title: RNA-seq siRNA DLX1 rep3

data_processing:
RNA-seq reads were aligned to hg19 genome assembly using Tophat2 after trimming raw reads, quality score <20 in Partek Flow version 3.
For RNA-seq, GENCODE v19 was used to quantify to transcriptome.
For RNA-seq, differentially expressed genes analyzed by using the Gene Specific Algorithm (Upper Quartile normalization) from Partek Flow version 3.
Genome_build: hg19
Supplementary_files_format_and_content: For RNA-seq, tab-delimited text files include normalized Upper Quartile for each gene.

extract_protocol:
For RNA-seq, RNA was extracted using Trizol reagent (15596-026) (Life technologies, Carlsbad, CA) following its protocol.
RNA-seq libraries were made using KAPA Stranded mRNA-Seq Kit with KAPA mRNA Capture Beads (KK8420) (Kapa Biosystems, Woburn, MA).

treatment_protocol: For transient knockdown, C4-2B cells were transfected with 100nM of siRNA oligonucleotides of human HOXC6 (L011871000005), DLX1 (L011871000005), ZFP41 (L018062020005) or control (D0018101005) using SMART pool Dharmafect transfection reagent 3 (Dharmacon, Lafayette, CO) for 72 h.

tag: transfection


title: H3K27Ac ChIP-seq C42B rep1

status: Public on Oct 26 2016

type: SRA

city: Los Angeles

first: Suhn

middle: K

last: Rhie

state: CA

address: 1450 Biggy Street NRT 3504

department: Biochemistry and Molecular Medicine

country: USA

institute: University of Southern California

library_source: genomic

data_processing:
ChIP-seq reads were aligned to hg19 genome assembly using bwa.
For ChIP-seq, Sole-Search (alpha=0.0001, FDR=0.0001, peakmergedistance=0, histoneblurlength=1200) was used to call peaks.
Genome_build: hg19
Supplementary_files_format_and_content: For ChIP-seq, tab-delimited text files include location of peaks

molecule: genomic DNA

organism: Homo sapiens

source_name: Human prostate cancer cell line C42B

growth_protocol: C42B cells were grown in RPMI 1640 supplemented with 10% fetal bovine serum.

extract_protocol:
For ChIP-seq, cells were crosslinked using 1% formaldehyde and lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq: Libraries were barcoded (NEXTflex™ DNA Barcodes) (Bio Scientific, Austin, TX).

tag: cell line

tag: antibody

tag: antibody vendor/catalog#


title: RNA-seq siRNA DLX1 rep2

library_source: transcriptomic

molecule: total RNA


title: RNA-seq siRNA HOXC6 rep3


title: RNA-seq siRNA HOXC6 rep2


title: H3K27Ac ChIP-seq MCF7+E2 rep2

source_name: H3K27Ac ChIP-seq MCF7+E2

growth_protocol: The human breast cancer MCF7 cells (ATCC # HTB-22) were grown in DMEM supplemented with 10% fetal bovine serum (FBS).

treatment_protocol: For estradiol stimulation, cells were grown in phenol red free medium with charcoal stripped serum for several days and treated with 100nM of estradiol for 45 min.

tag: cell type

value: Human breast cancer cell line

tag: treated with

value: 100nM of estradiol for 45 min

tag: chip antibody

value: H3K27Ac Abcam ab4729


title: RNA-seq siRNA DLX1 rep1


title: RNA-seq siRNA control rep2


title: A549 - Ctrl siRNA-1 - rep2

status: Public on Oct 25 2016

city: Gothenburg

first: Arghavan

last: Ashouri

address: Medicinaregatan 9A

department: Medical Biochemistry and Cell Biology

country: Sweden

institute: University of Gothenburg

data_processing:
Reads were aligned to hg19 genome using Hisat version 0.1.6-beta.
Number of reads mapping to each feature were calculated using htseq-count version 0.6.0.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files including raw counts for each sample.

source_name: A549 lung cancer cell line - Ctrl siRNA-1 - rep2

extract_protocol:
RNA was prepared using the RNeasy Mini kit.
8 strand-specific total RNA-seq libraries were generated using TruSeq Stranded Total RNA Sample Preparation Kit with Ribo-Zero Gold

treatment_protocol: 250,000 cells were transfected with Lipofectamine RNAiMAX reagent containing 5 nmol siRNA particles in a 6-well plate. Three transfections siRNAs targeting NFE2L2 were performed, using three independent duplexes, while four control transfections were done using two different control duplexes.

value: Human lung adenocarcinoma cell line


title: A549 - Ctrl siRNA-1 - rep1

source_name: A549 lung cancer cell line - Ctrl siRNA-1 - rep1


title: A549 - NFE2L2-siRNA-3

source_name: A549 lung cancer cell line - NFE2L2-siRNA-3


title: RNA-seq siRNA control rep3


title: RNA-seq siRNA control rep1


title: ChIP-seq Input C42B rep2


title: A549 - Mock transfection control

source_name: A549 lung cancer cell line - Mock transfection


title: A549 - Ctrl siRNA-2 - rep2

source_name: A549 lung cancer cell line - Ctrl siRNA-2 - rep2


title: A549 - NFE2L2-siRNA-1

source_name: A549 lung cancer cell line - NFE2L2-siRNA-1


title: A549 - NFE2L2-siRNA-2

source_name: A549 lung cancer cell line - NFE2L2-siRNA-2


title: MGT 2WK (Sample28)

city: Louisville

first: Tamer

middle: M

last: Mohamed

state: KY

address: 580 S. Preston St., Baxter II Bldg., Room 122

department: Cardiology

institute: University of Louisville

description: TM 578 mm9

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to the mouse-reference assembly mm9 or human-reference assembly hg19 using Tophat 2.0.13
we calculated differential expression P-values using edgeR
we first filtered out any genes without at least two samples with a CPM (counts per million) between 0.5 and 5000. CPMs below 0.5 indicates non-detectable gene expression, and CPM above 5000 is typically only seen in mitochondrial genes
Genome_build: mm9 and hg19
Supplementary_files_format_and_content: Excel files contain Raw counts, Normalized CPM and FPKM

organism: Mus musculus

source_name: reprogrammed fibroblasts

growth_protocol: induced cardiomyocytes (iCMs) generated in vitro or in vivo

extract_protocol:
RNA were extracted using Qiagen, miRNeasy Micro Kit #210874
Ovation RNA-seq System v2 Kit (NuGEN)

treatment_protocol: iCMs were generated in presence or absence of SB431542 and XAV939

tag: protocol

value: reprogramming in vitro

tag: time of reprogramming

value: 2 weeks reprogramming

value: fibroblasts reprogrammed into iCMs


title: MGT SB 3WK (Sample32)

description: TM 578 mm9

value: 3 weeks reprogramming


title: MGT 3WK (Sample31)

description: TM 578 mm9


title: MGT XAV 2WK (Sample30)

description: TM 578 mm9


title: Border picked 67 (Sample25)

description: TM 578 mm9

value: reprogramming in vivo

value: 12 weeks reprogramming


title: MGT SB 2WK (Sample29)

description: TM 578 mm9


title: No Border full 110 (Sample22)

description: TM 578 mm9


title: No border picked 67 (Sample27)

description: TM 578 mm9


title: Border full 110 (Sample20)

description: TM 578 mm9


title: Border picked 110 (Sample21)

description: TM 578 mm9


title: MGT SB 6WK (Sample18)

description: TM 578 mm9

value: 6 weeks reprogramming


title: A549 - Ctrl siRNA-2 - rep1

source_name: A549 lung cancer cell line - Ctrl siRNA-2 - rep1


title: MGT SBXAV 5WK (Sample16)

description: TM 578 mm9

value: 5 weeks reprogramming


title: MGT 6WK (Sample17)

description: TM 578 mm9


title: Border full 67 (Sample24)

description: TM 578 mm9


title: MGT XAV 3WK (Sample33)

description: TM 578 mm9


title: MGT SB 5WK (Sample15)

description: TM 578 mm9


title: RNA-seq siRNA HOXC6 rep1


title: MGT_1WK  (Sample11)

description: TM 578 mm9

value: 1 weeks reprogramming


title: MGT_SBXAV_3WK  (Sample10)

description: TM 471 mm9


title: MGT 5WK (Sample14)

description: TM 578 mm9


title: MGT_3WK  (Sample9)

description: TM 471 mm9


title: MGT_SBXAV_2WK _1 (Sample7)

description: TM 471 mm9


title: MGT_SBXAV_2WK _2 (Sample8)

description: TM 471 mm9


title: MGT_2WK  (Sample6)

description: TM 471 mm9


title: MGT SB 1 WK (Sample12)

description: TM 578 mm9


title: MGT_SBXAV_1WK _2 (Sample4)

description: TM 471 mm9


title: MGT_SBXAV_1WK _1 (Sample3)

description: TM 471 mm9


title: No Border picked 110 (Sample23)

description: TM 578 mm9


title: MGT_SBXAV_1WK _3 (Sample5)

description: TM 471 mm9


title: MGT SBXAV 6WK (Sample19)

description: TM 578 mm9


title: MGT_SBXAV_4WK  (Sample1)

description: TM 471 mm9

value: 4 weeks reprogramming


title: Tumor CDC7

city: Buffalo

first: Jianmin

last: Wang

state: NY

address: Elm and Carlton Streets

department: Bioinformatics and Biostatistics

institute: Roswell Park Comprehensive Cancer Center

data_processing:
Basecalls performed using CASAVA version 1.8
Raw reads passed quality filter was first pre-processed using tools FASTQC for quality control followed by sequence mapping using TopHat to the human reference genome and RefSeq annotation database
sequence counts are generated using HTSeq with intersection-strict option
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited text file with raw sequence counts.

source_name: kidney collecting duct tumor

extract_protocol:
Frozen patient tumor samples and matched normal kidney tissues were obtained from the tissue bank at the participating institutions.
The sequencing libraries were prepared from 1µg total RNA using a TruSeq Stranded Total RNA kit (Illumina Inc) according to the manufacturer’s instructions. After rRNA depletion from total RNA, the remaining RNA was purified, fragmented, and primed for cDNA synthesis.  Fragmented RNA was reverse transcribed into first strand cDNA using random primers.  The RNA template was then removed and a replacement strand synthesized, incorporating dUTP in place of dTTP to generate ds cDNA.  AMPure XP beads were used to separate the ds cDNA from the second-strand reaction mix resulting in blunt-ended cDNA.  A single ‘A’ nucleotide was then added to the 3’ ends of the blunt fragments.  Multiple indexing adapters, containing a single ‘T’ nucleotide on the 3’ end of the adapter, were ligated to the ends of the ds cDNA, preparing them for hybridization onto a flow cell.   Libraries were purified and validated for appropriate size on a 2100 Bioanalyzer High Sensitivity DNA chip (Agilent Technologies, Inc.).   The DNA library was quantitated using a KAPA Biosystems qPCR kit, and then pooled in an equimolar fashion to a final concentration of 2nM.  Each pool was denatured, diluted to 10pM, and clustered to individual lanes of a HiSeq Flow Cell using an Illumina cBot and the corresponding paired-end TruSeq V3 cluster kit.

tag: tumor stage

value: Kidney-Grade IV


title: Normal CDC6

source_name: Normal kidney collecting duct

value: paired normal sample


title: Normal CDC7


title: Tumor CDC5


title: Tumor CDC6


title: MGT XAV 1WK (Sample13)

description: TM 578 mm9


title: Normal CDC3


title: Tumor CDC4


title: Tumor CDC3

value: Kidney-Grade III


title: Normal CDC2


title: Tumor CDC2


title: Tumor CDC1


title: Normal CDC1


title: Normal CDC4


title: miR-control

city: Taipei

first: Yu-Chan

last: Chao

state: Taiwan

address: 128 Academia Road, Section 2, Nankang

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

data_processing:
Illumina Casava1.7 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the human herpes virus 4 type I (Epstein-Barr virus) genome using Bowtie 2 (Version 2.0.0-beta5), and low quality map reads with mapq < 20 were filtered out.
The output was converted to sequence alignment/map (SAM) format for further analysis.
The signal profile was performed on the open source software CisGenome.
Illumina reads were mapped to oriP 130-342 by CLC-bio version 4.3 with parameter Limit 8, Mismatch cost = 2, Global alignment = no, Alignment = ungapped
Genome_build: HHV4 (NC_007605.1), GeneBank ID: 82503188
Supplementary_files_format_and_content: bedGraph

source_name: synthesize DIG-labeled miRNA

growth_protocol: Human Akata cells were incubated in RPMI1640 medium at 37 °C, supplemented with 10 % FBS.

extract_protocol:
The cell lysates were incubated with 5 μg of anti-DIG antibody (Roche). Precipitated DNA was purified and subjected to next generation sequencing (NGS) on an Illumina instrument. The experiment was repeated using biotin-labeled miRNAs for transfection into Akata cells and PureProteomeä Streptavidin Magnetic Beads (Millipore) for immuno-precipitation. Immuno-precipitated DNA was purified and subjected to NGS.
The TruSeq® ChIP Library Preparation Kit (Illumina) was used for library construction. The procedure was following the standard protocol provided by Illumina.

treatment_protocol: Akata cells (1 x 107) were transfected with DIG-labeled (2nd generation DIG Oligonucleotide Tailing Kit, obtained from Roche) miR-155 mimic, miR-3117-3p mimic or miR-control using Fugene® 6 (Roche).

value: human Akata cells

tag: transfected with

value: DIG-labeled miR-control


title: miR-155

value: DIG-labeled miR-155 mimic


title: GBML8 CD133- sample 2

city: New York

first: Igor

last: Dolgalev

state: New York

address: 550 1st Ave

institute: NYU Grossman School of Medicine

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
The sequencing reads were aligned to the human genome (UCSC build hg19) using the TopHat aligner.
Mapped reads were analyzed using the Cufflinks package (using fragment bias and multi-read correction).
Genome_build: hg19
Supplementary_files_format_and_content: comma-delimited text file contains FPKM values for each sample

source_name: GBML8 primary GBM culture

growth_protocol: Established tumorsphere cultures were maintained in Neural Stem Cell media, supplemented with 20 ng/ml EGF and FGF2.

extract_protocol:
Total RNA was extracted using RNeasy Qiagen extraction kit according to the manufacturer's instructions.
Libraries were prepared using the mammalian RiboZero magnetic rRNA depletion kit (Epicenter, Madison, WI) following the manufacturer’s protocol.  Five nanograms of RiboZero-treated RNA were used to construct a library using Epicenter’s ScriptSeq v2 RNASeq Library Preparation Kit.

treatment_protocol: FACS isolation for CD133+ and CD133- cells

tag: cancer type

value: Glioblastoma multiforme

value: non-stem CD133- cells


title: GBML8 CD133- sample 1


title: GBML8 CD133+ sample 2

value: stem-like cells CD133+ cells


title: GBML8 CD133+ sample 1


title: MGT_1WK  (Sample2)

description: TM 471 mm9

value: reprogramming in vitro

value: fibroblasts reprogrammed into iCMs


title: Erα_Chipseq_Y537S_INPUT

city: London

first: Van

middle: Thuy Mai

last: Nguyen

address: 237 Fulham Rd, Chester Beatty Laboratories, third floor

department: Cancer Biology

country: United Kingdom

institute: Institute of cancer research

data_processing:
Sequenced reads were mapped to human genome hg19 using Bowtie 1.0. Peak detection was done with the Model -based Analysis of Chip-seq (MACS) algorithm using default settings.
Genome_build: hg19
Supplementary_files_format_and_content: Wig files

source_name: Y537S_MCF7 cells

growth_protocol: MCF-7 LUC /Y537S cells were cultured in DMEM containing 10%FCS.

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed in MCF7_LUC and MCF7_Y537S cell lines. The cells were seeded at 10X10^6 cells/plate on 150cm dishes in DMEM lacking of phenol-red with 10% dextran-coated charcoal stripped FCS for 72 hours, then treated with ethanol/oestrogen (10nM) for 45 mins prior to fixation. Lysates were collected from sonicated nuclei extracts and subsequently were immuno-precipitated with Erα antibody (HC-20, santacruz). DNA was then extracted using phenol-chloroform and sodium chloride precipitation method.
For Chip-seq, 10ng DNA from IP and input samples were used for library preparation. Libraries were prepared according to NEB (E7370S) multiplex library preparation protocol for DNA-seq preparation. Libraries were run on bioanalyzer for quality control. Finally, sequencing was performed on Ilumina Hiseq 2000 genome analyser (using 50b reads)

treatment_protocol: For Chip-seq experiments, cells were depleted of oestrogen by culturing in DMEM lacking phenol-red with 10% dextran-coated charcoal stripped FCS for 72 hours. 10nM estrogen or ethanol was treated and cells were fixed after treatment of 45 mins.

tag: mutation status (esr1)

tag: agent

value: Vehicle treatment


title: miR-3117

value: DIG-labeled miR-3117-3p mimic


title: Erα_Chipseq_Y537S_E2_CHROMATIN

value: E2 treatment


title: Erα_Chipseq_Y537S_ETOH_CHROMATIN


title: Erα_Chipseq_MCF7LUC_ETOH_CHROMATIN

source_name: MCF7 LUC cells

value: WT


title: Erα_Chipseq_MCF7LUC_INPUT


title: Erα_Chipseq_MCF7LUC_E2_CHROMATIN


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZSCAN5C [ZSCAN5C_rep1]

city: Montreal

first: Hamed

middle: S

last: Najafabadi

state: QC

address: 740 Dr. Penfield Avenue, Room 7202

department: Human Genetics

country: Canada

institute: McGill University

data_processing:
RNA-seq reads were mapped to the annotated human transcriptome using TopHat2, based on annotations from GENCODE v19.
Gene-level read counts were then quantified using HTSeq-count.
Genome_build: hg19
Supplementary_files_format_and_content: HTSeq-count output, indicating the number of reads mapping to each gene.
Supplementary_files_format_and_content: OE.vsd_normalized.log2.txt: Tab-delimited text file includes normalized gene expression matrix.

source_name: HEK293 cells expressing GFP-tagged protein

growth_protocol: HEK293 cells were cultured in Dulbecco's modified Eagle's medium with 10% fetal bovine serum and antibiotics. Gateway-compatible entry clones were cloned into the pDEST pcDNA5/FRT/TO-eGFP vector according to the manufacturer's instructions and co-transfected into Flp-In T-REx 293 cells together with the pOG44 Flp recombinase expression plasmid. Cells were selected for FRT site-specific recombination into the genome, following instructions by the manufacturer.

extract_protocol:
RNA was isolated from lysates using Trizol (Thermo Fisher Scientific) as described by the manufacturer.
Sequencing libraries were constructed using TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold or TruSeq RNA Library Preparation Kit v2.

treatment_protocol: Expression of the gene of interest was induced by addition of doxycycline to the culture medium 24 hours prior to harvesting.

tag: uniprotkb id

tag: library type

value: mRNA V2


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZSCAN22 [ZSCAN22_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF770 [ZNF770_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF778 [ZNF778_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF85 [ZNF85_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF768 [ZNF768_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF768 [ZNF768_rep2]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF76 [ZNF76_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF708 [ZNF708_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF692 [ZNF692_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF677 [ZNF677_rep3]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF680 [ZNF680_rep1]

value: stranded total RNA


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF684 [ZNF684_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF677 [ZNF677_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF675 [ZNF675_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF669 [ZNF669_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF669 [ZNF669_rep3]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF667 [ZNF667_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF669 [ZNF669_rep2]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF596 [ZNF596_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF582 [ZNF582_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF554 [ZNF554_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF582 [ZNF582_rep2]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF528 [ZNF528_rep2]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF513 [ZNF513_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF574 [ZNF574_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF502 [ZNF502_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF490 [ZNF490_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF467 [ZNF467_rep4]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF528 [ZNF528_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF677 [ZNF677_rep2]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF675 [ZNF675_rep2]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF467 [ZNF467_rep3]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF467 [ZNF467_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF454 [ZNF454_rep3]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF394 [ZNF394_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF454 [ZNF454_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF454 [ZNF454_rep2]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF419 [ZNF419_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF418 [ZNF418_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF543 [ZNF543_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF350 [ZNF350_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF502 [ZNF502_rep2]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF322 [ZNF322_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF324 [ZNF324_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF320 [ZNF320_rep3]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF329 [ZNF329_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF317 [ZNF317_rep2]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF317 [ZNF317_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF224 [ZNF224_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF213 [ZNF213_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF184 [ZNF184_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF273 [ZNF273_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF214 [ZNF214_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF320 [ZNF320_rep2]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF320 [ZNF320_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF454 [ZNF454_rep4]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF250 [ZNF250_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF257 [ZNF257_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF16 [ZNF16_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZFP82 [ZFP82_rep2]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZFP3 [ZFP3_rep4]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZFP3 [ZFP3_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF175 [ZNF175_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF134 [ZNF134_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZFP82 [ZFP82_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZFP3 [ZFP3_rep2]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZFP64 [ZFP64_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZBTB42 [ZBTB42_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged SP4 [SP4_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged MYNN [MYNN_rep2]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZFP28 [ZFP28_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged SP1 [SP1_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged KLF7 [KLF7_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged KLF12 [KLF12_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged MYNN [MYNN_rep1]


title: No border full 67 (Sample26)

description: TM 578 mm9

value: reprogramming in vivo

value: 12 weeks reprogramming


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged KLF10 [KLF10_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged GLIS1 [GLIS1_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZBTB12 [ZBTB12_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZFP3 [ZFP3_rep3]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged FEZF1 [FEZF1_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged YY1 [YY1_rep2]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged YY1 [YY1_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged SP2 [SP2_rep1]


title: ChIP-seq of GFP-tagged ZNF175 in HEK293 cells [ZNF175_rep1]

data_processing:
ChIP-seq reads were mapped to the human genome build hg19 using Bowtie 2. The 3’ end of reads were trimmed to a final length of 50 nucleotides, mapped with the Bowtie “--very-sensitive” preset of parameters, and duplicate reads were removed using SAMtools.
MACS v1.4 was used for peak calling, using experiment-specific background models constructed by pooling multiple control datasets.
Genome_build: hg19
Supplementary_files_format_and_content: MACS v1.4 output, containing the coordinates of peaks and summits based on hg19 genome assembly, as well as associated scores.
Supplementary_files_format_and_content: combined_summits.per_protein.hg19.tar: Tar of peak summits per protein.
Supplementary_files_format_and_content: combined_summits.motif_hits.per_protein.hg19.tar: Tar of motif hit locations within peaks per protein.
Supplementary_files_format_and_content: motifs.pfm.txt: Tab-delimited text file includes motifs identified for each protein.

extract_protocol:
Lysates were sonicated to a DNA fragment length range of 200-300 bp using a Bioruptor (Diagenode). GFP-tagged transcription factors were immunoprecipitated with a polyclonal anti-GFP antibody (ab290, Abcam) and Dynabeads Protein G (Invitrogen). Subsequently, crosslinks were reversed at 65°C over night and bound DNA fragments were purified (EZ-10 Spin Column PCR Product Purification kit, Bio Basic).
Sequencing libraries were constructed using the TruSeq ChIP-seq library kits (Illumina) according the manufacturer's instructions followed by PCR amplification and agarose gel size selection.

treatment_protocol: Expression of the gene of interest was induced by addition of doxycycline to the culture medium 24 hours prior to harvesting. HEK293 cells were cross-linked for 10 min in 1% formaldehyde.


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged SCRT1 [SCRT1_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged PRDM1 [PRDM1_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged KLF10 [KLF10_rep2]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged OSR2 [OSR2_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged EGR3 [EGR3_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged EGR2 [EGR2_rep1]


title: ChIP-seq of GFP-tagged ZNF281 in HEK293 cells [ZNF281_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged CTCF [CTCF_rep1]


title: RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZBTB48 [ZBTB48_rep1]


title: ChIP-seq of GFP-tagged ZNF257 in HEK293 cells [ZNF257_rep1]


title: ChIP-seq of GFP-tagged ZNF224 in HEK293 cells [ZNF224_rep1]


title: ChIP-seq of GFP-tagged KLF15 in HEK293 cells [KLF15_rep1]


title: ChIP-seq of GFP-tagged KLF12 in HEK293 cells [KLF12_rep1]


title: ChIP-seq of GFP-tagged ZBTB12 in HEK293 cells [ZBTB12_rep4]


title: ChIP-seq of GFP-tagged ZBTB12 in HEK293 cells [ZBTB12_rep5]


title: ChIP-seq of GFP-tagged ZNF257 in HEK293 cells [ZNF257_rep2]


title: ChIP-seq of GFP-tagged ZBTB12 in HEK293 cells [ZBTB12_rep1]


title: ChIP-seq of GFP-tagged ZBTB12 in HEK293 cells [ZBTB12_rep6]


title: ChIP-seq of GFP-tagged MYNN in HEK293 cells [MYNN_rep1]


title: ChIP-seq of GFP-tagged ZBTB12 in HEK293 cells [ZBTB12_rep3]


title: ChIP-seq of GFP-tagged KLF15 in HEK293 cells [KLF15_rep3]


title: ChIP-seq of GFP-tagged ZFP64 in HEK293 cells [ZFP64_rep1]


title: ChIP-seq of GFP-tagged ZNF214 in HEK293 cells [ZNF214_rep1]


title: ChIP-seq of GFP-tagged ZNF586 in HEK293 cells [ZNF586_rep1]


title: ChIP-seq of GFP-tagged ZFP64 in HEK293 cells [ZFP64_rep3]


title: ChIP-seq of GFP-tagged ZNF331 in HEK293 cells [ZNF331_rep1]


title: ChIP-seq of GFP-tagged ZFP64 in HEK293 cells [ZFP64_rep2]


title: ChIP-seq of GFP-tagged KLF15 in HEK293 cells [KLF15_rep2]


title: ChIP-seq of GFP-tagged PRDM6 in HEK293 cells [PRDM6_rep1]


title: ChIP-seq of GFP-tagged ZBTB26 in HEK293 cells [ZBTB26_rep1]


title: ChIP-seq of GFP-tagged PATZ1 in HEK293 cells [PATZ1_rep1]


title: ChIP-seq of GFP-tagged ZSCAN16 in HEK293 cells [ZSCAN16_rep3]


title: ChIP-seq of GFP-tagged ZNF768 in HEK293 cells [ZNF768_rep1]


title: ChIP-seq of GFP-tagged ZSCAN16 in HEK293 cells [ZSCAN16_rep2]


title: ChIP-seq of GFP-tagged ZSCAN16 in HEK293 cells [ZSCAN16_rep1]


title: ChIP-seq of GFP-tagged ZNF331 in HEK293 cells [ZNF331_rep2]


title: ChIP-seq of GFP-tagged ZNF350 in HEK293 cells [ZNF350_rep2]


title: ChIP-seq of GFP-tagged ZBTB26 in HEK293 cells [ZBTB26_rep2]


title: ChIP-seq of GFP-tagged ZNF341 in HEK293 cells [ZNF341_rep1]


title: ChIP-seq of GFP-tagged SCRT1 in HEK293 cells [SCRT1_rep1]


title: ChIP-seq of GFP-tagged ZNF184 in HEK293 cells [ZNF184_rep1]


title: ChIP-seq of GFP-tagged ZNF350 in HEK293 cells [ZNF350_rep1]


title: ChIP-seq of GFP-tagged ZNF382 in HEK293 cells [ZNF382_rep4]


title: ChIP-seq of GFP-tagged ZBTB18 in HEK293 cells [ZBTB18_rep2]


title: ChIP-seq of GFP-tagged ZSCAN31 in HEK293 cells [ZSCAN31_rep2]


title: ChIP-seq of GFP-tagged ZFP42 in HEK293 cells [ZFP42_rep2]


title: ChIP-seq of GFP-tagged ZNF778 in HEK293 cells [ZNF778_rep1]


title: ChIP-seq of GFP-tagged ZNF563 in HEK293 cells [ZNF563_rep1]


title: ChIP-seq of GFP-tagged ZNF502 in HEK293 cells [ZNF502_rep1]


title: ChIP-seq of GFP-tagged ZNF502 in HEK293 cells [ZNF502_rep2]


title: ChIP-seq of GFP-tagged ZNF418 in HEK293 cells [ZNF418_rep1]


title: ChIP-seq of GFP-tagged GTF3A in HEK293 cells [GTF3A_rep1]


title: ChIP-seq of GFP-tagged ZNF419 in HEK293 cells [ZNF419_rep1]


title: ChIP-seq of GFP-tagged OSR2 in HEK293 cells [OSR2_rep1]


title: ChIP-seq of GFP-tagged ZNF595 in HEK293 cells [ZNF595_rep1]


title: ChIP-seq of GFP-tagged ZNF34 in HEK293 cells [ZNF34_rep1]


title: ChIP-seq of GFP-tagged ZSCAN29 in HEK293 cells [ZSCAN29_rep1]


title: ChIP-seq of GFP-tagged ZNF680 in HEK293 cells [ZNF680_rep1]


title: ChIP-seq of GFP-tagged ZNF680 in HEK293 cells [ZNF680_rep2]


title: ChIP-seq of GFP-tagged GLIS1 in HEK293 cells [GLIS1_rep1]


title: ChIP-seq of GFP-tagged ZNF784 in HEK293 cells [ZNF784_rep1]


title: ChIP-seq of GFP-tagged ZNF329 in HEK293 cells [ZNF329_rep1]


title: ChIP-seq of GFP-tagged ZNF547 in HEK293 cells [ZNF547_rep1]


title: ChIP-seq of GFP-tagged ZNF449 in HEK293 cells [ZNF449_rep1]


title: ChIP-seq of GFP-tagged ZFP42 in HEK293 cells [ZFP42_rep1]


title: ChIP-seq of GFP-tagged ZNF774 in HEK293 cells [ZNF774_rep1]


title: ChIP-seq of GFP-tagged ZNF667 in HEK293 cells [ZNF667_rep1]


title: ChIP-seq of GFP-tagged ZNF394 in HEK293 cells [ZNF394_rep1]


title: ChIP-seq of GFP-tagged ZNF669 in HEK293 cells [ZNF669_rep1]


title: ChIP-seq of GFP-tagged ZNF528 in HEK293 cells [ZNF528_rep3]


title: ChIP-seq of GFP-tagged ZBTB6 in HEK293 cells [ZBTB6_rep3]


title: ChIP-seq of GFP-tagged ZBTB6 in HEK293 cells [ZBTB6_rep2]


title: ChIP-seq of GFP-tagged ZNF549 in HEK293 cells [ZNF549_rep1]


title: ChIP-seq of GFP-tagged ZNF574 in HEK293 cells [ZNF574_rep2]


title: ChIP-seq of GFP-tagged KLF1 in HEK293 cells [KLF1_rep1]


title: ChIP-seq of GFP-tagged EGR3 in HEK293 cells [EGR3_rep1]


title: ChIP-seq of GFP-tagged ZNF513 in HEK293 cells [ZNF513_rep1]


title: ChIP-seq of GFP-tagged ZBTB6 in HEK293 cells [ZBTB6_rep1]


title: ChIP-seq of GFP-tagged ZNF528 in HEK293 cells [ZNF528_rep4]


title: ChIP-seq of GFP-tagged ZNF33A in HEK293 cells [ZNF33A_rep1]


title: ChIP-seq of GFP-tagged ZNF85 in HEK293 cells [ZNF85_rep1]


title: ChIP-seq of GFP-tagged SP4 in HEK293 cells [SP4_rep2]


title: ChIP-seq of GFP-tagged ZNF554 in HEK293 cells [ZNF554_rep1]


title: ChIP-seq of GFP-tagged SP4 in HEK293 cells [SP4_rep3]


title: ChIP-seq of GFP-tagged ZNF41 in HEK293 cells [ZNF41_rep3]


title: ChIP-seq of GFP-tagged SP2 in HEK293 cells [SP2_rep1]


title: ChIP-seq of GFP-tagged ZNF528 in HEK293 cells [ZNF528_rep1]


title: ChIP-seq of GFP-tagged SP4 in HEK293 cells [SP4_rep1]


title: ChIP-seq of GFP-tagged ZNF136 in HEK293 cells [ZNF136_rep1]


title: ChIP-seq of GFP-tagged CTCF in HEK293 cells [CTCF_rep6]


title: ChIP-seq of GFP-tagged ZNF467 in HEK293 cells [ZNF467_rep2]


title: ChIP-seq of GFP-tagged ZNF41 in HEK293 cells [ZNF41_rep1]


title: ChIP-seq of GFP-tagged CTCF in HEK293 cells [CTCF_rep7]


title: ChIP-seq of GFP-tagged CTCF in HEK293 cells [CTCF_rep3]


title: ChIP-seq of GFP-tagged CTCF in HEK293 cells [CTCF_rep5]


title: ChIP-seq of GFP-tagged ZNF76 in HEK293 cells [ZNF76_rep1]


title: ChIP-seq of GFP-tagged CTCF in HEK293 cells [CTCF_rep4]


title: ChIP-seq of GFP-tagged ZNF816 in HEK293 cells [ZNF816_rep1]


title: ChIP-seq of GFP-tagged CTCF in HEK293 cells [CTCF_rep1]


title: ChIP-seq of GFP-tagged YY1 in HEK293 cells [YY1_rep2]


title: ChIP-seq of GFP-tagged YY1 in HEK293 cells [YY1_rep1]


title: ChIP-seq of GFP-tagged MZF1 in HEK293 cells [MZF1_rep2]


title: TLC-S 62.5 uM [AJ113]

city: Minneapolis

first: Anne

last: Sarver

state: MN

address: 420 Delaware St. MMC 195, S.E Minneapolis, MN-55455

department: Surgery

institute: University of Minnesota

data_processing:
adapter trimming with Cutadapt
aligned to the Mouse Dec. 2011 (GRCm38/mm10) Assembly genome using the Bowtie algorithm
Aligned reads were  quantified against the miRBase 21-transcript annotations for both precursor and mature miRNAs
Within each sample, reads from miRNA genes were normalized and scaled to counts per million. The mature miRNA that were found on multiple precursors were merged and their counts summed.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Files are tab delimited. raw: Raw miRNA expression counts for each sample. Counts are weighted so if a read aligns equally well to two miRNA then they are each given a count of 0.5.; norm: Normalized miRNA expression counts for each sample. Expression counts are Counts per Million within each sample (1000000 * raw_counts/total_raw_counts).; mature: The mature miRNA that are found on multiple Precursors have been merged and their counts summed.

source_name: Pancreatic acini

extract_protocol:
Total RNA was isolated from these samples using a mirVana (Life Technologies) kit according to the manufacturer’s instruction.
High-resolution quantification of miRNA expression was performed using small RNA-sequencing from 1 μg of each pool of total RNA from three independent acinar preparations. Small RNA libraries were sequenced (8-12 samples per lane, each sample had 10 million reads) on a High Seq 2000 (Illumina, San Diego, CA, USA).  Sequencing was done at Medical Genome Facility, Mayo Clinic, Rochester, USA.

value: TLC-S 62.5 uM

tag: strain

tag: tissue

value: pancreas

tag: age

value: 7-8 weeks


title: Caerulein 100 pM [AJ115]

value: Caerulein 100 pM


title: ChIP-seq of GFP-tagged CTCF in HEK293 cells [CTCF_rep2]

tag: cell line


title: ChIP-seq of GFP-tagged ZNF37A in HEK293 cells [ZNF37A_rep1]


title: Caerulein 100 nM [AJ114]

value: Caerulein 100 nM


title: TLC-S 250 uM [AJ112]

value: TLC-S 250 uM


title: Control [AJ111]


title: ChIP-seq of GFP-tagged MAZ in HEK293 cells [MAZ_rep1]


title: ChIP-seq of GFP-tagged ZNF22 in HEK293 cells [ZNF22_rep3]


title: Caerulein 100 pM [AJ15]


title: ChIP-seq of GFP-tagged EGR2 in HEK293 cells [EGR2_rep1]


title: ChIP-seq of GFP-tagged EGR2 in HEK293 cells [EGR2_rep2]


title: ChIP-seq of GFP-tagged ZBTB48 in HEK293 cells [ZBTB48_rep1]


title: TLC-S 62.5 uM [AJ13]


title: Caerulein 100 nM [AJ14]


title: ChIP-seq of GFP-tagged ZSCAN22 in HEK293 cells [ZSCAN22_rep4]


title: Control [AJ11]


title: TLC-S 250 uM [AJ12]


title: ChIP-seq of GFP-tagged ZSCAN22 in HEK293 cells [ZSCAN22_rep1]


title: ChIP-seq of GFP-tagged SNAI1 in HEK293 cells [SNAI1_rep3]


title: ChIP-seq of GFP-tagged YY1 in HEK293 cells [YY1_rep4]


title: ChIP-seq of GFP-tagged KLF7 in HEK293 cells [KLF7_rep1]


title: ChIP-seq of GFP-tagged ZNF22 in HEK293 cells [ZNF22_rep2]


title: ChIP-seq of GFP-tagged SP1 in HEK293 cells [SP1_rep1]


title: TLC-S 62.5 uM [AJ3]


title: TLC-S 250 uM [AJ2]


title: High Phosphate

city: Coimbatore

first: Manivannan

last: Jeganathan

state: Tamilnadu

address: Maruthamalai Road

department: Environmental Sciences

country: India

institute: Bharathiar University

description: H9c2 - High Pi

data_processing:
The Illumina HiSeq 2000 generates raw images utilizing HCS (HiSeq Control Software) for system control and base calling through an integrated primary analysis software called RTA (Real Time Analysis). The BCL (base calls) binary is converted into FASTQ utilizing Illumina package bcl2fastq.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using NGS Toolkit.
Sequencing reads obtained were mapped to the rat genome using TopHat (v2.1.1).
To assemble the mapped reads from RNA-seq against NCBI gene structure annotation, Cufflinks (v2.2.1) was used and expression level for each transcript was estimated. A Cufflinks based probabilistic model of paired-end sequencing was used to evaluate abundances of isoforms, and detect ambiguous isoforms.
Differentially expressed transcripts were identified using CuffDiff protocol. Fold change of 2 with a pvalue of <=0.05 was used as a cutoff to identify differentially expressed genes.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: *FPKM.txt: Tab-delimited text files include FPKM values for each Sample.

organism: Rattus norvegicus

source_name: H9c2 cardiomyoblast cells, high phosphate

growth_protocol: H9c2 cardiomyoblasts were cultured in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum and antibiotics under a humidified atmosphere of 95% air, 5% CO2 at 37 °C.

extract_protocol:
RNAs were extracted using the GenElute Mammalian total RNA Miniprep kit (Sigma cat: RTN10-1KT) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Control cells were treated with 0.9 mM phosphate and high phosphate group were treated with 2.5mM phosphate in serum-free DMEM for 12 hours.

value: embryonic cardiomyoblast cell line

tag: treatment

value: high phosphate (2.5mM)


title: ChIP-seq of GFP-tagged ZNF354A in HEK293 cells [ZNF354A_rep1]


title: ChIP-seq of GFP-tagged ZNF324 in HEK293 cells [ZNF324_rep1]


title: ChIP-seq of GFP-tagged PRDM1 in HEK293 cells [PRDM1_rep1]


title: Control [AJ1]


title: ChIP-seq of GFP-tagged ZBTB14 in HEK293 cells [ZBTB14_rep1]


title: Olig2-mOL-LPC

city: Xiamen

first: Ying

last: Chen

state: Fujian Provinee

address: XiangAn Nan Road

department: School of Life Sciences

country: China

institute: Xiamen University

data_processing:
All sequencing data were mapped to November 2004 rat genome assembly
Peak calling was performed using MACS version 1.4.2 with default parameters to get primary binding regions
Genome_build: rn4
Supplementary_files_format_and_content: bed files

source_name: oligodendrocytes, lysolecithin

growth_protocol: Mixed glial cells were cultured in 15% FBS medium for 5–7 days, then switched to B104 conditional medium for 2 days prior to isolating OPCs by mechanical dissociation. Isolated rat OPCs were grown in the OPC growth medium (Sato medium supplemented with mitogens 10 ng/ml PDGF-AA and 20 ng/ml bFGF) and differentiated in oligodendrocyte differentiation medium (Sato medium supplemented with 15 nM thyroid hormone T3 and 10 ng/ml ciliary neurotrophic factor).

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared using 5500 SOLiD Fragment Library Core Kit (PN 4464412) and then run on the 5500xl SOLiD sequencer from Life Technologies

treatment_protocol: Cultured oligodendrocytes were treated with LPC (12.5 mM) for 6h

tag: cell type

value: oligodendrocytes

tag: chip antibodies

value: Olig2 (Millipore)

value: Brain


title: Control

description: H9c2 - Control Pi

source_name: H9c2 cardiomyoblast cells, control phosphate

value: control phosphate (0.9 mM)


title: H3K4me1 pre-B input ChIP-seq

city: La Jolla

first: Salvatore

last: Loguercio

state: California

address: 10550 North Torrey Pines Rd

department: MB

institute: TSRI

description: H3K4me1 pre-B input ChIP-seq

data_processing:
Duplicated reads were removed before mapping.
Experimental and input control fastaq tags were aligned to the mouse reference genome (mm9) using Bowtie 0.12.9. Alignment parameters used:-a -v 2 -m 3 --best --strata
All reads mapping with their best alignment score at more than 3 sites in the genome were discarded.
Significant regions were called using HOMER (version 4.7) with parameter-style histone.
Genome_build: mm9
Supplementary_files_format_and_content: file format: bed; content: significant regions (as called by HOMER)

source_name: RAG-/-µ+ pre-B cells

growth_protocol: Bone marrow were isolated from 6 to 14 wk old C57BL/6 mice, including both males and females.

extract_protocol:
For bone marrow subset purification, B6.RAG-/- mice bearing a rearranged IgM transgene were used to obtain pre-B cells.
For each sample 1 - 10 ng of IP material or input control sample was prepared into sequencing libraries using the NEBNext Ultra DNA Library Prep Kit for Illumina following manufacturers protocol. Samples were amplified using 18 cycles of PCR and then size selected on 2% EX agarose gels (Thermo Fisher) and bands cut at 300bps (+ 25 bps) and cleaned up using DNA Clean & Concentrator-25  (Zymo Research). The prepared libraries were loaded onto an Illumina HiSeq2000 for single-end 100 base reads with 7 bases of the index read. Data was processed to generate Fastq files using CASAVA 1.8 and demultiplexed based on index sequences.

value: Pre-B cells

tag: genotype

tag: antibody


title: Olig2-mOL-Veh

source_name: oligodendrocytes, vehicle


title: ChIP-seq of GFP-tagged ZSCAN22 in HEK293 cells [ZSCAN22_rep3]


title: ChIP-seq of GFP-tagged ZNF263 in HEK293 cells [ZNF263_rep1]


title: H3K4me1 pre-B ChIP-seq

description: H3K4me1 pre-B ChIP-seq

value: H3K4me1 (Abcam (Ab8895))


title: ChIP-seq of GFP-tagged ZBTB42 in HEK293 cells [ZBTB42_rep1]


title: Caerulein 100 nM [AJ4]


title: H3K27Ac-mOL-Veh

value: H3K27Ac (Abcam)


title: RPMI_ctrl (Sample50)

description: TM 590 & 601 hg19

tag: protocol

value: reprogramming in vitro

tag: time of reprogramming

value: 3 weeks reprogramming

value: fibroblasts reprogrammed into iCMs


title: retro_2w_IP_C15

city: Brockport

first: Rongkun

last: Shen

address: 350 New Campus Dr

department: Biology

institute: SUNY Brockport

description: retrovirus B rep 2

data_processing:
Basecalls performed using CASAVA version 1.4
alignment by TopHat2 v2.0.10
Reads count by HTSEQ v0.5.4p1
filtering out low-expressed genes
DESeq v1.14.0
Genome_build: mm10
Supplementary_files_format_and_content: reads count data, tab-delimited text

source_name: batch B retrovirus infected hippocampus

growth_protocol: mouse model

extract_protocol:
Mouse sacrifized, hippocampus dissected, RNA extracted using Trizol, UPRT purification, SMARTer amplication
Illumina TruSeq v3 standard protocol
Illumina mulitplex indexed single-end sequencing

treatment_protocol: virus injection

tag: tissue type

value: Hippocampus


title: ChIP-seq of GFP-tagged ZNF320 in HEK293 cells [ZNF320_rep2]


title: retro_2w_IP_C14

description: retrovirus B rep 1


title: ChIP-seq of GFP-tagged ZNF320 in HEK293 cells [ZNF320_rep1]


title: rv2w_IP4

description: retrovirus A rep 4

source_name: batch A retrovirus infected hippocampus


title: ChIP-seq of GFP-tagged FEZF1 in HEK293 cells [FEZF1_rep1]


title: RPMI_7F_SBXAV_Rep1 (Sample48)

description: TM 590 & 601 hg19

source_name: reprogrammed fibroblasts


title: RPMI_7F_SB_Rep1 (Sample47)

description: TM 590 & 601 hg19


title: rv2w_IP3

description: retrovirus A rep 3


title: RPMI_7F (Sample46)

description: TM 590 & 601 hg19


title: H3K27Ac-mOL-LPC


title: prenatal heart (Sample45)

description: TM 590 & 601 hg19

source_name: tissue extract

value: in vivo

value: prenatal heart


title: Caerulein 100 pM [AJ5]

value: Caerulein 100 pM

value: pancreas

value: 7-8 weeks


title: lv2w_IP3

description: lentivirus rep 3

source_name: lentivirus infected hippocampus


title: TGF-beta and EGF treated shSmad3 replicate 1

city: Bethesda

middle: E

last: Zhang

state: Maryland

address: 37 Convent Dr., Bldg.37, Rm.2056

department: LCMB/CCR

institute: National Cancer Institute, NIH

description:
TGF-beta and EGF treated
processed data file: SHS3_SHS3TE.SE.MATS.ReadsOnTargetAndJunctionCounts.txt
processed data file: SHS3_SHS3TE.MXE.MATS.ReadsOnTargetAndJunctionCounts.txt
processed data file: SHS3_SHS3TE.A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt
processed data file: SHS3_SHS3TE.A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt
processed data file: SHS3_SHS3TE.RI.MATS.ReadsOnTargetAndJunctionCounts.txt

data_processing:
Demultiplexing was done allowing 1 mismatch in the barcodes. Sample reads were trimmed adapters and low quality bases using Trimmomatic software.
Paired-end RNA-seq sequencing reads were aligned with TopHat version 2.0.9 (http://tophat.cbcb.umd.edu/) against the reference human genome hg19, with UCSC known gene transcripts as the gene model annotation.
Quality of the RNA-seq data was assessed using Picard?s CollectRnaSeqMetrics package on alignment bam files (http://broadinstitute.github.io/picard/).
Alternative splicing events were assessed with rMATs (http://rnaseq-mats.sourceforge.net/) on TopHat aligned bam files and using UCSC known gene transcripts as the gene model annotation
File contents: IC_SAMPLE_1: inclusion counts for SAMPLE_1, replicates are separated by comma
File contents: SC_SAMPLE_1: skipping counts for SAMPLE_1, replicates are separated by comma
File contents: IC_SAMPLE_2: inclusion counts for SAMPLE_2, replicates are separated by comma
File contents: SC_SAMPLE_2: skipping counts for SAMPLE_2, replicates are separated by comma

source_name: Hela

growth_protocol: HeLa cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and 100 unit/ml penicillin-streptomycin.

extract_protocol:
RNA was isolated with RNeasy mini kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Hela cells stably expressing shNS, shPCBP1, shSmad3 were treated without or with TGF-beta (4ng/ml) and EGF (10nM) for 72 hours, in triplcates.

value: cervix

value: HeLa

tag: expression

value: TGF-beta and EGF


title: TGF-beta and EGF treated shSmad3 replicate 2


title: retro_2w_IP_B16

description: retrovirus B rep 3


title: shSmad3 replicate 3

description:
untreated
processed data file: SHS3_SHS3TE.SE.MATS.ReadsOnTargetAndJunctionCounts.txt
processed data file: SHS3_SHS3TE.MXE.MATS.ReadsOnTargetAndJunctionCounts.txt
processed data file: SHS3_SHS3TE.A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt
processed data file: SHS3_SHS3TE.A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt
processed data file: SHS3_SHS3TE.RI.MATS.ReadsOnTargetAndJunctionCounts.txt

value: untreated


title: Postnatal heart (Sample44)

description: TM 590 & 601 hg19

value: postnatal heart


title: ChIP-seq of GFP-tagged ZFP82 in HEK293 cells [ZFP82_rep1]


title: TGF-beta and EGF treated shSmad3 replicate 3


title: MGT_SBXAV (Sample43)

description: TM 590 & 601 hg19


title: lv2w_IP1

description: lentivirus rep 1


title: lv2w_IP2

description: lentivirus rep 2


title: shSmad3 replicate 2


title: RPMI_7F_XAV_Rep1 (Sample49)

description: TM 590 & 601 hg19


title: TGF-beta and EGF treated shPCBP1 replicate 1

description:
TGF-beta and EGF treated
processed data file: SHE_SHETE.SE.MATS.ReadsOnTargetAndJunctionCounts.txt
processed data file: SHE_SHETE.MXE.MATS.ReadsOnTargetAndJunctionCounts.txt
processed data file: SHE_SHETE.A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt
processed data file: SHE_SHETE.A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt
processed data file: SHE_SHETE.RI.MATS.ReadsOnTargetAndJunctionCounts.txt


title: iCM_ctrl (Sample42)

description: TM 590 & 601 hg19


title: shSmad3 replicate 1


title: rv2w_IP2

description: retrovirus A rep 2


title: rv2w_IP1

description: retrovirus A rep 1


title: iCM_7F_XAV (Sample41)

description: TM 590 & 601 hg19


title: iCM_7F_SB (Sample39)

description: TM 590 & 601 hg19


title: RPMI _7F_SBXAV_Rep 2 (Sample36)

description: TM 590 & 601 hg19


title: RPMI_7F_XAV_Rep 2 (Sample37)

description: TM 590 & 601 hg19


title: shPCBP1 replicate 1

description:
untreated
processed data file: SHE_SHETE.SE.MATS.ReadsOnTargetAndJunctionCounts.txt
processed data file: SHE_SHETE.MXE.MATS.ReadsOnTargetAndJunctionCounts.txt
processed data file: SHE_SHETE.A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt
processed data file: SHE_SHETE.A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt
processed data file: SHE_SHETE.RI.MATS.ReadsOnTargetAndJunctionCounts.txt


title: TGF-beta and EGF treated shNS replicate 3

description:
TGF-beta and EGF treated
processed data file: SHNS_SHNSTE.SE.MATS.ReadsOnTargetAndJunctionCounts.txt
processed data file: SHNS_SHNSTE.MXE.MATS.ReadsOnTargetAndJunctionCounts.txt
processed data file: SHNS_SHNSTE.A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt
processed data file: SHNS_SHNSTE.A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt
processed data file: SHNS_SHNSTE.RI.MATS.ReadsOnTargetAndJunctionCounts.txt

value: shNS


title: iCM_7F_SBXAV (Sample40)

description: TM 590 & 601 hg19


title: TGF-beta and EGF treated shNS replicate 1


title: TGF-beta and EGF treated shPCBP1 replicate 3


title: 4FSBXAV (Sample34)

description: TM 590 & 601 hg19


title: shPCBP1 replicate 3


title: Y537S E2_68

data_processing:
Illumina CASAVA 1.8.4 software used for basecalling
Quality control checks were performed on raw sequence reads using FastQC 0.11.3 and then reads were trimmed using FASTX trimmer 0.0.13 to remove biased sequence composition in the first 15 bases. All samples, except one Y537S E2 sample, passed quality control. This sample was removed from subsequent analysis.
Reads were aligned to the human genome (Homo sapiens UCSC hg19) using TopHat 2.0.14.
Aligned reads were counted by HTSeq 0.6.1.
Total read counts for each sample were obtained by adding together the read counts resulting from both sequencing lanes (5 and 6)
The R package ‘DESeq2’ was used to normalize counts using a regularized log transformation (rlog). Shrunken log2 fold changes were also calculated to determine DEGs (differentially expressed genes) between conditions, while minimizing the fold change variation of low expressed genes. For more information on DESeq2, see Love et al., 2014.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: Excel files include output from DESeq2 for DEGs between conditions (log2 fold changes, p-adjusted values)

source_name: MCF7-Luc cells

growth_protocol: Cell lines were routinely cultured in DMEM containing 10% FCS. For estrogen depletion experiments, the cells were transferred to DMEM lacking phenol red and containing 5% dextran-coated charcoal-stripped FCS (DSS) for 72 hours.

extract_protocol:
RNA was extracted using RNeasy Mini Kit (Qiagen), with DNase treatment to remove genomic DNA.
cDNA libraries were prepared using TruSeq® RNA Sample Preparation Kit v2 (Illumina, UK), according to manufacturer’s instructions.

treatment_protocol: 17ß-estradiol (E2), purchased from Sigma-Aldrich, was prepared in ethanol. Cells were treated with either E2 or ethanol, as vehicle control, for 8 hours before RNA extraction.

tag: mutation status (esr1)

value: 10nM E2


title: Y537S E2_67


title: TGF-beta and EGF treated shNS replicate 2


title: Y537S Veh_66

value: Ethanol


title: control shNS replicate 3

description:
untreated
processed data file: SHNS_SHNSTE.SE.MATS.ReadsOnTargetAndJunctionCounts.txt
processed data file: SHNS_SHNSTE.MXE.MATS.ReadsOnTargetAndJunctionCounts.txt
processed data file: SHNS_SHNSTE.A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt
processed data file: SHNS_SHNSTE.A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt
processed data file: SHNS_SHNSTE.RI.MATS.ReadsOnTargetAndJunctionCounts.txt


title: control shNS replicate 2


title: TGF-beta and EGF treated shPCBP1 replicate 2


title: control shNS replicate 1


title: shPCBP1 replicate 2


title: Y537S Veh_63


title: iCM_7F (Sample38)

description: TM 590 & 601 hg19

value: reprogramming in vitro


title: Y537S Veh_62


title: MCF7 E2_7

value: WT


title: MCF7 E2_10


title: RPMI_7F_SB_Rep 2 (Sample35)

description: TM 590 & 601 hg19

value: 3 weeks reprogramming

value: fibroblasts reprogrammed into iCMs


title: iPSCs from severe-FD patient

first: Lorenz

last: Studer

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using Tophat v1.3.3 with these parameters: -p8 -r 180 --library-type fr-unstranded --no-coverage-search --no-novel-juncs
BAM files were then compared using Cuffdiff
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited file with FPKM and fold change compared to control samples are provided.

source_name: induced pluripotent stem cells

extract_protocol:
RNA was extracted with Trizol and cleaned up using a Qiagen RNEasy column
RNA libraries were prepared for sequencing using standard Illumina protocols

value: iPSCs

tag: disease state

value: severe

tag: differention day


title: MCF7 Veh_3


title: NCs from control patient

value: normal


title: NCs from mild-FD patient

value: mild


title: NCs from severe-FD patient


title: Ueno201302_XENLA_st08

status: Public on Oct 24 2016

city: Ulsan

first: Taejoon

last: Kwon

address: 50 Unist-gil

department: Department of Biomedical Engineering

country: South Korea

institute: Ulsan National Institute of Science and Technology

description:
st08.U2
TairaUeno_XENLA_stage.JGIv18pV2_cdna_final.bwa_mem+rsem.indiv_tpm.txt.gz

data_processing:
Mapped paired-reads to primary transcripts with bwa mem (0.7.10)
Filtered out non-compatible hits for RSEM (local alignment, gapped alignment, multi hits, etc)
Calculate TPM with RSEM (1.2.19)
Genome_build: XENLA_JGIv18p (X. laevis JGI gene model version 1.8 primary transcripts; http://www.xenbase.org/)
Supplementary_files_format_and_content: TPMs calculated by RSEM for individual samples.  X. laevis has a genome duplication (a pair of large chromosome and small chromosome; see Fig 3 at http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3806017/). The consortium decided to call the gene with the suffix (L or S) of the type of chromosome.

molecule: polyA RNA

organism: Xenopus laevis

source_name: NF stage 08

extract_protocol:
Whole tissue was minced before mRNA extraction; mRNA was extracted with TRIzol protocol; the column purification was performed after extraction.
Standard non-strand-specific RNA-seq protocol for HiSeq 2000, with poly-A capturing method

value: J-strain

tag: developmental stage

value: NF stage 08

tag: clutch

value: Ueno


title: Ueno201210_XENLA_st20

description:
st20.U
TairaUeno_XENLA_stage.JGIv18pV2_cdna_final.bwa_mem+rsem.indiv_tpm.txt.gz

source_name: NF stage 20

tag: strain

value: NF stage 20


title: Ueno201210_XENLA_st15

description:
st15.U
TairaUeno_XENLA_stage.JGIv18pV2_cdna_final.bwa_mem+rsem.indiv_tpm.txt.gz

source_name: NF stage 15

value: NF stage 15


title: iPSCs from control patient


title: Ueno201210_XENLA_st12

description:
st12.U
TairaUeno_XENLA_stage.JGIv18pV2_cdna_final.bwa_mem+rsem.indiv_tpm.txt.gz

source_name: NF stage 12

value: NF stage 12


title: Ueno201210_XENLA_st08

description:
st08.U
TairaUeno_XENLA_stage.JGIv18pV2_cdna_final.bwa_mem+rsem.indiv_tpm.txt.gz


title: MCF7 E2_9


title: MCF7 Veh_6


title: Ueno201210_XENLA_st10

description:
st10.U
TairaUeno_XENLA_stage.JGIv18pV2_cdna_final.bwa_mem+rsem.indiv_tpm.txt.gz

source_name: NF stage 10.5

value: NF stage 10.5


title: Ueno201302_XENLA_st10

description:
st10.U2
TairaUeno_XENLA_stage.JGIv18pV2_cdna_final.bwa_mem+rsem.indiv_tpm.txt.gz

source_name: NF stage 10

value: NF stage 10


title: Ueno201210_XENLA_st35

description:
st35.U
TairaUeno_XENLA_stage.JGIv18pV2_cdna_final.bwa_mem+rsem.indiv_tpm.txt.gz

source_name: NF stage 35

value: NF stage 35


title: MCF7 Veh_4

value: Ethanol


title: Ueno201210_XENLA_st40

description:
st40.U
TairaUeno_XENLA_stage.JGIv18pV2_cdna_final.bwa_mem+rsem.indiv_tpm.txt.gz

source_name: NF stage 40

value: NF stage 40


title: Ueno201302_XENLA_st35

description:
st35.U2
TairaUeno_XENLA_stage.JGIv18pV2_cdna_final.bwa_mem+rsem.indiv_tpm.txt.gz


title: Ueno201210_XENLA_st30

description:
st30.U
TairaUeno_XENLA_stage.JGIv18pV2_cdna_final.bwa_mem+rsem.indiv_tpm.txt.gz

source_name: NF stage 30

value: NF stage 30


title: Ueno201210_XENLA_oo12

description:
oo12.U
TairaUeno_XENLA_stage.JGIv18pV2_cdna_final.bwa_mem+rsem.indiv_tpm.txt.gz

source_name: oocyte stage 1-2

value: oocyte stage 1-2


title: Ueno201210_XENLA_st09

description:
st09.U
TairaUeno_XENLA_stage.JGIv18pV2_cdna_final.bwa_mem+rsem.indiv_tpm.txt.gz

source_name: NF stage 09

value: NF stage 09


title: Ueno201210_XENLA_oo56

description:
oo56.U
TairaUeno_XENLA_stage.JGIv18pV2_cdna_final.bwa_mem+rsem.indiv_tpm.txt.gz

source_name: oocyte stage 5-6

value: oocyte stage 5-6


title: Taira201203_XENLA_st30

description:
st30.T
TairaUeno_XENLA_stage.JGIv18pV2_cdna_final.bwa_mem+rsem.indiv_tpm.txt.gz

value: Taira


title: Ueno201210_XENLA_oo34

description:
oo34.U
TairaUeno_XENLA_stage.JGIv18pV2_cdna_final.bwa_mem+rsem.indiv_tpm.txt.gz

source_name: oocyte stage 3-4

value: oocyte stage 3-4


title: Ueno201210_XENLA_egg

description:
egg.U
TairaUeno_XENLA_stage.JGIv18pV2_cdna_final.bwa_mem+rsem.indiv_tpm.txt.gz

source_name: unfertilized egg

value: J-strain

value: unfertilized egg


title: iPSCs from mild-FD patient

value: iPSCs

value: mild


title: Taira201203_XENLA_st20

description:
st20.T
TairaUeno_XENLA_stage.JGIv18pV2_cdna_final.bwa_mem+rsem.indiv_tpm.txt.gz

value: NF stage 20


title: Taira201203_XENLA_st35

description:
st35.T
TairaUeno_XENLA_stage.JGIv18pV2_cdna_final.bwa_mem+rsem.indiv_tpm.txt.gz


title: Taira201203_XENLA_st40

description:
st40.T
TairaUeno_XENLA_stage.JGIv18pV2_cdna_final.bwa_mem+rsem.indiv_tpm.txt.gz


title: Taira201203_XENLA_st12

description:
st12.T
TairaUeno_XENLA_stage.JGIv18pV2_cdna_final.bwa_mem+rsem.indiv_tpm.txt.gz

value: NF stage 12


title: Taira201203_XENLA_st25

description:
st25.T
TairaUeno_XENLA_stage.JGIv18pV2_cdna_final.bwa_mem+rsem.indiv_tpm.txt.gz

source_name: NF stage 25

value: NF stage 25


title: Taira201203_XENLA_st09

description:
st09.T
TairaUeno_XENLA_stage.JGIv18pV2_cdna_final.bwa_mem+rsem.indiv_tpm.txt.gz


title: Taira201203_XENLA_egg

description:
egg.T
TairaUeno_XENLA_stage.JGIv18pV2_cdna_final.bwa_mem+rsem.indiv_tpm.txt.gz


title: Ueno201210_XENLA_stomach

description: TairaUeno_XENLA_tissue.JGIv18pV2_cdna_final.bwa_mem+rsem.indiv_tpm.txt.gz

data_processing:
Mapped paired-reads to primary transcripts with bwa mem (0.7.10)
Filtered out non-compatible hits for RSEM (local alignment, gapped alignment, multi hits, etc)
Calculate TPM with RSEM (1.2.19)
Genome_build: XENLA_JGIv18p (X. laevis JGI gene model version 1.8 primary transcripts)
Supplementary_files_format_and_content: TPMs calculated by RSEM for individual samples.  X. laevis has a genome duplication (a pair of large chromosome and small chromosome; see Fig 3 at http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3806017/). The consortium decided to call the gene with the suffix (L or S) of the type of chromosome.

source_name: stomach

tag: tissue

value: stomach

value: Ueno


title: Ueno201210_XENLA_testis

source_name: testis

value: testis


title: Taira201203_XENLA_st10

description:
st10.T
TairaUeno_XENLA_stage.JGIv18pV2_cdna_final.bwa_mem+rsem.indiv_tpm.txt.gz

value: NF stage 10.5


title: Taira201203_XENLA_st08

description:
st08.T
TairaUeno_XENLA_stage.JGIv18pV2_cdna_final.bwa_mem+rsem.indiv_tpm.txt.gz

source_name: NF stage 08

value: NF stage 08


title: Ueno201210_XENLA_pancreas

source_name: pancreas

value: pancreas


title: Ueno201210_XENLA_ovary

source_name: ovary

value: ovary


title: Ueno201210_XENLA_st25

description:
st25.U
TairaUeno_XENLA_stage.JGIv18pV2_cdna_final.bwa_mem+rsem.indiv_tpm.txt.gz


title: Ueno201210_XENLA_skin

source_name: skin

value: skin


title: Ueno201210_XENLA_lung

source_name: lung

value: lung


title: Ueno201210_XENLA_intestine

source_name: intestine

value: intestine


title: Ueno201210_XENLA_kidney

source_name: kidney

value: J-strain

value: kidney


title: Ueno201210_XENLA_muscle

source_name: muscle

value: muscle


title: Ueno201210_XENLA_heart

source_name: heart

value: heart


title: Taira201203_XENLA_st15

description:
st15.T
TairaUeno_XENLA_stage.JGIv18pV2_cdna_final.bwa_mem+rsem.indiv_tpm.txt.gz

source_name: NF stage 15

value: NF stage 15

value: Taira


title: Taira201203_XENLA_testis


title: Ueno201210_XENLA_eye

source_name: eye

value: eye


title: Ueno201210_XENLA_brain

source_name: brain

value: brain


title: Taira201203_XENLA_stomach

value: stomach


title: Ueno201210_XENLA_spleen

source_name: spleen

value: spleen

value: Ueno


title: Taira201203_XENLA_ovary


title: Taira201203_XENLA_pancreas


title: Ueno201210_XENLA_liver

source_name: liver

value: liver


title: Miller201511_HYMBO_tadpole8

data_processing:
Mapped reads to de novo assembled transcripts using Kallisto (0.42.4), to calculate TPM
Genome_build: HYMBO_TrinityV1_cdna (de novo assembled transcripts)
Supplementary_files_format_and_content: FASTA file containing de novo assembled transcripts, and their TPM values among samples calculated by Kallisto

organism: Hymenochirus boettgeri

source_name: swimming tadpole replicate #2

extract_protocol:
Whole tissue was minced before mRNA extraction; mRNA was extracted with TRIzol protocol; the column purification was performed after extraction.
Standard strand-specific RNA-seq protocol for Illumina HiSeq, with poly-A capturing method

value: wild-type

value: swimming tadpole


title: Taira201203_XENLA_muscle


title: Miller201511_HYMBO_tadpole7

source_name: swimming tadpole replicate #1


title: MCF7_ChIP_ERa_sc543x_NA_E2_100nM_120min_Rep2

city: Quebec

first: Steve

last: Bilodeau

state: Quebec

address: 2260 boul. Henri-Bourassa

institute: Centre de recherche du CHU de Québec-Université Laval

data_processing:
All datasets were analyzed with the ChIP-Seq pipeline developed at the McGill University and Génome Québec Innovation Centre (https://bitbucket.org/mugqic/mugqic_pipelinest) (version 2.1.0)
All samples were processed using Trimmomatic 0.33 with the following parameters: LEADING=30, TRAILING=30, SLIDINGWINDOW=4:30, MINLEN=30. Reads were mapped against the hg19 build of the human reference genome using BWA 0.7.12 with default parameters and MACS2 2.1.0 with default parameters was used for peak calling.
Genome_build: hg19
Supplementary_files_format_and_content: NarrowPeak files were generated with MACS2 2.1.0 with default parameters. The enrichment ratio of each replicate were calculated  with the 2 control files available for each cell line.

growth_protocol: HEPG2 were grown in DMEM (Gibco, 11965-092) and A549 were grown in F12K medium (Gibco, 21127022) as recommended by the supplier. All cell mediums were supplemented with 10% fetal bovine serum (Invitrogen, qualified 12483020), 100 μM MEM nonessential amino acids (Cellgro, 25-0250), 2 mM L-glutamine (Gibco, 25030-081), 100 U/ml penicillin, 100 μg/ml streptomycin (Gibco, 15170-063). MCF7 were kept in DMEM w/o phenol-red (Gibco, 31053-028) supplemented with 5% of Charcoal/Dextran treated FBS (Hyclone, AVH78911), 100 μM MEM nonessential amino acids (Cellgro, 25-0250) and 2 mM L-glutamine (Gibco, 25030-081) for 3 days prior to 100nM of Beta-Estradiol (SIGMA, E8875) for two hours.

extract_protocol:
Cells were crosslinked with 1% formaldehyde in culture medium for 10 minutes at room temperature. Cells were then lysed in 10 ml lysis buffer (0.1%SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris-HCl ph 8.0 and 150 mM NaCl) and chromatin was sheared to 200-600 bp fragments using a Bioruptor Sonicator (Diagenode). Chromatin extract from 5x10^7 cells was incubated overnight at 4oC with 100 ul of Dynabeads Protein G magnetic beads (Life Technologies, 10004D) previously incubated with 10 ug of selected antibodies. After ChIP, samples were washed and bound complex were reversed cross-linked and eluted in 10mM Tris-HCl pH 8
The TruSeq DNA sample prep kit with indexing adapters was used according to the manufacturer's recommendations (Illumina)

treatment_protocol: For EtOH treatment, 250 ul of 1% EtOH were added directly to cell medium (25 ml) and incubated for 1 hour at 37C. For estradiol treatment, 100nM of Beta-Estradiol (SIGMA, E8875) was added directly to cell medium and incubated for two hours at 37C.

tag: cell line

value: MCF7 (ATCC, HTB-22)

value: Breast adenocarcinoma-derived cells

tag: passages

tag: treated with

tag: chip antibody

value: Era (Santa-Cruz, sc543x, lot:


title: MCF7_ChIP_SMC1_A300-055A_NA_E2_100nM_120min_Rep2

tag: cell type

value: SMC1 (Bethyl, A300-055A, lot:3)


title: Taira201203_XENLA_lung

value: J-strain

value: lung


title: Taira201203_XENLA_liver


title: Taira201203_XENLA_skin

value: skin


title: MCF7_ChIP_MED1_A300-793A_NA_E2_100nM_120min_Rep2

value: MED1 (Bethyl, A300-793A, lot:2)


title: Miller201511_HYMBO_egg2

source_name: unfertilized egg replicate #2

value: unfertilized egg


title: Miller201511_HYMBO_8cells4

source_name: 8-cell stage replicate #2

value: 8-cell stage


title: MCF7_ChIP_NIPBL_A301-779A_NA_E2_100nM_120min_Rep2

value: NIPBL (Bethyl, A301-779A, lot:3)


title: Taira201203_XENLA_kidney

value: kidney

value: Taira


title: Taira201203_XENLA_spleen

value: spleen


title: MCF7_ChIP_WCE_NA_NA_E2_100nM_120min_Rep2


title: Taira201203_XENLA_intestine

value: intestine


title: Miller201511_HYMBO_st26a

source_name: NF stage 26 replicate #1

value: wild-type

value: NF stage 26


title: Taira201203_XENLA_heart

value: heart


title: Miller201511_HYMBO_8cells3

source_name: 8-cell stage replicate #1


title: Taira201203_XENLA_eye

value: eye


title: Miller201511_HYMBO_st26b

source_name: NF stage 26 replicate #2


title: MCF7_ChIP_ERa_sc543x_NA_E2_100nM_120min_Rep1

value: MCF7 (ATCC, HTB-22)

value: Breast adenocarcinoma-derived cells

value: Era (Santa-Cruz, sc543x, lot:


title: Miller201511_HYMBO_egg1

source_name: unfertilized egg replicate #1


title: MCF7_ChIP_SMC1_A300-055A_NA_E2_100nM_120min_Rep1

value: SMC1 (Bethyl, A300-055A, lot:3)


title: MCF7_ChIP_MED1_A300-793A_NA_E2_100nM_120min_Rep1


title: S067

city: Hamburg

first: Stefan

last: Scholten

address: Ohnhorststrasse 18

department: Biocenter Klein Flottbek

country: Germany

institute: University of Hamburg

description: Sample 22

data_processing:
Basecalls were performed using CASAVA (version 1.7 for samples 1-3,5-22; version 1.8.1 for samples 23-24; version 1.8.2 for sample 4,25-31).
Raw reads were trimmed from adapter and low quality nucleotide reads (<99.9%) using a custom Java program, all reads within 15-nt to 40-nt were retained and identical sequences merged to obtain raw read counts.
Read counts of samples 1-25 (“association_srna”) were quantile normalized and scaled to 1 Mio. normalized reads per library (qnrpm). Raw read counts of samples 26-31 („p1_hc-pro_suppressor“) were used for analyses.

organism: Zea mays

source_name: whole seedling

growth_protocol: Five biological replicates of each genotype (Sample 1-25) were grown in a climate chamber (Percival Scientific Inc., Perry, USA) under controlled conditions (25°C, 16h day, 8h night, 70% air humidity) for seven days, flash-frozen in liquid nitrogen, and pooled before RNA isolation. For Sample 26-31 nucellus tissue of P1/HC-Pro x H99 hybrids were isolated one day after pollination (dap) and transfered to plates with modified MS-medium. The transgenic viral suppressor was induced via 20 µM Dexamethasone to the medium, half of the plates was mock-treated with ethanol. Two days after germination (dag) the tissue was transfered into glass containes containing standard MS media and either Dexamethasone or ethanol. Whole seedlings were harvested 20 dag, flash-frozen in liquid nitrogen and stored until RNA isolation.

extract_protocol:
Total RNA isolation of all samples was performed using the miRVana miRNA Isolation Kit (Life technologies Corp., Carlsbad, USA).
sRNA sample library preparation was performed using the TruSeq SBS Kit v5 (Illumina Inc., San Diego, USA).

tag: genetic background

value: inbred line

value: whole seedling

tag: age

value: 7 days after germination


title: S028xF039

description: Sample 24

value: hybrid


title: P033xF047

description: Sample 23


title: S058

description: Sample 21


title: S044

description: Sample 17


title: S050

description: Sample 20


title: S028xL024

description: Sample 25


title: CtrA_ChIP-seq NR3057

city: Lausanne

first: Johann

last: Mignolet

address: Biophore Quartier UNIL-SORGE

department: DMF

country: Switzerland

institute: UNIL

data_processing:
Alignment: Bowtie-0.12.9, samtools-0.1.18
Peak calling and Tn-insertion calling: SeqMonk software (Braham Bionformatics Institute)
Peak refinement and annotation: SeqMonK output were processed by Java and Perl programs (decribed in Fumeau et al., Nat. Comm., 2014) to refine the peaks annotation and eliminate background
ChIPseq comparisons: Peaks list after being proccessed were scanned for common target, then ratio of each peak abundance were computed and reported as the log2 fold variation
Genome_build: Caulobacter crescentus : NC_011916.1
Supplementary_files_format_and_content: the xls files reporting probe annotations and transcription factor occupancy  were generated by SeqMonk software. The sheets  are organized in columns as follows:  column 1 : probe start  column 2 : probe end  column 3: gene name to which the probe is associated  column 4 : gene ortholog in Caulobacter crescentus CB15 strain  column 5 : orientation of the probe in regard to the associated gene   column 6 : Probe distance, the distance of the probe from ORF  column 7 : It is reported here the absolute value of reads per probe  column 8 : It is reported here the relative number of reads per probe expressed as the percentage of total reads number
Supplementary_files_format_and_content: the xls files reporting comparison peaks annotations and abundance between two strains were generated by Java and Perl programs (described in the Fumeau et al., Nat. Comm., 2014) . The file is organized in columns as follows:  column 1: gene name to which the peak is associated is reported in the reference genome used for the reads alignment  column 2 : probe start  column 3 : probe end  column 4 : Abundance of reads per probe expressed as the percentage of total reads number in one strain  column 5 : Abundance of reads per probe expressed as the percentage of total reads number in a second strain  column 6 : ratio between column 4 and 5  column 7 : log2 transformation of column 6
Supplementary_files_format_and_content: the xls files reporting Tn-insertion and insertion bias (IB) were generated by SeqMonk sofware.The sheet is organized in columns as follows:   column 1: gene name to which was assigned an IB  column 2 : probe start   column 3 : probe end  column 4 : gene size   column 5 : The gene strand of the gene associated to the peak (0 plus strand, 1 reverse strand)  column 6 : Abundance of Tn innsertion per probe in mutant background  column 7 : Abundance of Tn innsertion per probe in WT background  column 8 : Normalized abundance of Tn innsertion per probe in mutant background  column 9 : Normalized abundance of Tn innsertion per probe in WT background  column 10 : Ratio of Normalized abundance of Tn innsertion per probe in mutant versus WT background  column 11 : log2 transformation of column 10
Supplementary_files_format_and_content: Janakiraman_et_al_Supplementary_Data1.xlsx: abundance measurements, IB assessment
Supplementary_files_format_and_content: Janakiraman_et_al_Supplementary_Data2.xlsx: abundance measurements
Supplementary_files_format_and_content: Janakiraman_et_al_Supplementary_Data3.xlsx: abundance measurements
Supplementary_files_format_and_content: Janakiraman_et_al_Supplementary_Data4.xlsx: abundance measurements
Supplementary_files_format_and_content: Janakiraman_et_al_Supplementary_Data5.xlsx: abundance measurements, peaks annotation

organism: Caulobacter vibrioides NA1000

growth_protocol: Caulobacter crescentus and derivatives were grown at 30°C in PYE (Peptone yeast extract) or M2G

extract_protocol:
ChIP-seq : Mid-log phase cells were cross-linked in 10 mM sodium phosphate (pH 7.6) and 1%  formaldehyde at room temperature for 10 min and on ice for 30 min thereafter, washed  thrice in phosphate buffered saline (PBS) and lysed in a Ready-Lyse lysozyme solution  (Epicentre, Madison, WI) according to the manufacturer`s instructions. Lysates were  sonicated (Sonifier Cell Disruptor B-30; Branson Sonic Power. Co., Danbury, CT) on ice  using 10 bursts of 20 sec at output level 4.5 to shear DNA fragments to an average length  of 0.3-0.5 kbp and cleared by centrifugation at 14,000 rpm for 2 min at 4°C. Lysates were  normalized by protein content, diluted to 1 mL using ChIP buffer (0.01% SDS, 1.1%  Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl [pH 8.1], 167 mM NaCl plus protease  inhibitors (Roche) and pre-cleared with 80 μL of protein-A agarose (Roche, Switzerland)  and 100 uμg BSA. Ten % of the supernatant was removed and used as total chromatin  input DNA as described before (Radhakrishnan et al., 2008).  Two microliters of polyclonal antibodies to CtrA (Domian et al., 1997), SciP (Gora et al.,  2010; Tan et al., 2010) (note that for ChIP experiments reported in Table S6 we used  antibodies that we raised against His6-SUMO-SciP), FlbD (Davis and Viollier, 2011),  RpoC (Neoclone, Madison, WI), MucR1 or MucR2 were added to the remains of the  supernatant, incubated overnight at 4°C with 80 μL of protein-A agarose beads pre  saturated with BSA, washed once with low salt buffer (0.1% SDS, 1% Triton X-100, 2  mM EDTA, 20 mM Tris-HCl (pH 8.1), 150 mM NaCl), high salt buffer (0.1% SDS, 1%  Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.1), 500 mM NaCl) and LiCl buffer  (0.25 M LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, 10 mM Tris-HCl (pH  8.1) and twice with TE buffer (10 mM Tris-HCl (pH 8.1) and 1 mM EDTA). The  protein•DNA complexes were eluted in 500 μL freshly prepared elution buffer (1% SDS,  0.1 M NaHCO3), supplemented with NaCl to a final concentration of 300 mM and  incubated overnight at 65°C to reverse the crosslinks. The samples were treated with 2 μg  of Proteinase K for 2 h at 45°C in 40 mM EDTA and 40 mM Tris-HCl (pH 6.5). DNA  extracted using phenol:chloroform:453 isoamyl alcohol (25:24:1), ethanol-precipitated  using 20 ug glycogen as carrier and re-suspended in 100uL of water. For deep  sequencing (ChIP-seq) total chromatin input DNA was not saved.
Tn-seq: Tn collections of 100,000 kanamycin- and nalidixic acid-resistant clones were collected for NA1000 (WT) and ∆spmX strains, with the same protocol as previously described by Viollier et al., PNAS, 2004. For each collection, all Tn clones were harvested and chromosomal DNA extracted. Genomic DNAs were used to generate barcoded ChIP-Seq libraries and submitted to Illumina HiSeq 2000 sequencing (Fasteris, www.fasteris.com/). Tn insertion-specific reads (50 bp long) were sequenced using the himar-Tnseq primer generating several million reads that were mapped to Caulobacter crescentus NA1000 (NC_011916).
DNA libraries were prepared for sequencing using standard Illumina protocols by FASTERIS SA, Switzerland

tag: genotype

tag: mutations


title: S036

description: Sample 16


title: MCF7_ChIP_WCE_NA_NA_E2_100nM_120min_Rep1


title: P063

description: Sample 13


title: CtrA_ChIP-seq ∆spmX

description: Janakiraman_et_al_Supplementary_Data5.xlsx

value: deltaspmX


title: S028

description: Sample 15


title: P066

description: Sample 14


title: MCF7_ChIP_NIPBL_A301-779A_NA_E2_100nM_120min_Rep1

value: NIPBL (Bethyl, A301-779A, lot:3)


title: P048

description: Sample 12


title: TacA_ChIP-seq wild type

value: wild type


title: A549_ChIP_SMC1_A300-055A_NA_EtOH_60min_Rep2

value: Lung adenocarcinoma-derived cells


title: Tn-seq ∆spmX

description: Janakiraman_et_al_Supplementary_Data1.xlsx

source_name: Tn-seq


title: P046

description: Sample 11


title: Taira201203_XENLA_brain

value: J-strain

value: brain

value: Taira


title: P040

description: Sample 10


title: A549_ChIP_MED1_A300-793A_NA_EtOH_60min_Rep2

value: MED1 (Bethyl, A300-793A, lot:2)


title: S049

description: Sample 19


title: P033

description: Sample 9


title: A549_ChIP_NIPBL_A301-779A_NA_EtOH_60min_Rep2


title: F043

description: Sample 4


title: L024

description: Sample 6


title: A549_ChIP_WCE_NA_NA_EtOH_60min_Rep2


title: F047

description: Sample 5


title: Tn-seq wild type


title: L043

description: Sample 8


title: F039

description: Sample 3


title: L035

description: Sample 7


title: F037

description: Sample 2


title: A549_ChIP_NIPBL_A301-779A_NA_EtOH_60min_Rep1


title: A549_ChIP_SMC1_A300-055A_NA_EtOH_60min_Rep1


title: A549_ChIP_MED1_A300-793A_NA_EtOH_60min_Rep1


title: db/m glom rep 1

city: Houston

first: Shawn

middle: Samson

last: Badal

state: TX

address: 2121 W. Holcombe Blvd

department: Nephrology

institute: MD Anderson Cancer Center

data_processing:
The raw data quality was assessed using FastQC software.
Adaptor presence was tested using Trimmomatic. Reads from each sample were aligned to the NCBI mouse reference genome build 37.2 using Tophat2 v2.0.4.
Transcript quantification, normalization and assembly were carried out using Cufflinks.
Genome_build: mm9

source_name: Kidney Glomeruli

growth_protocol: All animal studies were conducted according to the “Principles of Laboratory Animal Care” (NIH publication No. 85023, revised 1985) and the guidelines of the IACUC of The University of Texas MD Anderson Cancer Center/Texas A&M Institute of Biosciences and Technology (IBT). Diabetic db/db mice and their control littermates, db/m, were obtained from Jackson Laboratories (Strain: BKS.Cg-Dock7m+/+Leprdb/J, Bar Harbor, ME). All mice used in experiments were male. Ages of mice are reported in figure legends or denoted in figure panels. Mice were 25 weeks old at the time of sacrifice. All animals were maintained on a normal chow diet and housed in a room with a 12:12-hour light/dark cycle and an ambient temperature of 22° C.

extract_protocol:
After placing mice under a surgical plane of anesthesia, mice were perfused by insertion of a butterfly needle into the left ventricle. Cold Perfusion solution consisted of 200ul of Dynabeads M-450 Tosylactivated (Life Technologies) diluted in 40 ml of Hank's Balanced Salt Solution (HBSS). After perfusion, kidneys were harvested on ice, minced and chemically digested. Dynabead perfused glomeruli were retreived by magnetic isolation and RNA extracted by Trizol Reagent, purified over PureLink RNA Easy mini columns (Life Tech)
The Illumina compatible libraries were prepared using Illumina’s TruSeq RNA Sample Prep kit v2, as per the manufacturer’s protocol. In brief, Poly-A RNA was enriched using Oligo-dT beads. Enriched Poly-A RNA was fragmented to a median size of 150bp using chemical fragmentation and converted into double stranded cDNA. Ends of the double stranded cDNA were polished, 5′-phosphorylated, and 3’-A tailed for ligation of the Y-shaped indexed adapters. Adapter ligated DNA fragments were PCR amplified, quantified and validated by qPCR, and sequenced on Illumina’s HiSeq 2000 in a paired-end read format for 76 cycles.

tag: phenotype

value: non-diabetic, normal control

value: heterozygous mutation in Leptin receptor (db)

value: 25 weeks

value: Kidney Glomeruli


title: B73

description: Sample 1


title: db/m glom rep 3


title: db/db glom rep 2

value: Type 2 diabetic

value: homozygous mutation in Leptin receptor (db)


title: A549_ChIP_WCE_NA_NA_EtOH_60min_Rep1


title: HEPG2_ChIP_SMC1_A300-055A_NA_NA_Rep2

value: HEPG2 (ATCC, HB-8065)

value: Hepatocellular carcinoma-dirived cells

value: SMC1 (Bethyl, A300-055A, lot:3)


title: db/db glom rep 3


title: db/db glom rep 1


title: HEPG2_ChIP_MED1_A300-793A_NA_NA_Rep2


title: gDNA-Input 2

description: ChIRP-Seq

data_processing:
After the sequencing platform generated the sequencing images, the stages of image analysis and base calling were performed using Off-Line Basecaller software (OLB V1.8).
After passing Solexa CHASTITY quality filter, the clean reads were aligned to mouse genome (UCSC mm10) using BOWTIE software (V2.1.0).
peak calling of the ChIRP regions using MACS V1.4.0. Statistically significant ChIRP-enriched regions (peaks) were identified by comparison to input, using a p-value threshold of 10-5.
The peaks in samples were annotated by the nearest gene using the newest UCSC RefSeq database
Genome_build: mm10
Supplementary_files_format_and_content: bed

source_name: Kidney podocyte

growth_protocol: Temperature Sensitive SV40-T antigen Immortalized podocytes were cultured first at 33 degrees in RPMI-1040 supplemented with 10% FBS and 1% Antibiotics, cells were thermoswitched to 37 degrees to induce differentiation and cultured for 10 days in DMEM (1g glucose/L) supplemented with 5% FBS and 1% Antibiotics.

extract_protocol:
Gluteraldehyde crosslinked cells were subjected to nuclear extraction protocol and nuclei were subjected to sonication by BioRuptor. 1% Input Chromatin was set aside and Chromatin was incubated with biotynilated Tug1-Even or Tug1-Odd oligos, DNA was reverse-crosslinked and purified by ethanol precipitation.
10 ng of DNA samples were prepared for Illumina sequencing as the following steps: 1) DNA samples were blunt-ended with T4 DNA polymerase and Klenow polymerase; 2) a dA base was added to the 3' end of each strand by Klenow (exo minus) polymerase; 3) Illumina's genomic adapters were ligated to the DNA fragments; 4) PCR amplification was performed to enrich ligated fragments; 5) Enriched product of ~200-400bp was cut out from gel and purified with QIAquick Gel Extraction Kit. The completed libraries were quantified by Agilent 2100 Bioanalyzer. The libraries were denatured with 0.1 M NaOH to generate single-stranded DNA molecules, captured on Illumina flow cell, amplified in situ. The libraries were then sequenced on the Illumina HiSeq 2000 following the TruSeq Rapid SBS Kit protocol.

value: Kidney podocyte

tag: immortilization

value: SV40-Temperature Sensitive T-Antigen Immortalized

tag: passage


title: gDNA-Input 1

description: ChIRP-Seq


title: HEPG2_ChIP_NIPBL_A301-779A_NA_NA_Rep2

value: NIPBL (Bethyl, A301-779A, lot:3)


title: Odd-Tug1-PD1

description: ChIRP-Seq


title: Even-Tug1-PD2

description: ChIRP-Seq


title: HEPG2_ChIP_WCE_NA_NA_NA_Rep2


title: HEPG2_ChIP_NIPBL_A301-779A_NA_NA_Rep1


title: KL1_LKB1_cDNA

city: Cambridge

first: Rahul

last: Karnik

state: MA

address: 419 Broadway

data_processing:
Reads aligned to human genome with tophat version 2.0.8 using mm9 gene annotation and default settings.
Aligned reads processed to Fragments Per Kilobase of exon per Million fragments mapped (FPKM) using cufflinks version 2.1.1 (http://cufflinks.cbcb.umd.edu/index.html) with the -G flag to use the hg19 reference annotation to estimate isoform expression and not assemble novel transcripts.
Genome_build: mm9
Supplementary_files_format_and_content: genes.fpkm_tracking files are tab delimited text files output by cufflinks in a generic FPKM tracking format with estimated gene-level expression values in the form of FPKM values

growth_protocol: Primary pancreatic ductal epithelial cells were isolated from two LSL-KRASG12D/+ or two LSL-KRASG12D/+;LKB1L/L mice as follows: In brief, mice were euthanized and the pancreata were rapidly collected, followed by microscopy-assisted removal of the bile duct. Tissues were washed once in PBS, suspended in 3-5 ml of 2 mg/ml collagenase in DMEM:F12 (filter sterilized) and incubated at 37oC for 15 min with rigorous agitation. 7-10 ml of PBS was added to each tube, the homogenate was left to settle for 5 min at room temperature and the supernatant containing mainly acinar cells was discarded. The remaining tissue was transferred in 6 cm plates, mechanically dissociated with blades/scissors, transferred to a new tube, suspended in 2 ml freshly prepared dispase solution (4 mg/ml in PBS, filter sterilized) and incubated at 37oC for 8-10 min with agitation. Dispase was inactivated by addition of 10 ml G solution (sterile HBSS, 0.9 μg/L Glucose, 1X Pen/Strep). To capture the largely intact ductal structures and clear out dissociated acinar cells, homogenate was filtered through a 100 μm strainer that retained only the ducts. After washing with G solution, ducts were recovered by inverting the strainer and washing it with 50 ml G solution followed by gently pelleting by centrifugation at 1000 rpm for 1 min. Supernatant was aspirated and ducts were washed twice more with 50 ml G solution each time. After the last wash, pellet was suspended in 2 ml trypsin, incubated for 5 min at room temperature then trypsin was inactivated by addition of 10 ml DMEM+10% FBS+1X Pen/Strep. Cells were collected by centrifugation, washed twice in ductal media (DMEM:F12, 5 mg/ml Glucose, 1.22 mg/ml nicotinamide, 5 nM 3,3,5-tri-iodo-L-thyronine, 1 μM Dexamethasone, 100 ng/ml cholera toxin, 5 ml/L ITS+, 1X Pen/Strep, 0.1 mg/ml trypsin inhibitor, 20 ng/ml mouse EGF, 5% NuSerum IV and 25 μg/ml bovine pituitary extract) and plated. To activate KRAS and/or delete LKB1 cultures were infected with Ade-CreGFP (1-5x106 pfu/ml) leading to generation of K and KL cells.

extract_protocol:
Cells were washed twice with ice cold PBS and collected in Trizol.
RNA libraries we prepared using the Illumina TruSeq RNA library V2 prep kit (cat no# RS-122-2001) using 1ug of total RNA

tag: strain background

tag: genotype/variation

value: LSL-KRASG12D/+;LKB1L/L (KL)

value: pancreas

value: Primary Pancreatic Ductal Epithelial Cells

tag: transduced with

value: full length LKB1 cDNA (rescue)


title: KL2_rep_2


title: KL2_rep_1


title: Even-Tug1-PD1

description: ChIRP-Seq


title: HEPG2_ChIP_SMC1_A300-055A_NA_NA_Rep1


title: GC138

data_processing:
Sequence reads were trimmed by 5bp at each end and aligned to the mouse genome (mm9) using bsmap.
CpG level methylation calls were calculated using mcall from the MOABS package.
Genome_build: mm9
Supplementary_files_format_and_content: chrom,start,end,ratio,totalC,methC,strand,next,Plus,totalC,methC,Minus,totalC,methC

source_name: KL_primary pancreatic ductal epithelium

extract_protocol: 200 ng of genomic DNA was fragmented using a Covaris S2 for 6 min according to the following program: duty cycle 5%; intensity 5; cycle per burst 200. The sheared DNA was purified using the DNA Clean & Concentrator kit from Zymo Research per the manufacturer’s recommendations. Bisulfite conversion of DNA was then conducted using the EZ DNA Methylation-Gold kit (Zymo Research) followed the instructions, eluting to 15 μl low TE buffer. To minimize continual loss during storage, the converted DNA was immediately processed for generating WGBS libraries using the Accel-NGS Methyl-Seq DNA library kit (Swift Biosciences) following the manufacturer’s protocol.

value: KRASG12D/+;LKB1-/- (KL)


title: K2_rep_2

source_name: KRASG12D/+ (K) 2

value: LSL-KRASG12D/+ (K)


title: db/m glom rep 2

value: non-diabetic, normal control

value: heterozygous mutation in Leptin receptor (db)


title: HEPG2_ChIP_WCE_NA_NA_NA_Rep1


title: KL2_LKB1_cDNA


title: GC137


title: KL1_rep_2


title: K2_rep_1


title: K1

source_name: KRASG12D/+ (K) 1


title: GC130

source_name: K_primary pancreatic ductal epithelium

value: KRASG12D/+ (K)


title: Odd-Tug1-PD2

description: ChIRP-Seq


title: GC131


title: Mouse Decidua OMLPS 48

city: Subiaco

first: Anthony

last: Bosco

state: WA

address: 100 Roberts Road

country: Australia

institute: Telethon Kids Institute

data_processing:
Illumina CASAVA pipeline version 1.8.2 was used for basecalling.
Sequencing reads were aligned to the reference genome (mm10) employing Subread, and summarized at the gene level using featureCounts, with Entrez gene annotation.
Differentially expressed genes were identified from gene-level counts employing edgeR.
Coexpression network analysis was performed on VST transformed counts (varianceStabilizingTransformation, DESeq2 package).
Genome_build: mm10
Supplementary_files_format_and_content: Data are provided as raw gene-level counts, and DESeq2 VST transformed counts

source_name: Decidua

extract_protocol:
Total RNA was extracted employing TRIzol followed by RNeasy
Libraries were prepared according to Illumina's TruSeq Stranded mRNA Protocol (RS-122-2101) at the Australian Genome Research Facility. Libraries were sequenced on the HiSeq 2500 with 50 bp single reads following the manufactures protocols.

tag: strain

value: Balb/c

value: Decidua

tag: treatment

value: OM85 pretreat plus LPS challenge

value: Gestational day 17.5


title: HEPG2_ChIP_MED1_A300-793A_NA_NA_Rep1

tag: cell line

value: HEPG2 (ATCC, HB-8065)

value: Hepatocellular carcinoma-dirived cells

value: MED1 (Bethyl, A300-793A, lot:2)


title: Mouse Decidua OMLPS 47

tag: tissue


title: KL1_rep_1


title: Mouse Decidua LPS 40

value: LPS challenge


title: Mouse Decidua LPS 42


title: Mouse Decidua LPS 41


title: Mouse Decidua OMLPS 46


title: Mouse Decidua OMLPS 44


title: Mouse Decidua OMLPS 45


title: Mouse Decidua OMLPS 43


title: Mouse Decidua LPS 38


title: Mouse Decidua LPS 39


title: Mouse Decidua Control 36

value: sham control


title: Mouse Decidua LPS 37


title: GEF_AZ1366_4

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 v1.4.1 using default settings
expression levels: Cufflinks v1.3.0 and cuffdiff using default settings
Genome_build: hg19 (Ucsc)
Supplementary_files_format_and_content: text file with FPKM values

source_name: NSCLC cell lines (HCC4006)

growth_protocol: HCC4006 were provided by Drs. John Minna and Adi Gazdar (University of Texas Southwestern Medical School, Dallas, USA) and were submitted for fingerprint analysis to verify their authenticity relative to established sources.  All cell lines were routinely cultured in RPMI-1640 growth medium supplemented with 10% fetal bovine serum at 37 °C 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: Cells were plated at 25% confluency, then grown for 24 hours without treatment.  Treatment with gefitinib (100 nM), AZ1366 (100 nM) or a combination thereof (100 nM each) took place for 24 hours.  Cells were trypsinzed and immediately flash frozen for downstream RNA analysis.

value: NSCLC

value: Gefitinib and AZ1366 treated


title: Mouse Decidua Control 34


title: Mouse Decidua Control 35


title: N_oNT_10

city: Baton Rouge

first: J. Michael

last: Salbaum

state: LA

address: 6400 Perkins Road

department: Regulation of Gene Expression

institute: Pennington Biomedical Research Center

data_processing:
Conversion of SOLiD 5500 XSQ files to csfasta/qual files was performed using perl and bash shell scripts that were developed in-house. These scripts make use of Life Technologies XSQ conversion tools, version 1.5.
alignment of sequence tags back to a reference genome was performed using a modified version of the Applied Biosystems SOLiD™ SAGE™ Analysis Software v1.10 that was developed in-house.
Filtering non-unique tags, and establishing counts per RefSeq gene was performed using a modified version of the Applied Biosystems SOLiD™ SAGE™ Analysis Software v1.10 that was developed in-house.
Genome_build: The following version of RefSeg RNA was used for mapping sequence tags: Mouse (mm9): ftp://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/ARCHIVE/BUILD.37.2/RNA/rna.fa.gz
Supplementary_files_format_and_content: processed data files contain the counts per gene for 26608 mouse RefSeq genes

source_name: E8.5 embryo, neural tube at anterior boundary of closure 1

growth_protocol: Diabetic and normal dams were mated, and the morning where presence of a vaginal plug was detected was designated as day 0.5 of gestation. Pregnant dams were single housed, and embryos were prepared at 8.5 days of gestation.

extract_protocol:
Total RNA was prepared using Trizol, RNA concentration was determined on a Qbit fluorometer, and 7ng RNA per sample was used for sequencing library construction.
Libraries were prepared using the Applied Biosystems SOLiDSAGE kit, according to AB's instructions for the SOLiD 4 System (except a 1:100 of Adaptor B dilution was used).
SOLiD SAGE Kit with Barcoding Adaptor Module (#4452811) and SOLiD RNA Barcode Kit (#4427046)

treatment_protocol: Cryosections of embryos at 8.5 days of gestation were used to prepare neural tube tissue by Laser microdissection. The anterior boundary of neural tube closure site 1 was determined and used as reference point to collect sections immediately anterior (open neural tube) and immediately posterior (closed neural tube) of closure site 1

value: FVB

tag: neural tube

value: open

tag: disease state

value: normal


title: S046

description: Sample 18

value: inbred line

value: whole seedling

value: 7 days after germination


title: GEF_AZ1366_2

tag: cell type


title: Mouse Decidua Control 33

value: Balb/c


title: N_cNT_12

value: closed


title: Mouse Decidua Control 32

value: Decidua


title: AZ1366_4

value: AZ1366 Treated


title: Mouse Decidua OM 29

value: OM85 pretreatment

value: Gestational day 17.5


title: D_oNT_14

value: diabetic


title: Mouse Decidua Control 31


title: N_oNT_09


title: AZ1366_3


title: AZ1366_2


title: Mouse Decidua OM 30


title: Mouse Decidua OM 26


title: N_cNT_11


title: D_oNT_13


title: Mouse Decidua OM 28


title: D_cNT_15


title: GEF_2

value: Gefitinib Treated


title: D_cNT_16


title: AZ1366_1


title: GEF_AZ1366_3


title: GEF_AZ1366_1


title: Mouse Decidua OM 27


title: GEF_3


title: GEF_4


title: Mouse Uterus OMLPS 23

source_name: Uterus

value: Uterus

value: OM85 pretreat plus LPS challenge


title: Mouse Uterus OMLPS 22


title: CTRL_3

value: NSCLC

value: DMSO


title: CTRL_4


title: GEF_1


title: Mouse Uterus OMLPS 20


title: Mouse Uterus OMLPS 24


title: CTRL_2


title: Mouse Uterus OMLPS 19


title: CTRL_1


title: Mouse Decidua OM 25


title: Mouse Uterus LPS 17

value: LPS challenge


title: Mouse Uterus LPS 16


title: Mouse Uterus LPS 13


title: Mouse Uterus LPS 15


title: CL3_DEX

city: Bristol

first: Lulu

last: Jiang

state: State...

address: Academic Renal Unit,Dorothy Hodgkin Building,Whitson Street

department: School of Clinical Sciences

institute: University of Bristol

data_processing:
The raw data was processed using Illumina software, RTA 1.17.21.3 with default filter and quality settings.
The reads were demultiplexed with CASAVA 1.8.2.
Read alignment is performed using Tophat. We use HTSeq to generate read counts, using the ENSEMBL GRCh37  annotations for reference.
Genome_build: GRCh37
Supplementary_files_format_and_content: csv file with raw read counts

source_name: Podocytes derived from human kidneys_dexamethasone

growth_protocol: Conditionally immortalized human podocytes were established from three healthy kidney transplant donors. Cells were grown to 70%-80% confluence at 33 Celsius degree in 5% CO2 before thermo-switching to 37 Celsius degree in 5% CO2 and allowed to differentiate for 10 days.

extract_protocol:
Total RNA was extracted from PBS and dexamethasone-treated podocytes using the TRIzol method. RNA samples were then subjected to DNase treatment (Ambion TURBO DNase, Life Technologies) and purification (RNeasy Mini Kit, QIAGEN) according to the manufacturer’s instructions.
The cDNA library preparation and the sequencing were performed following manufacturer’s instructions at the Bristol Genomics Facility, University of Bristol. Briefly, approximately 1μg of purified total RNA was prepared for sequencing using the Illumina TruSeq mRNA Seq v2 kit.  Sequencing of 100bp paired-end reads was performed with the Illumina HiSeq 2500 instrument.

treatment_protocol: Differentiated cells were then treated with PBS or 0.1μM dexamethasone (Sigma–Aldrich) for 24 hours, then subsequently used for RNA extraction and sequencing.

value: Podocytes

value: kidney


title: CL3_CON

source_name: Podocytes derived from human kidneys_control


title: CL2_DEX


title: CL2_CON


title: CL1_CON


title: CL1_DEX


title: Mouse Uterus OM 11


title: Mouse Uterus OM 12