title: Mouse random Hi-C ligation

first: Steven

middle: William

last: Wingett

state: Cambs

address: Francis Crick Avenue, Cambridge Biomedical Campus

department: Cell Biology

institute: MRC Laboratory of Molecular Biology

data_processing:
Library strategy: Hi-C
Hi-C analysis pipeline HiCUP v0.4.2 (running bowtie2 v2.2.3 for mixed human-mouse samples or bowtie v0.12.9 for other samples). HiCUP homepage: www.bioinformatics.babraham.ac.uk/projects/hicup
Hi-C normalisation used Hicpipe v0.93 (Hicpipe homepage: http://compgenomics.weizmann.ac.il/tanay/?page_id=283 )
Hi-C normalisation also used Homer (Homer homepage: http://homer.salk.edu/homer )
Genome_build: hg19 or mm9
Supplementary_files_format_and_content: The files with extension ".raw" provide the positions of interacting Hi-C read pairs (di-tags). The header line in each file describes each column.

source_name: Mouse foetal liver cells from C57BL/6 mouse embryos, (E14.5)

growth_protocol: H9 (WA09; WiCell) human ESCs were maintained using Pluripro fully-defined media and matrix (Cell Guidance Systems). Mouse foetal livers were dissected from C57BL/6 mouse embryos at day 14.5 (E14.5) of development.

extract_protocol:
Approximately 50 million human ESCs (at passage 56) were harvested with Accutase (Life Technologies), suspended in Pluripro media and directly processed for fixation. Mouse foetal liver cells were suspended in DMEM (Life Technologies) supplemented with 10% FBS, filtered through a cell strainer (70 µm) and directly fixed by addition of formaldehyde.
Thirty to 50 million cells were fixed in 2% formaldehyde for 10 min, quenched with 0.125 M glycine, spun down (400 x g, 5 min) and washed once with PBS. The cells were incubated in 50 ml permeabilisation buffer (10 mM Tris-HCl pH 8, 10 mM NaCl, 0.2% Igepal CA-630, Complete EDTA-free protease inhibitor cocktail [Roche]) for 30 min on ice with occasional agitation, spun down (650 x g, 5 min, 4˚C), and the cell pellets were resuspended in 358 µl of 1.25 x NEBuffer2 (NEB) per 5 million cell aliquot. Eleven µl of 10% SDS was added to each aliquot, followed by an incubation at 37˚C for 60 min with continuous agitation (950 rpm). To quench the SDS, 75 µl of 10% Triton X-100 was then added per aliquot, followed by an incubation at 37˚C for 60 min with continuous agitation (950 rpm). To digest chromatin, 1500 U of Hind III (NEB) was added per aliquot and incubated at 37˚C overnight with continuous agitation (950 rpm). After digestion, restriction sites were filled in with Klenow (NEB) in the presence of biotin-14-dATP (Life Technologies), dCTP, dGTP and dTTP (all 30 µM) for 60 min at 37˚C.   For in-solution ligation, 86 µl of 10% SDS was added per aliquot and incubated at 65˚C for 30 min with continuous agitation (950 rpm), followed by addition of 7.61 ml of ligation mix (745 µl of 10% Triton X-100, 820 µl of 10 x T4 DNA ligase reaction buffer [NEB], 82 µl of 10 mg/ml BSA [NEB] and 5.965 ml water) per aliquot and incubation at 37˚C for 60 min with occasional agitation. For in-nucleus ligation, 7.61 ml of ligation mix (820 µl of 10 x T4 DNA ligase reaction buffer [NEB], 82 µl of 10 mg/ml BSA [NEB] and 6.71 ml water) was added per aliquot (compared to the in-solution ligation, SDS addition and incubation at 65˚C were omitted). For the ligation reaction (both in-solution and in-nucleus variants), 50 µl of 1 U/µl T4 DNA ligase (Life Technologies) was added per aliquot, followed by incubation at 16˚C for 4 hrs.   The cross-links were reversed by adding 60 µl of 10 mg/ml proteinase K (Roche) per aliquot and incubating at 65˚C overnight. After overnight incubation, another 60 µl of proteinase K per aliquot was added, followed by incubation at 65˚C for an additional two hours. RNA was removed by adding 12.5 µl of 10 mg/ml RNase A (Roche) per aliquot and incubating at 37˚C for 60 min. DNA was isolated by a phenol (Sigma) extraction, followed by a phenol/chloroform/isoamylalcohol (Sigma) extraction and standard ethanol precipitation. The precipitated DNA was washed three times with 70% ethanol, and dissolved in 25 µl TE per aliquot. Subsequently all aliquots were pooled and the Hi-C DNA was quantified (Quant-iT Pico Green, Life Technologies). Biotin was removed from non-ligated restriction fragment ends by incubating 30 to 40 µg of Hi-C library DNA with T4 DNA polymerase (NEB) for 4 hours at 20˚C in the presence of dATP. After DNA purification (Qiagen PCR purification kit) and sonication (Covaris E220), the sonicated DNA was end-repaired with T4 DNA polymerase, T4 DNA polynucleotide kinase, Klenow (all NEB) and dNTPs in 1 x T4 DNA ligase reaction buffer (NEB). Double size selection of DNA was performed using AMPure XP beads (Beckman Coulter), before dATP-addition with Klenow exo- (NEB). Biotin-marked ligation products were isolated with MyOne Streptavidin C1 Dynabeads (Life Technologies) in binding buffer (5 mM Tris pH8, 0.5 mM EDTA, 1 M NaCl) for 30 min at room temperature, followed by two washes in binding buffer, and one wash in 1 x T4 DNA ligase reaction buffer (NEB). PE adapters (Illumina) were ligated onto Hi-C ligation products bound to streptavidin beads for 2 hours at room temperature (T4 DNA ligase in 1 x T4 DNA ligase reaction buffer [NEB], slowly rotating). After washes in wash buffer (5 mM Tris, 0.5 mM EDTA, 1 M NaCl, 0.05% Tween-20) and binding buffer, the DNA-bound beads were resuspended in NEBuffer 2. Bead-bound Hi-C DNA was amplified with 12 PCR amplification cycles using PE PCR 1.0 and PE PCR 2.0 primers (Illumina). The concentration and size distribution of Hi-C library DNA after PCR amplification was determined by Bioanalyzer profiles (Agilent Technologies) and quantitative PCR, and the Hi-C libraries were paired-end sequenced on Illumina Hi-Seq1000 or MiSeq platforms.

value: liver

value: embryo stage 14.5


title: ETC-159 treatment (Replicate 4)

status: Public on Aug 12 2015

type: SRA

city: Cardiff

first: NATHAN

last: HARMSTON

address: Museum Avenue

country: United Kingdom

institute: Cardiff University

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

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


title: 12_Rudnerlab_HindIII_HiC_BWX3209

city: Bloomington

first: Xindan

last: Wang

state: IN

address: 1001 E 3rd St

department: Biology

country: USA

institute: Indiana University at Bloomington

library_source: genomic

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).

molecule: genomic DNA

organism: Bacillus subtilis PY79

source_name: Bacillus subtilis PY79

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).
Standard library construction for Illumina Hiseq2500 sequencing platform. Illumina Truseq indexes were used.

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

tag: developmental stage

value: CH, 37C

tag: genotype

value: delta-parB::spec, pelB::Psoj mcherry-parB1(Vc) (cat)

tag: restriction enzyme

value: HindIII


title: Vehicle (Replicate 2)

value: Vehicle


title: Kdm5aRb1 DKO rep2 purified

city: Chicago

first: Elizaveta

middle: V

last: Benevolenskaya

state: IL

address: 900 S. Ashland Ave.

department: Biochemistry and Molecular Genetics

institute: University of Illinois at Chicago

description:
S12
mRNA
Myotubes isolated from a mixed cell population by size exclusion gravity.

data_processing:
Illumina Casava1.7 software used for basecalling.
Mapping of reads was done with TopHat (version 1.2.0) (Trapnell et al., 2009). Identified 36bp short reads were uniquely aligned allowing at best two mismatches to the UCSC (Lander et al., 2001) mouse reference genome (mm9). Sequence that matched more than one place with equally quality were discarded to avoid bias.
The reads that were not mapped to the genome were utilized to map against the transcriptome (junctions mapping) using EnsEMBL 59 (Hubbard et al., 2007) gene model.
Any residual mapping bias was checked using RSEQtools (Habegger et al., 2010).
Consistency between two replicate data on KO and WT were checked by Pearson correlation co-efficient by counting reads in 500 bp bins.
Reads are then subjected to count by Bioconductor package “Genominator” to get corrected (weighted) count. The weighted number of reads falling in the Ensembl gene model were then normalized (against matrix of total input read count) and differential expression were analyzed by Bioconductor package Deseq.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include weighted-normalized read count values for each Sample.

organism: Mus musculus

source_name: Mouse Embryonic Fibroblasts

growth_protocol: Standard growth meduim DMEM/10% FBS, at 10% CO2

extract_protocol:
Total RNA was isolated with Trizol (Invitrogen) following by purification on the RNeasy Micro column (Qiagen).
cDNA library was prepared using the NEBNext® mRNA Library Prep Master Mix Set for Illumina® (NEB). Agencourt AMPure XP Beads (Beckman Coulter) were used for DNA purification were appropriate.

treatment_protocol: MEFs were induced to differentiate into myotubes as follows. MEFs were transduced with Adeno-MyoD in differentiation media (DM: DMEM/2% horse serum, 10µg/ml insulin). After 24 hours, the DM containing Adeno-MyoD was replaced with fresh DM and cells were grown for additional 72 hours.

tag: cell type

value: Mouse Embryonic Fibroblasts

tag: strain

tag: rna fractionation

value: 1.5 µg of total RNA was purified using Dynabeads mRNA Purification Kit (Invitrogen) according to manufacturer’s protocol. RNA was subjected to two sequential rounds of hybridization with Dynabeads® Oligo(dT).

tag: library strategy

value: Synthesized cDNA was enriched by 15 cycles of PCR using Phusion DNA Polymerase (NEB) and PE primers designed for Illumina sequencing. Single-read sequencing for 36 bases was done on an Illumina Genome Analyzer II.

tag: treatment protocol

value: 24 hours before extraction, cells were trypsinized and fractionated by size exclusion gravity. Cells were allowed to recover in conditioned DM (that was kept on different MEFs for 48 hours) for 24 hours.


title: Induced 19 Days (by FICB) sample 1

city: Beijing

first: Yan-Tao

last: Ma

address: No. 5 Yiheyuan Road

country: China

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: chemically-induced cells from 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: WT rep2 purified

description:
S10
mRNA
Myotubes isolated from a mixed cell population by size exclusion gravity.

value: WT


title: Induced 48 hrs (by FICB)


title: 11_Rudnerlab_HindIII_HiC_BWX3208

value: delta-parB::spec, pelB::Psoj mcherry-parB(delta-parS) (cat)


title: Kdm5aRb1 DKO rep1 purified

description:
S11
mRNA
Myotubes isolated from a mixed cell population by size exclusion gravity.


title: WT rep1 purified

description:
S9
mRNA
Myotubes isolated from a mixed cell population by size exclusion gravity.


title: 10_Rudnerlab_HindIII_HiC_BDR2707

value: pelB::(parA parB G77S delta-parS) cat, delta-parAB::spec


title: Primary neuron

source_name: mouse primary cortical neurons


title: Induced 8 Days (by FICB)


title: Induced 4 Days (by FICB)


title: Kdm5aRb1 DKO rep1

description:
S7
ribo-minus RNA
MEFS subjected to differentiation protocol into myotubes, mixed cell population

value: 1.7 µg of total RNA was processed using the RiboMinus Eukaryote Kit for RNA-Seq (Ambion) according to manufacturer’s protocol.

value: Synthesized cDNA was integrated into the standard TruSeq Illuminal protocol at the step of adenylation of 3’ ends. Single-read sequencing for 40 bases was done on an Illumina HiSeq Analyzer.


title: 08_Rudnerlab_HindIII_HiC_BDR2292


title: Rbp2 WT_H3K4me3_ChIPSeq

description: Chromatin IP against H3K4me3

data_processing:
Alignment: Sequence reads were obtained using the Illumina Genome Analyzer Pipeline and reads were  mapped to the mouse (July, 2007) genomes (NCBI37/mm9) using BOWTIE aligner program (http://bowtie-bio.sourceforge.net/index.shtml) (Ref: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25.) All reads mapping uniquely with two or fewer mismatches were retained.
Peaks: Peak/significant island detection was performed with the program SICER (http://home.gwu.edu/~wpeng/Software.htm)
Genome Build:
H3K4me3_mmuES_ff_map-mm9.bed: mm9
H3K4me3_ff_mm9_ES.wig: mm9
H3K4me3_mmuES_ff_island.bed: mm9

source_name: Rbp2 f/f ES cells

growth_protocol: Wild-type (Rbp2 f/f) and Rbp2-/- (Rbp2 KO) ES cells were maintained on irradiated mouse embryonic fibroblast (IEF) feeders in standard ES medium (DMEM; Dulbecco's modified Eagle's medium) supplemented with 15% heat-inactivated fetal calf serum, 0.1 mM 2-mercaptoethanol, 2 mM L-glutamine, 0.1 mM non-essential amino acid, 1% of nucleoside mix (100X stock, Sigma), 1000U/ml recombinant leukemia inhibitory factor (LIF; Chemicon) and antibiotics. For ChIP assays, the cells were seeded on gelatin-coated plates.

extract_protocol: ChIP and genomic library preparation was performed as described (Beshiri, M.L, A. Islam A, D.C. DeWaal, W.F. Richter, Love J, N. Lopez-Bigas, and E.V. Benevolenskaya. 2010. Genome-wide Analysis using ChIP to Identify Isoform-specific Gene Targets. JoVE. 41. http://www.jove.com/index/details.stp?id=2101, doi: 10.3791/2101).  After adapter ligation DNA was PCR amplified with Illumina primers for 18 cycles and library fragments of ~320 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: genotype/variation

value: Rbp2 f/f wild type

value: embryonic stem cells

tag: chip antibody

value: Anti-trimethyl-Histone H3 (Lys4)

tag: chip antibody vendor

value: Upstate Tech

tag: chip antibody cat. #


title: Induced 0 Days

source_name: mouse fibroblasts


title: 09_Rudnerlab_HindIII_HiC_BWX3196

value: CH, 37C

value: parS-delta-9 (spec):parS-delta-8, +91degrees yhaX (delta-parS) (spec)


title: Rbp2 KO_H3K4me3_ChIPSeq

description: Chromatin IP against H3K4me3

data_processing:
Alignment: Sequence reads were obtained using the Illumina Genome Analyzer Pipeline and reads were  mapped to the mouse (July, 2007) genomes (NCBI37/mm9) using BOWTIE aligner program (http://bowtie-bio.sourceforge.net/index.shtml) (Ref: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25.) All reads mapping uniquely with two or fewer mismatches were retained.
Peaks: Peak/significant island detection was performed with the program SICER (http://home.gwu.edu/~wpeng/Software.htm)
Genome Build:
H3K4me3_mmuES_KO_map-mm9.bed: mm9
H3K4me3_KO_mm9_ES.wig: mm9
H3K4me3_mmuES_KO_island.bed: mm9

source_name: Rbp2 KO ES cells

value: Rbp2 -/- knockout


title: 07_Rudnerlab_HindIII_HiC_BWX2876

value: delta-parA (delta-soj132) no a.b.

value: HindIII


title: 15_Rudnerlab_HindIII_HiC_BWX3151_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: smcts02 (spec)


title: no-tag Myc for Cut14_Sfc6_Sfc2 ChIP-seq

city: Eugene

first: Hideki

last: Tanizawa

state: OR

address: 1370 Franklin Blvd

department: Institute of Molecular Biology

institute: University of Oregon

data_processing:
Basecalls performed using Illumina CASAVA version 8.
ChIP-seq reads were aligned to the S. pombe genome (20090706; download from http://ebi.edu.au/ftp/databases/pombase/pombe/Chromosome_contigs/OLD/20090706/) using Maq version 0.7.1 for MyC samples or aligned to the S. pombe genome (ASM294v1.18; download from ftp://ftp.ensemblgenomes.org/pub/fungi/release-18/fasta/schizosaccharomyces_pombe/dna/) using BWA version 0.6.2 with the option -n 100 for FLAG samples.
Fragment size was estimated by using HOMER version 4.4.
The scores of the peaks were determined by the subtraction of control read density from treatment read density and calculate 200bp window average.
Genome_build: 20090706
Supplementary_files_format_and_content: wig files. Scores represent subtraction of control read density from treatment read density.

organism: Schizosaccharomyces pombe

source_name: fission yeast cells, WT, no-tag Myc, Myc ChIP

growth_protocol: Fission yeast cells (5 x 10^8 cells at 1 x 10^7 cells/ml) were grown at 30°C in YEA medium for Myc ChIP samples. For FLAG ChIP samples, cells were grown at 30°C in EMM medium and further cultured in EMM containing 15 mM thiamine and 0.5 mM auxin (1-naphthaleneacetic acid) for 2 hours (5 x 10^8 cells at 1 x 10^7 cells/ml), followed by pFA fixation. Using an auxin-based degron system (Kanke et al., 2011, BMC Cell Biol vol.12: 8), endogenous Cnd2 proteins were depleted by adding auxin and thiamine into culture medium. Wild-type and mutant Cnd2 proteins tagged with 3FLAG at their C-termini were continuously expressed from plasmids carrying the endogenous cnd2 promoter.

extract_protocol:
Fission yeast cells grown at 30°C in YEA were shifted to 18°C for 5 min before 30 min fixation in 3% paraformaldehyde. Soluble chromatin fractions prepared from fixed cells were sonicated for 30 min by a Bioruptor (Diagenode). Tagged proteins were purified by each antibody and protein G-coupled Dynabeads (Life Technologies).
Libraries were prepared from 5 ng of DNA using the TruSeq DNA sample prep kit (Illumina) for Myc samples or using the NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina® with the NEBNext® Multiplex Oligos for Illumina® (index Primers Set 1) for FLAG samples, following manufacturer's protocol. Sequencing was performed by an Illumina Genome Analyzer II (Myc) or an Illumina HiSeq 2000 (FLAG).

tag: strain/background

value: h+N leu1-32 ade6-210 ura4-DS/E

tag: tagged protein

value: no-tag Myc

tag: culture condition

value: asynchronous cultures

value: rabbit polyclonal anti-Myc (Novus Biologicals, Cat. NB600-336, Lot. A5)


title: Sfc2-Myc ChIP-seq

source_name: fission yeast cells, WT, Sfc2-Myc, Myc ChIP

value: h+N leu1-32 ade6-210 ura4-DS/E Sfc2-13Myc::kanMX


title: 06_Rudnerlab_HindIII_HiC_BDR1873_S7sorb37C

treatment_protocol:
Cells were growing in S750 sorbitol medium at 37˚C, fixed by 3% formaldehyde for 30min at room temperature
None

value: S7sorbitol, 37C


title: Rb1 KO rep1

description:
S5
ribo-minus RNA
MEFS subjected to differentiation protocol into myotubes, mixed cell population

value: Mouse Embryonic Fibroblasts

value: 1.7 µg of total RNA was processed using the RiboMinus Eukaryote Kit for RNA-Seq (Ambion) according to manufacturer’s protocol.

value: Synthesized cDNA was integrated into the standard TruSeq Illuminal protocol at the step of adenylation of 3’ ends. Single-read sequencing for 40 bases was done on an Illumina HiSeq Analyzer.


title: Sfc6-Myc ChIP-seq

source_name: fission yeast cells, WT, Sfc6-Myc, Myc ChIP

value: h+N leu1-32 ade6-216 ura4-DS/E Sfc6-13Myc::kanMX


title: 05_Rudnerlab_HindIII_HiC_PY79_S7sorb37C

value: wild type


title: Induced 8 Days without F (FICB-F)


title: Rb1 KO rep2

description:
S6
ribo-minus RNA
MEFS subjected to differentiation protocol into myotubes, mixed cell population


title: Cut14-Myc ChIP-seq

source_name: fission yeast cells, WT, Cut14-Myc, Myc ChIP

value: h+N leu1-32 ade6-210 ura4-DS/E Cut14-13Myc::kanMX


title: Kdm5aRb1 DKO rep2

description:
S8
ribo-minus RNA
MEFS subjected to differentiation protocol into myotubes, mixed cell population


title: Kdm5a KO rep1

description:
S3
ribo-minus RNA
MEFS subjected to differentiation protocol into myotubes, mixed cell population


title: 03_Rudnerlab_HindIII_HiC_BDR1873

value: CH, 37C


title: Induced 8 Days without B (FICB-B)


title: no-tag Myc for Rpc25_Brf1 ChIP-seq


title: WT rep1

description:
S1
ribo-minus RNA
MEFS subjected to differentiation protocol into myotubes, mixed cell population

value: WT


title: Left_Mammary_Gland_4_NOD-SCID

city: Stockholm

first: Daniel

last: Ramsköld

address: Nobels väg 3

country: Sweden

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)

molecule: polyA RNA

source_name: left 4th mammary gland, cleared

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:
We minced the tissue in 200uL TRIzol (Ambion, cat. no. 15596-026) with a scalpel and passed the tissue solution through a 23-gauge needle ten times, then extracted RNA using PureLink RNA Mini Kit (Ambion, cat. no. 12183-018A)
We used the kit TruSeq RNA Sample Prep Kit v2–48, Set B (Illumina®, cat. no. RS-122-2002)

treatment_protocol: mammary fat pad clearing

tag: mouse strain

value: NSG-NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ

tag: tissue

value: mouse mammary tissue


title: Brf1-Myc ChIP-seq

source_name: fission yeast cells, WT, Brf1-Myc, Myc ChIP

value: mat1M leu1-32 ade6-216 his2 ura4-D18 Brf1-13Myc::kanMX


title: Induced 8 Days without C (FICB-C)


title: Rpc25-Myc ChIP-seq

source_name: fission yeast cells, WT, Rpc25-Myc, Myc ChIP

value: mat1M leu1-32 ade6-210 his2 ura4-D18 Rpc25-13Myc::kanMX


title: no-tag Myc for Tbp1 ChIP-seq

value: h+N leu1-32 ade6-210 ura4-DS/E

value: no-tag Myc


title: 01_Rudnerlab_HindIII_HiC_PY79

tag: developmental stage

value: HindIII


title: Induced 8 Days without I (FICB-I)


title: E16.5 Intermediate progenitor cell-derived neurons

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

data_processing:
Illumina Casava 1.9 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using TopHat v1.2.0 with default settings. Aligned reads were used to generate pileup for each base with Samtools v0.1.18.
Read counts for each refseq gene were summarized using custom built R scripts. The exons in all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the TMM method implemented in Bioconductor package "edgeR" .
Genome_build: mm9
Supplementary_files_format_and_content: Counts for each refseq genes

source_name: Cortex

extract_protocol:
Heterozygous Tbr2(Eomes)-GFP mice were bred with homozygous DCX-mRFP mice to yield GFP/RFP double positive embryos. The cortices derived from the double positive embryos were dissociated by trituration in HBSS with 2mM of EDTA and 25 ug/ml of DNase I. Cells were washed once with HBSS and re-suspended in DMEM/F12. Fluorescence-activated cell sorting (FACS) was used to acquire intermediate progenitor cell-derived neurons (IPNs, double color) and non-intermediate progenitor cell-derived neurons (non-IPNs, red color). One million of IPNs and non-IPNs at embryonic day 15.5 (E15.5) was accumulated, respectively. Total RNA was extracted using TRIzol. For E13.5 and E16.5, 10000 IPNs or non-IPNs were collected and whole transcriptome was amplified by Ovation RNA-Seq System V2 kit (NuGEN) before sending to sequencing.
Following Illumina's True-seq RNA-seq library prep kit

value: Neuron

tag: age

value: Embryonic day 16.5

tag: sample type


title: WT rep2

description:
S2
ribo-minus RNA
MEFS subjected to differentiation protocol into myotubes, mixed cell population

tag: cell type

value: Mouse Embryonic Fibroblasts

tag: genotype


title: 02_Rudnerlab_HindIII_HiC_PY79_rep1

tag: restriction enzyme


title: E16.5 non-IPC(intermediate progenitor cell)-derived neurons

tag: strain


title: Mouse-human mixture2: Hi-C in-solution ligation

city: Cambridge

description:
Mixture of mouse and human samples.
The human-mouse mixed samples were used to assess the level of experimental artefacts. The FASTQ files were mapped against a reference genome (creating a BAM file) and the interspecies contacts were counted.

data_processing:
Library strategy: Hi-C
Hi-C analysis pipeline HiCUP v0.4.2 (running bowtie2 v2.2.3 for mixed human-mouse samples or bowtie v0.12.9 for other samples). HiCUP homepage: www.bioinformatics.babraham.ac.uk/projects/hicup
Hi-C normalisation used Hicpipe v0.93 (Hicpipe homepage: http://compgenomics.weizmann.ac.il/tanay/?page_id=283 )
Hi-C normalisation also used Homer (Homer homepage: http://homer.salk.edu/homer )
Genome_build: hg19 and mm9
Supplementary_files_format_and_content: The files with extension ".raw" provide the positions of interacting Hi-C read pairs (di-tags). The header line in each file describes each column.

organism:
Homo sapiens
Mus musculus

source_name: H9 (WA09; WiCell) human ESCs and Mouse foetal liver cells from C57BL/6 mouse embryos, (E14.5)

value: mixture of human ESC and mouse embryonic liver

tag: cell line

value: H9 (wa09; wicell)

value: human ESC and mouse embryo stage 14.5


title: Mouse sample2: Hi-C in-nucleus ligation

source_name: Mouse foetal liver cells from C57BL/6 mouse embryos, (E14.5)

value: liver

value: embryo stage 14.5


title: Kdm5a KO rep2

description:
S4
ribo-minus RNA
MEFS subjected to differentiation protocol into myotubes, mixed cell population

tag: rna fractionation

value: 1.7 µg of total RNA was processed using the RiboMinus Eukaryote Kit for RNA-Seq (Ambion) according to manufacturer’s protocol.

tag: library strategy

value: Synthesized cDNA was integrated into the standard TruSeq Illuminal protocol at the step of adenylation of 3’ ends. Single-read sequencing for 40 bases was done on an Illumina HiSeq Analyzer.


title: E13.5 non-IPC(intermediate progenitor cell)-derived neurons

value: Embryonic day 13.5


title: 04_Rudnerlab_HindIII_HiC_BDR1873_rep1

source_name: Bacillus subtilis PY79

value: CH, 37C


title: ETC-159 treatment (Replicate 1)

source_name: Colorectal cancer patient-derived xenograft

value: Colorectal cancer PDX

tag: condition


title: Mouse-human mixture2: Hi-C in-nucleus ligation


title: Mouse sample1: Hi-C in-solution ligation


title: Human sample1: Hi-C in-nucleus ligation

source_name: H9 (WA09; WiCell) human ESCs

value: ESC

value: embryo


title: E15.5 Intermediate progenitor cell-derived neurons

extract_protocol:
Heterozygous Tbr2(Eomes)-GFP mice were bred with homozygous DCX-mRFP mice to yield GFP/RFP double positive embryos. The cortices derived from the double positive embryos were dissociated by trituration in HBSS with 2mM of EDTA and 25 ug/ml of DNase I. Cells were washed once with HBSS and re-suspended in DMEM/F12. Fluorescence-activated cell sorting (FACS) was used to acquire intermediate progenitor cell-derived neurons (IPNs, double color) and non-intermediate progenitor cell-derived neurons (non-IPNs, red color). One million of IPNs and non-IPNs was accumulated, respectively. Total RNA was extracted using TRIzol.
Following Illumina's True-seq RNA-seq library prep kit

value: Embryonic day 15.5


title: Mouse sample1: Hi-C in-nucleus ligation


title: E15.5 non-IPC(intermediate progenitor cell)-derived neurons


title: Mouse32_IgG

source_name: Stroma and tumor of MBA-MB-231 cells injected into the left intact 4th inguinal mammary fat pad, treated with unspecific IgG antibody, mouse 32

extract_protocol:
We used the “Lysis and Homogenization: 10-100mg Frozen or Fresh Fibrous Tissue, Mortar and Pestle Protocol” of the PureLink RNA Mini Kit (Ambion, cat. no. 12183-018A)
We used the kit TruSeq RNA Sample Prep Kit v2–48, Set B (Illumina®, cat. no. RS-122-2002)

treatment_protocol: cells in PBS injected into the left intact 4th inguinal mammary fat pad; tumors were allowed to grow for 4-5 weeks (average tumor volume of 500mm3), treated with IgG antibody twice a week for a total of 8 times.

value: Fox Chase SCID Congenic-CB17/Icr-Prkdcscid/IcrIcoCrl

value: MDA-MB-231 tumor and mouse mammary tissue


title: Mouse sample2: Hi-C in-solution ligation


title: 41_Rudnerlab_ChIPseq_BWX3209

description: ChIP using mCherry antibodies

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.

source_name: Bacillus subtilis PY79, ∆parB::spec, pelB::Psoj mcherry-parB1(Vc) (cat)

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 37˚C, fixed by 3% formaldehyde for 30min at room temperature and subjected to chromatin immunoprecipitation as in Graham et al 2014 PMID 24829297, using anti-mCherry antibodies

value: delta-parB::spec, pelB::Psoj mcherry-parB1(Vc) (cat)


title: 40_Rudnerlab_ChIPseq_BWX3208

description: ChIP using mCherry antibodies

source_name: Bacillus subtilis PY79, ∆parB::spec, pelB::Psoj mcherry-parB(∆parS) (cat)

value: delta-parB::spec, pelB::Psoj mcherry-parB(delta-parS) (cat)


title: Mouse-human mixture1: Hi-C in-solution ligation

value: mixture of human ESC and mouse embryonic liver


title: Mouse22_IgG

source_name: Stroma and tumor of MBA-MB-231 cells injected into the left intact 4th inguinal mammary fat pad, treated with unspecific IgG antibody, mouse 22


title: Mouse13_IgG

source_name: Stroma and tumor of MBA-MB-231 cells injected into the left intact 4th inguinal mammary fat pad, treated with unspecific IgG antibody, mouse 13


title: Mouse-human mixture1: Hi-C in-nucleus ligation

data_processing:
Library strategy: Hi-C
Hi-C analysis pipeline HiCUP v0.4.2 (running bowtie2 v2.2.3 for mixed human-mouse samples or bowtie v0.12.9 for other samples). HiCUP homepage: www.bioinformatics.babraham.ac.uk/projects/hicup
Hi-C normalisation used Hicpipe v0.93 (Hicpipe homepage: http://compgenomics.weizmann.ac.il/tanay/?page_id=283 )
Hi-C normalisation also used Homer (Homer homepage: http://homer.salk.edu/homer )
Genome_build: hg19 and  mm9
Supplementary_files_format_and_content: The files with extension ".raw" provide the positions of interacting Hi-C read pairs (di-tags). The header line in each file describes each column.

value: H9 (wa09; wicell)


title: Mouse1_IgG

source_name: Stroma and tumor of MBA-MB-231 cells injected into the left intact 4th inguinal mammary fat pad, treated with unspecific IgG antibody, mouse 1


title: Tbp1-Myc ChIP-seq

source_name: fission yeast cells, WT, Tbp1-Myc, Myc ChIP

tag: genotype/variation

value: h+N leu1-32 ade6-210 ura4-DS/E Tbp1-13Myc::kanMX

value: asynchronous cultures

tag: chip antibody

value: rabbit polyclonal anti-Myc (Novus Biologicals, Cat. NB600-336, Lot. A5)


title: Human sample2: Hi-C in-solution ligation


title: Mouse3R_MCF7-EGFP

source_name: Stroma and tumor of MCF7-EGFP cells injected into right cleared 4th inguinal mammary fat pad, mouse 3

treatment_protocol: cells mixed with BD Matrigel Basement Membrane Matrix (BD Biosciences, cat. no. 356234) and injected into the left and right cleared 4th inguinal mammary fat pads; tumors were allowed to grow for 8 weeks (average tumor volume of 500mm3), supplemented with estrogen and progesterone pellets (Innovative Research of America) to support growth.

value: Nude Foxn1nu

value: MCF7-EGFP tumor and mouse mammary tissue


title: Human sample1: Hi-C in-solution ligation


title: Mouse3L_MCF7-EGFP

source_name: Stroma and tumor of MCF7-EGFP cells injected into left cleared 4th inguinal mammary fat pad, mouse 3


title: Mouse1R_MCF7-EGFP

source_name: Stroma and tumor of MCF7-EGFP cells injected into right cleared 4th inguinal mammary fat pad, mouse 1


title: Human sample2: Hi-C in-nucleus ligation


title: Mouse1L_MCF7-EGFP

source_name: Stroma and tumor of MCF7-EGFP cells injected into left cleared 4th inguinal mammary fat pad, mouse 1


title: Cnd2 C703R-FLAG ChIP-seq

data_processing:
Basecalls performed using Illumina CASAVA version 8.
ChIP-seq reads were aligned to the S. pombe genome (20090706; download from http://ebi.edu.au/ftp/databases/pombase/pombe/Chromosome_contigs/OLD/20090706/) using Maq version 0.7.1 for MyC samples or aligned to the S. pombe genome (ASM294v1.18; download from ftp://ftp.ensemblgenomes.org/pub/fungi/release-18/fasta/schizosaccharomyces_pombe/dna/) using BWA version 0.6.2 with the option -n 100 for FLAG samples.
Fragment size was estimated by using HOMER version 4.4.
The scores of the peaks were determined by the subtraction of control read density from treatment read density and calculate 200bp window average.
Genome_build: ASM294v1
Supplementary_files_format_and_content: wig files. Scores represent subtraction of control read density from treatment read density.

source_name: fission yeast cells, cnd2 degron, Cnd2 C703R-FLAG, FLAG ChIP

tag: strain/background

value: h- ade6-M26 ura4-D18 ade6::ade6+-Padh15-skp1-AtTIR1-2NLS-9myc::hphMX, nmt81-Cnd2-IAA17::kanMX + pcnd2-Cnd2C703R-3FLAG-Ura4-ars1-Leu2

tag: tagged protein

value: Cnd2 C703R-FLAG

value: mouse monoclonal anti-Flag M2 (Sigma, Cat. F3165, Lot. SLBH1191V)


title: MDA231_3T3DLL4_-DAPT

source_name: MDA-MB-231 cells cultured with 3T3-L1 cells transiently transfected with DLL4 plasmid, treated with DMSO control

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)

treatment_protocol: MDA-MB-231 cells cultured with 3T3-L1 cells transiently transfected with DLL4 plasmid, treated with DMSO (Sigma-Aldrich, cat. no. D4540) for 6 hours

value: MDA-MB-231 human breast adenocarcinoma cell line (ATCC, HTB-26) and 3T3-L1 mouse embryonic fibroblast cell line (ATCC, CL-173)


title: no-tag FLAG ChIP-seq

source_name: fission yeast cells, WT, no-tag FLAG, FLAG ChIP

value: h- ade6-M26 ura4-D18 ade6::ade6+-Padh15-skp1-AtTIR1-2NLS-9myc::hphMX, nmt81-Cnd2-IAA17::kanMX + pRep4

value: no-tag FLAG

tag: culture condition


title: Cnd2 F701R-FLAG ChIP-seq

source_name: fission yeast cells, cnd2 degron, Cnd2 F701R-FLAG, FLAG ChIP

value: h- ade6-M26 ura4-D18 ade6::ade6+-Padh15-skp1-AtTIR1-2NLS-9myc::hphMX, nmt81-Cnd2-IAA17::kanMX + pcnd2-Cnd2F701R-3FLAG-Ura4-ars1-Leu2

value: Cnd2 F701R-FLAG


title: E13.5 Intermediate progenitor cell-derived neurons

description: intermediate progenitor cell-derived neurons

source_name: Cortex

value: Neuron

value: Embryonic day 13.5


title: input DNA

description: input DNA

data_processing:
Alignment: Sequence reads were obtained using the Illumina Genome Analyzer Pipeline and reads were  mapped to the mouse (July, 2007) genomes (NCBI37/mm9) using BOWTIE aligner program (http://bowtie-bio.sourceforge.net/index.shtml) (Ref: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25.) All reads mapping uniquely with two or fewer mismatches were retained.
Peaks: Peak/significant island detection was performed with the program SICER (http://home.gwu.edu/~wpeng/Software.htm)
Genome Build:
mmuES_gDNA_map-mm9.bed: mm9
mmuES_gDNA.wig: mm9

source_name: Rbp2 f/f ES cells

value: Rbp2 f/f wild type

value: embryonic stem cells


title: MDA231_3T3DLL4_+DAPT

source_name: MDA-MB-231 cells cultured with 3T3-L1 cells transiently transfected with DLL4 plasmid, treated with DAPT

treatment_protocol: MDA-MB-231 cells cultured with 3T3-L1 cells transiently transfected with DLL4 plasmid, treated with 20μM DAPT (GSI-IX) (10mM stock, Selleck Chemicals, cat. no. S2215) for 6 hours

tag: tissue


title: MDA231_3T3GFP_+DAPT

source_name: MDA-MB-231 cells cultured with 3T3-L1 cells transiently transfected with GFP plasmid, treated with DAPT

treatment_protocol: MDA-MB-231 cells cultured with 3T3-L1 cells transiently transfected with GFP plasmid, treated with 20μM DAPT (GSI-IX) (10mM stock, Selleck Chemicals, cat. no. S2215) for 6 hours


title: Cnd2 wt-FLAG ChIP-seq

source_name: fission yeast cells, cnd2 degron, Cnd2 wt-FLAG, FLAG ChIP

value: h- ade6-M26 ura4-D18 ade6::ade6+-Padh15-skp1-AtTIR1-2NLS-9myc::hphMX, nmt81-Cnd2-IAA17::kanMX + pcnd2-Cnd2wt-3FLAG-Ura4-ars1-Leu2

value: Cnd2 wt-FLAG


title: JPN15_DMEM_0.5_BR1

status: Public on Aug 11 2015

city: Baltimore

first: Sean

last: Daugherty

state: Maryland

address: 801 W. Baltimore St.

department: Institute for Genome Sciences

institute: University of Maryland School of Medicine

data_processing:
Illumina reads were mapped to the E2348/69 genome using Bowtie
The mapped reads were counted using HTSeq and normalized and then the differential expression of each gene for one sample compared to another was determined using DESeq v. 1.5.24, and statistical analyses were performed using R-2.15.2, and was represented as the log2 of the fold-change values.
Genome_build: E2348/69

organism: Escherichia coli O127:H6 str. E2348/69

source_name: Escherichia coli cells

growth_protocol: The EPEC strains were grown overnight in Luria-Bertani (LB) media and were inoculated 1:100 into 250 ml of fresh LB or DMEM and were incubated with shaking (225 rpm) at 37˚C to a final optical density (OD600) of approximately 0.5.

extract_protocol:
RNA was isolated from cells grown in LB or DMEM using the Ribopure Bacteria kit (Ambion) and contaminating DNA was removed using the Ribopure Dnase I and also the Turbo DNA-free kit (Ambion).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Escherichia coli E2348/69 sub-strain JPN15


title: JPN15_LB_0.5_BR1


title: JPN15_DMEM_0.5_BR2


title: perABC_DMEM_0.5_BR2

value: Escherichia coli E2348/69, ΔperABC


title: perABC_LB_0.5_BR1


title: MDA231_3T3GFP_-DAPT

source_name: MDA-MB-231 cells cultured with 3T3-L1 cells transiently transfected with GFP plasmid, treated with DMSO control

treatment_protocol: MDA-MB-231 cells cultured with 3T3-L1 cells transiently transfected with GFP plasmid, treated with DMSO (Sigma-Aldrich, cat. no. D4540) for 6 hours


title: 19_Rudnerlab_HindIII_HiC_BWX3266_spo30C170m42C20m

source_name: Bacillus subtilis PY79

treatment_protocol:
Cells were growing in CH medium at 30˚C, resuspended in sporulation medium for 170min at 30˚C, shifted to 42˚C for 20min, fixed by 3% formaldehyde for 30min at room temperature
None

tag: developmental stage

value: sporulation, 30C 170min, 42C 20min

value: spoIIIE36, smcts02 (spec)

value: HindIII


title: perABC_DMEM_0.5_BR1


title: perABC_LB_0.5_BR2


title: E2348_DMEM_0.5_BR2

value: Escherichia coli E2348/69


title: E2348_DMEM_0.5_BR1


title: DL5324

city: Edinburgh

first: Charlotte

middle: Anne

last: Cockram

address: Mayfield Road

department: ICB

institute: University of Edinburgh

data_processing:
Adaptor Sequences were removed using fastx_clipper. (http://hannonlab.cshl.edu/fastx_toolkit/index.html) -  Example: fastx_clipper -a GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCTCGTATG -i DL4900_raw.fasta  -o DL4900_clipped.fasta
Data collapsed using fastx collapser to remove identical sequencing reads (http://hannonlab.cshl.edu/fastx_toolkit/index.html) - Example: fastx_collapser -i DL4900_clipped.fasta -o DL4900_clip_clp.fasta
reads were mapped to the E. coli K12 MG1655 (NC000913.3) genome using Novoalign version 2.07  (www.novocraft.com) - Example: (novoalign -f DL4900_clip_clp.fasta -d NC000913.3.nix -r Random > DL4900.novo)
yPileup was used to generate count data for the whole genome - Example:  pyPileup.py --file_type=novo -f DL4900.novo --tab=NC000913.3.tab --chr=Wholechom.txt.gz -- ignorestrand
Genome_build: Escherichia coli K12 MG1655 NC000913.3
Supplementary_files_format_and_content: txt files including count data for the whole genome

organism: Escherichia coli

source_name: bacterial cell lysates_RecA-ChIP-seq

growth_protocol: Cells were grown in M9 minimal media supplemented with 0.2% casamino acids, 0.5% glucose 5μM CaCl2 and 1mM MgSO4 at 37°C to and OD600nm of 0.2-0.25

extract_protocol:
Cells were collected by centrifugation and washed three times in ice-cold 1X PBS. The pellet was then re-suspended in 250 μl ChIP buffer (200 mM Tris-HCl (pH 8.0), 600 mM NaCl 4% Triton X, Complete protease inhibitor cocktail EDTA-free (Roche)). Sonication of crosslinked samples was performed using the Diagenode Bioruptor® at 30s intervals for 10 min at high amplitude. After sonication, 350 μl of ChIP buffer was added to each sample, the samples were mixed by gentle pipetting and 100 μl of each lysate was removed and stored as ‘input’. Immunoprecipitation was performed overnight at 4°C using 1/100 anti-RecA antibody (Abcam, ab63797). IP samples were then incubated with Protein G Dynabeads® (Life Technologies) for 2 h at room temperature. All samples were washed 3 times with 1 X PBS + 0.02% Tween-20 before re-suspending the Protein G dynabeads in 200 μl of TE buffer (10 mM Tris (pH 7.4), 1 mM EDTA) + 1% SDS. 100 μl of TE buffer was added to the input samples and all samples were then incubated at 65°C for 10 h to reverse formaldehyde crosslinks. DNA was isolated using the MinElute PCR purification kit (Qiagen). DNA was eluted in 50 μl of TE buffer using a 2-step elution. Samples were stored at -20°C.
All samples were processed following NEB’s protocol from the NEBNext® ChIP-Seq library preparation kit.

treatment_protocol: Protein DNA interactions were crosslinked for 10 min at 22.5C with 1% formaldehyde and quenched using glycine to a final concentration of 0.5M

tag: strain details

value: lacIq lacZχ- lacZ::246pal cynX::GmR lacZY::χχ  mhpA::χχχ codBχ- prpEχ- mhpCχ- cynXχ- rph+

value: anti-RecA antibody

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat.#


title: DL4900_input

source_name: bacterial cell lysates_input

value: lacIq lacZχ- lacZ::246pal cynX::GmR lacZY::χχχ  mhpA::χχχ rph+


title: DL5322

value: lacIq lacZχ- lacZ::246pal cynX::GmR lacZY::χ  mhpA::χχχ codBχ- prpEχ- mhpCχ- cynXχ- rph+


title: DL4900


title: E2348_LB_0.5_BR2


title: ΔgadX pH5.5 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.

source_name: ΔgadX pH5.5

growth_protocol: E. coli K-12 MG1655 WT, gadE, gadW and gadX mutant cells were grown to mid-log phase (OD600 = 0.3) aerobically (250 rpm) at 37°C in M9 minimal media supplemented with 0.2% glucose at pH 5.5.

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-gadX

tag: growth phase

value: mid-log phase (OD600 = 0.3)


title: ΔgadX pH5.5 1


title: E2348_LB_0.5_BR1


title: DL5330

value: lacIq lacZχ- lacZ::246pal cynX::GmR lacZY::χχχχχχ  mhpA::χχχ codBχ- prpEχ- mhpCχ- cynXχ- rph+


title: ΔgadE pH5.5 2

source_name: ΔgadE pH5.5

value: delta-gadE


title: ΔgadW pH5.5 2

source_name: ΔgadW pH5.5

value: delta-gadW


title: 409_rep1

city: Shanghai

first: Renyi

last: Liu

state: Shanghai

address: 3888 Chenhua Road

department: Bioinformatics

institute: Shanghai Center for Plant Stress Biology

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads were pre-processed to remove low quality regions and adapter sequences. Reads passed quality filtering and minimum length (Q > 17 and length >= 25 bp) were clean reads and used to map to the cucumber genome using TopHat. The genome data that we used were downloaded from the cucumber genome database (http://cucumber.genomics.org.cn/page/cucumber/index.jsp).
Genome_build: v2i
Supplementary_files_format_and_content: Fasta file with id and clean sequence; the normalized data (reads per million per gene), Cucumber_fruits_RPM.txt

organism: Cucumis sativus

source_name: fruit

growth_protocol: The cucumber line 408 and its near-isogenic line 409 were grown in the Jinliuhuan experimental station of Beijing under standard greenhouse condition. Pest control and water management were performed according to standard practices.

extract_protocol:
Frozen fruit samples were grinded in a mortar with liquid nitrogen, and total RNA was isolated using RNA extraction kit (Huayueyang, China). RNA degradation and contamination was checked on 1% agarose gels, followed by Nano Photometer spectrophotometer (IMPLEN, CA, USA) to examine RNA purity. Qubit RNA Assay Kit in Qubit 2.0 Flurometer (Life Technologies, CA, USA) was used to measure RNA concentration, and RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA) was used to evaluate RNA integrity. Only RNA samples that passed the quality test were chosen for RNA-SEQ analyses.
RNA-seq library construction was performed using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, Ispawich, USA) following manufacturer’s instruction and four index codes were added to attribute sequences to each sample45. Briefly, mRNA was enriched from 3ug total RNA using magnetic beads with Oligo (dT) (Life technologies, CA, USA), and then fragmented using divalent cations under elevated temperature in NEB proprietary fragmentation buffer. Double-stranded cDNAs were synthesized using random hexamers and M-MuLV Reverse Transcriptase (RNase H-), followed by DNA Polymerase I and RNase H. After adenylation of 3’ ends of DNA fragments, NEBNext adaptor oligonucleotides were ligated to cDNA fragments, and AMPure XP beads system (Beckman Coulter, Beverly, USA) were used to select cDNA fragments of approximately 200 bp in length. DNA fragments with ligated adaptor molecules on both ends were selectively enriched using NEB Universal PCR Primer and Index primer in a 10 cycles PCR reaction. Products were purified (AMPure XP beads system) and quantified using the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. RNA-seq library were sequenced on an Illumina Hiseq 2000 platform and 100 bp single-end reads were generated.

treatment_protocol: Early fruits about 2-4 cm were collected from 408 or 409 lines at the same time on the same day. Three-to-five fruits from different plants were pooled together as one biological sample for each cucumber line.

tag: cucumber line

value: fruits

tag: age

value: early fruits about 2-4cm


title: WT pH5.5 1

source_name: WT pH5.5

tag: strain

value: WT


title: DL5328

value: lacIq lacZχ- lacZ::246pal cynX::GmR lacZY::χχχχχ  mhpA::χχχ codBχ- prpEχ- mhpCχ- cynXχ- rph+


title: 409_rep2


title: ChIP-exo RpoS pH5.5 1

data_processing:
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(.).

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Immunoprecipitated DNA

growth_protocol: E. coli K-12 MG1655 WT, GadE-8-myc, GadW-8-myc, and GadX-8-myc tagged strains were grown to mid-log phase (OD600 = 0.3) aerobically (250 rpm) at 37°C in M9 minimal media supplemented with 0.2% glucose at pH 5.5.

extract_protocol: ChIP-seq libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: anti-RpoS (neoclone, WP009)


title: WT

city: Paris

first: Maxime

last: Wery

address: 26 rue d'Ulm

country: France

institute: Institut Curie

data_processing:
Adapter sequences were removed using cutadapt.
14-40 nt reads were mapped to the S. cerevisiae reference genome (retrieved from SGD) using the version 0.12.7 of Bowtie, with a tolerance of 3 mismatches.
Tag densities were obtained using uniquely mapped 19-23 nt reads, after normalization on the total number of 19-23 nt reads that uniquely mapped on ORFs.
Genome_build: S. cerevisiae S288C
Supplementary_files_format_and_content: text file with normalized tag densities

organism: Saccharomyces cerevisiae

source_name: Yeast cells_wildtype

extract_protocol: Small-RNA libraries were constructed according to the Small RNA Sample Preparation Guide (Illumina) using 10-40 nt small RNAs purified from total RNA on 15% TBE-urea PAGE or with a flashPAGE Fractionator (Ambion). Size selection was validated by qualitative analysis of a sample of the purified small RNA fraction on a Small RNA chip in a 2100 bioanalyzer (Agilent).

value: Wild-type


title: DL5326

value: lacIq lacZχ- lacZ::246pal cynX::GmR lacZY::χχχχ mhpA::χχχ codBχ- prpEχ- mhpCχ- cynXχ- rph+


title: ChIP-exo GadX pH5.5 2

value: anti-myc (Santa Cruz Biotech, sc-28207)


title: JPN15_LB_0.5_BR2

value: Escherichia coli E2348/69 sub-strain JPN15


title: ChIP-exo GadX pH5.5 1


title: DL5215

value: lacIq lacZχ- lacZ::246pal cynX::GmR lacZY::χχχ  mhpA::χχχ codBχ- prpEχ- mhpCχ- cynXχ- rph+

value: anti-RecA antibody

value: Abcam


title: ChIP-exo GadW pH5.5 1


title: DL4899

value: lacIq lacZχ- cynX::GmR lacZY::χχχ  mhpA::χχχ rph+


title: xrn1

source_name: Yeast cells_xrn1


title: ChIP-exo GadE pH5.5 1


title: 408_rep2


title: ΔgadW pH5.5 1

value: mid-log phase (OD600 = 0.3)


title: TNFR2-knockout rep3

first: Cambrian

middle: Yangshao

address: 5841 S Maryland Ave

department: Department of Medicine

institute: The University of Chicago

description: TNFR2-knockout colon, replicate 3

data_processing:
Reads were mapped to mm10 using Bowtie2 software with the -r 50 parameter.
A transcriptome assembly was generated with Cufflinks and compared to the reference assembly with Cuffmerge.
Cuffdiff2 was used to calculate FPKM and perform statistical tests for significance between the wildtype and TNFR2-knockout samples.
Genome_build: mm10
Supplementary_files_format_and_content: Comma-separated value file containing individual FPKM measurements for each sample, with statistics

source_name: Colon

extract_protocol:
Total RNA from distal colons of 8 week-old male wildtype C57Bl/6 and TNFR2-/- mice (n=3 each) was isolated using the PureLink RNA kit (Ambion, Life Technologies).
RNA samples were submitted to the Genomic Services Lab at the HudsonAlpha Institute for Biotechnology (Huntsville, AL) for multiplex library preparation, barcoding, mRNA enrichment, and sequencing. Standard Illumina protocols (as of January, 2013) were used.

value: Distal colon

value: 8 wks

tag: Sex

value: Male


title: ΔgadE pH5.5 1

value: delta-gadE


title: GR:KAN1 Mock Shade 2

city: Frederiksberg C

last: Straub

address: Thorvaldsensvej 40

department: Plant and Environmental Sciences

country: Denmark

institute: University of Copenhagen

data_processing:
Basecalls were performed using HiSeq Control Software v2.0.12.0
Quality was assessed using FastQC (v0.10.1) in Galaxy (https://usegalaxy.org, v15.05.rc1).
Galaxy's Tophat2 (v2.0.9) aligned above 90% read pairs of each sample.
Galaxy's Cufflink package (v0.0.7) was used to calculate FPKM and calling of differential expressed genes.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text file; Cuffdiff gene differential expression testing: includes AGI codes, FPKM values, log2 fold changes, test for significance

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Arabidopsis thaliana Columbia-0 and transgenic 35S::FLAG-GR-KAN1 seeds were surface sterilized and sown on Murashige & Skoog (MS) agar plates. After being sown, plates were kept at 4 C for three days, and then incubated at 22 C in long-day conditions.

extract_protocol:
RNA was isolated from seedlings using the roboklon GeneMATRIX universal RNA purification kit
Illumina TruSeq RNA Sample Prep protocol

treatment_protocol: 10-day old seedlings were induced with 50 M Dexamethasone (DEX) or mock (0.5% ethanol) solution for 90 min prior to harvesting for RNA extraction. For shade treatment, plants were mock or DEX treated 45 min prior to the expose to a true shade environment for another 45 minutes.

tag: ecotype


title: WT pH5.5 2

tag: genotype/variation


title: ChIP-exo RpoS pH5.5 2

tag: chip antibody


title: DCR1_AGO1

source_name: Yeast cells_DCR1_AGO1

value: DCR1 AGO1


title: xrn1_DCR1_AGO1

source_name: Yeast cells_xrn1_DCR1_AGO1

value: xrn1-delta DCR1 AGO1


title: WT rep3

description: Wildtype colon; replicate 3

value: Wildtype


title: ChIP-exo GadW pH5.5 2


title: E15.5 preSertoli cells_RNA-seq 3

first: Danielle

last: Maatouk

address: 303 E. Superior St., Lurie 7-250

institute: Northwestern University

data_processing:
Base calls were performed using CASAVA version 1.8.2.
For each sample, 57-63 million reads were generated and over 96% of reads had a quality score equal to or greater than Q30, with a mean quality score of 38, therefore no further filtering was performed.
Reads were aligned to the mm9 transcriptome using Bowtie version 0.12.7 (Langmead et al., 2009) with the following options: -v 3 -a -m 100 --best –strata.
Gene- and isoform-level abundance was estimated using RSEM version 1.2.0 (Li and Dewey, 2011). Expected counts were then quartile normalized and square-root transformed prior to further analysis.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited .txt file contains quartile normalized, square-root transformed expected count data.

source_name: E15.5 preSertoli cells

extract_protocol:
FACS purified E15.5 preSertoli cells were collected from ~165 embryos and pooled into 3 independent biological replicates (DM1, DM2, DM3), each containing ~1 million cells. RNA isolation was performed using the RNeasy Micro Kit according to the manufacturer’s protocol (Qiagen). The RNA was DNaseI digested. QC and quantitation was performed on the Thermoscientific NanoDrop 2000 and the Agilent Bioanalyzer.
Poly-A enriched mRNA libraries were generated from 0.8-1 µg of RNA using the standard Illumina Tru-Seq V2 protocol, then quantitated on the Agilent Bioanalyzer and adapted with index 23, 25 or 27. 7pM of the resulting library pool was run in a single Illumina HiSeq2000 lane to generate 50 bp single-end reads.

value: fetal testis

tag: cell type

value: preSertoli cells


title: 408_rep1

value: fruits

value: early fruits about 2-4cm


title: E15.5 preSertoli cells_RNA-seq 2


title: E15.5 preSertoli cells_RNA-seq 1


title: GR:KAN1 Mock WL 2


title: TNFR2-knockout rep2

description: TNFR2-knockout colon, replicate 2


title: ChIP-exo GadE pH5.5 2

value: anti-myc (Santa Cruz Biotech, sc-28207)


title: TNFR2-knockout rep1

description: TNFR2-knockout colon, replicate 1


title: Col-0 Mock Shade 1

value: wildtype


title: Col-0 DEX Shade 2


title: Col-0 Mock Shade 2


title: WT rep2

description: Wildtype colon; replicate 2


title: GR:KAN1 DEX WL 2


title: WT rep1

description: Wildtype colon; replicate 1


title: MGAS5314-3_OD1.8

status: Public on Aug 10 2015

city: Houston

first: Stephen

middle: B.

last: Beres

state: TX

address: 6670 Bertner Ave.

department: Pathology and Genomic Medicine

institute: Houston Methodist Research Institute

description: isolates are minimally passaged, that is only passaged to the extent required to isolate the bacteria from a normally sterile body site

data_processing:
multiplexed SE libraries were sequenced on an Illumina HiSeq 2500 instrument, basecalling and demultiplexing was done on the instrument, and the RNA-Seq data was output as fastq files
RNA-Seq reads from pre-epidemic M1 strains (MGAS1279, MGAS1438, MGAS5314, SF370)  and  epidemic M1 strains (MGAS1272, MGAS1526, and MGAS2221) were mapped to the epidemic M1 strain MGAS5005 genome (GenBank accession number CP000017) using CLC Genomics Workbench 7.0.4
raw and nomalized (RPKM) values for each gene were determined using CLC Genomics workbench

organism: Streptococcus pyogenes

source_name: cell pellet

growth_protocol: cells were grown in Todd-Hewitt broth supplemented with yeast extract (THY media) at 37 C in atmosphere supplemented with 5% CO2

extract_protocol:
pelleted cells were mechanically disrupted using silica beads, RNA was isolated using RNeasy kit, contaminating DNA was degraded using DNA-free, and rRNA was depleted using Ribo-Zero
resultant RNA was reverse transcribed to cDNA and sequencing libraries were generated using ScriptSeq RNA-seq preparation kit

treatment_protocol: at the desired growth stage, mid-exponential OD 600nm 1.0 or early-stationary OD600nm 1.8, the culture was treated with RNAprotect Bacteria Reagent and cells were harvested by centrifugation

tag: isolate

value: pre-epidemic

tag: sample type

value: invasive infection isolate

value: early-stationary


title: Col-0 DEX WL 2


title: Col-0 Mock WL 2


title: SF370-1_OD1.8


title: MGAS5314-2_OD1.8


title: MGAS2221-2_OD1.8

value: epidemic


title: GR:KAN1 Mock Shade 1


title: MGAS1526-3_OD1.8


title: Col-0 Mock WL 1


title: GR:KAN1 DEX WL 1


title: Col-0 DEX Shade 1


title: MGAS1526-2_OD1.8


title: GR:KAN1 Mock WL 1


title: MGAS2221-1_OD1.8


title: MGAS1526-1_OD1.8


title: MGAS1438-3_OD1.8


title: Col-0 DEX WL 1


title: MGAS1438-2_OD1.8


title: MGAS2221-3_OD1.8


title: SF370-2_OD1.8


title: MGAS1438-1_OD1.8


title: MGAS5314-1_OD1.8


title: GR:KAN1 DEX Shade 1


title: 1101 lard muscle

city: Guelph

first: Angela

last: Cánovas

state: ON

address: 50 Stone Road East

department: Animal Biosciences

country: Canada

institute: University of Guelph

data_processing:
Filtering for quality by NGS quality control tool of CLC Genomics workbench (CLC Bio, Aarhus, Denmark)
RNA-Seq analysis using CLC Genomics Workbench Ver. 7.0
RNA sequencing was performed in 4 sequencing lanes multiplexing 8 samples per lane (7 samples in one lane) on a HiSeq 2000 sequencer analyzer (Illumina, San Diego, CA). Sequence single reads (100 bp) were assembled on the annotated GRCm38 Mus musculus reference genome (release 71; ftp://ftp.ensembl.org/pub/release-71/genbank/mus_musculus/) ().   Quality control analysis was performed using procedures described by Cánovas et al., 2013 using the application NGS quality control tool of CLC Genomics workbench (CLC Bio, Aarhus, Denmark). This tool assesses sequence quality indicators based on the FastQC-project (http:// www.bioinformatics.babraham.ac.uk/projects/fastqc/). Quality was measured taking into account sequence-read lengths and base-coverage, nucleotide contributions and base ambiguities, quality scores as emitted by the base caller and over-represented sequences (Cánovas et al., 2014). All the samples analyzed passed all the QC parameters having the same length (100bp), 100% coverage in all bases, 25% of A, T, G and C nucleotide contributions, 50% GC on base content and less than 0.1% over-represented sequences, indicating a very good quality.
Transcripts levels were normalizing for RNA length and total reads in each sample, by calculating the reads per kilo base per million mapped reads’ (RPKM) for each gene (Mortazavi et al., 2008). To select expressed genes in a given sample a threshold of RPKM ≥ 0.2 was used (Wickramasinghe et al., 2012).  Differential expression analysis between Control vs CR-Soy and comparisons between pairs of CR diets were performed using t-test.
Genome_build: Sequence single reads (100 bp) were assembled on the annotated GRCm38. Mus musculus reference genome (release 71, ftp://ftp.ensembl.org/pub/release-71/genbank/mus_musculus/).
Supplementary_files_format_and_content: The .txt files report RPKMs and t-test results

source_name: lard muscle

extract_protocol:
Liver and the entire hindlimb skeletal muscle were removed and RNA was extracted from tissue samples using the Trizol Reagent (Invitrogen)
TrueSeq RNA Sample Preparation kit (Illumina, San Diego, CA)

tag: gender

value: male

tag: protocol

value: lard

tag: tissue

value: muscle


title: GR:KAN1 DEX Shade 2


title: 1125 fish liver

source_name: fish liver

value: fish

value: liver


title: otpR mutant

first: Qingmin

address: No. 2 Yuanming west Road

institute: China Agricultural University

data_processing:
Genome Analyzer System Software
All sequences were examined for possible sequencing errors. The raw sequence data was filtered by removing reads that contained adaptor sequences, consisted of >5% ambiguous residues (Ns), or had the majority base quality of <5.
Our reads were aligned with the B. melitensis 16M genome (NC_003317 and NC_003318) and annotated gene sets obtained from NCBI (ftp://ftp.ncbi.nlm.nih.gov/genomes/) using the Short Oligonucleotide Analysis Package (SOAP)
cDNAs with matches to the reference genome of >80% were retained for further analysis. Those sequencing reads that matched annotated genes in the B. melitensis 16M genome reflect the genes transcribed under the given experimental conditions.
Gene expression was quantified as reads per kilobase of coding sequence per million reads (RPKM algorithm);
Genome_build: NC_003317, NC_003318
file format and content: MapReadsStat files contain brief statistics of the total number of Sequencing reads and the result of alignment. Mismatches no more than 2 bases were allowed in the alignment. RPKM file has the coverage of each gene, expression of gene (RPKM), total number of reads that aligned to gene, the description of gene and so on. The Series GeneDiffExp file has the statistics of transcriptional level of genes in B. melitensis 16M and otpR.

organism: Brucella melitensis

source_name: Brucella melitensis otpR mutant

growth_protocol: Cells were grown in 100 mL of Tryptic Soy Broth (TSB; BDTM; BactosTM Tryptone 17 g/L, Bacto Soytone 3 g/L, NaCl 5 g/L, K2HPO4 2.5 g/L, glucose 2.5 g/L, final pH=7.3) into a 500-mL water bath shaker (180 rpm) at 37 0C until mid-log phase (OD=0.6~0.7).

extract_protocol:
The cell culture was then collected and RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany) was added to the cultures according to the manufacturer’s instructions. The Brucella RNAs for solexa/illumina sequence were isolated and purified with RNeasy Mini System (Qiagen, Hilden, Germany) according to the manufacture’s protocol. RNA was eluted from the column using RNase-free water. Total RNA was incubated with DNase (Ambion, Foster City, CA) to remove remaining DNA. Subsequently, RNA was purified using two phenol-chloroform extractions and one chloroform extraction, followed by the precipitation of RNA and resuspended in RNAase free TE buffer (10Mm Tris, 1Mm EDTA; pH 8.0; Ambion, Foster City, CA).
Each mRNA sample was fragmented into short sequences with divalent cations under elevated temperature. Using these short fragments as templates, first-strand cDNA was synthesized with random hexamer primers and reverse transcriptase (Invitrogen, Carlsbad, CA). The second-strand DNA was synthesized using RNase H (Invitrogen, Carlsbad, CA) and DNA polymerase I (New England Biolabs, Beverly, MA, USA), respectively. The amplified fragments were purified with QiaQuick PCR Purification kit (Qiagen, Hilden, Germany) and resolved with EB buffer for the end preparation and poly (A) addition. The DNA libraries were then prepared according to the manufactuer Illumina’s protocols.

treatment_protocol: Briefly, the total cells of each sample were harvested at stationary phase by centrifugation for 10 min at 5,000 rpm, washed in an equal volume of pH 4.4 TSB (for adapted culture), and reharvested. The pellets were resuspended in TSB (100 ml) at the same pH 4.4 and incubated for 2 h (37 0C). Adapted cultures were washed and resuspended in pH 3.4 TSB for challenge and incubated for another 2 h (370C).

value: otpR mutant


title: 16M

source_name: Brucella melitensis 16M


title: 1159 soy liver

source_name: soy liver

value: soy


title: SF370-3_OD1.8


title: MGAS1279-3_OD1.8


title: 1101 lard liver

source_name: lard liver


title: MGAS1279-1_OD1.8


title: 1121 control liver

source_name: control liver

value: control


title: 1121 control muscle

source_name: control muscle


title: MGAS1272-1_OD1.8


title: MGAS1272-2_OD1.8


title: 1141 soy muscle

source_name: soy muscle


title: 1130 lard muscle


title: MGAS1272-3_OD1.8


title: 1141 soy liver


title: SF370-2_OD1.0

value: mid-exponential


title: SF370-3_OD1.0


title: SF370-1_OD1.0


title: 1124 fish liver


title: MGAS5314-3_OD1.0


title: 1120 control liver


title: 1120 control muscle


title: 1124 fish muscle

source_name: fish muscle


title: MGAS5314-1_OD1.0


title: MGAS1279-2_OD1.8


title: MGAS5314-2_OD1.0


title: MGAS2221-3_OD1.0


title: 1102 lard muscle


title: MGAS2221-1_OD1.0


title: MGAS2221-2_OD1.0


title: 1073 soy muscle


title: 1102 lard liver


title: MGAS1526-3_OD1.0


title: MGAS1526-2_OD1.0


title: 1123 fish muscle


title: 1130 lard liver


title: 1123 fish liver


title: MGAS1438-3_OD1.0


title: P15 (SRSF2 P95H)

city: New York

first: James

middle: L.

last: Manley

state: New York

address: 1212 Amsterdam Ave

department: Dept. of Biological Sciences

institute: Columbia University

data_processing:
We use RTA (Illumina) for base calling and bcl2fastq for converting BCL to fastq format, coupled with adaptor trimming.
Reads were mapped to the human genome (NCBI GRCh37) using TopHat v2.0.4 with the arguments “--max-multihits 10 --no-coverage-search --mate-inner-dist 100”.
The number of read fragments mapping to each gene was counted using HTSeq 0.6.1p1.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include counts of read pairs

source_name: K562_SRSF2 P95H mutant

extract_protocol:
Total RNA was isolated using the miRNeasy Mini Kit (Qiagen).
Poly(A)+ RNAs were selected and Illumina libraries were prepared using TruSeq RNA Sample Prep Kit. Libraries were then sequenced using Illumina HiSeq2000.

tag: cell line

value: CML-derived K562

tag: tissue source

value: bone marrow

value: erythroleukemia cells

value: mutant SRSF2 P95H


title: 1095 control liver


title: P9 (SRSF2 P95H)


title: MGAS1438-2_OD1.0

value: pre-epidemic

tag: growth phase


title: P38 (SRSF2 P95H)


title: P22 (SRSF2 P95H)


title: W42 (wild-type SRSF2)

source_name: K562_wild type SRSF2

value: wild-type SRSF2


title: 1071 control muscle


title: MGAS1438-1_OD1.0

value: invasive infection isolate


title: 1073 soy liver


title: cph2 deletion mutant rep 2

city: Irvine

first: Haoping

address: Med. Sci. I, Rm D234

department: Dept. of Biological Chemistry

institute: University of California

data_processing:
Processing & Demultiplexing: Illumina Casava 1.7
Alignments: Illumina Eland v2e with default parameters
Gene Expression Results / RPKM values: Illumina Casava VDC 1.7 on the reference genome Ca21
Differential Analysis: Cyber-T
Genome_build: C. albicans SC5314 A21 (Ca21)
Supplementary_files_format_and_content: tab-delimited text file that contain differential analysis of WT vs Cph2 deletion

organism: Candida albicans

source_name: fungus

growth_protocol: Wild type and cph2 mutant cells were grown in YPD overnight to OD600 >10

extract_protocol:
Total RNA was extracted using the RiboPure kit from Amgion along with Dnase digestion as in the manual
Library was constructed using the NuGen Encore Complete RNA-Seq Library Systems kit
RNA-Seq was carried out using the Illumina HiSeq2500

treatment_protocol: mRNA was enriched using the Invitrogen Dynabeads mRNA purification kit

value: cph2 deletion mutant


title: cph2 deletion mutant rep 1


title: W36 (wild-type SRSF2)


title: MGAS1279-3_OD1.0

value: epidemic


title: wild type rep 2

value: wild type


title: 1067 fish liver

value: male


title: MGAS1279-2_OD1.0


title: W33 (wild-type SRSF2)


title: W19 (wild-type SRSF2)


title: 1100 lard liver

value: lard


title: dCas9-VPR>Quas 2

city: Boston

first: Norbert

last: Perrimon

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

description: cells were transfected with Actin:dCas9-VPR together with the sgRNAs targeting luciferase reporter promoter, serving as negative control

data_processing:
align to genome with tophat v2 using default parameters, with self built bowtie2 genome database according to drosophila melanogaster genome assembly r5.51.
read number counts obtained with Htseq, with --mode=union, --stranded=no
data normalization and identifying DEG with Deseq package with built in functions
Genome_build: Drosophila genome r5.51 from flybase
Supplementary_files_format_and_content: tab deliminated .txt file with gene name and read number count for each gene

organism: Drosophila melanogaster

source_name: S2R+ cells

extract_protocol:
Total RNA extracted with TRIZOL, followed by purification using Qiagen Rneasy MinElute Cleanup Kit, including on-column DNAse treatment.
Standard multiplexing mRNA sequencing library following Illumina protocol

treatment_protocol: Cells were transfected with Actin:dCas9-VPR, together with a non-targeting sgRNA (negative control), or a pool of 5 sgRNAs targeting either Twist, Snail, or a combination of both pools.

tag: guide rna

value: a pool multiple guides targeting upstream region of luciferase reporter

tag: treatment

value: transfected with Actin:dCas9-VPR together with the sgRNAs targeting luciferase reporter promoter (serving as negative control)

value: S2R+ cells


title: wild type rep 1


title: 1095 control muscle

tag: strain

value: control

value: muscle


title: 1100 lard muscle


title: MGAS1526-1_OD1.0

value: mid-exponential


title: K562 parental cells

source_name: K562 parental cells

value: CML-derived K562

value: bone marrow


title: 1067 fish muscle

value: fish


title: MGAS1272-3_OD1.0

value: pre-epidemic


title: MGAS1279-1_OD1.0


title: 1065 soy liver

value: soy

value: liver


title: MGAS1272-2_OD1.0

value: invasive infection isolate


title: dCas9-VPR>Quas 1


title: dCas9-VPR>Twist&Snail 2

description: cells were transfected with Actin:dCas9-VPR together with the sgRNAs to activating both Snail and Twist

value: a pool of multiple guides targeting upstream region of gene snail and twist

value: transfected with Actin:dCas9-VPR together with the sgRNAs to activate both Snail and Twist


title: 1065 soy muscle

value: male


title: MGAS1272-1_OD1.0


title: DN_thymocytes_rep2

city: Durham

first: Zachary

last: Carico

state: North Carolina

address: 207 Research Drive

department: Immunology

institute: Duke University

description:
HindIII-digested DNA
library strategy: 4C-seq

data_processing:
Basecalls performed using CASAVA
Viewpoint sequences were trimmed from 5' end of reads using fastx_trimmer
Alignment to genome was performed using Bowtie with parameters -v 0 -m 10 --all --best --strata
Reads were mapped to HindIII restriction fragments using Python scripts from Stadhouders et al., Multiplexed chromosome conformation capture sequencing for rapid genome-scale high-resolution detection of long-range chromatin interactions, Nature Protocols 8 (509-524), 2013. In short, genome-wide maps of HindIII fragments were generated and aligned reads were mapped to these fragments. Output generated is in .bed format.
Reads were normalized to mapped reads per million.
Genome_build: mm9

source_name: thymocytes

extract_protocol:
Thymocytes from litters of 3 week old C57BL/6 Rag2-/- mice were crosslinked and chromatin was subject to HindIII restriction digest. Sticky ends were religated using T4 DNA ligase and DNA was purified from nuclear lysates. DNA was subsequently digested with DpnII and re-ligated with T4 DNA ligase to make 4C library templates.
Inverse PCR using primers containing Illumina HiSeq adaptors was performed on 4C templates. Libraries were amplified from 4 viewpoints: TEA, INT1, INT2, and E-delta.

value: thymocytes


title: naïve_B_rep2

source_name: spleen

value: wild type


title: dCas9-VPR>Twist 1

description: cells were transfected with Actin:dCas9-VPR together with the sgRNAs to activating Twist

value: a pool of multiple guides targeting upstream region of gene twist

value: transfected with Actin:dCas9-VPR together with the sgRNAs to activate Twist


title: dCas9-VPR>Snail 2

description: cells were transfected with Actin:dCas9-VPR together with the sgRNAs to activating Snail

value: a pool of multiple guides targeting upstream region of gene snail

value: transfected with Actin:dCas9-VPR together with the sgRNAs to activate Snail

value: S2R+ cells


title: naïve_B_rep1


title: dCas9-VPR>Twist 2


title: DN_thymocytes_rep1


title: OKMS MEF rep 2

status: Public on Aug 08 2015

first: Keisuke

last: Kaji

address: Edinburgh Bioquarter, 5 Little France Drive

department: MRC Centre for Regenerative Medicine

data_processing:
Read processing was performed as described in Islam et al. Genome Research, 21, 1160-1167, doi:10.1101/gr.110882.110 (2011).
Sequenced reads were trimmed for adaptor sequence, then mapped to mm10 whole genome using bowtie v0.12.7 with parameters --phredQualityScoreBase-quals -k MaxAlternativeMappings -v MaxAlignmentMismatches --best --strata. Unmapped reads were discarded.
Gene expression read counts were exported and low expression transcripts (no more than 5 reads in any sample) were filtered out.
Genome_build: mm10_UCSC
Supplementary_files_format_and_content: tab-delimited text file includes read counts per gene

source_name: MEF_OKMS MEF

growth_protocol: MEFs and ES Cells were cultured in GMEM + 100Units LIF. Intermediate reprogramming samples were cultured in the presence of dox and VitC for 10 or 15 days.

extract_protocol:
Nucleospin RNA XS kit (Macherey-Nagel, Ref. 740902.10)  was used
Library was constructed as published in Islam et al. Genome Research, 21, 1160-1167, doi:10.1101/gr.110882.110 (2011).

treatment_protocol: 20,000 to 100,000 cells from each sample were sorted by flow cytometry.

value: mouse embryonic fibroblast cell (MEF)


title: wt MEF rep 2

source_name: MEF_wt MEF


title: OKMS iPSCs 2i rep 2

source_name: MEF_OKMS iPSCs 2i

value: induced Pluripotent Stem cells (iPSCs)


title: wt MEF rep 1


title: MKOS MEF rep 1

source_name: MEF_MKOS MEF


title: OKMS iPSCs -dox rep 2

source_name: MEF_OKMS iPSCs -dox


title: OKMS iPSCs 2i rep 1


title: OKMS iPSCs -dox rep 1


title: MKOS iPSCs -dox rep 2

source_name: MEF_MKOS iPSCs -dox


title: MKOS iPSCs -dox rep 1


title: MKOS iPSCs 2i rep 1

source_name: MEF_MKOS iPSCs 2i


title: OKMS MEF rep 1


title: MKOS iPSCs 2i rep 2


title: TNG MKOS ESCs rep 1

source_name: ESCs_TNG MKOS ESCs

value: embryonic stem cells (ESCs)


title: TNG ESCS rep 1

source_name: ESCs_TNG ESCS


title: dCas9-VPR>Snail 1


title: TNG OKMS ESCs rep 2

source_name: ESCs_TNG OKMS ESCs


title: TNG OKMS ESCs rep 1


title: 3N+ (Ecad+) OKMS rep 3

source_name: MEF_3N+ (Ecad+) OKMS

value: mouse embryonic fibroblast cell (MEF); intermediate reprogramming population

tag: cell subtype

value: CD44- ICAM1+, Nanog-GFP+


title: 2N- (Ecad-) OKMS rep 3

source_name: MEF_2N- (Ecad-) OKMS

value: CD44- ICAM1-, Nanog-GFP-


title: D6 rep 1


title: 3N- (Ecad+) OKMS rep 3

source_name: MEF_3N- (Ecad+) OKMS

value: CD44- ICAM1+, Nanog-GFP-


title: dCas9-VPR>Twist&Snail 1

source_name: S2R+ cells

value: a pool of multiple guides targeting upstream region of gene snail and twist


title: 3N- (Ecad-) OKMS rep 3

source_name: MEF_3N- (Ecad-) OKMS


title: TNG ESCS rep 2


title: 3N- (Ecad+) MKOS rep 3

source_name: MEF_3N- (Ecad+) MKOS


title: 2N- (Ecad+) OKMS rep 3

source_name: MEF_2N- (Ecad+) OKMS


title: MKOS MEF rep 2


title: 3N- (Ecad-) OKMS rep 2


title: 3N+ (Ecad+) MKOS rep 3

source_name: MEF_3N+ (Ecad+) MKOS


title: 3N+ (Ecad+) OKMS rep 2


title: E14 rep 2


title: E14 rep 1


title: 2N- (Ecad-) OKMS rep 2


title: 2N- (Ecad+) MKOS rep 2

source_name: MEF_2N- (Ecad+) MKOS


title: 2N- (Ecad+) OKMS rep 2


title: D6 rep 2


title: 3N- (Ecad+) OKMS rep 2


title: TNG MKOS ESCs rep 2


title: 3N+ (Ecad+) OKMS rep 1


title: 3N- (Ecad+) MKOS rep 2


title: 2N- (Ecad-) OKMS rep 1


title: 3N- (Ecad-) OKMS rep 1


title: 3N- (Ecad+) OKMS rep 1


title: 3N+ (Ecad+) MKOS rep 2


title: 2N- (Ecad+) MKOS rep 1


title: 3N+ (Ecad+) MKOS rep 1


title: 3N- (Ecad+) MKOS rep 1


title: 2N- (Ecad+) MKOS rep 3


title: Epi_2

status: Public on Aug 07 2015

first: Michael

last: Rendl

state: NY

address: 1428 Madison Avenue

institute: Mount Sinai School of Medicine

data_processing:
All raw RNA sequencing reads were mapped to the mouse genome (mm10) with TopHat v2.0.3 coupled with the Bowtie2 aligner with default parameters.
Transcriptomes were assembled and fragments per kilo-base per million reads (FPKM) for each gene were computed with Cufflinks v2.1.1 with default parameters.
Genome_build: mm10

source_name: E14.5 embryonic skin

extract_protocol:
Total RNA obtained from FACS-sorted cells was purified with the Absolutely RNA Nanoprep kit (Agilent), quantified with the NanoDrop spectrophotometer (Thermo Scientific) and measured for quality control by the Agilent Bioanalyzer. Samples with RIN (RNA integrity number) scores 8.8 and higher were further processed. 6ng starting material was reverse transcribed and amplified to 5-7µg cDNA with the RNA Ovation RNA-seq System V2 (NuGEN).
From 100ng amplified cDNA sequencing libraries were generated with 16 unique barcoded adapters (8 samples x 2 replicates) using the Ovation Ultralow DR Library System (NuGEN).

value: skin

tag: age

value: embryonic day 14.5


title: Mc_1


title: 2N- (Ecad+) OKMS rep 1


title: Sch_2


city: Yantai

first: Ye

last: Zhao

state: Shandong Province

address: Qingquan Road No.30

institute: Yantai University

description: Sample 1

data_processing:
The original image data was transferred into sequence data by base calling (using CASAVA version 1.5+), (defined as ‘raw reads’) and saved as fastq files that include the detailed reads sequences and the reads quality information.
To obtain clean reads, it is necessary to remove the dirty raw reads prior to data analysis. This process encompasses the following procedures: (1) remove reads with adaptors; (2) remove reads in which unknown bases are greater than 10%; (3) remove low-quality reads (the percentage of the low quality bases of quality value ≤ 5 is more than 50% in a read)
A comparison of “clean reads” by SOAPaligner/soap2(parameters:-m 0 -x 1000 -s 28 -l 32 -v 2 -r 2) was carried out using the reference databases from large-scale transcriptome profiling
genome build:PMID 22428017
Supplementary_files_format_and_content: details in the 'readme.txt'

organism: Apostichopus japonicus

source_name: Apostihopus japonicus intestine

extract_protocol:
Total RNA from NA,DA and AA intestines was extracted and DNase-treated using RNeasy Mini Kit and RNase-Free DNase Set (Qiagen, Germany), following the manufacturer’ s instructions.
The quality and concentration of RNA were measured by NanoDrop 1000 (Thermo) after which the mRNA in total RNA was enriched by using the oligo(dT) magnetic beads. After the addition of fragmentation buffer, the mRNA was interrupted and formed short fragments (~200 bp). The first strand cDNA was then synthesized by the random hexamer-primer, using the mRNA fragments as templates. Buffer, dNTPs, RNase H and DNA polymerase I were added to synthesize the second strand. The double strand cDNA was purified using the QiaQuick PCR extraction kit, and washed with EB buffer so as to facilitate end repair and the addition of a single nucleotide A (adenine). Finally, sequencing adaptors were ligated to the fragments. The required fragments were purified by means of agarose gel electrophoresis and enriched by PCR amplification.

tag: Stage

value: non-aestivation (NA)

value: intestine


title: Epi_1


title: AA

description: Sample 3

value: arousal from aestivation (AA)


title: Fb_2


title: DA

description: Sample 2

value: deep aestivation (DA)


title: Neg_2


title: Mc_2


title: DC_2


title: Sch_1


title: DCSch_1


title: Neg_1


title: Pc_1


title: DCSch_2


title: DC_1


title: Pc_2


title: Fb_1


title: Axin2rtTA- CAGATC

city: San Francisco

first: Bruce

middle: M

last: Wang

address: 513 Parnassus Ave

department: Medicine

institute: University of California San Francisco

data_processing:
Processing and analysis of FASTQ files were performed using Galaxy.
A custom Galaxy instance (UC Davis bioinformatics Core) was run on Amazon AWS.
Sequenced reads were trimmed for adaptor sequence using Scythe v1.21, then mapped to mm10 whole genome using TopHat v2.0.11.
Cuffdiff v2.2.2 was used for differential gene expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file.

source_name: Hepatocytes

extract_protocol:
Hepatocytes were isolated from 8 week old Axin2rtTA;TetO-H2B-GFP mice given doxycycline in drinking water for 7 days. After removal of non-parenchymal cells, the hepatocytes were sorted into GFP+ versus GFP- populations. RNA was isolated with QIAGEN RNAeasy Mini kit. cDNA barcoded libraries were made using TruSeq Stranded mRNA Sample Prep Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: post natal day 63


title: Axin2rtTA- GTGAAA


title: Axin2rtTA- CGATGT


title: Axin2rtTA+ GTGAAA


title: Axin2rtTA+ CGATGT


title: Axin2rtTA+ CAGATC


title: LNA-48

city: Chapel Hill

first: Praveen

last: Sethupathy

state: NC

address: 120 Mason Farm Rd

institute: UNC Chapel Hill

data_processing:
Mapsplice alignment to genome
Gene expression analysis using RSEM
Genome_build: mm9

source_name: liver, 20mg/kg LNA29a, 20mg/kg LNA29bc

extract_protocol: Livers were removed and flash frozen in liquid nitrogen. RNA was extracted with the Norgen Total RNA Purification kit.

treatment_protocol: mice were dosed iv tail vein with 20mg/kg LNA29a and 20mg/kg LNA29bc. Seven days later, the mice were fasted overnight and euthanized by cervical dislocation without anesthesia; organs were collected and flash frozen in liquid nitrogen.

tag: Sex

value: female


title: LNA-50


title: LNA-52


title: wt 49

source_name: liver, saline

treatment_protocol: mice were dosed iv tail vein with saline. Seven days later, the mice were fasted overnight and euthanized by cervical dislocation without anesthesia; organs were collected and flash frozen in liquid nitrogen.


title: wt 47


title: wt 53


title: wt 43


title: LNA-46


title: wt 45


title: Tox4 esiRNA (rep. 1)

city: Dresden

first: Maciej

last: Paszkowski-Rogacz

address: Tatzberg 47/49

department: UCC / Medical Faculty and University Hospital Carl Gustav Carus

country: Germany

institute: Technische Universität Dresden

data_processing:
Illumina Casava 1.8 software used for basecalling.
Reads were mapped to the mouse genome with STAR 2.3.0e, using transcriptome from Ensembl 73 as a reference.
Fragments Per Kilobase of an expressed transcript per Megabase of library size (FPKEM) were calculated using an in-house developed script. Counts of reads mapped to exons of each gene were normalized to a size of expressed and mappable portion of the gene and to a total number of reads in the sample. Mappable regions of genes were estimated using as a criteria existence of mapped reads in any of the analyzed samples.
Genome_build: GRCm38.p1
Supplementary_files_format_and_content: tab-delimited text files include FPKEM values for each Sample

source_name: Epiblast stem cells (OE7 )

growth_protocol: The Oct4-GFP EpiSCs line OE7 was cultured on Fibronectin (Millipore)-coated plates in N2B27 medium, supplemented with 20 ng/ml Activin A and 12 ng/ml Fgf2

extract_protocol:
RNA was isolated using RNeasy Mini kit (Qiagen), poly(A) fractions were purified by double selection on oligo(dT) beads and cDNA prepared as described previously (Marks et al., 2012)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 1.5x105 EpiSCs cells were reverse transfected with 1000 ng Luc esiRNA (control) and Tox4 esiRNA and  2 µl lipofectamine 2000 in fibronectin-coated 6-well plates.

tag: origin

value: isolated from mouse post-implantation embryo

value: Oct4-Gip transgene

tag: passages

tag: RNAi


title: Tox4 esiRNA (rep. 2)


title: Luc esiRNA (rep. 2)

value: Luc


title: human_fetal_panc_54to57dpc_RNAseq replicate 2

city: La Jolla

first: Maike

last: Sander

address: 2880 Torrey Pines Scenic Dr.

institute: UC San Diego

data_processing:
Quality Control. Quality of sequencing data is analyzed using the software FastQC v0.10.1. The results are examined to determine if samples are of questionable quality on an array of metrics.
Mapping. Alignment of sequencing data to reference genomes is performed with the software RNA-Star 2.3.0e. Parameters are set to default and reads are mapped to references along with splice junction databases.
Gene Expression Quantification. To obtain gene expression values, several quantification methods are used (Sailfish 0.6.3, Cufflinks 2.2.0). Expression values are calculated for entries in the gene annotation references.
Genome_build: hg19
Supplementary_files_format_and_content: Txt file of ensemble identifiers with RPKMs of samples used in study

source_name: Human fetal pancreata

growth_protocol: Human embryonic pancreata at day 54 to 57 of gestation were from the University of Washington Birth Defects Research Laboratory.

extract_protocol:
Human embryonic pancreata were lysed in Trizol (Life Technologies) for extraction of total RNA. Residual contaminating genomic DNA was removed using the Turbo DNase kit (Ambion). mRNA was isolated from 2 μg of DNA-free total RNA using the Dynabeads mRNA Purification kit (Life Technologies).
Strand-specific RNA-seq libraries were prepared as previously described (Parkhomchuk et al., 2009), with minor modifications. Briefly, following RNA purification, mRNA was primed with Olig(dT)s and random hexamers and reverse-transcribed to first-strand cDNA. Residual dNTPs were removed using Illustra MicroSpin G-25 columns (GE Healthcare). In the second-strand synthesis reaction, dUTPs were used instead of dTTPs. The double-strand cDNA was fragmented using a Bioruptor Sonicator for 60 cycles of 30 sec on and off. After end-repair and adenine base addition, the cleaved double-strand cDNA fragments were ligated to Pair-end Adaptor Oligo Mix (Illumina) and size-fractionated on a 2% agarose gel (Sigma). cDNA fragments of 200±25 bp were recovered, and incubated with uracil-N-glycosylase (UNG) to digest the second-strand cDNA. Purified single-strand cDNA was then used as template for 15 cycles of amplification using pair-end PCR primers (Illumina). The amplified products were separated on a 2% agarose gel and a band between 225-275 bp excised.

tag: developmental stage

value: fetus

value: 54-57 days post conception (gestation)

value: pancreas


title: Luc esiRNA (rep. 1)


title: hESC_derived_liverprogenitors_RNAseq replicate 1

description:
FGC0186_s_7
liver_day8_1

source_name: hESC-derived liver progenitors

growth_protocol: Hepatic endoderm was derived by treating the definitive endoderm stage (Day 2),with 50ng/ml BMP4 (Millipore) and 10ng/ml FGF2 (Millipore) in RPMI media (Mediatech) supplemented with 0.2% (vol/vol) FBS (HyClone) with daily feeding for six days. Suspension culture was used.

extract_protocol:
hESC-derived liver progenitors were lysed in Trizol (Life Technologies) for extraction of total RNA. Residual contaminating genomic DNA was removed using the Turbo DNase kit (Ambion). mRNA was isolated from 2 μg of DNA-free total RNA using the Dynabeads mRNA Purification kit (Life Technologies).
Strand-specific RNA-seq libraries were prepared as previously described (Parkhomchuk et al., 2009), with minor modifications. Briefly, following RNA purification, mRNA was primed with Olig(dT)s and random hexamers and reverse-transcribed to first-strand cDNA. Residual dNTPs were removed using Illustra MicroSpin G-25 columns (GE Healthcare). In the second-strand synthesis reaction, dUTPs were used instead of dTTPs. The double-strand cDNA was fragmented using a Bioruptor Sonicator for 60 cycles of 30 sec on and off. After end-repair and adenine base addition, the cleaved double-strand cDNA fragments were ligated to Pair-end Adaptor Oligo Mix (Illumina) and size-fractionated on a 2% agarose gel (Sigma). cDNA fragments of 200±25 bp were recovered, and incubated with uracil-N-glycosylase (UNG) to digest the second-strand cDNA. Purified single-strand cDNA was then used as template for 15 cycles of amplification using pair-end PCR primers (Illumina). The amplified products were separated on a 2% agarose gel and a band between 225-275 bp excised.

tag: cell type

value: hESC-derived liver progenitors