title: control_cross_L1_C

city: Mainz

first: Rene

last: Ketting

address: Ackermannweg 4

institute: IMB

data_processing:
The raw reads in FastQ format were filtered from 3’ adapter sequences and size-selected in the range 15-35 bases (plus 8 bases random barcodes) using cutadapt v.1.2.1 1using parameters: -a AGATCGGAAGAGCACACGTCT -O 8 -m 23 -M 43 . Subsequently, PCR clonal reads were deduplicated using Bash and Awk commands. All reads containing low-quality (Phred+33 score less than 20) bases were filtered with the FastX toolkit (http://hannonlab.cshl.edu/fastx_toolkit/; fastq_quality_filter -q 20 -p 100 -Q 33), then the files were reformatted from FastQ into tabular format, sorted and deduplicated based on full sequence identity (library insert plus 5’ and 3’ random barcodes of 4 nucleotides), and finally converted back to FastQ format for mapping. Quality assessment of the raw and processed data was done with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). Mapping to the C. elegans genome reference WS244 was performed using Bowtie v1 2 with parameters: -v0 -M1 --best --strata --nomaqround --tryhard --trimm5 4 --trim3 4. Unmapped reads where then filtered for the ones ending with a “T” using custom python scripts and remapped using bowtie using the same parameter but trimming one extra 3’ base. These newly mapped reads were considered mono-uridylated. This filtering/mapping cycle was performed 10 times in order to map up to penta-urydilated reads. All mapped reads where then annotated using bedtools intersect 3 with a customized WS244.gff3 (ftp://ftp.wormbase.org/pub/wormbase/releases/WS244/species/c_elegans/PRJNA13758/c_elegans/PRJNA13758.WS244.annotations.gff3.gz); using the following parameters: -abam -b[custom annotated gff3] -bed -wa -wb. Mapped and annotated reads were subsequently filtered for size and starting nucleotide using custom made python scripts and normalized to total of non-structural reads between 18 and 30 nucleotides. Structural reads were considered as reads that mapped rRNAs, tRNAs and snoRNAs. During the analysis we considered miRNA reads that were 22 to 24 nt long sense to annotated miRNAs, we considered piRNA reads that were 21 nt long, started with a “T” and were sense to annotated piRNAs, and 22G reads that were 20 to 23 nt long, started with a “G” and map antisense to genes, transposable elements or pseudogenes. In order to categorize genes, we retrieved WAGO-1 targets, ERGO-1 targets, mutator targets, ALG-3/4 targets and CSR-1 targets from Gu (2009),Vasale (2010), Phillips(2014), Conine (2010), Claycomb (2009)4–8 respectively. For each protein coding gene saw if it was a WAGO-1 target, if not we saw if it was an ERGO-1 target, if not we saw if it was a mutator target and so on, in the previously mention order. The validation of a gene in a category would automatically exclude it from the following categories; this was to insure that there would be no duplication, since some categories overlap partially.
Genome_build: WS240
Supplementary_files_format_and_content: read counts for: total mapped reads, mapped reads 18-30 nt, non structrural reads (18-30 nt), 18-30nt mapping genes_anti-sense, 18-30nt mapping genes_sense, 18-30 nt mapping pseudogenic_transcript_anti-sense, 18-30 nt mapping pseudogenic_transcript_sense, 18-30nt mapping to piRNAs_anti-sense, 18-30nt mapping to piRNAs_sense, 18-30nt mapping to transposable_elements_anti-sense, 18-30nt mapping to transposable_elements_sense, 18-30nt mapping to ncRNA_anti-sense, 18-30nt mapping to ncRNA_sense, 18-30nt mapping to snoRNA_anti-sense, 18-30nt mapping to snoRNA_sense, 18-30nt mapping to tRNA_anti-sense, 18-30nt mapping to tRNA_sense, 18-30nt mapping to antisense_RNA_anti-sense, 18-30nt mapping to antisense_RNA_sense, 18-30nt mapping to lincRNA_anti-sense, 18-30nt mapping to lincRNA_sense, 18-30nt mapping to miRNA_anti-sense, 18-30nt mapping to miRNA_sense, 18-30nt mapping to snRNA_anti-sense, 18-30nt mapping to snRNA_sense, 18-30nt mapping to rRNA_anti-sense, 18-30nt mapping to rRNA_sense, 18-30nt mapping to scRNA_anti-sense, 18-30nt mapping to scRNA_sense, piRNAs (20U-21U sense to annotated piRNAs), miRNA (20-24 nt mapping sense to annotated miRNAs), 20G-23G antisense to annotated transposons, 20G-23G antisense to annotated protein coding genes, 20G-23G antisense to ALG-3/4 targets, 20G-23G antisense to CSR-1 targets, 20G-23G antisense to ERGO-1 targets, 20G-23G antisense to WAGO-1 targets, 20G-23G antisense to mutator targets, 20G-23G antisense to other protein coding genes

organism: Caenorhabditis elegans

source_name: L1 animals

growth_protocol: worms were grown in NGM plates seeded with OP50

extract_protocol:
150 L1 or 50 L2 C. elegans larvae were washed in M9 buffer (22nM Na2HPO4, 33 mM KH2PO4, 86 mM NaCl, 1 mM MgSO4) and digested in lysis buffer (200mM NaCl, 100 mM Tris pH 8.5, 50 mM EDTA, 0.5 % SDS, 200 µg/mL Prot-K) for 3h at 65°C followed by 15 min at 95° C to denaturate the Prot-K. Lysate was then incubated with DNase I (NEB) for 30 min at 37° C. Total RNA was then isolated using TRIZOL-LS (Life Technologies) using the manufacturer instructions and dissolved in 8 µL of H2O.
For RIP-seq, HRDE-1 was precipitated from synchronized adult worms. 50 µL of packed worms were washed with M9 and sonicated in 200 µL of lysis buffer (25 mM Tris pH7.5, 150 mM NaCl, 1.5 mM MgCl, 1 mM DTT and cOmplete mini, EDTA free (Roche, 1 tablet per 100 mL) 5 times 30 sec ON, 30 sec OFF at the maximum energy setting. Lysates were centrifuged at 21000G for 5 min. 50 µL of the supernatant was used as input and 100 µL was incubated with 1 mg of anti-HRDE-1 antibody (Ashe et al. 2012) and 10 µL of Dynabeads Protein G (Life Technologies) for 2 hours. The beads were washed 5 times 10 min with wash buffer  (25 mM Tris pH7.5, 150 mM NaCl, 1.5 mM MgCl, 1 mM DTT and cOmplete mini, EDTA free (Roche, 1 tablet per 100 mL, 0.2 % Triton X-100). RNA was extracted from both input and IP with TRIZOL-LS (Life Technologies) using the manufacturer instructions and dissolved in 8µL of H2O.
All 8uL of total RNA was treated with 5 U of tobacco acid phosphatase (Epicenter) at 37°C for 2 h to digest 5’ tri- and di-phosphates to mono-phosphates. RNA was size-selected between 15- to 35-nt on 15% TBE-urea gel. Gel-purified RNA was eluted overnight in 300 mM NaCl and then precipitated with 100% isopropanol and Glycoblue for 1 h at -20°C. The pellet was washed once with 75% ethanol and dissolved in nuclease-free water. Then, this purified fraction was confirmed by Bioanalyzer Small RNA chip (Agilent). Library preparation was based on the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England BioLabs) with slight modification. In brief, small RNA was first ligated to the 3’ adapter and then the 5’ adapter, both of which contained 4 random bases and were chemically synthesized by Bioo Scientific. Adapter-ligated RNA was reverse-transcribed and PCR-amplified for 14 cycles using index primers. The PCR-amplified cDNA construct was purified using AMPure XP beads (Beckman Coulter). The purified PCR reaction was checked on the Bioanalyzer using High Sensitivity DNA chip (Agilent). Size selection of the small RNA library was done on LabChip XT instrument (Perkin Elmer) using DNA 300 assay kit. Only the fraction containing 140-165 bp was pooled in equal molar ratio. The resulting 10 nM pool was denatured and diluted to 10 pM with 5% PhiX spike-in and sequenced as single-read on HiSeq 2500 (Illumina) in rapid mode for 50 cycles using on-board cluster generation. Sample “L1 N2” was sequenced as single-read on Miseq (Illumina). After demultiplexing, on average 35 million passing filter reads were obtained per sample.

treatment_protocol: C. elegans L1 larvae were obtained by bleaching gravid adults and letting the eggs hatch in M9 over-night. L1 cross-offspring larvae were obtained single picking 200 eggs to an unseeded NGM plate, bleaching those eggs to remove any bacteria that was carried along, and allowed to hatch over-night. L1 larvae were then re-suspended in M9. To identify cross offspring, males were carrying the punc-119::GFP transgene.  L2 larvae were single picked and washed in M9 buffer for each sample. Cross offspring was identified by the presence of a marker carried only by the male.

value: RFK231_males x RFK240_herm

tag: genoptype/variation

value: L1 animals


title: sterile_cross_L1_B

status: Public on Aug 13 2015

type: SRA

country: Germany

library_source: transcriptomic

molecule: total RNA

tag: strain background

value: RFK231_males x RFK232_herm

tag: developmental stage


title: control_cross_L1_B


title: control_cross_L1_A


title: sterile_cross_L1_C


title: prg-1_L1_A


title: prg-1_L1_B


title: prg-1_cross_L1_B

value: N2 _males x SX922_herm


title: prg-1_cross_L1_C


title: prg-1_L1_C


title: prg-1_cross_L1_A


title: mut-7_L1_C

value: mut-7(pk204) III; mjSi22 [Pmex-5::mCherry::his-58::21UR-1_as::tbb-2(3’UTR)] I; otls45 [Punc119::GFP] V


title: 5%DMSO/0.1%Tween 20 in H20 - 1

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

country: USA

institute: University of Georgia

description: Stranded mRNA-seq

data_processing:
Raw fastq reads were trimmed for adapters, preprocessed to remove low quality reads using Trimmomatic v0.32
Genome_build: Z. mays AGPv3.25
Supplementary_files_format_and_content: tab delimited text file, see metafile for column headers

organism: Zea mays

source_name: Emergent but non-fully-expanded 4th leaf

growth_protocol: Zea mays Var. Golden Queen seeds were germinated in MetroMix 200 (Sun Gro Horticulture Distribution, Inc.) supplemented with 14-14-14 Osmocote (Scotts Miracle-Gro) and grown in a greenhouse with a 12-h photoperiod, minimum of 300 μmol m−2 s−1 of photosynthetically active radiation supplied by supplemental lighting, 70% relative humidity, and temperature cycle of 24 °C/28 °C (night/day).

extract_protocol: RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 µg, and all volumes were reduced to a third of the described quantity.

tag: tissue

value: Leaf

tag: age

tag: agent

value: Dimeythl sulfoxide/Tween 20/H2O

tag: cultivar

value: Golden Queen


title: mut-16_L1_A


title: mut-16_L1_B


title: wild-type_L1_B

value: otls45 [Punc119::GFP] V


title: mut-7_L2_B

source_name: L2 animals

value: mut-7(pk204) III

value: L2 animals


title: wild-type_L1_A


title: mut-7_L2_A


title: sterile_cross_L2_B


title: control_cross_L2_A

value: RFK258_males x RFK240_herm


title: mut-16_prg-1_L2_B


title: sterile_cross_L2_A


title: control_cross_L2_B


title: wild-type_L2_B

value: wild-type


title: mut-7_L1_A


title: DD6_ERRAS_4days-induced

city: Glasgow

first: Peter

last: Adams

address: Switchback Rd, Bearsden

country: United Kingdom

institute: University of Glasgow, Beatson Institute for Cancer Research

description: RNA-seq of RAS 4 day induced cells in mitosis

data_processing:
Reads were trimmed using Trim Galore (v0.3.0).
Paired-end reads are aligned to the human genome (hg19) using tophat2. Reference splice junctions were provided by a reference transcriptome (Ensembl build 73).
FPKMs were determined using cufflinks under default settings.
Differentially expressed genes were called using cuffdiff under default settings.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix of FPKMs for all six samples, as called by cufflinks. Differential gene expression for uninduced vs induced samples, as called by cuffdiff.

molecule: polyA RNA

organism: Homo sapiens

source_name: Fibroblasts

growth_protocol: Early passage IMR90 cells stably expressing tamoxifen-inducible RasV12 (ER:RAS) were maintained in DMEM supplemented with 20% fetal calf serum, 2 mM L-glutamine, 50 U/ml Pen-Strep and 0.5mg/ml G418, at 3% oxygen level. RasV12 expression was induced by 100 nM of tamoxifen.

extract_protocol:
RNA was isolated from cell pellets using RNAeasy kit (Qiagen), and DNA was removed using  RNase-free DNase set (Qiagen).
Quality of RNA was assessed on Agilent 2100 Bioanalyser using Agilent RNA 6000 Nano Kit (Agilen Technologis), before creating oligo-dT based cDNA library using Illumina TruSeq RNA Sample Prep Kit,v2.0. kit.
RNA-seq: the library was sequenced on a NextSeq500, using a NextSeq500 Mid Output kit 150 cycles flowcell.

treatment_protocol: Cells expressing RasV12 for 4 days, or uninduced control cells, were synchronised in mitosis using 1µM DME (Dimethylenastron), and unattached mitotic cells were collected by washout. MI>90% was confirmed microscopically.

tag: cell line


title: DD5_ERRAS_4days-induced


title: DD2_ERRAS_uninduced

description: RNA-seq of unindiced cells in mitosis


title: DD3_ERRAS_uninduced

description: RNA-seq of unindiced cells in mitosis


title: mut-7_L1_B


title: DD1_ERRAS_uninduced

description: RNA-seq of unindiced cells in mitosis


title: GRO.seq_shPAF1.1_HCT116_rep2

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

description: GRO-seq

data_processing:
Base-calling and quality filtering, default settings, Illumina Casava 1.8 for reads generated with Illumina HiSeq 2000
Base-calling and quality filtering, default settings, bcl2fastq version 2 for reads generated with Illumina NextSeq 500
ChIP-seq: Reads were aligned using Bowtie v0.12.9, allowing unique reads only and up to two mismatches in the entire read length. Alignments were extended to a total fragment length of 150 bases toward the interior of the sequenced fragment. UCSC bigWig files were created with 1bp resolution coverage across the genome and normalized to total reads per million (r.p.m).
Nascent and Total RNA-seq: Reads were aligned to the human genome (UCSC hg19) and Ensembl 72 GTF human annotations  using the Tophat aligner version 2.0.10, with the - g1 option. Alignments were not extended. UCSC bigWig files were created with 1bp resolution coverage across the genome and normalized to total reads per million (r.p.m).
Genome_build: UCSC hg19
Supplementary_files_format_and_content: http://genome.ucsc.edu/goldenPath/help/bigWig.html

molecule: nuclear RNA

growth_protocol: HCT116 and MCF7 cells were grown in DMEM supplemented with 10% FBS. S2 cell were grown in Schneider's media with 10% FBS at room temperature

extract_protocol:
For ChIP-seq, HCT116 cells were crosslinked with 1% paraformaldehyde for 10 minutes at room temperature with gentle rotation, and then quenched by 0.125 M glycine solution. After washing, nuclei were sonicated on a Misonix Sonicator 3000 Ultrasonic Cell Disruptor, and the supernatant was used for immunoprecipitation with the indicated antibody. ChIP-sequencing libraries were prepared with Illumina’s Tru-seq DNA sample prep kit. For nascent RNA-seq, HCT116 cells was harvested and washed 3 times with cold PBS, then suspended in 10 ml Buffer A (10 mM HEPES at pH=7.9, 10 mM KCl, 2 mM MgCl2, 1 mM DTT, 1× Complete protease inhibitors [Roche]). After incubating on ice for 15 minutes, the cells were homogenized in pre-cooled 15 ml Dounce tissue homogenizer for 15 times. Nuclei were then washed twice with Buffer B (10 mM HEPES at pH=7.9, 250 mM Sucrose, 1 mM DTT, 1× Complete protease inhibitors). The pellet was vigorously suspended with 1 ml NUN buffer (20 mM HEPES at pH=7.9, 7.5 mM MgCl2, 0.2 mM EDTA, 300 mM NaCl, 1 M Urea, 1% v/v Nonidet P40, 1 mM DTT, 20 U/ml SUPERase.In RNase Inhibitor [Ambion]) that was freshly prepared. The chromatin was then washed twice more with 5 ml NUN buffer each time. The supernatant was removed and RNA was purified. The RNA was subjected to polyA depletion with Oligo(dT) magnetic beads (Invitrogen) and DNase I treatment (NEB) for 20 minutes, and then was re-purified. For sequencing, 2 μg of resulting RNA was used for ribosomal RNA depletion with the RiboZero kit (Epicenter) and libraries were made with the TruSeq RNA sample Prep Kit (Illumina).
ChIP-sequencing libraries were prepared with Illumina’s Tru-seq DNA sample prep kit using standard protocols. Nascent and Total RNA-seq libraries were prepared with Illumina’s TruSeq RNA sample Prep Kit using standard protocols. The global nuclear run-on procedure and the preparation of Gro-seq libraries were previously described (Core et al., 2008; Gardini et al., 2014).

tag: cell type

value: colorectal cancer cell line

tag: shRNA

value: PAF1 shRNA #1


title: mut-16_prg-1_L2_A


title: N20_shSCR_starve_HCT116_ChIPSeq

description: ChIP of Total Pol II

library_source: genomic

molecule: genomic DNA

value: Scramble shRNA

tag: chip antibody

value: Pol II (Santa Cruz, sc-899)


title: N20_shSCR_MCF7_ChIPSeq

description: ChIP-seq of Total Pol II

value: breast cancer cell line


title: N20_shPAF1.1_MCF7_ChIPSeq

description: ChIP-seq of Total Pol II


title: GRO.seq_shPAF1.1_HCT116_rep1

description: GRO-seq


title: Input_shSCR_MCF7_ChIPSeq

description: Input DNA from whole cell extract

value: no antibody


title: N20_shSCR_serum_HCT116_ChIPSeq

description: ChIP of Total Pol II


title: N20_shPAF1.1_FP_HCT116_ChIPSeq

description: ChIP of Total Pol II


title: wild-type_L2_A


title: Input_shPAF1.1_DMSO_HCT116_ChIPSeq

description: Input DNA from whole cell extract


title: N20_shPAF1.1_DMSO_HCT116_ChIPSeq

description: ChIP of Total Pol II


title: DD4_ERRAS_4days-induced


title: CDK9_shSCR_HCT116_ChIPSeq

description: ChIP-seq of CDK9

value: CDK9 (Santa Cruz, sc-484)


title: LEO1_shSCR_HCT116_ChIPSeq

description: ChIP-seq of LEO1

value: LEO1 (Bethyl, A300-175A)


title: LEO1_shPAF1.1_HCT116_ChIPSeq

description: ChIP-seq of LEO1


title: Input_shSCR_DMSO_HCT116_ChIPSeq

description: Input DNA from whole cell extract


title: GRO.seq_shSCR_HCT116_rep1

description: GRO-seq


title: GRO.seq_shSCR_HCT116_rep2

description: GRO-seq


title: RNA-seq_Genistein_rep2

city: Boston

first: Paula

middle: Goodman

last: Fraenkel

state: MA

address: 330 Brookline Avenue, SLD 423B

department: Division of Hematology/Oncology

institute: Beth Israel Deaconess Medical Center

data_processing:
Pair-end, 36-bp reads from each sample were aligned to the human genome (hg18) using TopHat (version 1.1.0) and Bowtie.  Gene expression was quantified as fragments per kilobase of exon model per million mapped fragments (FPKM,) using Cufflinks (version 1.0.3).
Differential expression for BMP6-treated or genistein-treated biological replicates compared to DMSO-treated controls was determined using the Cufflinks tool Cuffdiff.  The criteria for differential expression were: a log2 fold-change of >0.58 or <-0.58 and a q-value < 0.05 when compared to the control condition.  We also required that the differentially expressed genes used for downstream analysis have an FPKM >0.1 in at least one of the conditions.
Genome_build: hg18
Supplementary_files_format_and_content: Processed data file are in the format of Cufflinks output.

growth_protocol: The human hepatocarcinoma cell line, HepG2, (American Type Culture Collection, Manassas, VA) was maintained in a-Minimum Essential Medium (α-MEM)/10% certified endotoxin-free fetal bovine serum (FBS)/1% penicillin-streptomycin (Life Technologies, Grand Island, NY) at 37ºC, 5% CO2.  HepG2 cells were seeded onto 12-well tissue culture treated plates at a density of 4x105 cells per well.

extract_protocol: After 18 hours of treatment, the cells were harvested for the extraction of total RNA using the RNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions.  DNA was eliminated by on-column RNase-free DNase treatment.  RNA quality was verified (RNA integrity number >8.5) using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).  Messenger RNA was isolated, converted to cDNA, and amplified using the mRNA Purification Kit (Illumina, San-Diego, CA) according to the manufacturer’s instructions.  A cDNA library was built and used to generate clusters on the Illumina flow cell according to the Illumina protocol and sequenced using a Genome Analyzer II (Illumina).

treatment_protocol: Twenty-four hours after plating, the culture medium was changed to low serum medium (alpha-MEM/1% FBS).  After 8 hours of equilibration, the cells were then treated for 18 hours with genistein (10 mM), bone morphogenic protein 6 (BMP6) 50 ng/ml, (both from R&D Systems, Minneapolis, MN), or vehicle only (1% DMSO).  All the samples included 1% DMSO to control for any potential effects of the vehicle.


title: RNA-seq_Genistein_rep1


title: RNA-seq_Control_rep2


title: RNA-seq_Control_rep3


title: RNA-seq_BMP6_rep2


title: RNA-seq_Control_rep1


title: RNA-seq_Genistein_rep3


title: N20_shSCR_DMSO_HCT116_ChIPSeq

description: ChIP of Total Pol II


title: EoP RNA Seq-2

city: Cincinnati

first: Patricia

middle: C.

last: Fulkerson

state: OH

address: 3333 Burnet Ave, ML 7028

institute: Cincinnati Children's Hospital Medical Center

data_processing:
RNA-Seq data: Fastq files from Illumina pipeline were aligned by STAR (version STAR_2.4.0c PMCID: PMC3530905) with ”--outFilterMultimapNmax 1 --outFilterMismatchNmax 2”. RefSeq annotation from UCSC genome browser (11/2012 PMID: 23155063) for mm10 genome was used. The --outFilterMultimapNmax parameter is used to allow uniq alignment only and --outFilterMismatchNmax parameter is used to allow at max 2 errors.
ChIP-Seq data: Fastq files from Illumina pipeline were aligned by bowtie (version 1.0.0 PMID: 19261174) with maximum one allowed error in a sequence and no more than one number of hits was allowed.
Genome_build: mm10
Supplementary_files_format_and_content: Data analysis was performed in BioWardrobe Experiment Management System (https://biowardrobe.com/)

organism: Mus musculus

source_name: pooled bone marrow

growth_protocol: GMPs (Lin-,CD34+, c-kithi, CD16/32+), EoPs (Lin-, CD34+, c-kitlo, CD125+) and Eos (Sigelc-F+, CCR3+) were sorted from pooled bone marrow of Balb/c mice, at least 1 x10e6 cells per analysis were used

extract_protocol: Total RNA was isolated via Direct-zol RNA MiniPrep. Chromatin was cross-linked with formaldehyde and sonication was performed in Covaris sonicator. Anti-H3K4me3 antibody (Millipore) was used to pull down marked chromatin in SX-8G IP-Star ChIP Robot.

treatment_protocol: No treatment, cells were sorted at homeostasis

tag: strain

value: Balb/c

tag: genotype/variation

value: EoPs sorted from pooled bone marrow (Lin-, CD34+, c-kitlo, CD125+)


title: GMP H3K4me3 ChIP Seq

value: GMPs sorted from pooled bone marrow (Lin-,CD34+, c-kithi, CD16/32+)

tag: antibody

value: Anti-H3K4me3 (Millipore)


title: Eos H3K4me3 ChIP Seq

value: Mature eosinophils sorted from pooled bone marrow (CCR3+, Siglec-F+)


title: EoP H3K4me3 ChIP Seq


title: Eos RNA Seq-1


title: EoP RNA Seq-1


title: CDK9_shPAF1.1_HCT116_ChIPSeq

description: ChIP-seq of CDK9


title: GMP RNA Seq-2


title: GMP RNA Seq-1


title: RNA-seq_BMP6_rep1


title: WT-st rep2

city: Mannheim

first: Francesca

last: Tuorto

address: Ludolf-Krehl-Str. 13-17

department: Division of Biochemistry  Mannheim Institute for Innate Immunoscience (MI3)

institute: Deutsches Krebsforschungszentrum

data_processing:
After quality and adapter trimming (AGATCGGAAGAGCACACGTCT), aligned to rRNA using Bowtie allowing 1 mismatch, discarding any mapped reads from further analysis.
The remaining reads were aligned with bowtie against the mouse mm9 UCSC Canonical gene track, allowing 1 mismatch and using 20nt as seed region.
Reads of length 26-30 nt whose 5' ends map from 15 nt downstream of the CDS start and those of length 31-32 nt whose 5' ends map 16 nt downstream of the CDS start were assigned to that gene.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file containing footprint counts assigned to each CDS for all samples.

source_name: Bone Marrow

growth_protocol: Tibias, femurs, and humeri were harvested from wild-type and Dnmt2-/- mice. Bone marrow was flushed and cells counted. Mononuclear cells were cultured in fully supplemented IMDM containing 20% FBS (.Invitrogen) and cytokines (5 ng/ml thrombopoietine and 10 ng/ml FLT-3Land  SCF) at 37¡C, 5% CO2 under humidified conditions.

extract_protocol:
Ribosome footprint was performed according to (Ingolia et al, 2011). 2x107 primary haematopoietic cells from each genotypes were treated with cycloheximide (100 µg/ml) for 5 minutes prior to lysis in 200 µl of 15 mM Tris-HCl (pH 7.4), 15 mM MgCl2, 300 mM NaCl, 1% Triton X-100, 0.1% 2-Mercaptoethanol, 100 µg/ml cycloheximide, 500 µg/ml Heparin, 1x Complete Protease Inhibitors (Roche). 400 µl aliquot of lysate was treated with 4 U DNase I (ThermoScientific) and 800 U of RNase I (Ambion), for 45 minutes at room temperature with gentle shaking.  800 U of RNasin ribonuclease inhibitor (Promega) was added to quench the reaction. The  samples were run on a 17.5-50% sucrose gradient to isolate monosome. Footprint monosome RNA was end using RNA were end-repaired with T4 polynucleotide kinase (TaKaRa), and size selected 28-31 nucleotide on a 15% polyacrylamide TBE-urea gel.
Small RNA libraries were performed according to the protocol using NEB NEXT Small RNA library Prep Set for Illumina (Multiplex Compatible) E7330, and size-selected (150 base pairs) before sequencing.

treatment_protocol: Suspension (ss) haematopoietic cells were harvested independently respect the stroma (st) attached cells.

value: primary bone marrow stroma cells

value: post natal day 8

value: wild type


title: Dnmt2-/-st rep2


title: BMDMs infected with R179T M.tb RT1

city: Bellville

first: Abhilasha

last: Madhvi

state: Western Cape

address: Francie van Zijl Drive. Tygerberg

country: South Africa

institute: Stellenbosch University

description: Differentiated to macrophages using L-CSF

data_processing:
Basecalling by SOLiD
Mapped using Lifescope, export .BAM files for mapped reads
Quantified to transcriptome in Partek (EM method)
Differential expression, Normalise RPKM, (Gene Specific Analysis- Partek), read count of 0 reset to 1.0E-4
Filer for data with FDR<0.05 and fold change >|2|
Genome_build: Mus Musculus mm10

source_name: BMDM

growth_protocol: BMDMs were allowed 7 days to differentiate prior to infection with M.tb.

extract_protocol:
BMDM RNA was extracted using the RNeasy® Plus Mini Kit and mRNA enrichment was performed using the Dynabeads® mRNA DIRECT™ Kit (Cat. No. 61012, Ambion, Life Technologies, Oslo, Norway)
AB Library Builder™ Whole Transcriptome Core Kit for 5500 Genetic Analysis Systems (Cat. No. 4472690, Applied Biosystems, Life Technologies), SOLiD® EZ Bead™ System (Cat. No. 4448419, Applied Biosystems, Life Technologies)

treatment_protocol: On day 7, BMDMs were infected with either R179T or R179NT M.tb for 12 hours

tag: m.tb strain

value: R179 Beijing M.tb

tag: infection period

tag: m.tb culturing coonditions

value: Tween 80 containing medium


title: Dnmt2-/- ss rep2

value: primary bone marrow suspension cells


title: BMDMs infected with R179T M.tb RT3


title: BMDMs infected with R179T M.tb RT2


title: Dnmt2-/-ss rep1


title: BMDMs infected with R179NT M.tb RNT4

value: Detergent-free medium


title: WT-ss rep1


title: Eos RNA Seq-2


title: WT-ss rep2


title: Uninfected BMDMs C3


title: BMDMs infected with R179NT M.tb RNT2


title: Dnmt2-/- rep1

description: total RNA

data_processing:
Basecalls performed using CASAVA version 1.8.3
Sequenced reads were trimmed for base quality and adaptor sequence
The reads were quality- and adapter trimmed, then mapped to gtrnadb tRNA reference (http://gtrnadb.ucsc.edu/) with bowtie. A per-base coverage of the tRNAs was computed and divided by the total number of reads, then multiplied by 100, leading to values that are comparable between samples (percentage). The base 0 is in this case the first base of the tRNA, because this is standard in Biopython.
Genome_build: n/a
Supplementary_files_format_and_content: The columns show in order:
Supplementary_files_format_and_content: Bone Marrow Dnmt2 knockout forward aligned reads reverse aligned reads wildtype forward aligned reads reverse aligned reads

extract_protocol:
Total RNA was extracted using Trizol reagents (Invitrogen) and treated with DNase I (Ambion). RNA were end-repaired with T4 PNK
Small RNA libraries were performed according to the protocol using NEB NEXT Small RNA library Prep Set for Illumina (Multiplex Compatible) E7330, and size-selected (120-170 base pairs) before sequencing.

tag: genotype

value: Bone Marrow


title: Dnmt2-/- rep2

description: total RNA


title: Uninfected BMDMs C2


title: WT rep2

description: total RNA


title: Uninfected BMDMs C1


title: WT rep1

description: total RNA


title: ctr_rep2_t30

city: Solna

first: Vicent

last: Pelechano

address: Nobels väg 16

department: MTC

country: Sweden

institute: ScilifeLab - Karolinska Institutet

description:
barcode:CGCCTG
Control sample, 30 min rapamycin, biological replicate 2

data_processing:
The python package HTSeq v0.5.3 [PMID: 25260700] was used for processing of the sequencing data. Reads contain in-line barcodes. De-multiplexed samples were trimmed to remove the adapter 20 sequences before alignment. Read alignment was carried out using the GSNAP aligner v2012-01-11. As a reference we used the S. cerevisiae S288c genome (SGD R64). Reads with low mapping quality (< 30) or which were composed of more than 80% As or Ts were filtered out. The uniquely aligned reads were then assigned to S. cerevisiae S288c genome gtf gene annotation file (based on SGD64) using BEDTools v2.17.0 [PMID: 20110278].
Genome_build: S. cerevisiae S288c genome (SGD R64)
Supplementary_files_format_and_content: Processed data contain a count table summaryzing the RNA-Seq reads assignment to S.cerevisiae genomic features and transcripts [Xu, et al 2009 PMID: 19169243]. Read counts are not normalized by S. Pombe spike-ins.

organism: Saccharomyces cerevisiae

growth_protocol: Yeast cells were cultivated at 30°C in YPAD

extract_protocol:
RNA was purified using the hot phenol method and DNase treated with TURBO DNA-free kit (Ambion). 0.1 μg S. pombe total RNA was added as spike-in per 10 μg total RNA for each sample. rRNA was removed using Ribo-Zero magnetic gold kit (Yeast) (Illumina) and the bulk of small RNAs removed by a single purification using the clean-up procedure from the PureLink RNA Mini kit (Ambion).
Library prep and sequencing Strand specific RNAseq libraries were prepared as previously described [PMID: 23295673]. 1.5 μg of rRNA depleted RNA was fragmented by incubating the samples at 80ºC for 4’ in the presence of RNA fragmentation buffer (40 mM Tris-acetate, pH 8.1, 100 mM KOAc, 30 mM MgOAc2). The fragmented RNA was purified using 1.5x Ampure XP Beads (Beckman Coulter Genomics) and eluted in Elution Buffer (EB) (10 mM Tris-HCl pH 8). 24 μl of eluted RNA was reverse transcribed with 1 μl random hexamers (3 μg/μl) and 2 μl 10 mM dNTPs. The samples were incubated at 65ºC for 5’ and transferred to ice. 8 μl 5x First strand buffer (Invitrogen), 4 μl DTT 0.1 M, 0.5 μl Actinomycin D (1.25 mg/ml) and 0.5 μl RNasin plus RNase inhibitor (Promega) were added to each sample and the samples were then incubated at 25ºC for 2’. Following this, 0.5 μl Superscript III RT (200 U/μl, Invitrogen) was added. Reverse transcription was carried out at 25ºC for 10’, at 42ºC for 50 min, and inactivated at 70ºC for 15’. After cleanup with 1.8x of Ampure XP beads, cDNA was eluted in EB. For producing the second cDNA strand, 19 μl of sample was mixed with 2.5 μl NEBNext Second Strand Synthesis 10x (dNTPFree), 1.5 μl of dNTPs (10 mM, incorporating dUTPs instead of dTTPs), 0.5 μl of RNaseH (5 U/μl, NEB), 1 μl of DNA polymerase I (10 U/μl, Fermentas) and 0.5 μl E.coli DNA ligase (10 U/μl NEB). The samples were incubated at 16ºC for 2.5 h and inactivated at 80ºC for 20’. Samples were purified with 1.8x of 19 Ampure XP beads and eluted in EB. To produce blunt DNA ends, 17 μl of sample was incubated with 2 μl End repair buffer and 1 μl End repair enzyme mix (NEBNext DNA Sample Prep Master Mix Set 1, NEB) at 20ºC for 30’. Samples were purified with 1.8x of Ampure XP beads and eluted in EB. To add a protruding A, 17 μL of sample was incubated with 2 μl dA tailing buffer (10x NEBuffer 2, NEB, and 0.2 mM dATP) and 1 μl Klenow Fragment (3´→5´ exo–) 5 U/μl (NEB) at 37ºC for 30’. Samples were purified with 1.8x of Ampure XP beads and eluted in EB. Then 20 μl of each sample was incubated with 2.5 μl 10x T4 DNA ligation buffer (NEB), 0.5 μl of forked PE multiplexed adaptors (40 μM) and 2 μl T4 DNA ligase 2000 U/μl (NEB) were added at 16ºC for 1h. The dUTPs of the second strand were hydrolyzed by adding to the ligation mix 1μl USER enzyme 1 U/μL (NEB), incubating at 37ºC 15’ and then inactivating the reaction at 95ºC for 5’. Samples were purified with 1.8x of Ampure XP beads and eluted in 50 μl EB. Enrichment PCR was performed using 24 μl of sample, 25 μl Phusion Master Mix 2x (NEB), 0.5 μl each of oligos PE1.0 and PE2.0 (10 μM, Illumina). The PCR program was 30 s at 96ºC, 18 cycles of (10 s at 96ºC, 30 s at 65ºC and 30 s at 72ºC) and 5‘ at 72ºC. The PCR product was purified with Ampure XP Beads. Libraries between 250 and 500 bp were size-selected using Ampure XP Beads and sequenced using a HiSeq 2000.

treatment_protocol: Cells were treated with rapamycin (1 μg/ml final concentration).

value: MATa tor1-1 fpr1::loxPLEU2-LoxP RPL13A-2xFKBP12::LoxP-TRP1-LoxP

tag: treatment

value: 30 min rapamycin


title: ctr_rep1_t30

description:
barcode:GTATAG
Control sample, 30 min rapamycin, biological replicate 1


title: WT-st rep1


title: Nab2AA_rep3_t30

description:
barcode:GCCTAA
NAB2-AA sample, 30 min rapamycin, biological replicate 2

value: MAT tor1-1 fpr1::loxPLEU2-LoxP RPL13A-2xFKBP12::LoxP-TRP1-LoxP NAB2-FRB::HIS


title: Dnmt2-/-st rep1


title: miR-196a2 GFP/GFP; miR-196b-/-   Biological replicate 3

city: South San Francisco

first: Vikram

last: Agarwal

state: CA

address: 1130 Veterans Blvd

institute: Calico Life Sciences

description:
a2Homo_bHomo_vs_a2Het.txt
Libraries were multiplexed and sequenced using an Illumina HiSeq 2000 instrument, 50bp single end reads.

data_processing:
Raw reads were aligned to the latest build of the mouse genome (mm10) using STAR v. 2.3.1n (options --outFilterType BySJout --outFilterMultimapScoreRange 0 --readMatesLengthsIn Equal --outFilterIntronMotifs RemoveNoncanonicalUnannotated --clip3pAdapterSeq TCGTATGCCGTCTTCTGCTTG --outSAMstrandField intronMotif --outStd SAM) (Dobin et al., 2013)
Pooling all replicates of a particular genotype, differential expression statistics were computed between two genotypes of interest using cuffdiff v. 2.1.1 (options -c 100 --library-type fr-unstranded -b mm10.fa -u --max-bundle-frags 100000000) (Trapnell et al., 2013), using mouse transcript models of protein-coding genes annotated in Ensembl release 72.
For each biological replicate, expression level data (measured in Fragments Per Kilobase Million, or FPKM) was computed using cufflinks v. 2.1.1 (options --library-type fr-unstranded -b mm10.fa -u --max-bundle-frags 100000000 --compatible-hits-norm) (Trapnell et al., 2010), using mouse transcript models of protein-coding genes annotated in Ensembl release 72.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file containing gene expression measurements (FPKM), log2(fold changes), and statistical significance values for differential expression comparisons

source_name: embryonic FACS sorted cells

extract_protocol:
Freshly dissected E9.5 embryos were dissociated in 0.25%Trypsin/2% chick serum, neutralized in DMEM+10% FBS and washed into PBS+2% FBS for FACS sorting. GFP positive cells were FACS sorted directly into RTL buffer (Qiagen) and RNA isolated using RNEasy with added on-column DNase treatment (Qiagen).
RNA quality was assessed using a Bioanalyser and 200 ng per individual embryo was used as input for mRNAseq library generation (unstranded Illumina TruSeq Kit).

value: embryonic FACS sorted cells


title: miR-196a2 GFP/GFP; miR-196b-/-   Biological replicate 4


title: miR-196a2 GFP/GFP; miR-196b-/-   Biological replicate 2


title: miR-196a2 GFP/GFP; miR-196b+/-   Biological replicate 4

description:
a2Homo_bHet_vs_a2Het.txt
Libraries were multiplexed and sequenced using an Illumina HiSeq 2000 instrument, 50bp single end reads.


title: Nab2AA_rep2_t0

description:
barcode:GCGTGG
NAB2-AA sample, biological replicate 2


title: Nab2AA_rep2_t15

description:
barcode:TGGAGC
NAB2-AA sample, 15 min rapamycin, biological replicate 2

value: 15 min rapamycin


title: miR-196a2 GFP/GFP; miR-196b+/-   Biological replicate 3


title: Nab2AA_rep1_t15

description:
barcode:CCAGCA
NAB2-AA sample, 15 min rapamycin, biological replicate 1


title: Nab2AA_rep1_t30

description:
barcode:CAAGTT
NAB2-AA sample, 30 min rapamycin, biological replicate 1


title: BMDMs infected with R179NT M.tb RNT3


title: miR-196a2 GFP/GFP; miR-196b+/-   Biological replicate 2


title: miR-196a2 GFP/GFP; miR-196b-/-   Biological replicate 1


title: miR-196a2 GFP/GFP; miR-196b+/-   Biological replicate 1


title: miR-196a2 +/GFP; miR-196b-/-   Biological replicate 3

description:
a2Het_bHomo_vs_a2Het.txt
Libraries were multiplexed and sequenced using an Illumina HiSeq 2000 instrument, 50bp single end reads.


title: miR-196a2 +/GFP; miR-196b-/-   Biological replicate 4


title: Nab2AA_rep1_t0

description:
barcode:AAGTGC
NAB2-AA sample, biological replicate 1


title: miR-196a2 +/GFP; miR-196b-/-   Biological replicate 1


title: miR-196a2 +/GFP; miR-196b-/-   Biological replicate 2


title: miR-196a1 GFP/GFP-; miR-196a2 GFP/GFP   Biological replicate 4

description:
a1Homo_a2Homo_vs_a1Het_a2Het.txt
Libraries were multiplexed and sequenced using an Illumina HiSeq 2000 instrument, 50bp single end reads.


title: ΔsoxS PQ 2

city: Ulsan

first: Donghyuk

last: Kim

address: 50 UNIST-gil, Eonyang-eup, Ulju-gun

department: Department of Chemical Engineering

country: South Korea

institute: UNIST

data_processing:
Sequenced reads were mapped onto NC_000913 reference genome sequence using bowtie v1.0.0 with parameters -X 1000 -n 2 -3 3 -S
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cufflinks v.1.3.0
Genome_build: NC_000913
Supplementary_files_format_and_content: comma-delimited text files include FPKM values for each Sample.

organism: Escherichia coli

source_name: ΔsoxS PQ

growth_protocol: E. coli K-12 MG1655 WT, ΔoxyR, ΔsoxR, and ΔsoxS were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation.

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA, USA) and genomic DNA was removed by gDNA Eliminator spin column in the RNeasy Plus Mini Kit. RNA quality and concentration was determined by analysis with a NanoDrop 1000 (Thermo Scientific Inc., Wilmington, DE, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The cell culture was treated with the RNAprotect reagent (Qiagen).

value: delta-soxS

tag: treated with


title: miR-196a1 GFP/GFP-; miR-196a2 GFP/GFP   Biological replicate 2


title: ΔsoxR PQ 2

source_name: ΔsoxR PQ

value: delta-soxR

value: 250 uM of paraquat at mid-log pahse for 20 min


title: ΔsoxS PQ 1


title: ΔsoxR PQ 1


title: miR-196a1 GFP/GFP-; miR-196a2 GFP/GFP   Biological replicate 1


title: ΔoxyR PQ 2

source_name: ΔoxyR PQ

value: delta-oxyR


title: miR-196a1 +/GFP-; miR-196a2 GFP/GFP   Biological replicate 4

description:
a1Het_a2Homo_vs_a1Het_a2Het.txt
Libraries were multiplexed and sequenced using an Illumina HiSeq 2000 instrument, 50bp single end reads.


title: WT PQ 2

source_name: WT PQ

value: WT


title: miR-196a1 +/GFP-; miR-196a2 GFP/GFP   Biological replicate 2


title: miR-196a1 +/GFP-; miR-196a2 GFP/GFP   Biological replicate 3


title: WT PQ 1


title: miR-196a1 +/GFP-; miR-196a2 +/GFP   Biological replicate 4

description:
a1Het_a2Homo_vs_a1Het_a2Het.txt
a1Homo_a2Homo_vs_a1Het_a2Het.txt
Libraries were multiplexed and sequenced using an Illumina HiSeq 2000 instrument, 50bp single end reads.


title: miR-196a1 +/GFP-; miR-196a2 GFP/GFP   Biological replicate 1


title: miR-196a1 +/GFP-; miR-196a2 +/GFP   Biological replicate 3


title: SoxS PQ 2

description: Immunoprecipitated DNA

data_processing:
library strategy: ChIP-seq (ChIP-exo)
ChIP-exo reads were aligned to the ASM584v2 genome reference sequence using using bowtie v1.0.0 with parameters  -S
MACE software (https://code.google.com/p/chip-exo/) was used to detect peaks with aligned output from bowtie mapping.
Read count was calculated for each genomic position from sequence alignment, and 95% strongest intensity was used as background intensity.
For each peak detected with MACE, binding intensity was calculated by averaging read counts from two biological replicates and dividing by background intensity.
Genome_build: ASM584v2
Supplementary_files_format_and_content: Tab-delimited text files in gff format which has 8 columns: sequence id, source(empty), feature (+/- strand), start position, end position, intensity score, strand(+/-), frame(.), attribute(.).

source_name: soxS-8myc-tagged_PQ treated

growth_protocol: A total of six samples were analyzed. oxyR-8myc, soxR-8myc, and soxS-8myc tagged cells were cultured in M9 minimal media with 0.2% glucose. Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation.

extract_protocol:
Crosslinked cells were then resuspended in 500 ul of lysis buffer (10 mM Tris-HCl (pH 7.5), 100 mM NaCl and 1 mM EDTA) with 40 ul of protease inhibitor cocktail (50 mg in 0.25 ml of DMSO and 0.75 ml of TDW). Cells were lyzed with 1 ul of lysozyme for 30 min at 37oC on a rocker. 0.55 ml of 2X IP buffer (100 mM Tris-HCl (pH 7.5), 200 mM NaCl, 2% Triton X-100 and 1 mM EDTA) were added to the sample, and then was sonicated to fragmentize genomic DNA. 0.3 ml of Wash buffer I (50 mM Tris-HCl (pH 7.5), 140 mM NaCl, 1% Triton X-100 and 1mM EDTA) was added to make the volume up to 1.4 ml. Only 0.7 ml was taken and transfered to a new tube, and 15 ul of Anti-c-myc mouse antibody was added, and the sample was incubated overnight at 4 oC to make Antibody-TF complex. 50 ul of Dynabeads Pan mouse IgG were washed 3 times with bead washing solution (250 mg BSA in 50 ml of PBS), and were added to the sample. Cell lysate with beads were incubated for 6 hours or overnight at 4oC to make Dynabead-antibody-TF complex. The beads were pulled down on a magnet stand, and washed 2 times with wash buffer I and with wash buffer II (50 mM Tris-HCl (pH 7.5), 500 mM NaCl, 1% Triton X-100 and 1mM EDTA), wash buffer III (10 mM Tris-HCl (pH 8.0), 250 mM LiCl, 1% Triton X-100 and 1mM EDTA), and wash buffer IV (10 mM Tris-HCl (pH 8.0), 1mM EDTA). The bead-bound TF-DNA complex was then end-repaired, dA-tailed, and ligated to the first adapter. Adapter-ligated sample was then treated with nick-repair reagent, and was treated with lambda exonuclease and RecJ exonuclease. Then DNA was eluted away from Dynabeads by incubating in 200 ul of elution buffer (50 mM Tris-HCl (pH 8.0), 1% SDS and 1 mM EDTA) at 65oC overnight. Protein was removed by treating 4 ul of protease K and being incubated at 55 oC for 2 hours, and by Phenol-Chloroform-IAA extraction. Purified DNA was used to bulid the second strand synthesis, followed by another dA-tailing, second strand ligation, and 3' overhang removal stpes. Then the sequencing library was amplified with PCR enrichment.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: E. coli cells were crosslinked in 1% formaldehyde for 25 minutes at RT on a rocker, then washed 3 times with 50 ml of ice-cold TBS (Tris buffered saline) each time.

value: 250 uM of paraquat at mid-log phase for 20 min

value: anti-myc

tag: chip antibody vendor

value: Santa Cruz Biotech

tag: chip antibody cat. #


title: SoxR PQ 1

description: Immunoprecipitated DNA

source_name: soxR-8myc-tagged_PQ treated


title: miR-196a1 +/GFP-; miR-196a2 +/GFP   Biological replicate 2

tag: age


title: SoxS PQ 1

description: Immunoprecipitated DNA


title: SoxR PQ 2

description: Immunoprecipitated DNA


title: miR-196a1 +/GFP-; miR-196a2 +/GFP   Biological replicate 1


title: miR-196a1 GFP/GFP-; miR-196a2 GFP/GFP   Biological replicate 3


title: miR-196a2 GFP/GFP    Biological replicate 5

description:
a2Homo_vs_a2Het.txt
Libraries were multiplexed and sequenced using an Illumina HiSeq 2000 instrument, 50bp single end reads.


title: OxyR PQ 2

description: Immunoprecipitated DNA

source_name: oxyR-8myc-tagged_PQ treated


title: E16.5_XY_KitW/KitWv_testis 2

city: Cambridge

first: Ying Qi Shirleen

last: Soh

address: 9 Cambridge Center

institute: Whitehead Institute

data_processing:
Sequenced reads were mapped to mm9 using Tophat with parameter -g1
FPKMs were calculated using Cufflinks
Genome_build: mm9
Supplementary_files_format_and_content: Cufflinks output

source_name: testis

extract_protocol:
Total RNA, of about 1 ug, was extracted using Trizol (Invitrogen) according to manufacturer’s instructions. Hemoglobin transcripts were selectively removed from total RNA by following GLOBINclear (Ambion) protocol recommendations.
As per the Illumina kit protocol, poly-A-selected mRNA was used to generate mRNA-seq cDNA libraries using random hexamer-primers. cDNA fragments of ~200 nucleotides were isolated and modified for sequencing following the mRNA-seq protocol (Illumina). Illumina Genome Analyzer II was used to sequence 36-mers from the mRNA-seq libraries by following the manufacturer's recommendations.

value: WWv

tag: timepoint

tag: tissue

value: testis


title: miR-196a2 GFP/GFP   Biological replicate 3

tag: cell type


title: OxyR PQ 1

description: Immunoprecipitated DNA


title: E16.5_XY_KitW/KitWv_testis 1


title: E16.5_XY_Kit+/Kit+_testis 1


title: E16.5_XY_Kit+/Kit+_testis 2


title: ΔoxyR PQ 1


title: miR-196a2 GFP/GFP    Biological replicate 2


title: E16.5_XX_KitW/KitWv_ovary 2

source_name: ovary

value: ovary


title: miR-196a2 GFP/GFP   Biological replicate 1


title: E16.5_XX_KitW/KitWv_ovary 1


title: miR-196a2 +/GFP  Biological replicate 4

description:
a2Homo_vs_a2Het.txt
a2Het_bHomo_vs_a2Het.txt
a2Homo_bHet_vs_a2Het.txt
a2Homo_bHomo_vs_a2Het.txt
Libraries were multiplexed and sequenced using an Illumina HiSeq 2000 instrument, 50bp single end reads.


title: miR-196a2 +/GFP   Biological replicate 2


title: E16.5_XX_Kit+/Kit+_ovary 2


title: E14.5_XY_KitW/KitWv_testis 2


title: E16.5_XX_Kit+/Kit+_ovary 1


title: E14.5_XY_KitW/KitWv_testis 1


title: miR-196a1 GFP/GFP    Biological replicate 5

description:
a1Homo_vs_a1Het.txt
Libraries were multiplexed and sequenced using an Illumina HiSeq 2000 instrument, 50bp single end reads.


title: miR-196a1 GFP/GFP    Biological replicate 3


title: miR-196a1 GFP/GFP    Biological replicate 2


title: miR-196a1 GFP/GFP    Biological replicate 4


title: E14.5_XY_Kit+/Kit+_testis 1


title: miR-196a2 GFP/GFP   Biological replicate 4


title: E14.5_XX_KitW/KitWv_ovary 2


title: miR-196a2 +/GFP   Biological replicate 1


title: miR-196a2 +/GFP  Biological replicate 5


title: miR-196a1 GFP/GFP   Biological replicate 1


title: E14.5_XX_Kit+/Kit+_ovary 2


title: E14.5_XX_KitW/KitWv_ovary 1


title: E14.5_XY_Kit+/Kit+_testis 2


title: E14.5_XX_Kit+/Kit+_ovary 1


title: miR-196a1 +/GFP   Biological replicate 4


title: miR-196a1 +/GFP   Biological replicate 2


title: E12.5_XY_KitW/KitWv_testis 2


title: miR-196a1 +/GFP   Biological replicate 3


title: miR-196a2 +/GFP  Biological replicate 3


title: E12.5_XY_KitW/KitWv_testis 1


title: E12.5_XY_Kit+/Kit+_testis 2


title: miR-196a1 +/GFP   Biological replicate 1


title: E12.5_XX_Kit+/Kit+_ovary 2


title: E12.5_XX_KitW/KitWv_ovary 1


title: E12.5 XX Female C57BL/6NTac WT Mouse ovary (posterior third) 1

source_name: ovary (posterior third)

value: ovary (posterior third)


title: E12.5_XX_Kit+/Kit+_ovary 1


title: miR-196a1 +/GFP   Biological replicate 5


title: E12.5 XX Female C57BL/6NTac WT Mouse ovary (anterior third) 2

source_name: ovary (anterior third)

value: ovary (anterior third)


title: HS5-1 Inversion rep1

city: Shanghai

first: Qiang

last: Wu

address: 800 Dongchuan Road

department: Institute of Systems Biomedicine

country: China

institute: Shanghai Jiao Tong University

data_processing:
Illumina GA Pipeline v1.5 was used for basecalling.
The resulting sequencing reads (49 bp, single-read) were mapped onto the human genome build GRCh37/hg19 using TopHat-v2.0.14 with the setting of “-N 0 –g 1 –x 1”.
The output data were then averaged among biological replicates and normalized to reads per million (RPM) by the genomeCoverageBed program.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files were generated using the genomeCoverageBed tool. Scores represent raw reads per million.

extract_protocol:
total RNA was extracted from cultured cells (inversion and wide type control in duplicates) using an RNeasy plus mini kit (Qiagen) according to the manufacturer’s protocol.
Messenger RNA was isolated from the total RNA by oligo (dT) magnetic beads, and fragmented under heating condition. After the first and second cDNA strand synthesis, as well as ends repairing, the 3’ ends of cDNA fragments were added with a single ‘A’ nucleotide to facilitate adapter ligation. The libraries were then generated by PCR amplification of the cDNA products, and were sequenced on the Illumina sequencing platform of HiSeq 2000.

value: HS5-1 Inversion

tag: cell line

tag: gender

value: female

value: adenocarcinoma


title: E13.5 XX Female C57BL/6NTac WT Mouse ovary (posterior third) 3

tag: strain


title: E13.5 XX Female C57BL/6NTac WT Mouse ovary (posterior third) 1

tag: genotype/variation


title: E13.5 XX Female C57BL/6NTac WT Mouse ovary (anterior third) 3


title: E13.5 XX Female C57BL/6NTac WT Mouse ovary (anterior third) 2


title: E12.5 XX Female C57BL/6NTac WT Mouse ovary (posterior third) 2


title: Wild type control rep1

value: Wild type control


title: E13.5 XX Female C57BL/6NTac WT Mouse ovary (posterior third) 2


title: total.RNA_shSCR_HCT116_rep1

description: Total RNA-seq

value: colorectal cancer cell line

tag: shRNA

value: Scramble shRNA


title: HS5-1 Inversion rep2


title: E13.5 XX Female C57BL/6NTac WT Mouse ovary (anterior third) 1


title: Wild type control rep2


title: E12.5 XX Female C57BL/6NTac WT Mouse ovary (anterior third) 1


title: E12.5_XY_Kit+/Kit+_testis 1


title: E12.5_XX_KitW/KitWv_ovary 2


title: total.RNA_shSCR_HCT116_rep2

description: Total RNA-seq


title: total.RNA_shPAF1.1_HCT116_rep2

description: Total RNA-seq

value: PAF1 shRNA #1


title: total.RNA_shPAF1.1_HCT116_rep1

description: Total RNA-seq


title: nascent.RNA_shSCR_HCT116_rep2

description: Nascent RNA-seq


title: nascent.RNA_shSCR_HCT116_rep1

description: Nascent RNA-seq


title: nascent.RNA_shPAF1.1_HCT116_rep2

description: Nascent RNA-seq


title: Ser2P_shSCR_HCT116_rep2_ChIPSeq

description: ChIP-seq of Ser2 Phosphorylated Pol II

tag: chip antibody

value: Ser2 Phosphorylated Pol II (Millipore, 04-1571)


title: Ser2P_shPAF1.1_HCT116_rep2_ChIPSeq

description: ChIP-seq of Ser2 Phosphorylated Pol II


title: Ser2P_shPAF1.1_HCT116_rep1_ChIPSeq

description: ChIP-seq of Ser2 Phosphorylated Pol II


title: N20_shSCR_N20shPAF1.2_N20shPAF1.1rep2_HCT116_ChIPSeq

description: ChIP of Total Pol II

value: Pol II (Santa Cruz, sc-899)


title: PAF1_WT_HCT116_ChIPSeq

description: ChIP-seq of PAF1

value: no shRNA

value: PAF1 (Abcam, ab137519)


title: N20_shPAF1.1_HCT116_rep2_ChIPSeq

description: ChIP of Total Pol II


title: N20_shPAF1.2_HCT116_ChIPSeq

description: ChIP of Total Pol II

value: PAF1 shRNA #2


title: N20_shSCR_HCT116_rep1_ChIPSeq

description: ChIP of Total Pol II


title: N20_shSCR_N20shBre1A_HCT116_ChIPSeq

description: ChIP of Total Pol II


title: N20_shBre1A.2_HCT116_ChIPSeq

description: ChIP of Total Pol II

value: BRE1A shRNA #2


title: N20_shPAF1.1_HCT116_rep1_ChIPSeq

description: ChIP of Total Pol II


title: N20_shBre1A.1_HCT116_ChIPSeq

description: ChIP of Total Pol II

value: BRE1A shRNA #1


title: H2Bub_shSCR_HCT116_rep1_ChIPSeq

description: ChIP-seq of H2Bub

value: H2Bub (Cell signaling, #5546)


title: H2Bub_shSCR_HCT116_rep2_ChIPSeq

description: ChIP-seq of H2Bub


title: H2Bub_shPAF1.1_HCT116_rep1_ChIPSeq

description: ChIP-seq of H2Bub


title: Input_shSCR_HCT116_rep2_ChIPSeq

description: Input DNA from whole cell extract

value: no antibody


title: Input_shPAF1.1_HCT116_rep2_ChIPSeq

description: Input DNA from whole cell extract


title: H2Bub_shPAF1.1_HCT116_rep2_ChIPSeq

description: ChIP-seq of H2Bub


title: Input_shSCR_HCT116_rep1_ChIPSeq

description: Input DNA from whole cell extract


title: nascent.RNA_shPAF1.1_HCT116_rep1

description: Nascent RNA-seq


title: ELL2_shSCR_HCT116_rep1_ChIPSeq

description: ChIP-seq of ELL2

value: ELL2 (homemade)


title: Input_shPAF1.1_HCT116_rep1_ChIPSeq

description: Input DNA from whole cell extract


title: ELL2_shSCR_HCT116_rep2_ChIPSeq

description: ChIP-seq of ELL2


title: ELL2_shPAF1.1_HCT116_rep1_ChIPSeq

description: ChIP-seq of ELL2


title: AFF4_shPAF1.1_HCT116_rep2_ChIPSeq

description: ChIP-seq of AFF4

value: AFF4 (homemade)


title: ELL2_shPAF1.1_HCT116_rep2_ChIPSeq

description: ChIP-seq of ELL2


title: Ser2P_shSCR_HCT116_rep1_ChIPSeq

description: ChIP-seq of Ser2 Phosphorylated Pol II


title: AFF4_shSCR_HCT116_rep1_ChIPSeq

description: ChIP-seq of AFF4


title: AFF4_shPAF1.1_HCT116_rep1_ChIPSeq

description: ChIP-seq of AFF4


title: cde-1_hrde-1_IP

source_name: adult worms

tag: strain background

tag: genoptype/variation

value: cde-1(tm1021) III

tag: developmental stage

value: adult worms

tag: rip antibody

value: HRDE-1 antibody

tag: rip antibody ref.


title: wt_hrde-1_IP

value: wild-type


title: Input_shPAF1.2_HCT116_ChIPSeq

description: Input DNA from whole cell extract

value: colorectal cancer cell line


title: wild-type_L1_C

source_name: L1 animals

value: L1 animals


title: AFF4_shSCR_HCT116_rep2_ChIPSeq

description: ChIP-seq of AFF4

value: Scramble shRNA


title: E14.5_XX_Stra8_wild-type_3

extract_protocol:
Total RNA, of about 1 ug, was extracted using Trizol (Invitrogen) according to manufacturer’s instructions. Hemoglobin transcripts were selectively removed from total RNA by following GLOBINclear (Ambion) protocol recommendations.
As per the Illumina TruSeq Sample Preparation kit protocol, poly-A-selected mRNA was used to generate mRNA-seq cDNA libraries using random hexamer-primers. cDNA fragments of ~200-400 nucleotides were isolated and modified for sequencing following the mRNA-seq protocol (Illumina). Illumina HiSeq was used to sequence 40-mers from the mRNA-seq libraries by following the manufacturer's recommendations.

value: Stra8 WT

value: ovary


title: SK

city: guangzhou

first: Li

last: Changpeng

address: kai yuan road

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

data_processing:
Base calling were performed using Off-Line Basecaller software (OLB V1.8)
ChIP-seq reads were aligned to human genome (UCSC hg19) using BOWTIE software (V2.1.0)
Statistically significant ChIP-enriched regions (peaks) were identified by SKS vs SK (p-value threshold of 10-2) or SK vs LO2 (p-value threshold of 10-3)
ChIP-enriched peaks were annotated by the nearest gene using the newest UCSC RefSeq database
Genome_build: The signal profile (at 10 bp resolution) with UCSC
Supplementary_files_format_and_content: WIG file format was generated from ChIP-seq data

source_name: HCC cancer cell line

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
10 ng of your DNA samples were prepared for library construction as the following steps: 1) DNA samples were blunt-ended with T4 DNA polymerase and Klenow polymerase; 2) a dA base was added to the 3' end of each strand by Klenow (exo minus) polymerase; 3) Illumina's genomic adapters were ligated to the DNA fragments; 4) PCR amplification was performed to enrich ligated fragments; 5) Enriched product of ~300-500bp was cut out from gel and purified with QIAquick Gel Extraction Kit.

value: H3K27me3 (Millipore, ChIP grade)


title: E14.5_XX_Stra8_wild-type_2


title: wt_input

extract_protocol:
150 L1 or 50 L2 C. elegans larvae were washed in M9 buffer (22nM Na2HPO4, 33 mM KH2PO4, 86 mM NaCl, 1 mM MgSO4) and digested in lysis buffer (200mM NaCl, 100 mM Tris pH 8.5, 50 mM EDTA, 0.5 % SDS, 200 µg/mL Prot-K) for 3h at 65°C followed by 15 min at 95° C to denaturate the Prot-K. Lysate was then incubated with DNase I (NEB) for 30 min at 37° C. Total RNA was then isolated using TRIZOL-LS (Life Technologies) using the manufacturer instructions and dissolved in 8 µL of H2O.
For RIP-seq, HRDE-1 was precipitated from synchronized adult worms. 50 µL of packed worms were washed with M9 and sonicated in 200 µL of lysis buffer (25 mM Tris pH7.5, 150 mM NaCl, 1.5 mM MgCl, 1 mM DTT and cOmplete mini, EDTA free (Roche, 1 tablet per 100 mL) 5 times 30 sec ON, 30 sec OFF at the maximum energy setting. Lysates were centrifuged at 21000G for 5 min. 50 µL of the supernatant was used as input and 100 µL was incubated with 1 mg of anti-HRDE-1 antibody (Ashe et al. 2012) and 10 µL of Dynabeads Protein G (Life Technologies) for 2 hours. The beads were washed 5 times 10 min with wash buffer  (25 mM Tris pH7.5, 150 mM NaCl, 1.5 mM MgCl, 1 mM DTT and cOmplete mini, EDTA free (Roche, 1 tablet per 100 mL, 0.2 % Triton X-100). RNA was extracted from both input and IP with TRIZOL-LS (Life Technologies) using the manufacturer instructions and dissolved in 8µL of H2O.
All 8uL of total RNA was treated with 5 U of tobacco acid phosphatase (Epicenter) at 37°C for 2 h to digest 5’ tri- and di-phosphates to mono-phosphates. RNA was size-selected between 15- to 35-nt on 15% TBE-urea gel. Gel-purified RNA was eluted overnight in 300 mM NaCl and then precipitated with 100% isopropanol and Glycoblue for 1 h at -20°C. The pellet was washed once with 75% ethanol and dissolved in nuclease-free water. Then, this purified fraction was confirmed by Bioanalyzer Small RNA chip (Agilent). Library preparation was based on the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England BioLabs) with slight modification. In brief, small RNA was first ligated to the 3’ adapter and then the 5’ adapter, both of which contained 4 random bases and were chemically synthesized by Bioo Scientific. Adapter-ligated RNA was reverse-transcribed and PCR-amplified for 14 cycles using index primers. The PCR-amplified cDNA construct was purified using AMPure XP beads (Beckman Coulter). The purified PCR reaction was checked on the Bioanalyzer using High Sensitivity DNA chip (Agilent). Size selection of the small RNA library was done on LabChip XT instrument (Perkin Elmer) using DNA 300 assay kit. Only the fraction containing 140-165 bp was pooled in equal molar ratio. The resulting 10 nM pool was denatured and diluted to 10 pM with 5% PhiX spike-in and sequenced as single-read on HiSeq 2500 (Illumina) in rapid mode for 50 cycles using on-board cluster generation. Sample “L1 N2” was sequenced as single-read on Miseq (Illumina). After demultiplexing, on average 35 million passing filter reads were obtained per sample.


title: E14.5_XX_Stra8_knock-out_3

value: Stra8 KO


title: SKS

source_name: HCC cancer cell line with EZH2 knocked down


title: E14.5_XX_Stra8_wild-type_1


title: E14.5_XX_Stra8_knock-out_1


title: E14.5_XX_Dazl_wild-type_3

value: Dazl WT


title: E14.5_XX_Stra8_knock-out_2


title: E14.5_XX_Dazl_wild-type_2


title: E14.5_XX_Dazl_knock-out_3

value: Dazl KO


title: E14.5_XX_Dazl_wild-type_1


title: LO2

source_name: normal immortalized liver cell


title: E14.5_XX_Dazl_knock-out_1


title: E14.5_XX_Dazl_knock-out_2


title: Input_dsLacZ_S2_rep1_ChIPSeq

description: Input DNA from whole cell extract

organism: Drosophila melanogaster

value: Drosophila melanogaster cell line

value: LacZ RNAi


title: Input_dsPAF1.1_S2_rep1_ChIPSeq

description: Input DNA from whole cell extract

value: PAF1 RNAi #1

value: no antibody


title: dRpb1_dsPAF1.1_S2_rep1_ChIPSeq

description: ChIP-seq of Total Pol II

value: Rpb1 (homemade)


title: dRpb1_dsLacZ_S2_rep1_ChIPSeq

description: ChIP-seq of Total Pol II


title: G1 DZ cells +anti-DEC-OVA second biological replicate

status: Public on Aug 12 2015

city: NEW YORK

first: Thiago

middle: Y

last: Oliveira

state: New York

address: 1230 YORK AVE

department: Immunology, Virology and Microbiology

institute: The Rockefeller University

description: B1-8hi DEC205+/+ DZ cells in G1 phase were purified 48 hours after anti-DEC-OVA treatment, second biological replicate

data_processing:
Sequenced reads were mapped to mm9 whole genome using STAR with default parameters
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Cufflinks
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample and differential expression test generated by cuffdiff

source_name: B1-8hi DEC205+/+ Fucci-tg, germinal center B cells with DZ phenotype (CXCR4-hi, CD86-lo) in G1 phase

growth_protocol: Ovalbumin (OVA)-primed wild-type mice received an adoptive transfer of B1-8hi DEC205+/+ Fucci-Tg B cells and B1-8hi DEC205-/- B cells. The following day mice were subcutaneously boosted with the hapten NP coupled to OVA to induce germinal centers

extract_protocol:
DZ G1 cells were sorted by FACS directly into Trizol LS
SMARTer Ultra Low Input RNA for illumina sequencing kit (Clontech Laboratories)

treatment_protocol: On day 6 of the germinal center response, mice were injected with anti-DEC-CS or anti-DEC-OVA followed by cell sorting 2 days later

tag: organ

value: draining lymph node


title: G1 DZ cells +anti-DEC-OVA first biological replicate

description: B1-8hi DEC205+/+ DZ cells in G1 phase were purified 48 hours after anti-DEC-OVA treatment, first biological replicate


title: G1 DZ cells +anti-DEC-CS second biological replicate

description: B1-8hi DEC205+/+ DZ cells in G1 phase were purified 48 hours after anti-DEC-CS control treatment, second biological replicate


title: cde-1_input

data_processing:
The raw reads in FastQ format were filtered from 3’ adapter sequences and size-selected in the range 15-35 bases (plus 8 bases random barcodes) using cutadapt v.1.2.1 1using parameters: -a AGATCGGAAGAGCACACGTCT -O 8 -m 23 -M 43 . Subsequently, PCR clonal reads were deduplicated using Bash and Awk commands. All reads containing low-quality (Phred+33 score less than 20) bases were filtered with the FastX toolkit (http://hannonlab.cshl.edu/fastx_toolkit/; fastq_quality_filter -q 20 -p 100 -Q 33), then the files were reformatted from FastQ into tabular format, sorted and deduplicated based on full sequence identity (library insert plus 5’ and 3’ random barcodes of 4 nucleotides), and finally converted back to FastQ format for mapping. Quality assessment of the raw and processed data was done with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). Mapping to the C. elegans genome reference WS244 was performed using Bowtie v1 2 with parameters: -v0 -M1 --best --strata --nomaqround --tryhard --trimm5 4 --trim3 4. Unmapped reads where then filtered for the ones ending with a “T” using custom python scripts and remapped using bowtie using the same parameter but trimming one extra 3’ base. These newly mapped reads were considered mono-uridylated. This filtering/mapping cycle was performed 10 times in order to map up to penta-urydilated reads. All mapped reads where then annotated using bedtools intersect 3 with a customized WS244.gff3 (ftp://ftp.wormbase.org/pub/wormbase/releases/WS244/species/c_elegans/PRJNA13758/c_elegans/PRJNA13758.WS244.annotations.gff3.gz); using the following parameters: -abam -b[custom annotated gff3] -bed -wa -wb. Mapped and annotated reads were subsequently filtered for size and starting nucleotide using custom made python scripts and normalized to total of non-structural reads between 18 and 30 nucleotides. Structural reads were considered as reads that mapped rRNAs, tRNAs and snoRNAs. During the analysis we considered miRNA reads that were 22 to 24 nt long sense to annotated miRNAs, we considered piRNA reads that were 21 nt long, started with a “T” and were sense to annotated piRNAs, and 22G reads that were 20 to 23 nt long, started with a “G” and map antisense to genes, transposable elements or pseudogenes. In order to categorize genes, we retrieved WAGO-1 targets, ERGO-1 targets, mutator targets, ALG-3/4 targets and CSR-1 targets from Gu (2009),Vasale (2010), Phillips(2014), Conine (2010), Claycomb (2009)4–8 respectively. For each protein coding gene saw if it was a WAGO-1 target, if not we saw if it was an ERGO-1 target, if not we saw if it was a mutator target and so on, in the previously mention order. The validation of a gene in a category would automatically exclude it from the following categories; this was to insure that there would be no duplication, since some categories overlap partially.
Genome_build: WS240
Supplementary_files_format_and_content: read counts for: total mapped reads, mapped reads 18-30 nt, non structrural reads (18-30 nt), 18-30nt mapping genes_anti-sense, 18-30nt mapping genes_sense, 18-30 nt mapping pseudogenic_transcript_anti-sense, 18-30 nt mapping pseudogenic_transcript_sense, 18-30nt mapping to piRNAs_anti-sense, 18-30nt mapping to piRNAs_sense, 18-30nt mapping to transposable_elements_anti-sense, 18-30nt mapping to transposable_elements_sense, 18-30nt mapping to ncRNA_anti-sense, 18-30nt mapping to ncRNA_sense, 18-30nt mapping to snoRNA_anti-sense, 18-30nt mapping to snoRNA_sense, 18-30nt mapping to tRNA_anti-sense, 18-30nt mapping to tRNA_sense, 18-30nt mapping to antisense_RNA_anti-sense, 18-30nt mapping to antisense_RNA_sense, 18-30nt mapping to lincRNA_anti-sense, 18-30nt mapping to lincRNA_sense, 18-30nt mapping to miRNA_anti-sense, 18-30nt mapping to miRNA_sense, 18-30nt mapping to snRNA_anti-sense, 18-30nt mapping to snRNA_sense, 18-30nt mapping to rRNA_anti-sense, 18-30nt mapping to rRNA_sense, 18-30nt mapping to scRNA_anti-sense, 18-30nt mapping to scRNA_sense, piRNAs (20U-21U sense to annotated piRNAs), miRNA (20-24 nt mapping sense to annotated miRNAs), 20G-23G antisense to annotated transposons, 20G-23G antisense to annotated protein coding genes, 20G-23G antisense to ALG-3/4 targets, 20G-23G antisense to CSR-1 targets, 20G-23G antisense to ERGO-1 targets, 20G-23G antisense to WAGO-1 targets, 20G-23G antisense to mutator targets, 20G-23G antisense to other protein coding genes

value: cde-1(tm1021) III

value: adult worms


title: G1 DZ cells +anti-DEC-CS first biological replicate

description: B1-8hi DEC205+/+ DZ cells in G1 phase were purified 48 hours after anti-DEC-CS control treatment, first biological replicate


title: non-induced fibroblast sample 2

city: Beijing

first: Yan-Tao

last: Ma

address: No. 5 Yiheyuan Road

institute: Peking University

data_processing:
The transcriptome reads were mapped using the TopHat2 program.
The gene expression level was calculated by using FPKM method.
Genome_build: mm10
Supplementary_files_format_and_content: fpkm_tracking files including FPKM values for the analysis of gene expression

source_name: mouse fibroblasts

extract_protocol:
Total RNA from each sample was isolated using the RNeasy Plus Mini Kit (QIAGEN).
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext®Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNaseH-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.


title: Induced 19 Days (by FICB) sample 3

source_name: chemically-induced cells from mouse fibroblasts


title: non-induced fibroblast sample 3


title: 38_Rudnerlab_HindIII_HiC_BWX3359_30C

city: Bloomington

first: Xindan

last: Wang

state: IN

address: 1001 E 3rd St

department: Biology

institute: Indiana University at Bloomington

data_processing:
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
For Hi-C, we mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) independently by Bowtie version 2.1.0 to preserve the order of reads. All the processing steps afterwards were performed using an in-house Perl scripts. For ChIP-seq, we mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) independently using CLC genomics workbench 8.0, and exported .csv file.
For Hi-C, the two resulting SAM files were then merged together. Unaligned reads were discarded.
For Hi-C, the Bacillus subtilis (PY79) genome was divided into restriction fragments (2398 HindIII fragments). Each aligned read was sorted into its corresponding restriction fragment. We inferred that a DNA fragment resulted from non-ligation or self-ligation if reads from both ends were from the same restriction fragment; these reads were discarded. Only DNA fragments for which the reads came from different restriction fragments were retained and used for construction of a Hi-C contact map.
For Hi-C, the genome of Bacillus subtilis (PY79) was then divided into bins 10 kb and the remaining reads were allocated to their corresponding bin. We then counted the number of fragments having reads with in different bins. A raw Hi-C contact map is the matrix of read counts in which each entry, mij, indicates the number of fragments with ends mapping to bins i and j. The raw Hi-C contact map/matrix is biased due to the uneven distribution of restriction enzyme sites and, to a lesser extent, differences in GC content and the mappability of individual reads. We normalized raw contact maps using an iterative normalization procedure (Imakaev et al., 2012 PMID: 22941365). Essentially, we converted the number of interactions, or read counts, into Hi-C scores by applying the following equation and iteratively repeating it for the resulting contact map after each cycle:  mij =mij * (total reads) / (total reads in bin i * total reads in bin j). The iterative procedure was repeated until the maximum relative error of the total number of Hi-C scores in a bin was less than 10-5. Resulting matrices were normalized so that Hi-C scores for each row and column sum to 1. Subsequent analysis and visualization was done using R scripts.
ChIP-Seq reads were mapped to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) independently using CLC genomics workbench 8.0, and exported .csv file.
Genome_build: NC_022898.1
Supplementary_files_format_and_content: Files ending with .matrix.txt: tab-delimited text files of the iteratively-corrected Hi-C contact maps/matrices. Each column represents a 10kb bin (0-10K, 10-20k, 20-30k, etc) of the B. subtilis genome  and each row is a 10kb bin of the Bacillus subtilis PY79 genome (0-10K, 10-20k, 20-30k, etc). The cells contain the normalized Hi-C interaction score.   Files ending with .csv: comma-separated values files of ChIP-seq result, where the columns headers are: genome position, number of reads at each position.

organism: Bacillus subtilis PY79

source_name: Bacillus subtilis PY79, parS∆9, -94˚parS no ab, smcts02 spec

growth_protocol: Bacillus subtilis strains were derived from the prototrophic strain PY79 (Youngman et al 1983, PMID: 6300908). Cells were grown in defined rich medium (CH) (Harwood and Cutting 1990, Molecular Biological Methods for Bacillus ) or minimal medium (S750) (Grossman and Losick, 1988, PMID:3132711) supplemented with 1% sorbitol. Sporulation was induced by resuspension according to the method of Sterlini-Mandelstam (Harwood and Cutting 1990, Molecular Biological Methods for Bacillus). For Hi-C experiments during sporulation, strains contained a mutant of the SpoIIIE DNA translocase (spoIIIE36) that engages the chromosome after polar division but does not transport DNA (Wu and Errington, 1994, PMID: 8160014).

extract_protocol:
Hi-C experiments were performed using HindIII according to previous publications (Le et al, 2013, PMID: 24158908). ChIP-seq experiments were performed using anti-mCherry antibodies according to previous publications (Graham et al, 2014 PMID 24829297).
Standard library construction protocol was used for Illumina Hiseq2500 sequencing platform (Hi-C) or Illumina Miseq (ChIP-seq). Illumina Truseq indexes were used.

treatment_protocol: Cells were growing in CH medium at 30˚C, fixed by 3% formaldehyde for 30min at room temperature

value: CH, 30C

tag: genotype

value: parS-delta-9, -94degrees parS no ab, smcts02 spec

tag: restriction enzyme

value: HindIII


title: Induced 19 Days (by FICB) sample 2


title: 39_Rudnerlab_HindIII_HiC_BWX3359_42C40min

treatment_protocol: Cells were growing in CH medium at 30˚C, shift to 42˚C for 40min,  fixed by 3% formaldehyde for 30min at room temperature

value: CH, 30C to 42C, 40min


title: 34_Rudnerlab_HindIII_HiC_BDR1050_spo37C150m

data_processing:
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
We mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) independently by Bowtie version 2.1.0 to preserve the order of reads. All the processing steps afterwards were performed using an in-house Perl scripts.
The two resulting SAM files were then merged together. Unaligned reads were discarded.
The Bacillus subtilis (PY79) genome was then divided into restriction fragments (2398 HindIII fragments). Each aligned read was sorted into its corresponding restriction fragment. We inferred that a DNA fragment resulted from non-ligation or self-ligation if reads from both ends were from the same restriction fragment; these reads were discarded. Only DNA fragments for which the reads came from different restriction fragments were retained and used for construction of a Hi-C contact map.
The genome of Bacillus subtilis (PY79) was then divided into bins 10 kb and the remaining reads were allocated to their corresponding bin. We then counted the number of fragments having reads with in different bins. A raw Hi-C contact map is the matrix of read counts in which each entry, mij, indicates the number of fragments with ends mapping to bins i and j. The raw Hi-C contact map/matrix is biased due to the uneven distribution of restriction enzyme sites and, to a lesser extent, differences in GC content and the mappability of individual reads. We normalized raw contact maps using an iterative normalization procedure (Imakaev et al., 2012 PMID: 22941365). Essentially, we converted the number of interactions, or read counts, into Hi-C scores by applying the following equation and iteratively repeating it for the resulting contact map after each cycle:  mij =mij * (total reads) / (total reads in bin i * total reads in bin j). The iterative procedure was repeated until the maximum relative error of the total number of Hi-C scores in a bin was less than 10-5. Resulting matrices were normalized so that Hi-C scores for each row and column sum to 1. Subsequent analysis and visualization was done using R scripts.
Genome_build: NC_022898.1
Supplementary_files_format_and_content: Files ending with .matrix.txt: tab-delimited text files of the iteratively-corrected Hi-C contact maps/matrices. Each column is a 10kb bin of the Bacillus subtilis PY79 genome (0-10K, 10-20k, 20-30k, etc). Each row is a 10kb bin of the Bacillus subtilis PY79 genome (0-10K, 10-20k, 20-30k, etc).

source_name: Bacillus subtilis PY79

extract_protocol:
Hi-C experiments were performed using HindIII  according to previous publications (Le et al, 2013, PMID: 24158908).
Standard library construction for Illumina Hiseq2500 sequencing platform. Illumina Truseq indexes were used.

treatment_protocol:
Cells were growing in CH medium at 37˚C, resuspended in sporulation medium for 150min at 37˚C, fixed by 3% formaldehyde for 30min at room temperature
None

value: sporulation, 37C 150min


title: RNA-Seq analysis from Cxcr4-KO Notch1-deltaE+ mouse T-ALL cells 8 (primary tumor)

city: New York

first: Thomas

last: Trimarchi

state: NY

address: 550 First Ave Smilow 1307

department: Pathology

institute: NYU School of Medicine

description:
KO_8
Strand-specific RNA-SEQ (dUTP method).
Processed data file: primaryTumorFpkmMatrix.txt

data_processing:
Basecalls performed using CASAVA.
RNA-seq reads were aligned to the mm9 genome assembly using Tophat.
Differential gene expression analysis was performed using cuffdiffv2.1.
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: Tab-delimited FPKM matrix text file for each RNA-Seq experiment as computed by cuffdiffv2.1.

source_name: mouse T-ALL, Cxcr4-KO

growth_protocol: Primary mouse T-ALL cells isolated from spleen were maintained on OP9 stromal cells in OptiMEM + GlutaMAX (Invitrogen) supplemented with 10% FBS, 5ng/ml IL-7, penicillin and streptomycin, and 55μM β-mercaptoethanol and passaged every 3-4 days onto a fresh feeder layer. OP9 cells were pre-treated with 7.5ng/mL mitomycin C (Sigma) to prevent feeder cell division.

extract_protocol:
RNeasy kit (Qiagen).
Poly-A+ (magnetic oligodT-containing beads (Invitrogen)) RNA was used for library preparation. cDNA preparation and strand-specific library construction were performed using the dUTP method. Libraries were sequenced on the Illumina HiSeq 2500 using 50bp single-read method.

tag: strain/background

value: Cxcr4-/- Notch1-deltaE+

value: T-cell acute lymphoblastic leukemia (T-ALL) cells


title: 37_Rudnerlab_HindIII_HiC_BWX3304_42C20min

source_name: Bacillus subtilis PY79, parS∆8, smcts02 spec

treatment_protocol: Cells were growing in CH medium at 30˚C, shift to 42˚C for 20min,  fixed by 3% formaldehyde for 30min at room temperature

value: CH, 30C to 42C, 20min

value: parS-delta-8, smcts02 spec


title: 35_Rudnerlab_HindIII_HiC_BWX3091_spo37C150m

value: spoIIIE36, delta-parAB::spec


title: RNA-Seq analysis from Cxcr4+/+ Notch1-deltaE+ mouse T-ALL cells 1 (primary tumor)

description:
WT_1
Strand-specific RNA-SEQ (dUTP method).
Processed data file: primaryTumorFpkmMatrix.txt

source_name: mouse T-ALL, Cxcr4+/+

value: Cxcr4+/+ Notch1-deltaE+


title: RNA-Seq analysis from vehicle-treated mouse Notch1-deltaE+ T-ALL cells 1 (ex vivo-treatment)

description:
Control_1
Strand-specific RNA-SEQ (dUTP method).
Processed data file: amdTreatmentFpkmMatrix.txt

source_name: mouse T-ALL, control treated

tag: treatment

value: vehicle


title: RNA-Seq analysis from vehicle-treated mouse Notch1-deltaE+ T-ALL cells 3 (ex vivo-treatment)

description:
Control_3
Strand-specific RNA-SEQ (dUTP method).
Processed data file: amdTreatmentFpkmMatrix.txt

tag: cell type


title: RNA-Seq analysis from Cxcr4-KO Notch1-deltaE+ mouse T-ALL cells 5 (primary tumor)

description:
KO_5
Strand-specific RNA-SEQ (dUTP method).
Processed data file: primaryTumorFpkmMatrix.txt


title: RNA-Seq analysis from vehicle-treated mouse Notch1-deltaE+ T-ALL cells 2 (ex vivo-treatment)

description:
Control_2
Strand-specific RNA-SEQ (dUTP method).
Processed data file: amdTreatmentFpkmMatrix.txt


title: 36_Rudnerlab_HindIII_HiC_BWX3304_30C


title: RNA-Seq analysis from AMD-treated mouse Notch1-deltaE+ T-ALL cells 2 (ex vivo-treatment)

description:
AMD_2
Strand-specific RNA-SEQ (dUTP method).
Processed data file: amdTreatmentFpkmMatrix.txt

source_name: mouse T-ALL, AMD treated


title: RNA-Seq analysis from AMD-treated mouse Notch1-deltaE+ T-ALL cells 1 (ex vivo-treatment)

description:
AMD_1
Strand-specific RNA-SEQ (dUTP method).
Processed data file: amdTreatmentFpkmMatrix.txt


title: E2+DOX_3

city: Chapel Hill

first: Erin

middle: K

last: Shanle

state: NC

address: 3010 Genetic Medicine, 120 Mason Farm Road

department: Biochemistry and Biophysics

institute: University of North Carolina at Chapel Hill

data_processing:
Align reads to hg19 genome using RSEM, 1.1.16
Determine differential expression using DESeq, 1.7.10
Genome_build: hg19
Supplementary_files_format_and_content: text file, RSEM output. Column headers are:gene_ID, raw_count, scaled_estimate, transcript_ID

growth_protocol: Cells were cultured in phenol red-free DMEM + 10% 6x charcoal stripped serum for 3 days prior to the experiment. For each experiment, cells were cultured in phenol red-free DMEM + 5% stripped serum.

extract_protocol:
Total RNA was extracted using the RNEasy Plus Kit from Qiagen
Illumina TruSeq Sample Preparation V2

treatment_protocol: For each experiment, cells were treated with or without 50 ng/mL doxycycline for 48 hr. Then, cells were treated with 0.1% DMSO or 10 nM E2 for 4 hr followed by total RNA extraction.

tag: cell line

value: triple negative breast cancer cell line


title: RNA-Seq analysis from AMD-treated mouse Notch1-deltaE+ T-ALL cells 3 (ex vivo-treatment)

description:
AMD_3
Strand-specific RNA-SEQ (dUTP method).
Processed data file: amdTreatmentFpkmMatrix.txt


title: 31_Rudnerlab_HindIII_HiC_BNS1733_30C

treatment_protocol:
Cells were growing in CH medium at 30˚C, fixed by 3% formaldehyde for 30min at room temperature
None


title: E2+DOX_1


title: E2+DOX_2


title: 32_Rudnerlab_HindIII_HiC_BNS1733_42C45m

treatment_protocol:
Cells were growing in CH medium at 30˚C, shift to 42˚C for 45min,  fixed by 3% formaldehyde for 30min at room temperature
None

value: CH, 30C to 42C, 45min


title: 30_Rudnerlab_HindIII_HiC_BWX3231

treatment_protocol:
Cells were growing in CH medium at 37˚C, fixed by 3% formaldehyde for 30min at room temperature
None

value: CH, 37C

value: parS-delta-9 no.a.b., -94degrees parS (kan), 90degrees parS (spec)


title: RNA-Seq analysis from Cxcr4-KO Notch1-deltaE+ mouse T-ALL cells 7 (primary tumor)

description:
KO_7
Strand-specific RNA-SEQ (dUTP method).
Processed data file: primaryTumorFpkmMatrix.txt


title: DMSO+DOX_2


title: N20_shPAF1.1_starve_HCT116_ChIPSeq

description: ChIP of Total Pol II

data_processing:
Base-calling and quality filtering, default settings, Illumina Casava 1.8 for reads generated with Illumina HiSeq 2000
Base-calling and quality filtering, default settings, bcl2fastq version 2 for reads generated with Illumina NextSeq 500
ChIP-seq: Reads were aligned using Bowtie v0.12.9, allowing unique reads only and up to two mismatches in the entire read length. Alignments were extended to a total fragment length of 150 bases toward the interior of the sequenced fragment. UCSC bigWig files were created with 1bp resolution coverage across the genome and normalized to total reads per million (r.p.m).
Nascent and Total RNA-seq: Reads were aligned to the human genome (UCSC hg19) and Ensembl 72 GTF human annotations  using the Tophat aligner version 2.0.10, with the - g1 option. Alignments were not extended. UCSC bigWig files were created with 1bp resolution coverage across the genome and normalized to total reads per million (r.p.m).
Genome_build: UCSC hg19
Supplementary_files_format_and_content: http://genome.ucsc.edu/goldenPath/help/bigWig.html

extract_protocol:
For ChIP-seq, HCT116 cells were crosslinked with 1% paraformaldehyde for 10 minutes at room temperature with gentle rotation, and then quenched by 0.125 M glycine solution. After washing, nuclei were sonicated on a Misonix Sonicator 3000 Ultrasonic Cell Disruptor, and the supernatant was used for immunoprecipitation with the indicated antibody. ChIP-sequencing libraries were prepared with Illumina’s Tru-seq DNA sample prep kit. For nascent RNA-seq, HCT116 cells was harvested and washed 3 times with cold PBS, then suspended in 10 ml Buffer A (10 mM HEPES at pH=7.9, 10 mM KCl, 2 mM MgCl2, 1 mM DTT, 1× Complete protease inhibitors [Roche]). After incubating on ice for 15 minutes, the cells were homogenized in pre-cooled 15 ml Dounce tissue homogenizer for 15 times. Nuclei were then washed twice with Buffer B (10 mM HEPES at pH=7.9, 250 mM Sucrose, 1 mM DTT, 1× Complete protease inhibitors). The pellet was vigorously suspended with 1 ml NUN buffer (20 mM HEPES at pH=7.9, 7.5 mM MgCl2, 0.2 mM EDTA, 300 mM NaCl, 1 M Urea, 1% v/v Nonidet P40, 1 mM DTT, 20 U/ml SUPERase.In RNase Inhibitor [Ambion]) that was freshly prepared. The chromatin was then washed twice more with 5 ml NUN buffer each time. The supernatant was removed and RNA was purified. The RNA was subjected to polyA depletion with Oligo(dT) magnetic beads (Invitrogen) and DNase I treatment (NEB) for 20 minutes, and then was re-purified. For sequencing, 2 μg of resulting RNA was used for ribosomal RNA depletion with the RiboZero kit (Epicenter) and libraries were made with the TruSeq RNA sample Prep Kit (Illumina).
ChIP-sequencing libraries were prepared with Illumina’s Tru-seq DNA sample prep kit using standard protocols. Nascent and Total RNA-seq libraries were prepared with Illumina’s TruSeq RNA sample Prep Kit using standard protocols. The global nuclear run-on procedure and the preparation of Gro-seq libraries were previously described (Core et al., 2008; Gardini et al., 2014).

value: colorectal cancer cell line

value: PAF1 shRNA #1

value: Pol II (Santa Cruz, sc-899)


title: RNA-Seq analysis from Cxcr4+/+ Notch1-deltaE+ mouse T-ALL cells 4 (primary tumor)

description:
WT_4
Strand-specific RNA-SEQ (dUTP method).
Processed data file: primaryTumorFpkmMatrix.txt


title: 29_Rudnerlab_HindIII_HiC_BWX3221

value: parS-delta-9 (spec), -94degrees parS (kan)

value: HindIII


title: DMSO+DOX_3


title: RNA-Seq analysis from Cxcr4+/+ Notch1-deltaE+ mouse T-ALL cells 2 (primary tumor)

description:
WT_2
Strand-specific RNA-SEQ (dUTP method).
Processed data file: primaryTumorFpkmMatrix.txt


title: E2_3


title: DMSO+DOX_1


title: 33_Rudnerlab_HindIII_HiC_BNS1733_42C120m

treatment_protocol:
Cells were growing in CH medium at 30˚C, shift to 42˚C for 120min,  fixed by 3% formaldehyde for 30min at room temperature
None

value: CH, 30C to 42C, 120min


title: 28_Rudnerlab_HindIII_HiC_BWX3172


title: E2_1


title: DMSO_1


title: 27_Rudnerlab_HindIII_HiC_BDR3007

value: parS-delta-8, delta-soj132 no a.b.


title: DMSO_3


title: 25_Rudnerlab_HindIII_HiC_BNS1657

value: parS-delta-8:spo0J (parS-delta), yycG (parS-delta) , rocR (parS-delta), cotF (parS-delta), metS (parS-delta), ybbC(parS-delta), ydaD(parS-delta), nfrA(parS-delta)


title: DMSO_2


title: 26_Rudnerlab_HindIII_HiC_BWX2761


title: Vehicle (Replicate 4)

city: Cardiff

first: NATHAN

last: HARMSTON

address: Museum Avenue

institute: Cardiff University

data_processing:
Reads were aligned against the human genome (hg19/GRCh37) and Ensembl annotated transcripts (build 75) using Tophat version 2.0.945 allowing two mismatches
Read counts were summarized at the level of individual genes using HTseq-count considering only reads that mapped unambiguously to the transcriptome
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited files containing raw counts for each gene

source_name: Colorectal cancer patient-derived xenograft

extract_protocol:
RNA-seq libraries were prepared using the Illumina TruSeq stranded Total RNA protocol with subsequent PolyA enrichment.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were treated with ETC-159 for 56h

tag: tissue

value: Colorectal cancer PDX

tag: condition

value: Vehicle


title: Vehicle (Replicate 3)


title: Vehicle (Replicate 1)


title: ETC-159 treatment (Replicate 3)


title: 22_Rudnerlab_HindIII_HiC_BDR2298_S7sorb22C

treatment_protocol:
Cells were growing in S750 sorbitol medium at 22˚C, fixed by 3% formaldehyde for 30min at room temperature
None

value: S7sorbitol, 22C


title: 23_Rudnerlab_HindIII_HiC_BDR2996

value: parS-delta-8, -1degree parB (wt parS)


title: E2_2


title: ETC-159 treatment (Replicate 2)


title: 24_Rudnerlab_HindIII_HiC_BDR2985

value: parS-delta-8, +4degrees  metS (wt parS)


title: 21_Rudnerlab_HindIII_HiC_PY79_S7sorb22C

value: wild type


title: 18_Rudnerlab_HindIII_HiC_BWX3266_spo30C190m

treatment_protocol:
Cells were growing in CH medium at 30˚C, resuspended in sporulation medium for 190min at 30˚C, fixed by 3% formaldehyde for 30min at room temperature
None

value: sporulation, 30C 190min

value: spoIIIE36, smcts02 (spec)


title: 20_Rudnerlab_HindIII_HiC_BWX3266_spo30C150m42C40m

treatment_protocol:
Cells were growing in CH medium at 30˚C, resuspended in sporulation medium for 150min at 30˚C, shifted to 42˚C for 40min, fixed by 3% formaldehyde for 30min at room temperature
None

value: sporulation, 30C 150min, 42C 40min


title: 16_Rudnerlab_HindIII_HiC_BWX3151_42C40m

treatment_protocol:
Cells were growing in CH medium at 30˚C, shift to 42˚C for 40min,  fixed by 3% formaldehyde for 30min at room temperature
None

value: CH, 30C to 42C, 40min

value: smcts02 (spec)


title: MDA_WT_Fc_3

city: Stockholm

first: Daniel

last: Ramsköld

address: Nobels väg 3

institute: Karolinska Institutet

data_processing:
Reads were aligned using STAR to genomes mm10 and hg19
Reads were separated for different species using S^3 (https://github.com/danielramskold/S3_species-specific_sequencing) with default settings (-Ms 1 -Mu 1 -D 2)
Unique reads were selected using mapping quality threshold 255
Gene expression values were calculated using rpkmforgenes.py (http://sandberg.cmb.ki.se/rnaseq)  with options -rmnameoverlap -bothendsceil and using RefSeq annotation from 1 July 2014
MicroRNAs and snoRNAs were removed
RPKM values were TMM normalized
Supplementary_files_format_and_content: RPKM expression values and read counts (tab-delimited text format)

source_name: MDA-MB-231 cells cultured on immobilized human IgG Fc fragment, replicate 2

growth_protocol: cells maintained in DMEM, high glucose, pyruvate (Gibco, cat. no. 41966-029) supplemented with 10% fetal bovine serum (Gibco, cat. no. 10270-106) and 1% penicillin-streptomycin (10,000 U/mL, Gibco, cat. no. 15140-122) at 37°C in a humidified 5% CO2 atmosphere

extract_protocol:
RNeasy Mini Kit (Qiagen, cat. no. 74104)
We used the kit TruSeq RNA Sample Prep Kit v2–48, Set B (Illumina®, cat. no. RS-122-2002)

value: MDA-MB-231 human breast adenocarcinoma cell line (ATCC, HTB-26)


title: MDA231_Fc_+DAPT

source_name: MDA-MB-231 cells cultured on immobilized human IgG Fc fragment, treated with DAPT

treatment_protocol: cells cultured on immobilized human IgG Fc fragment, treated with 20μM DAPT (GSI-IX) (10mM stock, Selleck Chemicals, cat. no. S2215) for 6 hours


title: MCF7WT_Fc_1

source_name: MCF7 cells cultured on immobilized human IgG Fc fragment, replicate 1

value: MCF7 human breast adenocarcinoma cell line (ATCC, HTB-22)


title: MDA231_Fc-DLL4_-DAPT

source_name: MDA-MB-231 cells cultured on immobilized human IgG Fc-gamma and extracellular domain of Delta-like-4 fusion protein (Fc-DLL4), treated with DMSO control

treatment_protocol: cells cultured on immobilized human IgG Fc-gamma and extracellular domain of Delta-like-4 fusion protein (Fc-DLL4), treated with DMSO (Sigma-Aldrich, cat. no. D4540) for 6 hours


title: 17_Rudnerlab_HindIII_HiC_BWX2080_42C20m

treatment_protocol:
Cells were growing in CH medium at 30˚C, shift to 42˚C for 20min,  fixed by 3% formaldehyde for 30min at room temperature
None

value: CH, 30C to 42C, 20min

value: smc (wt) (spec)

value: HindIII


title: MCF7WT_Fc

treatment_protocol: cells cultured on immobilized human IgG Fc fragment


title: MDA231_Fc_-DAPT

source_name: MDA-MB-231 cells cultured on immobilized human IgG Fc fragment, treated with DMSO control

treatment_protocol: cells cultured on immobilized human IgG Fc fragment, treated with DMSO (Sigma-Aldrich, cat. no. D4540) for 6 hours


title: MDA231_Fc-DLL4_+DAPT

source_name: MDA-MB-231 cells cultured on immobilized human IgG Fc-gamma and extracellular domain of Delta-like-4 fusion protein (Fc-DLL4), treated with DAPT

treatment_protocol: cells cultured on immobilized human IgG Fc-gamma and extracellular domain of Delta-like-4 fusion protein (Fc-DLL4), treated with 20μM DAPT (GSI-IX) (10mM stock, Selleck Chemicals, cat. no. S2215) for 6 hours


title: MDA_WT_Fc_2

source_name: MDA-MB-231 cells cultured on immobilized human IgG Fc fragment, replicate 1


title: non-induced fibroblast sample 1

source_name: mouse fibroblasts

tag: strain


title: 13_Rudnerlab_HindIII_HiC_BWX3151_30C

value: CH, 30C


title: 14_Rudnerlab_HindIII_HiC_BWX3151_42C10m

treatment_protocol:
Cells were growing in CH medium at 30˚C, shift to 42˚C for 10min,  fixed by 3% formaldehyde for 30min at room temperature
None

value: CH, 30C to 42C, 10min