title: 2742: U2OS2-6-3_RNA_mock_transfected_1


title: q83_14dpOBX injured olfactory epithelium

status: Public on Nov 22 2017

type: SRA

city: Boston

first: Brian

last: Lin

state: MA

address: 136 Harrison Avenue

department: DMCB

country: USA

institute: Tufts University

library_source: transcriptomic

data_processing:
Demultiplexed reads are FASTQC trimmed
Mapped using STAR-2.5.2a
Samples were combined and normalized for library size using Cuffnorm, in the Cufflinks-2.2.1 package to output normalized FPKM and count estimates.
Genome_build: MM9
Supplementary_files_format_and_content: merged csv with either normalized counts or normalized FPKM

molecule: polyA RNA

organism: Mus musculus

source_name: 14dpOBX injured olfactory epithelium

extract_protocol:
Cell Dissociation protocol: Cells were dissociated from donor animals anaesthetized with IP injection of a triple cocktail of ketamine (37.5 mg/kg), xylazine (7.5 mg/kg), and acepromazine (1.25 mg/kg) and perfused with cold Low Ca2+ Ringers solution (140mM NaCl, 5mM KCl, 10mM HEPES, 1mM EDTA, 10mM glucose, 1mM sodium pyruvate, pH7.2). The olfactory epithelium is isolated away from respiratory tissue, finely minced, and incubated in 0.05% Trypsin-EDTA for 10 minutes on an orbital shaker at 37°C where it forms a sticky ball. The supernatant was replaced with an enzyme cocktail containing (100 U/ml collagenase, 250 U/ml hyaluronidase, 75 U/ml DNase I, 0.1 mg/ml trypsin inhibitor, 2.5 U/ml Dispase II, 350 U/ml Collagenase Type I, 5U/ml papain; from Worthington Biochemical, Roche, and Sigma) in Regular Ringers solution (140mM NaCl, 5mM KCl, 10mM HEPES, 1mM EDTA, 10mM glucose, 1mM sodium pyruvate, 1mM CaCl2, 1mM MgCl2, pH7.2). The tissue was incubated in the enzyme cocktail on an orbital shaker at 37°C for 15 minutes, after which the supernatant was replaced with fresh enzyme cocktail and incubated once again for 15 minutes. The supernatant is stored on ice in the meantime. After the second incubation, the pooled supernatant is filtered through 30 µm filter and centrifuged at <500g on a swinging bucket rotor for 5 minutes. The pellet is resuspended in 1x HBSS containing 25 mM HEPES, 10 mM EDTA for FACS purification based on eGFP positivity.
RNA and cDNA were generated using standard Fluidigm C1-Autoprep protocols
Libraries were generated using standard Illumina Nextera XT kit protocols modified by published Fluidigm C1-Autoprep modifications

tag: strain

value: FVB Neurog1-eGFP

tag: tissue

value: olfactory epithelium

tag: age

value: 8 wk

tag: genotype


title: 2740: U2OS2-6-3_RNA_untransfected_1

city: Heidelberg

first: Nick

last: Kepper

address: Im Neuenheimer Feld 267 - BQ24

department: Chromatin Networks

country: Germany

institute: German Cancer Research Center

data_processing:
exclusion of reads aligning to transfected constructs using bowtie (no mismatches, multiple mapping allowed: bowtie -t -v 0 -M 1)
exclusion of reads aligning to the reporter construct described in (Janicki et al. 2004, Cell 116, 683-698), same mapping strategy as for the transfected constructs
mapping of remaining reads to the human reference genome using STAR (no mismatches, unique mapping: STAR --alignIntronMax 100000 --chimSegmentMin 1 --outFilterMultimapNmax 1 --outFilterMismatchNmax 0)
generation of count table using multibamcoverage (deeptools2.0) including strand information (multiBamCov -D -split -S)
filtering out gene predictions and transcripts with identical genomic start and end positions
addition of the two reporter genes (ECFP-SKL and MS2 loops) into the count table
application of DESeq2 for differential expression analysis
Genome_build: hg38
Supplementary_files_format_and_content: txt, result tables with genomic coordinates, RefSeq identifiers and DESeq2 results for each gene

molecule: total RNA

organism: Homo sapiens

source_name: U2OS 2-6-3 cell line

growth_protocol: U2OS 2-6-3 cells were cultured in DMEM medium containing 1 g/l glucose, supplemented with 10% doxycycline-free fetal bovine serum, 1x penicillin/streptomycin and 2 mM stable glutamine

extract_protocol:
NucleoSpin RNA Plus (Macherey-Nagel) according to the manufacturer's protocol
NEBNext Ultra II Directional RNA library Prep Kit (NEB) according to the manufacturer's protocol

treatment_protocol: cells were exposed to white light over night

value: U2OS 2-6-3 cell line

tag: transient transfection

tag: transfection protocol

tag: illuminated over night

value: yes


title: q81_14dpOBX injured olfactory epithelium


title: q79_5dpOBX injured olfactory epithelium

source_name: 5dpOBX injured olfactory epithelium


title: q78_5dpOBX injured olfactory epithelium


title: 2741: U2OS2-6-3_RNA_untransfected_2


title: q80_14dpOBX injured olfactory epithelium


title: q77_14dpOBX injured olfactory epithelium


title: q76_5dpOBX injured olfactory epithelium


title: q73_Uninjured olfactory epithelium

description: Uninjured

source_name: Uninjured olfactory epithelium


title: q74_5dpOBX injured olfactory epithelium


title: q72_Uninjured olfactory epithelium

description: Uninjured


title: q71_Uninjured olfactory epithelium

description: Uninjured


title: q70_5dpOBX injured olfactory epithelium


title: q69_Uninjured olfactory epithelium

description: Uninjured


title: q75_5dpOBX injured olfactory epithelium


title: q67_Uninjured olfactory epithelium

description: Uninjured


title: q66_5dpOBX injured olfactory epithelium


title: q68_5dpOBX injured olfactory epithelium


title: q65_5dpOBX injured olfactory epithelium


title: q85_14dpOBX injured olfactory epithelium


title: q86_5dpOBX injured olfactory epithelium


title: q82_14dpOBX injured olfactory epithelium


title: q64_5dpOBX injured olfactory epithelium


title: q63_Uninjured olfactory epithelium

description: Uninjured


title: q60_5dpOBX injured olfactory epithelium


title: q59_Uninjured olfactory epithelium

description: Uninjured


title: q61_5dpOBX injured olfactory epithelium


title: q57_Uninjured olfactory epithelium

description: Uninjured


title: q56_Uninjured olfactory epithelium

description: Uninjured


title: Pa097BS

city: Singapore

first: Sonia

last: Chothani

address: 8 College Road

country: Singapore

institute: Duke-NUS school of medicine

data_processing:
Alignment: High-quality reads were mapped to Ensembl human GRCh38 v78 reference genome using TopHat v2.0.12 with the following parameters: prefilter multihits, mate inner distance of 0 and read realign edit distance of 0 (default was used for the rest of parameters).
Gene level counts were computed by using HTSeq (version 0.6.1)
Genome_build: GRCh38 v78
Supplementary_files_format_and_content: 168_fibroblast_samples_gene_counts.txt : file with gene level counts, fibroblasts_samples_info.txt: technical, clinical covariates and samples treatment

source_name: right atrial appendage biopsies

extract_protocol: Libraries were constructed with TruSeq Stranded mRNA Library Prep kit (Illumina) using 0.8µg of total RNA. RNA-seq, barcoded libraries were multiplexed and sequenced as paired-end reads on Illumina HiSeq 2500 platform using NextSeq High output 150 cycles kit across 4 lanes.

treatment_protocol: Cardiac fibroblasts were cultured in serum-free media for 24 hours prior to treatment. They were further treated with TGFB1.

tag: race

value: Chinese

tag: gender

value: male

tag: cell type

value: Cardiac fibroblasts

tag: treatment

value: Control


title: Pa097ST

value: human recombinant TGFB1 (Serotec)


title: Pa095ST


title: Pa096ST


title: q53_Uninjured olfactory epithelium

description: Uninjured


title: q54_Uninjured olfactory epithelium

description: Uninjured


title: Pa095BS


title: Pa096BS


title: q55_Uninjured olfactory epithelium

description: Uninjured


title: Pa094ST

value: female


title: q52_Uninjured olfactory epithelium

description: Uninjured


title: Pa093ST


title: Pa093BS


title: q51_Uninjured olfactory epithelium

description: Uninjured


title: q50_Uninjured olfactory epithelium

description: Uninjured


title: q49_Uninjured olfactory epithelium

description: Uninjured


title: q48_Uninjured olfactory epithelium

description: Uninjured


title: Pa094BS


title: Pa092ST


title: q47_Uninjured olfactory epithelium

description: Uninjured


title: q62_5dpOBX injured olfactory epithelium


title: Pa092BS


title: q58_Uninjured olfactory epithelium

description: Uninjured


title: q45_Uninjured olfactory epithelium

description: Uninjured


title: q44_Uninjured olfactory epithelium

description: Uninjured


title: Pa091ST


title: q46_Uninjured olfactory epithelium

description: Uninjured


title: Pa091BS


title: Pa088ST

value: Indian


title: Pa088BS


title: q43_Uninjured olfactory epithelium

description: Uninjured


title: Pa087ST

value: Malay


title: q41_Uninjured olfactory epithelium

description: Uninjured


title: q42_Uninjured olfactory epithelium

description: Uninjured


title: q40_Uninjured olfactory epithelium

description: Uninjured


title: Pa086ST


title: q39_Uninjured olfactory epithelium

description: Uninjured


title: Pa086BS


title: q38_Uninjured olfactory epithelium

description: Uninjured


title: Pa087BS


title: q36_Uninjured olfactory epithelium

description: Uninjured


title: Pa081ST


title: Pa084BS


title: q35_Uninjured olfactory epithelium

description: Uninjured


title: Pa084ST


title: Pa080ST


title: Pa081BS


title: q37_Uninjured olfactory epithelium

description: Uninjured


title: q33_Uninjured olfactory epithelium

description: Uninjured


title: q34_Uninjured olfactory epithelium

description: Uninjured


title: q32_Uninjured olfactory epithelium

description: Uninjured


title: Pa080BS


title: Pa079ST


title: q31_Uninjured olfactory epithelium

description: Uninjured


title: Pa078ST


title: Pa079BS


title: q30_Uninjured olfactory epithelium

description: Uninjured


title: q29_Uninjured olfactory epithelium

description: Uninjured


title: q28_Uninjured olfactory epithelium

description: Uninjured


title: q27_Uninjured olfactory epithelium

description: Uninjured


title: Pa076ST


title: Pa077BS


title: Pa076BS


title: q24_Uninjured olfactory epithelium

description: Uninjured


title: q23_Uninjured olfactory epithelium

description: Uninjured


title: q22_Uninjured olfactory epithelium

description: Uninjured


title: Pa075ST


title: Pa074ST


title: Pa075BS


title: q21_Uninjured olfactory epithelium

description: Uninjured


title: Pa073ST


title: Pa074BS


title: Pa078BS


title: q19_Uninjured olfactory epithelium

description: Uninjured


title: q25_Uninjured olfactory epithelium

description: Uninjured


title: q18_Uninjured olfactory epithelium

description: Uninjured


title: Pa072ST


title: Pa070ST


title: Pa070BS


title: q14_5dpOBX injured olfactory epithelium


title: Pa069BS


title: q15_5dpOBX injured olfactory epithelium


title: q26_Uninjured olfactory epithelium

description: Uninjured


title: Pa069ST


title: Pa072BS


title: q13_Uninjured olfactory epithelium

description: Uninjured


title: q12_Uninjured olfactory epithelium

description: Uninjured


title: Pa073BS


title: Pa077ST


title: q17_Uninjured olfactory epithelium

description: Uninjured


title: q16_Uninjured olfactory epithelium

description: Uninjured


title: Pa068ST


title: Pa068BS


title: q20_5dpOBX injured olfactory epithelium


title: q11_Uninjured olfactory epithelium

description: Uninjured


title: Pa067ST


title: q10_Uninjured olfactory epithelium

description: Uninjured


title: q9_Uninjured olfactory epithelium

description: Uninjured


title: Pa066ST


title: Pa067BS


title: q8_Uninjured olfactory epithelium

description: Uninjured


title: Pa066BS


title: q7_Uninjured olfactory epithelium

description: Uninjured


title: q5_Uninjured olfactory epithelium

description: Uninjured


title: q6_Uninjured olfactory epithelium

description: Uninjured


title: q3_5dpOBX injured olfactory epithelium


title: q4_Uninjured olfactory epithelium

description: Uninjured


title: Pa064ST

value: not reported


title: Pa065ST


title: q2_Uninjured olfactory epithelium

description: Uninjured


title: Pa064BS


title: Pa060ST


title: Pa061ST


title: Pa061BS


title: Pa060BS


title: Pa059BS

value: Bruneian


title: Pa065BS


title: Pa062BS


title: Pa057ST


title: Pa058BS


title: Pa058ST


title: Pa055BS


title: Pa055ST


title: Pa057BS


title: Pa056ST


title: Pa056BS


title: Pa054ST


title: Pa054BS


title: Pa053ST


title: q1_Uninjured olfactory epithelium

description: Uninjured


title: Pa062ST


title: Pa052BS

value: Caucasian


title: Pa059ST


title: Pa053BS


title: Pa051BS


title: Pa052ST


title: Pa051ST


title: Pa050ST


title: Pa050BS


title: Pa049BS


title: Pa049ST


title: Pa048ST


title: MDA MB-436 rep4 (RNA-Seq)

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description: PolyA RNA-seq under basal growth conditions

data_processing:
FastQC
The reads were then mapped to the human reference genome (GRCh37/hg19) using the default parameters in Tophat (v2.0.12).  For expression analyses, we created a collection of annotations by merging Gencode (v.19) and a set of previously unannotated lncRNAs identified in MCF-7 cells (Sun et al., 2015).  FPKM values were calculated per gene using Cufflinks (v.2.1.2) using the merged annotation GTF file.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files for visualization

source_name: MDA MB-436 rep4

growth_protocol: All cell lines were purchased from the American Type Culture Collection (ATCC) and were maintained, propagated, and plated for experiments in the laboratory of Dr. Khandan Keyomarsi at the MD Anderson Cancer Center.  The use of a centralized cell culture core facility facilitated consistency and reproducibility among all of the labs in the LONESTAR consortium conducting assays for this work.  All collections of RNA, protein, chromatin, and nuclei were performed in the cell culture core facility and distributed to the different labs for use in the various assays described herein.  The two immortalized breast epithelial cell lines, MCF-10A and 76N-F2V, were grown in D medium (described below).  All other cell lines were grown in Alpha-MEM medium (Sigma, M8042).  All cells were grown as adherent cultures at 37oC with 6.5% CO2.     The D medium comprised a 1:1 mixture of Alpha-MEM medium (Sigma, M8042) and Ham’s F12 base medium (Fisher, MT10080CV) containing the following additives: 0.1 M HEPES, 2 mM L-glutamine, 1% fetal bovine serum (Sigma, F4135), 0.035 mg/ml of bovine pituitary extract (Hammond Cell Tech, 1078NZ), 0.01 mM ascorbic acid, 2 nM β-estradiol, 2.5 ng/mL sodium selenite, 10 nM triiodothryonine, ethanolamine, 1 μg/mL insulin, 1 ng/mL hydrocortisone, 0.1 mM phosphoethanolamine, 0.01 mg/mL transferrin, 12.5 ng/mL epidermal growth factor, and 1% Penicillin/Streptomycin.  The Alpha-MEM contained the following additives: 0.1 M HEPES, 10% fetal bovine serum (Sigma, F4135), 1% non-essential amino acids, 2 mM L-glutamine, 1% sodium pyruvate, 1 μg/mL insulin, 1 ng/mL hydrocortisone, 12.5 ng/mL epidermal growth factor, and 1% Penicillin/Streptomycin.

extract_protocol:
The cells were collected at ~70-80% confluence.  RNA isolation for RT-qPCR and RNA-seq was performed using the RNeasy Mini Kit (Qiagen).
Total RNA was isolated as described above.  The integrity of the RNA was assessed and verified using an Experion Automated Electrophoresis System (Bio-Rad) before mRNA-seq libraries were prepared using methods described previously (Zhong et al., 2011).  Briefly, polyA+ RNA was enriched using Dynabeads oligo(dT)25 (Invitrogen), heat fragmented, and reverse transcribed using random hexamers in the presence of dNTPs.  Second strand cDNA synthesis was performed with dNTPs, but replacing dTTP with dUTP.  After end-repair, dA-tailing, ligation to adaptors containing barcode sequences, and size selection using AMPure beads (Agencourt), the synthesized second-strand was digested using uracil DNA glycosylase (Enzymatics).  A final PCR reaction was performed using Phusion high-fidelity DNA polymerase (NEB).  After library quality control assessment using a Bioanalyzer (Agilent), the samples were subjected to 50 bp single-end sequencing using an Illumina HiSeq 2000 Sequencing System.  At least two biological replicates for each cell line were sequenced

treatment_protocol: Basal Growth Conditions

value: TNBC Claudin Low Breast Cancer Cell Line

tag: cell line

value: MDA MB-436


title: MDA MB-436 rep1 (RNA-Seq)

source_name: MDA MB-436 rep1


title: MDA MB-436 rep3 (RNA-Seq)

source_name: MDA MB-436 rep3


title: HCC1937 rep4 (RNA-Seq)

source_name: HCC1937 rep4

value: TNBC Basal Breast Cancer Cell Line


title: Pa048BS


title: Pa047ST


title: Pa047BS


title: HCC1937 rep3 (RNA-Seq)

source_name: HCC1937 rep3


title: MDA MB-231 rep2 (RNA-Seq)

source_name: MDA MB-231 rep2

value: MDA MB-231


title: MDA MB-436 rep2 (RNA-Seq)

source_name: MDA MB-436 rep2


title: MDA MB-231 rep1 (RNA-Seq)

source_name: MDA MB-231 rep1


title: Pa045ST


title: HCC1937 rep2 (RNA-Seq)

source_name: HCC1937 rep2


title: HCC1937 rep1 (RNA-Seq)

source_name: HCC1937 rep1


title: Pa045BS


title: MB468 rep3 (RNA-Seq)

source_name: MB468 rep3


title: MDA MB-231 rep4 (RNA-Seq)

source_name: MDA MB-231 rep4


title: Pa044BS


title: MDA MB-231 rep3 (RNA-Seq)

source_name: MDA MB-231 rep3


title: MB468 rep4 (RNA-Seq)

source_name: MB468 rep4


title: MB468 rep1 (RNA-Seq)

source_name: MB468 rep1


title: MB468 rep2 (RNA-Seq)

source_name: MB468 rep2


title: Pa042ST

source_name: right atrial appendage biopsies


title: Pa043ST


title: HCC1954 rep3 (RNA-Seq)

source_name: HCC1954 rep3

value: HER2+ Breast Cancer Cell Line


title: Pa042BS


title: HCC1954 rep4 (RNA-Seq)

source_name: HCC1954 rep4


title: Pa043BS


title: HCC1954 rep1 (RNA-Seq)

source_name: HCC1954 rep1


title: Pa041BS


title: AU565 rep3 (RNA-Seq)

source_name: AU565 rep3


title: AU565 rep4 (RNA-Seq)

source_name: AU565 rep4


title: Pa039ST


title: AU565 rep2 (RNA-Seq)

source_name: AU565 rep2


title: Pa040ST


title: Pa041ST


title: Pa040BS


title: Pa038ST


title: Pa039BS


title: AU565 rep1 (RNA-Seq)

source_name: AU565 rep1


title: SKBR3 rep4 (RNA-Seq)

source_name: SKBR3 rep4


title: Pa044ST


title: SKBR3 rep3 (RNA-Seq)

source_name: SKBR3 rep3


title: Pa038BS


title: Pa037ST


title: Pa037BS


title: SKBR3 rep2 (RNA-Seq)

source_name: SKBR3 rep2


title: SKBR3 rep1 (RNA-Seq)

source_name: SKBR3 rep1


title: Pa036ST


title: UACC812 rep4 (RNA-Seq)

source_name: UACC812 rep4

value: Luminal B Breast Cancer Cell line


title: HCC1954 rep2 (RNA-Seq)

source_name: HCC1954 rep2


title: UACC812 rep2 (RNA-Seq)

source_name: UACC812 rep2


title: UACC812 rep1 (RNA-Seq)

source_name: UACC812 rep1


title: Pa036BS

value: Chinese


title: MDA MB-361 rep4 (RNA-Seq)

source_name: MDA MB-361 rep4

value: MDA MB-361


title: MDA MB-361 rep3 (RNA-Seq)

source_name: MDA MB-361 rep3


title: Pa032ST

source_name: right atrial appendage biopsies

value: male

value: Cardiac fibroblasts


title: ZR751 rep4 (RNA-Seq)

source_name: ZR751 rep4

value: Luminal A Breast Cancer Cell line


title: Pa033ST

value: female

value: human recombinant TGFB1 (Serotec)


title: Pa034BS

value: Control


title: Pa035ST

value: Indian


title: Pa035BS


title: ZR751 rep2 (RNA-Seq)

source_name: ZR751 rep2


title: ZR751 rep3 (RNA-Seq)

source_name: ZR751 rep3


title: Pa034ST


title: Pa031ST

value: Malay


title: Pa032BS


title: MDA MB-361 rep1 (RNA-Seq)

source_name: MDA MB-361 rep1


title: ZR751 rep1 (RNA-Seq)

source_name: ZR751 rep1


title: Pa031BS


title: MCF-7 rep4 (RNA-Seq)

source_name: MCF-7 rep4


title: UACC812 rep3 (RNA-Seq)

source_name: UACC812 rep3


title: Pa033BS


title: Pa030ST


title: MCF-7 rep3 (RNA-Seq)

source_name: MCF-7 rep3


title: Pa030BS


title: Pa029ST


title: MCF-7 rep1 (RNA-Seq)

source_name: MCF-7 rep1


title: MCF-7 rep2 (RNA-Seq)

source_name: MCF-7 rep2


title: MDA MB-361 rep2 (RNA-Seq)

source_name: MDA MB-361 rep2


title: Pa029BS


title: MCF10A rep4 (RNA-Seq)

source_name: MCF10A rep4

value: Mammary Gland Fibrocystic


title: Pa028ST


title: MCF10A rep3 (RNA-Seq)

source_name: MCF10A rep3


title: Pa028BS


title: MCF10A rep1 (RNA-Seq)

source_name: MCF10A rep1


title: MCF10A rep2 (RNA-Seq)

source_name: MCF10A rep2


title: Pa026BS


title: 76NF2V rep3 (RNA-Seq)

source_name: 76NF2V rep3

value: Mammary Brest Epithelium


title: 76NF2V rep4 (RNA-Seq)

source_name: 76NF2V rep4


title: Pa025ST

source_name: right atrial appendage biopsies


title: 76NF2V rep1 (RNA-Seq)

source_name: 76NF2V rep1


title: Pa026ST


title: 76NF2V rep2 (RNA-Seq)

source_name: 76NF2V rep2


title: Pa024ST


title: MDA MB-436 rep4 (GRO-Seq)

description:
nascent RNA
Nacent RNA transcription under basal growth conditions

data_processing:
Library strategy: GRO-seq
FastQC
Adaptor trimming using Cutadapt
Alignment to the human reference genome (hg19) and one complete copy of an rDNA repeat (GenBank ID: U13369.1) using the BWA aligner. The replicates 1, 2 are biological replicates and replicates 3, 4 are technical replicates of replicates 1,2 respectively. All the replicates were pooled to consider as a single replicate after confirming positive correlation between them and used for further analysis.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files for visualization

source_name: MDA MB-436 rep4

extract_protocol:
Nuclei Preparation.  All cells were grown using the growth conditions listed above at the LONESTAR Consortium cell culture core facility.  The cells were collected at ~70-80% confluence.  Nuclei were isolated from fresh (not frozen) cells, as described previously (Luo et al., 2014).  Briefly, the cells were washed three times with ice-cold PBS and swollen in Hypotonic Lysis Buffer [10 mM Tris•HCl pH 7.4, 0.5% NP-40, 10% glycerol, 3 mM CaCl2, 2 mM MgCl2, 1 mM DTT, 1x protease inhibitor cocktail (Sigma-Aldrich), and SUPERase-In (Ambion)].  The swollen cells were collected by centrifugation at 500 x g for 10 min at 4°C.  The cell pellets were resuspended in 1.5 ml of Hypotonic Lysis Buffer and pipetted up and down through a narrow opening 30 to 50 times to release the nuclei.  The nuclei were collected by centrifugation and washed once with 1 mL of ice cold Lysis Buffer.  The nuclei were collected by again centrifugation and washed once with 1 mL of Hypotonic Lysis Buffer.  After a final collection by centrifugation, the resulting pelleted nuclei were resuspended in 500 μL of Freezing Buffer (50 mM Tris•HCl pH 8.3, 40% glycerol, 5 mM MgCl2, 0.1 mM EDTA, and 4 units/mL of SUPERase-In per mL), counted, frozen in liquid nitrogen in 100 μL aliquots containing 5 x 106 nuclei, and stored at -80°C until use.
Nuclear run-on and GRO-seq library preparation were performed as previously described (Hah et al., 2011), with modifications (Danko et al., 2013; Luo et al., 2014).  Libraries were prepared from two biological replicates using a circularized ligation-based protocol for adaptor addition for improved efficiency of library preparation, reduced sequence bias, and ease for barcoding.  Briefly, nuclear run-ons were extended for ~100 bases in the presence of Sarksoyl (to prevent reengagement of RNA polymerases), rNTPs, α32P-CTP, and 5-bromo-UTP.  The nascent RNAs were isolated, hydrolyzed to ~150 bases, and enriched using α-BrdUTP antibody-conjugated agarose beads (Santa Cruz).  Enriched run-on RNA was subjected to polyA tailing with E. coli PolyA Polymerase and subsequently converted to cDNA by reverse transcription using SuperScript III reverse transcriptase (Invitrogen) and an RT primer (pGATCGTCGGACTGTAGAACTCT/idSp/CCTTGGCACCCGAGAATTCCATTTTTTTTTTTTTTTTTTTTVN), where p indicates phosphorylation, idSp indicates dSpacer Furan, and VN indicates degenerate nucleotides.  Reverse transcribed cDNAs were size selected (120 to 400 bp) by denaturing PAGE and circularized with CircLigase (Epicentre) to position Illumina adapter sequences relative to the 5’ and 3’ ends of reverse-transcribed run-on cDNA.  The circularized cDNAs were re-linearized by with ApeI (NEB), purified by phenol-chloroform extraction, and PCR amplified using unique Illumina TrueSeq small RNA sample barcoded primers with Phusion high fidelity DNA polymerase (NEB).  The PCR products (175 bp to 300 bp) were separated by native PAGE, eluted, and purified.  After library quality control assessment using a Bioanalyzer (Agilent), the samples were subjected to 50 bp single-end sequencing using an Illumina HiSeq 2000 Sequencing System.  At least two biological replicates for each cell line were sequenced

value: TNBC Claudin Low Breast Cancer Cell Line

value: MDA MB-436


title: Pa023BS


title: Pa024BS


title: Pa023ST


title: Pa025BS


title: MDA MB-436 rep2 (GRO-Seq)

source_name: MDA MB-436 rep2


title: MDA MB-436 rep1 (GRO-Seq)

source_name: MDA MB-436 rep1


title: Pa022ST


title: Pa022BS


title: Pa021ST


title: MDA MB-231 rep3 (GRO-Seq)

source_name: MDA MB-231 rep3

value: MDA MB-231


title: Pa027BS


title: Pa027ST


title: Pa021BS


title: MDA MB-231 rep1 (GRO-Seq)

source_name: MDA MB-231 rep1


title: HCC1937 rep3 (GRO-Seq)

source_name: HCC1937 rep3

value: TNBC Basal Breast Cancer Cell Line


title: Pa020BS


title: Pa019ST


title: MDA MB-436 rep3 (GRO-Seq)

source_name: MDA MB-436 rep3


title: Pa018ST


title: Pa018BS


title: MB468 rep4 (GRO-Seq)

source_name: MB468 rep4


title: MB468 rep3 (GRO-Seq)

source_name: MB468 rep3


title: HCC1937 rep1 (GRO-Seq)

source_name: HCC1937 rep1


title: MDA MB-231 rep4 (GRO-Seq)

source_name: MDA MB-231 rep4


title: MB468 rep2 (GRO-Seq)

source_name: MB468 rep2


title: Pa017BS


title: Pa017ST


title: MDA MB-231 rep2 (GRO-Seq)

source_name: MDA MB-231 rep2


title: Pa016ST


title: MB468 rep1 (GRO-Seq)

source_name: MB468 rep1


title: HCC1937 rep4 (GRO-Seq)

source_name: HCC1937 rep4


title: Pa016BS

source_name: right atrial appendage biopsies


title: HCC1954 rep3 (GRO-Seq)

source_name: HCC1954 rep3

value: HER2+ Breast Cancer Cell Line


title: HCC1954 rep2 (GRO-Seq)

source_name: HCC1954 rep2


title: Pa020ST

value: Chinese


title: HUE-24_amiCYG12-6h-O2-b

city: Bochum

first: Anja

middle: Christine

last: Hemschemeier

address: Universitätsstr. 150

department: Plant Biochemistry

institute: Ruhr-University of Bochum

data_processing:
Illumina HiSeq 2500 Basecalling pipeline - HiSeq Control Software 2.2.38, - RTA 1.18.61.0, - CASAVA-1.8.2; Mode: HiSeq High Output (HO) Version 4; PhiX spikes
Bioinformatics were done by the company Fasteris SA, Switzerland. Mapping was done using Bowtie v2.0.5 (Langmead et al. (2009); PMID: 19261174), Tophat v2.0.6 and Samtools v1.2 against C. reinhardtii genome version 5.5 on Phytozome 11  (https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Creinhardtii)  using the assembly file: Creinhardtii_281_v5.0, and the annotation file: Creinhardtii_281_v5.5.gene_exons.gff3
Expression estimation, normalization and comparisons were done by the company Fasteris SA, Switzerland, using Cufflinks v2.1.1
Supplementary_files_format_and_content: excel spreadsheet containing FPKM values for each C. reinhardtii transcript (including isoforms) for each duplicate as well as fold-changes of different comparisons and their test statistics

organism: Chlamydomonas reinhardtii

source_name: C. reinhardtii CC-124 amiCYG12 cell suspension

growth_protocol: Liquid cultures in TAP medium (http://www.chlamycollection.org/methods/media-recipes/tap-and-tris-minimal/), 20°C, continuous light (alternating 1 Osram Fluora and 2 Osram Lumilux CoolWhite light bulbs), reciprocal shaker with bottom-up illumination of 20 µmoles of photons x m-2 x s-1

extract_protocol:
Total RNA and Dnase digestion: 50 ml of algae were harvested by centrifugation (2 min, 4°C, 3,220xg). Cell pellets were resuspended in 0.8 ml lysis buffer (50 mM Tris-HCl pH 8.0, 0.3 M NaCl, 5 mM EDTA), transferred to reaction tubes containing 0.15 ml of 20% (w/v) SDS, vortexed, and stored at -80°C. Then, samples were thawed on ice, 0.8 ml of acidic phenol were added, the mixtures were vortexed and then centrifuged for 15 min, 4°C, 14,046xg. Phenolization was repeated at least 2x. Chloroform : isoamylalcohol 24 : 1 (0.8 ml) was added twice to the aqueous phases, vortexed, and centrifuged for 8 min, 4°C, 14.046xg. Then, the aqueous phases were mixed with 2.5-fold volumes of ethanol, incubated overnight at -20°C, centrifuged for 45 min, 4°C, 20,817xg. 0.8 ml 70% (v/v) ethanol was applied to wash the pellets. Samples were centrifuged for 30 min, 4°C, 20,817xg, dried, and resuspended in chromatography-grade water. To digest DNA, 40 µg of nucleic acids in a total volume of 300 µl were treated with 2 U  µl-1 TURBOTM DNase from Ambion for 1.5 h at 37°C. EDTA, pH 8.0, was added to a final concentration of 15 mM and samples were heated for 15 min at 75°C. 0.3 M sodium acetate (pH 7.0) and 775 µl ethanol were added, solutions were incubated overnight at -20°C. Precipitation of the RNA was done as described above.
Library construction was done by the company Fasteris SA, Switzerland, according to Standard stranded mRNA protocol: poly-adenylated transcripts selection, cDNA library construction using illumina TruSeq Stranded mRNA Library Prep kit

treatment_protocol: see: characteristics: incubation conditions

tag: strain background

tag: genotype/variation

value: amiCYG12; CYG12 knockdown

tag: incubation conditions

value: incubation in darkness in gas-tight flasks for 6h (dark-anoxia)

tag: molecule subtype

value: total RNA, Dnase-digested, poly(A)-purified mRNA


title: Pa015ST

value: Cardiac fibroblasts


title: HCC1954 rep1 (GRO-Seq)

source_name: HCC1954 rep1


title: Pa015BS

value: female


title: HCC1937 rep2 (GRO-Seq)

source_name: HCC1937 rep2


title: Pa019BS

value: male


title: Pa014ST

value: human recombinant TGFB1 (Serotec)


title: AU565 rep4 (GRO-Seq)

source_name: AU565 rep4


title: HUE-23_amiCYG12-6h-O2-a


title: HUE-22_amiCYG12-6h+O2-b

value: incubation in darkness in open and well-stirred beakers for 6h (dark-aerobiosis)


title: AU565 rep3 (GRO-Seq)

source_name: AU565 rep3


title: Pa014BS

value: Malay

value: Control


title: AU565 rep2 (GRO-Seq)

source_name: AU565 rep2


title: HCC1954 rep4 (GRO-Seq)

source_name: HCC1954 rep4


title: HUE-21_amiCYG12-6h+O2-a


title: Pa013ST


title: Pa013BS


title: 3T9 Y27 rep2

city: milano

first: stefano

last: campaner

address: via adamello 16

department: Center for Genomic Science

country: Italy

institute: fondazione Istituto italiano di tecnologia

data_processing:
Read filtering with fastx toolkit 0.0.13.2: fastq_masker -Q33 -q 20 -r N -v
alignment with tophat version 2.0.8: tophat -r 170 -p 8 --no-novel-juncs --no-novel-indels --library-type fr-unstranded --transcriptome-index transcriptome_index reffile fastq_file_R1 fastq_file_R2
Removing duplicate reads: samtools rmdup -sS bamfile
Quantifying read counts over features with featureCounts v. 1.4.5-p1: featureCounts -T 2 -p -P -a gtffile
Idendifying Differentially Expressed Genes (DEG) using DESeq2 R Bioconductor package
Genome_build: mm9
Supplementary_files_format_and_content: excel file containing differential expression results (DESeq2) and expression quantification (reads per kilobase per million mapped reads: RPKM) of 3T9 genes treated with Y27 or VP

source_name: 3T9 Y27 rep2

growth_protocol: 3T9MycER murine fibroblast were grown in DMEM medium supplemented with 10% tetracyclin-free serum, penicillin/streptomycin and 2mM L-Gln

extract_protocol:
RNA was extracted with the RNeasy MinElute Spin columns from Qiagen according to the manufacturer and eluted in 14µl of RNase free water
Libraries for RNA-Seq were prepared with the TruSeq RNA Sample Preparation Kits v2 (Illumina) following manufacturer instruction (except for skipping the first step of mRNA purification with poly-T oligo-attached magnetic beads)

treatment_protocol: ROCK inhibitor Y27632 (used 50µM), and YAP-TEAD inhibitor Verteporfin (used 20µM) for 8 hours

value: immortalized embryonic fibroblasts


title: HUE-20_amiCYG12-0h-b

value: standard (light:20 µmoles of photons x m-2 x s-1; aerated; TAP-medium)


title: 3T9 Y27 +OHT rep1

source_name: 3T9 Y27 +OHT rep1


title: SKBR3 rep4 (GRO-Seq)

source_name: SKBR3 rep4


title: HUE-19_amiCYG12-0h-a


title: 3T9 Y27 rep1

source_name: 3T9 Y27 rep1


title: Pa011ST

value: Indian


title: HUE-18_Wt-6h-O2-b

source_name: C. reinhardtii CC-124 cell suspension

value: wild type


title: 3T9 VP +OHT rep2

source_name: 3T9 VP +OHT rep2


title: Pa011BS


title: 3T9 VP +OHT rep1

source_name: 3T9 VP +OHT rep1


title: SKBR3 rep2 (GRO-Seq)

source_name: SKBR3 rep2


title: Pa010ST

source_name: right atrial appendage biopsies


title: HUE-17_Wt-6h-O2-a


title: HUE-16_Wt-6h+O2-b


title: 3T9 Y27 +OHT rep2

source_name: 3T9 Y27 +OHT rep2


title: 3T9 VP rep2

source_name: 3T9 VP rep2


title: HUE-15_Wt-6h+O2-a


title: Pa010BS


title: AU565 rep1 (GRO-Seq)

source_name: AU565 rep1


title: 3T9 VP rep1

source_name: 3T9 VP rep1


title: Pa008ST


title: Pa008BS


title: HUE-14_Wt-0h-b


title: HUE-13_Wt-0h-a


title: UACC812 rep3 (GRO-Seq)

source_name: UACC812 rep3

value: Luminal B Breast Cancer Cell line


title: UACC812 rep2 (GRO-Seq)

source_name: UACC812 rep2


title: 3T9 DMSO + OHT rep1

source_name: 3T9 DMSO + OHT rep1


title: 3T9 DMSO + OHT rep2

source_name: 3T9 DMSO + OHT rep2


title: SKBR3 rep3 (GRO-Seq)

source_name: SKBR3 rep3

value: HER2+ Breast Cancer Cell Line


title: UACC812 rep1 (GRO-Seq)

source_name: UACC812 rep1


title: Pa007ST


title: S2-Snail-RNAi-Sco

city: Taipei

first: Hweijan

last: Hsu

address: no 128, Sec 2,  Academia Rd. Nankang

department: Institute of Cellular Biology

country: Taiwan

institute: Academia Research

description: Snail-SCO

data_processing:
Illumina bcl2fastq 2.1.7  software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by trimmomatics with parameter: LEADING:20 TRAILING:13 SLIDINGWINDOW:2:20 MINLEN:30
Genome mapping by tophat2 with  --no-novel-juncs --microexon-search --library-type fr-firststrand --b2-sensitive
Expression estimate by cufflinks with bias-detected: -N  -u --library-type fr-firststrand -b
Genome_build: BDGP6
Supplementary_files_format_and_content: tab-delimited text files include FPKM/Read count values for each Sample

organism: Drosophila melanogaster

source_name: OVARY

growth_protocol: Flies with the genotype: c587-GAL4/UAS-flp; FRT40A/ubiGFP FRT40A (control), c587-GAL4/UAS-flp; ScoFRT40A/ubiGFP FRT40A (experiment) and c587-GAL4/UAS-flp; uas-SnailRNAIScoFRT40A/ubi-GFPFRT40A flies were grew at 18 degree, after eclosion (Day 1)  then were maintained at 25 degree untip Day 7.

extract_protocol:
Total RNA were extracted by Trizol reagent (Invitrogen, USA) according to the instructions. RNA was quantified at by absorbance at 260 nm using a ND-1000 spectrophotometer (Nanodrop Techonology, USA) and quality was assessed using a Bioanalyzer 2100 (Agilent Technology, USA) with a RNA 6000 labchip kit (Agilent Technologies, USA)
Library construction for all samples was accomplished with Agilent’s SureSelect Strand Specific RNA library Preparation Kit for 75SE (Single-End or Paired-End) sequencing on Solexa platform

value: ovary

value: day 7

value: c587-GAL4/UAS-flp; usa-snailRNAi ScoFRT40A/ubiGFP FRT40A


title: MDA MB-361 rep4 (GRO-Seq)

source_name: MDA MB-361 rep4

value: MDA MB-361


title: SKBR3 rep1 (GRO-Seq)

source_name: SKBR3 rep1


title: S1-Snail-RNAi-Sco

description: Snail-SCO

value: c587-GAL4/UAS-flp; uas-snailRNAi ScoFRT40A/ubiGFP FRT40A


title: 3T9 DMSO rep2

source_name: 3T9 DMSO rep2


title: Pa006ST

value: Chinese

value: Cardiac fibroblasts


title: Pa007BS

value: male


title: S2-C587-Sco


title: 3T9 OHT DOX rep3

data_processing:
Read filtering with fastx toolkit 0.0.13.2: fastq_masker -Q33 -q 20 -r N -v
alignment with tophat version 2.0.8: tophat -r 170 -p 8 --no-novel-juncs --no-novel-indels --library-type fr-unstranded --transcriptome-index transcriptome_index reffile fastq_file_R1 fastq_file_R2
Removing duplicate reads: samtools rmdup -sS bamfile
Quantifying read counts over features with featureCounts v. 1.4.5-p1: featureCounts -T 2 -p -P -a gtffile
Idendifying Differentially Expressed Genes (DEG) using DESeq2 R Bioconductor package
Genome_build: mm9
Supplementary_files_format_and_content: excel file containing differential expression results (DESeq2) and DEG status (Y/N)

source_name: 3T9 OHT DOX rep3

treatment_protocol: MycER was activated by the addition of 400nM 4-hydroxytamoxifen, while YAPS127A was induced by 2 µg/ml doxycycline


title: MDA MB-361 rep3 (GRO-Seq)

source_name: MDA MB-361 rep3


title: Pa006BS

source_name: right atrial appendage biopsies


title: S1-C587-Sco


title: MDA MB-361 rep2 (GRO-Seq)

source_name: MDA MB-361 rep2


title: 3T9 OHT DOX rep2

source_name: 3T9 OHT DOX rep2


title: MDA MB-361 rep1 (GRO-Seq)

source_name: MDA MB-361 rep1


title: Pa005ST

value: human recombinant TGFB1 (Serotec)


title: S2-C587-40A

value: c587-GAL4/UAS-flp; FRT40A/ubiGFP FRT40A


title: 3T9 OHT DOX rep1

source_name: 3T9 OHT DOX rep1


title: Pa005BS

value: Control


title: ZR751 rep4 (GRO-Seq)

source_name: ZR751 rep4

value: Luminal A Breast Cancer Cell line


title: S1-C587-40A


title: Pa003ST


title: ZR751 rep3 (GRO-Seq)

source_name: ZR751 rep3


title: 3T9 DOX rep2

source_name: 3T9 DOX rep2

value: immortalized embryonic fibroblasts


title: 3T9 DOX rep3

source_name: 3T9 DOX rep3


title: Pa003BS

value: Indian


title: 3T9 DMSO rep1

source_name: 3T9 DMSO rep1


title: ZR751 rep2 (GRO-Seq)

source_name: ZR751 rep2


title: Prolific Jintang black goat No. 3

city: Chengdu

first: Xiang-dong

last: Zi

address: Yi Huan Lu

country: China

institute: Southwest University for Nationalities

data_processing:
Illumina HiSeqTM 2000 platform
All RNA-Seq data were preprocessed with adaptor trimming and low quality reads filtering using standard approaches. All the clean reads from two goat breeds were aligned to the goatv2 reference genome obtained from CGD (http://goat.kiz.ac.cn/GGD/) (Dong et al. 2013) using Tophat2 (v2.0.10)(Kim et al. 2013) with parameters “-very-sensitive -segment-length 30 -segment-mismatches 2 -r 20 -mate-std-dev 20 -g 200 --no-discordant --no-mixed”. Through Tophat, Bowtie v2.1.0 (Langmead & Salzberg 2012) was called with option “--b2-sensitive --b2-gbar 99999999 --b2-mp 1,1 --b2-np 1 --b2-score-min L,0,-0.1 ”
Using the software package RSEM 1.2.0 to estimate the gene expression levels for each breed of goats using the gene annotation data obtained from CGD (http://goat.kiz.ac.cn). After the transcripts were prepared using rsem-prepare- reference script, the reads counts that mapped on each gene and the FPKM (fragments per kilobase per million reads) value were calculated using rsem-calculate-expression script by mapping clean data back onto the transcripts
Genome_build: GCA_000317765.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Capra hircus

source_name: Ovary

extract_protocol:
The total RNA was extracted using TRIzol (Invitrogen, Carlsbad, CA, USA)，Approximately 20 μg of total RNA from each individual ovarian sample was used to construct a cDNA library
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina1 (NEB, USA) following manufacturer’s recommendations

tag: breed

value: Jintang black goat

tag: stage of estrous cycle

value: follicular phase


title: Prolific Jintang black goat No. 2

tag: tissue


title: ZR751 rep1 (GRO-Seq)

source_name: ZR751 rep1


title: Prolific Jintang black goat No. 1


title: 3T9 DOX rep1

source_name: 3T9 DOX rep1


title: Non-prolific Tibetan goat No. 3

value: Tibetan goat


title: Input DNA control in staged YA #2

city: New Haven

first: Valerie

last: Reinke

state: CT

address: 333 Cedar St

department: Genetics

institute: Yale University School of Medicine

description: a fraction of the input total chromatin that was used for OEF-1:GFP ChIP

library_source: genomic

data_processing:
FASTQ files were processed and mapped using BWA (Li et al., 2009), retaining only high quality alignments (Q ≥ 30).
Transcription factor binding sites were determined and scored using SPP peak caller (Kharchenko et al. 2008).
High confidence binding events were identified using IDR (Irreproducible Discovery Rate)
A cross-replicate threshold was obtained using a 5% IDR score threshold.  Additionally, a rescue threshold method was also determined using IDR scoring.  A final rank threshold for each data set was calculated by combining the cross-replicate and rescue threshold scores.  Finally, reads from all replicates were pooled and the SPP and IDR framework was applied again to rank peaks by signal-score. The final rank threshold score determined from the individual replicates was used as a significance threshold for the ranked pooled-data peaks.
Genome_build: WS220
Supplementary_files_format_and_content: WIG files were generated as an output of the SPP program

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: staged young adult (YA) from OP383 (OEF-1:GFP transgenic strain)

growth_protocol: Gravid adults were bleached and synchronized by L1 starvation.  Starved L1s were plated on peptone-enriched NGM plates seeded with OP50, and grown until the desired developmental stage(young adult) at 20˚C. Worms were harvested and washed free of bacteria in M9.

extract_protocol:
For all ChIP-seq samples, worms  were crosslinked in 2% formaldehyde in M9 buffer for 30 minutes rotating at room temperature.  Crosslinking was quenched with 1M Tris pH 7.5, followed by two washes with M9, and one wash with FA buffer containing protease inhibitors.  Final Triton X-100 concentration in all FA buffers used was  1%.  Worm pellets were flash-frozen in liquid nitrogen and stored at -80˚C.  Using the Fisher Scientific Sonic Dismembrator 550 (Pittsburgh, PA), samples were sonicated with a microtip on ice for sixteen cycles of 10 sec on, and 60 sec off on the “microtip” setting to fragment the majority of DNA within 200-800bp range.  Sonicated extract containing 2mg of protein was immunoprecipitated as previously described (Zhong et al., 2010) with 7.5µg of anti-GFP antibody (gift from Tony Hyman).
ChIP-seq library preparation for enriched DNA and the genomic DNA input control for at least two biological replicates was performed as described in (Zhong et al. 2010), except Qiagen MinElute PCR purification and gel extraction kits were used after the Klenow step.  Libraries were multiplexed as described in Lefrancois et al. (2009) in order to sequence four samples in a single flow cell using the Illumina Genome Analyzer II platform.

tag: developmental stage

value: YA

value: whole animal

tag: chipped factor

value: none - input

tag: strain


title: MCF-7 rep3 (GRO-Seq)

source_name: MCF-7 rep3


title: OEF-1 ChIP in staged YA rep 2

description: ChIP was performed with anti-GFP of GFP-tagged OEF-1

tag: antibody

value: GFP


title: MCF-7 rep2 (GRO-Seq)

source_name: MCF-7 rep2


title: 3T9 OHT rep3

source_name: 3T9 OHT rep3

tag: genotype


title: MCF-7 rep1 (GRO-Seq)

source_name: MCF-7 rep1


title: 3T9 OHT rep2

source_name: 3T9 OHT rep2


title: Non-prolific Tibetan goat No. 2

value: ovary


title: 3T9 OHT rep1

source_name: 3T9 OHT rep1


title: 6F_fst-48h-3

city: Cambridge

first: Peter

middle: W

last: Reddien

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description:
10F_ctrol_myoD_6F_ctrol_fst_0-6-24-48hpa_readcounts.txt
res_6F_ctrol_v_fst-48hpa.txt
res_6F_ctrol-00_v_48hpa.txt

data_processing:
Basecalling was performed by Illumina CASAVA
Sequenced reads were quality trimmed using cutadapt v1.8 with parameteres -m 20 -q 30,30 and mapped to the ddv4 transcriptome using Bowtie v1.1.1 with parameter --best
Raw read counts were generated with Samtools idxstats and transcripts from different isoforms were summed (sum of counts for dd_v4_Smed_XXX_Y_Z for all Z)
Differential expression was determined with DESeq
Genome_build: Dresden S. mediterranea Transcriptome Assembly (ddv4, Lui et al, Nature 2013) https://idisk.mpi-cbg.de/~brandl/planaria/dd_Smed_v4.nuc.fasta.zip
Supplementary_files_format_and_content: Tab-separated text files

organism: Schmidtea mediterranea

source_name: Wound tissue from tail fragment

growth_protocol: Standard planarian culture conditions

extract_protocol:
Total RNA extracted from wounds in tail fragments with TriZOL reagent with 5 wounds per replicate. Extracted RNA was quantified by NanoDrop and Agilent Bioanalyzer
Kapa Stranded mRNA-Seq Kit Illumina Platform (KapaBiosystems)

treatment_protocol: Animals fed in-vitro transcribed dsRNA 6 times in 3 weeks or 10 times in 5 weeks

value: Tail fragment

tag: hours post amputation (hpa)

value: 48 hpa

tag: RNAi

value: fst

tag: RNAi feedings


title: MCF10A rep4 (GRO-Seq)

source_name: MCF10A rep4

tag: cell type

value: Mammary Gland Fibrocystic


title: Non-prolific Tibetan goat No. 1


title: 6F_fst-48h-2


title: 3T9 CTRL rep3

source_name: 3T9 CTRL rep3

tag: cell line


title: MCF10A rep3 (GRO-Seq)

source_name: MCF10A rep3


title: 3T9 CTRL rep2

source_name: 3T9 CTRL rep2


title: 3T9 CTRL rep1

source_name: 3T9 CTRL rep1


title: 6F_fst-48h-1

description:
high H.sap contamination
10F_ctrol_myoD_6F_ctrol_fst_0-6-24-48hpa_readcounts.txt
res_6F_ctrol_v_fst-48hpa.txt
res_6F_fst-00_v_48hpa.txt


title: MCF10A rep2 (GRO-Seq)

source_name: MCF10A rep2


title: 6F_ctrol-48h-3

description:
10F_ctrol_myoD_6F_ctrol_fst_0-6-24-48hpa_readcounts.txt
res_6F_ctrol_v_fst-48hpa.txt
res_6F_fst-00_v_48hpa.txt


title: MCF10A rep1 (GRO-Seq)

source_name: MCF10A rep1


title: cells_3T9_input

data_processing:
Read filtering with fastx toolkit version 0.0.13.2: fastq_masker -Q33 -q 20 -r -N -v
Alignment to mm9 with bwa version 0.6.2; bwa aln -t 16 reffile fastqfile| bwa samse -n 1 reffile - fastqfile | samtools view -q 1 -ut reffile - |samtools sort - bamfile
Transcription factors (YAP, TEAD, MYC, Pol2) peak calling with MACS version 2.0.9; macs2 -t samplebam -c inputbam  --mfold=7,30 -g mm -p 0.00001
Histone marks (H3K4me1, H3K4me3, H3K27Ac, H3K27me3) peak calling with MACS version 2.0.9; macs2 -t samplebam -c inputbam  --auto-bimodal --broad -g mm -p 0.00000001
the input alignment file wass randomly downsampled to the size of the ChIP sample alignment file
Genome_build: mm9
Supplementary_files_format_and_content: *_peaks.txt files: bed files of transcription factors ChIP-Seq

extract_protocol:
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 250 bp were immunoprecipitated using different antibodies. For Myc, TEAD, Histone Marks, RNAPol2 ChIP, 3T9 fibroblasts or dissected liver/tumors were fixed with 1% formaldehyde. For YAP ChIP, fixation was performed by a double step approach with 0.5 M DSG (Di-(N-succinimidyl)-glutarate)  and 1% formaldehyde (FA).
Libraries were prepared for Illumina sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters, selection on gel and PCR with index primers

tag: chip antibody

value: IgG (Santa Cruz, sc-2027)


title: 6F_ctrol-48h-2


title: 76NF2V rep4 (GRO-Seq)

source_name: 76NF2V rep4

value: Mammary Brest Epithelium


title: cells_3T9_YAP_OHT_DOX_ChIP

value: YAP 63.7(Santa Cruz, sc101199)


title: 6F_ctrol-48h-1


title: OEF-1 ChIP in staged YA rep 1


title: 76NF2V rep3 (GRO-Seq)

source_name: 76NF2V rep3


title: 6F_fst-24h-3

description:
10F_ctrol_myoD_6F_ctrol_fst_0-6-24-48hpa_readcounts.txt
res_6F_ctrol_v_fst-24hpa.txt
res_6F_ctrol-00_v_24hpa.txt

value: 24 hpa


title: cells_3T9_TEAD_OHT_DOX_ChIP

value: immortalized embryonic fibroblasts

value: TEAD (ARP38276_P050, Aviva Systems Biology)


title: 76NF2V rep2 (GRO-Seq)

source_name: 76NF2V rep2


title: cells_3T9_Pol2_OHT_DOX_ChIP

value: RNAPol2 N20-X (Santa Cruz, sc-899)


title: 6F_fst-24h-2


title: 6F_fst-24h-1


title: 76NF2V rep1 (GRO-Seq)

source_name: 76NF2V rep1


title: 6F_ctrol-24h-3

description:
10F_ctrol_myoD_6F_ctrol_fst_0-6-24-48hpa_readcounts.txt
res_6F_ctrol_v_fst-24hpa.txt
res_6F_fst-00_v_24hpa.txt


title: Liver LapTTA TetMyc 4W rep2

data_processing:
Read filtering with fastx toolkit 0.0.13.2: fastq_masker -Q33 -q 20 -r N -v
alignment with tophat version 2.0.8: tophat -r 170 -p 8 --no-novel-juncs --no-novel-indels --library-type fr-unstranded --transcriptome-index transcriptome_index reffile fastq_file_R1 fastq_file_R2
Removing duplicate reads: samtools rmdup -sS bamfile
Quantifying read counts over features with featureCounts v. 1.4.5-p1: featureCounts -T 2 -p -P -a gtffile
Idendifying Differentially Expressed Genes (DEG) using DESeq2 R Bioconductor package
Genome_build: mm9
Supplementary_files_format_and_content: excel files containing RPKM values for alll samples and differential expression results (DESeq2) and DEG status (Y/N) after 2d of YAP overexpression only for the R26 samples.

source_name: Liver

value: liver

value: LAP-tTA;tet-Myc


title: 6F_ctrol-24h-2


title: Liver LapTTA TetMyc 4W rep1


title: HFLNJBCXX-1789-06-29-1

city: AUCKLAND

first: Larry

last: Chamley

address: 85 Park Road

department: Obstetrics and Gynaecology

country: New Zealand

institute: The University of Auckland

data_processing:
HiSeq Control Software used for base calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using bowtie 2
Differential expression analysis was normalizaed by DESeq2, EdgeR and Voom
Genome_build: hg38
Supplementary_files_format_and_content: csv files were generated with reads and normalized reads included

source_name: placental macro extracellular debris

growth_protocol: 400mg of placental explants were cultured within netwell inserts with 440um mesh in Advanced DMEM/F12 medium supplemented with 2% FBS for 17 hours, trophoblast debris was collected by low speed centrifuge of the conditioned medium in the bottom chamber

extract_protocol:
Total RNA was extraced and purified by Trizol and PureLink® RNA Mini Kit according to the manufacturer's instructions for total RNA extraction.
100ng of total RNA samples were used for small RNA libraries preparation, using the NEXTflex small RNA sequencing kit V2.

tag: primary cell type

value: trophoblast debris collected from placental explants culture

value: placenta

tag: patient state

value: healthy control


title: HFLNJBCXX-1789-07-29-1


title: 6F_ctrol-24h-1


title: HFLNJBCXX-1789-04-29-1

value: preeclampsia


title: Liver LapTTA TetYapMyc 4W rep3

value: LAP-tTA; tet-Myc; tet-YAP


title: 6F_fst-06h-3

description:
10F_ctrol_myoD_6F_ctrol_fst_0-6-24-48hpa_readcounts.txt
res_6F_ctrol_v_fst-06hpa.txt
res_6F_ctrol-00_v_06hpa.txt

value: Tail fragment

value: 6 hpa


title: Liver LapTTA TetYapMyc 4W rep2


title: 6F_fst-06h-2

value: fst


title: Liver LapTTA TetYapMyc 4W rep1


title: HFLNJBCXX-1789-03-29-1


title: 6F_fst-06h-1


title: Liver LapTTA TetYap Tumor7

value: LAP-tTA;tet-YAP


title: 6F_ctrol-06h-3

description:
10F_ctrol_myoD_6F_ctrol_fst_0-6-24-48hpa_readcounts.txt
res_6F_ctrol_v_fst-06hpa.txt
res_6F_fst-00_v_06hpa.txt


title: Liver LapTTA TetMyc 4W rep3


title: cells_3T9_MYC_OHT_DOX_ChIP

value: MycN262 (Santa Cruz, sc 764)


title: HFLNJBCXX-1789-01-29-1


title: 6F_ctrol-06h-2


title: 6F_ctrol-06h-1


title: HFLNJBCXX-1789-08-29-1


title: Liver LapTTA TetYap Tumor8


title: Liver LapTTA TetYap Tumor5


title: HFLNJBCXX-1789-02-29-1


title: 6F_fst-00h-3

description:
10F_ctrol_myoD_6F_ctrol_fst_0-6-24-48hpa_readcounts.txt
res_6F_ctrol_v_fst-00hpa.txt
res_6F_ctrol-00_v_06hpa.txt
res_6F_ctrol-00_v_24hpa.txt
res_6F_ctrol-00_v_48hpa.txt

value: 0 hpa


title: Liver LapTTA TetYap Tumor6


title: HFLNJBCXX-1789-05-29-1


title: Liver LapTTA TetYap Tumor4


title: Liver LapTTA TetYap Tumor1


title: Liver LapTTA TetYap Tumor2


title: 6F_ctrol-00h-3

description:
10F_ctrol_myoD_6F_ctrol_fst_0-6-24-48hpa_readcounts.txt
res_6F_ctrol_v_fst-00hpa.txt
res_6F_fst-00_v_06hpa.txt
res_6F_fst-00_v_24hpa.txt
res_6F_fst-00_v_48hpa.txt


title: Liver LapTTA TetYap 4W rep3


title: 6F_ctrol-00h-1


title: 6F_fst-00h-1


title: Liver LapTTA TetYap 4W rep2


title: 10F_ctrol-48h-2

description:
10F_ctrol_myoD_6F_ctrol_fst_0-6-24-48hpa_readcounts.txt
res_10F_ctrol_v_myoD-48hpa.txt
res_10F_ctrol-00_v_48hpa.txt

value: 48 hpa


title: Liver LapTTA TetYap 4W rep4


title: Liver LapTTA TetYap 4W rep1


title: 10F_ctrol-48h-1


title: 10F_ctrol-48h-3


title: 10F_myoD-48h-3

description:
10F_ctrol_myoD_6F_ctrol_fst_0-6-24-48hpa_readcounts.txt
res_10F_ctrol_v_myoD-48hpa.txt
res_10F_myoD-00_v_48hpa.txt

value: myoD


title: Liver LapTTA WT rep1

value: LAP-tTA;WT


title: Liver LapTTA WT rep2


title: Liver LapTTA WT rep3


title: 10F_myoD-48h-2


title: 10F_myoD-48h-1


title: 6F_fst-00h-2


title: 10F_ctrol-24h-3

description:
10F_ctrol_myoD_6F_ctrol_fst_0-6-24-48hpa_readcounts.txt
res_10F_ctrol_v_myoD-24hpa.txt
res_10F_ctrol-00_v_24hpa.txt

value: 24 hpa


title: Liver R26 TetYap 2d rep6

value: liver


title: Liver R26 TetYap 2d rep5


title: Liver R26 TetYap 2d rep4


title: Liver LapTTA TetYap Tumor3


title: 10F_ctrol-24h-1


title: 10F_ctrol-24h-2


title: 6F_ctrol-00h-2


title: Liver R26 TetYap 2d rep3


title: 10F_myoD-24h-3

description:
10F_ctrol_myoD_6F_ctrol_fst_0-6-24-48hpa_readcounts.txt
res_10F_ctrol_v_myoD-24hpa.txt
res_10F_myoD-00_v_24hpa.txt


title: Liver R26 TetYap 2d rep2


title: Liver R26 TetYap 2d rep1


title: 10F_myoD-24h-2


title: 10F_myoD-24h-1


title: 10F_ctrol-06h-3

description:
10F_ctrol_myoD_6F_ctrol_fst_0-6-24-48hpa_readcounts.txt
res_10F_ctrol_v_myoD-06hpa.txt
res_10F_ctrol-00_v_06hpa.txt


title: 10F_ctrol-06h-2


title: Liver R26 TetYapMyc 2d rep1


title: 10F_ctrol-06h-1


title: Liver R26 WT rep4


title: 10F_myoD-06h-3

description:
10F_ctrol_myoD_6F_ctrol_fst_0-6-24-48hpa_readcounts.txt
res_10F_ctrol_v_myoD-06hpa.txt
res_10F_myoD-00_v_06hpa.txt


title: Liver R26 WT rep3


title: Liver R26 WT rep1


title: 10F_myoD-06h-1


title: Liver R26 WT rep2


title: 10F_ctrol-00h-3

description:
10F_ctrol_myoD_6F_ctrol_fst_0-6-24-48hpa_readcounts.txt
res_10F_ctrol_v_myoD-00hpa.txt
res_10F_ctrol-00_v_06hpa.txt
res_10F_ctrol-00_v_24hpa.txt
res_10F_ctrol-00_v_48hpa.txt


title: Liver R26 TetMyc 2d rep3


title: 10F_myoD-06h-2


title: Liver R26 TetMyc 2d rep4


title: 10F_ctrol-00h-2


title: Liver R26 TetMyc 2d rep1


title: 10F_ctrol-00h-1


title: Liver R26 TetMyc 2d rep2


title: 10F_myoD-00h-3

description:
10F_ctrol_myoD_6F_ctrol_fst_0-6-24-48hpa_readcounts.txt
res_10F_ctrol_v_myoD-00hpa.txt
res_10F_myoD-00_v_06hpa.txt
res_10F_myoD-00_v_24hpa.txt
res_10F_myoD-00_v_48hpa.txt


title: 10F_myoD-00h-2


title: Liver_input

data_processing:
Read filtering with fastx toolkit version 0.0.13.2: fastq_masker -Q33 -q 20 -r -N -v
Alignment to mm9 with bwa version 0.6.2; bwa aln -t 16 reffile fastqfile| bwa samse -n 1 reffile - fastqfile | samtools view -q 1 -ut reffile - |samtools sort - bamfile
Transcription factors (YAP, TEAD, MYC, Pol2) peak calling with MACS version 2.0.9; macs2 -t samplebam -c inputbam  --mfold=7,30 -g mm -p 0.00001
Histone marks (H3K4me1, H3K4me3, H3K27Ac, H3K27me3) peak calling with MACS version 2.0.9; macs2 -t samplebam -c inputbam  --auto-bimodal --broad -g mm -p 0.00000001
the input alignment file was randomly downsampled to the size of the ChIP sample alignment file
Genome_build: mm9
Supplementary_files_format_and_content: *_peaks.txt files: bed files of transcription factors ChIP-Seq;  *_broad_peaks.bed files: bed files of histone marks ChIP-Seq

value: IgG (Santa Cruz, sc-2027)


title: Liver_YAP_TetYapMyc_ChIP

value: YAP 63.7(Santa Cruz, sc101199)


title: 10F_myoD-00h-1


title: Liver R26 TetYapMyc 2d rep3


title: 10F_myoD-h-5

description:
12F_ctrol_nkx_10F_ctrol_myoD_readcounts.txt
res_10F_ctrol_v_myoD.txt

source_name: whole planarian tissue

treatment_protocol: Animals fed in-vitro transcribed dsRNA in liver 10 times in 7 weeks (2x per week for 6 feedings, 1x per week for 4 feedings) or 12 times in 9 weeks (2x per week for 6 feedings, 1x per week for 6 feedings)

value: individual intact planarian


title: Liver R26 TetYapMyc 2d rep2


title: Liver_TEAD_TetYapMyc_ChIP

value: TEAD (ARP38276_P050, Aviva Systems Biology)


title: Liver_YAP_TetYap_ChIP


title: 10F_myoD-h-4


title: 10F_myoD-h-3


title: Liver_TEAD_TetYap_ChIP


title: 10F_myoD-h-2


title: Liver_Pol2_TetYapMyc_ChIP

value: RNAPol2 N20-X (Santa Cruz, sc-899)


title: Liver_Pol2_TetYap_ChIP


title: 10F_ctrol-h-6


title: 10F_myoD-h-1


title: 10F_ctrol-h-5


title: Liver_MYC_TetYapMyc_ChIP


title: 10F_ctrol-h-4


title: Liver_H3K4me3_TetYapMyc_ChIP

value: H3K4me3 (Active Motif, #39159)


title: Liver_H3K4me3_TetYap_ChIP


title: 10F_ctrol-h-2


title: 10F_ctrol-h-3


title: Liver_H3K27Ac_TetYapMyc_ChIP

value: H3K27ac (Abcam, ab4729)


title: 10F_myoD-h-6


title: 10F_ctrol-h-1


title: Liver_MYC_TetYap_ChIP


title: Liver_TEAD_WT_ChIP


title: 12F_nkx1-1-h-7

description:
12F_ctrol_nkx_10F_ctrol_myoD_readcounts.txt
res_12F_ctrol_v_nkx1-1.txt


title: cuticulosomes (pigeon 515)

city: Vienna

first: Thomas

middle: Rainer

last: Burkard

address: Dr. Bohrgasse 7

country: Austria

institute: IMBA

description:
34125
C890GANXX_1#34125_TAGGCATGTATCCTCT

data_processing:
Basecalling RTA VN:1.18.64.0
The reads were aligned with TopHat (v1.4.1) (Trapnell, Pachter et al. 2009) against the Columba livia genome (provided by M.D. Shapiro, University of Utah). A maximum of 6 miss matches and introns between 20-150000 bp were allowed. Maximum multihits were set to 1 and InDels and Microexon-search was permitted. Furthermore, a gene model was implemented as GTF (Shapiro).
Aligned reads were subjected to FPKM estimation with Cufflinks (v1.3.0) (Trapnell, Williams et al. 2010, Roberts, Trapnell et al. 2011) and bias detection and correction was performed. Only fragments compatible with annotation were accepted and counted towards the number of mapped hits used in the FPKM denominator
The aligned reads were counted with HTSeq (0.6.1p1)
The transcripts were subjected to differential expression analysis with DESeq2 (v1.10.1) (Anders and Huber 2010, Love, Huber et al. 2014). Since cuticulosome and non-cuticulosome cells were collected from the same birds, this was considered via blocking in the differential expression analysis.
Genome_build: Columba livia genome (provided by M.D. Shapiro, University of Utah)
Supplementary_files_format_and_content: TAB separated text containing DESeq2 results and FPKM values

organism: Columba livia

source_name: Inner ear (Basilar papilla)

extract_protocol:
RNA extractions of 30 isolated hair cells with and without cuticulosomes from 9 birds respectively (18 samples in total) were performed using the TRIZOL/Chloroform method and the RNA Clean and Concentrator-5 Kit (Zymo Research, R1015) according to manufacturer's protocol.
cDNA libraries were prepared employing a full length RNA-seq from single cells protocol (Picelli et al. 2014). Briefly, this method involved preamplification of reverse transcribed mRNA using a template switching oligo followed by fragmentation and adaptor ligation using a hyperactive derivative of the Tn5 transposase from the Nextera XT DNA Sample Preparation Kit (Illumina, FC-131-1096). Adapter-ligated DNA fragments were amplified by PCR using the Nextera XT DNA Sample Preparation Kit and the Nextera XT 24-index Kit (Illumina, cat. no: FC-131-1001). Sequencing was performed on an Illumina HiSeqV4 system with 50 base pair single-end reads using the True-Seq dual-index sequencing primers for single read runs (Illumina, FC-121-1003).

value: Auditory hair cells with cuticulosomes


title: without cuticulosomes (pigeon 515)

description:
34126
C890GANXX_1#34126_CGTACTAGAGAGTAGA

value: Auditory hair cells without cuticulosomes


title: Liver_TEAD_TetMyc_ChIP


title: 12F_nkx1-1-h-6


title: without cuticulosomes (pigeon 514)

description:
34124
C890GANXX_1#34124_GGACTCCTCTCTCTAT


title: 12F_nkx1-1-h-5


title: Liver_Pol2_TetMyc_ChIP


title: 12F_nkx1-1-h-4


title: Liver_Pol2_WT_ChIP


title: Liver_MYC_WT_ChIP


title: 12F_nkx1-1-h-3


title: cuticulosomes (pigeon 513)

description:
34121
C890GANXX_1#34121_CGTACTAGCTCTCTAT


title: 12F_nkx1-1-h-2


title: 12F_nkx1-1-h-1


title: Liver_H3K27Ac_TetYap_ChIP


title: Liver_H3K4me3_WT_ChIP


title: without cuticulosomes (pigeon 458)

description:
27408
27408_CGTACTAGCTCTCTAT_C6VFBANXX_6_20150513B_20150513


title: Liver_MYC_TetMyc_ChIP


title: without cuticulosomes (pigeon 451)

description:
27406
27406_GGACTCCTAGAGTAGA_C6VFBANXX_6_20150513B_20150513


title: 12F_ctrol-h-5


title: 12F_ctrol-h-4


title: cuticulosomes (pigeon 458)

description:
27407
27407_TAGGCATGTAGATCGC_C6VFBANXX_6_20150513B_20150513


title: Liver_H3K27Ac_TetMyc_ChIP


title: 12F_ctrol-h-3


title: Liver_H3K27Ac_WT_ChIP


title: cuticulosomes (pigeon 451)

description:
27405
27405_TCCTGAGCTATCCTCT_C6VFBANXX_6_20150513B_20150513


title: Liver_H3K4me3_TetMyc_ChIP


title: without cuticulosomes (pigeon 450)

description:
27404
27404_AGGCAGAACTCTCTAT_C6VFBANXX_6_20150513B_20150513


title: 12F_ctrol-h-1


title: cuticulosomes (pigeon 450)

description:
27403
27403_CGTACTAGTAGATCGC_C6VFBANXX_6_20150513B_20150513


title: without cuticulosomes (pigeon 513)

description:
34122
C890GANXX_1#34122_AGGCAGAATATCCTCT


title: without cuticulosomes (pigeon 435)

description:
25403
25403_CGTACTAGTATCCTCT_C6A5PANXX_4_20150303B_20150303


title: cuticulosomes (pigeon 435)

description:
25402
25402_GGACTCCTAGAGTAGA_C6A5PANXX_4_20150303B_20150303


title: cuticulosomes (pigeon 514)

description:
34123
C890GANXX_1#34123_TCCTGAGCAGAGTAGA


title: G1S RNA-seq rep2

city: Shanghai

first: Qi

last: Wang

state: Shanghai

address: 800 Dong Chuan Rd.

institute: Shanghai Jiaotong University

data_processing:
The two ends of the Hi-C reads were seperately mapped to the Drosophila melanogaster dm3 reference genome using Bowtie2(v2.2.9). An iterative mapping method was adopted with an initial length 25bp, if this region failed to map uniquely, an additional 25 bp was included in the next round of mapping. This procedure was continued until the full read length reached 150 bp.
Only reads with high mapping quality(MAPQ>30) were kept for further analysis. Reads mapped to the same restriction fragment and dangling reads seperated by less than 500bp and PCR duplicates were further removed.
The Hi-C contact maps were normalized using ICE(Imakaev et al, 2012), restriction fragments were treated as units instead of equally spaced bins.
Domains were called using Armatus(Filippova et al, 2014) with scaling parameter, gamma, set to 0.9. Domains interrupted by gaps were modified locally using gamma 0.6.
Adapters and low quality reads were removed by cutadapt (v1.8.3) and Trimmomatic (v0.36) using default parameters. Valid paired reads were mapped to the Drosophila melanogaster reference genome dm3 and Flybase gene annotation v5.57 using Tophat2 (v2.0.9) with default options and transcripts were assembled using Cufflinks (v2.2.1). Two replicates were merged for further analysis.
Genome_build: dm3
Supplementary_files_format_and_content: S2Rplus_G1S_domain.txt is a tab-delimited text file contains domain positions in synchronized G1S S2R+ cells. G1S_genes.txt is a tab-delimited text file contains positions, ids, names and expression levels(FPKM) of Flybase r5.57 annotated genes .

source_name: late embryonic cell line

growth_protocol: Drosophila late embryonic S2R+ cells were seeded at the density of 1X 10^6 cells/ml and grown in Schneider's medium ( Invitrogen) with 10% heat-inactivated fetal bovine serum (BI) at 25 °C. Cells were synchronized at G1/S by incubating with 1 µM Hydroxyurea (HU) for 18 h

extract_protocol:
Total RNA were extracted with Trizol reagent.
PolyA+ RNA-seq libraries were prepared using KAPA Stranded mRNA-seq kit following the manufacturer’s instructions.

tag: developmental time

value: embryo 20-24h

tag: drug for synchronization

value: Hydroxyurea


title: without cuticulosomes (pigeon 434)

description:
25401
25401_TAGGCATGAGAGTAGA_C6A5PANXX_4_20150303B_20150303


title: asynchronous Hi-C rep2

description: Hi-C chimeric DNA

extract_protocol:
The Hi-C chimeric DNA were prepared by "in-situ Hi-C" method with minor modifications, Briefly, nuclei released from ten million crosslinked cells were digested with DpnII (NEB). After biotin fill-in and ligation in nuclei, biotin labeled ligation product were fragmented with Cavrios M220, the molecular with size ranging from 300bp to 500bp were selected for the generation of library
The Hi-C library were prepared using NEBNext Ultra DNA Library Prep Kit for Illumina with modifications. Briefly, after end-repair and adaptor liagtion with NEB moduals, biotin labeled validated chimetric DNA were selected with Streptavidin C1 beads (Invitrogen). Hi-C library was amplified after DNA eluation by inculating at 98° C.


title: G1S RNA-seq rep1


title: cuticulosomes (pigeon 434)

description:
25400
25400_GGACTCCTTATCCTCT_C6A5PANXX_4_20150303B_20150303


title: asynchronous Hi-C rep1

description: Hi-C chimeric DNA


title: cuticulosomes (pigeon 433)

description:
25398
25398_AGGCAGAATATCCTCT_C6A5PANXX_4_20150303B_20150303


title: G1S Hi-C rep2

description: Hi-C chimeric DNA


title: Macrophages donor 1

status: Public on Nov 21 2017

city: Montreal

first: Eric

middle: A

last: Cohen

state: Quebec

address: 110 Ave des Pins Ouest

country: Canada

institute: IRCM

data_processing:
Basecalls performed using CASAVA version 1.8
Adaptor sequences and poor quality bases were trimmed with Cutadapt
Alignment of reads was performed using miRDeep2 (mapper.pl) on the GRCh37 human genome
Quantification of individual microRNAs were performed using miRDeep2
Differential expression measurements were performed with DESeq2 v1.4.5
Genome_build: GRCh37
Supplementary_files_format_and_content: Diff files with differential expression

source_name: Macrophages derived from blood monocytes above

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from blood samples (obtained from consenting healthy adults) by Ficoll-Paque; washed in phosphate-buffered solution (PBS) and monocytes separated by adhesion to cell culture plates (cultured in RPMI at 37 °C at 5% CO2). Non-adherent cells were washed out and monocytes cultured in RPMI supplemented with 5% corresponding blood donor plasma for 7 days in order to differentiate into macrophages. Macrophages were maintained in culture with RPMI supplemented with 5% fetal bovine serum (FBS).

extract_protocol:
RNA was extracted from cells using the QIAGEN Rneasy Plus kit using the Total RNA Containing Small RNAs from Cells (Appendix D of 12/2014 Handbook)
Illumina TruSeq Small RNA system; sequencing using PE50 on a HiSeq 2000 sequencer (Illumina technologies)

treatment_protocol: Monocytes were recovered by gentle scraping. Macrophages were recovered by Accutase/PBS-EDTA (1:1) treatment and gentle scraping, washed, and RNA extracted.

value: macrophages


title: 293T EV

city: Beijing

first: lili

last: Cao

address: Xueyuan road, haidian district

institute: Peking university health science center

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: cell line HEK293T

extract_protocol:
Peritoneal macrophages and 293T cells were prepared, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: cell line


title: 293T Mir221


title: 12F_ctrol-h-2

description:
12F_ctrol_nkx_10F_ctrol_myoD_readcounts.txt
res_12F_ctrol_v_nkx1-1.txt


title: Macrophages donor 2


title: Monocytes donor 2

source_name: Monocytes derived from human blood

value: monocytes


title: Monocytes donor 1


title: HMEC_8.1

city: New Orleans

first: Aaron

middle: E

last: Hoffman

state: LA

address: 1700 Tulane University

department: Epidemiology

institute: Tulane University

description: Each sample was sequenced twice using the paired-end format

data_processing:
Duplicate sequencing files were concatenated using the Linux cat command.
Paired-end reads were aligned using Novoalign V2.07.8 with novoindex hg19k14s1 for gene expression analysis
Picard was used to remove duplicates and sort the aligned files
Gene expression was quantified using SAMMate V2.6.1
Genome_build: hg19
Supplementary_files_format_and_content: Microsoft Excel file includes Read Counts and FPKM values for each sample

source_name: breast reduction mammoplasty

growth_protocol: Human Mammary Epithelial Cells (HMECs; Invitrogen Catalog # A10565) were maintained according to the manufacturer's instructions (http://tools.lifetechnologies.com/content/sfs/manuals/HMEC_man.pdf)

extract_protocol:
RNA was extracted from the cells according to manufacturer's instructions of Qiagen's Allprep RNA/DNA Mini Kit (Catalog # 80204)
RNA libraries were prepared for sequencing using standard Illumina protocols for TruSeq Poly(A) selection with 4x barcoding

treatment_protocol: The HMECs were temperature pulsed by incubating the cells at 38.5°C for 6 hours followed by incubation at the maintenace temperature of 36°C for the remainder of the experiment.  The cells were harvested every 4 hours for 36 hours, with only the samples from a 24 hour period (ZT8 to ZT36) being sequenced.

value: human mammary epithelial cells (HMECS), Invitrogen

tag: passages

tag: time post synchronization

tag: replicate


title: HMEC_8.2


title: HMEC_0.1


title: HMEC_4.1


title: HMEC_20.1


title: HMEC_16.2


title: HMEC_16.1


title: HMEC_24.1


title: HMEC_12.1


title: HMEC_20.2


title: HMEC_24.2


title: HMEC_12.2


title: without cuticulosomes (pigeon 433)

description:
25399
25399_TCCTGAGCAGAGTAGA_C6A5PANXX_4_20150303B_20150303


title: G1S Hi-C rep1

description: Hi-C chimeric DNA


title: WTCHG_82519_232_SHAM

city: Oxford

first: Georgios

last: Baskozos

address: Level 6, West Wing, John Radcliffe Hospital

department: NDCN

country: United Kingdom

institute: Oxford University

description:
Poly-A RNA
RAT_SHAM
toc_ENS_genes_rat_DRG.csv
LncRNAs_toc_rat_DRG.csv
lncs_res_SNT_vs_sham_rat.csv
ens_genes_res_SNT_vs_sham_rat.csv
Novel_lncRNAs_rat_DRG.gtf
SJ_regs_rat_DRG.gtf

data_processing:
Sequencing, base calling, demultiplexing and QC using Illumina HiSeq4000 analysis software version 3.3.52 and Illumina HiSeq2000 analysis software version 2.0.12.0
Demux of files and FastQ preparation by BcltoFastq 2.17.1.14 and BcltoFastq 1.8.4
Reads were mapped to mm10 genome (Mus_musculus.GRCm38.dna.primary_assembly.fa, Mus_musculus.GRCm38.87.chr.gtf) or rn6 genome (Rattus_norvegicus.Rnor_6.0.dna.toplevel.fa, Rattus_norvegicus.Rnor_6.0.90.chr.gtf) using STAR aligner
BAM files were merged across sequencing lanes and sorted using SAMtools
Features were counted using HTSeq with Intersection not empty strategy
All reads overlapping annotations:  RefSeq (Pruitt et al., 2014), XenoRefSeq, ENSEMBL genes (Harrow et al., 2012) were discarded. We then used the remaining subset of RNA-seq reads in order to identify islands of expression outside known gene models (continuously expressed regions) using a coverage window approach. Workflow generally described in (Cabili et al., 2011; Gerstein et al., 2014; Ilott and Ponting, 2013) with modifications to produce annotations at the gene level. Doing this we get a non-redundant annotation of unique genes of LncRNAs suitable for count based DE analysis (Anders et al., 2015; Love et al., 2014). The concept of islands of expression (I.o.E) is described in (Gerstein et al., 2014). Coverage cut-off has been set as in (Cabili et al., 2011)  Only properly paired and uniquely mapped reads were selected. We selected splicing junctions covered with > 2 reads. We discarded all reads overlapping know gene models. We then used the remaining subset of RNA-seq reads to identify I.o.E outside known gene models using a coverage window approach.  We selected continuous regions above the coverage threshold of more than a read-mate length to ensure that overlapping read-mates would not artificially increase coverage. I.o.E were collapsed and clustered as co-overlapping features connected by splicing junctions. In each cluster consensus introns were calculated by the relative frequency of each discrete segment of a set of splicing junctions. We then subtracted the genomic intervals of these consensus introns from the genomic intervals of the grouped (I.o.E) to reconstruct full length putative LncRNAs.   We included putative LncRNAs in this novel annotation only if they were present in all replicates a biological condition or strain. Annotations were exported in the Gene Transfer Format (GTF). Subsequently we filtered out transcripts with length < 200 bp and we used CPAT (Wang et al., 2013) to assess coding potential. The pipeline was scripted in R using bioconductor (Gentleman et al., 2004) packages and custom scripts.
Genome_build: mm10 for mouse, rn6 for rat
Supplementary_files_format_and_content: CSV files *res*.csv include DESeq2 results for both ENSEMBL genes (ens_genes_res) and novel LncRNAs (lncs_res). CSV files *toc*.csv include read-pairs counts calculated using HTSeq. GTF files Novel_LncRNAs_*.gtf included gene models of novel LncRNAs.

organism: Rattus norvegicus

source_name: DRG L5

extract_protocol:
RNA was extracted according to the hybrid method of combined phenol extraction (TriPure, Roche) and column purification (High Pure RNA tissue Kit, Roche) (Bartus et al., 2016). The concentration of RNA in the samples was measured using a nanodrop and proved sufficient for sequencing. According to the hybrid method, DRG tissue was first homogenized in TriPure and then mixed with chloroform, following the phenol extraction method. After centrifuging the aqueous liquid, which stays on the top of the tube and contains the nucleic acids, was removed. This solution was then subjected to the column purification method. Following this protocol, the clear aqueous liquid was placed in Roche High Pure RNA tissue Kit columns and washed several times in order to purify the RNA. RNA was then extracted with the mRNeasy kit and all samples were subjected to on-column DNAse digestion in order to prevent genomic contamination i.e. presence of DNA in the RNA samples.
RNA libraries were prepared for sequencing using standard Illumina protocols. Second strand cDNA  synthesis incorporated dUTP. The cDNA was end-repaired, A-tailed and adapter-ligated. Prior to amplification,  samples underwent uridine digestion. The prepared libraries were size selected, multiplexed and QC’ed before paired  end sequencing over eight lanes of a flow cell.

tag: tissue

value: DRG L5

tag: pooled

value: 3 pooled animals

value: Wistar

tag: Sex

value: Male

tag: condition

value: Sham surgery


title: WTCHG_86634_231_SNT

description:
Poly-A RNA
RAT_SNT
toc_ENS_genes_rat_DRG.csv
LncRNAs_toc_rat_DRG.csv
lncs_res_SNT_vs_sham_rat.csv
ens_genes_res_SNT_vs_sham_rat.csv
Novel_lncRNAs_rat_DRG.gtf
SJ_regs_rat_DRG.gtf

tag: strain

value: SNT surgery


title: WTCHG_86635_235_SHAM


title: 541_M14WT_NPC_H3K27me3 ChIP

first: Yue

last: Li

state: Massachusetts

address: 32 Vassar Street, 32-D528

institute: Massachusetts Institute of Technology

description:
batch (Mar-17)
YW37

data_processing:
RNA-seq alignment. Tuxedo-suite was used for the entire RNA-seq analyses (Trapnell et al. 2012). Specifically, TopHat2 (v2.1.0) was used to align RNA-seq reads to the mouse genome (mm10). To ensure correct alignment especially for assigning the spliced reads to the correct transcripts, we supplied the software with an existing transcript reference annotations from RefSeq with option --GTF. The RefSeq annotation is available as the iGenome project at the TopHat website (https://ccb.jhu.edu/software/tophat/igenomes.shtml). Other settings of the aligner were left to the default.
Transcript assembly. We then supplied the alignment BAM files from TopHat2 to Cufflinks to perform transcript assembly and expression estimation. The assembly was guided by the above RefSeq annotations with option --GTF-guide. We also turn on the multi-read correction (--multi-read-correct) and fragment bias correction options (--frag-bias-correct $genome) to correct for the sequencing biases. Other settings of the assembler were left to the default.
Differential analysis. We assembled transcripts in each sample library and biological replicate separately. In the end, we ran Cuffmerge to combine all assembled transcripts into a merged custom annotation file (merged.gtf) for the differential expression analysis. In particular, we ran Cuffdiff to compare between M14 knockout mutant and wild-type libraries using the read alignment files from TopHat2 as input and the above custom annotation file as reference. The 3 biological replicates per condition were used to estimate the dispersion in the negative binomial likelihood function modeled by Cuffdiff. We also enabled --multi-read-correct and --frag-bias-correct to improve estimation. The main output from Cuffdiff that were used for downstream analysis in this paper were the “gene_exp.diff” and “genes.read_group_tracking” (default output names from the software), which provide the differential expression statistical results and the actual expression estimate in terms of FPKM, respectively. Significant fold-change was determined based on FDR < 0.05 (as the default threshold of the Cuffdiff program).
ChIP-seq analysis. To align ChIP-seq DNA reads to the reference mm10 genome, we used Bowtie2 (v2.3.1) (Langmead and Salzberg 2012) with the default options except that “--broad” was turned on for calling broad peaks. Each ChIP library in each biological replicate was compared against the DNA input background library in the corresponding cell type + condition. Specifically, histone marks H3K4me1, H3K4me3, H3K27ac, and H3K27me3 in wild-type and M14 knockout (KO) mutant of mouse neural progenitor cell (NPC) were compared with the DNA input in wild-type and M14 KO NPC, respectively. Default cutoff of FDR < 0.05 were used to determine ChIP-seq peaks relative to the input libraries. The main outputs from MACS2 were the broadPeak files in BED format, which we used for downstream comparison among the experimental conditions and with other cognate genome-wide results (i.e., RNA-seq and RIP-seq).
For RIP-seq, we used Tophat2 to align reads to the mouse reference mm10 genome with default setting and RefSeq annotations as guide (i.e., the same method as in the RNA-seq analysis). To call RIP-seq peaks, we used MACS2 with default settings except for enabling the --broad option (i.e., the same as in the ChIP-seq analysis).
Genome_build: mm10
Supplementary_files_format_and_content: text or peak (bed) format

source_name: WT

extract_protocol:
Positive ES clones were used for injection into c57 blastocysts and generation of chimerical mice. To produce Mettl14 f/+ mice, the chimeras were crossed wild-type c57 for germ line transmission and then crossed with Atcb-Flpe transgenic mice (The Jackson Laboratory, # 003800) to remove FRT flanked selection cassette. Male Mettl14 f/+ were crossed to female EIIa-Cre transgenic mice (The Jackson Laboratory, # 003724) to obtain Mettl14 +/- and Mettl14 +/- mice were intercrossed to obtain Mettl14 conventional knockout mice. To conditional knockout Mettl14 in brain, floxed Mettl14 mice were bred with nestin-Cre transgenic mice (The Jackson Laboratory, # 003771) to generate Mettl14 f/f;nes-cre. Mice were maintained at the SANFORD BURNHAM PREBYS Medical Discovery Institute Institutional animal facility, and experiments were performed in accordance with experimental protocols approved by local Institutional Animal Care and Use Committees (IACUC).
Total RNA was isolated using TRIZOL (Invitrogen) and treated with DNaseI (Roche). Polyadenylated mRNA was purified using GenElute™ mRNA Miniprep Kit (Sigma-Aldrich) and residual ribosomal RNA was depleted with RiboMinus™ Eukaryote System v2 (Life Technologies). m6A protocol: Purified polyA+ RNA was blotted to a nylon membrane (Millipore) using Bio-Dot Microfiltration Apparatus (Bio-Rad). After crosslinking with a UV crosslinker (Spectroline), the membrane was blocked with non-fat milk in TBST and then incubated with antibody against m6A (Synaptic Systems, Cat. # 202 003, 1:1,000) then an HRP-conjugated antibody against rabbit IgG. After incubation with the Immobilon Western Chemiluminescent HRP Substrate (Millipore), the membrane was exposed to autoradiography film (Kodak). ChIP-seq: Histones were extracted from NSCs cultured for 7 days in vitro using Histone Extraction Kit (Abcam) following manufacturer’s protocols. Histone lysates were separated on SDS-PAGE gel, blotted onto Immobilon-FL PVDF membrane (Millipore, Cat. # IPFL00010) and incubated with primary antibodies including rat anti-H3 (Active Motif, Cat. # 61647; 1:2000), rabbit anti- H3K4me3 (Abcam, Cat. # Ab8580; 1:2000), rabbit anti-H3K27ac (Active Motif, Cat. # Ab8580; 1:2000), rabbit anti-H3K27me3 (Millipore, Cat. # 07-449; 1:2000), rabbit anti-H3K9me3 (Active Motif, Cat. # Ab8898; 1:2000) and rabbit anti-H3ac (Active Motif, Cat. # 39133; 1:2000). Secondary antibodies were conjugates of IRDye 680RD and 800CW (LI-COR Biosciences). Membranes were scanned by Odyssey Imager (LI-COR Biosciences) and quantified using Image Studio Lite (LI-COR Biosciences).

treatment_protocol: Mettl14 gene targeting vector was created by E. coli bacterial recombination as described1. NotI-ApaI fragment including intron 1 to 5 of Mettl14 in the fosmid WI1-205L1 (CHORI) was cloned into pGEM11-DTA2L vector2, yielding pGEM-Mettl14(1-5)-DTA. Two primer pairs (M14-L50F and M14-L50R, the left arm for bacterial recombination; LoxP-LF and LoxP-LR) were annealed and cloned into XhoI/HindIII of pBS-2xFRT-Zeo, derivative of pBS- 2xF5-Zeo3. The PCR fragment including Mettl14 intron 1 to 2 with LoxP site (primer pair, M14- ex2F and M14-ex2R-LoxP) digested by BstBI-MluI and right arm adaptor (annealed primer pair, Mettl14-R50F and Mettl14-R50R) were cloned into the vector with the left arm. The splice acceptor (SA)-internal ribosomal entry site (Ires)-hygromycin resistance gene (Hyg)-tandem polyadenylation signals (tpA) cassette of pGEM-SA-Ires-Hyg-tpA was cloned into NheI-PmlI of the vector with left and right arms 3. The bacterial targeting vector was digested by AgeI- NotI to remove vector backbone and was transfected into E.coli strain SW106 containing pGEM472 Mettl14(1-5)-DTA for bacterial recombination, yielding Mettl14 targeting vector for mouse ES cells. Mettl14 ES targeting vector was linearized by NotI and transfected into G4 male ES cells as described4, 5. 24 hours after transfection, 150 μg/ml Hygromycin was added to the ES medium. Hygromycin-resistant ES colonies were picked 10 days after transfection. Targeting of Mettl14 was confirmed by genomic PCR analysis using primer pairs: M14cF and SA-R for 5′-end; UptpA-F and M14-cR for 3′-end.

value: neural progenitor cell

tag: developmental stage

value: embryo

tag: genotype

value: WT


title: WTCHG_82518_226_SHAM


title: HMEC_0.2

tag: cell type


title: WTCHG_86634_229_SHAM


title: 541_M14WT_NPC_H3K27ac ChIP

description:
batch (Mar-17)
YW36


title: 534_M14KO_NPC_H3K27ac ChIP

description:
batch (Mar-17)
YW42

source_name: KO

value: Mettl14 KO


title: HMEC_4.2


title: WTCHG_82519_234_SNT


title: WTCHG_82518_228_SNT


title: 541_M14WT_NPC_5% Input

description:
batch (Mar-17)
YW33


title: ATAC-seq LPL Treg Ahr WT (rep2)

city: Gainesville

first: Liang

last: Zhou

state: FL

department: Department of Infectious Diseases and Immunology

institute: University of Florida

data_processing:
[ATAC-seq] ATAC-Seq reads were mapped to the mouse genome (mm9) with bowtie2 (Langmead and Salzberg, 2012). The mapped reads were filtered using samtools (Li et al., 2009), keeping only the uniquely aligned reads, and bedgraph files (scaled to 10 million reads) were made with bedtools (Quinlan and Hall, 2010).
Genome_build: mm9
Supplementary_files_format_and_content: [RNA-seq] Tab-delimited text file includes count values for each sample.  [ATAC-seq] bedgraph files for each sample

source_name: Lg. Int. Lamina Propria Treg

extract_protocol:
[RNA-seq] Lamina propria cells were isolated and sorted by flow cytometry.  Sorted Tregs were lysed in Trizol (Invitrogen), and RNA was subsequently extracted with RNAeasy Mini Kit (Qiagen).  [ATAC-seq]  Lamina propria cells were isolated and Tregs were sorted by flow cytometry.
[RNA-seq] Total RNA was treated with Ribo-zero kit and RNAseq libraries were generated using kits from Illumina. Barcoded samples were pooled and sequenced over 2 lanes on an Illumina HiSeq 2500 instrument to produce 50 bp single-end reads. [ATAC-seq] Large intestinal CD4+TCRβ+YFP+ Tregs were sorted and subjected to ATAC-Seq according to a published protocol (Buenrostro et al., 2013) with a modification in the library purification step. Briefly, 5x10^4 sorted Tregs were washed once with 50 ul PBS, and then lysed in lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) on ice. Pelleted nuclei were resuspended in transposition reaction mix with Tn5 transposase (Illumina) and incubated at 37℃ for 30 min with gentle shaking. The DNA was purified with MinElute PCR Purification Kit (Qiagen) and was used as a template of PCR with 10 cycles of amplification. The library was cleaned up with 1.2x SPRIselect beads (Beckman Coulter), to exclude the small fragments, before sequencing with Illumia HiSeq 2500.

value: Large Intestine

value: Treg

value: Ahrf/+ Foxp3Yfp-Cre


title: 530_M14KO_NPC_5% Input

description:
batch (Mar-17)
YW27


title: ATAC-seq LPL Treg Ahr KO

data_processing:
[ATAC-seq] ATAC-Seq reads were mapped to the mouse genome (mm9) with bowtie2 (Langmead and Salzberg, 2012). The mapped reads were filtered using samtools (Li et al., 2009), keeping only the uniquely aligned reads, and bedgraph files (scaled to 10 million reads) were made with bedtools (Quinlan and Hall, 2010).
processed data files format and content: [ATAC-seq] bedgraph files for each sample
Genome_build: mm9

extract_protocol:
[ATAC-seq]  Lamina propria cells were isolated and Tregs were sorted by flow cytometry.
[ATAC-seq] Large intestinal CD4+TCRβ+YFP+ Tregs were sorted and subjected to ATAC-Seq according to a published protocol (Buenrostro et al., 2013) with a modification in the library purification step. Briefly, 5x10^4 sorted Tregs were washed once with 50 ul PBS, and then lysed in lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) on ice. Pelleted nuclei were resuspended in transposition reaction mix with Tn5 transposase (Illumina) and incubated at 37℃ for 30 min with gentle shaking. The DNA was purified with MinElute PCR Purification Kit (Qiagen) and was used as a template of PCR with 10 cycles of amplification. The library was cleaned up with 1.2x SPRIselect beads (Beckman Coulter), to exclude the small fragments, before sequencing with Illumia HiSeq 2500.

value: Ahrf/- Foxp3Yfp-Cre


title: 532_M14WT_NPC_H3K27ac ChIP

description:
batch (Mar-17)
YW24


title: 530_M14KO_NPC_H3K27ac ChIP

description:
batch (Mar-17)
YW30


title: 532_M14WT_NPC_5% Input

description:
batch (Mar-17)
YW21


title: 534_M14KO_NPC_H3K27me3 ChIP

description:
batch (Mar-17)
YW43


title: ATAC-seq LPL Treg Ahr KO (rep2)


title: meRIP-seq of m6A IP in NPC2

description:
m6A-IP RNA
batch (Sep-15)
CZ3_m6A_IP_2


title: meRIP-seq of RNA input in NPC1

description:
m6A-IP RNA
batch (Sep-15)
CZ1_Input_1


title: 534_M14KO_NPC_5% Input

description:
batch (Mar-17)
YW39


title: meRIP-seq of m6A IP in NPC1

description:
m6A-IP RNA
batch (Sep-15)
CZ3_m6A_IP_1


title: 532_M14WT_NPC_H3K27me3 ChIP

description:
batch (Mar-17)
YW25


title: ATAC-seq LPL Treg Ahr WT


title: RNA-seq in NPC 534 Mettl14 homozygous knockout

description:
batch3 (Mar-17)
Processed data files: genes.read_group_tracking3, merged3.gtf
YW20


title: RNA-seq LPL Treg Ahr KO (rep 2)

data_processing:
[RNA-seq]  De-multiplexed raw data files from the sequencing core were concatenated and uploaded to the Galaxy website (Pennsylvania State University) for analysis (Blankenberg et al., 2010; Giardine et al., 2005; Goecks et al., 2010). Quality control data was generated with the NGS Toolbox quality control tools (Patel and Jain, 2012). Based on the quality analysis and recommendation of the sequencing core, low-quality 3’ bases were trimmed from each of the reads using the NGS Toolbox FASTQ trimmer tool (Patel and Jain, 2012). The trimmed reads were mapped (with TopHat2 fast splice junction mapper for RNA-Seq) to the January 2012 annotation of the Mus musculus genome (National Center for Biotechnology Information, mm9 assembly) and filtered for uniquely mapped reads (Kim et al., 2013a). Genome visualization tracks (bedgraph files) were uploaded to the University of California Santa Cruz (UCSC) Genome Browser for visual comparison of expression levels (Meyer et al., 2013; Patel and Jain, 2012). Quantitated relative mRNA expression levels (RPKM) were calculated based on exon regions using the SeqMonk software (Babraham Bioinformatics) and the mm9 reference genome annotations (Kent et al., 2002; Mortazavi et al., 2008). Significantly changed genes were found by the Intensity Difference method as outlined and recommended by SeqMonk documentation, and by DESeq analysis.
processed data files format and content: [RNA-seq] Tab-delimited text file includes count values for each sample.
Genome_build: mm9

extract_protocol:
[RNA-seq] Lamina propria cells were isolated and sorted by flow cytometry.  Sorted Tregs were lysed in Trizol (Invitrogen), and RNA was subsequently extracted with RNAeasy Mini Kit (Qiagen).
[RNA-seq] Total RNA was treated with Ribo-zero kit and RNAseq libraries were generated using kits from Illumina. Barcoded samples were pooled and sequenced over 2 lanes on an Illumina HiSeq 2500 instrument to produce 50 bp single-end reads.


title: RNA-seq LPL Treg Ahr KO (rep 1)


title: RNA-seq in NPC 541 wild type

description:
batch3 (Mar-17)
Processed data files: genes.read_group_tracking3, merged3.gtf
YW19


title: RNA-seq LPL Treg Ahr WT (rep 1)


title: RNA-seq LPL Treg Ahr WT (rep 2)


title: RNA-seq in NPC 532 wild type

description:
batch3 (Mar-17)
Processed data files: genes.read_group_tracking3, merged3.gtf
YW17


title: RNA-seq in NPC 308 Mettl14 homozygous knockout

description:
batch2 (Mar-16)
Processed data files: genes.read_group_tracking2, merged2.gtf
CZ6


title: RNA-seq in NPC 530 Mettl14 homozygous knockout

description:
batch3 (Mar-17)
Processed data files: genes.read_group_tracking3, merged3.gtf
YW18


title: STAT4 knockout 2

first: Vince

last: Schulz

address: 333 Cedar St. LMP 4085

department: Department of Pediatrics

institute: Yale University

data_processing:
Sequenced reads were mapped to the mouse genome (mm10 NCBI Build 38) using the BWA version 0.7.9a alignment program.
Reads mapping to the ENCODE project blacklist of repetitive regions and mitochondrial regions were removed
The MACS2 program version 2.1.0.20150420 was used to identify peaks using parameters --nomodel --shift -100 --extsize 200 with a q value of <0.05.
Read counts for open chromatin regions in all samples were obtained using the DiffBind version 2.0.7 package (Ross-Innes et al., 2012)with DESEQ2 normalization utilizing read counts in analyzed regions (parameter bFullLibrarySize=FALSE).  Statistically significant differentially accessible regions were identified by DiffBind using the DESEQ2 method with default parameters.
Bigwig files were created using bedtools genomeCoverageBed scaling per million read, followed by conversion to bigwig format using the UCSC bedGraphToBigWig program.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

source_name: STAT4 KO_Splenic Tfh cells

extract_protocol:
Sorted cells were lysed in buffer (10mM Tris-HCl, 10mM NaCl 3mM MgCL2 and 0.1% IGEPAL) for 15 minutes at 4C, then centrifuged and re-suspended with transposase reaction mix (2x tagmented DNA buffer, transposase [Ilumina Nextera]), and nuclease-free water) and incubated for 30 min at 37 degrees.
Cells were then added to MinElute column (Qiagen) and PCR amplified in KAPA HiFi 2x mix (Kapa Biosystems) with barcoding primers(Buenrostro et al., 2013) at 98C for 45 sec (45s) + 5 x at (98C for 15s + 63C for 30s + 72C for 30s) + 72C for 1 min. PCR products were cleaned with MinElute columns and size exclusion was performed with magJet NGS Cleanup and Size Selection kit (Thermo Fisher). Q-PCR library amplification test and PCR library amplification was performed as previously described(Buenrostro et al., 2015).

treatment_protocol: 2.5 x 10^4 naïve Stg TCR transgenic CD4 T cells were transferred to recipient mice via retro-orbital injection. Mice were infected i.p. with 2 × 10^5 pfu LCMV Armstrong 24 hours after transfer.

tag: strain background

tag: genotype/variation

value: STAT4 Knockout

tag: transferred with

value: naïve Stg TCR transgenic CD4 T cells

tag: infected with

value: LCMV Armstrong

tag: timepoint

value: Day 8 post LCMV infection

value: Splenic Tfh cells (CD4+PSGL1loLy6cloCXCr5hiPD-1hi)


title: RNA-seq in NPC 305 Mettl14 homozygous knockout

description:
batch2 (Mar-16)
Processed data files: genes.read_group_tracking2, merged2.gtf
CZ5

source_name: Het


title: meRIP-seq of RNA input in NPC2

description:
m6A-IP RNA
batch (Sep-15)
CZ1_Input_2


title: 530_M14KO_NPC_H3K27me3 ChIP

description:
batch (Mar-17)
YW31


title: STAT4 wild type 2

source_name: STAT4 WT_Splenic Tfh cells

value: Wild Type


title: STAT4 knockout 1


title: RNA-seq in NPC 301 Mettl14 heterozogous

description:
batch2 (Mar-16)
Processed data files: genes.read_group_tracking2, merged2.gtf
CZ4

value: Mettl14 Het


title: RNA-seq in NPC 299 Mettl14 heterozogous

description:
batch2 (Mar-16)
Processed data files: genes.read_group_tracking2, merged2.gtf
CZ3


title: Tbet knockout 1

data_processing:
Reads were aligned to the mm9 mouse genome using STAR version 2.41d
Unaligned reads were then aligned using TopHat version 2.1.0
Differential expression was computed with Quantify to annotation model Partek (E/M)
Genome_build: mm9
Supplementary_files_format_and_content: FPKM

source_name: Tbet KO_Splenic Tfh cells

extract_protocol:
RNA was extracted using the RNAeasy plus mini kit (Qiagen)
Paired end strand-specific RNA libraries were prepared for sequencing using standard Illumina protocols at the Yale Center for Genome Analysis.

value: Tbet Knockout


title: Tbet heterozygous 2

source_name: Tbet heterozyous_T_Splenic Tfh cells

value: Tbet Heterozygous


title: RNA-seq in NPC 307 wild type

description:
batch2 (Mar-16)
Processed data files: genes.read_group_tracking2, merged2.gtf
CZ2

value: neural progenitor cell


title: Tbet heterozygous 1


title: Tbet wild type 2

source_name: Tbet WT_Splenic Tfh cells


title: RNA-seq in NPC 48 Mettl14 heterozogous

description:
batch1 (Jun-15)
Processed data files: genes.read_group_tracking1, merged1.gtf
YW-8

value: embryo


title: RNA-seq in NPC 306 wild type

description:
batch2 (Mar-16)
Processed data files: genes.read_group_tracking2, merged2.gtf
CZ1

value: WT


title: Tbet knockout 2


title: Tbet wild type 1


title: RNA-seq in NPC 47 Mettl14 heterozogous

description:
batch1 (Jun-15)
Processed data files: genes.read_group_tracking1, merged1.gtf
YW-7


title: RNA-seq in NPC 67 Mettl14 homozygous knockout

description:
batch1 (Jun-15)
Processed data files: genes.read_group_tracking1, merged1.gtf
YW-4

value: Mettl14 KO


title: RNA-seq in NPC 73 Mettl14 homozygous knockout

description:
batch1 (Jun-15)
Processed data files: genes.read_group_tracking1, merged1.gtf
YW-5


title: RM_KO

city: Cincinnati

first: Jeff

last: Kuerbitz

state: OH

address: 3333 Burnet Ave

department: Developmental Biology

institute: Cincinnati Childrens Hospital

description:
rsem_expected_count_matrix.csv
rsem_TPM_matrix.csv

data_processing:
Illumina HiSeq Control Software used for base calling
Sequenced reads were trimmed for Nextera adaptor sequence and low quality regions using Trimmomatic-0.33 with the parameters:2:30:10:1:keepBothReads SLIDINGWINDOW:4:20
Reads were mapped to the genome and transcripts per million transcripts (TPM) and expected counts were calculated using rsem-1.2.22  with the --bowtie2 parameter
Genome_build: mm10

source_name: Amygdalar Intercalated Cells

extract_protocol:
E16.5 Embryos were harvested and stored on ice while tail tissue samples were used for genotyping.  Brains from Tshz1GFP/+ or Tshz1GFP/RA embryos were dissected, quickly embedded in low melting agarose at 36°C, and hardened on ice.  Brains were cut into 700µm coronal sections using a vibratome.  The ventro-lateral portions of caudal telencephalic sections containing the amygdala were dissected as depicted in Figure 6A.  Tissue from embryos of the same genotype was pooled in PBS and dissociated.  Cell suspensions were diluted to a concentration of approximately 1.5x106 cells/mL and GFP expressing cells were isolated by FACS sorting.  Sorted cells were collected in 350µL in buffer RLT with 1% (v/v) 2-mercaptoethanol and RNA was isolated using the Qiagen RNeasy Micro Kit.
Double stranded cDNA was generated and amplified with the NuGEN Ovation RNA-Seq System v2. The Nextera XT DNA Sample Preparation Kit, was used to create DNA library templates from the double stranded cDNA. The size of the libraries for each sample was measured using the Agilent HS DNA chip. The samples were placed in a pool, and the concentration of the pool was optimized to acquire at least 30-35 million reads per sample.

treatment_protocol: Animal protocols were conducted in accordance with guidelines set forth by the Cincinnati Children’s Hospital Medical Center Institutional Animal Care and Use Committee and the National Institutes of Health.  All mice used in this study were maintained on an outbred background. For staging of embryos, the day of vaginal plug detection was considered embryonic day 0.5 (E0.5)

value: amygdala intercalated cells

tag: age


title: WTCHG_86635_237_SNT

value: DRG L5

value: 3 pooled animals

value: Wistar

value: Male

value: SNT surgery


title: RM_Ctrl


title: QT_KO


title: STAT4 wild type 1

value: naïve Stg TCR transgenic CD4 T cells

value: LCMV Armstrong