title: Central Memory- Replicate 3

city: Nashville

middle: F

last: Spurlock III

state: Tennessee

address: 1161 21st Avenue South

department: Medicine

institute: Vanderbilt University School of Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Quality control to filter out bad samples and reads
Alignment to human genome (hg19) using Tophat 2
Read count quantification using HTSeq
Genome_build: hg19
Supplementary_files_format_and_content: text file, read count table

source_name: Peripheral whole blood

extract_protocol:
Peripheral whole blood was collected into BD Vacutainer tubes. Peripheral blood mononuclear cells were isolated using SepMate-50 tubes according to the manufacturer's supplied protocol (Stem Cell Technologies). CD4+ T cells were enriched using the EasySep Human CD4+ T cell enrichment kit and subsequently labeled with the BD Biosciences Naive/Memory T-cell panel (#561438) prior to fluorescence activated cell sorting.
Total RNA isolated using TriReagent (Molecular Research Center) and purified with the RNeasy MinElute Cleanup kit (Qiagen) using an on-column DNAse treatment to ensure absence of genomic DNA contamination according to the manufacturer’s supplied protocol.
The 3026 project library was constructed using the Illumina TruSeq Stranded Total RNA Library Prep kit (Cat. No. RS-122-2201) following the manufacturer's supplied protocol.

value: CD4+ Central Memory (CD45RA lo; CD197 (CCR7) hi)


title: Pub_2

status: Public on Jun 12 2017

type: SRA

city: Hefei

first: Fugui

last: Fang

state: Anhui

address: No. 130 of Changjiang West Road

department: College of Animal Sciences and Technology

country: China

institute: Anhui Agricultural University

library_source: transcriptomic

data_processing:
Total RNA was used as input material for the RNA sample preparations. Ribosomal RNA was removed by Epicentre Ribo-zero™ rRNA Removal Kit (Epicentre, USA). Sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). Products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the libraries were  sequenced on an Illumina Hiseq 4000 platform and 150 bp paired-end reads were generated.
Inorder to identify the lncRNAs,the preliminary scanning was conducted by Scripture (beta2) and Cufflinks (v2.1.1) in a reference-based approach, follwed by coding poteintial analysis using CNCI (v2), CPC (0.9-r2) and Pfam Scan (v1.3).
Cuffdiff (v2.1.1) was used to calculate FPKMs of both lncRNAs and coding genes in each sample (Trapnell,C.et al.2010).
Genome_build: CHIR_1.0
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample. The file lncRNA_sequence.txt contains the sequences for the lncRNA IDs contained in "lncRNA_FPKM.txt".

molecule: total RNA

organism: Capra hircus

source_name: Hypothalamus

extract_protocol:
Hypothalamic tissues were surgically removed immediately frozen, and. RNA derived from goat hypothalamus was obtained using TRIzol Reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Anhuai goats

tag: tissue

value: Hypothalamus

tag: development stage

value: Puberty


title: Effector Memory- Replicate 2

status: Public on Jun 11 2017

first: Charles

country: USA

organism: Homo sapiens

tag: cell type

value: CD4+ Effector Memory (CD45RA lo; CD197 (CCR7) lo)


title: Pub_3


title: Central Memory- Replicate 2


title: Naïve- Replicate 3

value: CD4+ Naive (CD45RA hi; CD197 (CCR7) hi)


title: Tbx16_ChIP (2 replicates)

city: Coventry

first: Andrew

middle: Christopher

last: Nelson

address: Gibbet Hill Campus

department: School of Life Sciences

country: United Kingdom

institute: University of Warwick

description: 2 replicates

library_source: genomic

data_processing:
Reads were mapped to the Zv9 version of the genome with Bowtie using the following parameters: -y -m2 -k2 --best.
Peaks were called for each ChIP sample relative to their paired input sample using MACS with the following parameters: --gsize 1.3e+9 –mfold 10 -pval 1e-4 for Tbx16.
Peak coordinates common to both ChIP replicates were identified for further analysis using custom Perl scripts
Genome_build: Zv9
Supplementary_files_format_and_content: Wig files for track visualization of ChIP and input data.

molecule: genomic DNA

organism: Danio rerio

source_name: whole zebrafish embryos

growth_protocol: Embryos grown in E3 embryo medium at 28.5 degrees celcius and heat-shocket for one hour at 37 degrees celcius prior to fixation

extract_protocol:
Sequential cytoplasmic and nuclear lysis, followed by sonication and centrifugal clarification was used to obtain chromatin of appropriate fragment size.  Desired protein-DNA complexes were isolated using a published anti-Tbx16 antibody (Amacher et al. 2002, Development).
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Embryos fixed in 1.85% formaldehyde for 15 mins prior to chromatin extraction

value: AB

tag: Stage

value: 75-85% epiboly


title: EV_RIPseq

city: Würzburg

first: Lars

last: Barquist

state: Bayern

address: Josef-Schneider-Straße 2 / Bau D15

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

data_processing:
Reads were trimmed for a Phred quality of 20 using the FASTX toolkit version 0.0.13
Adapter trimming using Cutadapt version 1.3
Reads were mapped using the READemption pipeline (Förstner et al., 2014), segemehl, and the lack remapper to the SL1344 genome and associated plasmids (NCBI references: NC_016810.1, NC_017718.1, NC_017719.1, NC_017720.1 )
Coverage plots (wig files) and read quantifications were produced by READemption
Genome_build: NCBI references: NC_016810.1, NC_017718.1, NC_017719.1, NC_017720.1
Supplementary_files_format_and_content: text files are tab delimited including raw read counts; RIP-seq and RNA-seq contain fractional read counts for multimapping reads, while dual RNA-seq counts were generated solely from uniquely mapped reads.

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: Arabinose-supplemented, OD 2

growth_protocol: Salmonella was routine grown in LB (220 rpm, 37C), supplemented with appropriate antibiotics. For RIP-seq, cultures were supplemented with 0.2% L-Arabinose at an OD of 0.2. Cultures were grown to OD 2.0 before harvesting RNA. For dual RNA-seq, OD 2 cultures were used to infect HeLa cells at a multiplicity of infection of 5 and centrifuged for 10 minutes. After 30 minutes at 37C, gentamicin was added to the media to kill extracellular bacteria, and RNA was harvested at the listed time points.

extract_protocol:
For RIP-seq: When the culture reached an OD600 of 2, bacteria were re-suspended in 800 µl of ice-cold lysis buffer (Tris, pH 8.0, 20 mM, KCl 150 mM, MgCl2 1 mM, DTT 1 mM), and disrupted with 1 ml glass beads (BioSpec Products, 0.1 mm diameter) by shaking at 30 Hz for 10 min. The cleared lysate obtained after centrifugation (16000 rcf, 15 min, 4°C) was incubated with 0.5 µl/OD anti-Flag antibody (Sigma, F1804) at 4°C for 30 min followed by incubation with 64 µl pre-washed Protein-A sepharose (Sigma, P6649) for another 30 min. After 5 washes with ice-cold lysis buffer, the sepharose was subjected to Phenol:Chloroform:Isopropanol extraction to isolate RNA (PCI 25:24:1, pH 4.5; Roth, X985.3). For RNA-seq: Total RNA was extracted with hot phenol and chloroform followed by DNase I treatment. For dual RNA-seq: Total RNA from the infected and sorted cells was isolated using the mirVana kit (Ambion).
The samples were rRNA depleted (RNA-seq and dual RNA-seq), then poly(A)-tailed using poly(A) polymerase and the 5’triphosphate (and eukaryotic cap) structures were removed using tobacco acid pyrophosphatase (TAP). Afterwards, an RNA adapter was ligated to the 5’monophosphate of the RNA. First-strand cDNA synthesis was performed using an oligo(dT)-adapter primer and the M-MLV reverse transcriptase (NEB). The resulting cDNA was PCR-amplified to about 20-30 ng/µL using a high fidelity DNA polymerase (barcode sequences for multiplexing were part of the 3’primers). The cDNA library was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and analyzed by capillary electrophoresis (Agilent Technologies).

tag: stategy

value: RIP-seq

tag: plasmid

tag: genotype/variation

value: WT

tag: fraction

value: anti-FLAG co-IPed RNA


title: Tbx16_input

extract_protocol:
Sequential cytoplasmic and nuclear lysis, followed by sonication and centrifugal clarification from was used to obtain chromatin of appropriate fragment size.  Desired protein-DNA complexes were isolated using antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.


title: Effector Memory- Replicate 3


title: PCAF_HCT_Asincro

status: Public on Jun 10 2017

city: Barcelona

first: Oriol

last: bachs

address: Casanova 143

department: Biomedical Sciences

country: Spain

institute: University of Barcelona

description:
asynchronously growing HCT116 cells
PCAF_HCT_Asincro_3969_CAGT

data_processing:
Basecalls performed using Illumina pipeline CASAVA version 1.4
Illumina pipeline analyzed short reads were uniquely aligned allowing at best two mismatches  to the UCSC human genome version hg18, using the program BOWTIE
Reads mapped to multiple locations were discarded
Peak caller algorithm MACS (version 1.4) was used to determine enriched peak region with parameters: --nomodel, --tsize=46, --bw=300
Shift size were determined using Pyicos strand correlation method. Enriched peaks were annotated to nearest EnsEMBL gene (EnsEMBL Biomart   version 54) using Bioconductor package ChIPpeakAnno. Distribution of enriched reads along the genomes and transcription start site (TSS) of RefSeq genes were determined using CEAS
Genome_build: mm9
Supplementary_files_format_and_content: wig

source_name: colon cancer cells

growth_protocol: HCT116 cells were grown to confluence and made quiescent by serum starvation durin 48h for ChIP-seq for p27. Asynchronously growing HCT116 cells were used for ChIP-seq for PCAF

extract_protocol:
Lysates were clarified from sonicated nuclei and chromatine-DNA complexes were isolated with anti-p27 and anti-PCAF antibodies
Libraries were prepared using the NEBNext ChIP-Seq Library Prep Reagent Set for Illumina kit (ref. E6200S) according to the manufacturer's protocol. Briefly, 10 ng of input and ChIP enriched DNA were subjected to end repair, addition of  "A" bases to 3' ends and ligation of PE adapters. All purification steps were performed using Qiagen PCR purification columns (refs. 5092816 and 50928006). Library size selection was done with 2% low-range agarose gel. Library amplification was performed by PCR on the size selected fragments. final libraries were analyzed using Agilent DNA 1000 chip to estimate the quantity and check size distribution, and were then quantified by qPCR using the KAPA Library Quantification Kit (ref. KK4835, KapaBiosystems) prior toamplification with Illumina's cBot. sequencing was done on the HiSeq2000, single Read, 50 nts

tag: cell line

value: colon cancer cell line HCT116

tag: cell growth

value: asynchronously growing

tag: chip antibody

value: PCAF (Abcam, catalog# ab12188, lot# GR88673-4)


title: inputPCAF_HCT_Asincro

description:
asynchronously growing HCT116 cells
input_HCT_Asincro_3975_ACGT


title: Ta_ChIP (2 replicates)

description: 2 replicates

data_processing:
Reads were mapped to the Zv9 version of the genome with Bowtie using the following parameters: -y -m2 -k2 --best.
Peaks were called for each Ta ChIP sample relative to their matched input sample using MACS with the following parameters: --gsize 1.3e+9 and –mfold 10 -pval 1e-8.
Peak coordinates common to both ChIP replicates were identified for further analysis using custom Perl scripts
Genome_build: Zv9
Supplementary_files_format_and_content: Wig files for track visualization of ChIP and input data.

extract_protocol:
Sequential cytoplasmic and nuclear lysis, followed by sonication and centrifugal clarification was used to obtain chromatin of appropriate fragment size.  Desired protein-DNA complexes were isolated using an anti-Ta antibody antibody (Schulte-Merker et al. 1992 Development).
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Paired-end libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.


title: Ta_input

data_processing:
Reads were mapped to the Zv9 version of the genome with Bowtie using the following parameters: -y -m2 -k2 --best.
Peaks were called for each Ta ChIP sample relative to this input sample using MACS with the following parameters: --gsize 1.3e+9 and –mfold 10 -pval 1e-8 for Ta.
Peak coordinates common to both ChIP replicates were identified for further analysis using custom Perl scripts
Genome_build: Zv9
Supplementary_files_format_and_content: Wig files for track visualization of ChIP and input data.

growth_protocol: Embryos grown in E3 embryo medium at 28.5 degrees celcius prior to fixation

extract_protocol:
Sequential cytoplasmic and nuclear lysis, followed by sonication and centrifugal clarification was used to obtain chromatin of appropriate fragment size.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.


title: Naïve- Replicate 2


title: Effector Memory- Replicate 1


title: Dnmt1N_MEF_NT_K4d_K6b_USP21_BrUTP_1

city: Cambridge

last: Bradshaw

address: Tennis Court Road

department: Gurdon Institute

institute: University of Cambridge

description: immunoprecipitated RNA

data_processing:
fastq file processed by filering out low quality reads (<Q20) and llow quality bases (<Q20) with sickle. Adaptors were removed with cutadapt 1.0.
RNA-seq data have been aligned to mus musculus mm9 and X. Laevis genome 6.1 background genome using TopHat 2.0.6
ChIP-seq  data have been aligned to X. Laevis genome 6.1 mus musculus mm9 and X. Laevis genome 6.1 background genome using BWA 0.6.2 with default options. Duplicate reads were then removed
Differential analysis was conducted using EdgeR package
Genome_build: mus musculus mm9 and X. Laevis genome 6.1
Supplementary_files_format_and_content: text files contain RPKMs
Supplementary_files_format_and_content: bw files contain coverage across genome binned in 50bp windows

organism:
Xenopus laevis
Mus musculus

source_name: Dnmt1N_MEF transplanted to Xenopus oocyte injected with K4d and K6b and USP21 and with BrUTP

extract_protocol: RNA extractions were performed using Qiagen RNeasy Mini kit (Qiagen, 74106) according to the manufacturer's protocol including the on column DNAse step. Illumina TruSeq RNA sample prep kit for RNA-seq.

tag: pairing of samples

tag: transferred nucleus/sample type

value: Dnmt1N_p53minus_ MEF

tag: starting material

value: pool of  16 oocytes

tag: developmental stage/condition

value: stage 5-6 xenopus Nuclear transfer oocytes

tag: antibody

value: anti-BrdUTP (Sc32323AC, Santa Cruz Biotechnology Inc)


title: MDAMB468_Nontarget_siRNA_Rep2

city: Huntsville

first: Joy

last: Agee

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

description: MDA468_MDA157_STAT3_Lib_List.txt.SharedGeneCounts.txt

data_processing:
RNA-seq paired-end FASTQ files were aligned to hg19 female using Tophat and Cufflinks
Sequence counts for each transcript were compiled across all experiments for each time point
Genome_build: hg19 female
Supplementary_files_format_and_content: [.txt] Gene transcript sequence counts for all genes across all experiments in each time point

source_name: MDA-MB-468 cells

growth_protocol: TNBC cells were grown under recommended growth conditions

extract_protocol:
ChIP-seq was performed as previously described (Reddy et al. Molecular Cell 2013). RNA-seq was performed as previously outlned (Gertz et al. 2012)
Illumina Single End for ChIP-seq, Illumina Paired End for RNA-seq

treatment_protocol: HCC70, MDA-MB-231, MDA-MB-468, MDA-MB-157, HCC1143 were treated with Ethanol, STAT3 pooled siRNA (L-003544-00-0005, GE Healthcare, Logan, UT), Nontargeting siRNA (D-001810-01-05, GE Healthcare, Logan, UT)

tag: treatment

value: Nontargeting siRNA

value: MDA-MB-468 (Human adenocarcinoma)


title: Central Memory- Replicate 1

value: CD4+ Central Memory (CD45RA lo; CD197 (CCR7) hi)


title: MDAMB157_STAT3_siRNA_Rep2

source_name: MDA-MB-157 cells

value: STAT3 pooled siRNA

value: MDA-MB-157 (Human Medulallary Carcinoma)


title: Hfq_RIPseq


title: Naïve- Replicate 1

value: CD4+ Naive (CD45RA hi; CD197 (CCR7) hi)


title: HCC1143_STAT3_siRNA_Rep2

description: HCC1143_STAT3_Lib_list.txt.SharedGeneCounts.txt

source_name: HCC1143 cells

value: HCC1143 (Human TNM stage IIA, grade 3, primary ductal carcinoma)


title: WT-mycelium-Dark-R1

city: Irapuato

first: Alfredo

last: Herrera-Estrella

state: Guanajuato

address: Libramiento Norte Carretera Leon Km 9.6

department: LANGEBIO

country: Mexico

institute: LANGEBIO

data_processing:
100-base-pair-long reads were obtained and mapped to the P. blakesleeanus genome V2 using bowtie
We performed the mapping of the readings resulting from the RNAseq
experiment using the fasta file of the genome deposited at
http://genome.jgi.doe.gov/pages/dynamicOrganismDownload.jsf?organism=Phybl2
Identifying the file as Phycomyces blakesleeanus NRRL1555 v2.0: Project:
401760, Phycomyces_blakesleeanus_v2_filtered_transcripts.fasta.gz 5 MB; Wed Mar 07 16:56:13 PST 2012.

The identifiers used are those appearing in the Phycomyces blakesleeanus
NRRL1555 v2.0 genome file and can be accessed individually at
http://genome.jgi.doe.gov/pages/search-for-genes.jsf?organism=Phybl2.
Alignment results were recorded in BAM format for further downstream analysis. Read counts per gene were calculated for each library using a shell script and collapsed into a table.
Differential expression analysis of gene expression in the wild type and madC strains in response to light was performed using the edgeR package
Enrichment analysis was performed on the differential genes using GOseq
Supplementary_files_format_and_content: read counts, differential expression

organism: Phycomyces blakesleeanus

source_name: WT strain in dark

growth_protocol: 104 activated spores (48 °C, 15 min) of each P. blakesleeanus strain were grown at 22 °C in minimal medium.

extract_protocol:
Mycelia were disrupted by two 0.5-min pulses in a cell homogenizer (FastPrep-24, MP Biomedicals) with 1.5 g of zirconium beads (0.5 mm diameter) using the RNeasy Plant Mini Kit (Qiagen) following the manufacturer procedure.
Libraries for RNAseq were prepared with RNA from mycelia of the wild type and the madC mutant strains using the TruSeq kit protocol (Illumina).

treatment_protocol: P. blakesleeanus dark-grown mycelia were exposed to blue light (2782.10 J/m2) at the age of 48 h for 30 min. After light exposure mycelia were collected and frozen in liquid nitrogen.

value: mycelium (Vegetative growth)


title: Mixl1_Input

data_processing:
Reads were mapped to the Zv9 version of the genome with Bowtie using the following parameters: -y -m2 -k2 --best.
Peaks were called for each Mixl1 ChIP sample relative to this input sample using MACS with the following parameters: --gsize 1.3e+9 and –mfold 10 -pval 1e-5
Peak coordinates common to both ChIP replicates were identified for further analysis using custom Perl scripts
Genome_build: Zv9
Supplementary_files_format_and_content: Wig files for track visualization of ChIP and input data.

extract_protocol:
Sequential cytoplasmic and nuclear lysis, followed by sonication and centrifugal clarification was used to obtain chromatin of appropriate fragment size.  Desired protein-DNA complexes were isolated using antibody.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq DNA Sample Prep Kit (Part# FC-121-2001) with the exception that Illumina adapters were diluted 1:100 prior to use.

tag: strain

value: AB

value: 30-50% epiboly


title: P27_HCT_G0

description:
G0 synchronized HCT116 cells
P27_HCT_G0_3971_CTTT

value: colon cancer cell line HCT116

value: G0 synchronized

value: p27 (Santa Cruz, catalog# sc-528, lot# I 2115)


title: HCC1143_STAT3_siRNA_Rep1


title: HCC1143_Nontarget_siRNA_Rep3


title: input P27_HCT_G0

description:
G0 synchronized HCT116 cells
input_HCT_G0_3970_ATAT


title: HCC1143_Nontarget_siRNA_Rep2


title: HCC1143_Nontarget_siRNA_Rep1


title: MDAMB468_STAT3_siRNA_Rep3


title: MDAMB468_STAT3_siRNA_Rep1


title: MDAMB468_STAT3_siRNA_Rep2


title: MDAMB157_Nontarget_siRNA_Rep3


title: MDAMB468_Nontarget_siRNA_Rep3


title: MDAMB157_STAT3_siRNA_Rep3


title: MDAMB157_Nontarget_siRNA_Rep2


title: MDAMB468_Nontarget_siRNA_Rep1


title: MDAMB157_STAT3_siRNA_Rep1


title: HCC70_Nontarget_siRNA_Rep2

description: LibList_HCC70_STAT3_siRNA_96hr.txt.SharedGeneCounts.txt

source_name: HCC70 cells

value: HCC70 (Human Tnm Stage Iiia, Grade 3, Primary Ductal Carcinoma)


title: MDAMB231_STAT3_siRNA_Rep2

description: LibList_MDA231_STAT3_siRNA_96hr.txt.SharedGeneCounts.txt

source_name: MDA-MB-231 cells

value: MDA-MB-231 (Human Adenocarcinoma)


title: MDAMB157_Nontarget_siRNA_Rep1


title: MDAMB231_STAT3_siRNA_Rep1


title: MDAMB231_Nontarget_siRNA_Rep2


title: Mixl1_ChIP (2 replicates)

description: 2 replicates

data_processing:
Reads were mapped to the Zv9 version of the genome with Bowtie using the following parameters: -y -m2 -k2 --best.
Peaks were called for each ChIP sample relative to the stage-matched input sample using MACS with the following parameters: --gsize 1.3e+9 –mfold 10 -pval 1e-5
Peak coordinates common to both ChIP replicates were identified for further analysis using custom Perl scripts
Genome_build: Zv9
Supplementary_files_format_and_content: Wig files for track visualization of ChIP and input data.

extract_protocol:
Sequential cytoplasmic and nuclear lysis, followed by sonication and centrifugal clarification was used to obtain chromatin of appropriate fragment size.  Desired protein-DNA complexes were isolated using anti-Mixl1 antibody antibody (Anaspec 55613).
Libraries were prepared according to Illumina's instructions accompanying the TruSeq DNA Sample Prep Kit (Part# FC-121-2001) with the exception that Illumina adapters were diluted 1:100 prior to use.


title: MDAMB231_Nontarget_siRNA_Rep1


title: HCC70_STAT3_siRNA_Rep3


title: HCC70_STAT3_siRNA_Rep2


title: HCC70_STAT3_siRNA_Rep1


title: HCC1143_STAT3_siRNA_Rep3


title: HCC70_STAT3_Rep2_Input_Control

data_processing:
ChIP-seq and ChIP input control FASTQ files were aligned to hg19 female genome using Bowtie
Peak Calling was performed using MACS peak caller
Genome_build: hg19 female
Supplementary_files_format_and_content: [.bedgraph] Chromosome number, start position, stop position, dataValue

value: ethanol

tag: chip-seq antibody

value: none (input)


title: MDAMB157_STAT3_Rep2_Input_Control

tag: cell type


title: MDAMB231_STAT3_siRNA_Rep3


title: HCC1143_STAT3_Rep1

value: anti-STAT3 (Santa Cruz Biotechnology, sc-482)


title: HCC70_Nontarget_siRNA_Rep1

value: Nontargeting siRNA


title: MDAMB231_Nontarget_siRNA_Rep3


title: HCC1143_STAT3_Rep2_Input_Control


title: HCC1143_STAT3_Rep1_Input_Control


title: MDAMB468_STAT3_Rep2_Input_Control

value: MDA-MB-468 (Human adenocarcinoma)


title: MDAMB468_STAT3_Rep1_Input_Control


title: A137_STAT3_Input_Control

source_name: A137 tumor cells

tag: tumor

value: Tumor A137


title: MDAMB157_STAT3_Rep2

value: MDA-MB-157 (Human Medulallary Carcinoma)


title: MDAMB231_STAT3_Rep2


title: HCC70_STAT3_Rep1_Input_Control


title: A139_STAT3_Input_Control

source_name: A139 tumor cells

value: Tumor A139


title: MDAMB231_STAT3_Rep2_Input_Control


title: HCC70_Nontarget_siRNA_Rep3


title: MDAMB231_STAT3_Rep1_Input_Control


title: MDAMB157_STAT3_Rep1_Input_Control


title: hnRNP Q1_RNA-seq

city: Tainan

first: Liang-Yi

last: Hung

address: No.1, University Rd.

department: Institute of Bioinformatics and Biosignal Transduction

country: Taiwan

institute: National Cheng Kung University

description:
immunoprecipitated RNA
GFP-hnRNP Q1 overexpression

data_processing:
Illumina GA Pipeline software CASAVA v1.8
The sequences generated went through a filtering process to obtain qualified reads. ConDeTri was implemented to trim or remove the reads according to the quality score.
Qualified reads after filtering low-quality data were analyzed using TopHat/Cufflinks for gene expression estimation.
The gene expression level was calculated as FPKM (Fragments Per Kilobase of transcript per Million mapped reads)
The reference genome and gene annotations were retrieved from Ensembl database.
Genome_build: Human_hg19 (GRCh37.69)
Supplementary_files_format_and_content: Excel file including each transcript FPKM and ranking

source_name: colon cancer cell line SW480

growth_protocol: SW480 cells were cultured in L-15 medium supplied with 10% FBS and 1% P/S

extract_protocol:
Cytoplasmic lysate were isolated for RNA-IP by anti-GFP antibody and then extracted the immunoprecipitated RNA by TRIsure according to manufacture's protocol.
All procedures were carried out according to the manufacture’s protocol from Illumina. Library construction of all samples were used by TruSeq RNA Sample Prep Kits v2

treatment_protocol: Cells were transfected with GFP-hnRNP Q1 for 24 hours

tag: Stage

value: Duke's type B

value: epithelial

tag: rna-ip

value: GFP (JL-8) antibody


title: MDAMB468_STAT3_Rep2


title: W_KO_P24_4

city: San Francisco

first: minwoo

last: Lee

state: CA

address: 555 Mission bay blvd south

department: CVRI

institute: University of California, San Francisco

description: Processed data file: ac_fat_raw_counts.txt

data_processing:
Base calling was performed using RTA2 (real time analysis), which is included in the Illumina software.
Reads were mapped to mm9 using Tophat version 2.1.0 (default parameters).
Gene levels counts were obtained using featureCounts (Subread package, parameters -t exon -g gene_id).
Data were normalized (TMM option) and differential expression evaluated at the gene level with the edgeR package.
P-values were adjusted for multiple hypothesis testing using the Benjamini-Hochberg false discovery control procedure.
Gene ontology term enrichment was performed with Funcassociate 2.0.
Alternative splicing patterns were visualized using the Integrated Genome Viewer.
Junction reads corresponding to alternative splice isoforms were tallied from SAM format files using in-house Python scripts.
Plots were generating using ggplot2.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Tab-delimited text file includes raw count for all samples.

organism: Mus musculus

source_name: Inguinal white adipose tissue, IL-33 KO, P24

extract_protocol:
Tissues were homogenized in TRIsure reagent (Bioline), and total RNA was extracted using isolate II RNA mini kit (Bioline).
Libraries were prepared according to Illumina TruSeq Stranded mRNA Library Prep Kit. RNA sequencing was performed by the Functional Genomics Core of UCSF.

tag: strain/background

tag: genotype/variation

tag: tissue

value: Inguinal white adipose tissue

tag: age

value: postnatal day 24


title: MDAMB157_STAT3_Rep1

tag: cell line


title: Twelve month wild type mouse cortex sample number two

city: Shenzhen

first: Yifei

last: Cai

address: No. 1120 Lianhua Road

institute: Shenzhen Peking University the Hong Kong University of Science and Technology Medical Center

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
RNA-seq reads were aligned to the Ensembl-RNA reference sequence 38 using FanSe2 with parameters: -L110 -E7 -U0 -S10
Gene and lncRNA abundance measurements were generationed and normalized using edgeR ; The normalized standard were Counts Per Million (CPM)
Differential gene and miRNA expression were analysed using edgeR function package in R program version 3.1.1
Genome_build: UCSC human Hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized CPM and counts for each Sample, FDR and log Fold Change for each transcript

growth_protocol: SPF animal husbandry condiction

extract_protocol:
Total RNA from the cortex was extracted with Qiagen RNeasy RNA mini kit
Following "TruSeq RNA Sample Preparation Guide".

treatment_protocol: Animals were anesthetized and dislocated before cortex dissection

tag: strain background

value: wild type

value: 12 months

value: Brain/cortex


title: Twelve month wild type mouse cortex sample number one


title: MDAMB468_STAT3_Rep1


title: A137_STAT3_Rep1


title: B_KO_P05_4

source_name: Brown adipose tissue, IL-33 KO, P0.5

value: Brown adipose tissue

value: postnatal day 0.5


title: HCC70_STAT3_Rep2

value: ethanol

value: HCC70 (Human Tnm Stage Iiia, Grade 3, Primary Ductal Carcinoma)


title: HCC1143_STAT3_Rep2

value: anti-STAT3 (Santa Cruz Biotechnology, sc-482)

value: HCC1143 (Human TNM stage IIA, grade 3, primary ductal carcinoma)


title: A139_STAT3_Rep1


title: MDAMB231_STAT3_Rep1

value: MDA-MB-231 (Human Adenocarcinoma)


title: B_KO_P05_3


title: Twelve month APP/PS1 mouse cortex sample number two

value: APP/PS1 transgenic


title: B_KO_P05_2


title: Twelve month APP/PS1 mouse cortex sample number one


title: HT1080 LINE-1 attH4x

city: Singapore

first: Shawn

last: Hoon

address: 61 Biopolis Street

country: Singapore

institute: Agency for Science Technology and Research

data_processing:
Library strategy: Amplicon-seq
Raw fastq files were processed with Trimmomatic with settings  LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
The overlapping paired reads were assembled and screened for matching adapters using the biopieces utility scripts "read_fastq -e base_33 -i bpa-1-paired.fastq  -j bpa-2-paired.fastq  |assemble_pairs|find_adaptor -f CTGCTTTATTTCATTAAGTTG -r CAACTTAATGAAATAAAGCAG|grab -K -p ADAPTOR_POS_RIGHT,ADAPTOR_POS_LEFT "
Reads that contain the junction of the puro cassette and the insertion point was identified and read with identical sequences were collapsed to remove PCR duplicates
The junction reads were then mapped to human genome (GRCh38) with blat aligner using default settings. The top hit for each sequence was kept.
The location of the top hit for each read was extracted and overlapping regions were merged with the mergeBed tool from the BEDTools suite.The number of regions merged were tabulated and this results is presented in bpa1-counts.xlsx
Genome_build: GRCh38
Supplementary_files_format_and_content: Spreadsheet xls format

source_name: PCR amplicon

extract_protocol: The first step of insertion mapping involves using a single biotinylated primer that binds in the known sequence of the inserted vector. The primer will extend, amplify and generate many molecules of the biotinylated ssDNA including the vector sequence and its point of integration into the genome. This ssDNA PCR was performed on genomic DNA from parental HT1080 cells, bulk cultures obtained from co-transfections of seamless vector attL4X-PGKssPuro with pCMVssIna and bulk cultures obtained from co-transfections of seamless vector attL4X-PGKssPuro with pCMVssInt-C3CNLS. Biotinylated primer Puro fwd 127 was used to generate the ssDNA extending from puro cassette to the junction of insertion of vector into the human genome. PCR was performed using Bioline Taq polymerase with Tris-based buffer (Vivantis) and the reaction conditions includes 95◦C, 120 seconds; 95◦C, 5 seconds; 50◦C, 30 seconds, 72◦C, 120 seconds; 50 cycles.   The second step includes the capture of ssDNA onto the streptavidin dynabeads (M-280 Streptavidin, Thermo Fisher Scientific), which includes the washing of dynabeads with 1X PCR buffer (Tris-based) followed by incubation of the PCR product generated in the first step with dynabeads for 3 hours on roller at room temperature. The phosphorylated primer pETF2-PH was used as an adaptor and 5’ adenylation was done using kit (NEB E2610S). The ligation of the 5’ adenylated oligo with captured ssDNA was done with the help of 5’ AppDNA ligase (NEB) at 65◦C for an hour. Semi-nested PCR was performed on beads with forward primer Puro fwd 128 and reverse primer petF2RC using Taq Polymerase (Bioline) and non-Tris based buffer (Bioline). PCR reaction conditions includes 95◦C, 120 seconds; 95◦C, 5 seconds; 55◦C, 30 seconds, 72◦C, 120 seconds; 34 cycles. Further, a nested PCR was carried with forward primer bpa1 and cs_attH4X_R1  and the PCR products were analyzed on 1% agarose in 0.5% TBE buffer. The PCR amplicon with the expected size was excised and purified. The amplicon was sheared and ligated with standard illumina adaptors for shortgun sequencing  with 100 Paired End reads.

value: HT1080 fibrosarcoma

tag: molecule

value: PCR DNA amplicon


title: B_WT_P05_3

source_name: Brown adipose tissue, WT, P0.5

value: Wild type


title: HCC70_STAT3_Rep1


title: W_KO_P24_2


title: W_WT_P24_2

source_name: Inguinal white adipose tissue, WT, P24


title: W_WT_P24_1


title: W_WT_P24_4


title: B_WT_P05_4


title: W_KO_P24_3


title: Day2_WaterLoaded1

city: Bethesda

first: Jae Wook

state: MD

address: 10 Center Drive, 6N314

institute: National Institutes of Health

description: Cortical collecting duct, Water-loaded rat #1, Day 2

data_processing:
Base-calling was performed using on-instrument real-time analysis (RTA) pipeline provided by Illumina HiSeq 2000.
Individual pair of FASTQ sequences was inspected and nucleotides with phred33 score lower than 30 were trimmed with Trimmomatic 0.32 (http://www.usadellab.org/cms/?page=trimmomatic) using the following command: java -jar trimmomatic-0.32.jar PE -threads 8 -phred33 sample_1.fastq.gz sample_2.fastq.gz sample1_p1.fastq. sample1_up1.fastq sample2_p2.fastq sample2_pup2.fastq TRAILING:30 MINLEN:35
Pairs of FASTQ sequences that survived the trimming process were mapped to rat reference genome (ensembl Rnor6.0) with STAR 2.4.0.1 using the following command: STAR --genomeDir <genome directory> --readFilesIn sample_p1.fastq sample_p2.fastq --runThread 8 --outFilterMismatchNmax 3 --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMismatchMax 3 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated
The raw mapping data was filtered for uniquely mapped reads using SAMtools.
HTSeq-count and R were used to count mapped reads and calculate FPKMs.
Genome_build: Ensembl Rnor6.0
Supplementary_files_format_and_content: vasopressin_escale_rn6_FPKM.txt is a tab-delimited text file that contains a matrix of fragments per kilobase exons per million mapped reads (RPKMs) for Ensembl Rnor6.0 genes. Vasopressin_escape_rn6_htseqcount.txt is a tab-delimited text file that contains a matrix of read counts for Ensemble Rnor6.0 genes.

organism: Rattus norvegicus

source_name: Microdissected cortical collecting duct

growth_protocol: Male Sprague-Dawley rats were grown and maintained in the Animal Facility of the NHLBI. Normal rat chow was fed to the animals. For vasopressin-escape experiment, 5-week-old rats were used.

extract_protocol:
Dissected tubules were lysed in buffer containing RNase inhibitors and universal primers. Reverse transcription was started in this cell lysate. See Tang F. et al. (2010). "RNA-Seq analysis to capture the transcriptome landscape of a single cell" Nature Protocol 5(3):517-35.
We followed an RNA-seq protocol developed for single-cell RNA-seq. See Tang F. et al. (2010). "RNA-Seq analysis to capture the transcriptome landscape of a single cell" Nature Protocol 5(3):517-35. cDNAs were sheared and made into adapter-ligated RNA-seq libraries using NuGen Mondrian machine and Ultralow Library System.

treatment_protocol: For vasopressin-escape experiment, subcutaneous minipumps containing DDAVP (5ng/hr) were implanted into the back of the rats. These rats received either water load ("WL", 50 mL/day) or normal amount of water ("C", 25 mL/day) in the form of gelled food. After 4 days of water load, the cortical collecting duct was microdissected.

value: Sprague-Dawley

tag: Sex

value: male

tag: developmental stage

value: adult

value: cortical collecting duct


title: Day4_Control3

description: Cortical collecting duct, Control rat #3, Day 4


title: Day4_WaterLoaded1

description: Cortical collecting duct, Water-loaded rat #1, Day 4


title: Day2_WaterLoaded3

description: Cortical collecting duct, Water-loaded rat #3, Day 2


title: Day4_WaterLoaded3

description: Cortical collecting duct, Water-loaded rat #3, Day 4


title: Day4_WaterLoaded2

description: Cortical collecting duct, Water-loaded rat #2, Day 4


title: Day4_Control1

description: Cortical collecting duct, Control rat #1, Day 4


title: Day2_WaterLoaded2

description: Cortical collecting duct, Water-loaded rat #2, Day 2


title: B_WT_P05_2


title: Day2_Control1

description: Cortical collecting duct, Control rat #1, Day 2


title: B_WT_P05_1


title: W_WT_P24_3

value: Inguinal white adipose tissue

value: postnatal day 24


title: Day2_WaterLoaded4

description: Cortical collecting duct, Water-loaded rat #4, Day 2


title: Day2_Control4

description: Cortical collecting duct, Control rat #4, Day 2


title: Day1_WaterLoaded3

description: Cortical collecting duct, Water-loaded rat #3, Day 1


title: B_KO_P05_1

value: Brown adipose tissue


title: Day4_Control2

description: Cortical collecting duct, Control rat #2, Day 4


title: Day1_Control2

description: Cortical collecting duct, Control rat #2, Day 1


title: Day1_WaterLoaded1

description: Cortical collecting duct, Water-loaded rat #1, Day 1


title: Sample 34 [CTRL 4 wks]

city: Martigny

first: Raphaelle

last: Luisier

state: Valais

address: Rue Marconi 19, PO Box 592

country: Switzerland

institute: Idiap Research Institute

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and then mapped to h19 ribosomal RNA using bowtie v1.1.2 with parameters -q -p 8 -v 0. Unmapped reads were finally mapped to hg19 whole genome using tophat2 with parameters  -g 1 -p 8  --library-type fr-firststrand.
For differential gene and transcript expression analysis we ran Kallisto and Sleuth. Kallisto was used to 1) build a transcript index from the Ensembl GRC38 release 85 Homo sapiens transcriptome (-k 31), 2) pseudo-align the RNA-seq reads to the transcriptome and 3) quantify transcript abundances (-b 100 --single -l 275 -s 50 --rf-stranded). We next identified differentially expressed transcripts and genes with Sleuth, a companion program that uses Kallisto results to differentiate between true biological expression differences and variation resulting from sources of experimental noise.
Genome_build: hg19
Supplementary_files_format_and_content: Relative transcript abundance and transcript per million as obtained from Kallisto software.

source_name: astrocytes

growth_protocol: Dermal fibroblasts were cultured in OptiMEM +10% FCS medium. The following episomal plasmids were transfected for iPSC generation: pCXLE hOct4 shp53, pCXLE hSK and pCXLE hUL (Addgene), as previously reported [15].Details of the lines used in thus study are reported in Supplementary table 1. Two of the control lines used (control 2 and control 3) are commercially available and were purchased from Coriell (cat. number ND41866*C ) and ThermoFisher Scientific (cat. number A18945) respectively. Induced PSCs were maintained on Geltrex (Life Technologies) with Essential 8 Medium media (Life Technologies) and passaged using EDTA (Life Technologies, 0.5mM).All cell cultures were maintained at 37°Cand 5% carbon dioxide.

extract_protocol:
Total RNA was extracted from cells using the Maxwell RSC simplyRNA cells kit (Promega), that includes DNase treatment, according to manufacturer’s instructions.
1 ug of total RNA was subjected to Ribo-Zero treatment TruSeq Stranded mRNA preparation Kit (Illumina).

treatment_protocol: AC differentiation was conducted using an adapted version of a previously published protocol (Gupta et al., 2012). Briefly, iPSCs were treated identically to the motor neurogenesis protocol but underwent an additional propagation phase (>60 days) with 10ng/ml FGF-2 (Peprotech) before terminal differentiation in 10ng/ml BMP4 and 10ng/ml LIF.

tag: patient id

value: Patient 4

tag: cell line id

value: CTRL 1

tag: genotype

value: Control

tag: days of differentiation


title: Sample 33 [CTRL 4 wks]

value: Patient 3

value: CTRL 2


title: Day1_Control1

description: Cortical collecting duct, Control rat #1, Day 1

tag: strain


title: Day1_Control3

description: Cortical collecting duct, Control rat #3, Day 1


title: Sample 35 [CTRL 4 wks]


title: Day2_Control3

description: Cortical collecting duct, Control rat #3, Day 2


title: CPT1A_81KD2

city: Cleveland

first: Jihye

last: Kim

state: Ohio

address: 9500 Euclid Ave.

department: Quantitative Health Sciences

institute: Cleveland Clinic

description: mRNA isolated using the miRNeasy Mini Kit (Qiagen)

data_processing:
alignment: TopHat v2.1.0 using default settings
expression levels: Cufflinks v2.2.1 and cuffdiff using default settings
significant genes are with FDR < 0.05
Genome_build: hg19 (Ucsc)
Supplementary_files_format_and_content: text file with FPKM values

source_name: Prostate cancer (PCa) cells

growth_protocol: Cell lines were obtained from the University of Colorado Cancer Center (UCCC) Tissue Culture Shared Resource (2014) and were authenticated by Single Tandem Repeat analysis. Cells were passaged in RPMI media containing 5% FBS supplemented with amino acids and Insulin (Hyclone). Cells were grown in a humidified 5% CO2 incubator.

extract_protocol:
Total RNA was extracted with the miRNeasy Kit (Qiagen) according to manufacturer's instructions.
RNA libraries were prepared for sequencing using TruSEQ RNA Sample Prep v2 using standard Illumina protocols.

treatment_protocol: TRCN0000036279 (CPTsh1), TRCN0000036281 (CPTsh2) CPT1A shRNAs and the non-targeting control SHC002 were purchased from the CU Functional Genomics Core.  Lentiviral transduction and selection were performed according to Sigma's MISSION protocol but using lentiviral packing plasmids pCMV-R8.74psPAX2 and VSV-G/pMD2.G and transfection reagent TransIT-LT1 (Mirius).

tag: treatment

value: TRCN0000036281 (CPTsh2) KnockDown


title: CPT1A_79KD1

value: TRCN0000036279 (CPTsh1) KnockDown


title: Day2_Control2

description: Cortical collecting duct, Control rat #2, Day 2


title: Day1_WaterLoaded2

description: Cortical collecting duct, Water-loaded rat #2, Day 1


title: RNAseq_NIPBL_Rep2

first: Nezar

last: Abdennur

state: MA

address: 77 Massachusetts Ave

institute: MIT

description:
ACAGTG
rRNA-depleted RNA
deseq2-gene.csv
NIPBL_all_star_genome_minusUniq.bw
NIPBL_all_star_genome_plusUniq.bw

data_processing:
Hi-C. Alignment: Hi-C reads were mapped using bowtie 2.2.8 and the iterative mapping strategy (Imakaev et al, 2011) implemented in the hiclib package. Filtering: PCR duplicates and reads mapped to multiple or zero locations were removed. After binning, low-coverage bins were removed using a maximum allowed median absolute deviation (MAD) filter on log genomic coverage, set to five MADs. To remove the short-range Hi-C artifacts we also filter contacts mapping to the same or adjacent genomic bins (i.e., first two diagonals). Binning: the filtered reads pairs were binned into 20kb and 100kb contact matrices using the cooler library and stored as binary cool HDF5 files. Normalization: the filtered 20kb and 100kb contacts matrices were then normalized using the iterative correction procedure (IC), such that the genome-wide sum of contact probability for each row/column equals 1.0.
ChIP-seq. We processed ChIP-seq data following the steps of the ENCODE pipeline [https://github.com/ENCODE-DCC/chip-seq-pipeline]. Alignment: we used bwa 0.7.12 (program bwa aln with parameters: -q 5 -l 32 -k 2). Filtering: PCR duplicates were marked using picardtools 2.7.1. Unmapped reads, non-primary alignments, and low quality alignments (mapQ < 30) were removed using samtools 1.3. Cross-correlation analysis was performed using phantompeakqualtools. Peaks and signal tracks were generated using MACS2. For Rad21, Smc3 and CTCF ChIP-seq, we followed the same steps with the following variations: reads from pooled mouse hepatocyte chromatin and HEK human chromatin (internal control and calibration) were mapped to the combined mm9 and hg19 assemblies using the bwa mem program. After filtering, reads were divided into those that mapped uniquely to either mm9 or hg19. A database of CTCF motif instances was produced by performing a PWM scan of the canonical mouse CTCF motif against the mm9 genome using the fimo tool from the MEME suite with default parameters. Peak files with motif annotations were generated by intersecting the peak files against the motif database using bedtools 2.26.0.
RNA-seq. We mapped the RNA-seq data to mm9 reference mouse genome assembly and GENCODE vM1 transcriptome using STAR v.2.5.0a and adapted scripts from the ENCODE RNA-Seq pipeline [https://www.encodeproject.org/pipelines/ENCPL002LSE/]. To obtain the tracks of local transcription, we aggregated the uniquely mapped reads into RPKM-normalized bigWig files using the built-in STAR functionality. To find differentially expressed genes, we aggregated the read counts at the gene level using HTSeq with the "union" option and called DE genes with DESeq2. Alignment with STAR v2.5.0.a was done using parameters: --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMunmapped Within --outFilterType BySJout --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM --sjdbScore 1. Signal tracks were generated using STAR with parameters: --runMode inputAlignmentsFromBAM --outWigType bedGraph --outWigStrand Stranded  --outWigReferencesPrefix chr.
Compartment eigenvectors. The compartment structure of Hi-C maps was detected using a modified procedure from (Imakaev et al, 2012). In short, compartments were quantified as the dominant eigenvector of the observed/expected 20kb and 100kb cis contacts maps upon subtraction of 1.0, as implemented in hiclib.
Domain detection. To identify contact domains, we used a segmentation that divides the genome into domains in such a way as to maximize a global domain scoring function. We used two different scoring functions: one was the corner score function from (Rao et al, 2014) and the other was based on network modularity, which is a metric widely used to detect communities in networks. The implementation of these and related algorithms is provided in the lavaburst package. To robustly call insulating boundaries across different conditions, we exploit the multi-resolution nature of the modularity score and compute the average marginal boundary scores on 20kb WT and ΔNipbl contact matrices sweeping over a range of gamma values to obtain a 1D boundary (i.e., insulation) track. Short intervals representing insulating loci were called by thresholding on the boundary score, and the common and unique loci to each condition were determined by interval intersection.
Genome_build: mm9
Supplementary_files_format_and_content: Cooler HDF5 files (extension .cool.HDF5) contain contact matrices and were generated using the cooler Python package; ChIP-seq signal track bigWigs were generated using MACS2, in units of SPMR; RNA-seq bigWig files were generated using STAR in units of RPM; Eigenvector text files are fixed step bedGraph-like files covering the whole genome with a column for the eigenvector in each condition (U=WT, T=TAM, N=NIPBL); TAD call text files are BED-like files where each row corresponds to a detected domain; the TAD boundary probabilities file is a bedGraph-like file covering the whole genome at 20kb with columns for the insulation tracks in conditions U=WT and N=NIPBL; The deseq2 CSV file contains estimated transcript abundances and differential expression statistics across the three conditions

source_name: NIPBL

extract_protocol:
Liver was dissected and the left lateral lobe was prepped for a two-step perfusion adapted from (Li et al 2010 & Goncalves et al 2007): First, the liver was perfused with an EDTA-containing buffer to remove Ca2+ from the tissue in order to weaken the integrity of the desmosomes, which were subsequently digested using a Ca2+ rich buffer containing collagenase. The freed hepatocytes were rinsed through a cell strainer and washed four times with ice-cold Ca2+ rich buffer without collagenase. For each wash, the cells were spun at low centrifugal force (60g for 1min) to enrich intact hepatocytes and reduce non-mesenchymal debris. Part of each sample was fixed with 1% PFA for 10 minutes at room temperature. Fixed and unfixed hepatocytes were aliquoted and frozen in liN2 for later use.
Hi-C: Roughly 100 million fixed hepatocytes per sample were processed according to (Kalhor et al, 2012) using HindIII. TCC libraries were PCR-amplified (12 cycles) and size selected. Equimolar pools of libraries were sequenced; ChIP-seq: Fixed aliquots of hepatocytes were hypotonically lysed and sonicated in 1% SDS/TE. An aliquot of each sample was reverse cross-linked in order to determine chromatin concentration and sonication efficiency. 20μg chromatin per sample was diluted in RIPA and incubated with 1.5μg of either αH3k4me3 antibody (C15410003-50, Diagenode) or αH3K27Ac antibody (ab4729, Abcam) at 4°C, overnight. The antibodies were retrieved with Dynabeads (IgA, Invitrogen) and bound chromatin was washed and eluted. After reverse cross-linking, the amount of ChIPped and input DNA was determined with Qubit (Thermo Fisher).  The libraries were prepared with NEBNext® ChIP-Seq Library Prep Kit for Illumina®. After amplification and size selection with E-Gel® SizeSelect™ (Thermo Fisher) their size-distributions were determined with Bioanalyzer. Equimolar pools of libraries were sequenced with Illumina HiSeq2000 (50bp, single end). RNA-seq: RNA integrity was tested with Bioanalyzer (Agilent RNA Nano Kit) and ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit (Illumina) prior to library preparation.  Strand-specific libraries were prepared with NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®. After amplification and size selection with Agencourt AMPure XP beads (Beckmann Coulter) their size-distributions were determined with Bioanalyzer. Equimolar pools of libraries were sequenced with Illumina HiSeq2000 (50bp, single end).

treatment_protocol: Treated 12 week old mice were injected with 1mg Tamoxifen (100μl of 10mg/ml Tamoxifen in corn oil) on 5 consecutive days. After keeping these mice for another 5 days without injection, they were sacrificed and the hepatocytes were harvested.

value: tamoxifen

value: 12 weeks

value: liver


title: CL_WdEpiB

city: New York

first: Yejing

last: Ge

state: NY

address: 1230 York Ave

institute: The Rockefeller University

description: RNAseq

data_processing:
50-bp sequences were aligned to mm10 using STAR and Gencode release M9 and counts generated from STAR output --quantMode GeneCounts.
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited, gene counts

source_name: Skin

growth_protocol:
Adult P60 (Refer to Yang et al eLife 2015 4:e10870 for published RNAseq data (SCC-SC and the rest of HFSC, EpdSC)
Adult P60 wound biopsy (Refer to Yang et al eLife 2015 4:e10870 for published RNAseq data (SCC-SC and the rest of HFSC, EpdSC)

extract_protocol:
Total RNA extracted via Trizol/Zymo RNA extraction kit
Illumina TruSeq RNA Sample Preparation
Single Read Clustering and 51 Cycles Sequencing (per lane)

value: female

tag: cell types

value: adult skin epidermal stem cells after wounding

tag: sort markers

value: Lineage Neg, IntA6Hi, YFP- (Sox9CreER;R26-YFP)


title: CTRL2

value: non-targeting(NT) shRNA


title: CPT1A_81KD1


title: CTRL1


title: Sample 32 [CTRL 4 wks]


title: CPT1A_79KD2


title: RNAseq_NIPBL_Rep4

description:
GGCTAC
rRNA-depleted RNA
deseq2-gene.csv
NIPBL_all_star_genome_minusUniq.bw
NIPBL_all_star_genome_plusUniq.bw


title: RNAseq_NIPBL_Rep3

description:
TTAGGC
rRNA-depleted RNA
deseq2-gene.csv
NIPBL_all_star_genome_minusUniq.bw
NIPBL_all_star_genome_plusUniq.bw


title: RNAseq_NIPBL_Rep1

description:
CCGTCC
rRNA-depleted RNA
deseq2-gene.csv
NIPBL_all_star_genome_minusUniq.bw
NIPBL_all_star_genome_plusUniq.bw


title: CL_WdEpiA

description: RNAseq


title: RNAseq_TAM_Rep4

description:
TAGCTT
rRNA-depleted RNA
deseq2-gene.csv
TAM_all_star_genome_minusUniq.bw
TAM_all_star_genome_plusUniq.bw

source_name: TAM


title: CL_BuA

description: RNAseq

value: adult skin hair follicle stem cells

value: Lineage Neg, IntA6Hi, CD34+Sca1-


title: RNAseq_TAM_Rep1

description:
CGATGT
rRNA-depleted RNA
deseq2-gene.csv
TAM_all_star_genome_minusUniq.bw
TAM_all_star_genome_plusUniq.bw


title: CL_WdBuB

description: RNAseq

value: adult skin hair follicle stem cells after wounding

value: Lineage Neg, IntA6Hi, YFP+ (Sox9CreER;R26-YFP)


title: ChIPseq_Input_histone_NIPBL

tag: chip antibody


title: RNAseq_TAM_Rep3

description:
ATCACG
rRNA-depleted RNA
deseq2-gene.csv
TAM_all_star_genome_minusUniq.bw
TAM_all_star_genome_plusUniq.bw


title: CL_WdBuA

description: RNAseq


title: RNAseq_TAM_Rep2

description:
GATCAG
rRNA-depleted RNA
deseq2-gene.csv
TAM_all_star_genome_minusUniq.bw
TAM_all_star_genome_plusUniq.bw


title: CL_EpiB

description: RNAseq

value: adult skin epidermal stem cells

value: Lineage Neg, IntA6Hi, CD34-Sca1+


title: ChIPseq_H3K27ac_NIPBL

value: H3K27ac (Abcam, ab4729)


title: ChIPseq_H3K4me3_NIPBL


title: CL_EpiA

description: RNAseq


title: RNAseq_WT_Rep4

description:
ATTCCT
rRNA-depleted RNA
deseq2-gene.csv
UNTR_all_star_genome_minusUniq.bw
UNTR_all_star_genome_plusUniq.bw

source_name: WT


title: ChIPseq_Input_histone_WT


title: siHdac4_3

city: Miami

first: Eleonore

last: Beurel

state: FL

address: 1011 NW 15th Street Gautier room 415

department: Psychiatry

institute: University of Miami, Miller School of Medicine

data_processing:
Paired-ends reads generated from sequencing on the Illumina Hiseq2000 were trimmed off the adaptor sequences using a custom script.
Trimmed reads were aligned to the mouse genome reference GRCm37 using TopHat 2.0.9.
Transcriptome for each sample was assembled using Cufflinks, which also provided transcripts abundance in fragments per kilobase of exon per million fragments mapped (FPKM)
Transcripts assemblies were merged using Cuffmerge.
Genes were annotated according to the ENSEMBL classification, and genes that were not annotated as protein coding genes, lincRNA or antisense RNA were filtered out.
Differential gene expression analysis was performed using Cuffdiff.
Genome_build: GRCm37
Supplementary_files_format_and_content: Excel file including RPKM values for each Sample

source_name: hippocampus

extract_protocol:
RNA were extracted using the TRIzol method
1mg of RNA was used to prepare poly-A selected directional libraries using the NEBNext Ultra Directional RNA Library Prep Kit (New England BioLabs)

treatment_protocol: mice were treated intranasally with 10 ug siRNAs against Bdnf, Hdac4 and a scramble siRNAs. After 3 days animals were sacrificed and RNA were extracted from hippocampus and sequenced

value: brain

tag: brain region

value: hippocampus


title: siHdac4_2

tag: tissue


title: siBdnf_4

value: siBDNF


title: RNAseq_WT_Rep3

description:
GTGAAA
rRNA-depleted RNA
deseq2-gene.csv
UNTR_all_star_genome_minusUniq.bw
UNTR_all_star_genome_plusUniq.bw

tag: age


title: CL_BuB

description: RNAseq


title: CO_MO_n3

city: Urbana

first: Stephanie

last: Ceman

state: IL

address: 601 S. Goodwin Ave

department: Cell and Developmental Biology

institute: University of Illinois-Urbana Champaign

data_processing:
The libraries were quantitated by qPCR and sequenced on one lane for 101 cycles from one end of the fragments on a HiSeq 4000 using a HiSeq 4000 sequencing kit version 1.
Fastq files were generated and demultiplexed with with the bcl2fastq v2.17.1.14 Conversion Software (Illumina), which also trims the adaptors (default 0.9 stringency) and removes resulting reads shorter than 35 bp.
All bases across the reads showed quality scores greater than Q30 (FASTQC version 0.11.4) and so quality trimming was not performed.
The single end reads were aligned to xenbase.org's X. laevis v9.1 repeat masked genome using STAR (v2.5.2a); index generation was done without gene models and default parameters. The gff3 of xenbase.org's 1.8.3.1 gene models was converted gtf format using the gff_read program from cufflinks2 (version 2.2.1). Alignment was done using parameters --sjdbGTFfeatureExon CDS, --sjdbGTFtagExonParentGene gene_id and –quantMode GeneCounts, the last of which outputs read counts per gene_id.
Genome_build: X. laevis v9.1
Supplementary_files_format_and_content: [.tab] tab-delimited text files of read counts per gene per sample were used directly in edgeR 3.15.2 for statistical analysis and thus are the "normalized" data.

organism: Xenopus laevis

growth_protocol: Fertilized eggs were collected from 2 separate mating pairs, dejellied and sorted for injection in 0.25X MMR media

extract_protocol:
Total RNA was prepared using TRIZOL reagent , followed by Phenol Chloroform extraction and Isopropanol precipitation. Total RNA was analyzed on a MOPS gel to rule out DNA contamination and submitted for Library Prep and sequencing.
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina).

treatment_protocol: Injections were done using 18ng of Control or Translation blocking MOV10 morpholino. The embryos were incubated in 0.25XMMR  till Stage 10.5. Three separate embryos were collected from both the Control and MOV10 MO injected conditions.

value: whole embryo

value: stage 10.5 embryo

value: Control Morpholino injection


title: CO_MO_n1


title: siScramble_2

value: siScramble


title: GW0742 rep 2

status: Public on Jun 09 2017

city: Nanchang

first: Yanyu

last: Dean

address: Lushanzhong888, Changbei district

institute: Jiangxi Agricultural University

data_processing:
Trimmed, clean reads were mapped to the pig reference genome (Sscrofa 10.2) using the SOAP2 software and allowing five mismatches(Li et al., 2009).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol (Mortazavi et al., 2008). 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.
A FDR of no more than 0.001 (FDR ≤ 0.001) and a difference ratio of the RPKM between the untreated (DMSO)and treated (GW0742) samples of no less than 1 (|log2 ratio| ≥ 1) were adopted as the significance thresholds to identify DEGs.
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: txt files include RPKM values for each Sample.

organism: Sus scrofa

source_name: Pig auricular cartilage primary cells

extract_protocol:
Total RNA was isolated from three untreated (DMSO) and three GW0742-treated primary cartilage cells using Trizol reagent (Invitrogen).
The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo(dT) magnetic beads. Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments(about 200 bp). Then the first strand of cDNA is synthesized by using random hexamer-primed reverse transcription. Buffer, dNTPs, RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation is then performed. After the previous step, adaptors are ligated to the end of these fragments. Next, ligation products were selected by size and purified on TAE-agarose gel. Finally, the fragments are enriched by PCR amplification, then purified by magnetic beads and dissolved in the appropriate amount of Epstein-Barr solution. During the QC step, Agilent 2100 Bioanaylzer are used to qualify and quantify of the sample library. The library products are ready for sequencing via Ion Proton platform.

tag: breed

value: Duroc x (Landrace x Large White)

tag: agent

value: PPARD agonist (GW0742)


title: GW0742 rep 1


title: RNAseq_WT_Rep1

description:
CAGATC
rRNA-depleted RNA
deseq2-gene.csv
UNTR_all_star_genome_minusUniq.bw
UNTR_all_star_genome_plusUniq.bw

value: 12 weeks

value: liver


title: siBdnf_1


title: ChIPseq_H3K27ac_WT


title: MOV10_MO_n2

value: MOV10 Morpholino injection


title: DMSO rep2

value: DMSO


title: siScramble_4


title: T-cell Input

city: Philadelphia

first: yinfei

last: tan

state: PA

address: 333 cottman ave

department: Genomic Core

institute: Fox Chase Cancer Center

data_processing:
Sequence Analysis: The 50-nt sequence reads identified by the Sequencing Service (using Illumina’s Hi-Seq) are mapped to the genome using the BWA algorithm with default settings. Alignment information for each read is stored in the BAM format. Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis. In addition, unless stated otherwise, duplicate reads (“PCR duplicates”) are removed.
Determination of Fragment Density: the tags are extended in silico (using Active Motif software) at their 3´ends to a length of 150-250 bp, depending on the average fragment length in the size selected library (normally 150 bp). To identify the density of fragments (extended tags) along the genome, the genome is divided into 32-nt bins and the number of fragments in each bin is determined
“Peak Finding”:  Intervals are defined by the chromosome number and a start and end coordinate. The two main peak callers used at Active Motif are MACS.  Both methods look for significant enrichments in the ChIP/IP data file when compared to the Input data file
Active Region Analysis:  To compare peak metrics between 2 or more samples, overlapping Intervals are grouped into “Active Regions”, which are defined by the start coordinate of the most upstream Interval and the end coordinate of the most downstream Interval
Annotations:  After defining the Intervals and Active Regions, their genomic locations along with their proximities to gene annotations and other genomic features are determined and presented in Excel spreadsheets.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig file

source_name: Lck-Dlx5 T-cell lymphoma

growth_protocol: mice were maintained under normal condition

extract_protocol:
Lysates were clarified from sonicated nuclei and Dlx5-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit

tag: cell type

value: T-cell lymphoma

tag: passage

value: primary tumor


title: T-cell MycTag


title: ChIPseq_H3K4me3_WT


title: siscramble_3


title: Reproductive phase buds rep2

city: college station

first: Xiuren

last: Zhang

state: Texas

address: 2123 tamu

department: biochemistry & biophysics

institute: texas a&m university

data_processing:
Adapters were trimmed by FASTX-Toolkit (ver. 0.0.14)
sRNAs with lengths between 19- to 28-nt were selected and mapped using bowtie (version 1.1.2) to the Malus genomic sequences
sRNAs reads mapped to selected genomic features or miRNAs were count by BED Tools (v2.26) with 1 bp overlapping
Genome_build: Malus domestica Whole Genome v1.0
Supplementary_files_format_and_content: Tab-delimited text files include raw reads counts for each Sample.

organism: Malus domestica

source_name: Reproductive phase buds

extract_protocol:
Tissues were ground to fine powder, pre-warmed (at 65°C) RNA extraction buffer (2% CTAB, 2% PVP40, 100 mM Tris-HCl, 25 mM EDTA, 2 M NaCl, 0.5 g/L spermidine, 2% β-mercaptoethanol, pH 8.0) was added, and the mixture was incubated for 20 min at 65°C. RNA was extracted by treating the slurry twice with an equal volume of chloroform/isoamyl alcohol (24∶1), and then precipitated with LiCl at a final concentration of 2.5 M. The pellet was dissolved in STE buffer (1 M NaCl, 10 mM Tris-HCl, 1 mM EDTA, pH 8.0) and extracted one more time with chloroform/isoamyl alcohol. RNA was further precipitated with ethanol and dissolved in DEPC H2O.
sRNAs of 19-24 nt were gel-purified and ligated to a pair of adapters at the 5’ and 3’ ends by using T4 RNA ligase (NEB). sRNAs with adapters were transcribed into cDNA and amplified by Illumina sequencing-compatible primers.

value: Reproductive phase buds


title: siHdac4_4


title: Reproductive phase buds rep1


title: Juvenile phase buds rep2

source_name: Juvenile phase buds

value: Juvenile-like sucker from the stem base


title: siHdac4_1

value: brain


title: RNAseq_WT_Rep2

description:
ACTTGA
rRNA-depleted RNA
deseq2-gene.csv
UNTR_all_star_genome_minusUniq.bw
UNTR_all_star_genome_plusUniq.bw


title: siBdnf_3

value: hippocampus


title: MOV10_MO_n3

tag: developmental stage


title: Juvenile phase buds rep1


title: CO_MO_n2


title: siBdnf_2

value: siBDNF


title: siScramble_1


title: JF-12

city: Los Angeles

first: Vasu

last: Punj

address: Biggy Street

institute: USC

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and  low-quality sequence, then mapped to mm 10 whole genome using TopHat 2
Read density as Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated following a method of Mortazavi et al 2008, Nature Methods 2008 using an exon model.
Genome_build: mm10
Supplementary_files_format_and_content: Txt file (File_1_normalized_RPKM_values_Vasu_J_Chai.txt) include RPKM values for each Sample.

source_name: dental pulp (mouse molar )

extract_protocol:
First mandibular molars at PN7.5 from Gli1-CreER;Bmpr1afl/fl and littermate Bmpr1afl/fl control mice were dissected out, and the apical half dental mesenchymel was cut with a fine blade and transferred to RNA stabilization reagent (Qiagen, 76104). Total RNA was extracted with an RNeasy Mini Kit (Qiagen, 74134).
RNA extracted from cells was polyA+ labelled and used to generate libraries  following the manufacturer’s protocols (Illumina).  The modified cDNA molecules were subjected to sequencing by Illumina Next-Seq 500 system

tag: littermate

value: Mixed background (C57Bl6/129S6/SvEvTac)

value: apical half of tooth germ

value: post natal day 7.5

value: control  Bmpr1afl/fl


title: GW0742 rep 3

value: Duroc x (Landrace x Large White)


title: DMSO rep1


title: JF-11

value: mutant Gli1-CreER;Bmpr1afl/fl


title: JF-7

value: control Bmpr1afl/fl


title: Exp 2 Control rep 1

city: Sydney

first: Susan

last: Corley

state: NSW

address: D26, Kensignton Campus

department: Biotechnology & Biomolecular Sciences

country: Australia

institute: UNSW

description: processed data file: Exp2_PE_count_matrix.txt, Exp2_SE_count_matrix.txt, Exp2_NS_count_matrix.txt,

data_processing:
The reads for Experiment 2 were mapped to the Ensembl Mus musculus genome (GRCm38). Mapping was performed with Tophat2 (v 2.0.12) [14] calling Bowtie2 (v 2.1.0)
The featureCounts function of Subread  was used to generate counts of reads uniquely mapped to annotated genes using the GRCm38 annotation gtf file.
Comparison of controls in the PE, and SE  datasets was performed using edgeR (v3.14.0). Comparison of the controls versus treated samples in each of the four experiments was performed using functions in the edgeR (v 3.14.0) [23] and limma (v 3.28.17) [17] Bioconductor packages
genome build: Ensembl Mus musculus genome (GRCm38)
processed data files format and content: Tab-delimited text file with read count for each sample.

source_name: Keratinocytes (primary)

extract_protocol:
RNA was extracted from the dissected mouse tissues using TRI-reagent (Sigma), following the manufacturer’s instructions, which included a chloroform phase separation and ethanol precipitation. RNA was resuspended in 70 μL of RNase-free water. RNA samples were assessed for quantity and quality using a NanoDrop UV spectrophotometer (Thermo Fisher Scientific Inc), conventional RNA electrophoresis and using a Bioanalyser (Agilent Technology Inc). All RNA integrity numbers (RIN) for the analysed samples ranged from 9 to 9.5
mRNA libraries were prepared at the Ramaciotti Centre for Genomics (UNSW University of New South Wales, Australia). The Illumina TruSeq Stranded Total RNA Prep Kit was used for Experiments 2 .The six RNA-Seq libraries in Experiments 2 were sequenced using the Illumina NextSeq 500. R1.fastq and R2.fastq files were produced for each sample.

tag: batch

tag: condition

value: Control

value: Keratinocytes


title: Exp 2 Treated rep 1

value: YAP2-5SA-DC transgenic mouse


title: Exp 2 Treated rep 3


title: Reproductive phase buds rep3


title: Exp 2 Control rep 2


title: DMSO rep3

value: DMSO


title: JF-8

tag: genotype


title: OmpR NaCl 1

city: Ulsan

first: Donghyuk

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

department: Department of Chemical Engineering

country: South Korea

institute: UNIST

description: Immunoprecipitated DNA

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

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

source_name: OmpR NaCl 1

growth_protocol: A total of two samples were analyzed. ompR-8myc tagged cells were cultured in M9 minimal media with 0.2% glucose. Then cells were treated with 0.3 M of NaCl at mid-log pahse for 30 min with agitation.

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

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

tag: strain

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


title: Exp 2 Treated rep 2


title: H3K4me3_ChIP

city: Cambridge

first: Julia

last: Joung

address: 75 Ames St

institute: Broad Institute

data_processing:
Bowtie v0.12.7 was used to align paired-end reads to the human hg19 UCSC genome with command line options “-q -X 500 --sam --chunkmbs 512”
Model-based analysis of ChIP-seq (MACS) was run with command line options “-g hs -B -S --call-subpeaks” to identify histone modifications.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files include ChIP peaks called by MACS

growth_protocol: A375 cells were cultured in RPMI supplemented with 10% FBS and 1% Pen/Strep

extract_protocol:
Formaldehyde was added directly to the growth media for a final concentration of 1% for 10 mins at 37C to initiate chromatin fixation. The entire two-day ChIP procedure was performed using the EZ-Magna ChIP HiSens Chromatin Immunoprecipitation Kit (Millipore 1710460) according to the manufacturer’s protocol. Samples were pulse sonicated with 2 rounds of 10 mins (30s on-off cycles, high frequency) in a rotating water bath sonicator (Diagenode Bioruptor) with 5 mins on ice between each round. To detect histone modifications, antibodies (H3K4me2: Millipore 17-677, H3K4me3: Millipore 04-745, H3K27ac: Millipore 17-683) were optimized individually for each antibody to be 0.5 μL for 1 million cells. 1 μL of IgG (Millipore 12-370) was used for negative control.
ChIP samples were prepped with NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB E7645S). DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A375 cells were not treated prior to ChIP-seq

value: Melanoma cells

tag: passages

value: H3K4me3 (Millipore 04-745)


title: H3K4me2_ChIP

value: H3K4me2 (Millipore 17-677)


title: Exp 2 Control rep 3


title: JF-10


title: GFP_S3

data_processing:
Bowtie v0.12.7 index was created based on the human hg19 UCSC genome and known gene and lncRNA transcriptome constructed as described above. Paired-end reads were aligned directly to this index using Bowtie with command line options “-q --phred33-quals -n 2 -e 99999999 -l 25 -I 1 -X 1000 --chunkmbs 512 -p 1 -a -m 200 -S”.
RSEM v1.2.22 was run with default parameters on the alignments created by Bowtie to estimate expression levels (TPM).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

molecule: polyA RNA

extract_protocol:
RNA was harvested using the RNeasy Plus Mini Kit (Qiagen 74134) and 1ug of RNA was used for RNA-seq. The 6 candidate lncRNA loci with detectable transcript upregulation were prepped with TruSeq Stranded Total RNA Sample Prep Kit with Ribo-Zero Gold (Illumina RS-122-2302) and all other samples were prepped with NEBNext Ultra RNA Library Prep Kit for Illumina (NEB E7530S) and NEBNext PAS mRNA Magnetic Isolation Module (NEB E7490S).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A375 cells were treated with 2uM PLX-4720 for 3 days before RNA-seq

tag: cell line


title: H3K27ac_ChIP

value: H3K27ac (Millipore 17-683)


title: ΔompR NaCl 2

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

source_name: Total RNA isolated from E. coli

growth_protocol: E. coli K-12 MG1655 WT and ΔompR were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. Then cells were treated with 0.3 M of NaCl at mid-log pahse for 30 min with agitation.

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

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

value: ompR deletion mutant


title: OmpR NaCl 2

description: Immunoprecipitated DNA

source_name: OmpR NaCl 2


title: WT NaCl 2

value: WT


title: ΔompR NaCl 1


title: GFP_S2


title: MOB3B_S3


title: MOB3B_S1


title: NR_026873_G3_S1


title: NR_026873_G3_S3


title: NR_026873_G2_S2


title: JF-9

value: Mixed background (C57Bl6/129S6/SvEvTac)

value: apical half of tooth germ


title: GFP_S1


title: MOB3B_S2


title: NR_026873_G3_S2


title: NR_026873_G2_S3


title: NR_026873_G2_S1


title: NR_026873_G1_S2


title: NR_026873_G1_S1


title: WT NaCl 1


title: NR_026873_G1_S3


title: TCONS_00006579_G3_S1


title: TCONS_00006579_G3_S2


title: NR_033834_G3_S2


title: TCONS_00006579_G3_S3


title: NR_033834_G3_S3


title: TCONS_00006579_G2_S3


title: TCONS_00006579_G2_S2


title: TCONS_00006579_G1_S3


title: NR_033834_G3_S1


title: TCONS_00006579_G2_S1


title: NR_033834_G1_S2


title: TCONS_00006579_G1_S2


title: NR_109890_G3_S2


title: TCONS_00006579_G1_S1


title: NR_109890_G2_S3


title: NR_109890_G3_S1


title: NR_033834_G2_S1


title: NR_033834_G2_S3


title: NR_109890_G1_S3


title: NR_033834_G2_S2


title: NR_033834_G1_S3


title: NR_033834_G1_S1


title: NR_109890_G2_S2


title: NR_109890_G2_S1


title: NR_125939_G2_S3


title: NR_109890_G3_S3


title: NR_109890_G1_S1


title: NR_125939_G2_S1


title: NR_125939_G1_S2


title: NR_125939_G2_S2


title: NR_125939_G1_S1


title: NR_125939_G3_S1


title: NR_125939_G3_S2


title: NT_G2_S15


title: NT_G2_S13


title: NT_G1_S15


title: NT_G2_S14


title: NT_G1_S14


title: TCONS_00009861_G3_S1


title: TCONS_00009861_G2_S2


title: TCONS_00009861_G1_S1


title: NR_125939_G3_S3


title: TCONS_00009861_G3_S3


title: NT_G2_S12


title: TCONS_00009861_G2_S3


title: NR_109890_G1_S2


title: NT_G1_S12


title: NT_G1_S10


title: TCONS_00010506_G3_S3


title: TCONS_00009861_G3_S2


title: NT_G1_S13


title: TCONS_00010506_G3_S1


title: NR_125939_G1_S3


title: TCONS_00010506_G2_S3


title: TCONS_00010506_G3_S2


title: TCONS_00010506_G1_S3


title: NT_G2_S11


title: TCONS_00009861_G2_S1


title: TCONS_00009861_G1_S3


title: NT_G2_S10


title: NT_G2_S7


title: TCONS_00010506_G2_S2


title: NT_G1_S7


title: TCONS_00010506_G2_S1


title: NT_G1_S8


title: TCONS_00010506_G1_S1


title: TCONS_00026344_G3_S2


title: TCONS_00026344_G3_S1


title: NT_G1_S11


title: NT_G2_S9


title: NT_G2_S8


title: TCONS_00026344_G1_S3


title: TCONS_00026344_G1_S2


title: TCONS_00009861_G1_S2


title: TCONS_00026344_G2_S2


title: TCONS_00026344_G2_S1


title: TCONS_00010506_G1_S2


title: TCONS_00015940_G3_S2


title: TCONS_00015940_G2_S1


title: TCONS_00015940_G1_S3


title: TCONS_00015940_G2_S2


title: TCONS_00015940_G1_S2


title: TCONS_00026344_G1_S1


title: NT_G2_S5


title: TCONS_00015940_G3_S1


title: TCONS_00015940_G2_S3


title: TCONS_00015940_G3_S3


title: NT_G1_S9


title: NT_G2_S6


title: NT_G2_S4


title: TCONS_00015940_G1_S1


title: TCONS_00011252_G2_S2


title: TCONS_00011252_G3_S3


title: TCONS_00011252_G3_S2


title: NT_G1_S4


title: NT_G1_S6


title: TCONS_00011252_G1_S3


title: NT_G1_S5


title: NT_G2_S3


title: TCONS_00011252_G2_S3


title: TCONS_00011252_G3_S1


title: NR_034078_G3_S1


title: TCONS_00011252_G2_S1


title: NR_034078_G3_S2


title: TCONS_00011252_G1_S2


title: NR_034078_G2_S2


title: NT_G2_S1


title: NT_G2_S2


title: NT_G1_S2


title: NT_G1_S3


title: NR_034078_G1_S1


title: NR_034078_G1_S2


title: NT_G1_S1


title: NR_034078_G2_S3


title: Exp 3Treated rep 1

description: processed data file: Exp3_PE_count_matrix.txt, Exp3_SE_count_matrix.txt, Exp3_NS_count_matrix.txt,

data_processing:
The reads for Experiment 3 were mapped to the Ensembl Home sapiens genome (GRCh38).  Mapping was performed with Tophat2 (v 2.0.12) [14] calling Bowtie2 (v 2.1.0)
The featureCounts function of Subread  was used to generate counts of reads uniquely mapped to annotated genes using the GRCh38 annotation gtf file.
Comparison of controls in the PE, and SE  datasets was performed using edgeR (v3.14.0). Comparison of the controls versus treated samples in each of the four experiments was performed using functions in the edgeR (v 3.14.0) [23] and limma (v 3.28.17) [17] Bioconductor packages
genome build: Ensembl Homo sapiens genome (GRCh38)
processed data files format and content: Tab-delimited text file with read count for each sample.

source_name: Hematopoietic cells (primary)

extract_protocol:
RNA was extracted from 1x10^5 – 1x 10^6 cells using the RNeasy® Plus Mini kit (Qiagen, Germany) according to the manufacturer’s directions. RNA was eluted from the RNeasy spin column in 30 μL of RNase-free H20 and precipitated in 2x volume 100% ethanol and 1/10x volume NaOAc for 30 min at -80ºC. Precipitated RNA was then centrifuged at 12 000 x g for 30 min at 4ºC, the pellet washed in 75% ethanol and then centrifuged at 8000 x g for 30 min at 4ºC. Supernatant was removed, RNA was air dried and resuspended in 30 μL of RNase free water.
mRNA libraries were prepared at the Ramaciotti Centre for Genomics (UNSW University of New South Wales, Australia). The Illumina TruSeq Stranded Total RNA Prep Kit was used for Experiments 3. The six RNA-Seq libraries in Experiments 2 were sequenced using the Illumina NextSeq 500. R1.fastq and R2.fastq files were produced for each sample.

value: Cells transduced with DKC1 overexpression lentiviral vectors

value: Hematopoietic cells


title: NR_034078_G1_S3


title: Exp 3 Treated rep 2


title: Exp 4 Control rep 1

description: processed data file: Exp4_PE_count_matrix.txt, Exp4_SE_count_matrix.txt, Exp4_NS_count_matrix.txt,

data_processing:
The reads for Experiment 4 were mapped to the Ensembl Home sapiens genome (GRCh38).  Mapping was performed with Tophat2 (v 2.0.12) [14] calling Bowtie2 (v 2.1.0)
The featureCounts function of Subread  was used to generate counts of reads uniquely mapped to annotated genes using the GRCh38 annotation gtf file.
Comparison of controls in the PE, and SE  datasets was performed using edgeR (v3.14.0). Comparison of the controls versus treated samples in each of the four experiments was performed using functions in the edgeR (v 3.14.0) [23] and limma (v 3.28.17) [17] Bioconductor packages
genome build: Ensembl Homo sapiens genome (GRCh38)
processed data files format and content: Tab-delimited text file with read count for each sample.

source_name: NuLi cells (cell line)

extract_protocol:
RNA was extracted from NuLi cells using the ReliaPrep™ RNA Cell Miniprep System (Promega Corporation) following the manufacturer’s instructions. RNA was eluted in 30 µL of RNAse-free water and stored at -80°C. RNA was quantified using a NanoDrop™ UV Spectrophotometer (Thermo Fisher Scientific Inc) and quality assessed using the Experion™ Automated Electrophoresis System (Bio-Rad Laboratories Pty Ltd). All RNA integrity numbers (RIN) for the analysed samples ranged from 9.7 to 10.
mRNA libraries  were prepared at the Ramaciotti Centre for Genomics (UNSW University of New South Wales, Australia). The Illumina TruSeq Stranded mRNA Prep Kit was used for Experiment 4. The six RNA-Seq libraries in Experiment 4 were sequenced  using the Illumina NextSeq 500. R1.fastq and R2.fastq files were produced for each sample.

value: lung epithelium


title: Exp 3 Treated rep 3


title: Exp 4 Control rep 3


title: Exp 4 Treated rep 1

value: Cells treated with DHL (Decanyl Homoserine Lactone)


title: Exp 4 Control rep 2

value: Control


title: Exp 4 Treated rep 2


title: Exp 3 Control rep 2


title: T_11_19_1_C

city: swon

first: Tea jun

last: Park

address: 206, World cup-ro, Yeongtong-gu

department: Biochemistry and Molecular Biology

institute: Ajou University School of Medicine

data_processing:
[raw read cleaning] Illumina TruSeq adapter sequence that may included in raw reads were trimmed by CutAdapt (https://pypi.python.org/pypi/cutadapt).
[mapping on the reference genome] Adapter trimmed reads were mapped by TopHat2 (http://tophat.cbcb.umd.edu) with bowtie2 (http://bowtie-bio.sourceforge.net).
[expression quantification] Normalized gene expression values were calculated by CuffLinks (http://cufflinks.cbcb.umd.edu) with default options.
Genome_build: hg19
Supplementary_files_format_and_content: [.xlsx] DEG test result file by CuffDiff

source_name: Papillary thyroid cancer central region

extract_protocol:
Total RNA was extracted from papillary thyroid cancer central and invasive regions using Macherey-Nagel RNA kit (Macherey-Nagel GmbH & Co. KG, Düren, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: group

value: PTC central region


title: T_11_19_1_P

source_name: Papillary thyroid cancer invasive region

value: PTC invasive region


title: T_11_12_P


title: Exp 3 Control rep 3


title: Exp 3 Control rep 1


title: T_72_C


title: NR_034078_G3_S3


title: 8d Control_6SA_3_1

first: Evangelia

last: Diamanti

address: Wellcome Trust / MRC Building, Hills Road

department: Haematology

institute: University of Cambridge

description: processed data header: No_Color_SA_3_1

data_processing:
RNA-seq reads were aligned to mm10 using GSNAP (version 2015-09-29) with parameters (-B 5 -t 24 -n 1 -Q -N 1).
Reads in features were counted with htseq-count (HTSeq version 0.5.3p3) with the parameter (-s no).
Genome_build: mm10
Supplementary_files_format_and_content: HT-Seq counts(.txt)

source_name: Dissociated pancreatic organoid cells

extract_protocol:
Three-dimensional cultures of pancreatic ductal cells (organoids, Huch et al 2013) were infected with GFP vectors (GFP only controls, GFP-WT-Ngn3 and GFP-6SA-Ngn3). Organoids were dissociated to single cells and GFP+ cells were separated by FACS Influx (BD Biosciences). Pool of 50 cells were sorted by FACS directly into individual wells of a 96-well plate containing lysis buffer. RNA-Seq analysis was performed as described previously (Picelli et al., 2014). Pooled libraries were then run on the Illumina Hi-Seq 2500.
RNA libraries were prepared for sequencing using the Illumina Nextera XT DNA preparation kit

tag: days of transgene induction

value: 8 days


title: 8d Control_6SA_2_2

description: processed data header: No_Color_SA_2_2


title: 8d Control_WT_3_1

description: processed data header: No_Color_WT_3_1


title: 8d GFP-6SA-Ngn3 infected organoids_2_2

description: processed data header: GFP_SA_2_2


title: 8d Control_6SA_2_1

description: processed data header: No_Color_SA_2_1


title: T_72_P


title: NR_034078_G2_S1


title: 8d Control_WT_2_2

description: processed data header: No_Color_WT_2_2


title: 8d Control_WT_2_1

description: processed data header: No_Color_WT_2_1


title: 8d GFP-6SA-Ngn3 infected organoids_3_1

description: processed data header: GFP_SA_3_1


title: 8d GFP-WT-Ngn3 infected organoids_2_1

description: processed data header: GFP_WT_2_1


title: 8d Control_6SA_1_3

description: processed data header: No_Color_SA_1_3


title: 8d Control_6SA_1_2

description: processed data header: No_Color_SA_1_2


title: 8d GFP-WT-Ngn3 infected organoids_2_2

description: processed data header: GFP_WT_2_2


title: 8d Control_6SA_1_1

description: processed data header: No_Color_SA_1_1


title: 8d GFP-6SA-Ngn3 infected organoids_2_1

description: processed data header: GFP_SA_2_1


title: T_11_12_C


title: 8d Control_WT_1_1

description: processed data header: No_Color_WT_1_1


title: 8d Control_WT_1_3

description: processed data header: No_Color_WT_1_3


title: Exp 4 Treated rep 3


title: 8d GFP-6SA-Ngn3 infected organoids_1_2

description: processed data header: GFP_SA_1_2


title: 8d GFP-WT-Ngn3 infected organoids_1_2

description: processed data header: GFP_WT_1_2


title: 8d GFP-6SA-Ngn3 infected organoids_1_1

description: processed data header: GFP_SA_1_1


title: 8d GFP-WT-Ngn3 infected organoids_3_1

description: processed data header: GFP_WT_3_1


title: 8d GFP-WT-Ngn3 infected organoids_1_1

description: processed data header: GFP_WT_1_1


title: 2d GFP-6SA-Ngn3 infected organoids_3_4

description: processed data header: SA_3_4

value: 2 days


title: 2d GFP-6SA-Ngn3 infected organoids_3_5

description: processed data header: SA_3_5


title: 2d GFP-6SA-Ngn3 infected organoids_3_2

description: processed data header: SA_3_2


title: 2d GFP-WT-Ngn3 infected organoids_3_5

description: processed data header: Ngn3_3_5


title: 2d GFP-6SA-Ngn3 infected organoids_3_1

description: processed data header: SA_3_1


title: 2d GFP-WT-Ngn3 infected organoids_3_4

description: processed data header: Ngn3_3_4


title: 2d GFP-6SA-Ngn3 infected organoids_3_3

description: processed data header: SA_3_3


title: TCONS_00011252_G1_S1

value: Melanoma cells


title: 2d GFP-WT-Ngn3 infected organoids_3_3

description: processed data header: Ngn3_3_3


title: 2d GFP-WT-Ngn3 infected organoids_3_2

description: processed data header: Ngn3_3_2


title: 2d GFP infected pancreatic organoids_3_4

description: processed data header: CTRL_GFP_3_4


title: 2d GFP infected pancreatic organoids_3_2

description: processed data header: CTRL_GFP_3_2


title: 2d GFP infected pancreatic organoids_3_3

description: processed data header: CTRL_GFP_3_3


title: 8d Control_WT_1_2

description: processed data header: No_Color_WT_1_2


title: 2d GFP infected pancreatic organoids_3_5

description: processed data header: CTRL_GFP_3_5


title: 2d GFP infected pancreatic organoids_3_1

description: processed data header: CTRL_GFP_3_1


title: 8d GFP-6SA-Ngn3 infected organoids_1_3

description: processed data header: GFP_SA_1_3


title: 2d GFP-6SA-Ngn3 infected organoids_1_6

description: processed data header: SA_1_6


title: 2d GFP infected pancreatic organoids_3_6

description: processed data header: CTRL_GFP_3_6


title: 2d GFP-6SA-Ngn3 infected organoids_1_4

description: processed data header: SA_1_4


title: 2d GFP-6SA-Ngn3 infected organoids_3_6

description: processed data header: SA_3_6


title: 2d GFP-6SA-Ngn3 infected organoids_1_2

description: processed data header: SA_1_2


title: 2d GFP-6SA-Ngn3 infected organoids_2_5

description: processed data header: SA_2_5


title: 2d GFP-6SA-Ngn3 infected organoids_2_6

description: processed data header: SA_2_6


title: 2d GFP-6SA-Ngn3 infected organoids_2_3

description: processed data header: SA_2_3


title: 2d GFP-WT-Ngn3 infected organoids_3_1

description: processed data header: Ngn3_3_1


title: 2d GFP-WT-Ngn3 infected organoids_1_6

description: processed data header: Ngn3_1_6


title: 2d GFP-WT-Ngn3 infected organoids_1_4

description: processed data header: Ngn3_1_4


title: 2d GFP-WT-Ngn3 infected organoids_1_3

description: processed data header: Ngn3_1_3


title: 2d GFP-6SA-Ngn3 infected organoids_2_2

description: processed data header: SA_2_2


title: 2d GFP-WT-Ngn3 infected organoids_1_1

description: processed data header: Ngn3_1_1


title: 2d GFP-WT-Ngn3 infected organoids_2_5

description: processed data header: Ngn3_2_5


title: 2d GFP-WT-Ngn3 infected organoids_2_6

description: processed data header: Ngn3_2_6


title: 2d GFP-WT-Ngn3 infected organoids_2_1

description: processed data header: Ngn3_2_1


title: 2d GFP infected pancreatic organoids_1_6

description: processed data header: CTRL_GFP_1_6


title: 2d GFP infected pancreatic organoids_1_5

description: processed data header: CTRL_GFP_1_5


title: 2d GFP-WT-Ngn3 infected organoids_2_4

description: processed data header: Ngn3_2_4


title: 2d GFP infected pancreatic organoids_1_4

description: processed data header: CTRL_GFP_1_4


title: 2d GFP infected pancreatic organoids_1_3

description: processed data header: CTRL_GFP_1_3


title: 2d GFP-6SA-Ngn3 infected organoids_1_5

description: processed data header: SA_1_5


title: 2d GFP-6SA-Ngn3 infected organoids_2_4

description: processed data header: SA_2_4


title: 2d GFP-WT-Ngn3 infected organoids_2_2

description: processed data header: Ngn3_2_2


title: 2d GFP-WT-Ngn3 infected organoids_1_5

description: processed data header: Ngn3_1_5


title: 2d GFP infected pancreatic organoids_2_6

description: processed data header: CTRL_GFP_2_6


title: 2d GFP infected pancreatic organoids_2_5

description: processed data header: CTRL_GFP_2_5


title: 2d GFP-WT-Ngn3 infected organoids_1_2

description: processed data header: Ngn3_1_2


title: 2d GFP infected pancreatic organoids_2_4

description: processed data header: CTRL_GFP_2_4


title: 2d GFP infected pancreatic organoids_2_3

description: processed data header: CTRL_GFP_2_3


title: 2d GFP-WT-Ngn3 infected organoids_2_3

description: processed data header: Ngn3_2_3


title: 2d GFP infected pancreatic organoids_2_2

description: processed data header: CTRL_GFP_2_2


title: 2d GFP infected pancreatic organoids_2_1

description: processed data header: CTRL_GFP_2_1


title: MA9+Alox5_rep2

city: Monrovia

first: Jianjun

last: Chen

department: Systems Biology

institute: Beckman Research Institute of City of Hope

description:
rep2
JC35
Barcode: ACTTGA

data_processing:
sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
the expression and p value  were calculated using Cufflinks 2.2.1  with default parameters
Genome_build: mm10
Supplementary_files_format_and_content: .txt file containing the expression and p value

source_name: mouse BM leukemic blast cells

extract_protocol:
RNA was extracted by mirVana miRNA Isolation Kit (Thermo Fisher, Grand Island, NY) with total RNA extraction protocol. NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Ipswich, MA) was used for polyA RNA purification.
Library was prepared by or NEBNext Ultra Directional RNA Library Prep Kit (New England BioLabs, Ipswich, MA).
Libraries at the final concentration of 15 pM were clustered onto a single read (SR) flow cell using Illumina TruSeq SR Cluster kit v3, and sequenced to 50 bp using TruSeq SBS kit on Illumina HiSeq system.

tag: tumor

value: acute monocytic leukemia

value: bone marrow

tag: treatment


title: MA9+Ctrl_rep2

description:
rep2
JC33
Barcode: TGACCA

tag: tissue


title: MA9+Alox5_rep1

description:
rep1
JC32
Barcode: CGATGT


title: 2d GFP infected pancreatic organoids_1_1

description: processed data header: CTRL_GFP_1_1


title: MA9+Ctrl_rep1

description:
rep1
JC31
Barcode: GGCTAC


title: 2d GFP-WT-Ngn3 infected organoids_3_6

description: processed data header: Ngn3_3_6