title: healthy control  patient neural crest cells_1

first: Jeffrey

last: Zhao

address: 1275 York Avenue

department: Genomics Core

data_processing:
The output data (FASTQ files) are mapped to the target genome using the rnaStar aligner [Dobin2012] that maps reads genomically and resolves reads across splice junctions.  We use the 2 pass mapping method outlined in [Engström2013] in which the reads are mapped twice. The first mapping pass uses a list of known annotated junctions from Ensemble. Novel junctions found in the first pass are then added to the known junctions and a second mapping pass is done.
After mapping we compute the expression count matrix from the mapped reads using HTSeq (www-huber.embl.de/users/anders/HTSeq) and one of several possible gene model databases.
The raw count matrix generated by HTSeq are then be processed using the R/Bioconductor package DESeq (www-huber.embl.de/users/anders/DESeq) which is used to both normalize the full dataset and analyze differential expression between sample groups.
Program versions: htseq/HTSeq-0.5.3, picard/picard-tools-1.124, R/R-3.2.0, star/STAR-STAR_2.5.0a, samtools/samtools-0.1.19
Genome_build: UCSC HG19
Supplementary_files_format_and_content: Raw and normalized read count data.

source_name: PSC-derived neural crest

growth_protocol: PSC differentiation protocol published in Zeltner et a., Journal of Visual Experimentation 2014

extract_protocol:
Cells were FACS sorted and frozen in Tryzol
RNA samples are used for Hi-Seq library construction with the TruSeq RNA Sample Prep Kit v2 (Illumina) following the manufacturer’s instructions. Samples are barcoded with TruSeq SBS Kit v3 (Illumina).

value: PSC-derived neural crest

tag: disease state

value: healthy control


title: healthy control  patient neural crest cells_3

status: Public on Nov 14 2016

type: SRA

city: New York

state: NY

country: USA

institute: Memorial Sloan Kettering Cancer Center

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell type


title: mild  patient neural crest cells_3

value: mild familial dysautonomia


title: healthy control  patient neural crest cells_2


title: NOMe-seq_Mouse_E11.5_PGC_rep2

city: Hangzhou

first: Hongshan

last: Guo

state: Zhejiang Province

address: No.1369, Wenyixi Road

department: School of Medicine, Zhejiang University

country: China

institute: Liangzhu Laboratory

description:
library strategy: NOMe-seq
bisulfite converted DNA

library_source: genomic

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Reads were trimmed to remove the adapter sequences and low quality bases.
For NOMe-seq, bisulfte-converted reads were first alignned to the hg19 or mm9 refference using Bismark (v0.7.6), and unique mapped reads were retained to calculate the endogenous DNA methylation information, and also to deduce the chromatin accessbility at the same DNA molecule. FOr RNA-seq, sequencing reads were first aligned to the hg19 or mm9 refference using Tophat, and the expression level of protein-coding genes was quantified using cufflinks tool.
Genome_build: hg19, mm9
Supplementary_files_format_and_content: bigWig file which contains the DNA methylation level of cytosine on WCG and GCH context, while .txt files contain the FPKM values of all the protein-coding genes in mouse and human.

molecule: genomic DNA

organism: Mus musculus

extract_protocol:
For NOMe-seq, nuclei DNA was extracted using the Genomic DNA Clean & Concentrator™-10 Kit (Zymo Research), while for bulk RNA-seq, the total RNA was isolated using the Rneasy Mini kit (Qiagen), for single cell RNA-seq, the RNA was released after the single cell was picked into the lysis buffer.
For NOMe-seq, the nuclei was first treated with the GpC methyltransferase (M.CviPI), and the isolated DNA was bisulfite converted using MethylCode Bisulfite Conversion Kit (ThermoFisher), and NOMe-seq library was constructed using PBAT protocol.The single cell RNA-seq was performed using the protocol we developed in 2009 (Tang et al, 2009), while the bulk RNA-seq was performed using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina.

value: primordial germ cell

tag: age

tag: gender

value: unknown

tag: oct4-gfp knock-in (yes or no)

value: yes

tag: bulk or single cell

value: bulk


title: NOMe-seq_Mouse_E11.5_PGC_rep1


title: brain_input_DNA_R2

city: Paris

first: Yuvia

middle: Alheli

last: Perez Rico

address: 26 rue d'Ulm

country: France

institute: Institut Curie

description:
Processed data file: adult_brain_H3K27ac_drerio_super_enhancers.bed
Processed data file: adult_brain_H3K27ac_drerio_typical_enhancers.bed
Processed data file: adult_brain_drerio_H3K27ac_normalized.wig

data_processing:
Basecalls were performed using CASAVA.
ChIP-seq reads were aligned to the Zv9 genome assembly using Bowtie2-2.1.0 configured for global alignment and allowing 1 mismatch in the seed alignment (seed size = 22). If a read aligned more than once in the genome, only the alignment with the best score was saved for further analyses. Aligned reads were saved in BAM format using samtools (version 0.1.8).
BAM files from biological replicates were merged with samtools and converted to BED format with bedtools (v2.24.0).
Peak calling was performed using SICER (V1.1) with the following parameters: redundancy threshold = 1, window size = 200, fragment size = 175 or 200, effective genome fraction = 0.7, gap size = 600 and FDR = 0.05.
After peak calling, peaks were discarded if 50% of the peak overlapped with the regions comprising 2 Kb upstream and 2 Kb downstream of TSSs (based on RefSeq annotations) and if the peak summit was within these regions.
To identify typical enhancers and super-enhancers, the ROSE algorithm was applied (Whyte et al. 2013; Lovén et al. 2013), setting the -t parameter to 2000.
Genome_build: Zv9
Supplementary_files_format_and_content: BED files with annotations for typical enhancers and super-enhancers were generated using ROSE. Scores represent the H3K27ac density in each enhancer region.
Supplementary_files_format_and_content: WIG file with the H3K27ac profile generated by SICER and normalized by library size per million.

organism: Danio rerio

source_name: Adult brain, input

extract_protocol:
Whole brains, hearts, intestines and testis were dissected from adult male AB zebrafish (brains, hearts and testis = 10-month-old; hearts and intestines = 1-year-old). Two biological replicates were prepared from brain, heart (1-year-old), intestine and testis, whereas one biological replicate was prepared from 10-month-old heart. Each biological replicate was prepared using: 12 brains, 20 hearts, 5 intestines and 8 testis. All tissues were homogenized and cross-linked in 1% formaldehyde, washed and lysed. Chromatin was sheared using a Covaris S220 ultrasonicator to a DNA fragment size of 175 bp (10-month-old samples) or 200 bp (1-year-old samples). ChIP-seq was performed as previously described (Guenther et al. 2008) using 5 ug Abcam H3K27ac antibody (ab4729, lot# GR259887-1) bound to Dynal Protein A linked beads (Invitrogen). Reverse cross-linked and phenol:chloroform purified chromatin was used for single-end library preparation following standard Illumina protocols.
DNA fragments with an average size of 175 bp or 200 bp were used for single-end library preparation following standard Illumina protocols.

tag: strain/background

value: AB

tag: genotype/variation

value: wild type

tag: Sex

value: male

value: adult

tag: tissue

value: brain

tag: chip antibody


title: brain_input_DNA_R1


title: brain_H3K27ac_ChIP-seq_R2

source_name: Adult brain, H3K27ac ChIP


title: mild  patient neural crest cells_2


title: #10_137

first: Barbara

last: Spitzer

address: 411 E 67th St

data_processing:
ChIP-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned using Bowtie2 version 2.1.0 with the default parameters.
To create density files, the reads were extended to 200 bp, the signal was then normalized to ten million mapped reads and converted to BigWig using BEDTools.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files containing read densities normalized to 10 million reads

source_name: MEF

growth_protocol: MEFs were grown in DME supplemented with 10% FCS, 4.5 g/L glucose, NEAA, and pen/strep, and passaged every 2-3 days

extract_protocol: ChIP-seq was performed as described (Deshpande et al 2014 Cancer Cell).  1-2×106 MEF cells were crosslinked using 1% formaldehyde, washed in 1 mL of wash buffer (20 mM Tris pH8.0, 167mM NaCl, 5mM EDTA, 1% SDS) and lysed in lysis buffer (20 mM Tris pH8.0, 167mM NaCl, 5mM EDTA, 0.66% SDS, 1% Triton X-100).  Chromatin was sheared to 200-400 bp using Covaris E220 sonicator and used for chromatin immunoprecipitation (ChIP) with Dnmt3a-specific antibodies ab13888 mouse mAbs and ab2850 rabbit pAbs  (Abcam) and Protein-A (Life Technologies) magnetic beads.  After washing, the immune complexes were eluted and DNA fragments recovered after de-crosslinking at 65°C for 4 hours and used for TruSeq libraries generated using NEBNext kit (New England BioLabs).  Libraries were sequenced using HiSeq2500 (Illumina) to generate approximately 4×107 single end (SE)50 reads per sample.

treatment_protocol: Cre-mediated recombination was carried out by retroviral transduction in SV40 large T-antigen-immortalized MEFs

value: Dnmt3a (Abcam ab2850, rabbit)

tag: strain

tag: genotype


title: #10_120

value: Dnmt3a (Abcam ab13888, mouse)


title: mild  patient neural crest cells_1


title: #16_137


title: brain_H3K27ac_ChIP-seq_R1


title: severe  patient neural crest cells_2

value: severe familial dysautonomia


title: #16_120


title: severe  patient neural crest cells_1


title: #11_137


title: #41-TKDA3-4 iPSC diff-1_RNA-seq

city: Stanford

first: Andrew

last: Gentles

state: CA

address: 1201 Welch Road

institute: Stanford University

description: Sample name: s40.S21.diff_iPS

data_processing:
Expression levels of genes were quantified using Sailfish (Patro et al., 2014), with Illumina iGenomes reference transcriptome based on the UCSC known genes annotation, and hg19 as the reference human genome (ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Homo_sapiens/UCSC/hg19/Homo_sapiens_UCSC_hg19.tar.gz)
TPMs were summed for gene-level quantification. TPM values were transformed using a moderated log function: log2(1+TPM)
Genome_build: hg19
Supplementary_files_format_and_content: log2 (1+TPM)

source_name: Diff normal iPS line_TKDA3 cell line

extract_protocol:
Total RNA from different cell populations was isolated using RNAeasy Micro kit (Qiagen) as per manufacturers recommendations.
50 ng of total RNA was used as input for cDNA preparation and amplification using Ovation RNA-Seq System V2 (NuGEN). 500 ng of sheared and size-selected cDNA were used as input for library preparation using NEBNext Ultra DNA Library Prep Kit for Illumina (New England BioLabs) as per manufacturer’s recommendations

value: Diff normal iPS line

tag: subject

value: TKDA3 cell line


title: #11_120


title: #39-JMC1 iPSC diff-1_RNA-seq

description: Sample name: s39.S20.diff_iPS

source_name: Diff normal iPS line_JMC1 cell line

value: JMC1 cell line


title: testis_H3K27ac_ChIP-seq_R1

description:
Processed data file: adult_testis_H3K27ac_drerio_super_enhancers.bed
Processed data file: adult_testis_H3K27ac_drerio_typical_enhancers.bed
Processed data file: adult_testis_drerio_H3K27ac_normalized.wig

source_name: Adult testis, H3K27ac ChIP

value: testis


title: cKI_Mx_pos_830

data_processing:
Raw reads were aligned to the mm10 genome using STAR RNA-seq aligner (v.2.3.0e) with default parameters
Counts per gene were computed using HTSeq count v0.5.3p3 using the "intersection-nonempty" parameter
Differential expression analysis was performed with the R Bioconductor DESeq2 package using default parameters
Genome_build: mm10, ENSEMBL Mus_musculus.GRCm38.75
Supplementary_files_format_and_content: Normalized count tables as computed by DESeq2

source_name: bone marrow

extract_protocol:
bone marrow was extracted from femurs, tibiae and iliac crests. After red blood cell lysis and magnetic lineage depletion cells were FACS-sorted to isolate Lin- Sca1+ cKit+ (LSK) cells. Total RNA was extracted using AllPrep Kit (Qiagen)
Libraries were constructed using TruSeq Stranded Total RNA with Ribo-Zero Gold from Illumina

treatment_protocol: Mx1-driven Cre-mediated recombination was induced by 5 IP injections of poly(I:C)

value: LSK


title: #38-H7 ES diff-2_RNA-seq

description: Sample name: s38.S19.diff_ES

source_name: Diff normal ES line_H7 cell line

value: Diff normal ES line

value: H7 cell line


title: wt_Mx_pos_825


title: cKI_Mx_pos_824


title: cKI_Mx_pos_829


title: cKI_Mx_pos_827


title: wt_Mx_pos_823


title: wt_Mx_pos_820


title: #36-SU223T-6_RNA-seq

description: Sample name: s34.SU223T.6.CAGATC_S4

source_name: Undiff T-cell iPS_SU223

value: Undiff T-cell iPS


title: #33-SU042T-5_RNA-seq

description: Sample name: s36.SU042T.5.GGCTAC_S6

source_name: Undiff T-cell iPS_SU042


title: #37-SU223T-3_RNA-seq

description: Sample name: s31.SU223T.3.ATCACG_S1


title: RNAseq Double LKO Rep3

city: Boston

first: Manashree

last: Damle

state: MA

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

data_processing:
RNAseq reads were aligned using RUM
Normalized counts and differential gene expression were calculated using edgeR
Genome_build: mm9
Supplementary_files_format_and_content: excel file with edgeR output (normalized counts and differential gene expression)

source_name: Mouse liver

extract_protocol:
For gene expression, total RNA were extracted with TRIzol following standard procedures.
Following cDNA generation with High-Capacity cDNA RT kit (Applied Biosystems), RNA sequencing libraries were prepared from 1 μg total RNA using the TruSeq RNA Sample Preparation Kit v2 (Illumina) according to manufacturer’s protocol.

treatment_protocol: Mice were injected with indicated AAV8 and sacrificed 10 days later under ad lib fed conditions. Livers were harvested and flash frozen.

value: HDAC3/SCAP floxed

value: Cre

value: Liver


title: cKI_Cre_neg_819


title: #31-SU042T-2_RNA-seq

description: Sample name: s35.SU042T.2.GATCAG_S5


title: RNAseq Double LKO Rep2


title: S_aureus_SH1000_sigB

city: Tampa

first: Andy

last: Weiss

state: Florida

address: 4202 East Fowler Avenue, ISA2015

department: Department of Cell Biology, Microbiology and Molecular Biology

institute: University of South Florida

description:
total RNA, rRNA-depleted
SH1000_WT_vs_sigB.xlsx

data_processing:
Raw data files (.fastq) were imported into the CLC Genomics Workbench software platform for analysis
Expression values for coding genes as well as sRNA track were caculated using the "RNA-Seq Analysis" function in CLC Genomics Workbench
Samples were compared using "Set Up Experiment" tool for transcriptomic analysis and standardized via quantile normalization using CLC Genomics Workbench
Expression values were exported into excel files
Genome_build: The S. aureus NCTC 8325 genome file was accessed from GenBank (Accesion number:NC_007795)
Supplementary_files_format_and_content: Expression values calculated for each gene are presented as RPKM values in excel format

organism: Staphylococcus aureus

source_name: Bacterial cells, pelleted

growth_protocol: Strains were grown in TSB medium at 37°C with shaking

extract_protocol:
Total bacterial RNA was isolated utilizing the Qiagen RNeasy mini kit and contaminating DNA was removed by treatment with Ambion DNA-free
Library construction was performed using the Ion Total RNA-Seq v2 Kit from Life Technologies

treatment_protocol: Samples were stored at -80°C prior to RNA extraction

tag: growth medium

value: TSB

tag: growth conditions (time/temp/shaking)


title: RNAseq SCAP LKO Rep4

value: SCAP floxed


title: #30-TKDA3-4 iPSC_RNA-seq

description: Sample name: s30.TKDA3.4iPSC_S23

source_name: Undiff iPS line_TKDA3 cell line

value: Undiff iPS line


title: #29-JMC1 iPSC_RNA-seq

description: Sample name: s29.JMC1iPSC_S22

source_name: Undiff iPS line_JMC1 cell line


title: S_aureus_SH1000_WT

value: wild-type


title: #43-WT3 iPSC diff-1_RNA-seq

description: Sample name: s41.S22.diff_iPS

source_name: Diff normal iPS line_WT3 cell line

value: WT3 cell line


title: #28-WT3 iPSC_RNA-seq

description: Sample name: s28.WT3iPSC_S21

source_name: Undiff iPS line_WT3 cell line


title: RNAseq SCAP LKO Rep3


title: #27-H1 ES_RNA-seq

description: Sample name: s27.H1ES_S20

source_name: Undiff ES line_H1 cell line

value: Undiff ES line

value: H1 cell line


title: RNAseq SCAP LKO Rep2


title: S_aureus_[delta]rpoZ

description:
total RNA, rRNA-depleted
USA300_WT_vs_rpoZ.xlsx

data_processing:
Raw data files (.fastq) were imported into the CLC Genomics Workbench software platform for analysis
Expression values for coding genes as well as sRNA track were caculated using the "RNA-Seq Analysis" function in CLC Genomics Workbench
Samples were compared using "Set Up Experiment" tool for transcriptomic analysis and standardized via quantile normalization using CLC Genomics Workbench
Expression values were exported into excel files
Genome_build: The S. aureus USA300 FPR3757 genome file was accessed from GenBank (Accesion number:CP000255)
Supplementary_files_format_and_content: Expression values calculated for each gene are presented as RPKM values in excel format

value: USA300 Houston

value: [delta]rpoZ


title: #26-H7 ES_RNA-seq

description: Sample name: s26.H7ES_S19

source_name: Undiff ES line_H7 cell line


title: #34-SU223T-4_RNA-seq

description: Sample name: s32.SU223T.4.TTAGGC_S2


title: S_aureus_WT


title: #35-SU223T-5_RNA-seq

description: Sample name: s33.SU223T.5.ACAGTG_S3


title: #25-SU223-B3 Ms2_RNA-seq

description: Sample name: s25.SU223.B3.Ms2.ATTCCT_S6

source_name: Engrafted diff iPS from AML_SU223

value: Engrafted diff iPS from AML


title: RNAseq SCAP LKO Rep1


title: cKI_Cre_neg_780

value: LSK


title: #24-SU223-B3 Ms008_RNA-seq

description: Sample name: s24.SU223.B3.Ms008.CGTACG_S5


title: RNAseq HDAC3 LKO Rep2

value: HDAC3 floxed


title: RNAseq HDAC3 LKO Rep4


title: RNAseq HDAC3 LKO Rep3


title: D3 rep3_miRNA

city: Santa Barbara

first: William

middle: C

last: Smith

state: California

address: Biological Sciences II

department: MCDB

institute: UCSB

description: small RNA

data_processing:
Raw reads were trimmed of adapter sequences and pre-processed for base quality according to the default software specifications.
The C. intestinalis (now called robusta) JGI genome version 2.0 and Ensembl transcript models (release 83) were used as references for alignment.
miRNA libraries were aligned and quantified using miRDeep2. Counts of novel miRNA’s were extracted from the PDF files output by miRDeep2 using a custom Python script.
Genome_build: Ciona intestinalis JGI version 2.0
Supplementary_files_format_and_content: tab-delimited text file including count values for all samples

organism: Ciona robusta

source_name: Oral siphon

growth_protocol: C. robusta were collected at the the Santa Barbara Yacht Harbor. Gametes from two adults were mixed and the resulting offspring were grown to approximately 6 months of age.

extract_protocol:
Amputated siphon samples were immediately frozen in liquid nitrogen then transferred to 1 mL RNAlater-ICE (Life Technologies) and stored at -20°C for one week. Total RNA was extracted from a pool of five tissue samples for each replicate using the miRvana total RNA extraction kit (Life Technologies).
Small RNAs (approximately 18-30 bp), including miRNAs, were isolated from 1 μg of total RNA by 1% Tris/Borate/EDTA-Acrylamide gel electrophoresis. Sequencing libraries were prepared with the Total RNAseq Kit v2.0 (Life Technologies). Libraries were sequenced in multiplex using an Ion Proton sequencer from Life Technologies.

treatment_protocol: Approximately 75 sibling animals ranging in size from 5-10 cm were selected for amputation and anesthetized in 0.04% MS222 for 30 min. During time-course experiments batches of animals were housed in five gallon buckets of seawater, changed daily and maintained at 15°C with a 12/12 hour artificial light/dark cycle.

value: Oral siphon

tag: Stage

value: 3 days post amputation

value: 6 months

value: Wild type


title: D8 rep2_miRNA

description: small RNA


title: D8 rep3_miRNA

description: small RNA

value: 8 days post amputation


title: D8 rep1_miRNA

description: small RNA


title: #23-SU223-A7 Ms5_RNA-seq

description: Sample name: s23.SU223.A7.Ms5.GTGGCC_S4


title: D3 rep2_miRNA

description: small RNA

value: 1 day post amputation


title: RNAseq Double LKO Rep1

value: HDAC3/SCAP floxed

value: Cre

value: Liver


title: RNAseq HDAC3 LKO Rep1


title: #22-SU223-A7 Ms1_RNA-seq

description: Sample name: s22.SU223.A7.Ms1.GTCCGC_S3


title: #21-SU223-A7 Ms006_RNA-seq

description: Sample name: s21.SU223.A7.Ms006.CCGTCC_S2


title: #20-SU223-B3_RNA-seq

description: Sample name: s20.SU223.B3.AGTTCC_S1

source_name: Undiff iPS from AML_SU223

value: Undiff iPS from AML


title: D3 rep1_miRNA

description: small RNA


title: RNAseq Double floxed GFP Rep5

value: GFP


title: D1 rep1_miRNA

description: small RNA

value: 0 days (immediately) post amputation


title: D1 rep2_miRNA

description: small RNA


title: #19-SU223-A7_RNA-seq

description: Sample name: s19.SU223.A7_S18


title: #18-SU042-4 Ms4_RNA-seq

description: Sample name: s18.SU042.4Ms4_S17

source_name: Engrafted diff iPS from AML_SU042


title: RNAseq SCAP floxed GFP Rep3

value: SCAP floxed


title: D0 rep2_miRNA

description: small RNA


title: #17-SU042-4 Ms3_RNA-seq

description: Sample name: s17.SU042.4Ms3_S16


title: RNAseq HDAC3 floxed GFP Rep2


title: RNAseq HDAC3 floxed GFP Rep1


title: D8 rep3

data_processing:
Raw reads were trimmed of adapter sequences and pre-processed for base quality according to the default software specifications.
mRNA libraries were first aligned to the C. robusta genome and set of Ensemble transcript models using Tophat (Trapnell et al., 2009) with strict parameters (“end-to-end” mode) to accommodate spliced reads.
Reads initially not aligned by Tophat were processed using Bowtie with relaxed parameters (“local” mode) to increase the overall robustness of alignment to the highly polymorphic Ciona genome.
Counts of each transcript were prepared using HTSeq-Count (Anders et al., 2015).
Genome_build: Ciona intestinalis JGI version 2.0
Supplementary_files_format_and_content: tab-delimited text file including count values for all samples

molecule: polyA RNA

extract_protocol:
Amputated siphon samples were immediately frozen in liquid nitrogen then transferred to 1 mL RNAlater-ICE (Life Technologies) and stored at -20°C for one week. Total RNA was extracted from a pool of five tissue samples for each replicate using the miRvana total RNA extraction kit (Life Technologies).
PolyA+ RNA was isolated from 5 μg of total RNA using Dynabeads (Life Technologies). Sequencing libraries were prepared with the Total RNAseq Kit v2.0 (Life Technologies). Libraries were sequenced in multiplex using an Ion Proton sequencer from Life Technologies.

tag: regeneration stage


title: #15-SU042-4 Ms5_RNA-seq

description: Sample name: s15.SU042.4Ms5_S14


title: D8 rep2


title: #14-SU042-2 Ms954_RNA-seq

description: Sample name: s14.SU042.2Ms954_S13


title: D8 rep1


title: #13-SU042-2 Ms950_RNA-seq

description: Sample name: s13.SU042.2Ms950_S12


title: HA ChIPseq Input Pool

data_processing:
Reads were aligned using Bowtie1
Peaks were called and ucsc visualization files were made using HOMER
Genome_build: mm9
Supplementary_files_format_and_content: bigwig and peaks.bed

extract_protocol:
Lysates were clarified from sonicated cells and DNA complexes were isolated with antibody.
ChIPed DNA was amplified according to ChIP sequencing sample preparation guide provided by Illumina, using adaptor oligo primers from Illumina, enzymes from New England biolabs and PCR purification kits from Qiagen. Biological replicates were barcoded and sequenced. Deep sequencing was performed by the functional Genomics Core of the Penn Diabetes Endocrinilogy Research Center using Illumina HiSeq2000.


title: RNAseq Double floxed GFP Rep6


title: HDAC3 ChIPseq in AAV8:HA-nSREBP1c rep3

tag: antibody

value: Anti-HDAC3, ab7030, Abcam


title: #12-SU042-2 Ms3_RNA-seq

description: Sample name: s12.SU042.2Ms3_S11

value: Engrafted diff iPS from AML


title: HDAC3 ChIPseq in AAV8:HA-nSREBP1c rep2


title: #11-SU042-4_RNA-seq

description: Sample name: s11.SU042.4_S10

source_name: Undiff iPS from AML_SU042


title: D3 rep3

tag: age


title: RNAseq SCAP floxed GFP Rep4


title: HDAC3 ChIPseq in AAV8:HA-nSREBP1c rep1


title: #10-SU042-2_RNA-seq

description: Sample name: s10.SU042.2_S9


title: #8-SU223 AML Ms4_RNA-seq

description: Sample name: s8.SU223AMLMs4_S8

source_name: Engrafted primary AML_SU223

value: Engrafted primary AML


title: HDAC3 ChIPseq in AAV8:GFP rep2


title: #7-SU223 AML Ms5_RNA-seq

description: Sample name: s7.SU223AMLMs5_S7


title: D1 rep3


title: D0 rep1_miRNA

description: small RNA


title: D1 rep2


title: D1 rep1


title: HDAC3 ChIPseq in AAV8:GFP rep3


title: HDAC3 ChIPseq in AAV8:GFP rep1


title: HA ChIPseq in AAV8:HA-nSREBP1c rep2

value: Anti-HA, A2095, Sigma-Aldrich


title: #6-SU042 AML Ms4_RNA-seq

description: Sample name: s6.SU042AMLMs4_S6

source_name: Engrafted primary AML_SU042


title: D0 rep3

value: Oral siphon


title: #16-SU042-4 Ms952_RNA-seq

description: Sample name: s16.SU042.4Ms952_S15


title: #5-SU042 AML Ms2_RNA-seq

description: Sample name: s5.SU042AMLMs2_S5


title: D0 rep2


title: HDAC3 ChIPseq Input Pool

value: C57Bl/6 HDAC3 floxed


title: D0 rep1

value: 6 months


title: D3 rep2

value: 3 days post amputation

value: Wild type


title: #3-SU042 AML Ms3_RNA-seq

description: Sample name: s3.SU042AMLMs3_S3


title: D3 rep1


title: HA ChIPseq in AAV8:HA-nSREBP1c rep1


title: Trim33-deficient rep1

city: Ann Arbor

first: Vesa

middle: Matti

last: Kaartinen

state: MI

address: 1011 N. University

department: BMS

institute: University of Michigan

data_processing:
mRNA and sequencing libraries were prepared by the University of Michigan DNA Sequencing Core and single end reads generated on Illumina HiSeq2000.
After quality assessment per sample, single-end, 52 base pair reads were aligned to mm9 (Mus musculus assembly July 2007) using STAR RNA Seq aligner (Dobin et al., 2013).
Genome_build: mm9 (Mus musculus assembly July 2007)
Read counts for differential expression were obtained using HTSeq program. Differential expression analyses were performed using the DESeq program in R Statistical Package. https://bioconductor.org/packages/3.3/bioc/vignettes/DESeq/inst/doc/DESeq.pdf.
Supplementary_files_format_and_content:
DESeq_results.txt: differentially expressed genes p<=0.05; *count.txt; raw counts from HtSeq

source_name: Trim33-deficient _Embryoid bodies_day7 in differentiation

growth_protocol: ES cell lines were established from mouse embryos, which were homozygous for the Trim33-flox allele and carried the UbcCreERT2 transgene. Cells were culutured without feeder cells in the presence of LIF and 2i. Embryoid bodies were generated using the ATCC protocol on low attachment dishes under differentiating conditions. EBs were harvested at day 7.

extract_protocol:
Equivalent amounts/number of embryoid bodies (EBs) were collected at Day 7, comprising control and Trim33-deficient (n=2 independent pairs), in 100-200 μl commercially available (Qiagen) RLT buffer. Total RNA was isolated using Qiagen RNeasy Mini Kit Cat. No 74104.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Trim33-deficiency was induced with 4OH-Tamoxifen on day 4.

value: outbred

tag: source cell line

value: embryonic stem (ES) cell line

tag: passages

value: embryoid bodies

tag: time point

value: day7 in differentiation


title: Trim33-deficient rep2


title: #4-SU042 AML Ms1_RNA-seq

description: Sample name: s4.SU042AMLMs1_S4


title: NR rep2

value: Non-regenerating


title: NR rep3


title: #1-SU042 AML_RNA-seq

description: Sample name: s1.SU042.AML_S1

source_name: Primary AML_SU042

value: Primary AML


title: Control rep1

source_name: control_Embryoid bodies_day7 in differentiation

value: wild type


title: NR rep1


title: Delta.2

status: Public on Nov 13 2016

city: Maastricht

first: Kasper

last: Derks

state: Limburg

address: P. Debyelaan 25

department: Clinical Genetics

country: Netherlands

institute: Maastricht University Medical Center

data_processing:
Alignment to the mouse genome using TopHat (version 1.3.1.Linux_x86_64, --coverage-search, -butterfly-search, --segment-mismatches 1, --segment-length 18)
SAMMate was used to detect and quantify transcripts
Differentially expressed genes were detected using the R package EdgeR
Genome_build: mm9
Supplementary_files_format_and_content: The processed data contains a tab delimited text file; containing the RefSeq identifiers for the genes; read counts aligning to the exonic regions of the gene per sample; log2 fold changes; p.value ;FDR values.

source_name: ventral mesencephalic area_Ercc1 delta/+

growth_protocol: Generation and characterization of NER mutants Ercc1 delta/+ mice has been previously described (Weeda et al 1997). Ercc1 delta/+ mice were generated in an FVB:C57BL/6J (50:50) genetic background. Animals were kept on a regular diet and housed at the Animal Resource Center (Erasmus University Medical Center), which operates in compliance with the “Animal Welfare Act” of the Dutch government, following the “Guide for the Care and Use of Laboratory Animals” as its standard.

extract_protocol:
Animals were sacrificed by cervical dislocation and brains were rapidly excised on an ice-cold plate. Total RNA was isolated from the ventral mesencephalic area of the mouse brain using the RNAqueous Kit (Ambion) according to manufactures directions. Briefly, ventral midbrain tissues were homogenized in RNA lysis buffer and stored at -80 degrees until the extraction procedure. RNA quality was assessed via the BioAnalyzer machine (Agilent 2100). Only samples with a RIN greater than 8 were used for further processing.
Total RNA was used for the messenger RNA sequencing sample preparation using the TruSeq mRNA sample preparation kit (Illumina) according to the manufacturer's protocols. Briefly, 1ug of total RNA for eacht sample was used for poly(A) RNA selection using magnetic beads coated with poly-dT, followed by thermal fragmentation. The fregmented poly(A) RNA enriched samples were subjected to cDNA synthesis using Illumina TruSeq preperation kit according to the manufacturer's protocol. Briefly, cDNA was synthesized by reverse transcriptase (Super-Script II) using poly-dT and random hexamer primers. The cDNA fragments were then blunt-ended through an end-repair reaction, followed by dA-tailing, Subsequently, specific double-stranded bar-coded adapters were ligated and library amplification for 15 cycles was performed. Pooled cDNA libraries, consisting of equal concentration bar-coded samples (wt and Ercc delta/+ samples), were sequenced in one lane on the HiSeq2000 (Illumina).

value: brain

tag: brain region

value: ventral mesencephalic area

value: Ercc1 delta/+


title: Delta.4


title: Delta.1


title: WT.3

source_name: ventral mesencephalic area_wildtype


title: WT.4


title: WT.1


title: AhRCA-HA_ChIP-seq_Keratinocyte_replicate2

city: Sendai

first: Eri

middle: H

last: Kobayashi

state: Miyagi

address: 2-1 Seiryo-machi, Aobaku

department: Medical Biochemistry

country: Japan

institute: Tohoku University Graduate School of Medicine

description: ChIP samples using antibody to HA obtained from AhRCA-HA-expressing keratinocytes, replicate 2

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using bwa version 0.5.9-r26.
Data were filtered using samtools version 0.1.19
Peaks were called using macs2 version 2.0.10
Genome_build: mm9
Supplementary_files_format_and_content: Wig files were generated using igvtools version 2.3.3

source_name: Primary keratinocytes trancduced with AhRCA-HA

growth_protocol: Primary keratinocytes were isolated from the epidermis of newborn ICR mice and cultured in MEM with Chelex-treated fetal calf serum and epidermal growth factor.

extract_protocol:
Lysates were clarified from sonicated nuclei, and protein-DNA complexes were isolated using antibody to HA and Dynabeads-proteinA and -proteinG
Libraries were prepared according to NuGEN's instructions accompanying the Ovation Ultralow DR Multiplex System 1-8 (NuGEN, 0330-32).

treatment_protocol: Primary keratinocytes were transfected with AhRCA-HA-expressing adenovirus.

tag: chip-antibody

value: HA (abcam, ab9110)

value: ICR

tag: cell type

value: Primary keratinocytes


title: Delta.3

tag: tissue


title: Control rep2

tag: genotype/variation


title: #2-SU223 AML_RNA-seq

description: Sample name: s2.SU223.AML_S2

source_name: Primary AML_SU223


title: Input_Keratinocyte_replicate3

description: Input DNA obtained from AhRCA-HA-expressing keratinocytes, replicate 3

tag: strain


title: IgG+ memory B cells replicate1

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

institute: Institut Pasteur

data_processing:
cleaning with clean_ngs (v 0.7)
alignment with tophat (v 1.4.1.1)
counting with htseq-count (v 0.6.1)
Genome_build: GRCm38 (Ensembl version 74)
Supplementary_files_format_and_content: Htseq-count file; txt file with name of gene and corresponding counting

source_name: lymphocytes_IgG+ memory B cells

extract_protocol:
Spleen cells were isolated and all mononuclear cells were stained with a combination of antibodies (anti-CD19, anti-IgM, anti-IgG). Then subsets of memory B cells were sorted as CD19+HEL+YFP+IgM+ or IgG+ and naive cells as CD19+HEL+YFP-IgM+ using a FACSAriaIII flow cytometer. The purity of the sorted populations varied from 90-95%.
Directional libraries were prepared using the TruSeq Stranded total RNA Sample preparation kit following the manufacturer’s instructions (Illumina). The libraries were quantified by fluorimetric measurements with the Qubit® dsDNA HS Assay Kit (ThermoFisher). 51-bp Single Read sequences were generated on the Hiseq2500 sequencer according to manufacturer’s instructions (Illumina).  Sequences were demultiplexed using the Illumina pipeline (Gerald, included in CASAVA version 1.7) giving FASTQ formatted reads.

value: 8 weeks after immunization

value: sorted B cells from spleen

tag: cell subtype

value: IgG+ memory B cells


title: IgG+ memory B cells replicate3


title: activated B cells replicate3

source_name: lymphocytes_activated B cells

value: activated B cells


title: B_45h

city: xiamen

first: yang

last: zhang

address: Daxue Road No. 178, Siming District

institute: Third Institute of Oceanography, State Oceanic Administration

description: The cells were cultured for 45hr, then harvested by centrifugation.

data_processing:
RTA(Real Time Analysis) 1.12 software used for basecalling.
The following reads will be filtered:  Reads with only adaptor; Reads with unknown base
map the clean Reads to reference by using BWA with no more than 1 mismatch
The RPKM(Reads per kilobase transcript per million mapped reads) of each gene was computed with the following formula: RPKM=the Reads number * 1M*1K /(the total reads number * the gene length)
Genome_build: Private assembly trasncriptome of Chlorella minutissima UTEX2341 (refer to the supplementary file, Ref.fasta)
Supplementary_files_format_and_content: The content of each column in gene expression .txt files:column 1, ID of gene; column 2,RPKM of gene; column 3, The total Reads number; column 4, The mapped Reads number; column 5, The length of gene

organism: Neodesmus pupukensis

growth_protocol: The cells were cultured fed-batch in 500 mL flasks containing 200 mL medium at 25°C for 5 days using an orbital shaker at 150 rpm.

extract_protocol:
Total RNA was extracted with TRIzol reagent (Life Technologies) according to the manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The cells were harvested using a centrifuge at 6000 rpm for 10 min and immediately frozen in liquid nitrogen and stored at -80°C until use.

value: The whole body

tag: culture

tag: lipid yield

value: nearly about 50% of total lipid content


title: C_57h

description: The cells were cultured for 57hr, then harvested by centrifugation.


title: activated B cells replicate1


title: D_88h

description: The cells were cultured for 88hr, then harvested by centrifugation.


title: A_14h

description: The cells were cultured for 14hr, then harvested by centrifugation.


title: WT.2

tag: genotype


title: IgG+ memory B cells replicate2

tag: Stage


title: AhRCA-HA_ChIP-seq_Keratinocyte_replicate3

description: ChIP samples using antibody to HA obtained from AhRCA-HA-expressing keratinocytes, replicate 3


title: Input_Keratinocyte_replicate1

description: Input DNA obtained from AhRCA-HA-expressing keratinocytes, replicate 1


title: Input_Keratinocyte_replicate2

description: Input DNA obtained from AhRCA-HA-expressing keratinocytes, replicate 2


title: IgM+ memory B cells replicate1

source_name: lymphocytes_IgM+ memory B cells

value: IgM+ memory B cells


title: IgM+ memory B cells replicate3


title: IgM+ memory B cells replicate2


title: activated B cells replicate2


title: naive B cells replicate3

source_name: lymphocytes_naive B cells

value: naive B cells


title: AhRCA-HA_ChIP-seq_Keratinocyte_replicate1

description: ChIP samples using antibody to HA obtained from AhRCA-HA-expressing keratinocytes, replicate 1


title: naive B cells replicate2


title: naive B cells replicate1


title: Heart, Sham, rep2

status: Public on Nov 12 2016

city: Lausanne

first: Frederic

last: Burdet

address: Quartier Sorge - Batiment Amphipole

country: Switzerland

institute: Swiss Institute of Bioinformatics

description: 12 week old mice, border zone of sham infarct, 2 weeks after surgery

data_processing:
Base calling was with Illumina GAP Pipeline Software v1.70
Sequence reads were processed to remove the adaptor sequences and reformatted to FASTA files using the FASTX-Toolkit
Sequences were aligned to mm9 reference genome using Tophat 2.0.5 with option -g with mm9 reference GTF
Novel transcripts were predicted with Cufflinks 2.0.2 with option -G with mm9 reference GTF
Novel transcripts predictions were merged with mm9 reference genome using Cuffmerge 2.0.2 with option -G with mm9 reference GTF
Counts were generated using htseq-count v0.5.4p2
Genome_build: mm9
Supplementary_files_format_and_content: Raw count data for genes were normalized to the relative size of each library using R/Bioconductor package DESeq, estimateSizeFactors function. Count data are provided in tab-delimited format

source_name: Heart, Sham

extract_protocol:
Total RNA was isolated using Trizol (Invitrogen). RNA quantities and quality were assessed using a NanoDrop ND-1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND-1000 spectrophotometer or an Agilent 2100 Bioanalyzer.
Sequencing libraries were prepared according to Illumina long RNA Seq library kit instructions with Poly(A) selection. Libraries were sequenced with the Illumina HiSeq2000 (2x100bp).

value: heart

tag: treatment

value: sham


title: Heart, Sham, rep4

description: 12 week old mice, border zone of infarct, 2 weeks after surgery


title: Patient 85, Lesion 85, gene expression

city: Sydney

first: Jason

last: Wong

state: NSW

address: Level 2, Lowy Cancer Research Centre, University of New South Wales

country: Australia

institute: UNIVERSITY OF NEW SOUTH WALES

description:
85T_RNAseq
processed data file: LST (IIa) project RNA-Seq.txt

data_processing:
MBD-seq data were aligned to hg19 using BWA with default parameters
RNA-seq data were aligned to hg19 using tophat with the following  parameters: tophat (version 1.3.1) -g 25 -r 20 --segment-length 45 -G "hg19_refseq.gtf"
For both MBD-seq and RNA-seq the gene were defined using the hg19 refseq gene models provided by HOMER
For MBD-seq data, all aligned reads were extended to 200bp prior to quantification
For MBD-seq data, genes were first separated into those with or without CpG island promoters. Genes with promoter CpG islands were defined as those with a CpG island (as defined by UCSC) within +/-1kb of the TSS. For genes with CpG islands, the methylation level was quantified based on the number of reads overlapping the CpG island. For non-CpG island promoter genes, the methylation level was quanitified based on the number of reads overlapping +/-1kb of the TSS.
For RNA-seq data, genes were quantified using HOMER.
For RNA-seq, read counts were TMM normalised using EdgeR
Genome_build: hg19
Supplementary_files_format_and_content: For MBD-seq raw read counts for all samples
Supplementary_files_format_and_content: For RNA-seq TMM normalized read counts for all samples

source_name: Patient 85, Lesion 85

extract_protocol:
RNA extraction using PureLink Micro Kit (Life Technologies, Catalog no. 12183-016)
Total RNA was amplified using the Ovation RNA-Seq system (Catalog no. 7102) prior to library construction

tag: individual

value: Patient 85

value: Adenoma


title: Patient 82, normal mucosa, gene expression

description:
82N_RNAseq
processed data file: LST (IIa) project RNA-Seq.txt

source_name: Patient 82, normal mucosa

value: Patient 82

value: Normal rectal mucosa


title: Patient 85, normal mucosa, gene expression

description:
85N_RNAseq
processed data file: LST (IIa) project RNA-Seq.txt

source_name: Patient 85, normal mucosa


title: Patient 81, Lesion 81, gene expression

description:
81T_RNAseq
processed data file: LST (IIa) project RNA-Seq.txt

source_name: Patient 81, Lesion 81

value: Patient 81


title: Heart, Sham, rep1


title: DGE of Kasa-1

city: Beijing

first: lili

last: hao

address: Beichen west road

institute: BIG

data_processing:
Library strategy: DGE
3' adaptor sequence removal: since Tags are only 21nt long while the sequencing reads are 35nt long, raw sequences are with 3' adaptor sequences
Empty reads removal (reads with only 3' adaptor sequences but no tags)
Low quality tags removal (Tags with unknown sequences 'N')
Removal of tags which are too long or too short, leaving Tags of 21nt long
Removal of Tags with a copy number of 1 (probably be sequencing error)
Genome_build: rice TIGR7.0
Supplementary_files_format_and_content: sequence count file, contain tag sequence information and the number of tags which are unambiguous clean tags mapped to the sequence

organism: Oryza sativa

source_name: leaf blades

extract_protocol:
Leaf samples taken from two-month-old plant were harvested for RNA extraction using TRIzol (Invitrogen) as described by the manufacturer.
Total RNA was extracted from Y103-1 and Kasa-1 with TRIZOL® Reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions. The RNA samples were incubated for 30 min at 37°C with 10 units of DNaseI (Takara, Dalian, China) to remove residual genomic DNA. The quality and quantity of the purified RNA were determined by measuring the absorbance at 260 nm/280 nm (A260/A280) using a Nanodrop® ND-1000 spectrophotometer (LabTech, Holliston, MA, USA). The samples had an average RIN value of 8.9 according to Labon-chip analysis using the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

tag: line

value: leaf blades

value: Kasalath


title: Heart, Sham, rep3


title: Patient 81, normal mucosa, gene expression

description:
81N_RNAseq
processed data file: LST (IIa) project RNA-Seq.txt

source_name: Patient 81, normal mucosa


title: Patient GNG, Lesion G2, gene expression

description:
GNG_G2_RNAseq
processed data file: LST (IIa) project RNA-Seq.txt

source_name: Patient GNG, Lesion G2

value: Patient GNG


title: Patient GNG, Lesion NG, gene expression

description:
GNG_NG_RNAseq
processed data file: LST (IIa) project RNA-Seq.txt

source_name: Patient GNG, Lesion NG


title: Patient GNG, Lesion G1, gene expression

description:
GNG_G1_RNAseq
processed data file: LST (IIa) project RNA-Seq.txt

source_name: Patient GNG, Lesion G1


title: Patient 82, Lesion 82, gene expression

description:
82T_RNAseq
processed data file: LST (IIa) project RNA-Seq.txt

source_name: Patient 82, Lesion 82


title: Patient GNG, normal mucosa, gene expression

description:
GNG_N_RNAseq
processed data file: LST (IIa) project RNA-Seq.txt

source_name: Patient GNG, normal mucosa


title: Patient 4, Lesion 4, gene expression

description:
ISTA04_IsB_RNAseq
processed data file: LST (IIa) project RNA-Seq.txt
ISTA04_IIa in processed data file

source_name: Patient 4, Lesion 4

value: Patient 4


title: Patient 5, normal mucosa, gene expression

description:
ISTA05_N_RNAseq
processed data file: LST (IIa) project RNA-Seq.txt

source_name: Patient 5, normal mucosa

value: Patient 5


title: Patient 5, Lesion 5, gene expression

description:
ISTA05_IIa_RNAseq
processed data file: LST (IIa) project RNA-Seq.txt

source_name: Patient 5, Lesion 5


title: Patient 3, Lesion 3, gene expression

description:
ISTA03_IIa_RNAseq
processed data file: LST (IIa) project RNA-Seq.txt

source_name: Patient 3, Lesion 3

value: Patient 3


title: Patient 3, normal mucosa, gene expression

description:
ISTA03_N_RNAseq
processed data file: LST (IIa) project RNA-Seq.txt

source_name: Patient 3, normal mucosa


title: Patient 4, normal mucosa, gene expression

description:
ISTA04_N_RNAseq
processed data file: LST (IIa) project RNA-Seq.txt

source_name: Patient 4, normal mucosa


title: Patient 2, Lesion 2, gene expression

description:
ISTA02_IIa_RNAseq
processed data file: LST (IIa) project RNA-Seq.txt

source_name: Patient 2, Lesion 2

value: Patient 2


title: Patient 1, Lesion 1, gene expression

description:
ISTA01_IIa_RNAseq
processed data file: LST (IIa) project RNA-Seq.txt

source_name: Patient 1, Lesion 1

value: Patient 1


title: Patient 1, normal mucosa, gene expression

description:
ISTA01_N_RNAseq
processed data file: LST (IIa) project RNA-Seq.txt

source_name: Patient 1, normal mucosa


title: Patient GNG, Lesion NG, DNA methylation

description:
GNG_NG_MBD
processed data file: LST (IIa) project MBD-Seq.txt

extract_protocol:
Phenol chloroform DNA extraction
Methylminer (Invitrogen, Catalog no. ME10025) methylated DNA enrichment. Enriched sonicated DNA was subject to size selection (350–450 bp) followed by adaptor ligation, flow cell hybridization and cluster amplification for 11–13 cycles using TruSeq SR Cluster Kit v3-cBot-HS (Illumina, Catalog no. GD-401-3001) prior to sequencing using the Illumina Hiseq2000 or Illumina Genome Analyzer IIx platform (single-end, 50 bp).


title: Patient GNG, Lesion G2, DNA methylation

description:
GNG_G2_MBD
processed data file: LST (IIa) project MBD-Seq.txt


title: Patient GNG, Lesion G1, DNA methylation

description:
GNG_G1_MBD
processed data file: LST (IIa) project MBD-Seq.txt


title: Patient 5, Lesion 5, DNA methylation

description:
ISTA05_IIa_MBD
processed data file: LST (IIa) project MBD-Seq.txt


title: Patient GNG, normal mucosa, DNA methylation

description:
GNG_N_MBD
processed data file: LST (IIa) project MBD-Seq.txt


title: Patient 5, normal mucosa, DNA methylation

description:
ISTA05_N_MBD
processed data file: LST (IIa) project MBD-Seq.txt


title: DGE of Y103-1


title: Patient 4, Lesion 4, DNA methylation

description:
ISTA04_IsB_MBD
processed data file: LST (IIa) project MBD-Seq.txt
ISTA04_Iia in processed data file


title: Patient 4, normal mucosa, DNA methylation

description:
ISTA04_N_MBD
processed data file: LST (IIa) project MBD-Seq.txt


title: Patient 3, Lesion 3, DNA methylation

description:
ISTA03_IIa_MBD
processed data file: LST (IIa) project MBD-Seq.txt


title: Patient 85, Lesion 85, DNA methylation

description:
85T_MBD
processed data file: LST (IIa) project MBD-Seq.txt

source_name: Patient 85, Lesion 85


title: Patient 2, Lesion 2, DNA methylation

description:
ISTA02_IIa_MBD
processed data file: LST (IIa) project MBD-Seq.txt


title: Patient 85, normal mucosa, DNA methylation

description:
85N_MBD
processed data file: LST (IIa) project MBD-Seq.txt

source_name: Patient 85, normal mucosa


title: Patient 3, normal mucosa, DNA methylation

description:
ISTA03_N_MBD
processed data file: LST (IIa) project MBD-Seq.txt


title: Patient 82, Lesion 82, DNA methylation

description:
82T_MBD
processed data file: LST (IIa) project MBD-Seq.txt


title: Patient 82, normal mucosa, DNA methylation

description:
82N_MBD
processed data file: LST (IIa) project MBD-Seq.txt

source_name: Patient 82, normal mucosa


title: Patient 1, Lesion 1, DNA methylation

description:
ISTA01_IIa_MBD
processed data file: LST (IIa) project MBD-Seq.txt


title: Patient 2, normal mucosa, DNA methylation

description:
ISTA02_N_MBD
processed data file: LST (IIa) project MBD-Seq.txt

source_name: Patient 2, normal mucosa


title: Patient 2, normal mucosa, gene expression

description:
ISTA02_N_RNAseq
processed data file: LST (IIa) project RNA-Seq.txt


title: Sample 35_H5

city: San Francisco

first: Charlie

last: Kim

address: 1001 Potrero Ave

department: Medicine

institute: University of California, San Francisco

data_processing:
Bases were called and reads were demultiplexed with Illumina CASAVA 1.8.2 and read quality assessed using FastQC
Reads were aligned to the transcriptome using STAR version 2.4.2a with default parameters as called by RSEM version 1.2.22
Gene expression per sample was modeled with RSEM version 1.2.22
Genome_build: Release GRCm38 of the mouse genome
Supplementary_files_format_and_content: Tab delimited text files showing tpm for all genes

source_name: Blood leukocytes

growth_protocol: Antigen-experienced CD4+ T cells were isolated from the blood of P. chabaudi-infected mice by double-sorting on a FACS AriaII.

extract_protocol:
Total RNA was isolated, converted to cDNA, and pre-amplified as described in the SMARTer Ultra-low input kit (Clontech PN 634833) but as modified for C1 (Fluidigm) single cell mRNA-seq analysis.
RNA libraries were prepared for sequencing following Illumina protocols.  cDNA libraries were diluted to 0.25ng/ul, fragmented with the Nextera XT DNA kit (Illumina PN FC-131-1024), multiplexed, and sequenced on a Hi-Seq2500

tag: strain background

tag: gender

value: female

tag: infected with

value: Plasmodium chabaudi

value: 6 days post-infection

value: Blood leukocytes

value: CD4+ T cells

tag: cell surface markers

value: TCRb+ CD4+ CD11a+ CD49d+


title: Sample 33_H2

tag: time point


title: Sample 32_H1

tag: cell type


title: Sample 34_H4

tag: tissue


title: Patient 81, normal mucosa, DNA methylation

description:
81N_MBD
processed data file: LST (IIa) project MBD-Seq.txt

source_name: Patient 81, normal mucosa


title: Patient 81, Lesion 81, DNA methylation

description:
81T_MBD
processed data file: LST (IIa) project MBD-Seq.txt

source_name: Patient 81, Lesion 81

value: Adenoma


title: Sample 31_G5


title: Sample 27_G1


title: Sample 29_G3


title: Sample 30_G4


title: Clone_4T1-T_shSlpi-2_B

city: Cold Spring Harbor

first: Simon

middle: Robert Vincent

last: Knott

address: 1 Bungtown Rd

department: Biology

institute: Cold Spring Harbor Laboratory

description: processed data file: Clone_4T1-T_shRNA_Normalized.txt

data_processing:
1) Reads were alligned to the mm10 genome using bowtie-2.
2) Each gene's read counts were determined using htseq -count (python) function.
3) Reads were normalized across samples using DESeq (bioconductor)
Genome_build: mm10
Supplementary_files_format_and_content: All_Clones_Normalized.txt: The first field is the RefSeq gene symbol. All other fields are the normalized read counts for a sample. Samples are indicated in the headers.
Supplementary_files_format_and_content: Clone_4T1-T_shRNA_Normalized.txt: The first field is the RefSeq gene symbol. All other fields are the normalized read counts for a sample. Samples are indicated in the headers

source_name: 4T1 Mammary Cancer Cell Line

growth_protocol: DMEM high glucose (Life Technologies) supplemented with 5% fetal bovine serum (Thermo Scientific), 5% fetal calf serum (Thermo Scientific), non-essential amino acids (Life Technologies) and penicillin streptomycin (Life Technologies)

extract_protocol:
RNA was purified and DNAse treated using the Qiagen RNeasy Mini Kit
The NuGEN Ovation RNA-Seq V2 protocol was carried out on 100 ng of total RNA. cDNA was fragmented using the Covaris LE220 sonicator according to the manufacturer’s instruction to yield a target fragment size of 200 bp. The fragmented cDNA was subsequently processed using the NuGEN Ovation Ultralow DR Multiplex System.
Libraries were analyzed on an Illumina Hiseq-2.0 using 76bp reads.

tag: clone

value: Clone 4T1-T (derived From Single Cell)

value: shRNA Infected (shSlpi-2)


title: Sample 25_F4


title: Sample 23_F2


title: Sample 26_F5


title: Clone_4T1-T_shSlpi-2_A


title: Sample 24_F3


title: Clone_4T1-T_shSlpi-1_B

value: shRNA Infected (shSlpi-1)


title: Clone_4T1-T_shSlpi-1_A


title: Sample 22_F1


title: Clone_4T1-T_shSerpine2-2_A

value: shRNA Infected (shSerpine2-2)


title: Sample 16_D4


title: Sample 17_D5


title: Clone_4T1-T_shSerpine2-2_B


title: Sample 19_E2


title: Sample 21_E5


title: Sample 28_G2


title: Sample 18_E1


title: Sample 15_D3


title: Clone_4T1-T_shSerpine2-1_B

value: shRNA Infected (shSerpine2-1)


title: Sample 11_C3


title: Sample 12_C4


title: Clone_4T1-T_shRenilla_B

value: shRNA Infected (shRenilla)


title: Sample 14_D1


title: Clone_4T1-T_shSerpine2-1_A


title: Sample 13_C5


title: Sample 9_C1


title: Sample 10_C2


title: Sample 8_B5


title: Clone_4T1-T_shRenilla_A


title: Sample 20_E3


title: Sample 5_B1


title: Sample 6_B2


title: Sample 4_A5


title: Sample 3_A3


title: Sample 1_A1


title: Meth_Clone_4T1-Parental_Round_1

description: Bisulphate Converted genomic DNA

data_processing:
1) Data was processed with Methpipe pipeline to calculate the methylation levels at each CpG and to call hypomethylated regions (Song, Q. et al. A reference methylome database and analysis pipeline to facilitate integrative and comparative epigenomics. PloS one 8, e81148, doi:10.1371/journal.pone.0081148 (2013)).
2) For clustering, the hypomethylated regions of different clones were collapsed together into a consensus set using the Bedtools intersectBed function (merging when a single base of overlap existed).
3) Reads were normalized across samples using DESeq (bioconductor)
4) For each clone, the average methylation levels of the CpGs within the consensus regions were calculated. The median absolute deviations (MAD) of the resultant methylation levels were then used to identify the top 10% most variable for clustering.
5) Promoter methylation levels were calculated as the average CpG methylation level within 1kbp of the transcription start site of each gene. The top 10% most variable promoter regions (based on MAD) were clustered.
Genome_build: mm10
Supplementary_files_format_and_content: HMR_Methylation.txt: field 1 is the chromosome location of the HMR, field 2 is the start position of the HMR, field 3 is the end position of the HMR. All other fields represent the average methylation levels of the different clones within the HMR region. Clones are annotated in the header.
Supplementary_files_format_and_content: Promoter_Methylation.txt: field 1 is the RefSeq gene symbol of the promoter. All other fields represent the average methylation levels of the different clones within the gene promoter region. Clones are annotated in the header.

extract_protocol:
Genomic DNA was purified using the QIAamp DNA Blood Mini Kit (Qiagen) and was fragmented using the Covaris LE220 sonicator according to the manufacturer’s instruction to yield a target fragment size of 300 bp.
The fragmented DNA was end repaired, A-tailored and ligated to methylated Illumina adapters. Ligated fragments were then bisulfite converted using the EZ-DNA Methylation-Gold Kit (Zymo).
Following PCR enrichment, each sample was sequenced on the Illumina HiSeq sequencer generating 76 nt paired-end (PE) reads.

tag: cell line

value: Parental Cell Line


title: Meth_Clone_4T1-T_Round_2

description: Bisulphate Converted genomic DNA

value: Clone-T (derived From Single Cell)

tag: intravasating capacity

value: Intravasating


title: 3C-TAP-D13

city: London

first: Martin

last: Allday

state: London

address: Norfolk Place

country: United Kingdom

institute: Imperial College London

description: Second donor repetition

data_processing:
Illumina CASAVA 1.8.2 software used for basecalling
Sequence reads were mapped to the human genome (vhg19) downloaded from UCSC using BWA
Binding regions were identified using the MACS v2.1.0 peak-calling algorithm comparing the sample to a control sample processed in the same way from an LCL not expressing tagged proteins. Peaks were defined as significant with a q value cut-off of 5.00e-02
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files for peaks including all with quantitative data produced by MACS algorithm

source_name: LCL

growth_protocol: Lymphoblastoid cell lines (LCLs) were created by recombinant EBV infection of isolated CD19 +ve B cells from buffy coat from two blood donors (D11 and D13).

extract_protocol:
ChIPs for the TAP-tagged EBNA3s were done as follows. A suspension of 15x10^6 fixed cells was made in 1ml swelling buffer (25M HEPES, pH7.8; 1.5mM MgCl2; 10mM KCl, 0.1% NP-40; 1mM DTT; 1mM PMSF; 1µg/ml aprotinin; 1µg/ml pepstatin A) and incubated at 4oC with rotation for 20 mins. They were then centrifuged at 375g for 5 min at 4oC and the supernatant discarded. The remaining nuclei were re-suspended in 1ml of sonication buffer (50mM HEPES pH7.9; 140mM NaCl; 1mM EDTA; 1% Triton X-100; 0.1% sodium deoxycholate; 0.1% SDS; 1mM PMSF; 1µg/ml aprotinin; 1µg/ml pepstatin A) and incubated on ice for 30 minutes.  Lysate was then sonicated for 1 hour using a Covaris M220 Focused-ultrasonicator with a milliTUBE holder (settings: peak power 75, duty factor 26, cycles/burst 200, set point temperature 6oC). Sonicated lysate was centrifuged at 12000g for 10 minutes at 4oC and supernatant was diluted with 3ml of sonication buffer. From the input sample 5% was kept at 4 oC as a control and the rest was incubated overnight with 16µg of α-FLAG antibody and 120µl of ChIP-grade protein G magnetic beads (NEB, #9006) at 4oC in a 15ml Falcon tube on rollers. The following day the beads were washed with standard ChIP wash buffers, 4ml buffer for each wash for 15 minutes at 4oC on rollers. Precipitated chromatin was eluted in 400µl of elution buffer, the eluate was treated with RNase, formaldehyde cross-links were reversed before proteinase K treatment and DNA was cleaned with a Qiagen PCR purification MinElute kit, for ChIP sample and input control.
DNA from ChIP was run on a 2% agarose gel (Bio-Rad Low Range Ultra, #161-3107) and DNA between 100-500bp was excised and purified using the Qiagen MinElute gel purification kit, according to manufacturing instructions. At least 1ng of DNA for each sample was then sent to the Harvard Biopolymers facility for library construction (ChIP-Seq Wafergen) and sequencing (Illumina HiSeq 2500, 50bp single-reads).

value: Lymphoblastoid cell line

tag: tagged protein

value: EBNA3C FLAG-Strep II tag, C-terminus

tag: chip antibody

value: DYKDDDDK (FLAG) Tag Antibody; NEB #2368

tag: donor


title: WT-D13

description: Second donor repetition

value: No tag


title: Meth_Clone_4T1-T_Round_1

description: Bisulphate Converted genomic DNA


title: Meth_Clone_4T1-Parental_Round_2

description: Bisulphate Converted genomic DNA


title: Meth_Clone_4T1-P_Round_2

description: Bisulphate Converted genomic DNA

value: Clone-P (derived From Single Cell)

value: Non-Intravasating


title: 3A-TAP-D13

description: Second donor repetition

value: EBNA3A FLAG-Strep II tag, C-terminus


title: 3A-TAP-D11


title: 3C-TAP-D11


title: WT-D11


title: Meth_Clone_4T1-L_Round_1

description: Bisulphate Converted genomic DNA

value: Clone-L (derived From Single Cell)


title: TAP-3B-D11

value: EBNA3B FLAG-Strep II tag, N-terminus


title: ARID1b Rep3

first: Gopuraja

last: Dharmalingam

address: Faculty of Medicine, Imperial College, Hammersmith Hospital Campus

department: Epigenetics section

institute: MRC London Institute of Medical Sciences

description: expression profile of IMR90 transduced with ARID1B cDNA

data_processing:
RNA-Seq sequencing reads were aligned to hg19 genome using Tophat v2.0.11 using parameters "--library-type fr-firststrand --b2-very-sensitive --b2-L 25" and using known transcripts annotation from ensembl gene v72
Number of reads counts on exons were summarised using HTSeq v0.5.3p9 with "--stranded=reverse" option and differentially expressed genes were identified using DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM

growth_protocol: IRM90 were grown in DMEM 10% FBS for 6 days. Media was changed at Day 4

extract_protocol: Libraries were prepared according to Illumina's kit instructions (mRNA stranded library prep kit)

treatment_protocol: At day 0 IMR90 cells were infected with an empty vector or ARID1B cDNA and selected with 0.8ug Puromycin for stable integrations until day 4

tag: time

value: 6 days after infection

tag: passage

tag: genotype/variation

value: ARID1B overexpression


title: Intact adult females, replicate 4

city: Salt Lake City

first: Richard

middle: M

last: Clark

state: Utah

department: Department of Biology

institute: University of Utah

description:
RNA from adult females
GHZ-118

data_processing:
Reads obtained with the Illumina method were aligned to the T. urticae reference genome (September 29, 2009 build) with STAR 2.4.1d in two-pass alginment mode, a maximum intron size of 20 kb, and independent of the refrerence annotation.
Read counts for genes in the October 29, 2015 annotation were obtained using HTSeq 0.6.1 with "--stranded=reverse" and "--feature=exon".
Genome_build: September 29, 2009 genome build and October 29, 2015 genome annotation as downloaded from the public ORCAE genome portal (http://bioinformatics.psb.ugent.be/orcae/).
Supplementary_files_format_and_content: Tab-delimited text file with raw gene counts.

organism: Tetranychus urticae

source_name: Whole body

growth_protocol: Spider mites were grown on the detacted leaves of the common bean (Phaseolus vulgaris).

extract_protocol:
Total RNA was extracted with the Qiagen RNeasy RNA extraction kit from the whole bodies of adult males (about 800 individuals) and females (about 200 individuals) per biological replicate. Briefly, more males were collected than for females to ensure enough RNA for Illumina library construction (males are markedly smaller than females). Adult mites were collected at the ages of 1-2 days for males, and 3 days for females, the time of maturity for each sex, respectively.
RNA-Seq libraries were prepared for sequencing with the Illumina strand-specific RNA-Seq protocol with oligo dT selection.

tag: developmental stage

value: adult

tag: Sex

value: female

tag: strain

value: London


title: Intact adult females, replicate 3

description:
RNA from adult females
GHZ-117


title: Sample 7_B4

tag: strain background

tag: gender

tag: infected with

value: Plasmodium chabaudi

value: 6 days post-infection

value: Blood leukocytes

value: CD4+ T cells

value: TCRb+ CD4+ CD11a+ CD49d+


title: Meth_Clone_4T1-K_Round_2

description: Bisulphate Converted genomic DNA

value: Clone-K (derived From Single Cell)


title: Sample 2_A2

tag: time point

tag: cell type

tag: cell surface markers


title: ARID1b Rep2

tag: cell line


title: Meth_Clone_4T1-K_Round_1

description: Bisulphate Converted genomic DNA

tag: clone

tag: intravasating capacity


title: ARID1b Rep1


title: Intact adult females, replicate 1

description:
RNA from adult females
GHZ-115


title: Intact adult males, replicate 4

description:
RNA from adult males
GHZ-114

value: male


title: Meth_Clone_4T1-I_Round_2

description: Bisulphate Converted genomic DNA

value: Clone-I (derived From Single Cell)


title: Intact adult males, replicate 3

description:
RNA from adult males
GHZ-113


title: Meth_Clone_4T1-P_Round_1

description: Bisulphate Converted genomic DNA

value: Clone-P (derived From Single Cell)

value: Non-Intravasating


title: Intact adult males, replicate 2

description:
RNA from adult males
GHZ-112


title: vector Rep2

description: expression profile of IMR90 transduced with empty vector

source_name: vector

value: control


title: Meth_Clone_4T1-E_Round_2

description: Bisulphate Converted genomic DNA

value: Clone-E (derived From Single Cell)

value: Intravasating


title: Meth_Clone_4T1-L_Round_2

description: Bisulphate Converted genomic DNA

value: Clone-L (derived From Single Cell)


title: vector Rep1

value: 6 days after infection


title: Meth_Clone_4T1-E_Round_1

description: Bisulphate Converted genomic DNA


title: Intact adult males, replicate 1

description:
RNA from adult males
GHZ-111

value: adult


title: Intact adult females, replicate 2

description:
RNA from adult females
GHZ-116

value: female

value: London


title: Sample_RNAseq_FT9

status: Public on Nov 11 2016

city: Rockville

first: Brandon

middle: W

last: Higgs

state: Maryland

address: 2273 Research Blvd Suite 220

institute: Immunocore, Ltd

description:
mRNA-seq
Processed data file: hepato_norm_counts.txt

data_processing:
Basecalls performed using CASAVA version 1.8.
Reads aligned using HISAT2.
Normalization of raw read counts with DESeq2.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: hepato_norm_counts.txt: Tab-delimited text file includes normalization of raw read counts with DESeq2.

source_name: Hepatoblastoma liver

extract_protocol:
Total RNA was isolated from fresh frozen liver tissues with hepatoblastoma (HBL) using the RNeasy RNA isolation kit (Qiagen, Valencia, CA).
RNA sequencing libraries were prepared from fresh frozen liver with HBL RNA (1ug) using a SureSelect Strand Specific RNA Library Preparation kit (Product# G9691A, Agilent Technologies, Santa Clara, CA) accordingly to the manufacturer's protocol.
Libraries were sequenced with HiSeq2500 system (Illumina) using TruSeq SBS Kit v3 - HS (200-cycles) (cat# FC-401-3001, Illumina, San Diego, CA) and TruSeq PE Cluster Kit v3 (Cat# PE-401-3001, Illumina, San Diego, CA).

tag: tissue

value: Hepatoblastoma liver


title: Sample_RNAseq_FT7


title: Exosome of non-invasive NFPAs

first: Yuan

last: Ren

state: Beijing

address: Dongcheng district, No.1, beishuaifuyuan

department: Neurosurgery

institute: Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College

data_processing:
Total exosomal RNA was extracted using the HiPure Serum/Plasma miRNA Kit (Magen R4317). RNA quality was assessed with the Qubit 3.0 (Thermo Scientific, Rockford, IL, USA) and the Agilent 2200 TapeStation. The NEBNext® Ultra™ RNA Library Prep Kit (Beverly, MA, USA) for Illumina was used to prepare an RNA-seq library. Finally, library sequencing was conducted on an Illumina HiSeq™ 3000 system.
Genome_build: Sequence data were mapped to a human reference genome hg19 with TopHat v2.0.13. gfold v1.1.2 was subsequently employed to count the number of reads mapped to each gene.
Supplementary_files_format_and_content: Differential expression was assessed via DEGseq using RPKM as the input. DEGs were chosen according to the criteria of a > 2-fold change and adjusted P-value < 0.05.

source_name: exosome

tag: sample type

value: non-invasive non-functional pituitary adenomas


title: Sample_RNAseq_FT13


title: Exosome of invasive NFPAs

extract_protocol: Total exosomal RNA was extracted using the HiPure Serum/Plasma miRNA Kit (Magen R4317). RNA quality was assessed with the Qubit 3.0 (Thermo Scientific, Rockford, IL, USA) and the Agilent 2200 TapeStation. The NEBNext® Ultra™ RNA Library Prep Kit (Beverly, MA, USA) for Illumina was used to prepare an RNA-seq library. Finally, library sequencing was conducted on an Illumina HiSeq™ 3000 system.

value: invasive non-functional pituitary adenomas


title: Sample_RNAseq_FT14


title: Sample_RNAseq_FT15


title: Sample_RNAseq_FT12


title: Sample_RNAseq_FT6


title: 791_NC_S3

source_name: Normal liver

value: Normal liver


title: Sample_RNAseq_FT10


title: pwr-H3K27ac ChIP

city: Madison

first: Xuehua

last: Zhong

state: WI

address: 330 N. Orchard St.

department: Epigenetics

institute: Wisconsin Institute for Discovery

data_processing:
ChIPseq reads were filtered for average QC score>30. Reads were mapped with Bowtie2 to the TAIR10 genome, with default parameters. Reads mapping to identical positions in the genome were collapsed into one read.bedtools was used to generate bedGraph file; UCSC "bedGraphToBigWig" scipt was used to generate bigwig file.
Genome_build: Arabidopsis TAIR10
Supplementary_files_format_and_content: BigWig file

organism: Arabidopsis thaliana

source_name: leaf

growth_protocol: Arabidopsis plants were grown on soil at 21 degree under continuous light.

extract_protocol:
ChIP genomic DNA protocols are followed by Zhong et al., Nat Struct Mol Biol, 2012, 19:870-850;
ChIP library and RNA library was construbuted by using the Ovation Ultralow Library Kit (NuGen, Part No. 0330)

value: pwr mutant

value: leaf

tag: antibody

value: H3K27ac antibody (Active motif, 39133)


title: hda9-H3K27ac ChIP

value: hda9 mutant


title: 785_NC_S2


title: Meth_Clone_4T1-I_Round_1

description: Bisulphate Converted genomic DNA

value: Clone-I (derived From Single Cell)

value: Non-Intravasating


title: hda9-ES-repeat2

data_processing:
ChIPseq reads were filtered for average QC score>30. Reads were mapped with Bowtie2 to the TAIR10 genome, with default parameters. Reads mapping to identical positions in the genome were collapsed into one read.bedtools was used to generate bedGraph file; UCSC "bedGraphToBigWig" scipt was used to generate bigwig file.
RNAseq fpkm were generated by tophat and cufflink by following Trapnell et al.(2012).
Genome_build: Arabidopsis TAIR10
Supplementary_files_format_and_content: RNA-seq (txt file: gene fpkm); ChIP-seq(BigWig file)

extract_protocol:
ChIP genomic DNA protocols are followed by Zhong et al., Nat Struct Mol Biol, 2012, 19:870-850; RNA was extracted by Trizol (ThermoFisher, 15596026) following the manufacturer’s instructions.
ChIP library and RNA library was construbuted by using the Ovation Ultralow Library Kit (NuGen, Part No. 0330) and Illumina Truseq RNA Library Prep Kit v2 (RS-122-2001), respectivly.

tag: Stage

value: early senesence


title: Col-ES-repeat2

tag: genotype/variation

value: Wild-type Columbia-0


title: pwr-ES-repeat1

value: pwr-mutant


title: hda9-ES-repeat1


title: Col-ES-repeat1


title: Col-YL-repeat2

value: young leaves (2 weeks)


title: vector Rep3

tag: time

value: 6 days after infection

tag: passage

value: control


title: hda9-YL


title: Col-YL-repeat1


title: pwr-ES-repeat2


title: Sample_RNAseq_FT8


title: Col-H3K27ac ChIP

value: wild-type Columbia-0


title: Col-CHIPSEQ-control

description: Genomic DNA isolicated from immnuoprecipitated chromatin using FLAG antibody

value: Wild-type Columbia-0 without FLAG tag


title: HDA9-FLAG-CHIPSEQ

value: Wild-type Columbia-0 with HDA9-FLAG transformed


title: Sample_RNAseq_FT11

value: Hepatoblastoma liver


title: 769_NC_S1

value: Normal liver


title: Hsf1_t30_3.0U

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

institute: Princess Maxima Center for Pediatric Oncology

description:
Nucleosome positioning in the Hsf1-FRB-GFP strain, 30 minutes after addition of rapamycin (7.5 uM final concentration). The DNA was digested using 3.0U of Mnase.
The anchor away system (Haruki et al., 2008) was recreated in the Saccharomyces cerevisiae S288C/BY4742 strain. To achieve this FPR1 was deleted, a tor1-1 mutation was introduced to desensitize the strain to rapamycin and RPL13A was tagged with 2xFKBP12 as in the original anchor away system (Haruki et al., 2008). This strain was the parental strain used to create the specific anchor away strains. This strain is referred to as wildtype (WT) throughout the study. In order to create the specific anchor away strains, Hsf1 was tagged with an FRB-yEGFP tag.

data_processing:
The Chip-seq reads were aligned using bwa (Li and Durbin, 2009; version 0.5.9-r16 aln) with the settings ‘-c –l 25 –k 2 –n 10’The Mnase-seq reads were mapped using bowtie2 (Langmead and Salzberg, 2012; version 2.2.5) with the settings ‘ --no-discordant --no-contain --maxins 1980 --trim5 5 --trim3 15 --end-to-end --sensitive’
Only read pairs with an insert size between 95-225 bp were used for subsequent analyses. To compare the occupancy of all samples, their numbers were scaled to 10 million mapped paired-end reads per sample using genomecov from the bedtools2 suite version 2.250 (Quinlan and Hall, 2010).
The nucleosome dyads (midpoints of the mate pairs) were determined and smoothed using a 31 bp running average using https://github.com/plijnzaad/phtools/blob/master/ngs/center+smooth.pl and converted to BigWig format using genomecov from the bedtools2 suite version 2.250 (Quinlan and Hall, 2010) and bedGraphToBigWig (Kent et al., 2010)
Genome_build: Saccharomyces cerevisiae, assembly R64 (aka sacCer3)
Supplementary_files_format_and_content: Processed data files represent the Hsf1 binding peaks, and nucleosome dyad positions, respectively

organism: Saccharomyces cerevisiae

source_name: cell culture

growth_protocol: Strains were streaked from -80oC stocks onto appropriate selection plates and grown for 3 days. Liquid cultures were inoculated with independent colonies and grown overnight (ON) in Synthetic Complete (SC) medium: 2 gr/L Drop out mix Complete and 6.71 gr/L Yeast Nitrogen Base without AA, Carbohydrate & w/AS (YNB) from US Biologicals (Swampscott, USA) with 2% D-glucose. The following day O/N cultures were used to inoculate 250 ml (ChIP-seq) or 70 ml (Mnase-seq) cultures of SC media at OD595=0.35 (ChIP-seq) or OD595=0.15 (Mnase-seq) and were grown for two doublings. All growth was done at 30oC.

extract_protocol:
ChIP was caried out as previously described (van Bakel et al., NAR 2008), Chromatin for Mnase digestion was prepared essentialy as described (Kent and Mellor, 1995)
Sequencing libraries were created from the purified DNA using the NextflexTM rapid DNA-Seq kit (Bioo Scientific) using a modified protocol.

treatment_protocol: For the Mnase-seq material: Hsf1 was depleted from the nucleus by adding rapamycin, dissolved in DMSO, to a final concentration of 7.5 µM. For the “t=0” samples no rapamycin, but the same volume of DMSO was added. Harvesting was done 30 minutes after addition of rapamycin.

tag: strain

tag: genotype

value: BY4742 tor1-1; fpr1del; RPL13A-FKBP12-NAT; HSF1-FRB-yEGFP-hphMX4

tag: mating type

value: MATalpha

tag: mnase concentration

tag: depletion time


title: fru-2h replicate 1

first: miaomiao

last: Zhou

address: Uppsalalaan 8

department: fungal physiology

institute: centre of fungal biodiversity, Utrecht, KNAW

description: Pyricularia oryza wild type on fructose 2 hours

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 Agaricus bisporus var bisporus (H97) v2.0  whole genome using SOAPaligner/SOAP2. No more than 2 mismatches were allowed in the alignment.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi et al., 2008.
Genome_build: Pyricularia oryzae (Magnaporthe oryzae) 70-15 (MG8); http://fungi.ensembl.org/Magnaporthe_oryzae/
Supplementary_files_format_and_content: excel file includes unique reads number for each sample.

organism: Pyricularia oryzae

growth_protocol: P. oryzae strain Guy11Δku80 was used for transcriptome analysis. All P. oryzae cultures were incubated at 25-26°C. TNK-YE (complete medium). For solid media, 1.5% (w/v) agar was added. The plates were inoculated with 2 μl containing 1x10^3 P. oryzae spores. Transcriptome analysis was performed on P. oryzae mycelium grown for 2, 4 or 8 h in liquid TNK-MM containing 25 mM L-arabinose as well as for 2 h in liquid TNK-MM with 25 mM D-fructose. For this, sporulating mycelium of one full-grown complete medium (TNK-YE and 1% D-glucose) agar plate was blended (Sorvall omni-Mixer, Newtown, USA) in a total volume of 50 ml H2O. Two 200-ml pre-cultures were inoculated with 20 ml of the blended mycelium solution. Pre-cultures were cultivated at 120 rpm in a rotary shaker. After 48 h of growth, the mycelium was harvested without suction over a piece of cheese-cloth, washed with TNK-MM (without carbon source) and 1.5 g mycelium (wet weight) was transferred to 250 ml Erlenmeyer flasks containing 50 ml TNK-MM with 25 mM D-fructose or L-arabinose. For RNA isolation, mycelium was harvested with suction over a piece of cheese-cloth, dried between tissue paper and directly frozen in liquid nitrogen.

extract_protocol:
Total RNA was extracted from mycelium ground in a Tissue Lyser II (Qiagen) using TRIzol reagent (Invitrogen) according to the instructions of the manufacturer. Total RNA samples were purified with NucleoSpin RNA Clean-up Kit (Macherey-Nagel, Germany). Contaminating DNA is removed by an rDNase solution directly on the silica membrane. RNA quality was checked with the RNA 6000 Nano LabChip Kit on a 2100 Bioanalyzer (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: P. oryzae was grown for 2 h, 4 h or 24 h in liquid TNK-MM containing 25 mM D-glucose or 0.5% arabinan with 5 mM L-arabinose. The culture supernatants were sampled and stored at -20˚C while the mycelium was harvested and directly frozen in liquid nitrogen.

tag: strain info.

value: WT; Guy11Δku80

value: mycelium

tag: sampling time

value: 2 hours

tag: growth media containing

value: 25 mM D-fructose


title: fru-2h replicate 2


title: ara-2h replicate 1

description: Pyricularia oryza wild type on arabinose 2 hours

value: 25 mM L-arabinose


title: Hsf1_t0_3.0U

description:
Nucleosome positioning in the Hsf1-FRB-GFP strain, without addition of rapamycin. The DNA was digested using 3.0 U of MNase.
The anchor away system (Haruki et al., 2008) was recreated in the Saccharomyces cerevisiae S288C/BY4742 strain. To achieve this FPR1 was deleted, a tor1-1 mutation was introduced to desensitize the strain to rapamycin and RPL13A was tagged with 2xFKBP12 as in the original anchor away system (Haruki et al., 2008). This strain was the parental strain used to create the specific anchor away strains. This strain is referred to as wildtype (WT) throughout the study. In order to create the specific anchor away strains, Hsf1 was tagged with an FRB-yEGFP tag.


title: ara-4h

description: Pyricularia oryza wild type on arabinose 4 hours

value: 4 hours


title: ara-8h

description: Pyricularia oryza wild type on arabinose 8 hours

value: 8 hours


title: Hsf1_t0_0.2U

description:
Nucleosome positioning in the Hsf1-FRB-GFP strain without addition of rapamycin. The DNA was digested using 0.1875 U of MNase.
The anchor away system (Haruki et al., 2008) was recreated in the Saccharomyces cerevisiae S288C/BY4742 strain. To achieve this FPR1 was deleted, a tor1-1 mutation was introduced to desensitize the strain to rapamycin and RPL13A was tagged with 2xFKBP12 as in the original anchor away system (Haruki et al., 2008). This strain was the parental strain used to create the specific anchor away strains. This strain is referred to as wildtype (WT) throughout the study. In order to create the specific anchor away strains, Hsf1 was tagged with an FRB-yEGFP tag.


title: Hsf1_t30_0.05U

description:
Nucleosome positioning in the Hsf1-FRB-GFP strain, 30 minutes after addition of rapamycin (7.5 uM final concentration). The DNA was digested using 0.046875U of MNase.
The anchor away system (Haruki et al., 2008) was recreated in the Saccharomyces cerevisiae S288C/BY4742 strain. To achieve this FPR1 was deleted, a tor1-1 mutation was introduced to desensitize the strain to rapamycin and RPL13A was tagged with 2xFKBP12 as in the original anchor away system (Haruki et al., 2008). This strain was the parental strain used to create the specific anchor away strains. This strain is referred to as wildtype (WT) throughout the study. In order to create the specific anchor away strains, Hsf1 was tagged with an FRB-yEGFP tag.


title: Hsf1_t0_0.8U

description:
Nucleosome positioning in the Hsf1-FRB-GFP strain without addition of rapamycin. The DNA was digested using 0.75 U of MNase.
The anchor away system (Haruki et al., 2008) was recreated in the Saccharomyces cerevisiae S288C/BY4742 strain. To achieve this FPR1 was deleted, a tor1-1 mutation was introduced to desensitize the strain to rapamycin and RPL13A was tagged with 2xFKBP12 as in the original anchor away system (Haruki et al., 2008). This strain was the parental strain used to create the specific anchor away strains. This strain is referred to as wildtype (WT) throughout the study. In order to create the specific anchor away strains, Hsf1 was tagged with an FRB-yEGFP tag.


title: Hsf1_t30_0.8U

description:
Nucleosome positioning in the Hsf1-FRB-GFP strain, 30 minutes after addition of rapamycin (7.5 uM final concentration). The DNA was digested using 0.75U of MNase.
The anchor away system (Haruki et al., 2008) was recreated in the Saccharomyces cerevisiae S288C/BY4742 strain. To achieve this FPR1 was deleted, a tor1-1 mutation was introduced to desensitize the strain to rapamycin and RPL13A was tagged with 2xFKBP12 as in the original anchor away system (Haruki et al., 2008). This strain was the parental strain used to create the specific anchor away strains. This strain is referred to as wildtype (WT) throughout the study. In order to create the specific anchor away strains, Hsf1 was tagged with an FRB-yEGFP tag.


title: ara-2h replicate 2


title: Hsf1_t0_0.05U

description:
Nucleosome positioning in the Hsf1-FRB-GFP strain, without addition of rapamycin. The DNA was digested using 0.046875U of MNase.
The anchor away system (Haruki et al., 2008) was recreated in the Saccharomyces cerevisiae S288C/BY4742 strain. To achieve this FPR1 was deleted, a tor1-1 mutation was introduced to desensitize the strain to rapamycin and RPL13A was tagged with 2xFKBP12 as in the original anchor away system (Haruki et al., 2008). This strain was the parental strain used to create the specific anchor away strains. This strain is referred to as wildtype (WT) throughout the study. In order to create the specific anchor away strains, Hsf1 was tagged with an FRB-yEGFP tag.


title: R3

city: Santa Cruz

first: Andrew

last: Wallace

address: University of California, Santa Cruz Molecular, Cell & Developmental Biology Sinsheimer Labs 1156 High Street

department: Molecular, Cell and Developmental Biology

institute: University of California, Santa Cruz

description:
Processed data file: merge_graphs_all_events_C3.confirmed.gff3
Processed data file: ref_assisted_293T_Rocio_hg19_merged.gtf
Processed data file: Supplemental Tables_RTMN et al.xlsx

data_processing:
RNAseq 1: The 100x100bp paired-end reads were not trimmed.
RNAseq 2: Reads mapping (by bowtie2) to human repeatMasker elements were discarded.
RNAseq 3: Reads were mapped to hg19 by STAR, aided by a gtf file based on Gencode V19 with 100bp overlap.
RNAseq 4: Duplicate reads were removed based on coincident mapping, and only one hit from multi-mapping reads was considered.
RNAseq 5: Differential gene expression analysis was performed using DEseq2.
RNAseq 6: The paired-end bam files were used as input to StringTie, which generated an augmented transcriptome annotation for each sample based off of Gencode v19.
RNAseq 7: Individual transcriptome annotations were merged using stringtie –merge to generate a single GTF.
RNAseq 7: The paired-end bam files and the augmented StringTie GTF were used as input to SplAdder to annotate splice events and determine percent-spliced-in (PSI) values for skipped exon, multiple skipped exon, mutually exclusive exons, alt3 prime, alt5 prime, and intron retention events.
RNAseq 8: The SplAdder output junction counts were used as input to rMATS-STAT – differential splice tests were performed in paired mode with three PSI thresholds: > 0.1, > 0.05, and > 0.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: ref_assisted_293T_Rocio_hg19_merged.gtf: GTF file contains the merged transcript annotations generated using StringTi.
Supplementary_files_format_and_content: merge_graphs_all_events_C3.confirmed.gff3: GFF3 file contains splicing event annotations for the combined samples generated using SplAdder.
Supplementary_files_format_and_content: Supplemental Tables_RTMN et al.xlsx: Excel file contains multiple spreadsheets including DEseq2 output, splicing event quantifications (PSI values from SplAdder, FDR values from rMATS-STAT differential tests), as well as their parent genes, transcripts, and genomic locations, as well as the gene set enrichment analysis results, mapping statistics, and primers used for validations.

molecule: cytoplasmic RNA

source_name: HEK 293 T cells, Rapamycin

growth_protocol: HEK 293 T cells were grown in DMEM 10% FBS.

extract_protocol:
RNA was extracted from cytoplasmic extracts employing TRIzol LS, re-purified and DNase treated employing miRNeasy Micro Kit (Qiagen).
TruSeq Stranded mRNA Library Prep Kit.

treatment_protocol: HEK 293 T cells were starved in DMEM 10% FBS No Glutamine medium for 24h. Rapamycin or vehicle (DMSO) was incubated during 30min at 37C 5% CO2 prior to feeding with complete medium containing glutamine. 50ng/mL emetine was added after 72h during 4h prior to harvesting. Cells were lysed in 0.5% NP40, 20 mM Tris-HCl pH 7.5,10 0mM KCl and 10 mM MgCl2 to obtain cytoplasmic extracts.

tag: cell line

value: HEK 293 T

tag: treatment

value: Rapamycin


title: R1


title: R2


title: E2

source_name: HEK 293 T cells, Emetine

value: Emetine


title: C1

source_name: HEK 293 T cells, Control

value: Control


title: C3


title: E1


title: Hsf1_input

description:
Input material for the Hsf1_ChIP sample
The anchor away system (Haruki et al., 2008) was recreated in the Saccharomyces cerevisiae S288C/BY4742 strain. To achieve this FPR1 was deleted, a tor1-1 mutation was introduced to desensitize the strain to rapamycin and RPL13A was tagged with 2xFKBP12 as in the original anchor away system (Haruki et al., 2008). This strain was the parental strain used to create the specific anchor away strains. This strain is referred to as wildtype (WT) throughout the study. In order to create the specific anchor away strains, Hsf1 was tagged with an FRB-yEGFP tag.


title: C2


title: FLCNKO_rep2

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

data_processing:
Fastq files were align to the mm9 referece geome using STAR and default parameters
Ensmebl v67 gene annotations were used for gene counts, gene counts were obtain using STAR
Raw gene counts were transformed using 'LIMMA-Voom' method
Supplementary_files_format_and_content: Voom transformed abundance measurements

source_name: ingWAT

extract_protocol:
ingWATs were harvested and RNA was isolated by using Trizol and purified by RNAeasy columns (QIAGEN)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: inguinal WAT


title: FLCNKO_rep1


title: Hsf1_ChIP

description:
ChIP sequencing of Hsf1-FRB-GFP (without depleting Hsf1 from the nucleus)
The anchor away system (Haruki et al., 2008) was recreated in the Saccharomyces cerevisiae S288C/BY4742 strain. To achieve this FPR1 was deleted, a tor1-1 mutation was introduced to desensitize the strain to rapamycin and RPL13A was tagged with 2xFKBP12 as in the original anchor away system (Haruki et al., 2008). This strain was the parental strain used to create the specific anchor away strains. This strain is referred to as wildtype (WT) throughout the study. In order to create the specific anchor away strains, Hsf1 was tagged with an FRB-yEGFP tag.


title: WT_rep2


title: AngII28D-1

status: Public on Nov 10 2016

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

data_processing:
he reads were sequenced using a stranded protocol and aligned against the mouse genome, mm8, using Tophat 2.0.12 with bowtie 0.12.9/1.1
The parameters used are --bowtie1 --prefilter-multihits --no-coverage-search --transcriptome-index --library-type firststrand
Readcounts were generated using a custom script based on the same strategy as HTSeq-count. Genes that have no expression across all samples are removed from the dataset.
Prior to analysis the provided processed data files were only normalized for sequencing depth, using the DESeq2 package, and normalized for batch effects (ex: sequencing run)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample …

source_name: Heart

extract_protocol:
WT mice were infused with Ang II subcutaneously (1000 ng/kg/min) for 0, 7, and 28 days with ALZET miniosmotic pumps (n=2). Hearts were collected for RNA extraction and Library construction. RNA libraries were then sequenced at 10pM on the Illumina HiSeq 2000.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: heart


title: WT_rep1


title: AngII28D-2

description: WT mice were infused with Ang II subcutaneously (1000 ng/kg/min) for 0, 7, and 28 days with ALZET miniosmotic pumps (n=2).


title: Hsf1_t30_0.2U

description:
Nucleosome positioning in the Hsf1-FRB-GFP strain, 30 minutes after addition of rapamycin (7.5 uM final concentration). The DNA was digested using 0.1875U of MNase.
The anchor away system (Haruki et al., 2008) was recreated in the Saccharomyces cerevisiae S288C/BY4742 strain. To achieve this FPR1 was deleted, a tor1-1 mutation was introduced to desensitize the strain to rapamycin and RPL13A was tagged with 2xFKBP12 as in the original anchor away system (Haruki et al., 2008). This strain was the parental strain used to create the specific anchor away strains. This strain is referred to as wildtype (WT) throughout the study. In order to create the specific anchor away strains, Hsf1 was tagged with an FRB-yEGFP tag.


title: AngII7D-2

treatment_protocol: WT mice were infused with Ang II subcutaneously (1000 ng/kg/min) for 0, 7, and 28 days with ALZET miniosmotic pumps


title: AngII7D-1


title: 0D-1


title: 0D-2


title: EB_Nkx2.5GFP_mTmG_85-H10

city: Pittsburgh

first: Guang

last: Li

address: 530 45th St. 8116 Rangos Research Center

department: Developmental Biology

institute: University of Pittsburgh

data_processing:
Basecalls performed using RTA (Real Time Analysis. v1.18)
Sequenced reads were demultiplexed, and mapped to mouse genome GRCm38.79 with STAR 2.4.0
The mapped reads of each gene were quantified with HTSeq
Genome_build: GRCm38.79
Supplementary_files_format_and_content: tab-delimited text files include count number for each gene in each Sample

source_name: embryoid body Nkx2.5GFP heart

extract_protocol:
Single cells derived from mouse embryonic hearts were captured, lysed, and pre-amplified in C1 microfluidic chips.
RNA libraries were prepared with Nextera XT reagent for illumina sequencing

tag: developmental stage

value: day 10

value: embryoid body


title: EB_Nkx2.5GFP_mTmG_85-H11


title: EB_Nkx2.5GFP_mTmG_85-H6


title: E3


title: EB_Nkx2.5GFP_mTmG_85-H2


title: EB_Nkx2.5GFP_mTmG_85-H9


title: EB_Nkx2.5GFP_mTmG_85-G8


title: EB_Nkx2.5GFP_mTmG_85-G9


title: EB_Nkx2.5GFP_mTmG_85-H1


title: EB_Nkx2.5GFP_mTmG_85-G2


title: EB_Nkx2.5GFP_mTmG_85-G10


title: EB_Nkx2.5GFP_mTmG_85-G7


title: EB_Nkx2.5GFP_mTmG_85-G11


title: EB_Nkx2.5GFP_mTmG_85-G1


title: EB_Nkx2.5GFP_mTmG_85-F9


title: EB_Nkx2.5GFP_mTmG_85-F8


title: EB_Nkx2.5GFP_mTmG_85-F7


title: EB_Nkx2.5GFP_mTmG_85-F3


title: EB_Nkx2.5GFP_mTmG_85-F6


title: EB_Nkx2.5GFP_mTmG_85-F11


title: EB_Nkx2.5GFP_mTmG_85-F10


title: EB_Nkx2.5GFP_mTmG_85-F1


title: EB_Nkx2.5GFP_mTmG_85-E9


title: EB_Nkx2.5GFP_mTmG_85-E8


title: EB_Nkx2.5GFP_mTmG_85-E6


title: EB_Nkx2.5GFP_mTmG_85-E12


title: EB_Nkx2.5GFP_mTmG_85-E10


title: EB_Nkx2.5GFP_mTmG_85-D8


title: EB_Nkx2.5GFP_mTmG_85-E11


title: EB_Nkx2.5GFP_mTmG_85-D7


title: EB_Nkx2.5GFP_mTmG_85-E5


title: EB_Nkx2.5GFP_mTmG_85-D5


title: EB_Nkx2.5GFP_mTmG_85-D12


title: EB_Nkx2.5GFP_mTmG_85-F2


title: EB_Nkx2.5GFP_mTmG_85-D10


title: EB_Nkx2.5GFP_mTmG_85-E1


title: EB_Nkx2.5GFP_mTmG_85-E3


title: EB_Nkx2.5GFP_mTmG_85-D6


title: EB_Nkx2.5GFP_mTmG_85-D11


title: EB_Nkx2.5GFP_mTmG_85-D9


title: EB_Nkx2.5GFP_mTmG_85-C9


title: EB_Nkx2.5GFP_mTmG_85-C5


title: EB_Nkx2.5GFP_mTmG_85-C7


title: EB_Nkx2.5GFP_mTmG_85-C4


title: EB_Nkx2.5GFP_mTmG_85-C8


title: EB_Nkx2.5GFP_mTmG_85-C3


title: EB_Nkx2.5GFP_mTmG_85-C11


title: EB_Nkx2.5GFP_mTmG_85-C2


title: EB_Nkx2.5GFP_mTmG_85-C12


title: EB_Nkx2.5GFP_mTmG_85-C10


title: EB_Nkx2.5GFP_mTmG_85-C1


title: EB_Nkx2.5GFP_mTmG_85-B9


title: EB_Nkx2.5GFP_mTmG_85-D2


title: EB_Nkx2.5GFP_mTmG_85-B6


title: EB_Nkx2.5GFP_mTmG_85-D3


title: EB_Nkx2.5GFP_mTmG_85-B8


title: EB_Nkx2.5GFP_mTmG_85-B7


title: EB_Nkx2.5GFP_mTmG_85-B5


title: EB_Nkx2.5GFP_mTmG_85-D1


title: EB_Nkx2.5GFP_mTmG_85-C6


title: EB_Nkx2.5GFP_mTmG_85-B12


title: EB_Nkx2.5GFP_mTmG_85-B1


title: EB_Nkx2.5GFP_mTmG_85-A5


title: EB_Nkx2.5GFP_mTmG_85-B11


title: EB_Nkx2.5GFP_mTmG_85-A4


title: EB_Nkx2.5GFP_mTmG_85-A9


title: EB_Nkx2.5GFP_mTmG_85-A8


title: EB_Nkx2.5GFP_mTmG_85-A7


title: EB_Nkx2.5GFP_mTmG_85-B10


title: EB_Nkx2.5GFP_mTmG_85-A6


title: EB_Nkx2.5GFP_mTmG_85-A3


title: EB_Nkx2.5GFP_mTmG_85-A12


title: EB_Nkx2.5GFP_mTmG_85-A11


title: EB_Nkx2.5GFP_mTmG_85-A10


title: EB_Nkx2.5GFP_mTmG_84-H7


title: EB_Nkx2.5GFP_mTmG_85-A1


title: EB_Nkx2.5GFP_mTmG_84-H2


title: EB_Nkx2.5GFP_mTmG_84-H3


title: EB_Nkx2.5GFP_mTmG_84-H10


title: EB_Nkx2.5GFP_mTmG_85-B4


title: EB_Nkx2.5GFP_mTmG_84-G2


title: EB_Nkx2.5GFP_mTmG_84-G8


title: EB_Nkx2.5GFP_mTmG_84-G3


title: EB_Nkx2.5GFP_mTmG_84-G7


title: EB_Nkx2.5GFP_mTmG_84-G12


title: EB_Nkx2.5GFP_mTmG_84-F9


title: EB_Nkx2.5GFP_mTmG_84-F7


title: EB_Nkx2.5GFP_mTmG_84-F8


title: EB_Nkx2.5GFP_mTmG_85-A2


title: EB_Nkx2.5GFP_mTmG_84-F2


title: EB_Nkx2.5GFP_mTmG_84-E12


title: EB_Nkx2.5GFP_mTmG_84-D9


title: EB_Nkx2.5GFP_mTmG_84-D7


title: EB_Nkx2.5GFP_mTmG_84-F10


title: EB_Nkx2.5GFP_mTmG_84-E8


title: EB_Nkx2.5GFP_mTmG_84-F1


title: EB_Nkx2.5GFP_mTmG_84-D2


title: EB_Nkx2.5GFP_mTmG_84-D10


title: EB_Nkx2.5GFP_mTmG_84-D11


title: EB_Nkx2.5GFP_mTmG_84-D12


title: EB_Nkx2.5GFP_mTmG_84-E1


title: EB_Nkx2.5GFP_mTmG_84-D3


title: EB_Nkx2.5GFP_mTmG_84-G1


title: EB_Nkx2.5GFP_mTmG_84-G9


title: EB_Nkx2.5GFP_mTmG_84-C8


title: EB_Nkx2.5GFP_mTmG_84-C9


title: EB_Nkx2.5GFP_mTmG_84-C7


title: EB_Nkx2.5GFP_mTmG_84-C4


title: EB_Nkx2.5GFP_mTmG_84-C5


title: EB_Nkx2.5GFP_mTmG_84-C3


title: EB_Nkx2.5GFP_mTmG_84-C2


title: EB_Nkx2.5GFP_mTmG_84-F3


title: EB_Nkx2.5GFP_mTmG_84-D8


title: EB_Nkx2.5GFP_mTmG_84-F4


title: EB_Nkx2.5GFP_mTmG_84-C1


title: EB_Nkx2.5GFP_mTmG_84-E9


title: EB_Nkx2.5GFP_mTmG_84-B8


title: EB_Nkx2.5GFP_mTmG_84-C10


title: EB_Nkx2.5GFP_mTmG_84-B2


title: EB_Nkx2.5GFP_mTmG_84-B11


title: EB_Nkx2.5GFP_mTmG_84-B6


title: EB_Nkx2.5GFP_mTmG_84-B7


title: EB_Nkx2.5GFP_mTmG_84-B3


title: EB_Nkx2.5GFP_mTmG_84-B10


title: EB_Nkx2.5GFP_mTmG_84-B5


title: EB_Nkx2.5GFP_mTmG_84-A9


title: EB_Nkx2.5GFP_mTmG_84-B1


title: EB_Nkx2.5GFP_mTmG_84-A7


title: EB_Nkx2.5GFP_mTmG_84-A6


title: EB_Nkx2.5GFP_mTmG_84-A8


title: EB_Nkx2.5GFP_mTmG_84-A4


title: EB_Nkx2.5GFP_mTmG_84-A5


title: EB_Nkx2.5GFP_mTmG_84-A3


title: EB_Nkx2.5GFP_mTmG_84-A2


title: EB_Nkx2.5GFP_mTmG_84-A12


title: EB_Nkx2.5GFP_mTmG_84-A1


title: EB_Nkx2.5GFP_mTmG_84-A10


title: EB_Nkx2.5GFP_mTmG_84-A11


title: EB_Nkx2.5_Cre_mTmG92-H4

source_name: embryoid body Nkx2.5Cre mTmG heart


title: EB_Nkx2.5GFP_mTmG_84-B4


title: EB_Nkx2.5GFP_mTmG_84-B12


title: EB_Nkx2.5_Cre_mTmG92-H2


title: EB_Nkx2.5_Cre_mTmG92-H3


title: EB_Nkx2.5_Cre_mTmG92-H11


title: EB_Nkx2.5_Cre_mTmG92-H10


title: EB_Nkx2.5_Cre_mTmG92-H12


title: EB_Nkx2.5_Cre_mTmG92-G8


title: EB_Nkx2.5_Cre_mTmG92-G12


title: EB_Nkx2.5_Cre_mTmG92-G3


title: EB_Nkx2.5_Cre_mTmG92-H1


title: EB_Nkx2.5_Cre_mTmG92-G11


title: EB_Nkx2.5_Cre_mTmG92-G7


title: EB_Nkx2.5_Cre_mTmG92-G6


title: EB_Nkx2.5_Cre_mTmG92-F9


title: EB_Nkx2.5_Cre_mTmG92-G1


title: EB_Nkx2.5_Cre_mTmG92-F8


title: EB_Nkx2.5_Cre_mTmG92-G5


title: EB_Nkx2.5_Cre_mTmG92-F4


title: EB_Nkx2.5_Cre_mTmG92-G4


title: EB_Nkx2.5_Cre_mTmG92-F3


title: EB_Nkx2.5_Cre_mTmG92-F6


title: EB_Nkx2.5_Cre_mTmG92-F7


title: EB_Nkx2.5_Cre_mTmG92-F2


title: EB_Nkx2.5_Cre_mTmG92-F12


title: EB_Nkx2.5_Cre_mTmG92-E8


title: EB_Nkx2.5_Cre_mTmG92-F11


title: EB_Nkx2.5_Cre_mTmG92-E7


title: EB_Nkx2.5_Cre_mTmG92-E9


title: EB_Nkx2.5_Cre_mTmG92-E5


title: EB_Nkx2.5_Cre_mTmG92-E3


title: EB_Nkx2.5_Cre_mTmG92-E12


title: EB_Nkx2.5_Cre_mTmG92-E11


title: EB_Nkx2.5_Cre_mTmG92-D9


title: EB_Nkx2.5_Cre_mTmG92-E10


title: EB_Nkx2.5_Cre_mTmG92-E1


title: EB_Nkx2.5_Cre_mTmG92-D8


title: EB_Nkx2.5_Cre_mTmG92-D5


title: EB_Nkx2.5_Cre_mTmG92-D2


title: EB_Nkx2.5_Cre_mTmG92-D6


title: EB_Nkx2.5_Cre_mTmG92-D7


title: EB_Nkx2.5_Cre_mTmG92-C9


title: EB_Nkx2.5_Cre_mTmG92-F10


title: EB_Nkx2.5_Cre_mTmG92-C5


title: EB_Nkx2.5_Cre_mTmG92-C7


title: EB_Nkx2.5_Cre_mTmG92-C3


title: EB_Nkx2.5_Cre_mTmG92-C4


title: EB_Nkx2.5_Cre_mTmG92-C8


title: EB_Nkx2.5_Cre_mTmG92-C2


title: EB_Nkx2.5_Cre_mTmG92-C6


title: EB_Nkx2.5_Cre_mTmG92-C11


title: EB_Nkx2.5_Cre_mTmG92-C10


title: EB_Nkx2.5_Cre_mTmG92-C12


title: EB_Nkx2.5_Cre_mTmG92-C1


title: EB_Nkx2.5_Cre_mTmG92-B6


title: EB_Nkx2.5_Cre_mTmG92-B8


title: EB_Nkx2.5_Cre_mTmG92-B9


title: EB_Nkx2.5_Cre_mTmG92-B3


title: EB_Nkx2.5_Cre_mTmG92-B4


title: EB_Nkx2.5_Cre_mTmG92-B11


title: EB_Nkx2.5_Cre_mTmG92-B5


title: EB_Nkx2.5_Cre_mTmG92-B1


title: EB_Nkx2.5_Cre_mTmG92-D4


title: EB_Nkx2.5_Cre_mTmG92-B2


title: EB_Nkx2.5_Cre_mTmG92-A7


title: EB_Nkx2.5_Cre_mTmG92-A5


title: EB_Nkx2.5_Cre_mTmG92-A3


title: EB_Nkx2.5_Cre_mTmG92-A9


title: EB_Nkx2.5_Cre_mTmG92-B10


title: EB_Nkx2.5_Cre_mTmG92-A1


title: EB_Nkx2.5_Cre_mTmG91-H9


title: EB_Nkx2.5_Cre_mTmG92-A11


title: EB_Nkx2.5_Cre_mTmG91-H1


title: EB_Nkx2.5_Cre_mTmG91-H3


title: EB_Nkx2.5_Cre_mTmG91-H8


title: EB_Nkx2.5_Cre_mTmG91-H10


title: EB_Nkx2.5_Cre_mTmG91-H7


title: EB_Nkx2.5_Cre_mTmG91-G9


title: EB_Nkx2.5_Cre_mTmG91-G8


title: EB_Nkx2.5_Cre_mTmG91-G3


title: EB_Nkx2.5_Cre_mTmG92-E2


title: EB_Nkx2.5_Cre_mTmG91-F9


title: EB_Nkx2.5_Cre_mTmG91-G6