC131


title: HIC051


title: HIC102

source_name: B-lymphoblasts


title: HIC050


title: HIC129


title: HIC130


title: HIC101


title: HIC052


title: HIC100


title: HIC049


title: HIC128


title: HIC098


title: HIC132


title: HIC124


title: HIC096


title: HIC046

value: agar in situ Hi-C - no crosslinking


title: HIC047


title: HIC095


title: HIC044


title: HIC094


title: HIC127


title: HIC126


title: HIC042


title: HIC045


title: HIC093


title: HIC122


title: HIC048


title: HIC099


title: HIC097


title: HIC092


title: HIC125


title: HIC043

value: in situ Hi-C - no crosslinking


title: HIC120


title: HIC123

value: in situ Hi-C


title: moDC_sh-Cebpb H3K4me1

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

institute: Weizmann Institute of Science

data_processing:
Basecalls performed using CASAVA version 1.4
alignment using bowtie 0.12 using default parameters
tdf command - igvtools count -w 5 -e 200
Genome_build: mm9
Supplementary_files_format_and_content: tdf

growth_protocol: Bone marrows were extracted from femora and tibiae of C57BL/6J female mice (6 to 10 weeks old), growth in presence of GM-CSF (for moDC) or Flt3L (for pDC).

extract_protocol:
Cells were fixated, lyzed and nuclei were sonicated. Sonicated nuclei were mixed with protein G magnetic dynabeads coupled to target antibbody.
Libraries were prepared for sequencing using a method developed at Dr. Ido Amit's lab, Weizmann Institute of Science

value: moDC

tag: tissue

value: Bone marrow

tag: strain


title: pDC_Cebpb

value: pDC

value: Cebpb


title: moDC_sh-control H3K4me1


title: HIC041


title: pDC_sh-Irf8 H3K4me1


title: HIC121


title: HIC091


title: HIC038


title: HIC119


title: pDC_sh-control H3K4me1


title: HIC117


title: HIC088


title: HIC040


title: HIC032

value: pellet in situ Hi-C


title: HIC039


title: HIC090


title: HIC089


title: HIC031

value: agar in situ Hi-C


title: HIC118


title: single cell whole genome sequencing data from E14 embryonic stem cell 14 obtained with the MALBAC protocol

city: Utrecht

first: Lennart

last: Kester

address: Uppsalalaan 8

institute: Hubrecht Institute

description:
Coverage data for 50kb bins
E14OMsc14

data_processing:
For bulk gDNA and MALBAC libraries, paired end sequencing reads were aligned to the genome release mm10 for mouse cells (E14) and to the genome release hg19 for human cells (SK-BR-3) using BWA with default parameters. For the single cell gDNA libraries processed by DR-Seq, paired end sequencing reads were aligned to a masked genome mm10 for mouse cells and to a masked genome hg19 for human cells using BWA with default parameters. The masked genomes mm10 and hg19 were created by replacing all the coding sequences within the genome with "N". This is because the fraction used to sequence gDNA contains sequences that could originate from the cDNA within coding regions. By masking the coding sequences within the genome, such ambiguous reads that might arise from either gDNA or cDNA are discarded computationally leaving only reads that arise from gDNA. This does not pose a problem for calling copy number variations since the coding region constitutes only approximately 2% of the genome.
All PCR duplicates within mapped reads from the bulk, MALBAC or DR-Seq libraries are removed. As the first step towards quantifying the gDNA data, the genome is divided into bins. To account for the masking of the genome in the DR-Seq data, the start and end coordinates of each bin are chosen such that the length of all bins are the same after excluding coding regions within each bin. Next, to further reduce amplification biases, we developed a coverage-based method to quantify the reads within bins. This coverage-based method significantly reduces bin-to-bin technical noise (see supplementary document). The reads are then corrected for GC bias. The corrected read distribution is then used to identify breakpoints using the circular binary segmentation (CBS) algorithm26. Finally, the median read counts for each segment are used to call copy number variations in single cells.
For bulk mRNA and CEL-Seq libraries, paired end sequencing reads were aligned to the transcriptome using Burrows-Wheeler Aligner (BWA) with default parameters. For single cell mRNA processed using DR-Seq, the Ad-2 adapter sequence was trimmed computationally from the right mate and then aligned to the transcriptome using BWA with default parameters. For the E14 cells, we used the RefSeq gene models based on the mouse genome release mm10. For the SK-BR-3 cells, we used the RefSeq gene models based on the human genome release hg19. For bulk mRNA sequencing both mates of each read were mapped to the transcriptome. For CEL-Seq and DR-Seq, the right mate of each read pair was mapped to the transcriptome and the ERCC spike-ins. The left mate was used to identify the cell from which the transcript came based on the cell-specific barcode. Reads mapping to more than one region were distributed uniformly.
For the bulk mRNA sequencing libraries, PCR duplicates were then removed to obtain the dataset used in all the analysis. The left mate of the CEL-Seq libraries also contained a 4-bp random sequence, introduced during reverse transcription, to count unique cDNA molecules, as previously described. Length-based identifiers were determined for each read in the single-cell mRNA libraries processed by DR-Seq using the first coordinate of the right mate after trimming off adapter Ad-2. The length-based identifiers were used to minimize amplification biases and achieve resolution close to identifying unique cDNA molecules.
Genome_build: mm10 and hg19
Supplementary_files_format_and_content: details included in the 'processed_data_files_description.txt' file.

source_name: Mouse Embryonic Stem Cell line

growth_protocol: E14 cells were cultured in DMEM (Gibco) supplemented with 15% FBS (Gibco), 2mM GlutaMax (Gibco), 0.1 mM MEM nonessential amino acids, 0.1 mM β-mercaptoethanol (Sigma), 1% Pen/Strep (Gibco) and 1000u LIF/ml (ESGRO) on gelatinized petri dishes. SKBR3 cells were cultured in McCoy's 5a Medium Modified (ATCC) with 10% FBS and 1% Pen/Strep. Cells were grown at 37C and 5% CO2.

extract_protocol:
MALBAC (Zong et al. Science 2012)
Trypsinized single cells were picked using a mouth pipet with a 30μm glass capillary under a stereomicroscope. Picked cells were deposited in the center of the lid of a 0.2ml PCR tube and snap frozen in liquid nitrogen.

value: Mouse Embryonic Stem Cell line


title: HIC033

value: supernatant Hi-C


title: HIC115


title: single cell mRNA sequencing data from single E14 embryonic stem cells obtained with the CEL-seq protocol

description:
Read counts for all the single cells
E14OCscmRNA

extract_protocol:
CEL-seq (Hashimshony et al., Cell reports 2012)
Trypsinized single cells were picked using a mouth pipet with a 30μm glass capillary under a stereomicroscope. Picked cells were deposited in the center of the lid of a 0.2ml PCR tube and snap frozen in liquid nitrogen.


title: moDC_Cebpb


title: pDC_Irf8


title: HIC116


title: moDC_Pu.1


title: in vivo pDC H3K27Ac

description: Cells  were extracted from spleen and dissociated into single splenocytes. An mPDCA-1+ fraction was obtained through separation with monoclonal anti-mouse mPDCA-1 antibodies coupled to magnetic beads using a MACS cell separator system (Miltenyi Biotech).

value: mPDCA+ splenic cells

value: spleen


title: HIC113

value: dilution Hi-C


title: Bulk mRNA sequencing data from E14 embryonic stem cells

description:
RPKM data
E14bkmRNA

extract_protocol:
Illumina stranded mRNA kit
Trypsinized single cells were picked using a mouth pipet with a 30μm glass capillary under a stereomicroscope. Picked cells were deposited in the center of the lid of a 0.2ml PCR tube and snap frozen in liquid nitrogen.


title: HIC114


title: moDC H3K27Ac


title: HIC111


title: pDC_Pu.1


title: single cell whole genome sequencing data from E14 embryonic stem cell 3 obtained with the MALBAC protocol

description:
Coverage data for 50kb bins
E14OMsc3


title: pDC H3K27Ac


title: HIC112


title: pDC H3K4me3


title: Bulk whole genome sequencing data from E14 embryonic stem cells

description:
Coverage data for 50kb bins
E14bkgDNA

extract_protocol:
NEBnext Ultra DNA library prep kit
Trypsinized single cells were picked using a mouth pipet with a 30μm glass capillary under a stereomicroscope. Picked cells were deposited in the center of the lid of a 0.2ml PCR tube and snap frozen in liquid nitrogen.


title: HIC109


title: HIC108


title: single cell whole genome sequencing data from E14 embryonic stem cell 2 obtained with the DR-seq protocol

description:
Coverage data for 50kb bins
E14sc2a4

extract_protocol:
DR-Seq. First strand cDNA synthesis was performed by adding 2 μL of reaction mix containing 0.2 μL first strand buffer (MessageAmp II, Life technologies), 0.4 μL of dNTP mix (MessageAmp II, Life technologies), 0.1 μL Arrayscript (MessageAmp II, Life technologies), 0.1 μL RNAse inhibitor (MessageAmp II, Life technologies), 0.2 μL RT primer with cell specific barcode (Ad-1x)13, 0.2 μL 1:500000 diluted ERCC spike-in mix 1 (Life technologies) and 0.05% IGEPAL in water. The first strand cDNA synthesis and lysis reaction mix together with the spike-in molecules were added directly to the drop in the lid of the tube containing a single cell. Samples were incubated in a PCR machine with lid and block set to 42C for 15 minutes after which the samples were spun down and incubated for another 105 minutes. After first strand synthesis, samples were incubated for 10 minutes at 80oC. Quasilinear amplification buffer containing 6.0 μL ThermoPol buffer (NEB) 1.0 μL 10 mM dNTP mix, 26 μL water and 0.15 μL 50 μM primer mix (Ad-2)7 was added to each sample. Samples were incubated for 3 minutes at 94 oC to denature the DNA. Seven cycles of quasilinear amplification was performed (10oC for 45 seconds,15oC for 45 seconds, 20oC for 45 seconds, 30oC for 45 seconds, 40oC for 45 seconds, 50oC for 45 seconds, 65oC for 2 minutes, 95oC for 20 seconds, 58oC for 40 seconds and then immediately quench on ice). Prior to each cycle 0.6 μL polymerase mix containing 2U Bst large fragment (NEB) and 0.8U Pyrophage 3173 exo- (Lucigen) was added. Note that the 58oC step for 40 seconds step, prior to quenching the reaction on ice, is not performed for the first quasilinear amplification round. After 7 sounds of quasilinear amplification, samples were split in two. One half of the sample was processed for gDNA sequencing, the other half was processed for mRNA sequencing. For mRNA sequencing, second strand synthesis of the quasilinear amplified cDNA was performed using the P1 primer (5' - CGATTGAGGCCGGTAATAC - 3') in a single cycle of PCR (94oC for 20 sec, 51oC for 20 sec, 72oC for 7 min). After this, samples with non-overlapping barcodes were pooled and cleaned up on a cDNA purification column (MessageAmp II, Life technologies), and eluted twice with 9 μL of  water at 55oC. Next, the volume of the sample was reduced to 6.4 μL using a SpeedVac®. In vitro transcription (IVT) mix containing 1.6 μL 10x IVT buffer, 1.6 μL ATP, 1.6 μL GTP, 1.6 μL CTP, 1.6 μL UTP and 1.6 μL enzyme mix (MessageAmp II, Life technologies) were added to the samples and incubated at 37oC for 13 hours. After IVT, samples were cleaned up using the aRNA clean up columns (MessageAmp II, Life technologies) and aRNA was eluted twice in 12 μL of warm water at 55oC. After clean up, aRNA quality was assessed on a bioanalyzer (Agilent) Eukaryote Total RNA Pico chip. Library preparation was performed as previously described in Hashimshony et al. Cell reports 2012. For DNA sequencing, the other half of the quasilinear amplification product was amplified further by PCR. PCR mix containing 1.0 μL 10mM dNTP, 3 μL Thermopol buffer (10X), 0.2 μL 100 μM primer P2 (5' - GTGAGTGATGGTTGAGGTAGTGTGGAG - 3') and 1.0 μL Deep VentR (exo-) polymerase (NEB) was added to each sample for a final volume of 68 μL. PCR was performed as follows, 21 cycles of (94oC for 20 seconds, 59oC for 20 seconds, 65oC for 1 minute, 72oC for 2 minutes), and 72oC for 5 minutes at the end. After PCR, the quality of the products were assessed by agarose gel electrophoresis and the samples were cleaned up using a PCR purification column. Next, to remove adapter Ad-2 from the PCR product prior to preparing Illumina libraries, another PCR was done starting with 80 ng of product from the previous step. PCR mix containing 0.3 μL of 50 μM primer P3 with a 5' biotinylated end (5' - GTGAGCTGGAGTTGAGGTAGTGTGGAG - 3'), 5 μL Thermopol buffer (10X), 1 μL 10mM dNTP and 1 μL Deep VentR (exo-) polymerase (NEB) was added to each sample for a final volume of 50 μL. PCR was performed as follows, 94oC for 2 minutes, then 4 cycles of (94oC for 20 seconds, 46oC for 20 seconds, 65oC for 1 minute and 72oC for 2 minutes) and 9 cycles of (94oC for 20 seconds, 59oC for 20 seconds, 65oC for 1 minute and 72oC for 2 minutes). The PCR product was sheared using a sonicator (Biorupter®) on the low power setting with 15  cycles of 1 minute (30 seconds On, 30 seconds Off) with constant cooling at 4oC. The sheared products was then cleaned up using a PCR purification column (Qiagen) and eluted in 50 μL water. The final product distribution was verified on a bioanalyzer (Agilent) High Sensitivity DNA chip to have an average product size of approximately 300 bp. The DNA products was then added to Dynabeads MyOne Streptavidin C1 beads (Life Technologies) in 50 μL 2X BW buffer (10 mM Tris-HCl, 1mM EDTA and 2mM NaCl). After immobilizing the DNA products on the beads for 15 minutes, the biotinylated DNA was separated using a magnetic stand and the supernatant was stored. The biotinylated DNA was digested on the magnetic beads and the beads were washed twice with 50 μL  1X BW buffer. These two washes were then combined with the first supernatant and purified using a PCR purification column (Qiagen). Finally, Illumina libraries were prepared with different index primers for each single cell using the NEBNext Ultra DNA Library Prep Kit for Illumina® (NEB).
Trypsinized single cells were picked using a mouth pipet with a 30μm glass capillary under a stereomicroscope. Picked cells were deposited in the center of the lid of a 0.2ml PCR tube and snap frozen in liquid nitrogen.


title: moDC H3K4me3


title: single cell whole genome sequencing data from E14 embryonic stem cell 5 obtained with the DR-seq protocol

description:
Coverage data for 50kb bins
E14sc5a10


title: moDC_Irf8


title: in vivo pDC H3K4me1


title: HIC030


title: HIC107


title: single cell mRNA sequencing data from single SKBR3 cells obtained with the DR-seq protocol

description:
Read counts for all the single cells
SKBRscmRNA

source_name: Breast Cancer cell line

value: Breast Cancer cell line


title: pDC H3K4me1


title: single cell whole genome sequencing data from E14 embryonic stem cell 2 obtained with the MALBAC protocol

description:
Coverage data for 50kb bins
E14OMsc2


title: HIC106


title: HA-Ctrl_ChIP-Seq

data_processing:
Base calling : Image analysis and base calling were performed using RTA 1.17.20 and CASAVA 1.8.2
Alignment : Reads were mapped to mm9 assembly of mouse genome using Bowtie aligner release<=1.0.0, with principle parameters: -m 1 --strata --best
Peak calling : Peaks were called using the Model-based Analysis of ChIP-Seq (MACS 1.4.2) algorithm. Small dataset(HA-Ctrl_ChIP-Seq) was scaled towards larger dataset(HA-Rfx6_ChIP-Seq).
Wig files: For all samples, aligned sequences were extended to 200bp downstream (with respect to read strand) and allocated into 25bp bins.
Genome_build: mm9
Supplementary_files_format_and_content: MACS 1.4.2 peak calling file with the following collumns: chr, start,end,length,summit,tags,-10*LOG10(pvalue),fold_enrichment,FDR(%),peak name.

source_name: pancreatic beta cell line

growth_protocol: Min6b1 cells were grown in DMEM with 25mM glucose supplemented With 15% Foetal calf serum, penicillin/streptomycin and 71μM β-mercaptoethanol, in a 5% CO2 incubator at 37°C. Min6b1 were transfected with 24μg of pCMV-Tag2A-3HA-Rfx6 plasmid using Lipofectamine 2000 (Invitrogen) and harvested two days later for anti-HA (12CA5) ChIP.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared using Truseq ChIP-Seq Sample Prep Kit (Illumina, IP-202-1012) 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 Poly Nucleotide Kinase . 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), then size selected and purified using Agencourt AMPure XP beads (#A63881, Beckman). Prior to analyses DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer (Agilent). The libraries were loaded in the flowcell at 7pM concentration and clusters were generated using the Cbot (Illumina, SY-301-2002 ) and sequenced on the Illumina Genome Hiseq2500 as single-end 50 base reads following Illumina’s instructions

value: Min6b1 cells

value: HA 12CA5


title: single cell mRNA sequencing data from single E14 embryonic stem cells obtained with the DR-seq protocol

description:
Read counts for all the single cells
E14scmRNA


title: HIC110


title: moDC H3K4me1


title: single cell whole genome sequencing data from E14 embryonic stem cell 11 obtained with the DR-seq protocol

description:
Coverage data for 50kb bins
E14sc11a12


title: HIC105


title: 10wk skin

city: BUFFALO

first: SATRAJIT

last: SINHA

address: 701 ELLICOTT STREET

institute: SUNY AT BUFFALO

description: Sample 3

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 genome using the Tophat algorithm v2.0.7 with parameters -G -p 16 and default settings  [Trapnell C, et al. (2012) Nat Protoc Mar 1;7(3):562-78.]
Fragments Per Kilobase of exon per Million fragments mapped (FPKM) were calculated using the Cufflinks algorithm (v2.1.1). [Trapnell C, et al. (2012) Nat Protoc Mar 1;7(3):562-78.]
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include average FPKM values for biological replicates

source_name: Mouse adult skin (10 weeks old)

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: FVB

value: skin


title: P3 skin

description: Sample 2

source_name: Mouse pup skin (3 days old)


title: Bulk mRNA sequencing data from SKBR3 cells

description:
RPKM data
SKBRbkmRNA


title: single cell whole genome sequencing data from SKBR3 cell 26 obtained with the DR-seq protocol

description:
Copy number data for 50kb bins
SKBRsc26a10


title: HA-Rfx6_ChIP-Seq

value: 3HA-Rfx6 transfected Min6b1 cells


title: WT_N_strv_TEX

city: Norman

first: James

last: Creecy

state: Oklahoma

address: 770 Van Vleet Oval

department: Microbiology

institute: University of Oklahoma

description:
Nitrogen starvation
RNA-seq via Illumina sequencing of libraries prepared by ligation based chemistry to provide strand-specific datasets.

data_processing:
The data output from the Illumina Hiseq System was obtained directly from Vertis
For alignment of the reads contained within the fastq files to the E. coli MG1655 reference genome (RefSeq NC_U00096.3), the short read alignment tool Bowtie2 was utilized under default settings.  Bowtie parameters were set to include only perfect matches and map once reads that map to more than one genome location, i.e., uniquely mapped reads are retained. The output Bowtie2 was a SAM files for each sample.
Used SAMTOOLS (Li, et al., PMID 1950593) to sort and index the SAM files obtained from Bowtie2 and convert them to BAM format.
Sequence data was processed by conversion of the sample alignment (BAM) files to strand-specific base count (BigWIG) files. To accomplish this an in-house script was created to extract strand-specific base count data from BAM files (outputs are positive and negative strand BigWIG files).
BigWIG files were viewed and annotated using Jbrowse and Integrated Genome Viewer.
Genome_build: Reference genome for E. coli MG1655 (RefSeq NC_000913.3).
Supplementary_files_format_and_content: BigWIG files are provided showing uniquely mapped sequence reads.

organism: Escherichia coli BW38028

source_name: Cell culture

growth_protocol: Wild type E. coli K-12 (strain BW38038) and BW39452(ΔrpoS) cultures were grown on MOPS glucose minimal medium with 0.2% glucose as sole carbon source at 37°C, pH was initially 7.4,  and the agitation speed was 500 rpm. Culture samples were harvested during logarithmic growth and  following entry into stationary phase for the WT and rpoS mutant. OD600 measurements were made on a Beckman Coulter DU 800 spectrophotometer. Samples were harvested directly into ice-cold RNAlater at a 1:1 dilution to protect RNA from degradation and cells then were pelleted by centrifugation at 8000rpm for 10 minutes. Cell pellets were stored at -80°C in an equal volume of RNAlater prior to RNA extraction.

extract_protocol:
All samples were extracted using the hot phenol extraction with DNA digestion, following standard protocol
cDNA libraries were constructed at Vertis in Germany using a ligation based stratagey for Illumina whole transcriptome sequencing. Total RNA (DNase I digested) was fragmented by RNase III. RNA samples labeled as TEX were also subsequently digested with Terminator Exonuclease (TEX). Pyrophosphate groups were removed from the 5′ terminus using tobacco acid pyrophosphatase (TAP), and an RNA adapter was ligated to the 5′ end of the RNA. First-strand synthesis was performed using standard Illumina protocols.

treatment_protocol: Prior to total RNA extraction harvested bacterial cells were stored at -80.0°C in an equal volume of RNAlater.

tag: genotype

value: wt

value: Nitrogen starvation

tag: growth phase

value: 30 min post stationary

tag: sample type

value: no RNA treatment


title: single cell whole genome sequencing data from SKBR3 cell 28 obtained with the DR-seq protocol

description:
Copy number data for 50kb bins
SKBRsc28a4


title: E18.5 skin

description: Sample 1

source_name: Mouse embryo skin (18.5 days old)


title: WT_glucose_stat_TEX

description:
Carbon starvation
RNA-seq via Illumina sequencing of libraries prepared by ligation based chemistry to provide strand-specific datasets.

value: Carbon starvation


title: BY4741_50mM_3

first: Paul

last: van Heusden

address: Sylviusweg 72

department: Institute of Biology

description: Sample 7

data_processing:
CLC genomic workbench (Aarhus, Denmark) software was used for processing raw data.
Reads were trimmed to 17 bp.
Reads were aligned to a virtual tag library obtained by in silico digestion by NlaIII, cutting at 5’-CATG-3’, of S. cerevisiae sequences corresponding to open reading frames plus 200 bp downstream sequences.
Genome_build: FASTA sequence files of the 16 nuclear chromosomes and mitochondrial genome (S. cerevisiae S288c)(release: 03-Apr-2012)(www.yeastgenome.org).
Supplementary_files_format_and_content: .txt file with the number of reads (normalized to reads per million) aligning to each gene for all samples.

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae BY4741_50mM

growth_protocol: Strain BY4741 was grown overnight at 30 °C in Translucent YNB medium (Navarrete et al 2010, FEMS Yeast Research 10, 508) containing 50 mM KCl, supplemented with leucine, histidine, methionie and uracil. This culture was used to inoculate two times 50 ml of supplemented YNB medium containing 50 mM KCl yielding A600nm 0.1. These cultures were grown to A600nm 0.5 and cells were isolated by centrifugation. Cells from one culture were washed twice with supplemented YNB medium containing 50 mM KCl and resuspended in 50 ml supplemented YNB medium containing 50 mM KCl. Cells from the other culture were washed twice with supplemented YNB medium lacking KCl and resuspended in 50 ml supplemented YNB medium lacking KCl. Both cultures were incubated at 180 rpm at 30 °C. After 60 min the cultures were poured into plastic tubes and frozen in liquid nitrogen. Prior to RNA isolation, the frozen cultures were thawed on ice and cells were collected by centrifugation and transferred to Eppendorf tubes using ice-cold water.

extract_protocol:
RNA was isolated using the Ambion RiboPure yeast RNA Purification Kit (Life Technologies).
1 μg of total RNA was incubated with oligo-dT beads to capture the polyadenlyated RNA fraction. First- and second-strand cDNA synthesis was performed while the RNA was bound to the beads. While on the beads, samples were digested with NlaIII to retain a cDNA fragment from the most 3’ CATG to the poly(A)-tail. Subsequently, the GEX adapter 1 was ligated to the free 5’-end of the RNA, and a digestion with MmeI was performed, which cuts 17 bp downstream of the CATG site. At this point, the fragments detach from the beads. After dephosphorylation and phenol extraction, the GEX adapter 2 was ligated to the 3’-end of the tag. A PCR amplification with 15 cycles using Phusion polymerase was performed with primers complementary to the adapter sequences to enrich the samples for the desired fragments.

tag: growth protocol

value: 50 mM KCl


title: BY4741_50mM_4

description: Sample 8


title: rpoS_N_strv_TEX

value: rpoS


title: single cell whole genome sequencing data from SKBR3 cell 25 obtained with the DR-seq protocol

description:
Copy number data for 50kb bins
SKBRsc25a9

tag: cell type


title: single cell whole genome sequencing data from SKBR3 cell 20 obtained with the DR-seq protocol

description:
Copy number data for 50kb bins
SKBRsc20a7


title: WT_glucose_log_TEX

description:
log phase sample
RNA-seq via Illumina sequencing of libraries prepared by ligation based chemistry to provide strand-specific datasets.

value: log phase sample

value: Log phase OD 0.4


title: BY4741_50mM_1

description: Sample 5


title: BY4741_50mM_2

description: Sample 6


title: single cell whole genome sequencing data from SKBR3 cell 13 obtained with the DR-seq protocol

description:
Copy number data for 50kb bins
SKBRsc13a6


title: BY4741_0mM_4

description: Sample 4

source_name: Saccharomyces cerevisiae BY4741_0mM

value: 0 mM KCl


title: P. chlororaphis 30-84_gacA_AB_rep1

city: College station

first: Dongping

last: Wang

address: Wellborn

institute: TAMU

description: Strand-specific cDNA libraries were constructed using the SOLiD Total RNA-Seq kit according to the manufacturer’s instructions with the following modifications: 1) For RNA fragmentation, 300 ng of rRNA-depleted RNA were incubated at 95˚C for 5 min. Bioanalyzer traces were used to confirm that the largest proportion of RNA fragments were around 200 bp. 2) Bioanalyzer traces following reverse transcription were used to confirm that hybrization and ligation of RNA adapters and subsequent reverse transcription of the RNA to cDNA was successful. 3) Amplification of cDNA was carried out following reverse transcription, but preceding the size-selection step. Samples were barcoded by replacing the SOLiD 3’ primer with the appropriate barcoding primer as directed in the SOLiD instructions. Size selection of DNA amplicons ranging from 200-300 bp was performed using an E-Gel iBase system (SYBR Safe 2% SizeSelect gel) (Life Technologies, Carlsbad, CA).  This step was repeated to ensure that adapter-adapter dimers were fully eliminated before sequencing. Paired-end sequencing was carried out by the University of Texas Genomic Sequencing and Analysis Facility (UTGSAF: http://www.ti3d.utexas.edu/facilities/gene-expression) on a Life Technologies SOLiD 5500xl sequencing system. Targeted sequencing depth was six-million paired-end reads per sample.

data_processing:
Paired-end sequencing was carried out by the University of Texas Genomic Sequencing and Analysis Facility (UTGSAF: http://www.ti3d.utexas.edu/facilities/gene-expression) on a Life Technologies SOLiD 5500xl sequencing system. Targeted sequencing depth was six-million paired-end reads per sample.
Filtering and alignment of the SOLiD 4 paired-end data was performed at the UTGSAF using the AB SOLiD BioScope Whole Transcriptome pipeline (v1.3), for whole-transcriptome RNA-seq analysis.
Based on gene annotation information, the pipeline produced genome alignment results as a compressed binary version of the Sequence Alignment Map (BAM files).
Mapped reads were visualized using BamView in Artemis 13.2.0 (Rutherford et al. 2000).
The number of reads per kb of transcript per million mapped reads (RPKM) was used to normalize the raw data (Mortazavi et al., 2008), and mean RPKM values were determined for both the wild-type and gacA mutant samples.
Genome_build: NCBI Genome Accession #: PRJNA67533
Supplementary_files_format_and_content: Excel file containing the RPKM values for each gene

organism: Pseudomonas chlororaphis subsp. aureofaciens 30-84

source_name: gacA mutant cells

growth_protocol: Three biological replicates of every strain were started from single colonies located on three separate plates containing AB + 2% CAA and then transferred to 10 ml AB + 2% CAA broth. All cultures were grown at 28˚C with shaking (150 rpm) to an approximate OD600 = 1.2.

extract_protocol:
Transfer 700 μl lysate into RNeasy Mini column place in a 2 ml collection tube and centrifuge for 30 s at highest speed. Add 350 μl Buffer RW1 to the column and centrifuge for 30 s. Discard flow-through and reuse the collection tube. Add 10 μl DNase stock solution to 70 μ l RDD Buffer. Add the DNase I solution into the column and incubate at RT for 15 min. Add 350 μl Buffer RW1 to the column and wait for 5 min, centrifuge for 30 s. Discard the flow-through and collection tubes. Place the RNeasy Mini spin column in a new 2 ml collection tube. Add 500 μl Buffer RPE to the column. Centrifuge for 30 s. Place the column in a new 1.5 ml tube, and centrifuge for 1 min to eliminate any residue ethanol. Place the column in a new collection tube. Add 50 μl RNase free water, centrifuge for 1 min. Store RNA samples at -20°C
Strand-specific cDNA libraries were constructed using the SOLiD Total RNA-Seq kit according to the manufacturer’s instructions with the following modifications: 1) For RNA fragmentation, 300 ng of rRNA-depleted RNA were incubated at 95˚C for 5 min. Bioanalyzer traces were used to confirm that the largest proportion of RNA fragments were around 200 bp. 2) Bioanalyzer traces following reverse transcription were used to confirm that hybrization and ligation of RNA adapters and subsequent reverse transcription of the RNA to cDNA was successful. 3) Amplification of cDNA was carried out following reverse transcription, but preceding the size-selection step. Samples were barcoded by replacing the SOLiD 3’ primer with the appropriate barcoding primer as directed in the SOLiD instructions. Size selection of DNA amplicons ranging from 200-300 bp was performed using an E-Gel iBase system (SYBR Safe 2% SizeSelect gel) (Life Technologies, Carlsbad, CA).  This step was repeated to ensure that adapter-adapter dimers were fully eliminated before sequencing.

tag: genotype/variation

value: gacA mutant

value: logarithm phase

tag: media

value: AB minimal medium + 2% casamino acids (CAA)


title: P. chlororaphis 30-84_gacA_AB_rep3


title: P. chlororaphis 30-84_gacA_AB_rep2


title: rpoS_N_strv


title: WT_N_strv


title: P. chlororaphis 30-84_WT_AB_rep3

source_name: wild type bacterial cells

value: wild type


title: single cell whole genome sequencing data from SKBR3 cell 10 obtained with the DR-seq protocol

description:
Copy number data for 50kb bins
SKBRsc10a5

value: Breast Cancer cell line


title: WT_glucose_stat


title: BY4741_0mM_3

description: Sample 3


title: single cell whole genome sequencing data from SKBR3 cell 3 obtained with the DR-seq protocol

description:
Copy number data for 50kb bins
SKBRsc3a2


title: P. chlororaphis 30-84_WT_AB_rep2


title: WT_glucose_log


title: BY4741_0mM_1

description: Sample 1


title: Bulk whole genome sequencing data from SKBR3 cells

description:
Copy number data for 50kb bins
SKBRbkgDNA


title: BY4741_0mM_2

description: Sample 2


title: Vitis vinifera Carignan infected by E. necator c-strain 6dpi-rep3

status: Public on Dec 10 2014

city: Berkeley

first: Abraham

last: Morales-Cruz

state: California

address: 1 Cyclotron Road

institute: Joint Genome Institute

description: Leaves were collected at 6 days post inoculation

data_processing:
Quality trimming of raw reads was done with Sickle v.1.210 with a threshold of 20 (Q>20).
Quality filtering was done with Scythe v.0.991 with a prior of 0.4
Predicted transcriptomes of Erysiphe necator c-strain (JNVN00000000) and V. vinifera (GCA_000003745.2) were combined and used as a reference for mapping PM-infected grape leaves reads.
Bowtie2 v.2.1.0  was used to map the processed reads to the combined references with the following options: -q --end-to-end --sensitive --no-unal. Only reads with a mapping score greater than 30 were retained
Read counts were extracted from the bowtie2 alignments using the script sam2counts.py v.0.91. Only reads with a mapping score greater than 30 were retained.
Genome_build: Reads were mapped on E. necator (JNVN00000000) and V. vinifera (GenBank Assembly ID: GCA_000003745.2) predicted transcriptomes. The study focused on E. necator gene expression. Mapping on V. vinifera scaffold was done to limit non-specific mapping of grape reads.  Only counts of uniquely mapped E. necator genes are reported.
Supplementary_files_format_and_content: GEO_En_c-strain_time_course_raw_counts.txt : tab delimited text file, raw read counts determined by mapping the sequencing reads, only E. necator reads.

organism: Vitis vinifera

source_name: Vitis vinifera cv. Carignan leaves inoculated with Erysiphe necator (isolate: c-strain)

growth_protocol: Carignan detach leaves were disinfected with a 3% sodium hypochlorite solution and placed in Petri dishes containing 8 g/L water agar. A portable paint sprayer was used to inoculated leaves with a 1x106 conidia/mL suspension of the C-strain isolate in 0.001% Tween. The leaves were maintained under ambient conditions.

extract_protocol:
Total RNA was extracted using a CTAB based protocol with a chloroform denaturation step. RNA was cleaned with RNeasy kit (Qiagen, US) including the Dnase treatment on column.
Illumina TruSeq RNA Sample Prep Kit v2 protocol

treatment_protocol: Leaves were collected at 12 hours, 24 hours, 3 days, and 6 days post inoculation.

tag: biological replicate

value: Leaves

tag: time point

value: 6 days post inoculation


title: Vitis vinifera Carignan infected by E. necator c-strain 24hpi-rep2

description: Leaves were collected at 24 hours post inoculation

value: 24 hours post inoculation


title: Vitis vinifera Carignan infected by E. necator c-strain 3dpi-rep1

description: Leaves were collected at 3 days post inoculation

value: 3 days post inoculation


title: Vitis vinifera Carignan infected by E. necator c-strain 6dpi-rep1


title: Vitis vinifera Carignan infected by E. necator c-strain 3dpi-rep2


title: Vitis vinifera Carignan infected by E. necator c-strain 3dpi-rep3


title: Vitis vinifera Carignan infected by E. necator c-strain 24hpi-rep3


title: Vitis vinifera Carignan infected by E. necator c-strain 24hpi-rep1


title: Vitis vinifera Carignan infected by E. necator c-strain 12hpi-rep3

description: Leaves were collected at 12 hours post inoculation

value: 12 hours post inoculation


title: Vitis vinifera Carignan infected by E. necator c-strain 12hpi-rep2


title: Vitis vinifera Carignan infected by E. necator c-strain 12hpi-rep1


title: ASC_Day9

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

data_processing:
reads aligned with tophat v2.0.8b with parameter –-b2-very-sensitive,
transcript abundance estimated with cufflinks v2.1.1 with parameter -–GTF-guide
reference gtf with cuffmerge v2.1.1 with parameters -g, -s
diffrential expression analysis with cuffdiff v2.1.1 with parameters -b, -s, -u
csv file created from columns 5,10,14,18,22 from cuffdiff output file genes.fpkm_tracking
Genome_build: hg19
Supplementary_files_format_and_content: csv with two columns; gene_short_name and fpkm value

source_name: Pre-adipocytes from liposuction material, cultured, 9 days after adipogenic stimulation (Day 9).

growth_protocol: Primary ASCs isolated from liposuction material were cultured in T175 flasks under proliferative conditions in high-glucose DMEM (4.5 g/l; Life Technologies-BRL) containing 20% FBS and 2 ng/ml basic fibroblast growth factor (Sigma-Aldrich). Cells at passage 5-7 were used for adipogenic induction. When cells reached confluency, adipogenic differentiation was induced by replacing growth medium with DMEM/F12 containing 10% FBS and by addition of 0.5 µM 1-methyl-3 isobutylxanthine (Dumex Alpharma), 1 µM dexamethasone (Dumex Alpharma), 10 µg/ml insulin (Novo Nordisk) and 100 µM (Dumex Alpharma) indomethacin for up to 9 days.

extract_protocol:
Total RNA was isolated using the Ambion TRIzol® Reagent RNA extraction kit (Life Technologies), quality checked using a BioAnalyzer 2100 and processed for library preparation.
RNAseq library was prepared according to the Illumina protocol, and sequenced on an Illumina HiSeq2500 at the Norwegian Sequencing Center.

treatment_protocol: Cells were cultured as described under Growth protocol. 10e6 cells were cultured to the indicated stages for total RNA isolation.

value: Pre-adipocytes

tag: passages

value: Cells in passage 5-7

value: adipogenic stimulation

tag: time

tag: differentiation state

value: Non-proliferating, differentiated for 9 days


title: ASC_Day0

source_name: Pre-adipocytes from liposuction material, cultured, undifferentiated, confluent, on day of adipogenic stimulation (Day 0).

value: The day of adipogenic stimulation (Day 0)