title: BT474 THZ 1250 nM 1

status: Public on May 21 2021

city: Albuquerque

first: Viswanathan

last: Palanisamy

state: NM

address: 2325 Camino de Salud NE,

department: Internal Medicine

institute: University of New Mexico

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Partek array software

label: biotin

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: SKBR3 and BT474 were cultured in RPMI-1640 (GIBCO) supplemented with 10% FBS and 1% penicillin/streptomycin.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Cells were treated with vehicle control (DMSO), lapatinib (1 μM) or THZ1 (250 nM) for 6 hrs.

tag: cell line

value: THZ 1250 nM


title: SKBR3 LAPA 1 uM 3

type: RNA

country: USA

description: replicate 3

molecule: total RNA

organism: Homo sapiens

tag: treatment

value: LAPA 1 uM


title: Bleomycin None 7 r2

status: Public on May 05 2021

type: SRA

city: Biberach an der Riss

first: Fidel

last: Ramírez

state: BW

address: Birkendorfer Str. 65

department: Computational Biology

country: Germany

institute: Boehringer Ingelheim Pharma GmbH & Co KG

library_source: transcriptomic single cell

data_processing:
CellRanger v2 was used to obtain cell matrices per sample. Seurat was used to process matrices.
Supplementary_files_format_and_content: .h5 cell ranger unfiltered count matrices

organism: Mus musculus

source_name: lung

extract_protocol:
Lungs were dissociated using the gentleMACS protocol; flushed through a 70 μm cell strainer and washed twice with HBSS/0.5% FCS/0.4% EDTA buffer, Lung immune cells were then isolated according to the Lymphocyte Separation Medium protocol  and cell pellets were washed to prepare cells for single cell RNA-seq.
Handling of the Chromium Controller and library preparation using the Single Cell 3’ Reagent Kits v2 (10x Genomics, Pleasanton, CA) were performed; The Single Cell 3’ Chip was loaded aiming to capture 5,000 cells. cDNA from captured immune cells was amplified during cDNA amplification (13 PCR cycles) and libraries were prepared from 110 ng of cDNA. 13 amplification cycles were performed during the final index PCR reaction. An additional and final cleanup step with 1 volume of SPRISelect Beads (Beckman Coulter, Brea, CA) was performed to remove any left-over primers and primer dimers.
Libraries were on average 450 bp in length and sequencing was performed on a HiSeq 4000 using a HiSeq 3000/4000 PE Cluster Kit and two 50-cycle SBS kits (Illumina, San Diego, CA). Paired-end sequencing included a 26 bp read 1 (16 bp cell barcode and 10 bp UMI), 8 bp index read and 98 bp read 2 (transcript sequence read).

tag: weight

tag: mouse train

value: C57BL/6J males

tag: days after treatment

tag: ntb [50 mg/kg]


title: Bleomycin Nintedanib 14 r2


title: Control None 7 r2


title: BT474 DMSO 2

description: replicate 2

value: DMSO


title: BT474 THZ 1250 nM 3

description: replicate 3


title: SKBR3 THZ 1250 nM 3

description: replicate 3


title: BT474 DMSO 3

description: replicate 3


title: BT474 LAPA 1 uM 2

description: replicate 2


title: BT474 THZ 1250 nM 2

description: replicate 2


title: SKBR3 LAPA 1 uM 1

description: replicate 1


title: BT474 LAPA 1 uM 1

description: replicate 1


title: SKBR3 THZ 1250 nM 2

description: replicate 2


title: Control None 14 r2


title: SKBR3 LAPA 1 uM 2

description: replicate 2


title: BT474 LAPA 1 uM 3

description: replicate 3


title: BT474 DMSO 1

description: replicate 1


title: Bleomycin Nintedanib 14 r3


title: SKBR3 DMSO 2

description: replicate 2


title: SKBR3 DMSO 3

description: replicate 3


title: SKBR3 DMSO 1

description: replicate 1


title: Bleomycin None 7 r1


title: Bleomycin None 14 r3


title: Control None 14 r3


title: Bleomycin Nintedanib 7 r2


title: Bleomycin None 7 r3


title: Bleomycin Nintedanib 14 r1


title: VUB14_5 (WT)

status: Public on Apr 06 2021

city: Brussels

first: Claudia

last: Spits

address: Laarbeeklaan 103

department: Research Group of Reproduction and Genetics

country: Belgium

institute: Vrije Universiteit Brussel

description:
processed data file: Raw_count_wt_vs_VUB03_S2.csv
processed data file: CPM_count_wt_vs_VUB03_S2.csv
processed data file: DE_wt_vs_VUB03_S2.csv

library_source: transcriptomic

data_processing:
Mapping sequences: STAR 2.5.3: STAR --runThreadN 8 --runMode alignReads \ --quantMode TranscriptomeSAM \ --twopassMode Basic \ --outSAMtype BAM SortedByCoordinate
Count tables: RSEM 1.3.0: rsem-calculate-expression -p 8 \ --alignments Aligned.toTranscriptome.out.ba
RNA seq analysis: edgeR and DESeq2
Genome_build: GRCh38.p10/hg19
Supplementary_files_format_and_content: Raw_count_wt_vs_VUB03_S2.csv
Supplementary_files_format_and_content: CPM_count_wt_vs_VUB03_S2.csv
Supplementary_files_format_and_content: DE_wt_vs_VUB03_S2.csv

source_name: hESC

growth_protocol: hESC cultured on Laminin-521 with Nutristem medium, refreshed every day. Passaged once a week in a 1:20 ratio.

extract_protocol:
Total RNA was extracted using the QIAGEN RNeasy Mini kit, following manufacturer's instructions.
Illumina sequencing library preparation using the QuantSeq 3' mRNA-Seq Library Prep Kits (Lexogen) according to manufacturer's protocol.

tag: cell type

value: hESC

tag: genotype/variation

value: wild type


title: Control None 14 r1


title: Bleomycin None 14 r2


title: Bleomycin None 14 r1


title: SKBR3 THZ 1250 nM 1

description: replicate 1


title: VUB14_3 (WT)


title: Bleomycin Nintedanib 7 r1


title: VUB03_S1_3 (WT)

description:
VUB03_3 in GSE116372
processed data file: Raw_count_wt_vs_VUB03_S2.csv
processed data file: CPM_count_wt_vs_VUB03_S2.csv
processed data file: DE_wt_vs_VUB03_S2.csv


title: VUB03_S1_2 (WT)

description:
VUB03_2 in GSE116372
processed data file: Raw_count_wt_vs_VUB03_S2.csv
processed data file: CPM_count_wt_vs_VUB03_S2.csv
processed data file: DE_wt_vs_VUB03_S2.csv


title: VUB03_S1_4 (WT)

description:
VUB03_4 in GSE116372
processed data file: Raw_count_wt_vs_VUB03_S2.csv
processed data file: CPM_count_wt_vs_VUB03_S2.csv
processed data file: DE_wt_vs_VUB03_S2.csv


title: Control None 7 r1


title: VUB03_S1_1 (WT)

description:
VUB03_1 in GSE116372
processed data file: Raw_count_wt_vs_VUB03_S2.csv
processed data file: CPM_count_wt_vs_VUB03_S2.csv
processed data file: DE_wt_vs_VUB03_S2.csv


title: VUB14_2 (WT)


title: VUB03_S2_4


title: VUB01_2 (WT)


title: VUB14_4 (WT)


title: VUB01_1 (WT)


title: VUB03_S2_2


title: VUB03_S2_3


title: VUB03_S2_5


title: VUB03_S2_1


title: VUB02_1 (WT)


title: VUB02_2 (WT)


title: VUB14_1 (WT)


title: GS3-PDX-E2

status: Public on Feb 21 2021

city: Duarte

first: Shiuan

last: Chen

state: CA

address: 1500 E Duarte Rd

department: Cancer Biology-BRI

institute: City of Hope National Medical Center

description: single cell RNA

data_processing:
bcl2fastq v2.20 (loaded by cellranger mkfastq (3.0.1)) software used for basecalling.
reads were aligned to refdata-cellranger-hg19-1.2.0 genome assembly using cellranger v3.0.1
Counting data of reference gene expression levels were generated by cellranger v3.0.1 (automatic identification of chemistry properties)
Genome_build: hg19 and mm10
Supplementary_files_format_and_content: Tab separated values; MatrixMarket

source_name: breast cancer

growth_protocol: Surgically resected brain metastasis tumor pieces were implanted into the 4th mammary fat pat of female NOD-scid/IL2Rγ-/- (NSG) mice, that were 6-8 weeks old, to establish PDX lines.

extract_protocol:
Cells were then loaded onto the Chromium Controller (10x Genomics) targeting 2000–5000 cells per lane.
The Chromium v2 single cell 3′ RNA-seq reagent kit (10x Genomics) was used to process samples into scRNA-seq libraries according to the manufacturer’s protocol. Libraries were sequenced with a Hiseq 2500 instrument (Illumina) with a depth of 50k–100k reads per cell.

treatment_protocol: After tumor volume reached approximately 200mm3, mice were randomized and implanted with an Placebo or E2 (1mg) or DHT (12.5mg) pellet on their backside. These treatments lasted 7 days for experiments on single cell analysis.

tag: tissue

value: tumor


title: GS3-PDX-Placebo

description: single cell RNA


title: ZAP-g3 knockout HFF, CMV infected 24hpi, replicate 1 [ZAP-g3-24hpi-rep1]

status: Public on Feb 01 2021

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

institute: Max Delbrück Center for Molecular Medicine

description:
RNAseq_ZAP191-KD-mock-rep1
processed data file:
RNAseq_hg19_readcounts.tsv
RNAseq_CMV-MF871618_readcounts.tsv

data_processing:
For bulk RNA-sequencing, alignments were done using hisat2 (Kim et al, 2015)
Sequencing reads were aligned to the hg19 version of the human genome using standard parameter, using the Refseq gtf file downloaded from the UCSC genome browser.
Reads were then quantified using quasR (Gaidatzis et al, 2015) and the above mentioned gtf file, or the HCMV TB40/E annotation (accession number MF871618).
Differential expression and corresponding p-values were calculated using edgeR (McCarthy et al, 2012).
For 4sU sequencing, reads were mapped to a combined index of the human genome (Hg38 / Ensembl v90) and the HCMV genome (accession number KF297339.1) using STAR (v2.5.3a) with parameters --outFilterMismatchNmax 20 --outFilterScoreMinOverLread 0.3 --outFilterMatchNminOverLread 0.3 --alignEndsType Extend5pOfReads12 --outSAMattributes nM MD NH.
We used GRAND-SLAM (v2.0.5d) (Jurges et al., 2018) to estimate the new-to-total RNA ratios.
We only used the parts of the reads that were sequenced by both mates in a read pair (parameter -double) for the estimation.
New RNA was computed by multiplying total RNA with the maximum a posteriori estimate of the new-to-total RNA ratio.
For further analyses, we removed all cellular genes that had less than 10 transcripts per million transcripts (TPM) in more than 6 (cellular genes) or 2 (viral genes) samples.
To remove artefacts due to imprecise quantification, we furthermore removed all viral genes with less than 100 new reads. Log2 fold changes were estimated using PsiLFC (Erhard, 2018) with uninformative prior (corresponding to no pseudocounts).
Normalization factors were computed from total RNA such that the median log2 foldchange was 0 and applied to both total and new RNA.
Genome_build: hg19 and HCMV MF871618 (bulk RNA-seq); hg38 and HCMV KF297339.1 (4sU seq)
Supplementary_files_format_and_content: tab-separated values

molecule: polyA RNA

source_name: ZAP-g3 knockout HFF, CMV infected 24hpi

growth_protocol:
Primary human foreskin fibroblasts (HFF-1) cells (ATCC SCRC-1041) were maintained in DMEM (high glucose) supplemented with 15% FCS, 1% P/S and 1% non‐essential amino acids (NEAA). Cells were cultured at 37°C and 7.5% CO2.
Knockouts of ZAP (ZC3HAV1) were done using CRISPR/Cas9, with components transduced by lentiviruses

extract_protocol:
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina
adapter sequence: GATCGGAAGAGCACACGT
For  RNA-sequencing, Cells were resuspended in Trizol (Invitrogen) and RNA extracted from Trizol.
RNA-sequencing libraries were constructed using commercial kits (New England Biolabs)

treatment_protocol: Cells were subjected to CMV infection and 4sU treatment as indicated

value: Primary human foreskin fibroblasts (HFF) cells

value: ZAP-g3 knockout

value: CMV infected 24hpi

tag: grna sequence forward

value: CACCGGCCGGGATCACCCGATCGG

tag: grna sequence reverse

value: AAACCCGATCGGGTGATCCCGGCC

tag: grna name

tag: 4su treatment

tag: cmv infection

value: yes

tag: harvesting timepoint


title: ZAP-g3 knockout HFF, CMV infected 24hpi, replicate 2 [ZAP-g3-24hpi-rep2]

description:
RNAseq_ZAP191-KD-mock-rep2
processed data file:
RNAseq_hg19_readcounts.tsv
RNAseq_CMV-MF871618_readcounts.tsv


title: ZAP-g1 knockout HFF, CMV infected 24hpi, replicate 1 [ZAP-g1-24hpi-rep1]

description:
RNAseq_ZAP2-KD-mock-rep1
processed data file:
RNAseq_hg19_readcounts.tsv
RNAseq_CMV-MF871618_readcounts.tsv

source_name: ZAP-g1 knockout HFF, CMV infected 24hpi

value: ZAP-g1 knockout

value: CACCGGCCGGGCCCGACCGCTTTG

value: AAACCAAAGCGGTCGGGCCCGGCC


title: VUB03_S1_5 (WT)

description:
VUB03_5 in GSE116372
processed data file: Raw_count_wt_vs_VUB03_S2.csv
processed data file: CPM_count_wt_vs_VUB03_S2.csv
processed data file: DE_wt_vs_VUB03_S2.csv


title: ZAP-g1 knockout HFF, CMV infected 24hpi, replicate 2 [ZAP-g1-24hpi-rep2]

description:
RNAseq_ZAP2-KD-mock-rep2
processed data file:
RNAseq_hg19_readcounts.tsv
RNAseq_CMV-MF871618_readcounts.tsv


title: GS3-PDX-DHT

description: single cell RNA


title: control knockout HFF, CMV infected 24hpi, replicate 2 [Ctrl-KD-24hpi-rep2]

description:
RNAseq_FFLuc-KD-mock-rep2
processed data file:
RNAseq_hg19_readcounts.tsv
RNAseq_CMV-MF871618_readcounts.tsv

value: control knockout

value: CACCGGATTCTAAAACGGATTACC

value: AAACGGTAATCCGTTTTAGAATCC

value: control


title: control knockout HFF, CMV infected 24hpi, replicate 1 [Ctrl-KD-24hpi-rep1]

description:
RNAseq_FFLuc-KD-mock-rep1
processed data file:
RNAseq_hg19_readcounts.tsv
RNAseq_CMV-MF871618_readcounts.tsv


title: parental wild type HFF, CMV infected 24hpi, replicate 2 [WT-24hpi-rep2]

description:
RNAseq_WT-mock-rep2
processed data file:
RNAseq_hg19_readcounts.tsv
RNAseq_CMV-MF871618_readcounts.tsv

value: parental wild type


title: parental wild type HFF, CMV infected 24hpi, replicate 1 [WT-24hpi-rep1]

description:
RNAseq_WT-mock-rep1
processed data file:
RNAseq_hg19_readcounts.tsv
RNAseq_CMV-MF871618_readcounts.tsv


title: B13: normal 7 (December 2020)

status: Public on Dec 15 2020

city: Beijing

first: Haihan

last: Xiao

address: NO.1 Beichen West Road, Chaoyang District

country: China

institute: Institute Of Microbiology, Chinese Academy Of Sciences

data_processing:
The pooling sequencing data from one lane was demultiplexed into FASTQ files of each sample according to index sequence in cellranger software package (10X genomics).
Clean raw data was generated after the reads with polluted adapter, Ns and low-quality were filtered out in Fastp package.
Extraction of cell barcodes (parameters using -1) and UMI (molecular barcode), reads mapping to human genome GRCh38.p13 and generation of count matrix were processed in the combined workflow of UMI-tools, STAR, Subread package and Samtools (https://github.com/CGATOxford/UMI-tools/blob/master/doc/Single_cell_tutorial.md).
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample.

source_name: Blood leucocytes

extract_protocol:
RNAprep pure Cell kit (DP430, TIANGEN) were used for extracting cellular total RNA of blood leucocytes, according to the manual. 50ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Fresh blood were obtained via vein puncture. Blood leucocytes were collected after being treated with ACK Lysis Buffer to remove red blood cells.

tag: patient

value: Patient 13

tag: gender

value: Male

tag: age

value: 1 Month

tag: cell counts /×109/l

value: Blood leucocytes


title: B12: normal 6 (December 2020)


title: B11: normal 5 (December 2020)


title: B2: sepsis 2 (December 2020)

value: Patient 7


title: B10: sepsis 6 (December 2020)


title: B9: sepsis 5 (December 2020)


title: ErbB3_V943R_1

status: Public on Nov 13 2020

city: Darlinghurst

first: Leonard

last: Goldstein

address: 384 Victoria St

country: Australia

institute: Garvan Institute of Medical Research

data_processing:
Illumina Casava 1.8
Illumina bcl2fastq 2.20
Reads were demultiplexed based on perfect matches to expected cell barcodes
Cell barcodes were filtered by requiring at least 10,000 reads
Transcript reads were aligned to the mouse reference genome (GRCm38) using GSNAP (2013-10-10) only considering uniquely mapped reads
Per-gene UMI counts were determined based on the number of unique UMIs for mapped reads overlapping exons in sense orientation, allowing for one mismatch when collapsing UMI sequences
UMI counts for each gene are divided by the total number of UMIs in that cell and multiplied by the median total UMI across cells
Genome_build: GRCm38
Supplementary_files_format_and_content: Gene x barcode matrix with UMI counts

source_name: mammary gland luminal epithelial cells

extract_protocol:
The thoracic and abdominal mammary glands from 6-week old ErbB3+/+;MMTV-Cre or ErbB3V943R/V943R;MMTV-Cre C57BL/6N mice (n = 3 per group) were pooled, minced, and collagenase-digested (Stem Cell Technologies) with constant agitation for 1 h.  The samples were further dissociated using an AutoMACS, followed by treatment with Trypsin-EDTA and DNAse I (StemCell Technologies) according to the manufacturer’s recommendations.  Epithelial populations were enriched using the EasySepTM mouse epithelial cell enrichment kit II (StemCell Technologies), and then FACS sorted for luminal epithelial populations.  Post-sorting, the density and viability of the single-cell suspensions was determined by Vi-CELL XR cell counter (Beckman Coulter), and the cell density was then used to impute the volume of single-cell suspension needed in the reverse transcription master mix, aiming to achieve ~6,000 cells per sample.
10x Genomics Chromium Single Cell 3' Library and Gel Bead Kit v2

tag: genotype


title: ErbB3_V943R_2


title: B8: normal 4 (December 2020)

value: Patient 12

value: 2 Month


title: ErbB3_WT_1


title: B6: normal 2 (December 2020)

value: Patient 10

value: Female

value: 3 Month


title: B7: normal 3 (December 2020)

value: Patient 11

value: 1 Day


title: B5: sepsis 4 (December 2020)

value: Patient 9

value: 29 Day


title: MDA-MB231 cells infected with pLL3.7 empty vector, replicate 1

status: Public on Jan 06 2021

city: Plainsboro

first: Yong

last: Wei

state: NJ

address: LTL227 Wathington Road

department: Molecular Biology

institute: Princeton University

hyb_protocol: Each cy5 labeled testing sample was mixed with equal amount cy3-labeled reference sample and fragmented and blocked (Agilent Gene Expression Hybridization Kit),  and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software (version 9.5.3.1).

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and linear Lowess normalization.

label_protocol: The testing RNA samples and universal mouse reference RNA (Agilent) were labeled with CTP-cy5 and CTP-cy3, respectively, Using Agilent Quick Amp Labeling Kit.

extract_protocol:
Cell preparation protocol: MDA-MB-231 breast cancer cells were infected with lenti-viral vector pLL3.7 with or without shRNAs against EPN1/2. The successful KD were confirmed by Western blot of the stable lines.
Total RNA were extracted using RNAeasy mini-prep kit from Qiagen

tag: tumor type

value: breast cancer

tag: cell line

tag: exogenous manipulation

source_name: Universal human Reference RNA

tag: cell lines

value: Mix of 10 human cell lines


title: SUM159 from 1st round lung met from P1 reinjection #1

status: Public on Jan 13 2021

hyb_protocol: Scanned on an Agilent G2505C scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version 11.0).

data_processing: Agilent Feature Extraction Software (v 11.0) was used for background subtraction and linear Lowess normalization.

label_protocol: Each Cy5 labeled testing sample was mixed with equal amount Cy3-labeled reference sample and fragmented and blocked (Agilent Gene Expression Hybridization Kit), and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially.

growth_protocol: SUM159 and derivative cells are cultured in F12 media with 10% FBS, 10 ug/mL Insulin and 20 ng/mL EGF. Subconfluent cells are lyzed with RLT buffer and collected.

extract_protocol: The testing RNA samples and Universal Human Reference RNA (Agilent Cat#740000) were labeled with CTP-Cy5 and CTP-Cy3, respectively, using Agilent Quick Amp Labeling Kit.

treatment_protocol: Total RNA were extracted using RNeasy mini-prep kit from Qiagen.

tag: parental cell line

tag: derivative

tag: lung metastasis

value: High

tag: bone metastasis

source_name: Universal Human Reference RNA

tag: sample type

value: Reference


title: B4: sepsis 3 (December 2020)

value: Patient 8

value: Male

value: 9 Month

tag: tissue


title: SUM159 from 2nd round mammary tumor from P1 reinjection

value: Low


title: B3: normal 1 (December 2020)

value: Patient 7

value: 1 Month

value: Blood leucocytes


title: SUM159 from 2nd round lung met from M1a reinjection

value: 2nd round lung met from M1a reinjection


title: B1: sepsis 1 (December 2020)


title: MDA-MB231 cells infected with shRNAs knocking down EPN1/2, replicate 1


title: Metastatic breast cancer; (9) ER+, (10) ER-, (11) ER-

status: Public on Aug 25 2020

city: Aurora

first: Kiran

last: Vinod Paul

institute: University of Colorado-Anschutz medical campus

data_processing:
Alignment  and UMI generation was done using CellRanger3
Pre-processing and QC was performed using Seurat 3
Normalize the raw counts using Seurat 3
ALRA imputation done using Seurat 3
UMAP projections made using Seurat 3
gene marker expression was determined in each cluster using Seurat 3
Marker genes were used for the interactome analysis
Genome_build: GRCh38
Supplementary_files_format_and_content: TSV files were generated for the raw expression counts and metadata

source_name: Peripheral blood

extract_protocol:
Cells from patient blood were filtered over a size exclusion filter and red blood cells were removed using ErythroClear™ Red Blood Cell Depeltion from STEMCELL Technologies.
Single cells were captured and libraries were constructed using the 10X Genomics, Chromium Box capture and library generation system.

tag: disease state

value: Breast cancer


title: SUM159 from 1st round lung met from P1 reinjection #2


title: SUM159 parental line expressing triple reporter

value: Expressing triple reporter


title: SUM159 from 1st round mammary tumor from TR injection


title: ErbB3_WT_2


title: MDA-MB231 cells infected with pLL3.7 empty vector, replicate 2


title: MDA-MB231 cells infected with shRNAs knocking down EPN1/2, replicate 2


title: SUM159 parental line

value: Parental


title: 1 Stage 2 ER+ breast cancer


title: 4 Metastatic ER+ breast cancer


title: 2 Metastatic ER+ breast cancer


title: 8 Metastatic ER- breast cancer


title: P21_2 skin sample (unwounded)

status: Public on Jul 01 2020

city: Pullman

first: Ryan

middle: Roy

last: Driskell

state: Washington

address: 100 Dairy Rd. BLS 202A

department: Molecular Biosciences

institute: Washington State University

description: 10X Genomics scRNA-Seq v2

data_processing:
Cellranger version 3.0.2 pipeline to generate output folders
Velocyto 0.17.5 run10x function was used to make loom files
Genome_build: mm10
Supplementary_files_format_and_content: loom files

source_name: skin

extract_protocol:
Cells were collected from dorsal skin (wounded or unwounded), single cells suspension according to protocol Jensen and Driskell 2010
scRNA libraries were constructed following 10X Genomics Protocol

treatment_protocol: 2mm circular full-thickness wound, collected 7dpw

value: dorsal skin

value: WT

tag: strain

tag: condition

value: unwounded


title: P21_1 skin sample (unwounded)

description: 10X Genomics scRNA-Seq v2


title: P21_3 skin sample (unwounded)

description: 10X Genomics scRNA-Seq v2


title: 7 Metastatic ER+ breast cancer


title: SMC09-N

status: Public on Apr 04 2020

city: Seoul

first: Yourae

last: Hong

address: 81, Irwon-ro

department: Samsung Genome Institute

country: South Korea

institute: Samsung Medical Center

data_processing:
Using CellRanger 2.1.0 pipeline (10X Genomics), fastq data was aligned to a human genome reference (GRCh38) and the unique molecular identifier (UMI) counts was quantified .
The raw gene expression matrix from the CellRanger pipeline was filtered using the Seurat R package (version 2.3) and selected according to the following criteria: cells with > 1000 UMI counts, > 200 genes, and < 6,000 genes, and < 20% of mitochondrial gene expression in UMI counts.
After filtering step, the raw gene expression matrix was normalized to the total UMI counts per cell and transformed to the natural log scale.
We combined the Seurat multiCCA and RCA pipelines for initial clustering and cell type identification and removed discordant cells from 2 methods.
To eliminate doublets, cells with a number of genes exceeding the outliers were removed.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-deliminated text file containing the raw gene expression and the normalized gene expression for QC filtered cells.

source_name: SMC09_Normal mucosa

extract_protocol:
After resection, tumor (n = 23) and non-malignant (n = 10) colon tissues were collected immediately and tissue dissociation was performed using a tumor dissociation kit (Miltenyi Biotech, Germany), according to the manufacturer’s instructions. Briefly, tissues were cut into 2-4 mm pieces and transferred to C tubes containing an enzyme mix (Enzyme H, R, and A in RPMI1640 media). Gentle MACS programs (h_tumor_01, 02, and 03) were run in a MACSmix tube rotator, with two 30-min incubation periods at 37°C between each run. The digested samples were filtered through a 70-µm strainer, purified via a Ficoll-Paque PLUS (GE healthcare. USA) gradient, and cryopreserved in cell bank (Zenoaq, Japan) before sequencing. The cryopreserved single cell dissociates were rapidly thawed, washed and loaded to Chomium system (10X genomics) targeting 5,000 cells.
Following the manufacturer’s instructions, barcoded sequencing libraries were generated using Chromium Single Cell 3’ v2 kits and sequenced across 8 lanes on a Hiseq 4000 platform (Illumina) targeting 100,000 reads per cell.

tag: tissue type

value: Normal mucosa


title: SMC24-T

source_name: SMC24_Colorectal cancer

tag: tumor stage

value: Colorectal cancer

tag: region

value: ascending

tag: pathologic

value: Well differentiated with mucin production (10%)


title: 6 Metastatic ER+ breast cancer


title: SMC02-N

source_name: SMC02_Normal mucosa


title: 5 Metastatic ER+ breast cancer


title: SMC01-N

source_name: SMC01_Normal mucosa


title: SMC10-N

source_name: SMC10_Normal mucosa


title: SMC20-T

source_name: SMC20_Colorectal cancer

value: Mucinous adenocarcinoma


title: SMC18-T

source_name: SMC18_Colorectal cancer

value: sigmoid

value: Moderately differenttiated


title: SMC08-N

source_name: SMC08_Normal mucosa


title: SMC07-N

source_name: SMC07_Normal mucosa


title: SMC15-T

source_name: SMC15_Colorectal cancer

value: Well differentiated


title: SMC14-T

source_name: SMC14_Colorectal cancer

value: rectosigmoid


title: SMC06-N

source_name: SMC06_Normal mucosa


title: SMC11-T

source_name: SMC11_Colorectal cancer


title: SMC05-N

source_name: SMC05_Normal mucosa


title: SMC10-T

source_name: SMC10_Colorectal cancer


title: SMC07-T

source_name: SMC07_Colorectal cancer


title: SMC03-N

source_name: SMC03_Normal mucosa


title: SMC06-T

source_name: SMC06_Colorectal cancer

value: hepatic flexure


title: SMC04-N

source_name: SMC04_Normal mucosa


title: SMC22-T

source_name: SMC22_Colorectal cancer


title: 3 Metastatic ER+ breast cancer

source_name: Peripheral blood


title: SMC23-T

source_name: SMC23_Colorectal cancer


title: SMC03-T

source_name: SMC03_Colorectal cancer

value: Poorly differntiated


title: SMC01-T

source_name: SMC01_Colorectal cancer

value: rectum


title: SMC19-T

source_name: SMC19_Colorectal cancer


title: SMC02-T

source_name: SMC02_Colorectal cancer


title: SMC21-T

source_name: SMC21_Colorectal cancer


title: SMC25-T

source_name: SMC25_Colorectal cancer


title: SMC17-T

source_name: SMC17_Colorectal cancer


title: SMC16-T

source_name: SMC16_Colorectal cancer


title: SMC09-T

source_name: SMC09_Colorectal cancer


title: SVF, 34-week HFD rep1

status: Public on Mar 19 2020

city: Boston

first: Stephen

middle: R

last: Farmer

state: MA

address: 72 E Concord St.

department: Biochemistry

institute: Boston University School of Medicine

description:
svf_thirty_four_week_tpm.tsv
S15

data_processing:
Raw sequencing reads were subjected to quality control analysis via FastQC and reports aggregated via MultiQC. Reads were then trimmed based on a sliding window and presence of adapter sequences using Trimmomatic set to the following parameters: ILLUMINACLIP::2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50. Salmon was used to quantify the expression of transcripts to a reference transcriptome containing protein coding and long non-coding RNAs from the gencode M10 annotation before aggregation to the gene level. Only genes with a raw count of greater than 5 and present in at least half of the replicates were used for downstream analysis. Normalization and differential expression were performed using DESeq2 set to default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: TPM matrixes for all samples generated by Salmon

source_name: visceral white adipose tissue

growth_protocol: C57BL/6J male mice were purchased from Jackson Laboratories (stock number  000664) and fed either a high fat diet (HFD) containing 60% kcal from fat (D12492;  Research Diets) or control chow diet (D12450B or D12450K; Research Diets) starting  from 6 weeks of age for 8, 20 or 34 weeks. Mice were maintained on a standard 12hr  light/dark cycle with ad libitum access to food and water. Bodyweights were measured  prior to study and at the end of the study under fed conditions. On the final day of each  study timepoint, mice were fasted for 6 hours (4:00 – 10:00am) by the removal of food  but with free access to water. Mice were euthanized using carbon dioxide asphyxiation  followed by cervical dislocation. All harvested tissues were wrapped in foil and  immediately snap-frozen in liquid nitrogen (LN2). At the completion of the study, tissues  were stored at -80C. All experimental protocols performed on animals were in accordance with  regulations and established guidelines and were reviewed and approved by Institutional  Animal Care and Use Committee (IACUC) at Pfizer Inc, Cambridge, MA.

extract_protocol:
Dissociation media was prepared by adding 2 grams of bovine serum albumin (BSA) to 100 mL of 4.5g/L glucose DMEM media (Invitrogen) and warmed in a 37C water bath to dissolve. Adipose tissue was dissected at the termination of the study. The fat pad was rinsed with PBS before being gently minced in dissociation media with scissors and a razor blade. The minced tissue was then digested by transferring to a 50 mL falcon tube containing 25 mL of 1 mg/mL type I collagenase (Worthington) dissolved in dissociation media and placed in a 37C water bath with gentle shaking for approximately 40 minutes. The dispersed tissue was then passed through a 100 µm mesh filter and centrifuged at 200xg for 10 minutes. The floating adipocytes were carefully removed and added to a tube containing approximately 5 volumes of trizol (Qiagen) and immediately snap frozen in a bath of LN2. The pelleted SVF was resuspended in erythrocyte lysing buffer (155 mM NH4Cl, 10 mM KHCO3, 1 mM EDTA), incubated at room temperature for 3 minutes and then centrifuged at 200xg for 10 minutes. Pelleted SVF was resuspended in 2 mL trizol (Qiagen) and immediately snap frozen in a bath of LN2. Cell fractions were stored at -80C.
cDNA libraries for RNA-seq analysis were prepared from total RNA (isolated as described above) according to Illumina TruSeq stranded mRNA sample prep LS protocol. Pooled sample libraries were sequenced on Nextseq 500 instrument with Nextseq 500/550 High output kit, 150 cycles (Illumina).

tag: treatment

value: HFD

tag: cell type

value: stromal vascular fraction

tag: time


title: SVF, 34-week CHOW rep5

description:
svf_thirty_four_week_tpm.tsv
S5

value: CHOW


title: SVF, 34-week HFD rep6

description:
svf_thirty_four_week_tpm.tsv
S20


title: SVF, 34-week HFD rep4

description:
svf_thirty_four_week_tpm.tsv
S18


title: SVF, 34-week HFD rep2

description:
svf_thirty_four_week_tpm.tsv
S16


title: SVF, 34-week CHOW rep4

description:
svf_thirty_four_week_tpm.tsv
S4


title: SMC08-T

source_name: SMC08_Colorectal cancer


title: SVF, 34-week CHOW rep2

description:
svf_thirty_four_week_tpm.tsv
S2


title: SMC05-T

source_name: SMC05_Colorectal cancer

value: Well differentiated with mucin production (<10%)


title: SMC04-T

source_name: SMC04_Colorectal cancer


title: SVF, 34-week CHOW rep6

description:
svf_thirty_four_week_tpm.tsv
S6


title: SVF, 34-week HFD rep5

description:
svf_thirty_four_week_tpm.tsv
S19


title: SVF, 34-week HFD rep3

description:
svf_thirty_four_week_tpm.tsv
S17


title: SVF, 34-week CHOW rep7

description:
svf_thirty_four_week_tpm.tsv
S7


title: SVF, 8-week HFD rep5

description:
svf_eight_twenty_week_tpm.tsv
S47


title: SVF, 8-week HFD rep6

description:
svf_eight_twenty_week_tpm.tsv
S48


title: SVF, 8-week HFD rep3

description:
svf_eight_twenty_week_tpm.tsv
S45


title: SVF, 34-week CHOW rep1

description:
svf_thirty_four_week_tpm.tsv
S1


title: SVF, 34-week CHOW rep3

description:
svf_thirty_four_week_tpm.tsv
S3


title: SVF, 8-week CHOW rep4

description:
svf_eight_twenty_week_tpm.tsv
S36


title: SVF, 8-week CHOW rep1

description:
svf_eight_twenty_week_tpm.tsv
S31


title: SVF, 20-week HFD rep6

description:
svf_eight_twenty_week_tpm.tsv
S24


title: SVF, 8-week HFD rep4

description:
svf_eight_twenty_week_tpm.tsv
S46


title: SVF, 8-week HFD rep2

description:
svf_eight_twenty_week_tpm.tsv
S44


title: SVF, 20-week HFD rep4

description:
svf_eight_twenty_week_tpm.tsv
S22


title: SVF, 20-week HFD rep5

description:
svf_eight_twenty_week_tpm.tsv
S23


title: SVF, 8-week CHOW rep3

description:
svf_eight_twenty_week_tpm.tsv
S34


title: SVF, 8-week CHOW rep2

description:
svf_eight_twenty_week_tpm.tsv
S33


title: SVF, 20-week HFD rep3

description:
svf_eight_twenty_week_tpm.tsv
S21


title: SVF, 8-week HFD rep1

description:
svf_eight_twenty_week_tpm.tsv
S43


title: SVF, 20-week HFD rep2

description:
svf_eight_twenty_week_tpm.tsv
S20


title: SVF, 20-week CHOW rep 5

description:
svf_eight_twenty_week_tpm.tsv
S12


title: SVF, 20-week CHOW rep2

description:
svf_eight_twenty_week_tpm.tsv
S8


title: SVF, 20-week HFD rep1

description:
svf_eight_twenty_week_tpm.tsv
S19


title: SVF, 20-week CHOW rep3

description:
svf_eight_twenty_week_tpm.tsv
S10


title: SVF, 20-week CHOW rep1

description:
svf_eight_twenty_week_tpm.tsv
S7


title: SVF, 20-week CHOW rep4

description:
svf_eight_twenty_week_tpm.tsv
S11


title: WT HuR-1

status: Public on Jan 06 2020

description:
sample identifier: B-4-S4
Group-B_vs_Group-A_1510.txt
Group-B_vs_Group-A_1514.txt

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads (fastq files) were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform (OnRamp Bioinformatics, San Diego, CA). OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data, including data validation and quality control and read alignment to the human genome (hg19) using blastx
The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene-level differential expression analyses.
Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p-value or q-value, which is the smallest false discovery rate (FDR) at which a transcript is called significant.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited .txt files include DESEQ2 output for each Comparison ...

source_name: Tongue

growth_protocol: WT and HuR KO mice exposed with 4NQO for 16 weeks and further waited for 12 weeks to develop oral tumors in tongue. After the tumor formation, both WT and HuR KO mice tongue with tumor tissues excised and used for RNA extraction.

extract_protocol:
Total RNA extracted from tongue tissues using RNAeasy kit Cat No./ID: 74104 (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols using Illumina's TruSeq RNA Library Prep Kit

value: Tongue

tag: age

value: ~34 weeks old

tag: genotype/variation

value: Wild-Type


title: WT-HuR-2

description:
sample identifier: B-5-S5
Group-B_vs_Group-A_1510.txt
Group-B_vs_Group-A_1515.txt


title: WT-HuR-3

description:
sample identifier: B-7-S6
Group-B_vs_Group-A_1510.txt
Group-B_vs_Group-A_1514.txt
Group-B_vs_Group-A_1515.txt


title: HuR KO-3

description:
sample identifier: A-7-S3
Group-B_vs_Group-A_1510.txt

value: Knock-out


title: HuR KO-2

description:
sample identifier: A-6-S2
Group-B_vs_Group-A_1510.txt
Group-B_vs_Group-A_1514.txt
Group-B_vs_Group-A_1515.txt


title: HuR KO-1

description:
sample identifier: A-4-S1
Group-B_vs_Group-A_1510.txt
Group-B_vs_Group-A_1514.txt
Group-B_vs_Group-A_1515.txt


title: P 5 Tumor tissue stem cells-Control

status: Public on Jul 21 2019

city: madrid

first: Alba

last: Costales

state: madrid

address: Arturo Duperier, 4

department: cancer genetics

country: Spain

institute: IIB

data_processing: Sequencing reads were aligned to the transcriptome with TopHat2. Novel transcript discovery was not attempted. TopHat was provided with known gene annotations and other transcript data obtained from Gencode (Version 26 - Ensembl 75) basic gene set for the GRCh37/hg19 human genome assembly. Gene expression level was calculated from TopHat alignments as the number of reads per gene computed using HTSeq using default settings and gene features as defined in the GRCh37.75 release of the human genome (gtf file). Differential gene expression analysis was performed with the Bioconductor DEseq2 package for the R statistical Software.

source_name: stem cell enriched primary culture

growth_protocol: Normal and tumor culture medium was changed every other day and it was composed of 50% Advanced DMEM/F12, 50% Wnt3a-conditioned medium, 10 mM HEPES, 10 mM Glutamax, 10 mM nicotinamide (Sigma-Aldrich), 1x N2 (Thermo Fisher Scientific), 1x B27 (Thermo Fisher Scientific), 1 mM N-acetyl-L-cysteine (Sigma-Aldrich), 1:100 Primocin, 0.1 μg/mL Noggin (Peprotech, NJ, USA), 1 μg/mL Gastrin (Tocris, Bristol, UK), 1 μg/mL RSPO1 (Sino Biological, Beijing, China), 50 ng/mL EGF (Peprotech), 0.02 μM PGE2 (Sigma-Aldrich), 1 μM LY-2157299 (Axon Medchem, VA, USA), 10 μM SB-202190 (Sigma-Aldrich) and 10 μM Y-27632 (Tocris). For passaging, we followed the protocol described by Jung et al. (2011) with modifications. Briefly, Matrigel-embedded organoids were collected using a scraper in a 50 mL conical tube and incubated with Cell Recovery Solution (Corning) for 30 min on ice and continuous shaking to remove Matrigel. After centrifugation at 1000 rpm 5 min at 4ºC, organoids were washed in washing buffer and centrifuged again. Next, organoids were incubated with disaggregation buffer (washing buffer solution containing 10 μM Y-27632 and 1 mg/mL Dispase (Thermo Fisher Scientific)) for 10 min at RT in orbital rotation. Right after 2 mM EDTA (Sigma-Aldrich) was added and the mixture was incubated for additional 5 min. Following this, the solution was homogenized by passing it through a 21G syringe 10 times, collected in a 15 mL conical tube, centrifuged at 1200 rpm for 5 min at 4ºC and washed twice in washing buffer in presence of 10 μM Y-27632. Pelleted cells were embedded in Matrigel and seeded on culture dishes.

extract_protocol:
Macherey-Nagel RNA extraction Kit was used in combination with TRIZOL. Both large and small RNA was extracted.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with 1,25(OH)2D3 [100nM] or vehicle (EtOH) for 96 hours. The treatment was started 48 hours after passage and 1,25(OH)2D3 was renewed every 48 houres.

value: Tumor left colon

tag: gender

value: male

tag: tnm

value: Vehicle


title: P 5 Tumor tissue stem cells- VitD


title: P 6 Tumor tissue stem cells-Control


title: P 6 Tumor tissue stem cells- VitD


title: WT-control shRNA2

description: Control

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads (fastq files) were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with CutAdapt and FASTQC.
Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform (OnRamp Bioinformatics, San Diego, CA). OnRamp’s advanced Genomics Analysis Engine utilized an automated miRNA  workflow basedon CAP-miRNA-seq  to process the data, including data validation and quality control and read alignment to the human genome (hg19) using blastx
Read analysis was performed via a custom implementaiton of  the CAP-miRNASeq protocols. The resulting SAM files were sorted and inputted into MIRDEEP program, then EdgeR for gene-level differential expression analyses.
Transcript count data from EdgeR analysis of the samples were sorted according to their adjusted p-value or q-value, which is the smallest false discovery rate (FDR) at which a transcript is called significant.
Genome_build: HG19
Supplementary_files_format_and_content: tab-delimited .txt files include EdgeR output for the WT vs FXR1-KD comparison

source_name: cancer cells

growth_protocol: HNSCC cell lines UMSCC-74B was obtained from University of Michigan. Cells were routinely grown in Dulbecco’s modified Eagle medium (DMEM-Hyclone) containing 10% fetal bovine serum (FBS) with 100U/ml penicillin and 100 μg/ml streptomycin. The passage was calculated and approximately 12 to 15 passages.  Two different shRNA constructs for FXR1 (TRCN0000158932 and TRCN0000159153) was obtained from Sigma Mission. Regular transduction was done with lentiviral particles with two shRNAs against FXR1.

extract_protocol:
Total RNA is prepared from HNSCC cell line UMSCC74B using miRNeasy mini kit (QIAGEN) by following manufacturer’s protocol. After elusion,    RNaeast minielute column used to purify >200nt fractions and subjected to library preparations.
miRNA libraries were prepared for sequencing using standard Illumina protocols using Illumina's TruSeq Small RNA Library Prep Kit

value: Oral cancer cells

tag: passages


title: WT-control shRNA1

description: Control


title: FXR1 KD-2

description: Knockdown


title: FXR1 KD-1

description: Knockdown


title: satellite cells, 4dpi+ActD+aN2

status: Public on Dec 25 2019

data_processing:
Illumina Casava 1.8
Illumina bcl2fastq 2.17
Reads were demultiplexed based on perfect matches to expected barcodes
Transcript reads were aligned to the mouse reference genome (GRCm38) augmented with the tdTomato reporter transgene sequence using GSNAP (2013-10-10) only considering uniquely mapped reads
Per-gene transcript counts were determined based on the number of unique UMIs for mapped reads overlapping exons in sense orientation, allowing for one mismatch when collapsing UMI sequences
Barcodes were filtered by requiring a minimum number of detected transcripts, where a sample-specific cutoff was set to 0.1 times the total transcript count for cells at rank 30 (the 99th percentile for 3,000 cells)
Barcodes were filtered by iterative clustering, removing clusters identified as non-myogenic cells or stressed cells based on the expression of known marker genes
Genome_build: GRCm38_tdTomato
Supplementary_files_format_and_content: Gene x barcode matrix with UMI counts

source_name: satellite cells

extract_protocol: 10x Genomics Chromium Single Cell 3' Library and Gel Bead Kit v2

tag: timepoint

tag: antibody treatment

tag: actd treatment

value: yes


title: satellite cells, 0dpi+ActD+aN2


title: satellite cells, 4dpi+ActD+aDll1-1


title: satellite cells, 4dpi+ActD+aRW-1

value: aRW


title: satellite cells, 4dpi-ActD+aRW

value: no


title: satellite cells, 4dpi+ActD+aRW-2


title: satellite cells, 4dpi+ActD+aDll1-2


title: satellite cells, 0dpi+ActD+aRW


title: satellite cells, 4dpi-ActD


title: satellite cells, 4dpi-ActD+aN2


title: satellite cells, 0dpi-ActD


title: P 6 Healthy tissue stem cells- VitD

tag: tissue

value: Healthy left colon


title: P 4 Tumor tissue stem cells- VitD


title: P 5 Healthy tissue stem cells- VitD


title: P 5 Healthy tissue stem cells-Control


title: P 6 Healthy tissue stem cells-Control


title: P 4 Tumor tissue stem cells-Control


title: P 4 Healthy tissue stem cells- VitD


title: P 3 Tumor tissue stem cells-Control


title: P 3 Healthy tissue stem cells- VitD


title: P 3 Tumor tissue stem cells- VitD


title: P 2 Tumor tissue stem cells- VitD


title: P 3 Healthy tissue stem cells-Control


title: P 2 Tumor tissue stem cells-Control


title: P 1 Tumor tissue stem cells-Control

value: female


title: P 2 Healthy tissue stem cells- VitD


title: P 1 Tumor tissue stem cells- VitD


title: P 1 Healthy tissue stem cells-Control


title: ATAC-Seq_iPSC-CM_iPSCORE_2_3_UDID067

status: Public on Jul 12 2019

city: La Jolla

first: Kelly

middle: Ann

last: Frazer

address: 9500 Gilman Drive

department: Pediatrics

institute: UC San Diego

description:
ATAC-Seq  in iPSC-CM subject iPSCORE_2_3 sample UDID067
ATAC_iPSC-CM.bed

library_source: genomic

data_processing:
ATAC-Seq reads were aligned using STAR to hg19. Duplicate reads, reads mapping to blacklisted regions from ENCODE, reads mapping in chromosome other than chr1-chr22, chrX, chrY, and read-pairs with mapping quality Q<30 were filtered. To restrict the analysis to regions spanning only one nucleosome, we required an insert size no larger than 140 bp. Peak calling was performed using MACS2 on BAM files of iPSC and iPSC-CM combined samples with the command ‘macs2 callpeak --nomodel --nolambda --keep-dup all --call-summits -f BAMPE -g hs –q 0.01’
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files

molecule: genomic DNA

source_name: iPSC-CM

extract_protocol: Frozen nuclear pellets of 100,000 cells were thawed on ice, suspended in 25 mL transposition reaction mix (2.5 mL Tn5 transposase from Nextera DNA Library Preparation Kit in permeabilization buffer containing digitonin), and incubated for 30-60 min at 37°C in a thermomixer (500 RPM shaking). Reactions were purified using AMPure XP beads, eluted in 12 mL of DNA Elution Buffer (Zymo) and amplified using the NEBNext® High-Fidelity 2X PCR Master Mix (NEB) with barcoded adaptors. PCR reactions were terminated after 10 to 12 cycles and purified and size selected using AMPure XP beads. Libraries were sequenced on an Illumina HiSeq4000 to an average depth of 20 M 100-150 bp paired end reads.

value: iPSC-CM

tag: individual


title: ATAC-Seq_iPSC-CM_iPSCORE_2_7_UDID045

description:
ATAC-Seq  in iPSC-CM subject iPSCORE_2_7 sample UDID045
ATAC_iPSC-CM.bed


title: ATAC-Seq_iPSC-CM_iPSCORE_2_1_UDID007

description:
ATAC-Seq  in iPSC-CM subject iPSCORE_2_1 sample UDID007
ATAC_iPSC-CM.bed


title: ATAC-Seq_iPSC-CM_iPSCORE_2_3_UDID044

description:
ATAC-Seq  in iPSC-CM subject iPSCORE_2_3 sample UDID044
ATAC_iPSC-CM.bed


title: ATAC-Seq_iPSC_iPSCORE_2_3_UDID044

description:
ATAC-Seq  in iPSC subject iPSCORE_2_3 sample UDID044
ATAC_iPSC.bed

source_name: iPSC

extract_protocol: Frozen nuclear pellets of 25,000 cells were thawed on ice, suspended in 25 mL transposition reaction mix (2.5 mL Tn5 transposase from Nextera DNA Library Preparation Kit in permeabilization buffer containing digitonin), and incubated for 30-60 min at 37°C in a thermomixer (500 RPM shaking). Reactions were purified using AMPure XP beads, eluted in 12 mL of DNA Elution Buffer (Zymo) and amplified using the NEBNext® High-Fidelity 2X PCR Master Mix (NEB) with barcoded adaptors. PCR reactions were terminated after 10 to 12 cycles and purified and size selected using AMPure XP beads. Libraries were sequenced on an Illumina HiSeq4000 to an average depth of 20 M 100-150 bp paired end reads.

value: iPSC


title: P 4 Healthy tissue stem cells-Control


title: ATAC-Seq_iPSC-CM_iPSCORE_2_2_UDID053

description:
ATAC-Seq  in iPSC-CM subject iPSCORE_2_2 sample UDID053
ATAC_iPSC-CM.bed


title: ATAC-Seq_iPSC-CM_iPSCORE_2_6_UDID029

description:
ATAC-Seq  in iPSC-CM subject iPSCORE_2_6 sample UDID029
ATAC_iPSC-CM.bed


title: ATAC-Seq_iPSC-CM_iPSCORE_2_1_UDID043

description:
ATAC-Seq  in iPSC-CM subject iPSCORE_2_1 sample UDID043
ATAC_iPSC-CM.bed


title: ATAC-Seq_iPSC-CM_iPSCORE_2_3_UDID020

description:
ATAC-Seq  in iPSC-CM subject iPSCORE_2_3 sample UDID020
ATAC_iPSC-CM.bed


title: ATAC-Seq_iPSC-CM_iPSCORE_2_1_UDID048

description:
ATAC-Seq  in iPSC-CM subject iPSCORE_2_1 sample UDID048
ATAC_iPSC-CM.bed


title: ATAC-Seq_iPSC_iPSCORE_2_7_UDID045

description:
ATAC-Seq  in iPSC subject iPSCORE_2_7 sample UDID045
ATAC_iPSC.bed


title: ATAC-Seq_iPSC_iPSCORE_2_3_UDID067

description:
ATAC-Seq  in iPSC subject iPSCORE_2_3 sample UDID067
ATAC_iPSC.bed


title: NKX2-5_ChIPSeq_iPSC-CM_iPSCORE_2_2_FS005_B

description:
NKX2-5 ChIPSeq in iPSC-CM subject iPSCORE_2_2 sample FS005B
NKX2-5.bed

data_processing:
ChIP-Seq reads were mapped to the hg19 reference using BWA. Duplicate reads, reads mapping to blacklisted regions from ENCODE, reads mapping in chromosome other than chr1-chr22, chrX, chrY, and read-pairs with mapping quality Q<30 were filtered. Peak calling was performed using MACS2 (‘macs2 callpeak -f BAMPE -g hs -B --SPMR --verbose 3 --cutoff-analysis --call-summits -q 0.01’) from combined samples of the same cell type and with reads derived from sonicated chromatin not subjected to IP used as negative control.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files

extract_protocol: 10-20 million formaldehyde-fixed cells were lysed in 300 µl RIPA buffer (1xPBS, 1% NP-40, 0.5% DOC, 0.1% SDS, RCPI) and sonicated for 70-80 min using Bioruptor 200. 5µg of NKX2-5 antibody (Santa Cruz Biotechnology, sc-8697x) were incubated with Dynabeads for 2 hours and washed with BSA 0.5% in PBS. Chromatin was diluted to 1 ml of RIPA buffer and added to the beads for overnight IP. Five washes were performed with washing buffer (50 mM Hepes pH 8, 1% NP-40, 0.7% DOC, 0.5M LiCl, 1mM EDTA and 1x RCPI), followed by one wash with TE. DNA was eluted and reverse crosslinked in elution buffer (10 mM Tris-HCl pH 8, 1 mM EDTA, 1% SDS) at 65˚C, followed by RNAse A and Proteinase K treatment. DNA was purified using Qiagen MinElute PCR Purification kit. Libraries were prepared using KAPA Hyper Library preparation kit and sequenced on an Illumina HiSeq2500 to an average of 35 M 100 bp paired-end reads per sample.


title: ATAC-Seq_iPSC_iPSCORE_2_2_UDID053

description:
ATAC-Seq  in iPSC subject iPSCORE_2_2 sample UDID053
ATAC_iPSC.bed


title: ATAC-Seq_iPSC_iPSCORE_2_1_UDID007

description:
ATAC-Seq  in iPSC subject iPSCORE_2_1 sample UDID007
ATAC_iPSC.bed


title: NKX2-5_ChIPSeq_iPSC-CM_iPSCORE_2_4_FS015_B

description:
NKX2-5 ChIPSeq in iPSC-CM subject iPSCORE_2_4 sample FS015B
NKX2-5.bed


title: NKX2-5_ChIPSeq_iPSC-CM_Pool_Input control

description:
Input DNA from iPSC-CMs for NKX2-5 ChIP-Seq
NKX2-5.bed

value: Pool of samples


title: ATAC-Seq_iPSC_iPSCORE_2_1_UDID048

description:
ATAC-Seq  in iPSC subject iPSCORE_2_1 sample UDID048
ATAC_iPSC.bed


title: NKX2-5_ChIPSeq_iPSC-CM_iPSCORE_2_9_FS008

description:
NKX2-5 ChIPSeq in iPSC-CM subject iPSCORE_2_9 sample FS008
NKX2-5.bed


title: NKX2-5_ChIPSeq_iPSC-CM_iPSCORE_2_6_FS018_B

description:
NKX2-5 ChIPSeq in iPSC-CM subject iPSCORE_2_6 sample FS018B
NKX2-5.bed


title: NKX2-5_ChIPSeq_iPSC-CM_iPSCORE_2_7_FS014

description:
NKX2-5 ChIPSeq in iPSC-CM subject iPSCORE_2_7 sample FS014
NKX2-5.bed


title: P 2 Healthy tissue stem cells-Control


title: NKX2-5_ChIPSeq_iPSC-CM_iPSCORE_2_7_FS011

description:
NKX2-5 ChIPSeq in iPSC-CM subject iPSCORE_2_7 sample FS011
NKX2-5.bed


title: NKX2-5_ChIPSeq_iPSC-CM_iPSCORE_2_1_FS016

description:
NKX2-5 ChIPSeq in iPSC-CM subject iPSCORE_2_1 sample FS016
NKX2-5.bed


title: ATAC-Seq_iPSC_iPSCORE_2_3_UDID020

description:
ATAC-Seq  in iPSC subject iPSCORE_2_3 sample UDID020
ATAC_iPSC.bed


title: NKX2-5_ChIPSeq_iPSC-CM_iPSCORE_2_6_FS018_A

description:
NKX2-5 ChIPSeq in iPSC-CM subject iPSCORE_2_6 sample FS018A
NKX2-5.bed


title: NKX2-5_ChIPSeq_iPSC-CM_iPSCORE_2_3_FS003

description:
NKX2-5 ChIPSeq in iPSC-CM subject iPSCORE_2_3 sample FS003
NKX2-5.bed


title: NKX2-5_ChIPSeq_iPSC-CM_iPSCORE_2_2_FS005_A

description:
NKX2-5 ChIPSeq in iPSC-CM subject iPSCORE_2_2 sample FS005A
NKX2-5.bed


title: human Fetal RPE H3K27ac ChIP-seq

status: Public on Mar 30 2019

data_processing:
ChIP-Seq reads were mapped to the hg19 reference using BWA. Duplicate reads, reads mapping to blacklisted regions from ENCODE, reads not mapping to chromosomes chr1-chr22, chrX, chrY, and read-pairs with mapping quality Q <30 were filtered. Peak calling was performed for each sample using MACS263 (‘macs2 callpeak -f BAMPE -g hs -B --SPMR --verbose 3 --cutoff-analysis --call-summits -q 0.01’) with reads derived from sonicated chromatin not subjected to IP (ie input chromatin) from a pool of samples used as a negative control.

Genome_build: hg19
Supplementary_files_format_and_content: bigWig, tpm, FPKM

source_name: fetal RPE

extract_protocol: For H3K27ac, 5-15 x 106 formaldehyde crosslinked iPSC-RPE cells were lysed and sonicated in 110 µl of SDS Lysis Buffer (0.5% SDS, 50mM Tris-HCl pH 8.0, 20mM EDTA, 1x cOmplete™ Protease Inhibitor Cocktail (Sigma)) using Covaris E220 Focused-ultrasonicators (Covaris) for 14 cycles, 1 min per cycle, duty cycle 5. For each sample, H3K27ac antibody (Abcam ab4729, lot GR00324078) was coupled for 4 hours to 20µl of Protein G Dynabeads (Thermo Scientific) and used for overnight chromatin immunoprecipitation in IP buffer (1% Triton X-100, 0.1% DOC, 1x TE buffer, 1x cOmplete™ Protease Inhibitor Cocktail). Beads with immunoprecipitated chromatin were washed with six times with 150 µl of ChIP wash buffer (50mM HEPES pH 8.0, 1% NP-40, 0.7% DOC, 400mM LiCl, 1mM EDTA, 1x cOmplete™ Protease Inhibitor Cocktail) and twice with 1X TE buffer (10mM Tris-HCl pH 8.0, 1mM EDTA). Next, samples were eluted in 150 µl of ChIP Elution Buffer (1% SDS, 10mM Tris-HCl pH 8.0, 1mM EDTA) and reverse crosslinked by incubation for 15 min at 65˚C with rotation and subsequent incubation with 5 µl RNAse (Sigma) for 1h at 37˚C and Proteinase K Solution (20 mg/mL, Thermo Fisher Scientific) for 1h at  55˚C. After reverse crosslinking samples were purified with 2X Agencourt AMPure XP DNA beads (Beckman Coulter), eluted in 30 µl of H2O and Qubit (Thermo Scientific) quantified. Libraries were generated using KAPA Hyper Prep Kit (KAPA Biosystems) and KAPA Real Time Library Amplification Kit (KAPA Biosystems) following manufacturers manual. Libraries were barcoded using TruSeq RNA Indexes (Illumina). Libraries were sequenced on an Illumina HiSeq 4000 to an average of 40 M 150 bp Paired-End reads per sample.

value: fetal RPE

tag: antibody

value: human fetal RPE


title: NKX2-5_ChIPSeq_iPSC-CM_iPSCORE_2_9_FS007

description:
NKX2-5 ChIPSeq in iPSC-CM subject iPSCORE_2_9 sample FS007
NKX2-5.bed


title: iPSC-RPE RPE006 ATAC-seq

data_processing:
Libraries were sequenced to approximately 80M 150bp paired end reads on the HiSeq 4000 (Illumina) platform. ATAC-seq reads were aligned using STAR to hg19. Duplicate reads, reads mapping to blacklisted regions from ENCODE, reads mapping in chromosome other than chr1-chr22, chrX, chrY, and read-pairs with mapping quality Q<30 were filtered. In addition, to restrict the analysis to regions spanning only one nucleosome, we required an insert size no larger than 140 bp, as we observed that this filtering improved sensitivity to call peaks and reduced noise. Peak calling was performed using MACS2 on BAM files with the command ‘macs2 callpeak --nomodel --nolambda --keep-dup all --call-summits -f BAMPE -g hs’, and peaks were filtered by enrichment score (q < 0.01). Samples were required to have a fraction of reads within peaks greater than 2% (range observed: 6.6-23%). Public data sets were also processed through this pipeline prior to analysis.

Genome_build: hg19
Supplementary_files_format_and_content: bigWig, tpm, FPKM

source_name: iPSC-RPE

extract_protocol: We performed ATAC-seq using the protocol from Buenrostro et al. (Buenrostro et al., 2013) with small modifications. Frozen nuclear pellets of 5 x 104 cells each were thawed on ice and tagmented in permeabilization buffer containing digitonin. Tagmentation was carried in 25µl using 2.5µl of Tn5 from Nextera DNA Library Preparation Kit (Illumina) for 60 min at 37°C in a thermomixer (500 RPM shaking). To eliminate confounding effects due to index hopping, all libraries within a pool were indexed with unique i7 and i5 barcodes. Libraries for iPSC-RPE were amplified for 12 cycles. Libraries were sequenced to approximately 80M 150bp paired end reads on the HiSeq 4000 (Illumina) platform.

value: iPSC-RPE


title: iPSC-RPE RPE008 ATAC-seq


title: human Fetal RPE ATAC-seq


title: NKX2-5_ChIPSeq_iPSC-CM_iPSCORE_2_1_FS009

description:
NKX2-5 ChIPSeq in iPSC-CM subject iPSCORE_2_1 sample FS009
NKX2-5.bed


title: NKX2-5_ChIPSeq_iPSC-CM_iPSCORE_2_3_FS010

description:
NKX2-5 ChIPSeq in iPSC-CM subject iPSCORE_2_3 sample FS010
NKX2-5.bed


title: NKX2-5_ChIPSeq_iPSC-CM_iPSCORE_2_3_FS024

description:
NKX2-5 ChIPSeq in iPSC-CM subject iPSCORE_2_3 sample FS024
NKX2-5.bed


title: iPSC-RPE RPE007 ATAC-seq


title: iPSC-RPE RPE007 H3K27ac ChIP-seq R2


title: iPSC-RPE RPE001 ATAC-seq


title: human Fetal RPE RNA-seq

data_processing:
RNA-seq reads were aligned using STAR (Dobin et al., 2013) with a splice junction database built from the Gencode v19 gene annotation (Harrow et al., 2012a). Transcript and gene-based expression values were quantified using the RSEM package (1.2.20) (Li and Dewey, 2011) and normalized to transcript per million bp (TPM).

Genome_build: hg19
Supplementary_files_format_and_content: bigWig, tpm, FPKM

extract_protocol: Total RNA was isolated using the Quick-RNA Mini Prep Kit (Zymo) from frozen RTL plus pellets, including on-column DNAse treatment step. RNA was eluted in 40 µl RNAse-free water and run on a Bioanalyzer (Agilent) to determine integrity. Concentration was measured by Qubit. Illumina Truseq Stranded mRNA libraries were prepared and sequenced on HiSeq4000, to an average of 40 M 150 bp paired-end reads per sample.


title: iPSC-RPE RPE007 H3K27ac ChIP-seq


title: iPSC-RPE RPE001 H3K27ac ChIP-seq R2


title: iPSC-RPE RPE001 H3K27ac ChIP-seq


title: iPSC-RPE RPE005 H3K27ac ChIP-seq


title: iPSC-RPE RPE006 H3K27ac ChIP-seq


title: iPSC-RPE RPE006 H3K27ac ChIP-seq R2


title: iPSC-RPE RPE003 ATAC-seq


title: NKX2-5_ChIPSeq_iPSC-CM_iPSCORE_2_4_FS015_A

description:
NKX2-5 ChIPSeq in iPSC-CM subject iPSCORE_2_4 sample FS015A
NKX2-5.bed


title: iPSC-RPE RPE003 H3K27ac ChIP-seq


title: iPSC-RPE RPE008 RNA-seq


title: iPSC-RPE RPE003 RNA-seq


title: iPSC-RPE RPE008 H3K27ac ChIP-seq


title: iPSC-RPE RPE005 ATAC-seq


title: iPSC-RPE RPE006 RNA-seq


title: iPSC-RPE RPE001 RNA-seq


title: iPSC-RPE RPE007 RNA-seq


title: e86d9c4d-d0ca-4122-b729-9b1f0fbee934_iPSC-CM (ChIP-seq)

status: Public on Jan 24 2019

data_processing: ChIP-Seq reads were mapped to the hg19 reference using BWA62. Duplicate reads, reads mapping to blacklisted regions from ENCODE, reads not mapping to chromosomes chr1-chr22, chrX, chrY, and read-pairs with mapping quality Q <30 were filtered. Peak calling was performed using MACS263 (‘macs2 callpeak -f BAMPE -g hs -B --SPMR --verbose 3 --cutoff-analysis --call-summits -q 0.01’) using pooled BAM files from all iPSC or iPSC-CM samples and with reads derived from sonicated chromatin not subjected to IP (ie input chromatin) from a pool of samples used as a negative control.

extract_protocol: For H3K27ac, 2 x 10e6 fixed cells were lysed in 60 µl of MAGnify™ Chromatin Immunoprecipitation System Lysis Buffer (Thermo Scientific) and sonicated using Bioruptor 200 (Diagenode) for 35-45 min of 30 sec on/30 sec off cycles. H3K27ac antibodies (Abcam ab4729, lots GR183922-2 (1.75 µg) or GR184333-2 (1 µg)) were coupled for 2 hours to ProteinG Dynabeads (Thermo Scientific), and used for overnight chromatin immunoprecipitation in IP buffer (1% Triton-X, 0.1% DOC, 1x TE, 1x Roche Complete Proteinase Inhibitor tablets (RCPI)). Beads were washed five times with washing buffer (50 mM Hepes pH 8, 1% NP-40, 0.7% DOC, 0.5M LiCl, 1mM EDTA and 1x RCPI) and once with TE buffer. For transcription factors, 1-2 x 10e7 cells were lysed in 300 µl RIPA buffer (1xPBS, 1% NP-40, 0.5% DOC, 0.1% SDS, RCPI) and sonicated for 70-80 min with instrument and setting as above. Five µg of SRF antibody (Santa Cruz Biotechnology, sc-335x, lot I1014) were incubated with Dynabeads for 2 hours and washed with BSA 0.5% in PBS. Chromatin was diluted to 1 ml of RIPA buffer and added to the beads for overnight IP. Five washes were performed with washing buffer (100 mM Tris pH 7.5, 500 mM LiCl, 1% NP-40, 1% DOC and 1x RCPI), followed by one wash with TE. DNA was eluted and reverse crosslinked overnight in elution buffer (10 mM Tris-HCl pH 8, 1 mM EDTA, 1% SDS) at 65˚C. DNA was purified using Qiagen MinElute PCR Purification kit, quantified by Qubit (Thermo Scientific) and submitted to library preparation and barcoding using KAPA Hyper Library preparation kit (KAPA Biosystems). Libraries were sequenced on an Illumina HiSeq2500 or a HiSeq4000 to an average of 35 M 100 bp paired-end reads per sample.

tag: chip antibody


title: iPSC-RPE RPE005 RNA-seq


title: dd8bcb5e-15bf-4be6-97ac-94f54ed811eb_iPSC (ChIP-seq)

value: H3K27ac antibodies (Abcam ab4729, lots GR183922-2 (1.75 µg) or GR184333-2 (1 µg))


title: e9586b34-11fc-4cdf-907a-beb5643ee3ae_iPSC-CM (ChIP-seq)


title: aa613f3f-2ff5-4d09-84bc-008c30c6ef66_iPSC (ChIP-seq)


title: e241faad-584b-41b5-9d1d-07f8ce5ecd30_iPSC (ChIP-seq)


title: c92b23f5-206f-4892-ba1b-90dfb8cfe2ee_iPSC-CM (ChIP-seq)


title: a8241e50-58c1-40de-9551-573d41ea4f19_iPSC (ChIP-seq)


title: a1d6f499-3f5f-494f-a182-1e3211bd5ae1_iPSC-CM (ChIP-seq)


title: a80bc6f4-b918-4461-ab7b-c1f16136bed6_iPSC-CM (ChIP-seq)


title: 960c428e-6eba-4fd6-b926-f8776fc20cbc_iPSC (ChIP-seq)


title: 962cd048-2790-4ef4-8c06-acf9ec1b7bc2_iPSC-CM (ChIP-seq)


title: 7d2f5a9b-831d-4859-9451-3c7dcc0a00ed_iPSC-CM (ChIP-seq)


title: 955ebdbe-26c8-43c3-8a1d-207728297dc0_iPSC (ChIP-seq)


title: 76a804b4-b3ec-4b54-9c70-92b11cf82f33_iPSC (ChIP-seq)


title: 881424e7-e3cb-482c-830b-69c6897eb772_iPSC-CM (ChIP-seq)


title: 6d634ac7-1854-4d2c-b7db-1d9913dc8dc6_iPSC-CM (ChIP-seq)


title: 7a1966dd-3453-4d30-8e77-6870ee9cd790_iPSC-CM (ChIP-seq)


title: 6a65308f-37d0-4b06-94b3-c5301d760afd_iPSC-CM (ChIP-seq)


title: b56fb523-1e03-4812-a745-1f97314359e7_iPSC-CM (ChIP-seq)


title: 4a049ce8-ac3f-4d2b-8bc8-76a2c376bed9_iPSC (ChIP-seq)


title: f8db3685-37ed-409c-8216-c0d045108403_iPSC (ChIP-seq)


title: 1a75c25e-c463-47ab-b838-0fdf7af5ea24_iPSC-CM (ChIP-seq)


title: 31ae89ae-0296-415c-b202-e9668ab4461c_iPSC (ChIP-seq)


title: 093b028a-b5e8-496e-b2cb-aa5e0d4da368_iPSC (ChIP-seq)


title: 03a95c32-f31e-4846-b4e7-6991a7bbbd86_iPSC (ChIP-seq)


title: 262ead42-62d0-45fb-a309-dfb9fdeceb28_iPSC-CM (ChIP-seq)


title: 36f8c31d-b865-4424-a829-8e55cbba6411_iPSC (ChIP-seq)


title: 079927aa-29e1-462c-8b15-af1a3d8f1b20_iPSC (ChIP-seq)


title: 036253ba-25d4-4b93-9127-adc21527a082_iPSC-CM (ChIP-seq)


title: MDA-MB231-1833 cells with GLG1 KO by CRISPR, seeded on E-Selectin

status: Public on Feb 22 2019

description:
See Agilent Cat#740000 for product details
Cells  transduced with CRISPR vectors targeting Glg1 or Control were seeded on E-selectin or IgG (10 ug/mL) coated plates for 12 h

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version 11.0).

extract_protocol: Total RNA were extracted using RNAeasy mini-prep kit from Qiagen

tag: parental cell line

tag: subline

tag: crispr ko

value: E-Selectin

source_name: Universal human Reference RNA

tag: cell lines

value: Mix of 10 human cell lines


title: SUM1315-M1a cells with GLG1 KO by CRISPR, seeded on IgG

tag: treatment

value: IgG


title: MDA-MB231-1833 cells with GLG1 KO by CRISPR, seeded on IgG


title: SUM1315-M1a cells with GLG1 KO by CRISPR, seeded on E-Selectin


title: MDA-MB231-1833 cells with non-targeting CRISPR, seeded on E-Selectin

value: non-targeting


title: SUM1315-M1a cells with non-targeting CRISPR, seeded on IgG


title: fada091d-3477-48cc-8de1-42d76bb87587.tpm_iPSC-CM (RNA-seq)

data_processing: RNA-Seq reads were aligned using STAR59 with a splice junction database built from the Gencode v19 gene annotation60. Transcript and gene-based expression values were quantified using the RSEM package (1.2.20)61 and normalized to transcript per million bp (TPM).

extract_protocol: Total RNA was isolated using the Qiagen RNAeasy Mini Kit from frozen RTL plus pellets, including on-column DNAse treatment step. RNA was eluted in 60 µl RNAse-free water and run on a Bioanalyzer (Agilent) to determine integrity. Concentration was measured by Nanodrop. Illumina Truseq Stranded mRNA libraries were prepared and sequenced on HiSeq2500 or HiSeq4000, to an average of 40 M 100 bp paired-end reads per sample. RNA-Seq reads were aligned using STAR60 with a splice junction database built from the Gencode v19 gene annotation.

tag: cell type


title: fbcd3e04-9962-4169-a792-ef2b09681221.tpm_iPSC (RNA-seq)


title: eb81d0ea-7263-4459-bb83-3de9894c60b2.tpm_iPSC (RNA-seq)


title: cadea57b-d7a5-4838-8a2f-bf019bdd2b28.tpm_iPSC-CM (RNA-seq)


title: d98f48f5-de74-491e-be50-678d8127ca00.tpm_iPSC-CM (RNA-seq)


title: d7e18ad6-6137-43bc-bd0a-de8885494d51.tpm_iPSC-CM (RNA-seq)


title: MDA-MB231-1833 cells with non-targeting CRISPR, seeded on IgG


title: 2d5dda6b-f7cb-428b-8c85-380325c4926a_iPSC (ChIP-seq)


title: SUM1315-M1a cells with non-targeting CRISPR, seeded on E-Selectin


title: af741e10-f00c-4099-802d-4c42d68b4aea.tpm_iPSC (RNA-seq)


title: daf0d3bc-7233-46b7-bfbc-42cf43103e71.tpm_iPSC (RNA-seq)


title: 232f80c9-44f3-45e5-ac7c-88c3b27950ea_iPSC-CM (ChIP-seq)


title: 8fd94ff1-9f53-4b85-bdb1-69be4cd62f10.tpm_iPSC-CM (RNA-seq)


title: 8bcaed11-47e9-4a38-a2b0-d0949a74235a.tpm_iPSC (RNA-seq)


title: 7855c945-e8f9-4df0-9532-98e1966b3bf8.tpm_iPSC (RNA-seq)


title: abfc59bf-9fec-4a49-8855-93f27530772f.tpm_iPSC (RNA-seq)


title: 9e5035d3-9ced-4b81-b77b-87d6aaf2631d.tpm_iPSC (RNA-seq)


title: 96869dde-d2bf-49a2-846b-36f7f1b53df7.tpm_iPSC (RNA-seq)


title: 20f37c64-0c86-4cb7-9501-6132d1801b84_iPSC-CM (ChIP-seq)


title: 82323342-825f-4ec9-8b7f-5a827a0c979d.tpm_iPSC-CM (RNA-seq)


title: 903a9f7a-bec4-4dd3-98c7-80bc712137bf.tpm_iPSC (RNA-seq)


title: 7ed45406-0db1-4e52-9d2b-fd113e2df425.tpm_iPSC-CM (RNA-seq)


title: 683d39a0-cc9d-4e6b-8778-f7bb98101a94.tpm_iPSC (RNA-seq)


title: 68db8f6f-5e8a-4354-babb-9515ae48df2a.tpm_iPSC (RNA-seq)


title: 4d562aa3-9c2a-4154-acb2-1c14a12c58cc.tpm_iPSC-CM (RNA-seq)


title: 42b68828-6c5e-4004-ae2e-96e1a0f47391.tpm_iPSC (RNA-seq)


title: 389af0a1-6076-4bae-9bb2-d8b42229f17a.tpm_iPSC-CM (RNA-seq)


title: 3538d9a9-0e7d-47b4-991e-562d9c6892b2.tpm_iPSC (RNA-seq)


title: 1d39387d-681a-4576-a921-8db18c31de3e.tpm_iPSC (RNA-seq)


title: 349de0b8-ea4a-45eb-9631-8259b539f7b8.tpm_iPSC (RNA-seq)


title: 4ed6cbf7-7622-491c-ba65-dd64e219d99a.tpm_iPSC (RNA-seq)


title: 1d040183-856b-4510-a6a2-9eef729bfc45.tpm_iPSC (RNA-seq)


title: 0bcc0b58-b278-4fd7-9e31-19d9fa7b20f1.tpm_iPSC-CM (RNA-seq)


title: 1198c156-b1d3-440e-804f-5c66457eebe7.tpm_iPSC-CM (RNA-seq)


title: d7a034e7-2916-409d-9197-51c6b3b8e173_iPSC-CM (ChIP-seq)


title: 142e5ecb-d354-4b16-9d4e-ee0110fd07d8.tpm_iPSC (RNA-seq)


title: f0f2cac5-03e9-4334-8dfe-0d4c13c9a511_iPSC (ChIP-seq)


title: a0bfb58f-bf49-4f7c-9b64-c8a7b8af9ea4_iPSC (ATAC-seq)

data_processing: ATAC-Seq reads were aligned using STAR to hg19 and filtered using the same protocol as for ChIP-Seq. In addition, to restrict the analysis to regions spanning only one nucleosome, we required an insert size no larger than 140 bp, as we observed that this improved sensitivity to call peaks and reduced noise. Peak calling was performed using MACS2 on merged BAM files of iPSC and iPSC-CM meta-samples with the command ‘macs2 callpeak --nomodel --nolambda --keep-dup all --call-summits -f BAMPE -g hs’, and peaks were filtered by enrichment score (q < 0.01).

extract_protocol: Frozen nuclear pellets of 5 x 10e4 cells each were thawed on ice, suspended in 50 uL transposition reaction mix (2.5 uL Tn5 transposase in 1x TD buffer, Illumina Cat# FC-121-1030), and incubated for 30 min at 37C. Reactions were purified using Qiagen MinElute kit, eluted in 10 uL water and amplified using the KAPA real-time library amplification kit (KAPA Biosystems) with barcoded adaptors. PCR reactions were terminated after 10 to 13 cycles and purified using AmPure XP beads (Beckman Coulter). Samples were size selected using SPRIselect beads (Beckman Coulter) to a size range of 150 to 850 kbp and sequenced on an Illumina HiSeq2500 or HiSeq4000 to an average depth of 30 M 100 bp paired end reads.


title: 04ec8b03-6878-4707-af15-418fd78aac97.tpm_iPSC-CM (RNA-seq)


title: 15898f77-a5f6-4c94-b3da-687fb0c88945.tpm_iPSC (RNA-seq)


title: 77654a6d-933a-4d7f-bfd2-8b9c5901fc87_iPSC (ATAC-seq)


title: cc566b8a-fc54-4941-8328-f57401635839_iPSC-CM (ChIP-seq)


title: 52298625-e109-48b6-9b4c-f3bc7191692c_iPSC (ATAC-seq)


title: 00d5b244-97b4-42eb-9a21-370776533f09.tpm_iPSC-CM (RNA-seq)


title: 989f8246-9010-4cc3-be5a-62316bf3a02d_iPSC-CM (ATAC-seq)


title: 70a36144-e2ae-4fa2-a1e2-6eb972fc96d2.tpm_iPSC (RNA-seq)


title: d56606a1-e263-4da9-acf9-2d6f14a822cb_iPSC-CM (ChIP-seq)


title: 4bedc357-aa29-4139-a901-f9b88fd1fdc0.tpm_iPSC-CM (RNA-seq)


title: ac83d79a-3621-4eb2-8245-5bcccc209d58_iPSC-CM (ChIP-seq)


title: aeeaf78e-a3ae-4071-b364-5d4e35e06799_iPSC (ChIP-seq)


title: 7ba84fca-758f-4068-a7ef-914e68be9c3e_iPSC-CM (ChIP-seq)


title: 84943ee6-4aef-468e-ba30-55d150e879b5_iPSC-CM (ChIP-seq)


title: a31d0ae6-a7ef-4054-98f0-2928ccf16cf4_iPSC-CM (ChIP-seq)


title: 32ddc48c-0759-4444-ad25-465c591b9d7a_iPSC (ChIP-seq)


title: 190c0665-f7ff-48af-925f-a50607fe9af3_iPSC (ChIP-seq)


title: e8d0daf3-5f47-44eb-afdd-f060c0d8a3f9_iPSC (ChIP-seq)


title: 0441cd83-9d1a-416b-a82d-856f7f04f6e4_iPSC-CM (ChIP-seq)


title: b958f299-3ced-4ab9-9901-fe7008745909.tpm_iPSC-CM (RNA-seq)


title: c20abef2-dd3b-4235-9853-bf297b6bf3a6.tpm_iPSC-CM (RNA-seq)


title: 4ee11143-6657-4375-b56e-51b1c35c8f3d_iPSC (ChIP-seq)


title: b46b88ad-cd7e-406f-8be6-c3da5f8bf1ab.tpm_iPSC (RNA-seq)


title: 936f69d3-5ca1-4464-b090-325880a42c11.tpm_iPSC-CM (RNA-seq)


title: d08fcfb6-1540-4174-bc73-b625da9d9ab9_iPSC-CM (ChIP-seq)


title: b6641cf0-9356-4888-8b24-e8b70a39faeb.tpm_iPSC (RNA-seq)


title: b37fa297-2a4d-4bda-9b98-479ac1d6c8a6.tpm_iPSC-CM (RNA-seq)


title: 7ef7df12-fdf8-4ca3-aa00-cff58603bb99.tpm_iPSC (RNA-seq)


title: 6aaf5dd4-ba88-47ee-98fe-e7ff4094adc0.tpm_iPSC-CM (RNA-seq)


title: ef1f05e2-fa53-4aa0-9490-2cd02eb9d8d5.tpm_iPSC-CM (RNA-seq)


title: b389c69b-47cc-4b1e-ae53-bc0a8b23f88a_iPSC-CM (ChIP-seq)


title: 4f7327ef-84bf-4b64-ae5f-50812d0dbf6d.tpm_iPSC-CM (RNA-seq)


title: 670a7249-feee-42be-84c1-32b9a6beae2a.tpm_iPSC (RNA-seq)


title: 6997242e-da3d-4cb6-865b-bb44998ef92f.tpm_iPSC (RNA-seq)


title: 614b916c-62e4-4565-8039-04c47b6daf6b.tpm_iPSC-CM (RNA-seq)


title: 34dc9f1a-5203-4354-8c9a-d2df18f0c645.tpm_iPSC-CM (RNA-seq)


title: 3b973ee0-2859-4316-bdeb-4404ac0157cc.tpm_iPSC (RNA-seq)


title: 28e21163-cd01-4302-a75b-440b772d54fb.tpm_iPSC-CM (RNA-seq)


title: 1342ed09-a675-4e07-b342-757895f4fa3d.tpm_iPSC (RNA-seq)


title: 0ad04243-b101-4c41-be59-7029d943df10.tpm_iPSC-CM (RNA-seq)


title: 02e9fa84-3521-4f36-bea2-5b0462869aa2.tpm_iPSC (RNA-seq)


title: 013eb23c-4ff0-493b-b106-9c8c9c2176d6.tpm_iPSC-CM (RNA-seq)


title: iPSC-CM_iPSC-CM (Hi-C)

data_processing: For each sample, Hi-C reads were first aligned to human reference genome hg19 using BWA-MEM (version 0.7.15) with default parameters. Forward and reverse reads from the paired-end data were aligned independently to allow for identification of split reads that represent ligations between two genomic loci due to spatial proximity. Paired-end reads were then reconstructed, processed, and filtered using the Juicer pipeline, resulting in the removal of: unmapped reads, abnormal split reads (split reads that cause ambiguous positioning of the contact), read pairs within the same restriction enzyme fragment, low mapping quality read pairs (MAPQ < 30), and duplicate reads. Subsequently, read pairs that were less than 2kb apart were removed to avoid self-ligated fragments. These filtered read pairs (contacts) were subsequently used to generate chromatin contact maps for each sample via Juicer. To create Hi-C contact maps on a per individual basis, contacts were pooled across all samples of a particular cell type for each individual, and to create maps of iPSC and iPSC-CM, contacts were pooled across individuals within the respective cell type. These processes resulted in a set of binary .hic files, which were utilized to obtain raw and Knight-Ruiz (KR) normalized counts as well as normalization vectors of contact frequency matrices via Juicebox command line tools67 at various resolutions used throughout this study.

extract_protocol: We performed in situ Hi-C on 2-5 million cells. Cells were crosslinked at a final concentration of 1% formaldehyde and quenched using 200 mM glycine. Crosslinked cells were then lysed and nuclei were digested with 100U MboI overnight at 37°C. Next, fragmented ends were biotinylated for 90min at 37°C, and the sample was diluted and proximity ligated for 4 hours at room temperature. Crosslinks were reversed by the addition of SDS, ProteinaseK, and NaCl, and allowed to incubate overnight at 68°C. Samples were then purified by ethanol precipitation, resuspended in 100uL 1X Elution Buffer, fragmented using a Covaris S2 instrument, and size selected using AmpureXP beads. Subsequently, biotinylated ligation junctions were pulled down using T1 Streptavidin beads. Hi-C libraries were prepared using streptavidin beads by performing end-repair, dA-tailing, and adapter ligation, following which PCR amplification and purification was performed. The resulting libraries were sequenced on an Illumina HiSeq 4000 machine to obtain 150bp paired-end reads.


title: iPSC_iPSC (Hi-C)


title: iPSCORE_2_7.CM_iPSC-CM (Hi-C)


title: a5e7b56f-dd4b-42bd-9c13-afe3436ac9c0.tpm_iPSC-CM (RNA-seq)


title: iPSCORE_2_9.iPSC_iPSC (Hi-C)


title: iPSCORE_2_7.iPSC_iPSC (Hi-C)


title: iPSCORE_2_6.iPSC_iPSC (Hi-C)


title: iPSCORE_2_4.CM_iPSC-CM (Hi-C)


title: iPSCORE_2_3.CM_iPSC-CM (Hi-C)


title: iPSCORE_2_2.CM_iPSC-CM (Hi-C)


title: iPSCORE_2_3.iPSC_iPSC (Hi-C)


title: iPSCORE_2_2.iPSC_iPSC (Hi-C)


title: iPSCORE_2_1.CM_iPSC-CM (Hi-C)


title: ffbe88c6-49c0-4fce-8542-56bb2930ee4a_iPSC-CM (ATAC-seq)


title: eaa627a7-7f87-418c-a79f-cf54db079ab4_iPSC (ATAC-seq)


title: bf276c4d-c784-481c-bcc3-a2a1028ad058_iPSC (ATAC-seq)


title: 917c5313-4a1b-4a27-8e68-df83b7f135f4_iPSC (ATAC-seq)


title: d95d608f-a645-4459-bd3b-79999e2d400a_iPSC-CM (ATAC-seq)


title: 77486cbe-cd49-4414-afcc-1d85438ff286_iPSC (ATAC-seq)


title: iPSCORE_2_9.CM_iPSC-CM (Hi-C)


title: 63bbec42-175e-48e8-990d-432be9154380_iPSC (ATAC-seq)


title: 5d47b014-54e5-47b3-814c-a1de280537ba_iPSC-CM (ATAC-seq)


title: 5baf0dab-42ba-4419-8d27-bc9406d61d44_iPSC-CM (ATAC-seq)


title: iPSCORE_2_6.CM_iPSC-CM (Hi-C)


title: 29c2aa2a-2d29-4261-a806-9f5204de2a7d_iPSC (ATAC-seq)


title: 1dc9a2ea-0225-4250-a17e-821dd8eec27a_iPSC-CM (ATAC-seq)


title: 244bb06f-40c8-4f55-a350-39b3b352ca1d_iPSC-CM (ATAC-seq)


title: iPSCORE_2_4.iPSC_iPSC (Hi-C)


title: f1e0d609-fe23-4a50-9316-e59094738d07_iPSC (ATAC-seq)


title: iPSCORE_2_1.iPSC_iPSC (Hi-C)


title: e8df8eb0-a9c4-4231-bf83-6bf30ecaeae2_iPSC-CM (ATAC-seq)


title: 29f6f3bb-de7e-4204-adf3-19149bf7c143_iPSC-CM (ATAC-seq)


title: 26c6cb3d-7ca1-4051-9bb9-98ffb18f6d46_iPSC (ATAC-seq)


title: P 1 Healthy tissue stem cells- VitD

tag: age

value: Vehicle


title: Lung metastasis #3 by Tinagl1 overexpressed LM2 cells

status: Public on Dec 31 2018

data_processing: Agilent Feature Extraction Software (v 11.0) was used for background subtraction and linear Lowess normalization.

extract_protocol:
Lungs with metastatic lesions that formed by Tinagl1 overexpressed or vector control cells were dissected from NSG mice. GFP expressing tumor cells were sorted using GFP based FACS.
Total RNA were extracted using RNAeasy mini-prep kit from Qiagen

tag: tinagl1 overexpression

value: Yes


title: 429d0e1c-3e06-496a-b819-f31e88a2fed0_iPSC-CM (ATAC-seq)


title: Lung metastasis #3 by LM2 cells with empty vector

value: No


title: Lung metastasis #2 by LM2 cells with empty vector


title: EpRAS mutant with disrupted Zeb1/miR-200c feedback loop equilibrium, treated with 100pM TGFb, replicate 1

status: Public on Nov 08 2018

extract_protocol: Total RNA were extracted using RNAeasy mini-prep kit from miRVANA kit

treatment_protocol: EpRAS mutant was generated by deletion of the Z-box-2 in -354nt of miR-200c2 promoter by CRISPR/Cas9, and thus lose response to Zeb1 mediated repression. The EpRAS control and mutant cells were treated with mock PBS or 100pM TGFb for 3 Days.

tag: cell line

value: EpRAS

tag: cell manipulation

value: Deletion of Z-box2 in miR-200c promoter

value: TGFbeta (pmol/l):100

source_name: Universal Mouse Reference RNA

value: Mix of 11 mouse cell lines


title: Lung metastasis #1 by Tinagl1 overexpressed LM2 cells


title: OA_10_WGBS

status: Public on Apr 30 2018

first: Gary

middle: S

last: Firestein

state: California

address: 9500 Gilman Dr

institute: UCSD

data_processing:
Adapter and primer sequences are removed from the sequence reads, and bases with poor quality are trimmed
Sequence reads are transformed into a C-to-T and G-to-A version
Then reads are mapped to reference genome hg19 using the BISMARK tool with the default parameters
PCR duplicates are removed
Mapped reads are processed with DSS package in R
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file include methylation information

source_name: OA patient Fibroblast-like synoviocytes

extract_protocol: The sample preparation for WGBS was performed using standard Illumina protocols by GATC BIOTECH (Konstanz, Germany) according to the manufacturer’s instructions.

tag: subject diagnosis

value: Osteoarthritis (OA) patient

value: Fibroblast-like synoviocytes


title: EpRAS treated with 100pM TGFb, replicate 2

value: Wild type


title: OA_09_WGBS


title: EpRAS mutant with disrupted Zeb1/miR-200c feedback loop equilibrium, treated with PBS, replicate 2

value: TGFbeta (pmol/l):0


title: OA_11_WGBS


title: EpRAS treated with PBS, replicate 1


title: Lung metastasis #2 by Tinagl1 overexpressed LM2 cells


title: EpRAS treated with PBS, replicate 3


title: EpRAS treated with 100pM TGFb, replicate 1


title: EpRAS treated with 100pM TGFb, replicate 3


title: OA_08_WGBS


title: EpRAS mutant with disrupted Zeb1/miR-200c feedback loop equilibrium, treated with PBS, replicate 1


title: Lung metastasis #1 by LM2 cells with empty vector


title: EpRAS treated with PBS, replicate 2


title: EpRAS mutant with disrupted Zeb1/miR-200c feedback loop equilibrium, treated with PBS, replicate 3


title: OA_05_WGBS


title: OA_04_WGBS


title: OA_01_WGBS


title: Macrophage (F4/80+) from mammary gland of female Dll1-conditional KO mice, replicate 2

status: Public on Oct 05 2018

description: See Agilent Cat#740100 for product details

growth_protocol:
Single cell suspensions were prepared from the mammary glands of virgin mice using mechanical and enzymatic dissociation as detail described in Tiede BJ et al., 2009, PLoS ONE 4(11): e8035. doi:10.1371/journal.pone.0008035
Various subpopulations of mammary epithelial cells were sorted using flow cytometry based on combination of a set of surface markers. The marker profiles and FACS gating parameters are detailed in Tiede BJ et al., 2009, PLoS ONE 4(11): e8035. doi:10.1371/journal.pone.0008035

tag: strain

tag: mg condition

value: Virgin

value: Macrophage

tag: rna source


title: OA_07_WGBS


title: RA_09_WGBS

source_name: RA patient Fibroblast-like synoviocytes

value: Rheumatoid arthritis (RA) patient


title: Macrophage (F4/80+) from mammary gland of female Dll1-conditional KO mice, replicate 1


title: OA_03_WGBS


title: High Dll1 fraction (mCherry+) of subpopulation P4 (CD24+CD29hi) from Dll1-mCherry female mice.

value: MaSC


title: Low Dll1 fraction (mCherry-) of subpopulation P4 (CD24+CD29hi) from Dll1-mCherry female mice.


title: EpRAS mutant with disrupted Zeb1/miR-200c feedback loop equilibrium, treated with 100pM TGFb, replicate 3


title: Macrophage (F4/80+) from mammary gland of female wild type littermates of Dll1-conditional KO mice, , replicate 1


title: Macrophage (F4/80+) from mammary gland of female wild type littermates of Dll1-conditional KO mice, , replicate 2


title: OA_06_WGBS


title: EpRAS mutant with disrupted Zeb1/miR-200c feedback loop equilibrium, treated with 100pM TGFb, replicate 2


title: RA_11_WGBS


title: RA_05_WGBS


title: RA_02_WGBS


title: RA_01_WGBS


title: RA_03_WGBS


title: RA_06_WGBS


title: OA_10_RNA

data_processing:
Data was demultiplexed using Illlumina’s CASAVA software
Raw read quality was evaluated using FastQC
Adapter and low quality bases below a quality score of 15 were trimmed from raw RNA-seq reads using Cutadapt.After trimming, reads with less than 30bp were further discarded
The remaining reads were aligned to human reference genome hg19 using STAR (2.3.0) and assembled and quantified by HTSeq (0.5.4p5)
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file include raw counts for each sample

extract_protocol:
Total RNA was extracted, sequencing libraries were prepared using TruSeq Stranded Total RNA RiboZero protocol from Illumina with an input of 400 ng RNA, libraries were pooled and sequenced with an Illumina HiSeq 2000 with paired-end 100 bp flow cell.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: OA_11_RNA


title: RA_04_WGBS


title: OA_08_RNA


title: OA_07_RNA


title: OA_06_RNA


title: OA_09_RNA


title: RA_08_WGBS


title: OA_04_RNA


title: OA_02_RNA


title: OA_05_RNA


title: OA_03_RNA


title: RA_11_RNA


title: RA_10_RNA


title: RA_01_RNA


title: RA_03_RNA


title: RA_08_RNA


title: RA_06_RNA


title: OA_11_H3K4me3

data_processing:
Raw reads were mapped to hg19 genome using bwa (0.7.7-r441).
Peaks were called using MACS2 (2.1.0.20150420.1).
To assess the library complexity and the enrichment of the data, quality control was done using several metrics, including non-redundant fraction of reads, fraction of reads that fall into peak regions, PCR bottleneck coefficient, normalized strand cross-correlation coefficient and the relative strand cross-correlation coefficient.
Genome_build: hg19
Supplementary_files_format_and_content: Peak files generated by MACS2

extract_protocol: The sample preparation for ChIP-seq was performed using the Zymo-spin ChIP kit (Zymo Research, Irvine, CA) according to the manufacturer’s instructions.


title: OA_11_H3K9me3


title: RA_02_RNA


title: RA_04_RNA


title: RA_05_RNA


title: RA_07_RNA


title: OA_11_Input


title: OA_11_H3K27me3


title: OA_11_H3K27ac


title: OA_10_H3K9me3


title: OA_10_H3K4me3


title: OA_11_H3K4me1


title: OA_10_Input


title: OA_09_Input


title: OA_09_H3K9me3


title: OA_10_H3K36me3


title: OA_11_H3K36me3


title: OA_10_H3K27me3


title: OA_10_H3K27ac


title: OA_09_H3K4me3


title: OA_10_H3K4me1


title: OA_09_H3K36me3


title: OA_09_H3K27me3


title: OA_09_H3K4me1


title: OA_09_H3K27ac


title: OA_08_Input


title: OA_08_H3K9me3


title: OA_07_Input


title: OA_07_H3K4me3


title: OA_08_H3K27ac


title: OA_07_H3K27me3


title: OA_08_H3K27me3


title: OA_06_Input


title: OA_07_H3K9me3


title: OA_07_H3K36me3


title: OA_08_H3K4me1


title: OA_08_H3K4me3


title: OA_07_H3K4me1


title: OA_06_H3K4me1


title: OA_06_H3K9me3


title: OA_08_H3K36me3


title: OA_06_H3K36me3


title: OA_06_H3K27me3


title: OA_05_H3K4me3


title: OA_06_H3K4me3


title: OA_05_H3K36me3


title: OA_06_H3K27ac


title: OA_05_H3K4me1


title: OA_05_H3K9me3


title: OA_05_H3K27me3


title: OA_05_H3K27ac


title: OA_04_Input


title: OA_04_H3K9me3


title: OA_07_H3K27ac


title: OA_04_H3K4me3


title: OA_04_H3K36me3


title: OA_05_Input


title: OA_04_H3K27me3


title: OA_04_H3K27ac


title: OA_03_Input


title: OA_04_H3K4me1


title: OA_03_H3K9me3


title: RA_10_Input


title: OA_02_Input


title: RA_10_H3K4me1


title: OA_03_H3K27ac


title: RA_11_H3K4me3


title: OA_01_H3K4me3


title: RA_11_H3K36me3


title: OA_02_H3K4me1


title: OA_01_Input


title: RA_10_H3K9me3


title: OA_01_H3K4me1


title: OA_01_H3K27ac


title: OA_02_H3K27ac


title: OA_01_H3K36me3


title: RA_11_H3K4me1


title: OA_01_H3K27me3


title: OA_03_H3K4me1


title: OA_03_H3K36me3


title: OA_01_H3K9me3


title: RA_11_H3K27me3


title: OA_02_H3K9me3


title: OA_02_H3K4me3


title: RA_11_H3K27ac


title: RA_11_Input


title: RA_10_H3K27me3


title: OA_03_H3K4me3


title: RA_10_H3K36me3


title: OA_02_H3K36me3


title: RA_10_H3K4me3


title: RA_11_H3K9me3


title: RA_09_H3K9me3


title: RA_09_H3K4me3


title: RA_10_H3K27ac


title: RA_08_Input


title: RA_06_H3K36me3


title: RA_08_H3K4me1


title: RA_08_H3K27me3


title: RA_09_Input


title: RA_06_H3K4me3


title: RA_07_H3K4me3


title: RA_09_H3K4me1


title: RA_08_H3K27ac


title: RA_07_H3K36me3


title: RA_09_H3K27me3


title: RA_06_H3K4me1


title: RA_07_H3K27ac


title: RA_08_H3K9me3


title: RA_09_H3K27ac


title: RA_06_H3K9me3


title: RA_08_H3K4me3


title: RA_07_Input


title: RA_07_H3K27me3


title: RA_06_H3K27ac


title: RA_07_H3K9me3


title: RA_08_H3K36me3


title: RA_07_H3K4me1


title: RA_06_H3K27me3


title: RA_06_Input


title: RA_05_Input


title: RA_09_H3K36me3


title: RA_05_H3K9me3


title: RA_05_H3K27ac


title: RA_04_H3K9me3


title: RA_05_H3K36me3


title: RA_05_H3K4me3


title: RA_05_H3K4me1


title: RA_04_Input


title: RA_05_H3K27me3


title: RA_03_Input


title: RA_03_H3K9me3


title: RA_04_H3K27ac


title: RA_04_H3K36me3


title: RA_03_H3K4me3


title: RA_03_H3K36me3


title: RA_03_H3K4me1


title: RA_04_H3K4me1


title: RA_04_H3K27me3


title: RA_02_H3K4me1


title: RA_03_H3K27ac


title: RA_02_H3K36me3


title: RA_02_H3K4me3


title: RA_02_H3K9me3


title: RA_02_Input


title: RA_02_H3K27me3


title: RA_01_Input


title: RA_01_H3K9me3


title: RA_02_H3K27ac


title: RA_01_H3K4me3


title: RA_04_H3K4me3


title: RA_03_H3K27me3


title: RA_01_H3K4me1


title: OA_11_ATAC

data_processing:
Raw reads were mapped to hg19 genome using Bowtie and read depth was normalized.
Peaks were called using MACS2 (2.1.0.20150420.1).
To assess the library complexity and the enrichment of the data, quality control was done using several metrics, including non-redundant fraction of reads, fraction of reads that fall into peak regions, PCR bottleneck coefficient, normalized strand cross-correlation coefficient and the relative strand cross-correlation coefficient.
Genome_build: hg19
Supplementary_files_format_and_content: Peak files in bed format

extract_protocol: The sample preparation for ATAC-seq was performed by Epinomics (San Francisco, CA) according to the manufacturer’s instructions.


title: OA_10_ATAC


title: OA_08_ATAC


title: RA_01_H3K27ac


title: OA_09_ATAC


title: OA_07_ATAC


title: RA_09_ATAC


title: RA_08_ATAC


title: OA_03_ATAC


title: RA_10_ATAC


title: RA_11_ATAC


title: OA_05_ATAC


title: OA_01_ATAC


title: RA_07_ATAC


title: OA_02_ATAC


title: RA_04_ATAC


title: RA_05_ATAC


title: OA_04_ATAC


title: RA_03_ATAC


title: RA_06_ATAC


title: RA_02_ATAC


title: RA_01_ATAC


title: RA_01_H3K27me3


title: RA_01_H3K36me3


title: MOLM13_DMSO.R2

status: Public on Mar 07 2018

city: Toronto

first: Shabana

last: Vohra

state: Ontario

address: 101 College St

country: Canada

institute: University Health Network

description: Ribosomal-depleted RNA

data_processing:
Sequences were aligned to the human genome (assembly hg19) using RNA-seq aligner STAR  (version 2.4.0) allowing a mismatch of 2
genomeCoverageBed with split option was used to create bigwig files from uniquely mapped reads.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig

growth_protocol: MV411, MOLM13, K562 were cultured at 37 °C and 5% CO2 in RPMI1640 (Sigma) supplemented with 10% dialyzed fetal bovine serum (FBS) (Sigma) and 1% penicillin/streptomycin/glutamine.

extract_protocol:
Bulk cell line was used for RNA extraction.  RNA was extracted using Qiagen RNeasy Plus Mini kits with genomic DNA depletion
dUTP directional method and RiboZero depletion

treatment_protocol: MV411, MOLM13 cells were treated for 18hrs with AC220 1nM or vehicle control. K562 were treated for 18hrs with Imatinib 2uM or vehicle control.

value: MOLM13 Human cell line

tag: tumor type

value: AML

tag: mutation

value: FLT3ITD positive

tag: agent

value: DMSO


title: MOLM13_DMSO.R1

description: Ribosomal-depleted RNA


title: MV411_AC220.R2

description: Ribosomal-depleted RNA

value: MV411 Human cell line


title: MOLM13_AC220.R2

description: Ribosomal-depleted RNA


title: MV411_DMSO.R1

description: Ribosomal-depleted RNA


title: MOLM13_AC220.R1

description: Ribosomal-depleted RNA


title: MV411_AC220.R1

description: Ribosomal-depleted RNA


title: MV411_DMSO.R2

description: Ribosomal-depleted RNA


title: OA_06_ATAC


title: K562_DMSO.R2

description: Ribosomal-depleted RNA

value: K562 Human cell line

value: CML Blast Crisis

value: BCR-ABL Positive


title: K562_DMSO.R1

description: Ribosomal-depleted RNA


title: K562_IMATINIB.R2

description: Ribosomal-depleted RNA

value: IMATINIB


title: WT_B.LowIn.EXPR.R2

status: Public on Dec 13 2017

description: Ribosomal-depleted RNA

data_processing:
RNA-Seq:RNA-Seq reads were trimmed for adaptor sequence and masked for low-quality sequence.Paired end reads were aligned to mm10  genome STAR version 2.4.0.
To generate the bigwig file, we first extended each read to 200 bp along 5' end and generated bedgraph file using  genomeCoverageBed and converted to bigwig  using the wigToBigwig software
genome build: mm10

source_name: B220+ B cells low input

extract_protocol:
FACS of B220+ splenocytes
Ovation Mouse RNA-Seq System (0348-32, NuGEN)

tag: genotype

value: Wild type (CBPfl/fl:Mx-Cre-)

value: B220+ B cells low input


title: WT_Tumor.EXPR.R1

description: Ribosomal-depleted RNA

source_name: LPD bulk tissue

extract_protocol:
Bulk splenocytes
Rapid Directional RNA-seq Kit (5138-08 NEXTflex)

value: LPD bulk tissue


title: LEU_B.EXPR.R2

description: Ribosomal-depleted RNA

value: Crebbp-/- (CBPfl/fl:Mx-Cre+)


title: Mac1B220.EXPR.R2

description: Ribosomal-depleted RNA

source_name: Mac1+ B220+ pre-malignant cells

extract_protocol:
FACS of B220+ Mac1+ splenocytes
Ovation Mouse RNA-Seq System (0348-32, NuGEN)

value: Mac1+ B220+ pre-malignant cells


title: WT_Tumor.EXPR.R2

description: Ribosomal-depleted RNA


title: LEU_B.EXPR.R1

description: Ribosomal-depleted RNA


title: WT_B.H3K56ac.R1

data_processing:
Chip-seq: Sequenced reads were trimmed for adaptor sequence and masked for low-quality sequence. Reads were aligned to mm10  genome using Bowtie  version 2.1.0 allowing two mismatch. Duplicates were removed using PICARD tools.  -seq: Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10  genome using Bowtie  version 2.1.0 with parameters -k 2 -N 1
Peaks were called using MACS version 2.0.10
To generate the bigwig file, we first extended each read to 200 bp along 5' end and generated bedgraph file using  genomeCoverageBed and converted to bigwig  using the wigToBigwig software
genome build: mm10

source_name: B220+ B cells

extract_protocol:
FACS of B220+ splenocytes
ChIP-Seq libraries were prepared for sequencing using standard Illumina protocols

value: B220+ B cells

tag: chip antibody

value: anti-H3K56ac  #ab76307, Abcam


title: WT_B.H3K56ac.R2


title: WT_B.EXPR.R2

description: Ribosomal-depleted RNA

extract_protocol:
FACS of B220+ splenocytes
Rapid Directional RNA-seq Kit (5138-08 NEXTflex)


title: LEU_B.H3K56ac.R1

extract_protocol:
Bulk splenocytes
ChIP-Seq libraries were prepared for sequencing using standard Illumina protocols


title: K562_IMATINIB.R1

description: Ribosomal-depleted RNA


title: WT_B.LowIn.EXPR.R1

description: Ribosomal-depleted RNA


title: Mac1B220.EXPR.R1

description: Ribosomal-depleted RNA


title: CRE_LP.EXPR.R1

description: Ribosomal-depleted RNA

source_name: Lin- IL7ra+ lymphoid progenitors

extract_protocol:
Lineage-depleted bone marrow cells were isolated followed by fluorescence activated cell sorting (FACS)  of Lin- IL7Ra+ cells.
Ovation Mouse RNA-Seq System (0348-32, NuGEN)

value: Lin- IL7ra+ lymphoid progenitors


title: CRE_LP.EXPR.R2

description: Ribosomal-depleted RNA


title: LEU_B.H3K18ac.R1

value: anti-H3K18ac  #ab1191, Abcam


title: WT_B.CBP

value: anti-CBP #sc-369, Santa Cruz


title: WT_LP.EXPR.R2

description: Ribosomal-depleted RNA


title: WT_B.Input


title: WT_B.EXPR.R1

description: Ribosomal-depleted RNA


title: WT_LP.EXPR.R1

description: Ribosomal-depleted RNA


title: LEU_B.H3K18ac.R2


title: WT_B.H3K18ac.R2


title: LEU_B.H3K56ac.R2


title: WT_B.H3K18ac.R1


title: LEU_B.H3K27ac.R2

value: anti-H3K27ac  #ab4729, Abcam


title: WT_B.H3K27ac.R2


title: LEU_B.H3K27ac.R1


title: WT_B.H3K27ac.R1


title: CRE.LP.H3K27ac

extract_protocol:
Lineage-depleted bone marrow cells were isolated followed by fluorescence activated cell sorting (FACS)  of Lin- IL7Ra+ cells.
ChIP-Seq libraries were prepared for sequencing using standard Illumina protocols


title: SUMxCNT

status: Public on Dec 27 2017

description: See Agilent Cat#740000 for product details

hyb_protocol: Each cy5 labeled testing sample was mixed with equal amount cy3-labeled reference sample and fragmented and blocked (Agilent Gene Expression Hybridization Kit),  and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed in sequence

data_processing: Agilent Feature Extraction Software (v 11.0) was used for background subtraction and linear Lowess normalization. The data were loaded with GeneSpring12 without additional normalization or transformation

label_protocol: The testing RNA samples and universal human reference RNA (Agilent) were labeled with CTP-cy5 and CTP-cy3, respectively, Using Agilent Quick Amp Labeling Kit.

extract_protocol:
Cell preparation protocol: SUM1315 breast cancer cells (GFP labeled) were cultured alone or co-cultured with MC3T3E1 bone marrow stroma cells, and treated with control saline or 10uM cisplatin for 48hours.Tumor cells were sorted out based on GFP labeling.
Total RNA were extracted from cancer cells using RNAeasy mini-prep kit from Qiagen

value: control (saline)

value: breast cancer

value: Mix of 10 human cell lines


title: WT.LP.H3K27ac


title: SUMxCDDP

value: cisplatin (10uM x 48hrs)


title: SUM+MCxCNT

value: co-cultured with MC3T3E1 were treated with control (saline)


title: SUM+MCxCDDP

value: co-cultured with MC3T3E1 were treated with cisplatin (10uM x 48hrs)


title: Subpopulation P4 (Lin-CD24+CD29hi) from virgin wild type FVB mice, replicate 1

status: Public on May 05 2017

hyb_protocol: Using  Agilent’s miRNA Complete Labeling and Hyb Kit, labeled total RNA samples were mixed with blocking reagent and RPM hybridization buffer and assembled with miRNA array for hybridization. The hybridization assembly were rotate at 20rpm in 55C oven for 20hrs. The array were washed with prewarmed washing buffers and dried for scan.

data_processing: Agilent Feature Extraction Software (v 11.0) was used to extract the signal and GeneSpring v13 were used to process the data. The processing is using Agilent technology miRNA 46065 with Threshold 1.0, logbase 2, Normalization shift to 90 percentile and baseline transformation is conducted based on median of all samples.

source_name: MaSC enriched P4 population of wild type virgin mice

label_protocol: The testing RNA samples were labeled with Cy3-pCp using Agilent’s miRNA Complete Labeling and Hyb Kit. Briefly, total RNA is dephosphrylated with CIP and then ligated to Cy3-pCp with T4-RNA ligase. Labeled RNA sample were purified and dried.

extract_protocol:
Cell preparation protocol: Single cell suspensions were prepared from the mammary glands of virgin wild type and transgenic mice using mechanical and enzymatic dissociation as detail described in Tiede BJ et al., 2009, PLoS ONE 4(11): e8035. doi:10.1371/journal.pone.0008035
FACS sorting protocol: Various subpopulations of mammary epithelial cells were sorted using flow cytometry based on combination of a set of surface markers. The marker profiles and FACS gating parameters are detailed in Tiede BJ et al., 2009, PLoS ONE 4(11): e8035. doi:10.1371/journal.pone.0008035
miRNA enriched Total RNA were extracted using mirVana™ miRNA Isolation Kit from Ambion

value: FVB/N-J

value: Virgin

tag: enrichment

value: MaSC enriched P4 population

tag: genotype/variation

value: wild type


title: Subpopulation P4 (Lin-CD24+CD29hi) from virgin wild type FVB mice, replicate 2


title: Subpopulation P5 (Lin-CD24+CD29lo) from virgin wild type FVB mice, replicate 3

source_name: Luminal enriched P5 population of wild type virgin mice

value: Luminal progenitor enriched P5 population


title: Subpopulation P5 (Lin-CD24+CD29lo) from virgin wild type FVB mice, replicate 2


title: Subpopulation P5 (Lin-CD24+CD29lo) from virgin wild type FVB mice, replicate 1