title: EN28

city: Irvine

first: Bogi

last: Andersen

address: 250 Sprague Hall

department: Department of Biological Chemistry

institute: University of California, Irvine

description:
EN ZT28
R114-L8-P3-GTGGCC

data_processing:
RNA-Seq short reads were mapped to mouse genome mm10 by Tophat2 (Kim et al., 2013), and rRNA reads were removed from the bam file via RSeQC (Wang et al., 2012). The reads with mapping quality less than 5 were removed with SAMtools (Li et al., 2009)
Then the exon and intron gene reads and the reads for the antisense region of the whole gene body were counted with HOMER (Heinz et al., 2010). Transcripts were annotated using the UCSC known canonical gene set (31872 total; 22526 with introns).
The reads were normalized into RPKM (Reads Per Kilobase per Million) by CQN (Hansen et al., 2012).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file with raw count or RPKM for each gene for each Sample

source_name: EN ZT28

growth_protocol: Twenty-three day old C57BL/6NCrl mice (Charles River Laboratories, strain code 027) were acclimated to the mouse facility for 1 to 2 weeks before starting the RF schedules. The mice were housed under 12h:12h light/dark cycles (Light on at 6:30am, ZT0, and off at 6:30pm, ZT12) with free access to water during the whole experiment, and free access to food before restricted feeding. The restricted access to food according to the designed RF schedules was continued for 18 to 21 days; skin was sampled at the end of the experiment during the second telogen when mice were at age around Day 54; the telogen state of the skin was verified by histology. Regular chow was used in all experiments.

extract_protocol:
RNA was isolated with Trizol reagent. Total RNAs with RNA integrity number (RIN) higher than 6.5 were pooled, treated with RNase-Free DNase (Qiagen cat. No. 79254), and cleaned with RNeasy Mini Elute Cleanup Kit (Qiagen).
Illumina TruSeq Stranded Total RNA Sample Prep Kit was used with pooled RNA for library construction.

treatment_protocol: Hair was shaved before sampling and the sample was kept in RNAlater until RNA extraction.

tag: strain

value: whole back skin

tag: age

value: 8 weeks

tag: genotype/variation

value: wild type

tag: growth phase

value: telogen

tag: gender

value: male

tag: feeding window

tag: sampling time


title: DLD1-0nM-1

status: Public on Aug 01 2017

type: SRA

city: Boston

first: David

middle: T

last: Ting

state: MA

address: 149 E 13th street

department: Cancer Center

country: USA

institute: Massachusetts General Hospital

library_source: transcriptomic

data_processing:
The paired-end reads were aligned to the human_g1k_v37.fasta reference genome from http://www.1000genomes.org using BSMAP version 2.74 with default settings.
Duplicate reads were marked using the MarkDuplicates tool in picard-tools-1.8.4 and were removed.
BSMAP’s methratio.py script was used to extract methylation ratio data from the mapped reads with the --zero-meth, --remove-duplicate, and --combine-CpG options.
CpG-specific methylation data was extracted by taking the rows of the methratio.py output that had a value of “+” in the strand field and had a sequence context that began with “..CG”.
Each CpG in the CpG methylation data table was annotated with repeat masker information (ucsc_repeatmasker_2014-06-23.txt from the UCSC genome browser (https://genome.ucsc.edu) and its distance from the nearest Gencode annotation (gencode.v19.annotation.gtf from http://www.gencodegenes.org).
CpG methylation fractions for specific repeat types were averaged over all repeats of the given type. Distances to the nearest annotated genes were binned in 5,000-base increments from 0 to 100,000 bases, and CpG methylation fractions were averaged by distance bin within each repeat class.
Genome_build: hg19
Supplementary_files_format_and_content: CSV file of average percent CpG methylation for repeats annotated in repeat masker

molecule: total RNA

organism: Homo sapiens

source_name: Colon cancer Cell line DLD1

growth_protocol: RPMI-1640 + 10% FBS + 1% Pen/Strep

extract_protocol:
DNA extracted using Qiagen DNA micro kit
Methyl sequencing with the EZ DNA Methylation-Lightning Kit (Zymo Research) followed by Illumina library construction using the EpiGnome Methyl-Seq Kit (Epicentre/Illumina) .  Sequencing on MiSeq 75 bp pair-end

treatment_protocol: AZA as indicated

tag: aza concentration

value: 0 nM


title: DLD1-0nM-2


title: EN12

state: CA

description:
EN ZT12
R114-L7-P2-GCCAAT

organism: Mus musculus

source_name: EN ZT12

tag: tissue


title: EN20

description:
EN ZT20
R114-L8-P1-ATCACG

source_name: EN ZT20


title: EN16

description:
EN ZT16
R114-L7-P3-ATGTCA

source_name: EN ZT16


title: EN08

description:
EN ZT8
R114-L7-P1-ACAGTG

source_name: EN ZT8


title: ED28

description:
ED ZT28
R114-L6-P1-CGATGT

source_name: ED ZT28


title: ED24

description:
ED ZT24
R114-L5-P3-CGTACG

source_name: ED ZT24


title: ED16

description:
ED ZT16
R114-L5-P1-ACTTGA

source_name: ED ZT16


title: EN00

description:
EN ZT0
R114-L6-P2-CAGATC

source_name: EN ZT0


title: RNAseq_Myc_sgMll3/Cas9_3

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

description:
Myc Mll3 2T1
Processed data file: deseq2_mll3li_p53.txt

data_processing:
Resulting RNA-Seq data was analyzed by removing adaptor sequences using Trimmomatic (Bolger et al. 2014). RNA-seq reads were then aligned to GRCm38.75/mm10 with STAR (Dobin et al. 2012). Genome-wide transcript counting was performed by HTSeq to generate RPKM matrix. Differentially expressed genes were identified by DESeq2 (v.1.8.2 ,package in R).
Genome_build: GRCm38.75/mm10
Supplementary_files_format_and_content: rpkm.txt: Tab-delimited text file includes RPKMs from each experiment.
Supplementary_files_format_and_content: deseq2_mll3li_p53.txt: Tab-delimited text file includes differentially expressed genes.

source_name: Liver tumor cell line, Myc;sgMll3/Cas9

growth_protocol: Derived primary proliferating cells were cultured in complete DMEM (10% FBS, 1x Penicillin/Streptomycin), maintained on collagen-coated plates (PurCol, Advanced Biomatrix), and passaged until visibly free from fibroblasts. RNA from independent triplicates was extracted.

extract_protocol:
Cells were lysed by adding RLT buffer directly to the culture dish. RNA was extracted using RNeasy Qiagen Kit.
RNA samples were used for HiSeq 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).

tag: strain/background

tag: cell type

value: Liver tumor cell line

tag: viral transduction

value: in vivo hydrodynamic transfection with px330_sgMll3

tag: treatment


title: MtbRvRho

city: Bangalore

first: Valakunja

last: Nagaraja

state: Karnataka

address: C V Raman Avenue

department: Department of Microbiology and Cell Biology

country: India

institute: Indian Institute of Science (IISc)

description: Chromatin immunoprecipitation against Rho

library_source: genomic

data_processing:
Illumina Genome Analyzer Iix
Data processing Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to M.tb H37Rv genome (NCBI accession NC_000962.2)
Mapping done using the Bowtie2 program (Version = 2.0.5) with default parameters
Coverage calculated using Bedtools ( Version : 2.17.0 )
Genome_build: M.tb H37Rv genome (NCBI accession NC_000962.2)
Supplementary_files_format_and_content: Coverage calculated using Bedtools ( Version : 2.17.0 ). M.tb H37Rv genome (NCBI accession NC_000962.2) is used as the genome build

molecule: genomic DNA

organism: Mycobacterium tuberculosis H37Rv

source_name: Log/exponential phase Mtb H37Rv cells

growth_protocol: Mycobacterium tuberculosis H37Rv was grown at 37°C in 7H9 broth (Difco) supplemented with 0.2% glycerol, 0.05% Tween 80 and 10% albumin-dextrose-catalase (ADC, Middlebrook) or on 7H10 plates supplemented with 0.5% glycerol and 10% oleic acid-albumin-dextrose-catalase (OADC, Middlebrook). Logarithmic-phase cultures (exponential phase) were harvested at an optical density (OD600) of 0.4-0.6.

extract_protocol:
Crosslinked bacteria cells were sonicated and protein-DNA complexes were isolated with No antibody (Mock) or anti-TopoI or anti-gyrA antibodies.
Libraries were prepared according to Illumina's instructions.

treatment_protocol: M. tuberculosis cultures, either in exponential or stationary phase, were cross-linked with 1% formaldehyde for ten minutes at 37°C.

tag: antibody

value: antibody:anti-Rho(Polyclonal) ,lot no. AMVN2009

value: Exponential phase


title: ED20

description:
ED ZT20
R114-L5-P2-GGCTAC

source_name: ED ZT20


title: EN24

description:
EN ZT24
R114-L8-P2-TAGCTT

source_name: EN ZT24


title: ED12

description:
ED ZT12
R114-L4-P3-ACTGAT

source_name: ED ZT12


title: EN04

description:
EN ZT4
R114-L6-P3-GTGAAA

source_name: EN ZT4


title: ski2; PGK-CGA

city: St Louis

first: Hani

last: Zaher

state: MO

address: 1 Brookings Drive

department: Biology

institute: Washington University in St Louis

description: processed.xls; '3(CGA)_3end' spreadsheet

data_processing:
Fastx-toolkit V0.0.13 used to trim terminal nt from barcode reads
Reads were processed with Cutadapt 1.12 to prep for Novoalign (no trimming)
Reads were demultiplexed with novobarcode V3.03.00 with Distance 1 and Format N 5
Trim Illumina adapter sequence with cutadapt 1.12 (ATTGATGGTGCCTACAG) with max 10% errors, single end mode
Align reads to custom reference seqeunce (reporter gene seqeunce) using nonoalign V3.03.00
Filter reads, convert sam to bam, sort and index bam file with samtools-1.13
Convert bam files to bed files with bedtools
Genome_build: N/A
Supplementary_files_format_and_content: Processed data is in an excel file, one sheet per dataset, with position of read relative to the reference seqeunce ATG and number of reads at that position

organism: Saccharomyces cerevisiae

source_name: BY4741 ski2delta_whole cell

growth_protocol: Cells were grown in defined media (-ura) containing 2%galactose and 2%raffinose to OD~0.8.

extract_protocol:
RNA was extracted using hot phenol followed by chloroform extraction and ethanol precipitation.
An adenylated DNA oligo was ligated to extracted RNA. cDNA was amplified using primers designed for the Illumina HiSeq platform that contain sequence complementary to the adaptor and to position 585 of PGK1.

value: BY4741; ski2delta

value: expressing a PGK-stall seqeunce reporter gene

tag: stalling reporter type

tag: barcode

value: CAGCAT


title: ED08

description:
ED ZT8
R114-L4-P2-GATCAG

source_name: ED ZT8


title: ski2; PGK-SL

description: processed.xls; '2(SL)_3end' spreadsheet

value: a stem loop

value: ATCAGT


title: ski2; PGK-AAA

description: processed.xls; '4(AAA)_3end' spreadsheet

value: CGACGT


title: ED00

description:
ED ZT0
R114-L3-P3-GTGGCC

source_name: ED ZT0


title: ED04

description:
ED ZT4
R114-L4-P1-TTAGGC

source_name: ED ZT4


title: MD24

description:
MD ZT24
R114-L3-P1-ATCACG

source_name: MD ZT24


title: MD20

description:
MD ZT20
R114-L2-P3-ATGTCA

source_name: MD ZT20


title: MD12

description:
MD ZT12
R114-L2-P1-ACAGTG

source_name: MD ZT12


title: MD16

description:
MD ZT16
R114-L2-P2-GCCAAT

source_name: MD ZT16


title: MD00

description:
MD ZT0
R114-L1-P1-CGATGT

source_name: MD ZT0


title: MD04

description:
MD ZT4
R114-L1-P2-CAGATC

source_name: MD ZT4


title: Lateral entorhinal cortex layer II, P45, replicate 4

city: Trondheim

first: Lene

middle: Christin

last: Olsen

address: Erling Skjalgsons gt. 1

department: Medical Faculty

country: Norway

institute: Norwegian University of Science and Technology - NTNU

data_processing:
Base calling using bcl2fastq-1.8.4
Adapter sequences, reads below 20 nt, and low quality bases at the ends were removed using Trimmomatic (v0.33)
Alignment to reference genome rn6 using STAR aligner v. 2.4.0 using settings --outFilterType BySJout --chimSegmentMin 30 --runThreadN 12 --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04  --alignIntronMin 20 --alignIntronMax 1000000 --sjdbGTFfile RefSeq.gtf
Annotated and counted reads using featureCounts program in the Subread package (v.1.4.6-p1) using RefSeq gene annotations downloaded from UCSC on April 8, 2015. Used featureCounts settings -p -B -C -O -a RefSeq.gtf -t exon -s 2 -T 24 -g gene_id
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited txt-files contain read counts for each gene_id

organism: Rattus norvegicus

source_name: Entorhinal cortex

extract_protocol:
Total RNA was extracted using Ambion's RNAqueous®-Micro kit, following the manufacturer's recommendations except for an extra 1 minute incubation with wash buffer, and the ethanol added for precipitation was increased to 1.25x lysis buffer volume to include small RNAs. RNA was eluted with 2x10μl RNAqueous Elution Buffer. The amount of RNA in all samples was analyzed on the Qubit, and the quality of the RNA on the BioAnalyzer Nano Chip
Libraries were constructed using the Illumina Ribo-Zero Gold Human/Rat/Mouse kit and sequenced on the Illumina HiSeq 2500, all according to Illumina's recommended protocols (100 ng input). Illumina's dual index system was used for barcoding the samples, and all samples were run across all lanes.
Illumina TruSeq® Stranded Total RNA HT with Ribo-Zero Gold

treatment_protocol: Long Evans rats were deeply anesthetized and sacrificed by guillotine. The brain was immediately placed in oxygenated ACSF, sliced on a microtome (400μm) and placed in RNAlater. Layer slices were then dissected under a microscope.

tag: region

value: Lateral

tag: layer

value: II


title: Medial entorhinal cortex layer II, P45, replicate 4

tag: age

value: Medial


title: Lateral entorhinal cortex deep layers, P45, replicate 3

value: Deep


title: Lateral entorhinal cortex layer II, P45, replicate 3


title: Medial entorhinal cortex layer II, P45, replicate 3


title: Medial entorhinal cortex deep layers, P45, replicate 3


title: Medial entorhinal cortex deep layers, P45, replicate 1


title: Lateral entorhinal cortex deep layers, P45, replicate 1


title: Lateral entorhinal cortex deep layers, P45, replicate 2


title: Medial entorhinal cortex layer II, P45, replicate 2


title: Lateral entorhinal cortex layer II, P45, replicate 1


title: Lateral entorhinal cortex deep layers, P23, replicate 3


title: Medial entorhinal cortex layer II, P45, replicate 1


title: Medial entorhinal cortex deep layers, P45, replicate 2


title: Medial entorhinal cortex layer II, P23, replicate 3


title: Lateral entorhinal cortex deep layers, P23, replicate 2


title: Lateral entorhinal cortex layer II, P45, replicate 2


title: MD28

description:
MD ZT28
R114-L3-P2-TAGCTT

source_name: MD ZT28

tag: strain

value: whole back skin

value: 8 weeks

tag: genotype/variation

value: wild type

value: telogen


title: Lateral entorhinal cortex layer II, P23, replicate 3


title: Lateral entorhinal cortex layer II, P23, replicate 2


title: Lateral entorhinal cortex deep layers, P45, replicate 4


title: MD08

description:
MD ZT8
R114-L1-P3-GTGAAA

source_name: MD ZT8

tag: growth phase

tag: gender

value: male


title: Medial entorhinal cortex deep layers, P23, replicate 2


title: Lateral entorhinal cortex deep layers, P23, replicate 1


title: Medial entorhinal cortex deep layers, P45, replicate 4


title: Medial entorhinal cortex layer II, P23, replicate 1


title: Medial entorhinal cortex deep layers, P9, replicate 4


title: Medial entorhinal cortex deep layers, P23, replicate 3


title: Lateral entorhinal cortex layer II, P9, replicate 3


title: Lateral entorhinal cortex deep layers, P9, replicate 3


title: Medial entorhinal cortex deep layers, P9, replicate 3


title: Medial entorhinal cortex layer II, P9, replicate 3


title: Medial entorhinal cortex layer II, P9, replicate 4


title: Lateral entorhinal cortex layer II, P9, replicate 2


title: Lateral entorhinal cortex deep layers, P9, replicate 2


title: Medial entorhinal cortex layer II, P9, replicate 2


title: Medial entorhinal cortex layer II, P23, replicate 2


title: Lateral entorhinal cortex deep layers, P9, replicate 1


title: Medial entorhinal cortex deep layers, P9, replicate 2


title: chronic GVHD PSGL-1loCD4+ T, 2

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

description:
chronic GVHD PSGL-1loCD4+ T
11256_WTCD-extra2

data_processing:
Illumina Casava 1.9 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using TopHat v1.2.0 with default settings. Aligned reads were used to generate pileup for each base with Samtools v0.1.18.
Read counts for each refseq gene were summarized using custom built R scripts. The exons in all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the TMM method implemented in Bioconductor package "edgeR" .
Genome_build: mm9
Supplementary_files_format_and_content: Normalized counts for each refseq genes

source_name: chronic GVHD mice

growth_protocol: in vivo alloreactive T cell expansion

extract_protocol:
Using miRNeasy Mini Kit purchased from Qiagen (Valencia, USA)
Ribozero RNA-seq

value: Speen

value: CD4 T cells

tag: cell subtype

value: PSGL-1loCD4+ T


title: Medial entorhinal cortex deep layers, P9, replicate 1


title: Medial entorhinal cortex layer II, P9, replicate 1


title: Lateral entorhinal cortex deep layers, P2, replicate 5


title: Lateral entorhinal cortex layer II, P9, replicate 1


title: Medial entorhinal cortex layer II, P2, replicate 5


title: Lateral entorhinal cortex layer II, P23, replicate 1


title: Lateral entorhinal cortex deep layers, P2, replicate 4


title: Lateral entorhinal cortex layer II, P2, replicate 5


title: Medial entorhinal cortex deep layers, P2, replicate 5


title: Medial entorhinal cortex deep layers, P23, replicate 1


title: Lateral entorhinal cortex layer II, P2, replicate 4


title: Lateral entorhinal cortex deep layers, P9, replicate 4


title: A384T Treg_2_Input (ChIP-seq)

city: Yokohama

first: Shohei

last: Hori

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

country: Japan

institute: RIKEN Center for Integrative Medical Sciences

data_processing:
Basecalls performed using Illumina offline basecaller (OLB) version 1.9.4.
DNA sequence reads were aligned to the mouse reference genome (UCSC mm9) using the Bowtie 2 software (Langmead and Salzberg, 2012).
FoxP3 ChIP-seq peaks were called with Model-based Analysis for ChIP-Seq (MACS) (Zhang et al., 2008) (v2.1.0) using input chromatin as control and FDR q-value of <10e-10.
Genome_build: mm9
Supplementary_files_format_and_content: Tabular files in txt format generated by the MACS2 peak-calling program, which contains information about called peaks.

source_name: Treg cells from FoxP3A384T:hCD2 mice

growth_protocol: freshly isolated cells

extract_protocol:
Magnetically sorted hCD2(+) WT and A384T Treg cells (approx. 1x10e7 cells per reaction, prepared in triplicates) were fixed for 30 min at room temperature with 1% formaldehyde, washed with PBS, and stored at -80 °C. Cells were resuspended in lysis buffers and sonicated for solubilization and shearing of crosslinked DNA. The cell extract was incubated overnight at 4 °C with 4 µg of the anti-FoxP3 antibodies and then with Dynabeads protein G (Dynal). Bound complexes were washed and eluted from the magnetic beads by heating at 65°C with occasional vortexing and crosslinking was reversed by overnight incubation at 65°C. The immunoprecipitated DNA and whole-cell extract input DNA were treated with RNase A and proteinase K, purified using MinElute PCR purification kit (QIAGEN)
ChIP-seq libraries were prepared using NEBNext ChIP-Seq Library Prep Reagent Set for Illumina (NEB) according to the manufacturer's instructions.

value: lymph nodes and spleen cells

value: CD4(+)hCD2(+) Treg cells

tag: sorted from

value: FoxP3A384T:hCD2 mice

tag: chip antibody


title: A384T Treg_3_Input (ChIP-seq)

tag: tissue


title: A384T Treg_1_Input (ChIP-seq)

tag: cell type


title: Medial entorhinal cortex deep layers, P2, replicate 4


title: Lateral entorhinal cortex layer II, P9, replicate 4


title: Lateral entorhinal cortex deep layers, P2, replicate 3


title: Medial entorhinal cortex layer II, P2, replicate 4


title: Medial entorhinal cortex layer II, P2, replicate 3


title: Medial entorhinal cortex deep layers, P2, replicate 3


title: Lateral entorhinal cortex layer II, P2, replicate 3


title: Lateral entorhinal cortex layer II, P2, replicate 2


title: Medial entorhinal cortex deep layers, P2, replicate 2


title: Lateral entorhinal cortex deep layers, P2, replicate 2


title: WT Treg_3 (ChIP-seq)

source_name: Treg cells from FoxP3WT:hCD2 mice

value: FoxP3WT:hCD2 mice

value: FoxP3 (affinity purified rabbit polyclonal antibody, generated in house)


title: A384T Treg_3 (ChIP-seq)


title: Medial entorhinal cortex layer II, P2, replicate 2


title: WT Treg_1_Input (ChIP-seq)


title: A384T Treg_1 (ChIP-seq)


title: A384T Treg_2 (ChIP-seq)


title: WT Treg_2_Input (ChIP-seq)


title: WT Treg_2 (ChIP-seq)


title: Lateral entorhinal cortex layer II, P2, replicate 1

value: Lateral


title: Medial entorhinal cortex deep layers, P2, replicate 1


title: Lateral entorhinal cortex deep layers, P2, replicate 1


title: CASTInj3 [miRNA-seq]

city: Santa Barbara

first: Kenneth

middle: S.

last: Kosik

state: California

address: UC Santa Barbara

department: NRI

institute: UCSB

data_processing:
reads were mapped to mature miRNAs extracted from mirbase v20 using bowtie2
mapped reads were summarized using the summarizeOverlaps R package
Genome_build: mirbase 20
Supplementary_files_format_and_content: abundance measurements

source_name: CAST_Injured_dorsal root ganglia

extract_protocol:
dorsal root ganglia were removed and dissociated. RNA was extracted using the miRVana kit according to manufacturer’s instruction.
Libraries were prepared using the Ion Total RNA-Seq kit (Life technologies) according to manufacturer’s instruction

treatment_protocol: The left sciatic nerve of adult C57BL/6 and CAST/Ei male mice (8-10 weeks) was exposed at the sciatic notch and crushed with smooth forceps for 30 s

value: CAST/Ei

value: injured

value: dorsal root ganglia


title: Medial entorhinal cortex layer II, P2, replicate 1

value: Medial

value: II


title: WT Treg_1 (ChIP-seq)


title: CASTNaive3 [miRNA-seq]

source_name: CAST_Naive_dorsal root ganglia


title: CASTNaive2 [miRNA-seq]


title: WT Treg_3_Input (ChIP-seq)


title: C57Inj3 [miRNA-seq]

source_name: C57_Injured_dorsal root ganglia


title: CASTInj2 [miRNA-seq]


title: C57Inj2 [miRNA-seq]


title: CASTInj1 [miRNA-seq]


title: C57Naive5 [miRNA-seq]

source_name: C57_Naive_dorsal root ganglia


title: C57Naive4 [miRNA-seq]


title: C57Naive3 [miRNA-seq]


title: Histone H3K4me3 ChIP-seq Cdk7as Rep2

city: Aurora

middle: L.

last: Bentley

state: CO

department: Biochemistry and Mol. Genetics

institute: U. Colorado School of Medicine

description: Chromatin IP against histone H3K4me3

data_processing:
Single-end 50 base reads (after removing barcodes) or 151 base reads (after removing barcodes and trimming adaptor sequences) were mapped to the hg19 UCSC human genome with Bowtie version 0.12.5 for ChIP-seq and with Hisat2 version 2.0.4 for RNA-seq
Genome_build: GRCh37/hg19 assembly
Supplementary_files_format_and_content: bigwig files for ChIP-seq, TDF files for RNA-seq

source_name: HCT116 Cdk7as (Larochelle et al Mol. Cell 25:839, 2007)

growth_protocol: McCoy's 10% FCS, 10mM NM-PP1, 24hr

extract_protocol:
cross-linked Chromatin was sonicated with a Bioruptor
1-2 mg of cross-linked extract was immunoprecipitated, and prepared for illumina library construction by repair with Klenow, T4 DNA polymerase and T4 polynucleotide kinase, A-tailing with Klenow exo-, ligation to branched adaptors, gel purification of ~200bp fragments, and amplification (18cycles) with Illumina Tru-seq primers using Phusion DNA polymerase.

treatment_protocol: WT HCT116 and Cdk7as cells were treated with 10mM NM-PP1 for 24 hr before cross-linking and harvesting for ChIP-seq or RNA-seq

tag: cell line

tag: genotype

value: Cdk7as mutant

value: rabbit anti  H3K4me3 (Zhang et al EMBO J, 24:2379, 2005)


title: RNA pol II ChIP-seqCdk7as Rep2

description: Chromatin IP against RNA pol II

tag: antibody

value: rabbit anti pan CTD (Schroeder eta l Genes Dev. 14:2435, 2000)


title: Histone H3K4me3 ChIP-seq WT Rep2

description: Chromatin IP against histone H3K4me3

value: wildtype


title: Histone H3K4me3 ChIP-seq Cdk7as Rep1

description: Chromatin IP against histone H3K4me3


title: C57Naive1  [miRNA-seq]

tag: treatment


title: RNA of Camelia Beebread

city: Nanjing

first: Zhen

last: Zhou

state: Jiangsu

address: 22th,Hankou Road

department: School of Lifesciences

country: China

institute: Nanjing University

data_processing:
Illumina Casava1.6 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then aligned to pre-miRNA sequence in miRBase_v21
Sequenced reads with no mismatches and no more than 2 shifts were identified as one miRNA and formed the final miRNA expression profiles.
Genome_build: miRBase_v21
Supplementary_files_format_and_content: tab-delimited text files include microRNA names, sequences and counts in each sample

organism: Camellia japonica

source_name: Camelia Beebread

extract_protocol:
Total RNA was extracted from 10g of Royal Jelly/Honey/Bee Bread/Pollen using the Trizol Reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: product/source

value: Beebread


title: RNA of Camelia Pollen

source_name: Camelia Pollen

value: Pollen


title: RZB0003 Female

city: Singapore

first: Justin

middle: Jeyakani

last: Joseph Gnanakkan

state: Singapore

address: 60, Biopolis street

department: Computational and Systems Biology

country: Singapore

institute: Genome Institute of Singapore

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were uniquely mapped to Zv9 genome using tophat v1.4.1.
Mapped reads were filtered of reads duplication, quality threshold <= 30, and loaded to Genespring  NGS Reads per kilobase per megabase (RPKM) was calculated, and normalized using  the DeSeq normalization procedure.
Genome_build: Zv9
Supplementary_files_format_and_content: tab-delimited text files include Raw RPKM values and normalized RPKM for each Sample.

organism: Danio rerio

source_name: Female brain tissue

extract_protocol:
Brain from Male and female fish were extracted for RNA extraction. Brain tissues from 5 fish were collected and pooled.
RNA-Seq library preparation protocol: Total RNA was extracted using TRIzol® Reagent (Invitrogen, USA). RNA concentrations were determined using NanoDrop 2000 (Thermo Scientific). The integrity of RNA samples was determined using an Agilent RNA 6000 Nano chip on an Agilent 2100 Bioanalyzer. Samples with RNA Integrity Number (RIN) value of 8-9 was used for RNA seq library preparation. Messenger RNA sequencing library was prepared using TruSeq total RNA sample preparation kit (Illumina; Total RNA sample preparation guide) as per the manufacturers instructions with 3 microgram input RNA per library. Quality of RNA seq library was checked following company recommended protocols. RNA sequencing of male and female samples were performed on the Illumina HiSeq2000 (Illumina, USA) (one sample per lane) machine with single ended 51 bp read length.

value: Wild type

tag: Sex

value: female

value: Brain


title: RZB0002 Male

source_name: Male brain tissue

value: male


title: Mono_day 10 batch2

city: Beijing

first: Jia

last: Yu

address: Dong Dan San Tiao 5, Dongcheng District

institute: Peking Union Medical College

description: CD34-positive HSC induced to monocytic differentiation for 10 days

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using Trim Galore v0.3.7 with parameters -q 25 --stringency 5 --length 50 --paired --phred33, and filtered for low-quality sequence, then mapped to hg38 whole genome of GENCODE v25 using tophat v2.1.0 with parameters -p 14 --splice-mismatches 1 --segment-mismatches 2 --mate-inner-dist 50 --mate-std-dev 20 --library-type fr-unstranded
Non-normalized raw counts were calculated using featureCounts v1.5.0 with parameters -T 7 --primary. In short, exons from all isoforms of a gene were merged to create one meta-transcript. Fragments Per Kilobase of exon model per Million (FPKM) mapped reads were calculated using cufflinks v2.2.1 with parameters -p 10 -u --library-type fr-unstranded -G gencode.v24.annotation.gtf.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include non-normalized raw counts and FPKM values for each Sample.

extract_protocol:
Trizol reagent
polyA-enriched RNA
illumina RNA-seq library

treatment_protocol: G-CSF and M-CSF

tag: developmental stage

value: Monocytic middle stage

value: hematopoietic systerm

tag: batch


title: RNA pol II ChIP-seq WT Rep2

description: Chromatin IP against RNA pol II


title: Mono_day 5 batch2

description: CD34-positive HSC induced to monocytic differentiation for 5 days

value: Monocytic early stage


title: RNA of Camelia Honey

source_name: Camelia Honey

value: Honey


title: RNA of Camelia Royal Jelly

source_name: Camelia Royal Jelly

value: Royal Jelly


title: C57Inj1 [miRNA-seq]

tag: strain

value: injured

value: dorsal root ganglia


title: Mono_day 10 batch1

source_name: CD34-positive HSC induced to monocytic differentiation for 10 days


title: Gran_day 15 batch2

description: CD34-positive HSC induced to granulocytic differentiation for 15 days

value: Granulocytic late stage


title: Gran_day 5 batch2

description: CD34-positive HSC induced to granulocytic differentiation for 5 days

value: Granulocytic early stage


title: Gran_day 10 batch2

description: CD34-positive HSC induced to granulocytic differentiation for 10 days

value: Granulocytic middle stage


title: Gran_day 15 batch1

source_name: CD34-positive HSC induced to granulocytic differentiation for 15 days


title: Histone H3K36me3 ChIP-seq WT Rep1

description: Chromatin IP against histone H3K36me3

value: wildtype

value: rabbit anti  H3K36me3 (Kim et al PNAS 108:13564, 2011)


title: Histone H3K36me3 ChIP-seq Cdk7as Rep1

description: Chromatin IP against histone H3K36me3

value: Cdk7as mutant


title: Gran_day 5  batch1

source_name: CD34-positive HSC induced to granulocytic differentiation for 5 days


title: d2c2_SUVH9_rep2

city: Montpellier

first: Daniel

last: Grimanelli

address: 911 Av Agropolis

country: France

institute: IRD

description: chromatin

data_processing:
Quality filtering and base-calling performed by Fasteris SA (CASAVA pipeline v.1.8.2)
Reads with Q>30 were mapped to the reference genome -TAIR10- using Bowtie2. parameters used: 1 mismatch
Bining and read counts /coverage relative to annotations performed using bedtools2
Genome_build: TAIR10
Supplementary_files_format_and_content: BED files with coordinates and coverage

organism: Arabidopsis thaliana

source_name: Arabidopsis inflorescences, WT

extract_protocol:
500 ug of inflorescence tissues were collected for each genotype and cross linked with 1% formaldehyde in water for 10 min with vacuum. Cross linking was stopped by adding glycine to a final concentration of 0.125M. Liquid Nitrogen was used to grind the tissues  to a fine powder, which was mixed to 30ml of Extraction Buffer 1 (0.4M sucrose, 10mM Tris-HCl pH 8, 10mM MgCl, 5mM BME, 0.1mM PMSF, 1 tab Protease inhibitors (Roche Biochemicals) per 50mls), mixed gently and let on ice for 15 min. The solution was filtered twice with Miracloth into a fresh 50ml falcon tube, and spinned for 20 minutes at 4000 rpm in a centrifuge at 4°C. The pellet was resuspended in 1ml of Extraction Buffer 2 ( 0.25M sucrose, 10mM Tris-HCl pH 8, 10mM MgCl2, 1% Triton X-100, 5mM BME, 0.1mM PMSF, Protease inhibitors (Roche Biochemicals, 1 mini tab per 5mls) and transferred to 1.5ml eppendorf tube, followed by 10 min centrifugation (12,000 g at 4 degrees). The resulting pellet was resuspend in 300ul of Extraction Buffer 3 (1.7M sucrose, 10mM Tris-HCl pH 8, 0.15% Triton X-100, 2mM MgCl2, 5mM BME, 0.1mM PMSF, protease inhibitor (Roche Biochemicals, 1 mini tab per 5mls), layered on top of 300ul of Extraction Buffer 3 in a clean tube and spin for 1 hour at 16,000 at 4 degrees. The chromatin pellet was then resuspended in 300ul of Nuclei Lysis Buffer (50mM Tris-HCl ph 8, 10mM EDTA, 1% SDS, Protease inhibitors (Roche Biochemicals, 1 mini tab per 5mls) and sonicated with a Diagenode Bioruptor machine (10 cycles, 30 seconds/1 minute ON/OFF), spinned at full speed for 5 minutes at 4 degrees to pellet debris, the supernatant collected to a fresh tube, and the chromatin solution brought to 3ml with ChIP Dilution Buffer (1.1% Triton X-100, 1.2mM EDTA, 16.7mM Tris-HCl pH 8, 167mM NaCl). 1ml of chromatin was added to new low-binding tubes and pre-cleared with 50ul of agorose beads for 1h on a rotating wheel. 1ml of pre-cleared chromatin was mixed with 80µl of equilibrated agarose beads and 3µg of anti-GFP antibody, and incubated overnight at 4°C on a ratting wheel. Beads were washed with the following sequence: twice 5min with Low Salt Wash Buffer (150mM NaCl, 0.1% SDS, 1% TritonX-100, 2mM EDTA, 20mM Tris-HCl pH8.1), twice 5min with High Salt Wash Buffer (500mM NaCl, 0.1% SDS, 1% TritonX-100, 2mM EDTA, 20mM Tris-HCl (pH8.1)), twice 5min with LiCl Wash Buffer (0.25 LiCl, 1% NP40, 1% sodium deoxycholate, 1mM EDTA, 10mM Tris-HCl pH 8.1), and twice 5min with TE Buffer:  (10mM Tris-HCl pH 8, 1mM EDTA). Immune complexes were eluted twice with 250ul of Elution Buffer (1% SDS, 0.1 M NaHCO3) by incubating 65 degrees for 15 minutes with gentle agitation (mix tubes during incubation), and combining both two eluates. 20ul 5M NaCl was added to the combined eluates, which were reverse-cross linked at 65°C overnight, and treated with 2ul of 10mg/ml proteinase K for one hour at 45°C.  Note:  Don’t forget to get your total DNA out of the freezer and reverse X-link with other samples (Add 500 ul of Elution buffer + 20ul 5M NaCl). The resulting DNA fragments were purified using Diagenode ChIP purification kit (catalogue #C03010011), and resuspended in 50ul of distilled water.
Library constructed using Illumina’s TruSeq ChIP Sample Prep Kit, and following manufacturer’s protocol.

tag: tissues

value: inflorescences

tag: genotypes

value: d2c2,; SUVH9-VENUS

tag: antibodies

value: Chromotek, GFP-Trap


title: SUVH9_rep1

description: chromatin

value: WT; SUVH9-VENUS


title: Mono_day 15 batch2

description: CD34-positive HSC induced to monocytic differentiation for 15 days

value: Monocytic late stage


title: input_d2c2_SUVH9_rep2

description: chromatin


title: Lpin_B

status: Public on Jul 31 2017

city: Ramat Gan

first: Ofir

last: Hakim

address: Bar-Ilan University

country: Israel

institute: Bar-Ilan University

data_processing:
Library strategy: 4C-seq
Reads were sorted into different fastq files for each viewpoint and time point according to the bait and barcode sequences
Alignment was done using Bowtie with --5 option to trimm the seqcence from the 5'end until the HindIII site
Custom perl script was used to count the reads at each genomic HindIII site. To avoid possible quantitative PCR or sequencing bias the data was transformed to unique coverage (>1 reads per HindIII site was set to 1)
p score (= -log10 p-value) was calculated for each HindIII site using one tail binomial test with 100Kb running window centered at the HindIII site and the entire specific chromosome as background. Since intra- and inter-chromosomal  associations are typically different in intensity and size, the top 10% intra-chromosomal and the top 5% inter-chromosomal HindIII sites were considered  positive (FDR ~0.04). Contact regions were determined as clusters of consecutive positive HindIII sites of 100Kb or more. To avoid loci with high p score that may result from low HindIII content, only clusters of 15 HindIII sites or more were considered.
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph files include normalize P value at each HindIII site. The files can be viewed by the UCSC genome browser
Supplementary_files_format_and_content: tab-delimited text files (RE coverge) include number of reads at each HindIII site for each Sample

source_name: B lymphocytes cell line

growth_protocol: 3T3-L1 cells were maintained in DMEM supplemented with calf serum

extract_protocol: The 4C assay was performed according to the method previously described (Simonis et al. 2006; Hakim et al. 2011). Cells were fixed with 2% formaldehyde for 10 min, cross-linked chromatin was digested overnight with excess of HindIII enzyme (New England Biolabs) and then DNA ends were ligated under dilute conditions that favor junctions between cross-linked DNA fragments. The ligation junctions were then circularized by digestion with the DpnII four-base restriction enzyme (New England Biolabs) followed by ligation. Baits were amplified with specific primers listed in the method section

treatment_protocol: Differentiation of 3T3‐L1 fibroblasts to adipocytes was achieved as described previously (Helledie et al, 2002). Namely, 2-day post-confluent 3T3-L1 cells (designated day 0 cells) were exposed to DMEM containing 10% FCS (Invitrogen) supplemented with 1 μM dexamethasone (Sigma), 0.5 mM 3-isobutyl-1-methylxanthine (Aldrich), and 1 μg/ml insulin (Roche Molecular Biochemicals). At day 2, cells were fed DMEM containing FCS and 1 μg/ml insulin, thereafter cells were maintained in DMEM and FCS.

value: B lymphocytes cell line

tag: differentiation stage

tag: time

tag: bait

value: Lpin


title: SUVH9_rep2

description: chromatin


title: Lpin_day6

source_name: Preadipocyte cell line

value: 3T3-L1 preadipocyte cell line

value: Mature adipocyte

value: day 6


title: Lpin_day2

value: Intermediate stage

value: day 2


title: Lpin_day0

value: Preadipocyte

value: day 0


title: C57Naive2 [miRNA-seq]

tag: tissue

value: dorsal root ganglia


title: Mono_day 5 batch1

source_name: CD34-positive HSC induced to monocytic differentiation for 5 days

value: Monocytic early stage

value: hematopoietic systerm


title: Ifng_B

value: Ifng


title: Ifng_day6


title: Lpin_day1

value: day 1


title: Gran_day 10 batch1

source_name: CD34-positive HSC induced to granulocytic differentiation for 10 days

value: Granulocytic middle stage


title: Ifng_day0


title: Ifng_day1


title: pparg_B

value: pparg


title: pparg_day6


title: pparg_day0


title: pparg_day1


title: pparg_day2


title: PGE2 Rep2

city: Philadelphia

first: Bing

last: He

state: PA

address: 3501 Civic Center Blvd

institute: Children's Hospital of Philadelphia

data_processing:
Basecalls performed using Illumina Casava version 1.8
RNA-Seq reads were mapped to mouse genome (mm9) using Tophat. Only uniquely mapped reads with fewer than 2 mismatches were used for downstream analyses.
Transcripts were assembled using Cufflinks using mapped fragments outputted by Tophat. Refseq annotation was used as the source of annotated genes and transcript isoforms.
Genome_build: mm9
Supplementary_files_format_and_content: text files of FPKM values were generated for each sample.

source_name: LSC

growth_protocol: Lineage negative BM cells were cultured in IMDM medium with 15% fetal bovine serum, 50 ng/ml stem cell factor and 20 ng/ml thrombopoietin for 48 hrs. During the incubation time, at time 0 and 24 hr time point, the cells were retrovirally transduced with the p210 BCR-ABL retrovirus.

extract_protocol:
LSCs were surface-stained and sort-purified, and total RNA was extracted using standard Qiagen RNease columns
RNA libraries were prepared for sequencing using stardard Illumina protocol

treatment_protocol: The LSCs established from control BM cells were treated with DMSO, 20µM PGE1 or 20 µM PGE2 for 6 hrs

tag: cell type

value: BM cells

value: wild type


title: PGE1 Rep3


title: PGE1 Rep2


title: Mono_day 15 batch1

source_name: CD34-positive HSC induced to monocytic differentiation for 15 days

value: Monocytic late stage


title: PGE2 Rep1


title: DMSO Rep2

value: DMSO


title: dKO Rep3


title: Ifng_day2

tag: cell line

value: 3T3-L1 preadipocyte cell line


title: dKO Rep1

tag: genotype


title: WT Rep3


title: WT Rep1


title: M-E-Nras-p53WT-72hr-CX2

city: Canberra

first: Nadine

last: Hein

state: ACT

address: Garran Road

department: CBTx

country: Australia

institute: JCSMR

description: Veh_CX_72h_p53WT EdgeR

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were aligned to the mm9 genome assembly using bowtie with default parameters
Reads were counted using HTSeq
Differential expressed genes were identified using EdgeR
Genome_build: mm9
Supplementary_files_format_and_content: Tab delimited read counts from Htseq
Supplementary_files_format_and_content: Table with differential expression determined by EdgeR

source_name: p53WT MLL/ENL Nras

growth_protocol: syngeneic transplant of p53WT MLL/ENL Nras or p53null MLL/ENL Nras acute myeloid leukemia cells into recipient C57Bl/6 mice

extract_protocol:
GFPpositive tumour cells FACS sorted from the bone marrow of treated mice
Libraries were prepared using TruSeq RNA Sample Prep Kit v2 (Illumina)

treatment_protocol: Mice with established disease (either MLL/ENL Nras p53WT or p53null AML)  were treated with CX-5461 or vehicle  for 10 and 72 hr prior to sacrifice

tag: model

value: AML

value: p53 WT


title: Mouse Mid-gestation 1

city: West Haven

first: Gunter

last: Wagner

state: CT

address: 300 Heffernan Drive, ISTC 108

department: Systems Biology Institute, EEB

institute: Yale University

data_processing:
Basecalls performed using CASAVA
mRNA-seq reads were aligned to the rabbit (OryCun2.0), opossum (MonDom5.69) mouse (Mus38.69) and armadillo (DasNov3.0) cDNA builds using Tophat2
Number of reads overlapped with known features (gene counts) was counted using HTSeq
transcripts per million (TPM) values were calculated according to Wagner et al (2012) Theor. Biosci.
Genome_build: Genome_build: rabbit (OryCun2.0), opossum (MonDom5.69) mouse (Mus38.69) and armadillo (DasNov3.0)
Supplementary_files_format_and_content: Supplementary_files_format_and_content: Comma-delimited csv files include read counts for each sample.

molecule: polyA RNA

source_name: cervix

extract_protocol:
Tissues were harvested and kept in RNAlater until extraction of RNA using Qiagen RNeasy extraction kit.
RNA libraries were prepared for sequencing using standard illumina protocols.

value: cervix

tag: gestation stage

value: Mid-gestation (E15)


title: M-E-Nras-p53WT-72hr-V3

description: Veh_CX_72h_p53WT EdgeR


title: M-E-Nras-p53WT-72hr-V2

description: Veh_CX_72h_p53WT EdgeR


title: CX4-10-hr-Cyl-53

description: Veh_CX_10h p53NULL EdgeR

source_name: p53null MLL/ENL Nras

value: p53 null


title: Mouse Non-pregnant 2

value: Non-pregnant


title: M-E-Nras-p53WT-72hr-CX1

description: Veh_CX_72h_p53WT EdgeR


title: M-E-Nras-p53WT-72hr-CX3

description: Veh_CX_72h_p53WT EdgeR


title: CX1-10-hr-Cyl-53

description: Veh_CX_10h p53NULL EdgeR


title: CX2-10-hr-Cyl-53

description: Veh_CX_10h p53NULL EdgeR


title: V5-10-hr-Cyl-53

description: Veh_CX_10h p53NULL EdgeR


title: WT Rep2

tag: treatment


title: V4-10-hr-Cyl-53

description: Veh_CX_10h p53NULL EdgeR


title: DMSO Rep1


title: PGE1 Rep1


title: dKO Rep2


title: CASTNaive1 [miRNA-seq]

source_name: CAST_Naive_dorsal root ganglia

value: CAST/Ei

value: dorsal root ganglia


title: Kelly

city: Rochester

first: Hu

last: Li

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

data_processing:
alignment TopHat v2.0.6
htseq-count
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited gene counts

source_name: cell line

extract_protocol:
RNA was extracted from human neuroblastoma BE2C cells with programed expression of LMO1 or vector control as well as parental BE2C cells and Kelly cells. Total RNA was extracted using the RNAeasy Plus Mini Kit (QIAGEN, Germantown, MD, USA), as per manufacturer’s instructions. RNA integrity (RIN) was verified on an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and 100-200 ng of RNA (RIN ≥ 7.0) in a 5 μl volume was used for library preparation and RNA sequencing (RNAseq).
Paired-end sequencing libraries were prepared using the TruSeq Stranded Total Sample Preparation kit (Illumina) by the Mayo Clinic sequencing core facilities (Rochester, MN) followed by quality control, cluster generation and sequencing on the Illumina HiSeq 2000 platform. The reads were de-multiplexed and converted to FASTQ format using CASAVA software from Illumina (by the Mayo Clinic core).

value: Neurablastoma cell line

value: Kelly


title: DMSO Rep3


title: Be2C


title: M-E-Nras-p53WT-72hr-V1

description: Veh_CX_72h_p53WT EdgeR


title: Histone H3K4me3 ChIP-seq WT Rep1

first: David

description: Chromatin IP against histone H3K4me3

value: wildtype

tag: antibody

value: rabbit anti  H3K4me3 (Zhang et al EMBO J, 24:2379, 2005)


title: Opossum Late-gestation 2

description:
Md_LG_2
Illumina HiSeq 2000 and Illumina HiSeq 2500 (reran and combined)

organism: Monodelphis domestica

value: Late-gestation


title: v1-10-hr-Cyl-53

description: Veh_CX_10h p53NULL EdgeR


title: CX3-10hr-Cyc-41

description: Veh_CX_10h EdgeR with coumts


title: CX4-10hr-Cyc-41

description: Veh_CX_10h EdgeR with coumts


title: Opossum Late-gestation 1


title: Opossum Late-gestation 3


title: v5-10hr-Cyc-41

description: Veh_CX_10h EdgeR with coumts


title: Hela100_0_Pfx2

city: Curitiba

first: Christian

middle: Macagnan

last: Probst

state: PR

address: Rua Professor Algacyr Munhoz Mader, 3775

country: Brazil

institute: Instituto Carlos Chagas

description: Oligo-ME aRNA

data_processing:
Illumina 2x100 paired-end RNA-seq reads were aligned to the  T. cruzi Dm28c genome (GenBank accession number MBSY00000000) and human genome (version 19) using Bowtie2 v. 2.3.0 [35] in local mode, within three different settings: using default parameters, --very-fast-local and --very-sensitive-local. SOLiD Reads were aligned using the SHRIMP2 v2.2.3, with default parameter, except –strata -h 80% --max-alignments 1000 --local
Sample read count normalization was performed by edgeR v. 3.12.0, Bioconductor suite, R v 3.2.3
These samples were used to access errors in mapping, and we have stopped just after the mapping process, without processing any further.
Genome_build: MBSY00000000
Supplementary_files_format_and_content: n/a

source_name: HeLa lineage cell

growth_protocol: Parasite culture: T. cruzi Dm28c epimastigotes [32] were cultured at 28°C in LITB medium supplemented with 10% heat-inactivated fetal bovine serum (FBS) as previously described [33]. Tissue culture-derivedCell derived trypomastigote forms were obtained by infection of cultured Vero cell (ATCC® CCL-81™) at 37ºC in a humidified 5% CO2 atmosphere using a multiplicity of infection (MOI) of 10 parasites per host cell. Cell derived tTrypomastigotes were recovered after 4 days of infection, in the cell burst peak. HeLa culture: the human derived epithelial cell ATCC® CCL-2™ were grownth in 75 cm2 culture bottles at 37ºC in a humidified 5% CO2 atmosphere using DMEM medium supplemented with 10% FBS. When confluent, cells were detached from the culture flask by enzymatic treatment (0.01% trypsin, 0.1% EDTA in PBS), washed in PBS and passed to new bottles at cell density of 106 HeLa cells for each 75 cm2 culture bottle.

extract_protocol:
Total RNA was extracted from T. cruzi epimastigote and trypomastigote forms (5 × 108 cells) and from confluent HeLa cells with the RNeasy kit (Qiagen, Hilden, Germany), according to the manufacturer’s instructions, with an additional on-column DNase digestion step. Total RNA from HeLa cells were obtained from MessageAmpTM II aRNA Amplification Kit from Life Technologies® (#AMB1751-5). RNA integrity was assessed on an Agilent 2100 Bioanalyzer with RNA 6000 Nano LabChip kit, according to the manufacturer’s instructions. Polyadenylated RNA were purified from at least 50 µg of total RNA using PolyA+Track® mRNA Isolation System III from Promega® (#Z5300), according to the manufacturer's instructions. Polyadenylated RNA were purified from at least 50 µg of total RNA using PolyA+Track® mRNA Isolation System III from Promega® (#Z5300), according to the manufacturer's instructions. All mRNA amplification reactions were done using reagents from MessageAmpTM II aRNA Amplification Kit from Life Technologies® (#AMB1751-5). For classic Eberwine amplification method, first-strand cDNA was synthesized using a T7oligo(dT) primer that contains a T7 RNA polymerase promoter upstream to the poly-T tract; this promoter will further direct the in vitro mRNA synthesis (amplification). First, 100 ng of total RNA (in 11 µl) were mixed with first-strand cDNA reaction mix containing 1 µl of T7oligo(dT) primer, 2 µl first-strand buffer, 4 µl dNTPs, 1 µl RNase inhibitor and 1 µl ArrayScript Reverse Transcriptase and incubated for 2 hours at 42ºC. Second-strand cDNA was then synthesized for 2 hours at 16ºC using the total 20 µl first-strand product plus 80 µl of second strand mix containing 63 µl water, 10 µl second-strand buffer, 4 µl dNTPs, 2 µl DNA Polymerase and 1 µl of RNase H. Double-strand cDNA was then purified using PureLink® PCR Micro Kit from Life Technologies (#K310250) according manufacturer’s instructions. Eluted cDNA was adjusted to 16 µl and used as template for amplification reaction in a total volume of 40 µl containing 16 µl NTPs, 4 µl amplification buffer and 4 µl of T7 RNA polymerase; in vitro transcription took 14 hours at 37ºC. Amplified RNA (aRNA) was then purified using RNeasy MinElute CleanUp Kit (Qiagen, #74204), according to the manufacturer’s instructions. For specific amplification of spliced leader containing mRNA, we used a custom designed primer complementary to the last 21 bases of T. cruzi spliced leader (in bold) with an upstream T7 RNA polymerase promoter (in gray) (5'-GGCCAGTGAATTGTAATACG ACTCACTATAGGGAGGCGGTACAGTTTCTGTACTATATTG-3'), which we named T7SL. In this case, T7SL was used for second-strand cDNA synthesis, while first-strand cDNA was produced using random primers, accordingly to the second round amplification protocol of MessageAmpTM II aRNA Kit. Template total RNA was adjusted to 10 µl, mixed with 2 µl of "second round primers" (random primers) and incubated at 70ºC for 10 minutes followed by snap cool on ice to allow annealing of random primers to RNA. Then, 8 µl of reverse transcription master mix was added and first-strand cDNA synthesized at 42ºC for 2 hours. RNase H was added (1 µl) and sample incubated at 37ºC for 30 minutes to specifically degrade the remaining RNA. T7SL primer was added to a final concentration of 1 µM and the sample was incubated at 70ºC for 10 minutes and then placed on ice. Second-strand cDNA master mix without RNase H was added (74 µl) and the reaction incubated for 2 hours at 16ºC. Double-strand cDNA purification, in vitro transcription and aRNA purification was performed as described above.
Negative control aRNA samples, generated from pure HeLa RNA, were sequenced in Omega Bio-Tek Inc (Norcross, GA, USA) using the Illumina 2x100 paired-end sequencing method. Total RNA-Seq Kit (Life Technologies, #4445374) was used accordingly to manufacturer instructions. Briefly, RNA was fragmented using RNase III and cleaned up with Invitrogen RiboMinus™ Concentration Module. Strand-specific adaptors were hybridized and ligated to both extremities of RNA in an overnight reaction, followed by first-strand cDNA synthesis with reverse transcriptase. cDNA was purified using MinElute® PCR Purification Kit (Qiagen) and gel-based selected for size using a Novex TBE-Urea 6% gel (#EC6865bOX). On-gel cDNA was amplified by PCR using SOLiDTM RNA barcoding kit primers (Life Technologies, #4427046 and #4453189) and purified with Invitrogen PureLink® PCR Micro Kit. Amplified DNA was quantified with Qubit® dsDNA HS Assay Kit on a Qubit® 2.0 Fluorometer. Equal masses of each sample, containing specific barcodes, were pooled together and the mixture used as DNA template for emulsion PCR on Applied Biosystems SOLiD® EZ Bead™ E80 system  (#4453095). After 3' end modification with terminal transferase, template beads were deposited onto glass slides and libraries sequenced on a SOLiDTM 4 system using multiplex fragment sequencing protocol that generates about 700 millions 50 bases short reads per run.

treatment_protocol: No treatment

tag: mixture

value: no


title: Hela100_0_Pfx1

description: Oligo-ME aRNA


title: Opossum Non-pregnant 4


title: v4-10hr-Cyc-41

description: Veh_CX_10h EdgeR with coumts


title: Opossum Non-pregnant 3


title: CX5-10hr-Cyc-41

description: Veh_CX_10h EdgeR with coumts


title: Opossum Mid-gestation 1

value: Mid-gestation


title: Opossum Mid-gestation 3


title: Sample_Mixture_EDC_S1_L001_R1_001

city: santiago

first: Julio

middle: Buñay

last: Noboa

state: Santiago

address: Alameda 340

department: Physiology

country: Chile

institute: Pontificia Univerisidad Catolica de Chile

data_processing:
MiSeq-Illumina sequencer
The quality control of raw sequence data were examined using the FastQC program (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Adapter trimming was performed using cutadapt software (Martin, Marcel. 2011. “Cutadapt Removes Adapter Sequences from High-Throughput Sequencing Reads.” EMBnet.journal 17 (1): 10). Reads shorter than 12 nucleotides were removed. Trimmed reads were aligned to mouse genome (mm10) using bowtie aligner, allowing up to three mismatches
Identification and quantification of pre-miRNAs and mature miRNA was performed using HTSeq (Anders et al. 2015) using a general feature format file downloaded from miRBase 21 (Kozomara and Griffiths-Jones 2014). Data normalization and differential expression analysis was performed using DeSeq tool of the R/Bioconductor software package (Anders and Huber 2010; Anders et al. 2013).
Genome_build: mm10
Supplementary_files_format_and_content: Excel-files include miRNAs reads values for each sample

extract_protocol:
Testis were decapsulated testis, and RNA was harvested using TRIzol® Reagent (Invitrogen, Carlsbad, CA). RNA concentrations were verified by measuring the absorvance (A260/280 ratio) on a NanoDrop Spectrophotometer ND-1000 (NanoDrop) and the integrity of RNA was determined by Bio-analyzer 2100 (Agilent).
small RNA-seq libraries generation 1.5 µg of RNA (RIN>9) isolated from a pool of testis from control or exposed animals to the mixture of EDCs were prepared following the Illumina protocols (www.illumina.com/ support). Small RNA-seq was using a MiSeq-Illumina sequencer by single-end mode and read length of 65 nt.

tag: exposed to

value: mixtures of Endocrine disruptors compounds (EDCs)

value: Testis

tag: age

value: Post natal day 60


title: Sample_Control_S2_L001_R1_001

tag: strain

value: water (with vehicles); control


title: ChIP PolII siRRP40 replicate 1

city: Macclesfield

first: Muhammad

middle: Ahmad

last: Maqbool

address: Alderley Park

department: Cancer Research UK Manchester Institut

country: United Kingdom

institute: University of Manchester

description: Pol II ChIP from Hela cells with knock down of RRP40 with siRNA.

data_processing:
All sequencing reads were aligned to the hg19 genome assembly using Bowtie2 (allowing 2 mismatches, keeping uniquely aligned reads only).
For ChIP-seq experiments, all samples were input subtracted and signals were scaled so that the same number of units appeared in each experiment after merging of the replicates.
Genome_build: hg19
Supplementary_files_format_and_content: WIG files of scaled (input samples) or scaled and background-subtracted (ChIP sample) values.

source_name: Hela Kyoto cells

growth_protocol: Human HeLa Kyoto cells were grown under standard conditions.

extract_protocol: ChIP-seq libraries were prepared with Illumina's ChIP Sample Prep Kit according to standard protocol.

treatment_protocol: HeLa Kyoto cells were transfected with 15nM siRNA using Lipofectamine 2000 reagent. Transfection was repeated after 48 hours of first transfection and cells were harvested 36 hours after second transfection. Factor depletion efficiencies were evaluated by western blotting.

tag: chip antibody

value: PolII (Santa Cruz sc-899)

tag: sirna

value: knock down of RRP40 with siRNA.


title: ChIP PolII siFFL replicate 6

description: Pol II ChIP from Hela cells with mock knock down with siRNA.

value: mock knock down with siRNA.


title: ChIP PolII siFFL replicate 4


title: ChIP PolII siFFL replicate 3


title: ChIP PolII siZC3H18 replicate 2

description: Pol II ChIP from Hela cells with knock down of ZC3H18 with siRNA.

value: knock down of ZC3H18 with siRNA.


title: ChIP PolII siRRP40 replicate 2


title: Input siZC3H18 replicate 2

description: Input DNA from Hela cells with knock down of ZC3H18 with siRNA.


title: v3-10hr-Cyc-41

description: Veh_CX_10h EdgeR with coumts

value: AML

value: p53 WT


title: ChIP PolII siFFL replicate 5


title: Input siFFL replicate 3

description: Input DNA from Hela cells with mock knock down with siRNA.


title: ChIP PolII siZC3H18 replicate 1


title: ChIP PolII siFFL replicate 2


title: Input siZC3H18 replicate 1


title: Input siFFL replicate 1


title: ChIP PolII siFFL replicate 1


title: ChIP PolII siARS2 replicate 2

description: Pol II ChIP from Hela cells with knock down of Ars2 with siRNA.

value: knock down of Ars2 with siRNA.


title: Input siFFL replicate 2


title: M1L/shRen RNA-Seq

city: Seoul

first: Jae Seok

last: Roe

address: Yonsei-ro, 50

country: South Korea

institute: Yonsei University

data_processing:
Raw reads were mapped to the reference mouse (mm9) or human (hg19) genome assembly with Tophat, and rpkm values were calucated with Cufflink
Genome_build: mm9 and hg19

source_name: M1L/shRen organoid

growth_protocol: Mouse/human PDA organoids or cell lines were cultured in conditions as described in this study.

extract_protocol:
Total RNAs were extracted using Trizol reagent
Libraries were made following the instructions of Illumina TruSeq RNA sample prep kit v2

treatment_protocol: For cDNA overepxression, cDNAs were retrovirally introduced and selected with G418. For shRNA expression, shRNAs were retrovirally introduced and selected with puromycin. For sgRNA expression, sgRNAs were lentivirally introduced and GFP-sorted with FACS.

value: Mouse PDA liver metastasis (M1L)

tag: peturbation

value: Transduced with miR-E/shRen retrovirus


title: M1L/shFoxa1 RNA-Seq

source_name: M1L/shFoxa1 organoid

value: Transduced with miR-E/shFoxa1.2959 retrovirus


title: Input siARS2 replicate 1

description: Input DNA from Hela cells with knock down of Ars2 with siRNA.


title: M1L/sgFoxa1 RNA-Seq

source_name: M1L/sgFoxa1 organoid

value: Cas9-expressing Mouse PDA liver metastasis (M1L-Cas9)

value: Transduced with sgFoxa1 e2.4 lentivirus


title: LMO1-Be2C2

extract_protocol:
RNA was extracted from human neuroblastoma BE2C cells with forced overexpression of LMO1 or vector control. Total RNA was extracted using the RNAeasy Plus Mini Kit (QIAGEN, Germantown, MD, USA), as per manufacturer’s instructions. RNA integrity (RIN) was verified on an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and 100-200 ng of RNA (RIN ≥ 7.0) in a 5 μl volume was used for library preparation and RNA sequencing (RNAseq).
Paired-end sequencing libraries were prepared using the TruSeq Stranded Total Sample Preparation kit (Illumina) by the Mayo Clinic sequencing core facilities (Rochester, MN) followed by quality control, cluster generation and sequencing on the Illumina HiSeq 2000 platform. The reads were de-multiplexed and converted to FASTQ format using CASAVA software from Illumina (by the Mayo Clinic core).

value: Neurablastoma cell line

tag: genotype/variation

value: overexpression of LMO1


title: vector-Be2C2

value: overexpression of vector control


title: LMO1-Be2C1


title: T23/GATA5 RNA-Seq

source_name: T23/GATA5 organoid

value: Mouse PDA primary tumor organoid (T23)

value: Transduced with MSCV/FLAG-GATA5 retrovirus


title: T3/GATA5 RNA-Seq

source_name: T3/GATA5 organoid

value: Mouse PDA primary tumor organoid (T3)


title: vector-Be2C1


title: Input siARS2 replicate 2


title: T23/emp RNA-Seq

source_name: T23/emp organoid

value: Transduced with MSCV/emp retrovirus


title: T23/FOXA1-GATA5 RNA-Seq

source_name: T23/FOXA1-GATA5 organoid

value: Transduced with MSCV/V5-FOXA1-(P2A)-FLAG-GATA5 retrovirus


title: T3/FOXA1-GATA5 RNA-Seq

source_name: T3/FOXA1-GATA5 organoid


title: KPC-2D/FOXA1 RNA-Seq (rep1)

source_name: KPC-2D/FOXA1 cells

value: Monolayer-cultured cells established from mouse PDA primary tumor organoid (T3)

value: Transduced with MSCV/FOXA1 retrovirus

tag: biological replicate


title: M1L/sgRosa RNA-Seq

source_name: M1L/sgRosa organoid

value: Transduced with sgRosa lentivirus


title: T23/FOXA1 RNA-Seq

source_name: T23/FOXA1 organoid

value: Transduced with MSCV/V5-FOXA1 retrovirus


title: T3/FOXA1 RNA-Seq

source_name: T3/FOXA1 organoid


title: T3/emp RNA-Seq

source_name: T3/emp organoid


title: M10P RNA-Seq

source_name: M10P organoid

value: Mouse PDA peritoneum metastasis (M10P)


title: KPC-2D/emp RNA-Seq (rep1)

source_name: KPC-2D/emp cells


title: KPC-2D/FOXA1 RNA-Seq (rep2)


title: KPC-2D/emp RNA-Seq (rep2)


title: M6P RNA-Seq

source_name: M6P organoid

value: Mouse PDA peritoneum metastasis (M6P)


title: M3P RNA-Seq

source_name: M3P organoid

value: Mouse PDA peritoneum metastasis (M3P)


title: M3L RNA-Seq

source_name: M3L organoid

value: Mouse PDA liver metastasis (M3L)


title: M1L RNA-Seq

source_name: M1L organoid

value: Mouse PDA liver metastasis (M1L)


title: T34 RNA-Seq

source_name: T34 organoid

value: Mouse PDA primary tumor organoid (T34)


title: T23 RNA-Seq

source_name: T23 organoid


title: T19 RNA-Seq

source_name: T19 organoid

value: Mouse PDA primary tumor organoid (T19)


title: N6 RNA-Seq

source_name: N6 organoid

value: Mouse normal pancreatic organoid (N6)


title: P2 RNA-Seq

source_name: P2 organoid

value: Mouse PanIN organoid (P2)


title: M1L/shFoxa1 Ipt ChIP-Seq

data_processing:
Raw reads were mapped to the reference mouse (mm9) or human (hg19) genome assembly using Bowtie allowing two-mismatches for only unique alignment; -v 2 -m 1 -best --strata. To avoid clonal artifacts introduced in the library amplification steps, duplicated mapped reads were further discarded using SAMtools (http://samtools.sourceforge.net).
HOMER suite (http://homer.salk.edu/homer/) was used for overall analysis. Details were described in the experimental procedues of this study.
Genome_build: mm9 and hg19
Supplementary_files_format_and_content: bigWig

source_name: M1L/shFoxa1 organoid

extract_protocol:
Lysates were prepared from ~1 millon single cell dissociated of organoid cultures, or ~5 million of monolayer cultures. Sonicated nuclei with Bioruptor were further proceeded to ChIP assay with apporiate antibodies.
Libraries were prepared according to Illumina's instructions of TruSeq ChIP Sample Prep kit.

value: Transduced with miR-E/shFoxa1.2959 retrovirus

value: Ipt genomic DNA


title: N5 RNA-Seq

source_name: N5 organoid

value: Mouse normal pancreatic organoid (N5)


title: T3 RNA-Seq

source_name: T3 organoid

value: Mouse PDA primary tumor organoid (T3)


title: M1L/shFoxa1 FOXA1 ChIP-Seq

value: FOXA1 (ab23738; Abcam)


title: M15D RNA-Seq

source_name: M15D organoid

value: Mouse PDA peritoneum metastasis (M15D)


title: T6 RNA-Seq

source_name: T6 organoid

value: Mouse PDA primary tumor organoid (T6)


title: M1L/shFoxa1 H3K27ac ChIP-Seq (rep2)

value: H3K27ac (ab4729; Abcam)


title: M1L/shFoxa1 H3K27ac ChIP-Seq (rep1)


title: M1L/shRen FOXA1 ChIP-Seq

source_name: M1L/shRen organoid

value: Transduced with miR-E/shRen retrovirus


title: T3/FOXA1-GATA5 Ipt ChIP-Seq

source_name: T3/FOXA1-GATA5 organoid

value: Transduced with MSCV/V5-FOXA1-(P2A)-FLAG-GATA5 retrovirus


title: M1L/shRen H3K27ac ChIP-Seq (rep1)


title: M1L/shRen H3K27ac ChIP-Seq (rep2)


title: T23/GATA5 Ipt ChIP-Seq

source_name: T23/GATA5 organoid

value: Mouse PDA primary tumor organoid (T23)

value: Transduced with MSCV/FLAG-GATA5 retrovirus


title: M1L/shRen Ipt ChIP-Seq

value: Mouse PDA liver metastasis (M1L)


title: T3/FOXA1 Ipt ChIP-Seq

source_name: T3/FOXA1 organoid

value: Transduced with MSCV/V5-FOXA1 retrovirus


title: T23/FOXA1 Ipt ChIP-Seq

source_name: T23/FOXA1 organoid


title: T23/emp Ipt ChIP-Seq

source_name: T23/emp organoid

value: Transduced with MSCV/emp retrovirus


title: T33 RNA-Seq

source_name: T33 organoid

value: Mouse PDA primary tumor organoid (T33)


title: T3/emp Ipt ChIP-Seq

source_name: T3/emp organoid


title: T3/GATA5 Ipt ChIP-Seq

source_name: T3/GATA5 organoid


title: T23/FOXA1-GATA5 H3K27ac ChIP-Seq

source_name: T23/FOXA1-GATA5 organoid


title: T3/FOXA1-GATA5 H3K27ac ChIP-Seq


title: T23/GATA5 H3K27ac ChIP-Seq


title: T3/GATA5 H3K27ac ChIP-Seq


title: P3 RNA-Seq

source_name: P3 organoid

value: Mouse PanIN organoid (P3)


title: T23/FOXA1 H3K27ac ChIP-Seq


title: T3/FOXA1 H3K27ac ChIP-Seq


title: ChIP PolII siARS2 replicate 1

source_name: Hela Kyoto cells

value: PolII (Santa Cruz sc-899)

value: knock down of Ars2 with siRNA.


title: T3/emp H3K27ac ChIP-Seq


title: KPC-2D/emp Ipt ChIP-Seq

source_name: KPC-2D/emp cells

value: Monolayer-cultured cells established from mouse PDA primary tumor organoid (T3)

value: Ipt genomic DNA


title: KPC-2D/FOXA1 FOXA1 ChIP-Seq (rep2)

source_name: KPC-2D/FOXA1 cells

value: Transduced with MSCV/FOXA1 retrovirus

value: FOXA1 (ab23738; Abcam)


title: KPC-2D/emp FOXA1 ChIP-Seq (rep1)


title: KPC-2D/FOXA1 FOXA1 ChIP-Seq (rep1)


title: KPC-2D/FOXA1 H3K27ac ChIP-Seq (rep2)


title: KPC-2D/FOXA1 H3K27ac ChIP-Seq (rep1)


title: KPC-2D/emp H3K27ac ChIP-Seq (rep2)


title: KPC-2D/emp H3K27ac ChIP-Seq (rep1)


title: T23/FOXA1-GATA5 Ipt ChIP-Seq


title: T6/sgp53 H3K27ac ChIP-Seq

source_name: T6/sgp53 organoid

value: Cas9-expressing mouse PDA primary tumor organoid (T6-Cas9)

value: Transduced with sgp53 lentivirus


title: T6/sgRosa Ipt ChIP-Seq

source_name: T6/sgRosa organoid

value: Transduced with sgRosa lentivirus


title: T6/sgRosa H3K27ac ChIP-Seq

value: H3K27ac (ab4729; Abcam)


title: M15D Ipt ChIP-Seq

source_name: M15D organoid

value: Mouse PDA peritoneum metastasis (M15D)


title: M10P Ipt ChIP-Seq

source_name: M10P organoid

value: Mouse PDA peritoneum metastasis (M10P)


title: T6/sgp53 Ipt ChIP-Seq


title: M6P Ipt ChIP-Seq

source_name: M6P organoid

value: Mouse PDA peritoneum metastasis (M6P)


title: T34 Ipt ChIP-Seq

source_name: T34 organoid

value: Mouse PDA primary tumor organoid (T34)


title: M3L Ipt ChIP-Seq

source_name: M3L organoid

value: Mouse PDA liver metastasis (M3L)


title: M3P Ipt ChIP-Seq

source_name: M3P organoid

value: Mouse PDA peritoneum metastasis (M3P)


title: M1L Ipt ChIP-Seq

source_name: M1L organoid

value: Mouse PDA liver metastasis (M1L)


title: KPC-2D/emp FOXA1 ChIP-Seq (rep2)

value: Transduced with MSCV/emp retrovirus


title: P2 Ipt ChIP-Seq

source_name: P2 organoid

value: Mouse PanIN organoid (P2)


title: N5 Ipt ChIP-Seq

source_name: N5 organoid

value: Mouse normal pancreatic organoid (N5)


title: T33 Ipt ChIP-Seq

source_name: T33 organoid

value: Mouse PDA primary tumor organoid (T33)

value: Ipt genomic DNA


title: T23/emp H3K27ac ChIP-Seq

source_name: T23/emp organoid

value: Mouse PDA primary tumor organoid (T23)


title: KPC-2D/FOXA1 Ipt ChIP-Seq

value: Monolayer-cultured cells established from mouse PDA primary tumor organoid (T3)

value: Transduced with MSCV/FOXA1 retrovirus


title: T23 Ipt ChIP-Seq

source_name: T23 organoid


title: T19 Ipt ChIP-Seq

source_name: T19 organoid

value: Mouse PDA primary tumor organoid (T19)


title: T6 Ipt ChIP-Seq

source_name: T6 organoid

value: Mouse PDA primary tumor organoid (T6)


title: T3 Ipt ChIP-Seq

source_name: T3 organoid

value: Mouse PDA primary tumor organoid (T3)


title: P3 Ipt ChIP-Seq

source_name: P3 organoid

value: Mouse PanIN organoid (P3)


title: M10P H3K4me1 ChIP-Seq

value: Mouse PDA peritoneum metastasis (M10P)

value: H3K4me1 (ab8895; Abcam)


title: T6 H3K4me1 ChIP-Seq


title: N6 Ipt ChIP-Seq

source_name: N6 organoid

value: Mouse normal pancreatic organoid (N6)


title: M10P FOXA1 ChIP-Seq

value: FOXA1 (ab23738; Abcam)


title: M1L FOXA1 ChIP-Seq

value: Mouse PDA liver metastasis (M1L)


title: M3P FOXA1 ChIP-Seq

value: Mouse PDA peritoneum metastasis (M3P)


title: M10P H3K27ac ChIP-Seq

value: H3K27ac (ab4729; Abcam)


title: M3P H3K4me1 ChIP-Seq


title: T23 H3K4me1 ChIP-Seq


title: T6 FOXA1 ChIP-Seq


title: T3 FOXA1 ChIP-Seq


title: M1L H3K27ac ChIP-Seq


title: T3 H3K4me1 ChIP-Seq


title: T23 FOXA1 ChIP-Seq


title: M3P H3K27ac ChIP-Seq


title: M3L H3K27ac ChIP-Seq

value: Mouse PDA liver metastasis (M3L)


title: M15D H3K27ac ChIP-Seq

source_name: M15D organoid

value: Mouse PDA peritoneum metastasis (M15D)


title: T34 H3K27ac ChIP-Seq

value: Mouse PDA primary tumor organoid (T34)


title: P2 H3K27ac ChIP-Seq

value: Mouse PanIN organoid (P2)


title: M1L H3K4me1 ChIP-Seq


title: T3 H3K27ac ChIP-Seq


title: T6 H3K27ac ChIP-Seq


title: M10P ATAC-Seq

data_processing:
Raw reads were mapped to the reference mouse (mm9) genome assembly using Bowtie allowing two-mismatches for only unique alignment; -v 2 -m 1 -best --strata. To avoid clonal artifacts introduced in the library amplification steps, duplicated mapped reads were further discarded using SAMtools (http://samtools.sourceforge.net).
HOMER suite (http://homer.salk.edu/homer/) was used for overall analysis. Details were described in the experimental procedues of this study.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

source_name: M10P organoid

extract_protocol:
Nuclear extract were prepared from 50,000 single cell dissociated of organoid cultures, incubated with Tn5 transposase, and purified with Qiagen MinElute kit for library construction.
Sequencing libraries were constructed using a modified version of the Illumina Nextera DNA Sample prep kit, as originally described in Buenrostro et al. (2013).


title: T23 H3K27ac ChIP-Seq

value: Mouse PDA primary tumor organoid (T23)


title: T19 H3K27ac ChIP-Seq


title: P3 H3K27ac ChIP-Seq


title: P3 ATAC-Seq


title: N5 H3K27ac ChIP-Seq

value: Mouse normal pancreatic organoid (N5)


title: M1L ATAC-Seq


title: T3 ATAC-Seq


title: N6 H3K27ac ChIP-Seq


title: KO3

city: Cambridge

first: Michael

last: Hemann

state: Massachusetts

address: 500 Main St, Building 76 Room 301

department: Koch Institute

institute: Massachusetts Institute of Technology

data_processing:
read alignment with bowtie2
ATAC signal peaks were called using macs2
nucleosome signals were called using NucleoATAC
Genome_build: mm9
Supplementary_files_format_and_content: GFF file containing TSS nucleosome signals in 10bp bins, spanning +/-1kb of annotated TSSs

source_name: BCR-ABL1 transformed p19 null preB-ALL

growth_protocol: RPMI-1640 supplemented with 10% FBS, 4mM L-glutamine, 50µM 2-mercaptoethanol, 100U/mL penicillin and 100ug/mL streptomycin.

extract_protocol: 500,000 nuclei were lysed and transposed with the Nextera DNA library preparation kit (Illumina).

value: pre-B cell leukemia

value: BCR-ABL1 overexpressed p19 null PHF6 null


title: T6 ATAC-Seq

value: Mouse PDA primary tumor organoid (T6)


title: T33 H3K27ac ChIP-Seq

value: Mouse PDA primary tumor organoid (T33)


title: M6P H3K27ac ChIP-Seq

source_name: M6P organoid

value: Mouse PDA peritoneum metastasis (M6P)


title: P2 ATAC-Seq


title: M3P ATAC-Seq


title: N6 ATAC-Seq


title: KO1


title: KO2


title: WT_UUO_1

city: Boston

first: John

middle: N

last: Hutchinson

address: 201 Wachusett Street

institute: Diamond Age Data Science

description: Total RNA from mouse kidney from wildtype mice after 7 days unilateral uretal obstruction

data_processing:
Alignment and soft-trimming, STAR aligner version 2.4.1d, with options: --runThreadN 6 --outFilterMultimapNmax 10 --sjdbOverhang 74  --outSAMstrandField intronMotif  --quantMode TranscriptomeSAM
Feature counting with featureCounts, version 1.4.4, from the SUBREAD package with options: -s 0
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text files with EnsemblIDs and raw feature counts

source_name: kidney

extract_protocol:
Total RNA was extracted from frozen kidney tissue using the RNeasy Mini Kit (Qiagen). The quantity and quality of the RNA were assessed by NanoDrop 2000 (ThermoScientific) and the Bioanalyzer RNA 6000 Pico Kit (Agilent), respectively.
Libraries were prepared from 330 ng total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturers instructions. Quality and quantity of the library were assessed by the High Sensitivity DNA Analysis Kit (Agilent) and by

treatment_protocol: Male Balb/c mice (25-29 g) received a single intraperitoneal (ip) injection of 250 mg/kg folic acid (FA) dissolved in a 0.3 M sodium bicarbonate solution. Mice were sacrificed at day 7 following administration.

value: Wildtype


title: WT_UUO_2


title: WT3

value: BCR-ABL1 overexpressed p19 null


title: WT1


title: WT_normal_2

description: Total RNA from untreated mouse kidney from wildtype mice


title: T23 ATAC-Seq


title: WT_normal_1


title: SMOC2_UUO_4

description: Total RNA from mouse kidney from SMOC2 transgenic mice after 7 days unilateral uretal obstruction

value: SMOC2 Transgenic


title: SMOC2_UUO_3


title: WT_normal_3


title: SMOC2_UUO_2


title: WT_UUO_3


title: SMOC2_normal_1

description: Total RNA from untreated mouse kidney from SMOC2 transgenic mice


title: WT_UUO_4


title: SMOC2_normal_4


title: N5 ATAC-Seq


title: cells after 12hr recovery replicate 3

city: Santa Barbara

first: Kenneth

last: Kosik

institute: UCSB

description:
I3R12-c
total RNA with rRNA depletion

data_processing:
TopHat v2.0.13 was used for the innitial mapping, refseq genes were provided as transcriptome reference for tophat
unmapped reads aligned to genome by using bowtie2 --local --very-sensitive-local --mm
alighments from tophat and bowtie2 were conbined
RPKM_count.py from RSeQC was used to get read numbers for each genes
Genome_build: hg19
Supplementary_files_format_and_content: txt, gene expression in each sample

source_name: Hela cells

growth_protocol: MEM+Glutamax supplemented with 10% FBS and Pen/Strep

extract_protocol:
Total RNA was extracted using mirVana miRNA isolation kit (Thermo Fisher Scientific) then treated with TURBO Dnase (Thermo Fisher Scientific) to get rid of the genomic DNA. Ribosomal RNA (rRNA) was removed using RiboMinus Eukaryote System v2 (Thermo Fisher Scientific).
cDNA libraries used for sequencing were made from rRNA-depleted RNA using Ion Total RNA-seq kit v2 (Thermo Fisher Scientific)

treatment_protocol: To induce apoptosis, 4.3% ethanol was added to cells for 3hrs. The mock treatment group were added growth medium only. After 3hr ethanol treatment, medium containing ethanol was carefully aspirated, and fresh growth medium was added to allow cells to recover.

value: 12hr recovery after 3hr ethanol treatment

value: HeLa


title: cells after 12hr recovery replicate 2

description:
I3R12-b
total RNA with rRNA depletion


title: cells after 12hr recovery replicate 1

description:
I3R12-a
total RNA with rRNA depletion


title: SMOC2_UUO_1


title: cells after 8hr recovery replicate 2

description:
I3R8-b
total RNA with rRNA depletion

value: 8hr recovery after 3hr ethanol treatment


title: cells after 8hr recovery replicate 3

description:
I3R8-c
total RNA with rRNA depletion


title: cells after 4hr recovery replicate 2

description:
I3R4-b
total RNA with rRNA depletion

value: 4hr recovery after 3hr ethanol treatment


title: cells after 4hr recovery replicate 3

description:
I3R4-c
total RNA with rRNA depletion


title: SMOC2_normal_3


title: cells after 2hr recovery replicate 2

description:
I3R2-b
total RNA with rRNA depletion

value: 2hr recovery after 3hr ethanol treatment


title: cells after 8hr recovery replicate 1

description:
I3R8-a
total RNA with rRNA depletion


title: cells after 2hr recovery replicate 3

description:
I3R2-c
total RNA with rRNA depletion


title: cells after 3hr recovery replicate 2

description:
I3R3-a-2
total RNA with rRNA depletion

value: 3hr recovery after 3hr ethanol treatment


title: cells after 3hr recovery replicate 1

description:
I3R3-a-1
total RNA with rRNA depletion


title: cells after 2hr recovery replicate 1

description:
I3R2-a
total RNA with rRNA depletion


title: cells after 3hr recovery replicate 3

description:
I3R3-b
total RNA with rRNA depletion


title: cells after 1hr recovery replicate 2

description:
I3R1-b
total RNA with rRNA depletion

value: 1hr recovery after 3hr ethanol treatment


title: cells after 1hr recovery replicate 1

description:
I3R1-a
total RNA with rRNA depletion


title: apoptotic cells replicate 3

description:
I3R0-c
total RNA with rRNA depletion

value: 4.3% ethanol treatment for 3hrs


title: apoptotic cells replicate 2

description:
I3R0-b
total RNA with rRNA depletion


title: cells after 4hr recovery replicate 1

description:
I3R4-a
total RNA with rRNA depletion


title: mock-treated cells replicate 1

description:
I0R0-a
total RNA with rRNA depletion

value: mock treatment (growth medium only) for 3hrs


title: DIP2C +/- Cl. A6-C9

city: Uppsala

first: L.

address: Dag Hammarskjölds Väg 20

country: Sweden

institute: Uppsala University

description: DIP2C +/- Cl. A6-C9

data_processing:
The reads were aligned to the human genome hg19 assembly (https://genome.ucsc.edu) using Tophat2 software (version 2.0.4)
The normalized counts summary and statistical tests were performed using the Cufflinks tool (version 2.2.1)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with normalized counts values for each Sample.

source_name: DIP2C +/- Cl. A6-C9

extract_protocol:
Total RNA was extracted using an RNeasy Plus Mini kit (Qiagen). The RNA integrity and concentration was determined on a Bioanalyzer instrument (Agilent) using an RNA 6000 Nano kit.
For preparation of samples for RNA sequencing, 1 x10e6 cells were plated and    grown for 48 h. The cells were then detached by trypsination and 2  106    cells were pelleted for RNA isolation. RNA samples were prepared using the    Qiagen RNeasy Mini kit with on-column DNase treatment according to the    provided protocol. RNA quality and concentration was determined by analysis    on a Bioanalyzer 2100 instrument using the RNA 6000 nano chip (Agilent).

value: human colorectal cancer cell line RKO

value: DIP2C +/-


title: 2242-1_Thy1_Day_250 (bulk)

city: Atlanta

first: Steven

last: Sloan

state: GA

address: 615 Michael Street, Whitehead Building Room 375

department: Human Genetics

institute: Emory University

description: bulk

data_processing:
Processing and read alignment Fastq files first groomed, and then reads were aligned to the hg19 genome with Tophat2 using default settings (anchor length =8, minimum intron length =70, indel search with max insertion/deltion length = 3, mismatches per segment = 2, min length read segments = 25)
Per-gene read assignment: aligned reads were converted to FPM for every gene using Cufflinks (default settings; length correction applied), with hg19 as reference genome
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with FPKM values for each sample

source_name: iPSC-derived coritical spheroids (hCS)

growth_protocol: human cortical spheroids (hCS) were generated as described in (Pasca, Sloan et al., 2015)

extract_protocol:
A single cell suspension of hCS was generated using papain digestion as described in (Zhang, Sloan et al., 2016). Cell types were then purified using immunopanning with either anti-Thy1 antibody (neurons) or anti-HepaCAM antibody (astroctyes)
Total RNA was extracted using the miRNeasy kit (Qiagen 217084) under the protocols of the manufacturer. The quality of the RNA was assessed by Bioanalyzer. Samples with integrity number higher than 8 were used for library construction. cDNA was prepared according to the manufacturer's instructions accompanying the Ovation® RNA-seq system V2 (Nugen 7102) to perform first and second-strand cDNA synthesis. Libraries were prepared according to the manufacturer's instructions accompanying the NEB Next Ultra RNA-seq library prep kit for Illumina (NEB E7530) and NEBNext® multiplex oligos for Illumina (NEB E7335 E7500). In brief, library generation involved end repair, adaptor ligation, and 6 cycles of PCR enrichment. Indexed DNA fragments were subsequently purified and run on Bioanalyzer to assess library quality. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina NextSeq 500 following the manufacturer's protocols.

treatment_protocol: None; RNA from cells was harvested immediately after purification

tag: iPSc-line

tag: day of differentiation

tag: immunopanning antibody

value: Thy1 (neuron)


title: DIP2C +/- Cl. G1-A5

description: DIP2C +/- Cl. G1-A5

source_name: DIP2C +/- Cl. G1-A5

tag: cell line


title: RKOparental-2

value: parental control


title: DIP2C -/- Cl. C10

description: DIP2C -/- Cl. C10

source_name: DIP2C -/- Cl. C10

value: DIP2C -/-


title: mock-treated cells replicate 2

address: UC Santa Barbara

description:
I0R0-b
total RNA with rRNA depletion


title: DIP2C +/- Cl. F6-A7

description: DIP2C +/- Cl. F6-A7

source_name: DIP2C +/- Cl. F6-A7


title: mock-treated cells replicate 3

description:
I0R0-c
total RNA with rRNA depletion


title: DIP2C +/- Cl. A9-A12

description: DIP2C +/- Cl. A9-A12


title: DIP2C +/- Cl. H9-A4

description: DIP2C +/- Cl. H9-A4

source_name: DIP2C +/- Cl. H9-A4


title: DIP2C -/- Cl. E3

description: DIP2C -/- Cl. E3

source_name: DIP2C -/- Cl. E3


title: 2242-1_Thy1_Day_160b (bulk)

description: bulk


title: cells after 1hr recovery replicate 3

description:
I3R1-c
total RNA with rRNA depletion


title: 2242-1_Thy1_Day_160 (bulk)

description: bulk


title: 8858-3_Hepa_Day_100 (bulk)

description: bulk

value: HepaCAM (astrocyte)


title: 8858-1_Thy1_Day_100 (bulk)

description: bulk


title: 8858-3_Hepa_Day_130 (bulk)

description: bulk


title: 8858-1_Thy1_Day_450 (bulk)

description: bulk


title: 2242-1_Thy1_Day_100 (bulk)

description: bulk


title: 8858-1_Thy1_Day_93 (bulk)

description: bulk


title: 8858-1_Thy1_Day_82 (bulk)

description: bulk


title: 2242-1_Hepa_Day_495 (bulk)

description: bulk


title: 2242-1_Hepa_Day_450 (bulk)

description: bulk


title: RKOparental-1


title: 8858-1_Hepa_Day_180 (bulk)

description: bulk


title: 2242-1_Hepa_Day_377 (bulk)

description: bulk


title: 2242-1_Hepa_Day_295 (bulk)

description: bulk


title: apoptotic cells replicate 1

description:
I3R0-a
total RNA with rRNA depletion


title: 2242-1_Hepa_Day_172 (bulk)

description: bulk


title: 2242-1_Hepa_Day_193 (bulk)

description: bulk


title: 2242-1_Hepa_Day_120 (bulk)

description: bulk


title: 2242-1_Hepa_Day_137 (bulk)

description: bulk


title: 2242-1_Hepa_Day_96 (bulk)

description: bulk


title: 2242-1_Hepa_Day_224 (bulk)

description: bulk


title: 2242-1_Hepa_Day_102 (bulk)

description: bulk


title: 1001000291.E5 (single cell)

description:
hCS-derived cell
Single cell

data_processing:
Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65).  We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore  (--stringency 1).
Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ).
Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample

source_name: human cortical spheroid-derived cell

extract_protocol:
single-cell sorting in 96-well plates followed by cDNA preparation using Smart-seq2
Smart-Seq2 for preparation of cDNA followed by library preparation using Nextera XT
Nextera tagmentation according to the standard protocol for single cell RNA-seq following Smart-Seq2

tag: plate id

tag: well

tag: tissue

value: hCS

value: Day 130

tag: selection type

value: HEPACAM

tag: cell type

value: glia

tag: glial cluster


title: 1001000291.B11 (single cell)

description:
hCS-derived cell
Single cell

tag: age


title: 1001000291.F2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.C7 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.E11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.G3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.D10 (single cell)

description:
hCS-derived cell
Single cell

value: neuron


title: 1001000291.G10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.H2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.F5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.G6 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.F12 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.E2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.E9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.B4 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.B12 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.A7 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.C1 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.A11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.D11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.A4 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.C8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.F8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.G12 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.H10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.B3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.F1 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.G7 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.D8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.A3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.F4 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.E3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.H3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.C10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.A12 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.G4 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.G1 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.C4 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.C9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.A5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.H4 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.B9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.B6 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.D7 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.A10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.D2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.F10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.F7 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.B7 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.A8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.C2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.E12 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.D3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.C3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.E7 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.G8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.F3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.G2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.H5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.G9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.B8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.E10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.A9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.H1 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.B10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.B2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.G5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.B1 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.F6 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.D4 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.C5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.A6 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.D12 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.E1 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.C12 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.H7 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.E8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.E4 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.B5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.F11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.H8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.A9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.H6 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.C8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.H7 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.G1 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.E7 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.H11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000291.A2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.A6 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.F7 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.B9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.B5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.C6 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.D6 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.D2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.H10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.G10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.C3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.F6 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.H3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.E1 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.B11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.E11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.C10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.D5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.G2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.G9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.A8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.D1 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.B12 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.F5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.A3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.A5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.H5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.E2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.G5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.E9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.C9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.C12 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.E10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.A12 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.A7 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.C4 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.D4 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.B6 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.F10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.B4 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.B2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.A2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.H2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.A11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.D9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.D12 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.H9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.E5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.D10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.B7 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.F2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.B8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.D3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.D11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.F12 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.C11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.C5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.H1 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.H8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.B10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.E12 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.D8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.F11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.G11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.F8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.C2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.A1 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.D7 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.G8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.B4 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.E11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.F1 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.D10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.F3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.H3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.F2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.C8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.G9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.B11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.E6 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000290.B3 (single cell)

description:
hCS-derived cell
Single cell