title: Round spermatids

description: Gene expression data from round spermatids

data_processing:
Basecalling using Illumina Casava1.8.2 software
Map to mouse genome mm10 using Tophat(v 2.0.9)
Bam to Bedgraph using genomeCoverageBed
Bedgraph to bigwig using UCSC bedGraphToBigWig
For each gene, we first merged all exons from different isoforms, then counted the mapping reads and normalized as RPKM values.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig file (UCSC bigwig in an indexed binary format. http://genome.ucsc.edu/goldenPath/help/bigWig.html)

extract_protocol:
Total RNAs from cultured cells (0.5 x 10^6 - 1 x 10^7) were extracted with Trizol (Invitrogen) according to the manufacturer’s instruction, followed by DNase I treatment at 37 °C for 30 mins (Ambion, DNA-freeTM Kit). The polyadenylated RNA population was purified by oligo(dT) magnetic beads (Invitrogen) from 5 μg of total RNAs.
Library was prepared by using Illumina TruSeq Stranded Total RNA HT Sample Prep Kit (P/N 15031048) and Illumina TruSeq Small Sample Prep Kit (P/N 15004197).


title: mouse_liver_nuclei_totalRNA_miCLIP

status: Public on Jun 29 2015

type: SRA

city: Heidelberg

first: Bastian

last: Linder

address: Meyerhofstraße 1

department: Genome Biology Unit

country: Germany

institute: European Molecular Biology Laboratory (EMBL)

description: Nuclei were prepared by Iodixanol gradient as described in Graham 2001 [PMID: 18228353]. Total RNA was extracted using Trizol and depleted of (pre-)rRNA using RiboMinus (Invitrogen).

library_source: transcriptomic

data_processing:
Basecalls performed with Casava 1.8.2
Reads were trimmed for adaptor sequence using flexbar 2.5 (flexbar -r PE_R1.fastq -p PE_R2.fastq -f i1.8  -a flexbar_adapters.fasta --pre-trim-phred 30 -n 36 -s).
Paired-end fastq files were demultiplexed according to their experimental barcode using pyBarcodeFilter.py (pyBarcodeFilter.py -f PE_R1_trimmed.fastq -r PE_R2_trimmed.fastq -b pyCRAC_barcode.txt) and the random barcode was transferred to the header of the forward reads (awk -F "##" '{sub(/.../,"##"$2, $2); getline($3); $4 = substr($3,1,2); $5 = substr($3,3); print $1 $2 $4"\n"$5}').
For the HEK293 mRNA experiment, data from the four replicates was combined before PCR duplicate removal.
PCR-duplicates were removed based on their sequence with the pyFastqDuplicateRemover.py script of the pyCRAC suite [Webb et al. 2014; PMID 24393166].
Headers compatible for subsequent analysis with the CIMS software were generated using in-house bash scripts.
For paired end data, reverse reads were reverse complemented and assigned with the reverse complement of the random barcode using custom bash and perl scripts. This avoids collapsing of read pairs in the alignment-based PCR duplicate removal step of the CIMS analysis (see below).
Reads were aligned in single-end mode using Novoalign (novoalign parameters:  -t 85 F FA -l 16 -s 1 -o Native -r None -c 36 -a).
The CIMS pipeline [Moore et al. 2014; PMID: 24407355] was used to collapse PCR duplicates based on their mapped coordinates and to determine the unique tag coverage (k) and the number of C-->T transitions (m) for each nucleotide. No FDR filter was applied.
C-->T transition sites were filtered by the number transitions observed (m) and the ratio of transitions to unique tags covering that position (m/k). The filter for the HEK293 dataset was, m >=2 and 1% >=mk >= 50%. The filter used for the mouse nuclear RNA was m2 and 1.6% >=mk >= 50%
For CITS miCLIP, reads were processed and mapped identically. The CITS pipeline [Weyn-Vanhentenryck et al. 2014; PMID: 24613350] was then used to determine sites with significant (p < 0.05) crosslinking-induced cDNA truncations.
genome build: hg19 , mm10 and a custom build of human 18S and 28S rRNA (Acc.No. NR_003286.2 and NR_003287.2)
bedgraph files of unique CIMS miCLIP tags. Score represents the number of reads covering that position.
bedgraph files of unique CITS miCLIP tags. Score represents the number of reads covering that position.
bedgraph files of C-->T transitions observed in CIMS miCLIP. Score represents the number of transitions at that position.
bedgraph files of cDNA truncations observed in CITS miCLIP. Score represents the number of reads starting at that position.
Bed files of m6A sites detected in CIMS miCLIP.
Bed files of m6A sites detected in CITS miCLIP.

molecule: total RNA

organism: Mus musculus

source_name: Liver cell nuclei

extract_protocol:
Total RNA was extracted using Trizol and either subjected directly to miCLIP or used for oligo(dT)-purification of mRNA and subsequent miCLIP.
Libraries were constructed using the iCLIP cloning strategy [Huppertz et al. 2014; PMID: 24184352]. Briefly, RNA was ligated to a 3'-adapter and reverse transcribed. cDNA was size-selected, circularized, re-linearized and PCR-amplified as described [Huppertz et al. 2014; PMID: 24184352].

tag: tissue

value: liver

tag: subcellular compartment

value: nucleus

tag: rip antibody

value: Abcam rabbit polyclonal anti-m6A (ab151230)

tag: iclip barcode

value: NNNACCTNN


title: HEK293_mRNA_mICLIP_rep4

description:
mRNA
HEK293_mRNA.tag.uniq.bedgraph
HEK293_mRNA.C2T.bedgraph
HEK293_mRNA_low-stringency_m6A.bed
HEK293_mRNA_high-stringency_m6A.bed

organism: Homo sapiens

source_name: HEK293 cells

value: embryonic kidney cells

value: whole cell

tag: cell line


title: H19△DMR-IG△DMR-OG3-2

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

country: China

institute: Fudan University

description: Gene expression data from  AG-haESCs

source_name: Haploid embryonic stem cells derived from  androgenetic blastocysts_DKO2

growth_protocol: Mouse androgenetic haploid embryonic stem cells (AG-haESCs) were cultured on feeder in ES medium supplemented with 2i.

treatment_protocol: ES cells were washed by DPBS (GIBCO), trypsinized, and collected by centrifugation.

tag: strain

tag: passages

tag: type

value: Embryonic stem cells


title: HEK293_mRNA_miCLIP_rep3

value: NNNCAATNN


title: H19△DMR-IG△DMR-AGH-4_RRBS

description: DNA methylation data from  AG-haESCs

library_source: genomic

data_processing:
Basecalling using Illumina Casava1.8.2 software
Map the reads to mouse genome mm10 using Bismark v0.12.2
Ectract CpG sites by bismark methylation extractor script
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include methylated counts, unmethylated counts and methylated level for sequenced CpG sites

molecule: genomic DNA

source_name: Haploid embryonic stem cells derived from  androgenetic blastocysts_DKO1

extract_protocol:
Total DNA was extracted and purified using DNA extraction kit according to the manufacturer's instructions.
Genomic DNA was digested using MspI restriction enzyme, then repaired the end and ligated with methylated adapters. The ligation products were purified and size-selected by agarose gel electrophoresis. Purified DNA from gel fragment was bisulfite-treated followed by PCR amplification.


title: IG△DMR-H19△DMR-AGH-2

description: Gene expression data from  AG-haESCs

source_name: Haploid embryonic stem cells derived from  androgenetic blastocysts_DKO3


title: H19△DMR-IG△DMR-AGH-4

description: Gene expression data from  AG-haESCs


title: HEK293_mRNA_miCLIP_rep1

value: NNNGGTTNN


title: HEK293_mRNA_miCLIP_rep2

value: NNNTTGTNN


title: DR1-PMS

city: Seoul

first: Jisun

last: Kim

address: Anam-Dong, Sungbuk-Gu

department: Environmental Science and Ecological Engineering

country: South Korea

institute: Korea university

data_processing:
Base-calling: CASAVA v1.6
Alignment: CLC Genomics Workbench 4.5; reads aligned against Acinetobacter oleivorans DR1 chromosome, complete genome RefSeq (NC_014259.1).
Generation of normalized abundance measurement: CLC Genomics Workbench 4.5
The relative transcript abundance was measured in reads per kilobase of exon per million mapped sequence reads (RPKM).
Genome_build: ASM19679v1
Supplementary_files_format_and_content: .txt files report RPKMs

organism: Acinetobacter oleivorans DR1

source_name: DR1 treated with PMS

extract_protocol:
Total RNA was isolated from 5 ml of stationary cells, using the RNeasy Mini kit (QIAGEN, USA), according to the manufacturer’s instructions.
The RNA was subjected to a subtractive Hyb-based rRNA removal process using the MICROBExpress Bacterial mRNA Enrichment Kit (Ambion). RNA sequencing was performed using the Illumina Genome Analyzer IIx to generate single-ended 50-bp reads.

tag: genotype

value: Wild type

tag: growth phase

value: exponential

tag: treatment

value: phenazine methosulfate (200 μM) over a period of 15 min.

tag: rna isolated from

value: stationary cells


title: IG△DMR-H19△DMR-AGH-2_RRBS

description: DNA methylation data from  AG-haESCs


title: IFNg TLR replicate 1

city: New York

first: Xiaodi

last: Su

state: NY

address: 535 East 70th Street

department: Arthritis and Tissue Degeneration Program

country: USA

institute: Hospital for Special Surgery

data_processing:
Mirdeep2 was used to align the sequencing reads to human precursor miRNAs (miRBase release 21); allow one mismatch
Mirdeep2 was used to calculate the read counts and cpm for each miRNA
Genome_build: miRBase release 21
Supplementary_files_format_and_content: excel file includes cpm values for each sample (8 in total)

source_name: human primary macrophages

growth_protocol: Cells were maintained in RPMI1640 supplemented with 10% FBS and 20ng/ml MCSF, under 5% CO2 at 37C.

extract_protocol:
Total RNA was extracted by using mirVana miRNA isolation kit
miRNA libraries were prepared by using TruSeq small RNA library prep kit (Illumina)

treatment_protocol: Cells cultured for 24h were stimulated with or without Pam3Cys (10ng/ml) for 4h

tag: tlr stimulation

value: TLR2 stimulated


title: Mock TLR replicate 1


title: AGH-OG3

description: Gene expression data from  AG-haESCs

source_name: Haploid embryonic stem cells derived from  androgenetic blastocysts_wildtype


title: AGH-2_RRBS

description: DNA methylation data from  AG-haESCs


title: HEK293_total_RNA_miCLIP_SySy

description:
total RNA
HEK293_rRNA_SySy.C2T.bedgraph

value: Synaptic Systems rabbit polyclonal anti-m6A (Cat. No. 202 003)

value: NNNTTAGNN


title: AGH-2

description: Gene expression data from  AG-haESCs


title: IFNg UT replicate 1

value: unstimulated


title: DR1-PQ

source_name: DR1 treated with PQ

value: paraquat (1 mM) over a period of 15 min.


title: EUE control, biological replicate 3

status: Public on Jun 28 2015

city: Gent

first: Patrick

last: Willems

address: Technologiepark 927

department: PSB

country: Belgium

institute: Ghent University

description: Sample name: EUE control BR3

data_processing:
FastX Trimmer (v0.10.0) trimming 10bp at 3', yielding 80bp PE reads.
Read mapping was done using GSNAP (unique mapping (-n 1, -Q), maximum of 5 mismatches allowed (-m 5)
Only unique concordantly mapping reads were retained
To calculate the number of mapped transcript reads, samtools idxstats was used
Genome_build: Combined non-redudant gene set B. rapa and B. oleracea (see Brassica_combined.fasta linked as supplementary file on the Series record)
Supplementary_files_format_and_content: Read counts

molecule: polyA RNA

organism: Brassica napus

source_name: leaf tissue

growth_protocol: Seedlings were grown for 2 weeks on agar in half-strenght MS medium supplemented with 2% sucrose and then transferred to soil, growing 12 days under standard greenhouse conditions.

extract_protocol:
Polysomal RNA was isolated using a protocol adapted from de Jong et al. (2006). Grinded leaf 4 material from 26 day-old control and selected lines was solubilized in an equal volume of extraction buffer (pH 8.5) containing 0.2 M Tris, 0.1 M KCl, 70 mM Mg-acetate, 50 mM EGTA,  0.25 M sucrose, 10 mM DTT, 100 ug/ml cycloheximide (Sigma-Aldrich, St Louis, MO, USA) and 100 U/ml SUPERase-In (Ambion, Austin, TX, USA). The slurry was allowed to thaw on ice and gently mixed to enhance homogenization. The suspension was strained through two layers of Miracloth via successive centrifugation for 1 min at 100 g (4C) and 5 min at 1000 g (4C) in 50 ml sterile tubes. The cleared supernatant was centrifuged for 15 min at 8 400 g (4C) to pellet additional debris, made to 1% v/v Triton X-100 and incubated on ice for 10 min. After centrifugation at 14 000 rpm (4C) in an eppendorf tabletop centrifuge the supernatant was loaded on discontinuous sucrose gradients in SW41 Ultra-Clear tubes (Beckman Coulter). The gradients consisted of 0.6 ml 1.65 M sucrose and 1.0 ml 1.00 M sucrose both buffered with 10x concentrated sucrose salts buffer (pH 8.5, autoclaved) containing 0.4 M Tris, 1 M KCl, 0.3 M Mg-acetate and 50 mM EGTA. To maintain RNA integrity, 10 mM DTT, 100 ug/ml cycloheximide and 100 U/ml SUPERase-In (Ambion) were added to these sucrose solutions. The gradients were centrifuged for 4 h at 150 000 g (4C) in an ultracentrifuge (Beckman Coulter; type L8–50 M/E) to pellet the polysomes. The polysomal pellets were resuspended in 100 ul extraction buffer and polysomal RNA was isolated with a RNeasy kit (Qiagen). The quantity of polysomal RNA was investigated using a nanodrop and the quality with a bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA, USA) using the RNA 6000 Nano Assay kit (Agilent Technologies).
The RNA-Seq were performed at the Beijing Genome Institute (BGI) (Shenzhen, China). Complementary DNA sequencing libraries were prepared from the polysomal RNA using the mRNA-Seq Sample Preparation Kit (Illumina, San Diego, CA) and run on an Illumina GAIIx.

treatment_protocol: No treatment

tag: age

value: 26 days

tag: cultivar

value: L. spp. oleifera (Metzg) Sinsk. f. biennis

tag: line

value: Control line for EUE epiline

value: leaf


title: EUE epiline, biological replicate 3

description: Sample name: EUE epiline BR3

value: EUE selected epiline


title: EUE control, biological replicate 2

description: Sample name: EUE control BR2


title: EUE epiline, biological replicate 2

description: Sample name: EUE epiline BR2


title: PEG-2, biological replicate 1

description: Sample name: PEG-2 BR1

value: PEG2 selected epiline


title: Control line, no antibody

description: Sample name: Control no antibody

data_processing:
Peak calling was performed using MACS version 2.0, the genome size (-g) was set at 2.0e8 and 3.7e8 for B. rapa and B. oleracea, respetively. Other parameters were set at their default values using the BAMPE format option.
For differential histone mark binding analysis the MACS version 2.0 bdgdiff module with default settings was used.
Peak annotation was performed by overlapping the peak summits reported by MACS with the B. rapa or B. oleracea annotation. A peak was assigned to the closest gene, taking into account both up- and downstream regions of the genes. When a peak is located within the boundaries of a gene, it was assigned to this gene.
Genome_build: Combined non-redudant gene set B. rapa and B. oleracea
Supplementary_files_format_and_content: BED files were generated by MACS

extract_protocol:
The protocol for native chromatin immunoprecipitation was adapted from Bernatavichute et al., 2008. Leaf 4 material of 26 day-old wild-type and PEG1 plants was harvested, frozen in liquid nitrogen and ground to powder (1.5 g). Plant tissue was resuspended in 15 ml of HBM buffer (25 mM Tris-Cl pH 7.5, 440 mM sucrose, 10 mM MgCl2, 0.1% Triton-X, 10 mM beta-mercaptoethanol, 2 mM spermine, 1 mM PMSF, 1 ug/ml pepstatin, 1 ug/ml aprotinin and 1 ug/ml leupeptin), homogenized and filtered twice through Miracloth (Calbiochem). After spinning at 3000 rpm for 5 min (4°C, SS-34, Sorvall), the pellet was resuspended in 5 ml of NIB buffer (20 mM Tris-Cl pH 7.5, 250 mM sucrose, 5 mM MgCl2, 5 mM KCl, 0.1% Triton-X, 10 mM beta-mercaptoethanol, 1 mM PMSF, 1 ug/ml pepstatin, 1 ug/ml aprotinin and 1 ug/ml leupeptin), applied to a 15/50% Percoll (GE Healthcare) gradient in NIB and spun 2000 rpm for 20 min (4 C, SS-34, Sorvall). Isolated nuclei were washed three times in NIB buffer and flash frozen in liquid nitrogen in HBC buffer (25 mM Tris-Cl pH 7.5, 440 mM sucrose, 10 mM MgCl2, 0.1% Triton-X, 10 mM beta-mercaptoethanol, 20% glycerol). Nuclei from each preparation were diluted 2-fold in digestion buffer (20 mM Tris-Cl pH 7.5, 0.22 M sucrose, 50 mM NaCl, 5 mM MgCl2, 1 mM CaCl2, 5 mM Na butyrate), spun 600 g for 5 min (4°C, Eppendorf, 5415R) and resuspended in 0.25 ml digestion buffer for Micrococcal Nuclease (30 U, Affymetrix) digestion for 10 minutes at 37 °C stopped with 10 mM EDTA. Mononucleosomes were released by treating nuclei with 0.1% Triton-X for 2 hours in the cold, and then pelleting the debris by centrifuging at 10000 rpm for 5 min (4°C, Eppendorf, 5415R). The supernatants were diluted to 0.5ml in incubation buffer (20 mM Tris-Cl pH 7.5, 50 mM NaCl, 5 mM EDTA, 0.1% Triton, 20 mM Na butyrate, 0.1 mM PMSF, 1 ug/ml pepstatin, 1 ug/ml aprotinin and 1 ug/ml leupeptin) and overnight incubated in the cold with and without 2.5 ug of the anti-H3K4m3 antibody (#07-473, Millipore). 50 ul of Dynabeads Protein G (Invitrogen) were applied, incubated for 3 hours in the cold and washed three times with 500 ul wash buffer (50 mM Tris-Cl pH 7.5, 10 mM EDTA, 5mM Na butyrate, 0.1 mM PMSF, 1 ug/ml pepstatin, 1 ug/ml aprotinin and 1 ug/ml leupeptin) with increasing concentrations of NaCl (50 mM, 100 mM and 150 mM), subsequently. Final wash was done in TE buffer (10 mM TrisCl pH8, 500 mM NaCl, 1 mM EDTA) and immunocomplexes were eluted and reverse crosslinked by incubation overnight at 65°C in 0.25 ml 10 mM TrisCl pH8, 1 mM EDTA, 0.5 M NaCl, 1% SDS + 1 µl RNAse A (100 mg/ml). Eluates were incubated with 100 µg Proteinase K for 2 h at 42°C and the DNA extracted by phenol/chloroform/IAA followed by purification using Qiaquick PCR purification kit and DNA quantification by the Quant-iT dsDNA High Sensitivity kit (Invitrogen).
Standard Illumina Protocol

value: Control line

tag: chip antibody

value: none (input)


title: Control line, H3K4me3

description: Sample name: Control H3K4me3

tag: tissue

value: anti-H3K4me3  (Millipore, catalog# 07-473, lot# JBC1888194)


title: PEG-2, biological replicate 2

description: Sample name: PEG-2 BR2


title: EUE control, biological replicate 1

description: Sample name: EUE control BR1


title: PEG-1, biological replicate 2

description: Sample name: PEG-1 BR2

value: PEG1 selected epiline


title: PEG1 epiline, H3K4me3

description: Sample name: PEG1 H3K4me3


title: PEG control, biological replicate 2

description: Sample name: PEG control BR2

value: Control line for PEG1/2 epilines


title: Leghorn biological rep 1 & 2

city: Beijing

first: Jinxiu

last: Li

state: Beijing

address: Yuanmingyuan west road 2#

department: College of biological sciences

institute: China Agricutural University

data_processing:
Basecalls performed using CASAVA version 1.6.0
Sequenced reads were aligned to the galGal4 genome assembly using BWA version 0.6.2-r126 with the following configurations: aln -t 4 -n 5 -l 32 -k 2 -o 0
Pileup format of the aligned reads were generated by samtools version 0.1.16
Binomial distribution was used to identify the methylation site,and then false discovery rate (FDR) was used to correct it (p = 0.01)
Genome_build:  galGal4
Supplementary_files_format_and_content: Tab-delimited text files include chromosome, strand,and position of methylcytosines which were identified for each chicken line (LC represents Leghorn chicken; FC represents Fayoumi chicken).Two biological replicates were pooled to identified the methylcytosines. Further more, the methylcytosines were divided into CG, CHG, and CHH contexts (where H is A, C, or T),each context had its own document (LC_all_chr.real_chg, LC_all_chr.real_chh, and LC_all_chr.real_cg).

organism: Gallus gallus

source_name: Lung

extract_protocol:
DNA from lung tissue was isolated by phenol-chloroform extraction.
Libraries were prepared as below. Five μg DNA was sonicated to produce 200-400 bp fragments, followed by end repair with a nucleotide triphosphate mix free of dCTP. Cytosine methylated adapters provided by Illumina (Illumina, San Diego, CA) were ligated to the sonicated DNA according to the manufacturer’s instructions for genomic DNA library construction. Adapter-ligated DNA with the length of 320-500 bp was isolated by 2% agarose gel electrophoresis, and sodium bisulfite conversion was performed on it using the MethylEasy Xceed kit (Human Genetic Signatures, NSW, Australia) was used according to the manufacturer’s instructions. The 300 ng of bisulfite-converted, adapter-ligated DNA molecules were enriched by 14 cycles of PCR with the following reaction composition: 2.5 U of uracil-insensitive Pfu TurboCx Hotstart DNA polymerase (Stratagene), 5 μL of 10× Pfu Turbo reaction buffer, 25 μM dNTPs, 1 μL of Primer 1.1, and 1 μL of Primer 2.1 (50 μL final). The thermocycling parameters were as follows: 98°C for 2 min, followed by 4 cycles of 98°C for 15 s, 60°C for 30 s, and 72°C for 1 min, ending with incubation at 72°C for 10 min. The reaction products were purified using the MinElute PCR purification kit (Qiagen, Valencia, CA) and then separated by 2% agarose gel electrophoresis and purified by the MinElute gel purification kit (Qiagen, Valencia, CA). DNA library prepared above was sequenced using the Illumina Genome Analyzer II (GA II) according to the manufacturer’s instructions. Each sample had two technical replicates (a and b).

treatment_protocol: Two Leghorn and two Fayoumi birds were euthanized at 3 weeks, and lungs were harvested. The animal experiment was performed according to the guidelines approved by the Institutional Animal Care and Use Committee, Texas A&M University.

value: Lung

value: 3 weeks

value: Leghorn GB2


title: embryo SC12-039

status: Public on Jun 27 2015

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

description: Human embryo

data_processing:
Sequencing was performed on the Illumina HiSeq 2000
Reads were aligned using TopHat software, with hg19 as the reference genome and mapping fragments per kilobase per million mapped reads (FPKM) as output.
FPKM were log2-transformed, normalized, and baselined to the median expression of the average of each class of samples (GMP, induced, and BM Progenitor/ProMyelocytes, iPSC, and mesoderm-like induced differentiated cells).
Differentially expressed genes were idntified from a starting pool of all transcripts with more than 3 FPKM in at least 2 of the 9 myeloid samples.
Genome_build: GRCh37
Supplementary_files_format_and_content: Each fastq file has two associated text files: one text file contains FPKM, one text file contains data that has been log2-transformed, normalized and baselined.

source_name: embryo

growth_protocol: Hematopoietic progenitors derived from control iPSCs were cultured in myeloid expansion medium containing 50ng/mL SCF, 10ng/mL IL-3 and 10ng/mL GM-CSF for 5 days. The cells at this point were stained for CD45-Pacific blue, CD34-PECy7, CD33-AP, CD11b-APC-Cy7, CD15-FITC. 7-AAD was used to eliminate the dead cells. The promyelocytic population (CD45+CD34-CD33+CD11b-CD15+/lo) was sorted

extract_protocol:
Total RNA was extracted from sorted popylations derived from bone marrow or iPSC using RNAeasy minikit (Qiagen) or Trizol as determine by the number of available cells.  RNA quality and concentration were measured by Agilent Bioanalyzer 2100 using the RNA 6000 Nano Assay.  For specimens obtained from less than 50,000 cells, a linear amplification protocol was performed.
RNA sequencing libraries were prepared using the Illumina TruSeq RNA preparation kit

tag: cell type

value: embryo

tag: cell origin

tag: description

value: iPSC

tag: origin


title: CD34+ iPSC from Cord blood SC13-045

description: Human CD34+ iPSC cord blood

source_name: Cord blood

value: CD34+ iPSC

value: cord blood


title: mesoderm differentiated cells from PBMC SC12-037MESO

description: Human mesoderm differentiated cells made from CD34+ PBMC-derived induced pluripotent stem cells

source_name: PBMC

value: mesoderm differentiated cells

value: Mesodermal differentiated iPSC


title: mesoderm differentiated cells from Fibroblast SC12-022

description: Human mesoderm differentiated cells made from fibroblast-derived induced pluripotent stem cells

source_name: Fibroblast

value: fibroblast


title: mesoderm differentiated cells from Fibroblast SC12-030MESO

value: made from fibroblast-derived induced pluripotent stem cells


title: iPSC from Fibroblast SC12-030

description: Human iPSC fibroblast


title: EUE epiline, biological replicate 1

description: Sample name: EUE epiline BR1

value: 26 days

value: L. spp. oleifera (Metzg) Sinsk. f. biennis

value: EUE selected epiline

value: leaf


title: FACS sorted CD (45+/34+/33+/123+) from Bone marrow SC12-042.2-GMP

description: Human FACS sorted CD (45+/34+/33+/123+) prepared from human bone marrow

source_name: Bone marrow

value: prepared from human bone marrow

value: GMP promyelocytes sorted from BM

value: human bone marrow


title: mesoderm differentiated cells from Cord blood SC13-045MESO

description: Human mesoderm differentiated cells made from CD34+ cord blood-derived induced pluripotent stem cells


title: T24_NEG_REP1

city: Exeter

first: Darren

middle: Mark

last: Soanes

address: RILD Building, RD&E Hospital Wonford, Barrack Road

department: College of Medicine and Health

country: United Kingdom

institute: University of Exeter

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Reads were filtered using the fastq-mcf program from the ea-utils package (http://code.google.com/p/ea-utils/) applying –x 0.01, –q 20, –p 10, and –u
Reads were mapped to the Magnaporthe oryzae 70-15 reference genome version 8 using the TopHat2 package
Counts of reads mapping to each gene in the M. oryzae genome were generated using the htseq-count function of the HTSeq package
Relative gene expression was quantified using DESeq
Genome_build: Magnaporthe oryzae 70-15 reference genome version 8 (http://www.broadinstitute.org/annotation/genome/magnaporthe_comparative/MultiHome.html)
Supplementary_files_format_and_content: pkc_expression_all.txt: tab-delimited text file containing relative gene expression (baseMean) of each gene for all time points, generated by DESeq
Supplementary_files_format_and_content: *sorted.bam.sam.count.txt: tab-delimited text file containing raw counts for each gene (output from htseq-count)

organism: Pyricularia oryzae

extract_protocol:
Total RNA was then extracted using Qiagen RNeasy Plant Mini kit, according to manufacturer's instructions. RNA-seq  libraries were prepared using 5 µg of total RNA with ScriptSeq RNA-Seq Library Preparation Kit from Illumina according to manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

tag: genotype/variation

value: containing analogue-sensitive PKC1 allele (pkc1AS)

value: mycelium

tag: treated with

value: none (control)

tag: time point

value: 24 hrs


title: T24_POS_REP1

value: 500 nM 1NA-PP1


title: CD34+ iPSC from PBMC SC12-037

description: Human CD34+ iPSC PBMC

value: CD34+ iPSC

value: PBMC

value: iPSC


title: CD34+ iPSC from PBMC SC12-036

description: Human CD34+ iPSC PBMC


title: PEG control, biological replicate 1

description: Sample name: PEG control BR1

value: Control line for PEG1/2 epilines


title: T24_POS_REP2


title: iPSC from Fibroblast SC12-031

description: Human iPSC fibroblast

value: fibroblast


title: CD34+ iPSC from Cord blood SC13-044

description: Human CD34+ iPSC cord blood

value: cord blood

value: bone marrow


title: PEG-1, biological replicate 1

description: Sample name: PEG-1 BR1

value: 26 days

value: L. spp. oleifera (Metzg) Sinsk. f. biennis

value: PEG1 selected epiline


title: HEK293_total_RNA_miCLIP_Abcam

description:
total RNA
HEK293_rRNA_Abcam.C2T.bedgraph

value: embryonic kidney cells

tag: subcellular compartment

value: whole cell

tag: cell line

tag: rip antibody

value: Abcam rabbit polyclonal anti-m6A (ab151230)

tag: iclip barcode

value: NNNGGTCNN


title: T24_NEG_REP2

value: containing analogue-sensitive PKC1 allele (pkc1AS)

value: mycelium

value: none (control)


title: T12_NEG_REP2

value: 12 hrs


title: Fayoumi biological  rep 1 & 2

value: Lung

tag: age

value: 3 weeks

value: Fayoumi M43


title: FACS sorted CD (45+/34-/33+/11b-/15+)  from Bone marrow RN20-BM080

description: Human FACS sorted CD (45+/34-/33+/11b-/15+)  prepared from human bone marrow

value: prepared from human bone marrow

value: promyelocytes sorted from BM

value: human bone marrow


title: FACS sorted CD (45+/34-/33+/11b-/15+)  from Bone marrow RN19-BM109


title: T12_NEG_REP1


title: FACS sorted CD (45+/34-/33+/11b-/15+)  from PBMC RN18-35

description: Human FACS sorted CD (45+/34-/33+/11b-/15+)  made from CD34+ PBMC-derived induced pluripotent stem cells

value: promyelocytes-differentiated from iPSC


title: T12_POS_REP2

value: 500 nM 1NA-PP1


title: FACS sorted CD (45+/34-/33+/11b-/15+)  from PBMC RN17-34

value: made from CD34+ PBMC-derived induced pluripotent stem cells


title: T3_NEG_REP2

value: 3 hrs


title: FACS sorted CD (45+/34+/33+)  from PBMC RN1-13-La

description: Human FACS sorted CD (45+/34+/33+)  made from CD34+ PBMC-derived induced pluripotent stem cells

value: myeloid progenitors-differentiated from iPSC


title: FACS sorted CD (45+/34+/33+)  from PBMC RN3-5


title: T6_POS_REP2

value: 6 hrs


title: ikras_shh_plus_rep4

city: Manchester

first: Hui Sun

last: Leong

address: Wilmslow Road

department: The University of Manchester

institute: Cancer Research UK Manchester Institute

description: strand-specific RNA-seq

data_processing:
Basecalling was performed using Illumina CASAVA version 1.8.2
13~20 millions paired-end sequencing reads (101 nt) were obtained from all sequencing libraries and aligned to the mouse reference genome GRCm38/mm10 using the splice alignment software TopHat (version 2.0.9) with default parameters, except for options specifying library type (fr-firststrand). Gene annotation was taken from Ensembl release 74.
The expression of a gene or feature was measured by the Reads Per Kilobase Per Million Mapped (RPKM) score, which was calculated by counting the number of uniquely mapped reads in a given feature and normalizing by transcript length and the total read count in the library prep.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Tab-delimited text files of raw sequencing read counts and RPKM values for all samples

source_name: Epithelial cancer cells

extract_protocol:
Cells were trypsinized and rapidly resolved using a FACSAria (BD Biosciences) according to their GFP and RFP expression. The mCherry channel was used for optimal separation of the PSC+RFP cells. Analyses were performed using FlowJo (Tree Star Inc.). iKRAS+GFP mono-populations were instantly lysed, passed through a QIAshredder and snap-frozen.
Indexed PolyA Seq libraries were prepared using 500ng of Total RNA and 12 cycles of amplification using the NEB Next Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs Inc.  Cat No: E7420S). Then, libraries were quantified by qPCR using a Kapa Library Quantification Kit for Illumina sequencing platforms (Kapa Biosystems Inc. Cat No: KK4835). Pooled libraries were clustered at 15pM on the cBot. 2 x 101bp sequencing was carried out using the High Throughput mode of a HiSeq 2500 using TruSeq SBS Kit v3 chemistry (Illumina inc.).

treatment_protocol: iKRAS+GFP cells were co-cultured with PSC+RFP 20 μg/mL SHH-neutralizing antibody (R&D Systems MAB4641) (biological n = 4) in +0.5% dialyzed FBS for 72 hours.

value: FVB/B6 mix

value: p48Cre tetO_LKrasG12D ROSA_rtTAL+ p53L+

value: iKRAS epithelial cancer cells

tag: treatment

value: No SHH antibody

tag: replicate


title: T1_NEG_REP1

value: containing analogue-sensitive PKC1 allele (pkc1AS)

value: mycelium

value: none (control)

value: 1 hr


title: T3_POS_REP1


title: T3_POS_REP2


title: FACS sorted CD (45+/34+/33+) from PBMC RN2-13Lb

description: Human FACS sorted CD (45+/34+/33+) made from CD34+ PBMC-derived induced pluripotent stem cells


title: FACS sorted CD (45+/34+/33+/123+) from Bone marrow SC12-042.1-GMP

value: prepared from human bone marrow

value: GMP promyelocytes sorted from BM


title: T6_NEG_REP2


title: T1_POS_REP2


title: T6_NEG_REP1


title: LncPHx2_Even probe pool_ pull-down

city: Carlsbad

first: Sagar

middle: S

last: Damle

state: CA

address: 2855 Gazelle Ct

institute: Ionis Pharmaceuticals

description: RNA interactome analysis with probes targeting LncPHx2 (Pool of even number probes)

data_processing:
Reads were aligned to mm10 genome using STAR v2.3.0e
Coverage was computed from mapped reads using bedtools genomecov
Coverage was normalized by total number of mapped reads
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files contain RNA pulldown coverage

source_name: Hepa 1-6 cells

growth_protocol: Hepa1-6 (ATCC) were cultured in DMEM containing 1% L-glutamine, 10% fetal bovine serum, and 100 units/ml penicillin/streptomycin in 5% CO2 at 37 °C.

extract_protocol:
RNA-interactome analysis
cDNA libraries for RNA-seq were made using SMARTer Universal Low Input RNA Kit (Clonetech).

value: Hepa 1-8


title: ikras_shh_plus_rep3

description: strand-specific RNA-seq


title: ikras_shh_minus_rep4

description: strand-specific RNA-seq

value: With SHH antibody


title: T1_NEG_REP2


title: LncPHx2_Odd probe pool_ pull-down

description: RNA interactome analysis with probes targeting LncPHx2 (Pool of odd number probes)

value: Hepa 1-7


title: ikras_shh_plus_rep1

description: strand-specific RNA-seq


title: ikras_shh_minus_rep3

description: strand-specific RNA-seq


title: T12_POS_REP1

value: 500 nM 1NA-PP1

value: 12 hrs


title: T6_POS_REP1


title: T3_NEG_REP1

value: 3 hrs


title: ikras_shh_plus_rep2

description: strand-specific RNA-seq


title: T1_POS_REP1


title: ko3a_hsc_l4 RNA-Seq

city: Houston

first: deqiang

last: sun

state: TX

address: 2121 W Holcombe Blvd

institute: Texas A&M University

description: technical replicate of biological replicate 2

data_processing:
RUM to make alignments; Customized script to count fragments on gene; DESEQ to do differential expression test;
Genome_build: mm9
Supplementary_files_format_and_content: Tab separated text file for gene's count and fpkm for each sample; XLS file for two sample comparison testing if a gene is differentially expressed;

source_name: Dnmt-KO Hematopoietic Stem Cells

growth_protocol: Freshly sorted wild type and Dnmt3a-KO mouse HSCs (SP-KSL-CD150+)

extract_protocol:
Extract RNA using Qiagen Rneasy Micro kit.
Tru-Seq RNA sample prep kit

treatment_protocol: PolyA selection

value: Murine bone marrow derived primary HSCs

tag: cell surface marker


title: LacZ probe pull-down

description: RNA interactome analysis with probes targeting LacZ as negative control

value: Hepa 1-6


title: ikras_shh_minus_rep2

description: strand-specific RNA-seq

value: FVB/B6 mix

value: p48Cre tetO_LKrasG12D ROSA_rtTAL+ p53L+


title: ko3a_hsc_l3 RNA-Seq


title: T0_REP1

tag: tissue


title: ko3a_hsc_l1 RNA-Seq

description: technical replicate of biological replicate 1

tag: cell type


title: T0_REP2


title: ikras_shh_minus_rep1

description: strand-specific RNA-seq

value: iKRAS epithelial cancer cells


title: LncPHx2_ASO1 PHx_3

status: Public on Jun 26 2015

description: Liver RNAs from mice treated with LncPHx2_ASO1 subcutaneously, and operated with partial hepatectomy surgery.

data_processing:
Reads were aligned to mm10 using STAR v2.3.0e and reference annotation based transcriptome assembly was performed with Cufflinks v2.1.1
Differential gene expression was computed using cuffdiff v2.1.1 with default parameters
Genome_build: mm10
Supplementary_files_format_and_content: cuffdiff_genes.fpkm_tracking: Tab-delimited file containing replicate-averaged FPKM values for each condition. cuffdiff_gene_exp.diff: tab-delimited file containing fold-change values, p-values, q-values and significance calls of comparisons between different conditions. This file contains data for all samples; scroll down to find each data set.

source_name: mouse liver_LncPHx2ASO1_PHx

growth_protocol: Male Balb/c mice, 7-9 weeks of age.

extract_protocol:
Mouse livers were homogenized in guanidine isothiocyanate solution (Invitrogen) supplemented with 8% 2-mercaptoethanol (Sigma-Aldrich). Total RNA was prepared using the Qiagen RNeasy columns.
Library was prepared using Illumina True-seq protocol

treatment_protocol: Mice were treated subcutaneously with two doses of LncPHx2_ASO1 or PBS, and then performed PHx or Sham surgery. Liver samples were collected 48 hours after surgery.

value: Balb/c

value: liver

tag: developmental stage

value: adult, 7-9 weeks


title: LncPHx2_ASO1 PHx_1


title: LncPHx2_ASO1 PHx_2


title: G. barbadense 21 day post anthesis cotton fiber biological pool 3

city: Raleigh

first: Candace

middle: Hope

last: Haigler

state: NC

address: 101 Derieux Place

department: Crop Science

institute: North Carolina State University

description:
Sample name: Gb21p3
Fiber pooled from 3 plants
RNA-Seq of Gossypium barbadense 21 day post anthesis cotton fiber biological pool 3

data_processing:
Illumina Casava1.8.2 software was used for basecalling and demultiplexing
Raw reads were mapped to the combined cotton A and D EST reference using Burrows Wheeler Aligner version 0.6.2 (http://bio-bwa.sourceforge.net/) allowing maximum 4% mismatch
Mapped reads against individual reference gene were then counted through BEDTOOLS version 2.17.0 (https://code.google.com/p/bedtools/) after file format conversion using SAMTOOLS (http://samtools.sourceforge.net/).
Transcript counts were normalized by RPKM (Reads Per Kilo bases per Million reads) using a PERL script
RPKM values from three technical sequencing replicates per sample were averaged
The samWrapper function in the R DEGseq package (http://bioconductor.org/packages/release/bioc/manuals/DEGseq/) was used to determine differential gene expression
Genome_build: Graimondii2_0 (http://www.ncbi.nlm.nih.gov/assembly/GCA_000327365.1)
Genome_build: Gossypium arboreum transcriptome shotgun assembly - Bioproject PRJNA269608 and TSA accession GBYK00000000
Supplementary_files_format_and_content: Processed data files with read abundances for the inividual samples contain:1)  the transcript name (Reference_ID) derived from the Gossypium raimondii genome  or a Gossypium arboreum contig assembly (TSA accession GBYK00000000), 2) the mean read count from three technical sequencing replicates normalized as reads per kilobase of transcript per million reads mapped (RPKM), 3)The most homologous gene ID from the Arabidopsis Information Resource (www.arabidopsis.org, Homologous_TAIR_ID), 4) the corresponding Arabidopsis gene name (Arabidopsis_Gene_Name), and 5) the corresponding annotation imported from www.phytozome.net for Gossypium raimondii transcript identifiers or TAIR for Gossypium arboreum contig identifiers (Annotation).
Supplementary_files_format_and_content: Processed data files from differential expression analysis contain: 1) the transcript ID (Reference_ID), 2) fold change ratio for a given comparison derived from the means of three biological replicates (Fold Change),  3) the associated q-value from the pair-wise statistical comparison (q-value),  4) The most homologous gene ID from the Arabidopsis Information Resource (www.arabidopsis.org, Homologous_TAIR_ID), 5) the corresponding Arabidopsis gene name (Arabidopsis_Gene_Name), and 6) the corresponding annotation imported from www.phytozome.net for Gossypium raimondii transcript identifiers or TAIR for Gossypium arboreum contig identifiers (Annotation).

organism: Gossypium barbadense

source_name: cotton fiber

growth_protocol: Plants were grown in a temperature controlled greenhouse with day/night temperatures of 26/22C and ambient daylength supplemented to 14 hours by a bank of 16 x 500W metal halide lamps. Plants were potted in 10" diameter pots of peat-lite and gravel and were watered with Hoagland's solution once in the morning and once in the afternoon (http://www.ncsu.edu/phytotron/manual.pdf). Plants were rotated weekly to minimize the positional effects within the greenhouse.

extract_protocol:
Ovules and fibers from first position bolls were removed from cotton bolls, flash frozen in liquid nitrogen and gently ground within 5 minutes of boll dissection. Ovules were removed during the grinding process and the remaining ground fiber was stored at -80C until RNA extraction. Fiber RNA was extracted using the Spectrum Plant Total RNA kit (http://www.sigmaaldrich.com/) and the manufacturer's instructions for protocol A with 750µl of binding buffer and an on-column DNase I treatment using DNASE70 (www.sigmaaldrich.com).
RNA libraries were prepared for sequencing using the Illumina TruSeq RNA sample prep kit v2 (www.illumina.com). Total RNA (1 µg) was purified using poly-T oligo-attached magnetic beads to isolate poly-A containing mRNA. The mRNA was chemically fragmented using divalent cations and fragments were reverse transcribed into first strand cDNA using random primers. Second strand synthesis was carried out using DNA Polymerase I and RNaseH. Ends were repaired on the double-stranded cDNA to convert overhangs into blunt ends, 3’ ends were adenylated, and adapters with indexes for multiplexing were ligated. The library was amplified with a PCR reaction and then small fragments were removed (AmpureXP beads; www.beckmancoulter.com). The final library was quantified on the Agilent Bioanalyzer High Sensitivity DNA Chip; (www.agilent.com) prior to pooling.

value: 21 days post anthesis

value: cotton seed fiber

value: transition from primary to secondary cell wall deposition

tag: cultivar

value: PHYTOGEN 800


title: G. barbadense 21 day post anthesis cotton fiber biological pool 1

description:
Sample name: Gb21p1
Fiber pooled from 3 plants
RNA-Seq of Gossypium barbadense 21 day post anthesis cotton fiber biological pool 1


title: LncPHx2_ASO1 Sham_1

description: Liver RNAs from mice treated with LncPHx2_ASO1 subcutaneously, and operated with sham surgery.

source_name: mouse liver_LncPHx2ASO1_sham


title: LncPHx2_ASO1 Sham_2


title: PBS PHx_2

description: Liver RNAs from mice treated with PBS subcutaneously, and operated with partial hepatectomy surgery.

source_name: mouse liver_PHx


title: PBS Sham_3

description: Liver RNAs from mice treated with PBS subcutaneously, and operated with sham surgery.

source_name: mouse liver_sham


title: PBS PHx_3


title: G. barbadense 21 day post anthesis cotton fiber biological pool 2

description:
Sample name: Gb21p2
Fiber pooled from 3 plants
RNA-Seq of Gossypium barbadense 21 day post anthesis cotton fiber biological pool 2


title: G. barbadense 18 day post anthesis cotton fiber biological pool 3

description:
Sample name: Gb18p3
Fiber pooled from 3 plants
RNA-Seq of Gossypium barbadense 18 day post anthesis cotton fiber biological pool 3

value: 18 days post anthesis


title: PBS PHx_1


title: G. barbadense 10 day post anthesis cotton fiber biological pool 2

description:
Sample name: Gb10p2
Fiber pooled from 3 plants
RNA-Seq of Gossypium barbadense 10 day post anthesis cotton fiber biological pool 2

value: 10 days post anthesis

value: elongation and primary cell wall deposition


title: G. barbadense 10 day post anthesis cotton fiber biological pool 3

description:
Sample name: Gb10p3
Fiber pooled from 3 plants
RNA-Seq of Gossypium barbadense 10 day post anthesis cotton fiber biological pool 3


title: PBS Sham_1


title: G. barbadense 10 day post anthesis cotton fiber biological pool 1

description:
Sample name: Gb10p1
Fiber pooled from 3 plants
RNA-Seq of Gossypium barbadense 10 day post anthesis cotton fiber biological pool 1


title: G. barbadense 18 day post anthesis cotton fiber biological pool 2

description:
Sample name: Gb18p2
Fiber pooled from 3 plants
RNA-Seq of Gossypium barbadense 18 day post anthesis cotton fiber biological pool 2


title: G. barbadense 18 day post anthesis cotton fiber biological pool 1

description:
Sample name: Gb18p1
Fiber pooled from 3 plants
RNA-Seq of Gossypium barbadense 18 day post anthesis cotton fiber biological pool 1


title: G. barbadense 28 day post anthesis cotton fiber biological pool 2

description:
Sample name: Gb28p2
Fiber pooled from 3 plants
RNA-Seq of Gossypium barbadense 28 day post anthesis cotton fiber biological pool 2

value: 28 days post anthesis

value: secondary cell wall deposition


title: ko3a_hsc_l2 RNA-Seq

value: Murine bone marrow derived primary HSCs


title: G. barbadense 15 day post anthesis cotton fiber biological pool 3

description:
Sample name: Gb15p3
Fiber pooled from 3 plants
RNA-Seq of Gossypium barbadense 15 day post anthesis cotton fiber biological pool 3

value: 15 days post anthesis


title: PBS Sham_2


title: G. barbadense 28 day post anthesis cotton fiber biological pool 3

description:
Sample name: Gb28p3
Fiber pooled from 3 plants
RNA-Seq of Gossypium barbadense 28 day post anthesis cotton fiber biological pool 3


title: G. barbadense 28 day post anthesis cotton fiber biological pool 1

description:
Sample name: Gb28p1
Fiber pooled from 3 plants
RNA-Seq of Gossypium barbadense 28 day post anthesis cotton fiber biological pool 1


title: G. barbadense 15 day post anthesis cotton fiber biological pool 2

description:
Sample name: Gb15p2
Fiber pooled from 3 plants
RNA-Seq of Gossypium barbadense 15 day post anthesis cotton fiber biological pool 2


title: G. barbadense 15 day post anthesis cotton fiber biological pool 1

description:
Sample name: Gb15p1
Fiber pooled from 3 plants
RNA-Seq of Gossypium barbadense 15 day post anthesis cotton fiber biological pool 1


title: LncPHx2_ASO1 Sham_3


title: G. hirsutum 21 day post anthesis cotton fiber biological pool 2

description:
Sample name: Gh21p2
Fiber pooled from 3 plants
RNA-Seq of Gossypium hirsutum 21 day post anthesis cotton fiber biological pool 2

organism: Gossypium hirsutum

value: DELTAPINE 90


title: G. hirsutum 18 day post anthesis cotton fiber biological pool 3

description:
Sample name: Gh18p3
Fiber pooled from 3 plants
RNA-Seq of Gossypium hirsutum 18 day post anthesis cotton fiber biological pool 3


title: G. hirsutum 21 day post anthesis cotton fiber biological pool 1

description:
Sample name: Gh21p1
Fiber pooled from 3 plants
RNA-Seq of Gossypium hirsutum 21 day post anthesis cotton fiber biological pool 1


title: G. hirsutum 10 day post anthesis cotton fiber biological pool 2

description:
Sample name: Gh10p2
Fiber pooled from 3 plants
RNA-Seq of Gossypium hirsutum 10 day post anthesis cotton fiber biological pool 2


title: G. hirsutum 10 day post anthesis cotton fiber biological pool 3

description:
Sample name: Gh10p3
Fiber pooled from 3 plants
RNA-Seq of Gossypium hirsutum 10 day post anthesis cotton fiber biological pool 3


title: G. hirsutum 18 day post anthesis cotton fiber biological pool 1

description:
Sample name: Gh18p1
Fiber pooled from 3 plants
RNA-Seq of Gossypium hirsutum 18 day post anthesis cotton fiber biological pool 1


title: G. hirsutum 18 day post anthesis cotton fiber biological pool 2

description:
Sample name: Gh18p2
Fiber pooled from 3 plants
RNA-Seq of Gossypium hirsutum 18 day post anthesis cotton fiber biological pool 2


title: G. hirsutum 10 day post anthesis cotton fiber biological pool 1

description:
Sample name: Gh10p1
Fiber pooled from 3 plants
RNA-Seq of Gossypium hirsutum 10 day post anthesis cotton fiber biological pool 1


title: G. hirsutum 28 day post anthesis cotton fiber biological pool 1

description:
Sample name: Gh28p1
Fiber pooled from 3 plants
RNA-Seq of Gossypium hirsutum 28 day post anthesis cotton fiber biological pool 1


title: G. hirsutum 28 day post anthesis cotton fiber biological pool 2

description:
Sample name: Gh28p2
Fiber pooled from 3 plants
RNA-Seq of Gossypium hirsutum 28 day post anthesis cotton fiber biological pool 2


title: Bisection - 96 hour - replicate 1

city: Kansas City

first: Alejandro

last: Sánchez Alvarado

state: Missouri

address: 1000 E 50th Street

institute: The Stowers Institute for Medical Research

description:
Sample name: 96h-1
PolyA RNA
Processed data file: counts_table.txt
Processed data file: all_genes_expression.txt

data_processing:
Single end reads from each time point were aligned to the transcriptome using Bowtie2 with default parameters.
Alignments were quantified using Samtools. Isoform counts were summed to generate a 'per gene' count.
Differential expression analysis was performed using the R package DESeq2.
All time points were contrasted with the zero hour (0h) time point.
Genome_build: The Transcriptome Shotgun Assembly (TSA) project has been deposited at DDBJ/EMBL/GenBank under the accession GDGM00000000. The version described in this paper is the first version, GDGM01000000.
Supplementary_files_format_and_content: counts_table.txt: Raw counts of sequencing reads; tab-delimited text file.
Supplementary_files_format_and_content: all_genes_expression.txt: Normalized abundance measurements; tab-delimited text file.

organism: Ptychodera flava

source_name: Bisected posterior piece, 96 hours

growth_protocol: Animals were collected into 50 ml tubes and carried back to the lab with the tubes immersed in a cooler with sea water.

extract_protocol:
Four healthy, intact animals were bisected and total RNA was isolated from the cut site of the posterior half to serve as reference controls. RNA was isolated from the tissue using either a Promega SV Total RNA Isolation System, catalog number Z3100, or a USB PrepEase RNA Spin Kit, part number 78766 1 KT. RNA was analyzed on a NanoDrop ND-1000 spectrophotometer for nucleic acid concentration and purity and then stored at -80°C until cDNA was synthesized using the SuperScript® III First- Strand Synthesis System for RT-PCR by Invitrogen.
Libraries for sequencing were prepared with the TruSeq Stranded mRNA Library Preparation kit v2 (RS-122-2101).

treatment_protocol: Animals were bisected at the level of the anterior hepatic sacs and allowed to regenerate for various time points. Regenerating worms were kept in running seawater tanks at Kewalo Marine Laboratory at 27°C during regeneration. Some worms were collected and shipped to the University of Washington in Seattle, WA and kept at 26°C while regenerating.

tag: collection location

value: Paiko Peninsula in Honolulu, Hawaii

value: bisected posterior piece

value: adult

value: 96 hours


title: G. hirsutum 28 day post anthesis cotton fiber biological pool 3

description:
Sample name: Gh28p3
Fiber pooled from 3 plants
RNA-Seq of Gossypium hirsutum 28 day post anthesis cotton fiber biological pool 3


title: G. hirsutum 15 day post anthesis cotton fiber biological pool 2

description:
Sample name: Gh15p2
Fiber pooled from 3 plants
RNA-Seq of Gossypium hirsutum 15 day post anthesis cotton fiber biological pool 2


title: Bisection - 96 hour - replicate 3

description:
Sample name: 96h-3
PolyA RNA
Processed data file: counts_table.txt
Processed data file: all_genes_expression.txt


title: Bisection - 96 hour - replicate 4

description:
Sample name: 96h-4
PolyA RNA
Processed data file: counts_table.txt
Processed data file: all_genes_expression.txt


title: G. hirsutum 15 day post anthesis cotton fiber biological pool 1

description:
Sample name: Gh15p1
Fiber pooled from 3 plants
RNA-Seq of Gossypium hirsutum 15 day post anthesis cotton fiber biological pool 1


title: Bisection - 72 hour - replicate 1

description:
Sample name: 72h-1
PolyA RNA
Processed data file: counts_table.txt
Processed data file: all_genes_expression.txt

source_name: Bisected posterior piece, 72 hours

value: 72 hours


title: Bisection - 48 hour - replicate 3

description:
Sample name: 48h-3
PolyA RNA
Processed data file: counts_table.txt
Processed data file: all_genes_expression.txt

source_name: Bisected posterior piece, 48 hours

value: 48 hours


title: Bisection - 72 hour - replicate 3

description:
Sample name: 72h-3
PolyA RNA
Processed data file: counts_table.txt
Processed data file: all_genes_expression.txt


title: Bisection - 48 hour - replicate 4

description:
Sample name: 48h-4
PolyA RNA
Processed data file: counts_table.txt
Processed data file: all_genes_expression.txt


title: Bisection - 72 hour - replicate 4

description:
Sample name: 72h-4
PolyA RNA
Processed data file: counts_table.txt
Processed data file: all_genes_expression.txt


title: Bisection - 48 hour - replicate 5

description:
Sample name: 48h-5
PolyA RNA
Processed data file: counts_table.txt
Processed data file: all_genes_expression.txt


title: Bisection - 48 hour - replicate 1

description:
Sample name: 48h-1
PolyA RNA
Processed data file: counts_table.txt
Processed data file: all_genes_expression.txt


title: Bisection - 24 hour - replicate 5

description:
Sample name: 24h-5
PolyA RNA
Processed data file: counts_table.txt
Processed data file: all_genes_expression.txt

source_name: Bisected posterior piece, 24 hours

value: 24 hours


title: Bisection - 48 hour - replicate 2

description:
Sample name: 48h-2
PolyA RNA
Processed data file: counts_table.txt
Processed data file: all_genes_expression.txt


title: G. hirsutum 21 day post anthesis cotton fiber biological pool 3

description:
Sample name: Gh21p3
Fiber pooled from 3 plants
RNA-Seq of Gossypium hirsutum 21 day post anthesis cotton fiber biological pool 3

value: 21 days post anthesis

value: cotton seed fiber

value: transition from primary to secondary cell wall deposition


title: Bisection - 24 hour - replicate 4

description:
Sample name: 24h-4
PolyA RNA
Processed data file: counts_table.txt
Processed data file: all_genes_expression.txt


title: wor-Gal4_Dam

city: Hobart

first: Owen

last: Marshall

state: Tas

address: 17 Liverpool St

country: Australia

institute: Menzies Institute for Medical Research

data_processing:
FASTQ files were processed using the damidseq_pipeline software, v1.2, using the parameters –len=350.
Genome_build: Dm_r5.57
Supplementary_files_format_and_content: GFF files were generated using the damidseq_pipeline software, at 75nt bin and GATC fragment resolution.  Score represents the normalised log2(Dam-fusion/Dam) enrichment

organism: Drosophila melanogaster

source_name: 3rd instar larvae

growth_protocol: Larvae were grown for 7 days at 18°C before shifting to 29°C for 16 hours

extract_protocol:
DNA was extracted from the anterior half of torn larvae via Qiagen Blood and Tissue kits as per manufacturers' instructions, digested with DpnI, DamID adaptors ligated, digested with DpnII and amplified via PCR.
DNA was sonicated to an average size of 350bp using a Diagenode Bioruptor and DamID adaptors removed via Sau3AI digestion, before processing with an Illumina TruSeq LT kit as per manufacturer's protocols

value: brain

value: 3rd instar larvae


title: wor-Gal4_Dam-polII


title: Bisection - 96 hour - replicate 2

description:
Sample name: 96h-2
PolyA RNA
Processed data file: counts_table.txt
Processed data file: all_genes_expression.txt


title: G. hirsutum 15 day post anthesis cotton fiber biological pool 3

description:
Sample name: Gh15p3
Fiber pooled from 3 plants
RNA-Seq of Gossypium hirsutum 15 day post anthesis cotton fiber biological pool 3

value: elongation and primary cell wall deposition


title: Bisection - 24 hour - replicate 3

description:
Sample name: 24h-3
PolyA RNA
Processed data file: counts_table.txt
Processed data file: all_genes_expression.txt


title: Bisection - 24 hour - replicate 2

description:
Sample name: 24h-2
PolyA RNA
Processed data file: counts_table.txt
Processed data file: all_genes_expression.txt


title: Bisection - 24 hour - replicate 1

description:
Sample name: 24h-1
PolyA RNA
Processed data file: counts_table.txt
Processed data file: all_genes_expression.txt


title: Bisection - 72 hour - replicate 2

description:
Sample name: 72h-2
PolyA RNA
Processed data file: counts_table.txt
Processed data file: all_genes_expression.txt


title: Bisection - 12 hour - replicate 2

description:
Sample name: 12h-2
PolyA RNA
Processed data file: counts_table.txt
Processed data file: all_genes_expression.txt

source_name: Bisected posterior piece, 12 hours

value: 12 hours


title: Bisection - 12 hour - replicate 4

description:
Sample name: 12h-4
PolyA RNA
Processed data file: counts_table.txt
Processed data file: all_genes_expression.txt


title: H3K79me2 ckit.neg

city: Stanford

first: Stephen HK

last: WONG

state: California

address: G2035 SIM1 Bldg

department: Pathology

institute: Stanford University

data_processing:
Sequencing was carried out at the Stanford Genome Center.
ChIP-seq reads were aligned to the mm9 genome assembly using commercial tool, DNANexus (https://www.dnanexus.com)
Only best reads that pass statistical criteria were used for peak mapping
Peaks calling were performed following recommendation of commerical too
Genome_build: mm9
Supplementary_files_format_and_content: bed files generated represend statistically mapped ChIP-seq reads and scores were assigned for each mapped reads

source_name: In-vivo leukemia cells from spleen

extract_protocol: 0.7% Fixed leukemia cells were lysed for 20 min in nuclear lysis buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS) containing freshly added 1x proteinase inhibitor cocktail (Roche) on ice, then sonicated to generate DNA fragments of 150-500 base pair using a Diagenode Bioruptor XL sonicator for a total duration of 60 cycles (30 seconds ON and 30 seconds OFF). The soluble chromatin was diluted 10-fold with ChIP dilution buffer (20m M Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 0.01% SDS, 1% Triton-x 100) containing 1x proteinase inhibitor cocktail, and the diluted duration of 60 cycles (30 seconds ON and 30 seconds OFF). The soluble chromatin was diluted 10-fold with ChIP dilution buffer (20m M Tris-HCl pH 8.0, 150 chromatin (1 mL equivalent to 2 million cells) was subjected to immunoprecipitation using various ChIP grade antibodies coupled with protein A magnetic beads (Invitrogen). DNA was used for ChIP-seq library construction based on manufacturer's protocol with modifications to account for limited number of cells (Schmidt et al., 2009).

tag: disease state

value: MLL-AF10 leukemia

tag: antibody

value: H3K79me2 (Abcam, ab3594)


title: RNA Pol II ckit.neg

value: RNA Pol II (Abcam, ab817)


title: Bisection - 12 hour - replicate 3

description:
Sample name: 12h-3
PolyA RNA
Processed data file: counts_table.txt
Processed data file: all_genes_expression.txt

value: Paiko Peninsula in Honolulu, Hawaii


title: H3K36me3 ckit.neg

value: H3K36me3 (Abcam, ab9050)


title: Bisection - 6 hour - replicate 4

description:
Sample name: 6h-4
PolyA RNA
Processed data file: counts_table.txt
Processed data file: all_genes_expression.txt

source_name: Bisected posterior piece, 6 hours

value: bisected posterior piece

value: adult

value: 6 hours


title: H3K27me3 ckit.neg

value: H3K27me3 (Millipore, 07-449)


title: H3K4me3 ckit.neg

value: H3K4me3 (Abcam, ab8580)


title: Bisection - 6 hour - replicate 3

description:
Sample name: 6h-3
PolyA RNA
Processed data file: counts_table.txt
Processed data file: all_genes_expression.txt


title: Bisection - 12 hour - replicate 1

description:
Sample name: 12h-1
PolyA RNA
Processed data file: counts_table.txt
Processed data file: all_genes_expression.txt


title: H3K4me2 ckit.neg

value: H3K4me2 (Abcam, ab7766)


title: Bisection - 6 hour - replicate 2

description:
Sample name: 6h-2
PolyA RNA
Processed data file: counts_table.txt
Processed data file: all_genes_expression.txt


title: Input ckit.neg


title: H3AcK27 ckit.neg

value: H3K27ac (Abcam, ab4729)


title: Bisection - 4 hour - replicate 3

description:
Sample name: 4h-3
PolyA RNA
Processed data file: counts_table.txt
Processed data file: all_genes_expression.txt

source_name: Bisected posterior piece, 4 hours

value: 4 hours


title: Bisection - 4 hour - replicate 2

description:
Sample name: 4h-2
PolyA RNA
Processed data file: counts_table.txt
Processed data file: all_genes_expression.txt


title: Bisection - 2 hour - replicate 4

description:
Sample name: 2h-4
PolyA RNA
Processed data file: counts_table.txt
Processed data file: all_genes_expression.txt

source_name: Bisected posterior piece, 2 hours

value: 2 hours


title: H3K79me2 ckit.pos


title: RNA Pol II ckit.pos


title: Bisection - 2 hour - replicate 2

description:
Sample name: 2h-2
PolyA RNA
Processed data file: counts_table.txt
Processed data file: all_genes_expression.txt


title: H3K4me3 ckit.pos


title: H3K27me3 ckit.pos


title: Bisection - 2 hour - replicate 3

description:
Sample name: 2h-3
PolyA RNA
Processed data file: counts_table.txt
Processed data file: all_genes_expression.txt


title: H3K36me3 ckit.pos


title: Bisection - 2 hour - replicate 1

description:
Sample name: 2h-1
PolyA RNA
Processed data file: counts_table.txt
Processed data file: all_genes_expression.txt


title: H3K4me2 ckit.pos


title: H3AcK27 ckit.pos


title: H3AcK18 ckit.pos

value: H3K18ac (Abcam, ab1191)


title: Bisection - 6 hour - replicate 1

description:
Sample name: 6h-1
PolyA RNA
Processed data file: counts_table.txt
Processed data file: all_genes_expression.txt


title: H3AcK18 ckit.neg


title: Intact bisection - 0 hour - replicate 1

description:
Sample name: 0h-1
PolyA RNA
Processed data file: counts_table.txt
Processed data file: all_genes_expression.txt

source_name: Bisected posterior piece, 0 hours

value: 0 hours


title: MSC_TGF_rp3

city: Naples

first: Nicola

last: Normanno

address: via Mariano Semmola

country: Italy

institute: INT PASCALE

data_processing:
Whole-transcriptome reads were aligned to the version 19 of the human genome (hg19) with the SOLiD LifeScope Genomic Analysis Software version 2.5 (Life Technologies) using the parameters recommended in the user’s manual.
The automatic quantification of transcriptional events across the entire genome was performed with LifeScope.
The number of observed counts (number of reads/gene) was normalized for the length of the transcript and the number of mapped reads (RPKM) (Reads Per Kilobase per Million of mapped reads).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: MSC

growth_protocol: Bone marrow-derived MSCs were purchased from Lonza (Verviers, Belgium) and maintained in MSCGM bullet kit (Lonza) in a humidified atmosphere at 37 °C and 5% CO2, as suggested by the provider.

extract_protocol:
Total RNA was extracted from untreated or TGFα-treated MSCs using TRIReagent, according to the manufacturer’s protocol (Ambion/Life Technologies, Milan, Italy). Poly(A) RNA was isolated using the Ambion MicroPoly(A) Purist Kit (LifeTechnologies).
RNA libraries were prepared for sequencing using standard Applied Biosystems SOLiD 5500xl protocols

treatment_protocol: MSCs were starved overnight in serum free medium and treated for 1 hour with recombinant human TGFα (PeproTech,Rocky Hill, NJ, USA) at a concentration of 10 ng/ml.

value: MSC

value: TGFa

value: Bone marrow


title: Bisection - 4 hour - replicate 4

description:
Sample name: 4h-4
PolyA RNA
Processed data file: counts_table.txt
Processed data file: all_genes_expression.txt


title: MSC_TGF_rp2


title: MSC_CTRL_rp4

value: control


title: MSC_CTRL_rp3


title: MSC_TGF_rp1


title: Input ckit.pos

value: MLL-AF10 leukemia


title: MSC_TGF_rp4


title: MSC_CTRL_rp1


title: MSC_CTRL_rp2


title: WT batch (DNA)

status: Public on Jun 25 2015

city: Adelaide

first: Long

last: Bui

state: South Australia

address: North Terrace Campus

department: Microbiology

institute: University of Adelaide

data_processing:
Library strategy: DNA-seq
Bowtie2 to align reads from samples
Genome_build: NC_007795; WCH-SK2 batch and WCH-SK2 SCV sequence
Supplementary_files_format_and_content: excel files (comma seperated values files) and excel worksheet files; fasta files are available on the series record.

organism: Staphylococcus aureus

growth_protocol: Strain WCH-SK2 was cultured in batch culture condition and in a prologned continuous culture (chemostat) for 60 days

extract_protocol:
Whole genomic DNA extraction and purification were performed according to manufacturers protocols (Blood and Cell culture DNA Maxi kit PN13362 and QIAGEN Genomic-tip 500/G columns, QIAGEN
SMRT sequencing from sequencing service provider (DNA Link, South Korea).

treatment_protocol: Cells were harvested and treated with RNA protect (Qiagen)

tag: strain

tag: phenotype

value: MRSA

tag: medium

value: batch culture - TSB

tag: stress

value: no stress


title: stable SCV (DNA)

value: day 55 of continuous culture -CDM

value: high level of stress (0.03%)


title: ChIP-seq, InVitroCistromics_ATF4_0.02uL_plusCEBPb_0.1uL

city: Philadelphia

first: David

middle: J

last: Steger

state: PA

address: 12-193 SCTR 3400 Civic Center Blvd

department: Institute of Diabetes, Obesity, and Metabolism

institute: University of Pennsylvania

data_processing:
Reads were mapped to the hg19 genome using Bowtie. Ambiguous alignments were excluded for TF ChIP-seq tracks. For H3K27Ac, reads were included with alignment locations of up to 3 possible loci.
Redundant reads were removed from TF ChIP-seq datasets using the makeTagDirectory script in HOMER. Redundant reads were preserved only for the H3K27Ac dataset.
Bed files for TF ChIP-Seq peaks were generated using the FindPeaks script in HOMER.
Bedgraph file for H3K27Ac was generated using the makeUCSCfile script in HOMER.
RNAPII.peaks.bed file was produced using a slope-based feature detection algorithm in Galaxy, see Cohen et al. ELife for details.
Input bias regions were manually curated from genomic regions showing strong ChIP enrichment on the genome browser independently of ChIP antibody.
Genome_build: hg19
Supplementary_files_format_and_content: 1 )TF ChIP-seq peak files in BED format 2) H3K27Ac in BEDGRAPH format

source_name: hMSC

growth_protocol: hMSCs were cultured in low glucose DMEM supplemented with 1% glutamine, and 10% FBS. For cell seeding density experiments, low cell density refers to 3000 cells/cm2, and high density to 35000 cells/cm2.

extract_protocol:
Cell pellets were prepared from 1.8x106 cells, crosslinked in 1 % formaldehyde for 15 minutes. A 5 minute quench was performed with 125mM glycine. Cells were harvested from 10 or 15cm dishes in DPBS using a cell scraper. To prepare ChIP extracts, nuclei were suspended SDS lysis buffer (50 mM HEPES/NaOH pH 7.5, 1% SDS, 10 mM EDTA, Complete protease inhibitor), incubated at 4 C for 10 min, and subjected to microtip probe sonication under conditions optimized for IP efficiency.
ChIP-Seq libraries were produced and sequenced according to Illumina protocols. Libraries were multiplexed for sequencing.

treatment_protocol: hMSCs were treated with DMI adipogenic induction medium for 24 hours (RNAPII) or 6 hrs (CEBPb, GR).

value: Human Mesenchymal Stem Cells

tag: chip antibody

value: ATF4, sc-200, Santa Cruz


title: ChIP-seq, InVitroCistromics_CEBPb_0.1uL_plusATF4_0.2uL

value: CEBPb, sc-150, Santa Cruz


title: ChIP-seq, RNAPII_HighDensity_DMI

value: RNAPII, sc-899, sc-9001, Santa Cruz


title: ChIP-seq, InVitroCistromics_ATF4_0.2uL_plusCEBPb_0.1uL


title: ChIP-seq, ATF4_HighDensity_noDMI


title: Intact bisection - 0 hour - replicate 2

description:
Sample name: 0h-3
PolyA RNA
Processed data file: counts_table.txt
Processed data file: all_genes_expression.txt

value: Paiko Peninsula in Honolulu, Hawaii

value: bisected posterior piece

value: adult

tag: time point


title: ChIP-seq, CEBPb_HighDensity_noDMI


title: ChIP-seq, InVitroCistromics_CEBPb_0.1uL_plusATF4_0.02uL


title: ChIP-seq, RNAPII_LowDensity_DMI


title: ChIP-seq, RNAPII_HighDensity_noDMI


title: ChIP-seq, InVitroCistromics_ATF4_5uL


title: ChIP-seq, InVitroCistromics_CEBPb_0.1uL_plusATF4_0.002uL


title: Intact bisection - 0 hour - replicate 3

description:
Sample name: 0h-4
PolyA RNA
Processed data file: counts_table.txt
Processed data file: all_genes_expression.txt

tag: age

value: 0 hours


title: ChIP-seq, RNAPII_LowDensity_noDMI


title: ChIP-seq, InVitroCistromics_CEBPb_1.0uL


title: Stomach_20wkB

first: Linda

last: Szabo

address: Beckman Center, B400 279 W. Campus Dr. MC: 5307

department: Biochemistry

data_processing:
Raw fastq files were processed using TrimGalore version 0.3.7 and cutAdapt version 1.5 to remove adapter sequences and trim poor-quality bases.  All default values were used, with the exceptions that the length parameter was set to exclude reads where either mate had a trimmed length of less than 50
Circular and linear junction reads were called using custom scripts available with publication
Genome_build: hg19
Supplementary_files_format_and_content: txt files were generated by custom scripts available with publication; in denovo report files, pvalue represents the p-value from the naïve method (high p-value indicates high confidence in this splice); in other report files, pvalue represents the posterior probability from the GLM method (high posterior probability indicates high confidence)

source_name: Stomach

extract_protocol:
Fetal tissue samples <100 mg in size were placed into DNase- and RNase-free 1.5 ml microfuge tubes containing 1 ml of RNAlater RNA Stabilization Reagent (Qiagen) within 1 hour of the pregnancy termination procedure. After storage at room temperature for a period of 24-72 h, excess RNAlater was removed from the microfuge tubes and the samples were placed in the -80oC freezer for storage until RNA isolation was performed. The tissues were lysed in mirVana (Life Technologies) lysis buffer, using a Mini-Beadbeater-16 (Biospec), with agitation for 1 min in the presence of 1 mm zirconia beads. Samples were then centrifuged at maximum speed in a tabletop microcentrifuge for 1 min and the lysed solution was transferred to a fresh microfuge tube. The remainder of the extraction was per the manufacturer's protocol for the mirVana kit (Life Technologies).
Following RNA isolation (mirVana miRNA Isolation Kit, Life Technologies, Inc.), the RNA was quantified (Qubit RNA Assay Kit, Life Technologies, Inc.), and quality controlled (RNA6000 Nano Kit and BioAnalyzer 2100, Agilent). 200 ng to 1000 ng was used as input for the Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold sample prep kit (Illumina, Inc.) and sequencing libraries were created according to the manufacturer’s protocol. Briefly, first both cytoplasmic and mitochondrial rRNA was removed by selectively hybridizing biotinylated probes to target sequences and using magnetic beads to capture the bound products. Following rRNA removal, the RNA was fragmented and copied into first strand cDNA using random primers and reverse transcriptase. Next, second strand cDNA synthesis was completed using DNA Polymerase I and RNase H. The cDNA was then ligated to Illumina supplied adapters and enriched with PCR to create the final cDNA libraries. The libraries were then pooled and sequenced on a HiSeq 2000 (Illumina, Inc.) instrument as per manufacturer’s instructions. Sequencing was performed up to 2 X 101 cycles.

tag: age in weeks


title: Stomach_20wkA


title: ChIP-seq, InVitroCistromics_CEBPb_0.25uL


title: ChIP-seq, InVitroCistromics_CEBPb_0.1uL


title: Stomach_16wk


title: ChIP-seq, InVitroCistromics_CEBPb_10uL


title: Stomach_10wkB


title: Stomach_18wk


title: D14_cardio_3_4

data_processing:
Raw fastq files were processed using TrimGalore version 0.3.7 and cutAdapt version 1.5 to remove adapter sequences and trim poor-quality bases.  All default values were used, with the exceptions that the length parameter was set to exclude reads where either mate had a trimmed length of less than 50
Circular and linear junction reads were called using custom scripts available with publication
Genome_build: hg19
Supplementary_files_format_and_content: txt files were generated by custom scripts available with publication; pvalue represents the posterior probability from the GLM method (high posterior probability indicates high confidence)

source_name: RUES2 human embryonic stem cells

growth_protocol: RUES2 human embryonic stem cells were maintained in mouse embryonic fibroblast-conditioned media

extract_protocol:
Between 1-3 million cells per sample were pelleted for each sample. RNA was extracted as per the manufacturer's protocol for the mirVana kit (Life Technologies). After extraction, RNA was quantified using the Quant-iT RNA BR Assay Kit (Life Technologies). RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent) using RNA Nano-chips. Following RNA isolation (mirVana miRNA Isolation Kit, Life Technologies, Inc.), the RNA was quantified (Qubit RNA Assay Kit, Life Technologies, Inc.), and quality controlled (RNA6000 Nano Kit and BioAnalyzer 2100, Agilent)
200 ng to 1000 ngwas used as input for the Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold sample prep kit (Illumina, Inc.) and sequencing libraries were created according to the manufacturer’s protocol. Briefly, first both cytoplasmic and mitochondrial rRNA was removed by selectively hybridizing biotinylated probes to target sequences and using magnetic beads to capture the bound products. Following rRNA removal, the RNA was fragmented and copied into first strand cDNA using random primers and reverse transcriptase. Next, second strand cDNA synthesis was completed using DNA Polymerase I and RNase H. The cDNA was then ligated to Illumina supplied adapters and enriched with PCR to create the final cDNA libraries. The libraries were then pooled and sequenced on a HiSeq 2000 (Illumina, Inc.) instrument as per manufacturer’s instructions. Sequencing was performed up to 2 X 101 cycles.

treatment_protocol: The differentiation set up was initiated by plating undifferentiated hESCs as single cells. The cultures were treated with CHIR-99021 (Cayman chemical,13122) for 24 hours before reaching confluence. Cells were induced to differentiate (designated day 0) by replacing the culturing media with RPMI media (Invitrogen, 11875-119) containing 100 ng/mL Activin A (R&D SYSTEMS, 338-AC-050), 1:60 diluted Matrigel (BD), and insulin-free B27 supplement (Invitrogen, 0050129SA). An RPMI media change the following day (17 hours) included different 5 ng/mL BMP4 (R&D SYSTEMS, 314-BP-050), 1 uM CHIR-99021, and insulin-free B27 supplement. On day 3 of differentiation media was changed to RPMI media containing 1 uM XAV-939 (Tocris, 3748) and insulin-free B27 supplement. RPMI containing insulin-free B27 supplement was utilized until differentiation day 7 in which the media is replaced with RPMI containing a B27 supplement that includes insulin (Invitrogen, 17504044).  Subsequent media changes included the insulin-containing supplement.

tag: differentiation stage

value: definitive cardiomyocyte


title: Lung_20wkB

source_name: Lung


title: D14_cardio_3_3


title: Stomach_10wkA


title: D14_cardio_3_2


title: D14_cardio_3_5


title: Stomach_20wkC


title: Lung_20wkA


title: D14_cardio_2_6


title: Lung_17wkB


title: D14_cardio_3_1


title: D14_cardio_2_5


title: Lung_10wkB


title: Lung_17wkA


title: Lung_10wkA


title: D14_cardio_2_2


title: D14_cardio_2_1


title: D14_cardio_2_3


title: D14_cardio_1_5


title: Kidney_16wk

source_name: Kidney


title: D14_cardio_1_4


title: D14_cardio_1_3


title: Intestine_17wk

source_name: Intestine


title: Intestine_15wk


title: D5_progen_3_8

value: cardiac progenitor


title: D14_cardio_1_1


title: Intestine_11wk


title: D14_cardio_2_4


title: D5_progen_3_7


title: D5_progen_3_6


title: Intestine_20wkA


title: Intestine_10wkA


title: Kidney_20wk


title: D5_progen_3_5


title: Heart_20wkA

source_name: Heart


title: Heart_20wkC


title: D5_progen_3_4


title: D5_progen_3_3


title: Heart_20wkB


title: Intestine_10wkB


title: Intestine_20wkB


title: D5_progen_3_2


title: Heart_17wk


title: Heart_18wk


title: Heart_11wk


title: D5_progen_2_6


title: Heart_10wk


title: D14_cardio_1_2


title: D5_progen_3_1


title: Kidney_10wk


title: D5_progen_2_4


title: D5_progen_2_2


title: D5_progen_2_3


title: D5_progen_2_5


title: D5_progen_2_1


title: Adrenal_20wkA

source_name: Adrenal


title: Adrenal_16wk


title: D5_progen_1_1


title: Adrenal_10wk


title: D5_progen_1_2


title: D5_progen_1_3


title: D3_meso_3_7

value: mesoderm


title: D3_meso_3_6


title: D3_meso_3_2


title: D3_meso_3_4


title: D3_meso_3_1


title: D2_meso_2_5


title: D2_meso_1_4


title: D2_meso_2_4


title: D2_meso_1_5


title: D2_meso_2_2


title: D2_meso_2_1


title: D2_meso_1_3


title: D2_meso_1_2


title: Adrenal_18wk


title: D2_meso_1_1


title: D0_undiff_3_5

value: undifferentiated


title: Adrenal_20wkB


title: D0_undiff_3_6


title: D0_undiff_3_4


title: D0_undiff_3_3


title: D0_undiff_3_2


title: D0_undiff_3_7


title: D0_undiff_2_7


title: D0_undiff_2_6


title: D0_undiff_3_1


title: D0_undiff_2_4


title: D0_undiff_2_5


title: D3_meso_3_5


title: D2_meso_2_3


title: D0_undiff_2_2


title: D0_undiff_1_7


title: D0_undiff_1_5


title: D0_undiff_1_4


title: D3_meso_3_3


title: ChIP-Bcl3

city: Taipei

first: Chen-Yun

last: Chen

address: 128 Sec. 2, Academia Rd.

department: Institute of Biomedical Science

country: Taiwan

institute: Acdemia Sinica

data_processing:
DNA reads were trimmed for adaptor and low-quality sequence, then mapped to mouse reference genome mm9 with Burrows-Wheeler transform.
CisGenome was then used for peak detection.
Genome_build: mm9
Supplementary_files_format_and_content: xlsx file with peak data

source_name: embryonic stem cells_ChIP

growth_protocol: CGR8 mouse embryonic stem cells were cultured on 0.1% gelatin (Sigma) coated dishes in maintenance medium; Glasgow Minimum Essential Medium (Sigma) supplemented with 15% knock-out serum replacement (Invitrogen), 1x non-essential amino acids (Invitrogen), 1 mM sodium pyruvate (Invitrogen), 1x penicillin/streptomycin (Invitrogen), 0.1 mM β-mercaptoethanol (Invitrogen) and 1000 U/ml leukemia inhibitory factor (Millipore).

extract_protocol:
Lysates were clarified from enzyme-digested nuclei and protein-DNA complexes were pulled-down with antibody (anti-Bcl3, catalog number GTX108293, GeneTex)
Libraries were prepared according to Illumina's instructions, including end repair, 3' end adenylation, ligation with adaptors and DNA enrichment.

tag: cell line

value: embryonic stem cells


title: KD-poly(I:C)

city: Davis

first: Huaijun

last: Zhou

address: Meyer 3307, One shields Ave.

institute: UC Davis

data_processing:
Paired-end raw reads were aligned against the galGal4 reference chicken genome, Ensembl gene model (version 75), by Tophat2 (Version 2.1.0)
FPKM values were mesured by the Cufflinks program (Version 2.1.0).
Differential expression analysis were also performed by Cufflinks program using embeded cuffdiff tool.
Genome_build: Galgal4, Ensembl gene model annotation (versin 75)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample. Default output file of cufflinks genes.fpkm_traking file

source_name: DF-1 cell line

growth_protocol: DMEM, 10% FBS

extract_protocol:
Direct-zol™ RNA MiniPrep Kit (Zymo research, Irvine, CA) was used to isolate RNA from cell lines.
NEBNext® Ultra™ Directional RNA Library Prep Kit (New England Biolabs, Ipswich, MA) to generate cDNA library from the total RNA extracted.

treatment_protocol: Apply poly(I:C) into the growth medium

value: immortalized chicken embryonic fibroblast

tag: treatment

value: 6h post induction of poly(I:C) (1µg/mL(Invivogen))

tag: modification

value: IRF7 knockdown shRNA transfected


title: NS-poly(I:C)

tag: cell type

value: non-specific shRNA transfected


title: KD-Mock

value: Mock (media)


title: Input

source_name: embryonic stem cells_input


title: D0_undiff_1_3


title: OE-poly(I:C)

value: IRF7 overexpressed


title: NS-Mock


title: D0_undiff_2_1


title: D0_undiff_1_2


title: Control-Mock

value: empty DNA vector


title: D0_undiff_1_1


title: H3K9me3_ChIPSeq_noTam_R4

city: Suzhou

first: Xiaoqin

last: Yang

state: Jiangsu

address: No. 199, Ren'ai Road

institute: Suzhou Medical College of Soochow University

data_processing:
Basecalls performed using Off-Line Basecaller 1.9.4
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie version 0.12.7
peaks were called using MACS version 2.1.0 with the following setting: broad, extsize (146), q-value (0.01)
Genome_build: mm9
Supplementary_files_format_and_content: bigwiggle files were generated by MACS2, the score represents number of bp fall into the single base pair region.

growth_protocol: The iKO ES cells were cultured feeder-free in 60 mm or 100 mm tissue culture dishes at 37 C with 5% CO2. The culture surface was pre-coated with 0.1% (w/v) gelatin in PBS. The ES cell culture medium consists of Dulbecco's modified Eagle's medium supplemented with 15% fetal bovine serum, 1 mM glutamine, 0.1 mM β-mercaptoethanol, 0.1 mM non-essential amino acid, 50 U/mL penicillin plus 50 µg/mL streptomycin, and 1000 units ESGRO (LIF).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
For ChIP-seq libraries, 10 ng of input chromatin DNA or ChIP DNA were processed using the ChIP-seq sample prep kit (Illumina). Gel-purified ChIP-seq library DNA was further purified by phenol-chloroform extraction and ethanol precipitation, and processed for cluster generation, 15-cycle sequencing, and sequence analysis using Illumina Hiseq.

treatment_protocol: To induce the ablation of Setdb1, cells were treated with 2.5 μM tamoxifen (Tam) (Sigma), with DMSO used as the solvent control

tag: genotype/variation

value: inducible SetDB1 KO

value: ES cells

tag: treated with

value: none (noTam)


title: F1_Cvi_Col_1_NS

city: Versailles

first: Francisco

middle: A.

last: Cubillos

address: Route de St Cyr

country: France

institute: INRA-IJPB

data_processing:
Aligment was peformed using Palmapper v.0.4 using Col-0 and seudo-Cvi-0 genomes as references
Reads were called as either Col or Cvi based on SNP data from the re-sequencing of Cvi-0
Genome_build: TAIR10
Supplementary_files_format_and_content: allele specific expression ASE of Col-0 vs. Cvi-0

organism: Arabidopsis thaliana

source_name: 3-week old plants

growth_protocol: Samples were grown in the Phenoscope platform for 21 days under short day periods.

extract_protocol:
RNeasy Plant mini kit (Qiagen kit #74904)
Libraries were prepared according to Illumina's protocol for HiSeq2000

treatment_protocol: Water was automatically controlled and images were taken every day.

value: Control

tag: sample type

value: individual plant

value: 3 wk

tag: genetic background

value: F1 hybrids between Col-0 and Cvi-0

tag: tissue

value: whole plant


title: F1_Col_Cvi_3_NS


title: D0_undiff_1_6

value: undifferentiated


title: F1_Col_Cvi_3_S

value: drought stress


title: H3K9me3_ChIPSeq_noTam_R3

tag: strain

value: H3K9me3 (Active Motif:39161)


title: F1_Col_Cvi_1_S


title: H3K9me3_ChIPSeq_noTam_R2


title: Mnase-0.75X_Small

city: Berkeley

first: Xavier

last: Darzacq

address: 475D Li Ka Shing Center

department: Molecular and Cell Biology

institute: University of California, Berkeley

description:
Sample 90
processed data file: Micro-C interactions vs. distance for MNase titrations.xlsx
NDR-spanning reads for all replicates.xlsx

data_processing:
library strategy: Micro-C
OLB 1.9/CASAVA_v1.8.2 were used for base calling
Barcoded libraries were demultiplexed by Novobarcode.
Paired reads were mapped to sacCer3 genome separately by Bowtie2
Parse SAM files and remove duplicate reads.
Mate unique paired mates and generate interaction matrix.
Genome_build: S288C (sacCer3)
Supplementary_files_format_and_content: readme.txt file contains additional description of how each processed data file was generated.

organism: Saccharomyces cerevisiae

growth_protocol: 100mL yeast culture were grown to midlog phase ~OD 0.55 in YPD media at 30 C.

extract_protocol:
DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis.
Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers.
Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads.

treatment_protocol: Yeast cells were fixed with 3% formaldehyde for 15 min, and quenched with 125 mM glycine for 5 min. Cells were pelleted, spheroplasted with Zymolyase, and treated with a level of MNase yielding >95% mononucleosom. After stopping MNase, chromatin supernatant was dephosphorylated using Antarctic phosphatase. Crosslinked chromatin was subject to T4 DNA polymerase / T4 PNK enzyme mix solution to generate blunt ends. Crosslinked chromatin was diluted into 10 mL and treated with T4 DNA ligase. After heat inactivation, chromatin was concentrated to 250uL, and treated with 100U of exonuclease III for 5 min to eliminate biotinylated ends of unligated DNA. Proteinase K was then added and incubated for 65 C overnight.

tag: media

value: YPD


title: F1_Col_Cvi_2_NS


title: Mnase-0.25X_Small

description:
Sample 88
processed data file: Micro-C interactions vs. distance for MNase titrations.xlsx
NDR-spanning reads for all replicates.xlsx


title: Mnase-0.5X_Small

description:
Sample 89
processed data file: Micro-C interactions vs. distance for MNase titrations.xlsx
NDR-spanning reads for all replicates.xlsx


title: F1_Col_Cvi_1_NS


title: Pool_Col_Cvi_4_S

value: pool of plants

value: Pool of equal amounts of cDNA from parental Col-0 and Cvi-0 plants


title: Mnase-1X_Tri-Tetra

description:
Sample 87
processed data file: Micro-C interactions vs. distance for MNase titrations.xlsx
NDR-spanning reads for all replicates.xlsx


title: OE-Mock

value: immortalized chicken embryonic fibroblast

value: Mock (media)


title: Pool_Col_Cvi_3_S


title: Mnase-0.75X_Tri-Tetra

description:
Sample 86
processed data file: Micro-C interactions vs. distance for MNase titrations.xlsx
NDR-spanning reads for all replicates.xlsx


title: Control-poly(I:C)

value: 6h post induction of poly(I:C) (1µg/mL(Invivogen))

value: empty DNA vector


title: Mnase-0.5X_Tri-Tetra

description:
Sample 85
processed data file: Micro-C interactions vs. distance for MNase titrations.xlsx
NDR-spanning reads for all replicates.xlsx


title: Pool_Col_Cvi_1_NS


title: D0_undiff_2_3


title: Mnase-1X_Small

description:
Sample 91
processed data file: Micro-C interactions vs. distance for MNase titrations.xlsx
NDR-spanning reads for all replicates.xlsx


title: F1_Col_Cvi_2_S


title: Mnase-0.5X_Monomer

description:
Sample 81
processed data file: Micro-C interactions vs. distance for MNase titrations.xlsx
NDR-spanning reads for all replicates.xlsx


title: Mnase-0.25X_Monomer

description:
Sample 80
processed data file: Micro-C interactions vs. distance for MNase titrations.xlsx
NDR-spanning reads for all replicates.xlsx


title: Mnase-1X_Monomer

description:
Sample 83
processed data file: Micro-C interactions vs. distance for MNase titrations.xlsx
NDR-spanning reads for all replicates.xlsx


title: Mnase-0.75X_Monomer

description:
Sample 82
processed data file: Micro-C interactions vs. distance for MNase titrations.xlsx
NDR-spanning reads for all replicates.xlsx


title: Mnase-0.25X_Dimer

description:
Sample 76
processed data file: Micro-C interactions vs. distance for MNase titrations.xlsx
NDR-spanning reads for all replicates.xlsx


title: rgr1-100-37C_rep1

description:
Sample 68
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for temperature-sensitive dataset.xlsx

value: rgr1-97, ts-allele mutant


title: Mnase-0.75X_Dimer

description:
Sample 78
processed data file: Micro-C interactions vs. distance for MNase titrations.xlsx
NDR-spanning reads for all replicates.xlsx


title: Mnase-0.5X_Dimer

description:
Sample 77
processed data file: Micro-C interactions vs. distance for MNase titrations.xlsx
NDR-spanning reads for all replicates.xlsx


title: top1d_rep1

description:
Sample 63
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: ssu72-2_rep3

description:
Sample 62
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx

value: ssu72-2, ts-allele mutant


title: ssu72-2_rep1-2

description:
Sample 59
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: ssu72-2_rep2

description:
Sample 60
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: ssu72-2_rep2-2

description:
Sample 61
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: rtt109d_rep2-2

description:
Sample 56
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: rtt109d_rep3

description:
Sample 57
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: Mnase-0.25X_Tri-Tetra

description:
Sample 84
processed data file: Micro-C interactions vs. distance for MNase titrations.xlsx
NDR-spanning reads for all replicates.xlsx


title: rtt109d_rep1-2

description:
Sample 54
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: ssu72-2_rep1

description:
Sample 58
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: sth1-2-37C_rep2

description:
Sample 75
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for temperature-sensitive dataset.xlsx

value: sth1-2, ts-allele mutant


title: sth1-2-37C_rep1

description:
Sample 74
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for temperature-sensitive dataset.xlsx


title: top1d_rep2

description:
Sample 64
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: rtt109d_rep2

description:
Sample 55
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: rpd3d_rep1

description:
Sample 50
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: rtt109d_rep1

description:
Sample 53
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: Mnase-1X_Dimer

description:
Sample 79
processed data file: Micro-C interactions vs. distance for MNase titrations.xlsx
NDR-spanning reads for all replicates.xlsx


title: rpd3d_rep2

description:
Sample 52
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: rpd3d_rep1-2

description:
Sample 51
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: BY4741-37C_rep1

description:
Sample 65
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for temperature-sensitive dataset.xlsx


title: rsc8-21-37C_rep2

description:
Sample 71
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for temperature-sensitive dataset.xlsx

value: rsc8-21, ts-allele mutant


title: rnh201d_rep2

description:
Sample 49
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: rnh201d_rep1

description:
Sample 48
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: med1d_rep2-2

description:
Sample 46
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: med1d_rep3

description:
Sample 47
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: rgr1-100-37C_rep2

description:
Sample 69
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for temperature-sensitive dataset.xlsx


title: med1d_rep1-2

description:
Sample 44
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: BY4741-37C_rep2

description:
Sample 66
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for temperature-sensitive dataset.xlsx


title: med1d_rep1

description:
Sample 43
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: BY4741-37C_rep3

description:
Sample 67
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for temperature-sensitive dataset.xlsx


title: med1d_rep2

description:
Sample 45
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: H4Q93E

description:
Sample 38
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: scc2-4-37C_rep2

description:
Sample 73
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for temperature-sensitive dataset.xlsx

value: scc2-4, ts-allele mutant


title: H4R23A_rep2

description:
Sample 41
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: H4R23A_rep1

description:
Sample 39
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: H4K16Q_rep1-2

description:
Sample 37
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: H4K16Q_rep1

description:
Sample 36
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: scc2-4-37C_rep1

description:
Sample 72
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for temperature-sensitive dataset.xlsx


title: H4R23A_rep1-2

description:
Sample 40
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: W303_rep1

description:
Sample 29
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: H4d4-14_rep1-2

description:
Sample 33
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: H4d4-14_rep1

description:
Sample 32
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: H4-WT

description:
Sample 31
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx

value: S288C strain, H3/H4 plasmid


title: H4d4-14_rep2-2

description:
Sample 35
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: H4d4-14_rep2

description:
Sample 34
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx