title: s0617_mouse3_MDAMB231_Metastases_2cells

description:
Fluidigm C1 platform
well521

source_name: Metastases


title: s0615_mouse3_MDAMB231_Metastases_1cells

status: Public on May 13 2022

type: SRA

city: Basel

first: Mohamed

last: Bentires-Alj

address: Hebelstrasse 20

department: DBM

country: Switzerland

institute: University Hospital Basel

description:
Fluidigm C1 platform
well519

library_source: transcriptomic single cell

data_processing:
Reads were aligned to human genom with STAR. Following observation under the microscope, wells containing more than 1 cell or debris were marked and removed from further analyses.
Following observation under the microscope, wells containing more than 1 cell or debris were marked and removed from further analyses.
Cell cycle of individual cells were inferred using sets of known cell cycle-regulated genes known to peak in transcription at given cell cycle stages obtained from (PMID: 12058064, PMID:11416145)
The cell cycle and library complexity (percentage of detected genes) were modeled as covariates and regressed out of the log-normalized counts using glm.fit (R package glm).
Differential gene expression between single cell clusters was performed using pairwise t-test implemented in FindMarkers function from R package scran.
Gene set enrichment was performed with bioconductor packages fgsea and msigdb
Assembly: hg38
Supplementary files format and content: counts_raw.csv is a matrix containing raw counts after alignment. counts_afterQC are counts for the cells passing QC. Cccorected_logcounts.csv contains logcounts  of the cells that passed QC after the cell-cycle correction. metadata.csv contains addition information on the column names of counts_raw.csv  and CCcorected_logcounts.csv.

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: MDA-MB-231 and PDX models were implanted in the 4th mammary fat pad (cleared) of 4-8 week-old NSG mice. Primary tumors were resected. Lung metastasis cells were isolated out of the dissected lung at a later time (when mice reached ethical endpoints)

extract_protocol:
Primary tumors and lung metastases were mechanically and enzymatically digested with a collagenase/hyaluronidase solution (Stem Cell Technologies, 07912). Human cancer cells were recovered by FACS sorting, based CD298 or GFP expression.
Single cell isolation was performed on the Fluidigm C1 platform according to  manufacturer protocol. mRNA was isolated with the Takara SMART-Seq Ultra Low RNA kit (Takara Bio; 634833) . Libraries for Illumina sequencing were prepared with the Nextera XT DNA Library Preparation Kit (Illumina; FC-131-1096).

tag: tissue

value: Metastases

tag: cell line

tag: cell type

value: cancer cells


title: 786-0-RNA-08102018

city: Houston

first: Cheryl

middle: L

last: Walker

state: TX

address: 1 Baylor Plaza

department: Center for Precision Environmental Health

country: USA

institute: Baylor College of Medicine

library_source: transcriptomic

data_processing:
Samples were trimmed using TrimGalore!
After trimming samples were aligned to hg38 using HISAT2
Features were quantified using featureCounts
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include featureCounts values for each Sample

molecule: total RNA

source_name: clear-cell renal cell carcinoma (ccRCC) cells

growth_protocol: Cells grown in Dulbecco's Modified Eagle Medium (DMEM, Gibco) supplemented with 10% Fetal Bovine Serum (FBS).

extract_protocol:
Total RNA was extracted using TRIzol reagent (Ambion) and cleaned up using RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
RNA libraries were prepared with QIAseq Stranded Total RNA library Kit (Qiagen) using 100 ng input RNA

tag: genotype

value: Wild-type


title: s0613_mouse3_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well517


title: s0612_mouse3_MDAMB231_Metastases_2cells

description:
Fluidigm C1 platform
well516


title: 786-0-RNA-08092018


title: s0611_mouse3_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well515


title: s0610_mouse3_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well514


title: s0608_mouse3_MDAMB231_Metastases_2cells

description:
Fluidigm C1 platform
well512


title: vWAT; sham injection; day 14; rep. 3

city: New York

first: Mary

last: Teruel

state: NY

address: 1300 York Avenue, Room A-403

institute: Weill-Cornell Medical College, Cornell University

data_processing:
FastQC
For alignment, used Kallisto (v0.44.0) with the quantification algorithm enabled, the number of bootstraps set to 100, and ran in paired-end mode
The Kallisto output files were imported to R with Sleuth, and the transcripts per million (TPM) were used for downstream differential expression analysis
All downstream analysis was done on transcripts that were considered significant from the DESeq2 analysis (likelihood ratio test with a FDR less than 0.05).
Outlier samples were identified by both clustering and PCA analysis and removed.
Assembly: Mus_musculus.GRCm38.cdna
Supplementary files format and content: tab-delimited text files including length, effective length, estimated counts and TPM for each Sample

organism: Mus musculus

source_name: vWAT

extract_protocol:
Fat depots (BAT and vWAT) were removed, flash frozen in N2, and RNA was extracted using the RNeasy Lipid Tissue Mini Kit (Qiagen, Hilden, Germany). mRNA samples were concentrated to ≤ 5 µl by MinElute column (QIAGEN, Cat. 74204).
For generation of RNA-seq libraries, polyadenylated mRNA was isolated from 300 ng of total RNA by incubation with oligo-DT attached magnetic beads and followed by strand-specific library preparation using the TruSeq Stranded mRNA Library Preparation kit (Ilumina, Cat. 20020595).  Samples were pooled and sequenced on the Illumina NextSeq 500/550 High Output platform (Illumina, FC-404-2002) up to 18 samples per lane with 1% PhiX spike as a control.

tag: strain

value: vWAT

tag: treatment

value: sham injection for 14 days


title: E5-RNA-08102018


title: vWAT; sham injection; day 14; rep. 2


title: vWAT; sham injection; day 14; rep. 1


title: vWAT; sham injection; day 14; rep. 4


title: s0605_mouse3_MDAMB231_Metastases_2cells

description:
Fluidigm C1 platform
well509


title: s0603_mouse3_MDAMB231_Metastases_2cells

description:
Fluidigm C1 platform
well507


title: s0604_mouse3_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well508


title: s0607_mouse3_MDAMB231_Metastases_2cells

description:
Fluidigm C1 platform
well511


title: s0606_mouse3_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well510


title: vWAT; sham injection; day 7; rep. 3

value: sham injection for 7 days


title: vWAT; sham injection; day 7; rep. 1


title: vWAT; sham injection; day 7; rep. 2


title: vWAT; sham injection; day 7; rep. 4


title: vWAT; sham injection; day 3; rep. 4

value: sham injection for 3 days


title: s0601_mouse3_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well505


title: hCM-HAND1OE_H3K27ac_ChIP_rep2

city: Guangzhou

first: Lei

last: Jiang

address: No.106 Zhongshan 2nd Road

country: France

institute: Guangdong Provincial People's Hospital

library_source: genomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Single-end reads were mapped to the hg19 reference genome using the bwa2 mem. The duplicated reads were removed using the Picard Toolkit (https://broadinstitute.github.io/picard/), whereas the reads with a quality lower than 20 were filtered. The ChIP-seq peaks were called using the default (narrow) setting in MACS2.
Genome_build: hg19
Supplementary_files_format_and_content: hic forrmat for visualization in Juicebox
Supplementary_files_format_and_content: bigwig format for visualization in IGV or washU Genome Browser

molecule: genomic DNA

source_name: iPSC-derived cardiomyocyte

growth_protocol: The left ventricular (LV) heart samples were collected from DCM patients during surgery and the LV tissues were immediately dissected and snap frozen in liquid nitrogen.

extract_protocol: ChIP-seq: Chromatin (8 μg) was precleared with protein A agarose beads (Invitrogen). Genomic DNA regions of interest were precipitated using 4 μg of antibody against H3K27Ac (Active Motif, Cat# 39133) or 10 μg of antibody again HAND1 (Abconal, Cat#A9855). The complexes were washed, eluted from the beads with 1% SDS buffer and subjected to RNase and proteinase K treatment overnight at 65°C. The ChIPed DNA was purified by phenol-chloroform extraction and ethanol precipitation. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K in a similar way as ChIPed DNA. Illumina sequencing libraries were prepared from the ChIP products by the standard consecutive enzymatic steps of end-repair, A tailing, and adaptor ligation using the KAPA Hyper Prep Kit (Roche, CKK8504). Following a final PCR amplification step, the PCR products were purified and the size was selected by 0.5X SPRI followed by 0.9X SPRI beads.

value: iPSC-derived cardiomyocyte

tag: method

value: ChIP-Seq

tag: factor

tag: condition

value: Transfected with HAND1 overexpressing adenovirus


title: s0600_mouse3_MDAMB231_Metastases_2cells

description:
Fluidigm C1 platform
well504


title: vWAT; sham injection; day 3; rep. 1


title: s0599_mouse3_MDAMB231_Metastases_2cells

description:
Fluidigm C1 platform
well503


title: vWAT; sham injection; day 3; rep. 2


title: vWAT; cort injection; day 14; rep. 4

value: corticosterone injection for 14 days


title: s0598_mouse3_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well502


title: s0609_mouse3_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well513


title: vWAT; cort injection; day 14; rep. 3


title: s0597_mouse3_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well501


title: s0602_mouse3_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well506


title: vWAT; sham injection; day 3; rep. 3


title: vWAT; cort injection; day 7; rep. 4

value: corticosterone injection for 7 days


title: s0596_mouse3_MDAMB231_Metastases_2cells

description:
Fluidigm C1 platform
well500


title: vWAT; cort injection; day 14; rep. 2


title: s0595_mouse3_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well499


title: vWAT; cort injection; day 7; rep. 3


title: vWAT; cort injection; day 14; rep. 1


title: s0594_mouse3_MDAMB231_Metastases_2cells

description:
Fluidigm C1 platform
well498


title: s0591_mouse3_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well495


title: s0593_mouse3_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well497


title: vWAT; cort injection; day 7; rep. 2


title: vWAT; cort injection; day 7; rep. 1


title: s0592_mouse3_MDAMB231_Metastases_2cells

description:
Fluidigm C1 platform
well496


title: s0590_mouse3_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well494


title: s0588_mouse3_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well492


title: vWAT; cort injection; day 3; rep. 2

value: corticosterone injection for 3 days


title: vWAT; cort injection; day 3; rep. 1


title: vWAT; cort injection; day 3; rep. 4


title: s0589_mouse3_MDAMB231_Metastases_2cells

description:
Fluidigm C1 platform
well493


title: s0587_mouse3_MDAMB231_Metastases_3cells

description:
Fluidigm C1 platform
well491


title: s0586_mouse3_MDAMB231_Metastases_2cells

description:
Fluidigm C1 platform
well490


title: vWAT; sham pellet; day 14; rep. 3

value: sham pellet for 14 days


title: vWAT; sham pellet; day 14; rep. 2


title: vWAT; sham pellet; day 14; rep. 1


title: s0584_mouse3_MDAMB231_Metastases_2cells

description:
Fluidigm C1 platform
well488


title: s0585_mouse3_MDAMB231_Metastases_2cells

description:
Fluidigm C1 platform
well489


title: vWAT; sham pellet; day 7; rep. 4

value: sham pellet for 7 days


title: vWAT; cort injection; day 3; rep. 3


title: s0583_mouse3_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well487


title: s0582_mouse3_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well486


title: vWAT; sham pellet; day 7; rep. 3


title: vWAT; sham pellet; day 7; rep. 2


title: s0579_mouse3_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well483


title: vWAT; sham pellet; day 7; rep. 1


title: s0580_mouse3_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well484


title: s0578_mouse3_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well482


title: vWAT; sham pellet; day 3; rep. 3

value: sham pellet for 3 days


title: vWAT; sham pellet; day 14; rep. 4


title: s0577_mouse3_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well481


title: vWAT; sham pellet; day 3; rep. 4


title: vWAT; sham pellet; day 3; rep. 2


title: vWAT; cort pellet; day 14; rep. 2

value: corticosterone pellet for 14 days


title: vWAT; sham pellet; day 3; rep. 1


title: s0576_mouse3_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well480

value: Metastases


title: s0573_mouse3_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well477

value: cancer cells


title: s0575_mouse3_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well479


title: vWAT; cort pellet; day 14; rep. 1


title: s0572_mouse2_MDAMB231_Metastases_0cells

description:
Fluidigm C1 platform
well476


title: s0581_mouse3_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well485


title: s0571_mouse2_MDAMB231_Metastases_0cells

description:
Fluidigm C1 platform
well475


title: vWAT; cort pellet; day 7; rep. 4

value: corticosterone pellet for 7 days


title: s0570_mouse2_MDAMB231_Metastases_0cells

description:
Fluidigm C1 platform
well474


title: s0568_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well472


title: vWAT; cort pellet; day 7; rep. 1

value: vWAT


title: hCM-HAND1OE_H3K27ac_ChIP_rep1


title: s0569_mouse2_MDAMB231_Metastases_2cells

description:
Fluidigm C1 platform
well473


title: vWAT; cort pellet; day 7; rep. 3


title: vWAT; cort pellet; day 7; rep. 2


title: vWAT; cort pellet; day 3; rep. 1

value: corticosterone pellet for 3 days


title: vWAT; cort pellet; day 14; rep. 3


title: s0567_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well471


title: vWAT; cort pellet; day 3; rep. 3


title: vWAT; cort pellet; day 3; rep. 2


title: s0574_mouse3_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well478


title: vWAT; cort pellet; day 3; rep. 4


title: vWAT; day 0; rep. 4

value: no pellet/injection


title: vWAT; day 0; rep. 3


title: s0566_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well470


title: s0565_mouse2_MDAMB231_Metastases_0cells

description:
Fluidigm C1 platform
well469


title: s0562_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well466


title: s0563_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well467


title: vWAT; day 0; rep. 1


title: BAT; sham injection; day 14; rep. 4

source_name: BAT

value: BAT

value: sham injection for 14 days


title: s0560_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well464


title: s0559_mouse2_MDAMB231_Metastases_2cells

description:
Fluidigm C1 platform
well463


title: BAT; sham injection; day 14; rep. 3


title: s0557_mouse2_MDAMB231_Metastases_2cells

description:
Fluidigm C1 platform
well461


title: BAT; sham injection; day 14; rep. 2


title: BAT; sham injection; day 7; rep. 4

value: sham injection for 7 days


title: BAT; sham injection; day 7; rep. 3


title: s0556_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well460


title: BAT; sham injection; day 14; rep. 1


title: s0564_mouse2_MDAMB231_Metastases_0cells

description:
Fluidigm C1 platform
well468


title: vWAT; day 0; rep. 2


title: s0552_mouse2_MDAMB231_Metastases_0cells

description:
Fluidigm C1 platform
well456


title: s0554_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well458


title: s0553_mouse2_MDAMB231_Metastases_2cells

description:
Fluidigm C1 platform
well457


title: s0561_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well465


title: s0555_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well459


title: BAT; sham injection; day 7; rep. 2


title: BAT; sham injection; day 7; rep. 1


title: BAT; sham injection; day 3; rep. 3

value: sham injection for 3 days


title: s0548_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well452


title: s0549_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well453


title: s0551_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well455


title: BAT; sham injection; day 3; rep. 1


title: BAT; cort injection; day 14; rep. 4

value: corticosterone injection for 14 days


title: BAT; cort injection; day 14; rep. 3


title: s0547_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well451


title: BAT; cort injection; day 14; rep. 2


title: s0546_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well450


title: s0545_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well449


title: s0544_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well448


title: BAT; sham injection; day 3; rep. 4


title: BAT; sham injection; day 3; rep. 2


title: s0550_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well454


title: BAT; cort injection; day 7; rep. 2

value: corticosterone injection for 7 days


title: s0542_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well446


title: BAT; cort injection; day 7; rep. 3


title: s0541_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well445


title: s0540_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well444


title: s0537_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well441


title: s0539_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well443


title: BAT; cort injection; day 3; rep. 3

value: corticosterone injection for 3 days


title: s0538_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well442


title: BAT; cort injection; day 3; rep. 4


title: BAT; sham pellet; day 14; rep. 4

value: sham pellet for 14 days


title: BAT; cort injection; day 3; rep. 1


title: s0536_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well440


title: BAT; cort injection; day 3; rep. 2


title: s0535_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well439


title: BAT; sham pellet; day 14; rep. 3


title: s0534_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well438


title: BAT; cort injection; day 14; rep. 1


title: s0533_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well437


title: s0543_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well447


title: BAT; sham pellet; day 14; rep. 1


title: s0532_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well436


title: BAT; sham pellet; day 14; rep. 2


title: BAT; cort injection; day 7; rep. 4


title: BAT; sham pellet; day 7; rep. 4

value: sham pellet for 7 days


title: BAT; cort injection; day 7; rep. 1


title: s0531_mouse2_MDAMB231_Metastases_2cells

description:
Fluidigm C1 platform
well435


title: BAT; sham pellet; day 7; rep. 3


title: s0529_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well433


title: BAT; sham pellet; day 7; rep. 2


title: s0530_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well434


title: s0528_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well432


title: BAT; sham pellet; day 7; rep. 1


title: BAT; sham pellet; day 3; rep. 4

value: sham pellet for 3 days


title: BAT; sham pellet; day 3; rep. 3


title: s0526_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well430


title: s0524_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well428


title: BAT; sham pellet; day 3; rep. 2


title: BAT; cort pellet; day 14; rep. 4

value: corticosterone pellet for 14 days


title: s0522_mouse2_MDAMB231_Metastases_2cells

description:
Fluidigm C1 platform
well426

value: Metastases


title: s0525_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well429

value: cancer cells


title: s0521_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well425


title: s0558_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well462


title: BAT; sham pellet; day 3; rep. 1


title: s0520_mouse2_MDAMB231_Metastases_2cells

description:
Fluidigm C1 platform
well424


title: s0519_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well423


title: BAT; cort pellet; day 7; rep. 3

value: corticosterone pellet for 7 days


title: BAT; cort pellet; day 7; rep. 4


title: s0518_mouse2_MDAMB231_Metastases_2cells

description:
Fluidigm C1 platform
well422


title: BAT; cort pellet; day 7; rep. 2


title: BAT; cort pellet; day 7; rep. 1


title: s0517_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well421


title: s0527_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well431


title: BAT; cort pellet; day 3; rep. 4


title: BAT; cort pellet; day 3; rep. 2


title: s0516_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well420


title: BAT; cort pellet; day 3; rep. 3


title: s0523_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well427


title: s0515_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well419


title: s0514_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well418


title: s0513_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well417


title: BAT; cort pellet; day 14; rep. 3


title: BAT; cort pellet; day 14; rep. 1


title: BAT; day 0; rep. 4


title: BAT; cort pellet; day 3; rep. 1


title: BAT; cort pellet; day 14; rep. 2


title: s0511_mouse2_MDAMB231_Metastases_2cells

description:
Fluidigm C1 platform
well415


title: s0512_mouse2_MDAMB231_Metastases_2cells

description:
Fluidigm C1 platform
well416


title: BAT; day 0; rep. 3


title: s0510_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well414


title: BAT; day 0; rep. 2


title: BAT; day 0; rep. 1


title: s0509_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well413


title: s0507_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well411


title: s0508_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well412


title: s0506_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well410


title: s0503_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well407


title: s0504_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well408


title: s0502_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well406


title: s0501_mouse2_MDAMB231_Metastases_2cells

description:
Fluidigm C1 platform
well405


title: s0500_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well404


title: s0499_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well403


title: s0498_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well402


title: s0497_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well401


title: s0496_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well400


title: s0494_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well398


title: s0495_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well399


title: s0492_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well396


title: s0493_mouse2_MDAMB231_Metastases_2cells

description:
Fluidigm C1 platform
well397


title: s0491_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well395


title: s0489_mouse2_MDAMB231_Metastases_2cells

description:
Fluidigm C1 platform
well393


title: s0488_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well392


title: s0487_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well391


title: s0484_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well388


title: s0505_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well409


title: s0490_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well394


title: s0483_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well387


title: s0485_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well389


title: s0486_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well390


title: s0481_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well385


title: s0479_mouse2_MDAMB231_Metastases_2cells

description:
Fluidigm C1 platform
well383


title: s0478_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well382


title: s0380_mouse1_MDAMB231_Metastases_0cells

description:
Fluidigm C1 platform
well380


title: s0480_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well384


title: s0379_mouse1_MDAMB231_Metastases_0cells

description:
Fluidigm C1 platform
well379


title: s0377_mouse1_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well377


title: s0376_mouse1_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well376


title: s0375_mouse1_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well375


title: s0372_mouse1_MDAMB231_Metastases_0cells

description:
Fluidigm C1 platform
well372


title: s0373_mouse1_MDAMB231_Metastases_0cells

description:
Fluidigm C1 platform
well373


title: s0374_mouse1_MDAMB231_Metastases_0cells

description:
Fluidigm C1 platform
well374


title: s0477_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well381


title: s0370_mouse1_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well370


title: s0371_mouse1_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well371


title: s0369_mouse1_MDAMB231_Metastases_2cells

description:
Fluidigm C1 platform
well369


title: s0368_mouse1_MDAMB231_Metastases_0cells

description:
Fluidigm C1 platform
well368


title: s0367_mouse1_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well367


title: s0366_mouse1_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well366


title: s0362_mouse1_MDAMB231_Metastases_0cells

description:
Fluidigm C1 platform
well362


title: s0363_mouse1_MDAMB231_Metastases_0cells

description:
Fluidigm C1 platform
well363


title: s0365_mouse1_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well365


title: s0482_mouse2_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well386


title: s0359_mouse1_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well359


title: s0357_mouse1_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well357


title: s0353_mouse1_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well353


title: s0361_mouse1_MDAMB231_Metastases_0cells

description:
Fluidigm C1 platform
well361


title: s0360_mouse1_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well360


title: s0356_mouse1_MDAMB231_Metastases_0cells

description:
Fluidigm C1 platform
well356


title: s0378_mouse1_MDAMB231_Metastases_0cells

description:
Fluidigm C1 platform
well378


title: s0355_mouse1_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well355


title: s0354_mouse1_MDAMB231_Metastases_0cells

description:
Fluidigm C1 platform
well354


title: s0348_mouse1_MDAMB231_Metastases_0cells

description:
Fluidigm C1 platform
well348


title: s0349_mouse1_MDAMB231_Metastases_0cells

description:
Fluidigm C1 platform
well349


title: s0351_mouse1_MDAMB231_Metastases_3cells

description:
Fluidigm C1 platform
well351


title: s0345_mouse1_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well345


title: s0344_mouse1_MDAMB231_Metastases_0cells

description:
Fluidigm C1 platform
well344


title: s0350_mouse1_MDAMB231_Metastases_0cells

description:
Fluidigm C1 platform
well350


title: s0347_mouse1_MDAMB231_Metastases_0cells

description:
Fluidigm C1 platform
well347


title: s0340_mouse1_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well340


title: s0358_mouse1_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well358


title: s0339_mouse1_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well339


title: s0338_mouse1_MDAMB231_Metastases_0cells

description:
Fluidigm C1 platform
well338


title: s0341_mouse1_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well341


title: s0343_mouse1_MDAMB231_Metastases_0cells

description:
Fluidigm C1 platform
well343


title: s0342_mouse1_MDAMB231_Metastases_0cells

description:
Fluidigm C1 platform
well342


title: s0364_mouse1_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well364


title: s0337_mouse1_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well337


title: s0336_mouse1_MDAMB231_Metastases_0cells

description:
Fluidigm C1 platform
well336


title: s0335_mouse1_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well335


title: s0352_mouse1_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well352


title: s0333_mouse1_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well333


title: s0334_mouse1_MDAMB231_Metastases_0cells

description:
Fluidigm C1 platform
well334


title: Sirt6KD mESCs rep2 H3K56ac

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

country: Germany

institute: Justus-Liebig-University Giessen

data_processing:
Quality control of FASTQ files was done using FastQC.
Removal of low quality reads was done using fastx_toolkit-0.06
Reads were aligned to a pre-compiled index of the mouse mm10 genome using Bowtie (options: -k 1 -m 1) 0.12.5.
Duplicate reads were removed with Samtools' rmdup function.
Samtools was used to convert aligned reads to BAM format.
The bamCoverage tool of the Deeptools suite was used for extracting coverage vectors (bigwig format).
Genome_build: Genome_build: mm10
Supplementary_files_format_and_content: Supplementary_files_format_and_content: ChIP-seq peaks are supplied as BED and coverage vectors as bigwig files

source_name: Sirt6KD mESCs H3K56ac

growth_protocol: Undifferentiated mESCs were culture on feeder with growth medium (High glucose DMEM,15% Fetal Calf  Serum, Glutamax ,100 μ M Non-essential amino acids, 0.1 mM 2-mercaptoethanol Stock, 10³ units/ml LIF)

extract_protocol:
ChIPed DNA was purified by the mini-elute PCR kits (Qiagen)
TruSeq ChIP Library Preparation Kit (Illumina)

treatment_protocol: Undifferentiated mESCs infected with lentivirus expressing scramble or Sirt6 shRNAs

value: Embryonic stem cells V6.5

value: Sirt6 knockdown

tag: antibody

value: H3K56ac (EpiGentek A-4026-050-EP)


title: s0331_mouse1_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well331


title: s0346_mouse1_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well346


title: Sirt6KD mESCs input DNA

source_name: Sirt6KD mESCs input DNA


title: Scramble mESCs rep1 H3K56ac

source_name: Scramble H3K56ac

value: Scramble


title: s0329_mouse1_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well329


title: MuScs_Control rep2 input DNA rep 2

data_processing:
Quality control of FASTQ files was done using FastQC.
Removal of low quality reads was done using fastx_toolkit-0.06
Reads were aligned to a pre-compiled index of the mouse mm10 genome using Bowtie (options: -k 1 -m 1) 0.12.5.
Duplicate reads were removed with Samtools' rmdup function.
Samtools was used to convert aligned reads to BAM format.
The bamCoverage tool of the Deeptools suite was used for extracting coverage vectors (bigwig format).
Genome_build: Genome_build: mm10
Supplementary_files_format_and_content: ChIP-seq peaks are supplied as BED and coverage vectors as bigwig files

source_name: MuSCs_Control input DNA

growth_protocol: Freshly isolated MuSCs

extract_protocol:
ChIPed DNA was purified by the mini-elute PCR kits (Qiagen)
ChIP-seq libraries were generated using the Ion ChIP-Seq Library Preparation Kit (Thermo Fisher)

tag: strain background

value: Wild type

value: freshly isolated Muscle stem cells (MuSCs)

value: no


title: s0326_mouse1_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well326


title: Sirt6KD mESCs rep1 H3K56ac


title: MuScs_Control rep2 H3K56ac

source_name: MuSCs_Control H3K56ac


title: s0324_mouse1_MDAMB231_Metastases_0cells

description:
Fluidigm C1 platform
well324


title: s0332_mouse1_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well332


title: s0323_mouse1_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well323


title: s0322_mouse1_MDAMB231_Metastases_0cells

description:
Fluidigm C1 platform
well322


title: s0321_mouse1_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well321


title: MuScs_Sirt6mKO rep1 H3K56ac

source_name: MuSCs_Sirt6mKO H3K56ac


title: s0320_mouse1_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well320


title: s0330_mouse1_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well330


title: Scramble mESCs rep2 H3K56ac


title: s0328_mouse1_MDAMB231_Metastases_0cells

description:
Fluidigm C1 platform
well328


title: Scramble mESCs input DNA

source_name: Scramble input DNA


title: s0327_mouse1_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well327


title: MuScs_Control rep1 input DNA rep 1


title: Sirt6mKO ATAC-seq rep2

data_processing:
Quality control was done using FastQC.
Quality aware trimming and adaptor removal werde done using trim_galore (v0.4.1).
Reads were aligned with bwa (v0.5.9).
Coverage vectors were extracted with DeepTools bamCoverage function.
Peak calling was performed using Macs2.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig (read coverage)

extract_protocol:
50.000 cells were used for ATAC-seq
Library preparation using Tn5 Transposase from Nextera DNA Sample Preparation Kit (Illumina)


title: s0325_mouse1_MDAMB231_Metastases_0cells

description:
Fluidigm C1 platform
well325


title: MuScs_Control rep1 H3K56ac


title: s0318_mouse1_MDAMB231_Metastases_0cells

description:
Fluidigm C1 platform
well318


title: MuScs_Sirt6mKO rep2 input DNA

source_name: MuSCs_Sirt6mKO input DNA


title: 64EAT-07-19_S64

city: Corvallis

first: Andrey

last: Morgun

state: OR

address: 1601 SW Jefferson Way

institute: Oregon State University

data_processing:
De-multiplexed sequencing reads were generated using Illumina bcl2fastq (released version 2.18.0.12) allowing no mismatches in the index read.
Sequences were processed to remove adapter, polyA and low-quality bases by BBTools (https://jgi.doe.gov/data-and-tools/bbtools/)
Reads were aligned to mouse genome and transcriptome using Tophat (v2.1.1)
Number of reads assigned to mouse genes were counted using HTSeq (v 0.6.0) and relativised per million.
Genome_build: ENSEMBL NCBIM37
Supplementary_files_format_and_content: comma-delimited text file include relativized counts per million values for each Sample

source_name: EAT

extract_protocol:
RNA was extracted using an OMNI Bead Ruptor and 2.8 mm ceramic beads (OMNI International) followed by RNeasy Lipid Tissue Mini Kit using Qiacube (Qiagen automated extraction according to the manufacturer’s specifications with DNase treatment (RNase-Free DNase Set, QIAGEN).
RNA libraries were prepared with QuantSeq 3’mRNA-Seq Library Prep Kit (Lexogen) for the Apollo 324 NGS Library Prep System.

value: C57BL/6J SPF

tag: age

value: Adult

tag: Sex

value: male

tag: group

value: WD+MMP12 inhibitor

tag: ID

tag: cohort

value: WD+mmp12 inh2


title: 63EAT-07-19_S63


title: MuScs_Sirt6mKO rep1 input DNA


title: MuScs_Sirt6mKO rep2 H3K56ac


title: 60EAT-07-19_S60


title: s0312_mouse1_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well312


title: 61EAT-07-19_S61


title: Sirt6mKO ATAC-seq rep1


title: s0311_mouse1_MDAMB231_Metastases_0cells

description:
Fluidigm C1 platform
well311


title: s0310_mouse1_MDAMB231_Metastases_0cells

description:
Fluidigm C1 platform
well310


title: s0319_mouse1_MDAMB231_Metastases_0cells

description:
Fluidigm C1 platform
well319


title: Control ATAC-seq rep2

value: wild type


title: s0317_mouse1_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well317


title: Control ATAC-seq rep1


title: s0316_mouse1_MDAMB231_Metastases_0cells

description:
Fluidigm C1 platform
well316


title: s0308_mouse1_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well308


title: s0315_mouse1_MDAMB231_Metastases_0cells

description:
Fluidigm C1 platform
well315


title: s0313_mouse1_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well313


title: s0309_mouse1_MDAMB231_Metastases_0cells

description:
Fluidigm C1 platform
well309


title: s0314_mouse1_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well314


title: 62EAT-07-19_S62


title: 56EAT-07-19_S56

value: WD+vehicle


title: s0306_mouse1_MDAMB231_Metastases_0cells

description:
Fluidigm C1 platform
well306

value: Metastases


title: s0305_mouse1_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well305

value: cancer cells


title: s0307_mouse1_MDAMB231_Metastases_0cells

description:
Fluidigm C1 platform
well307


title: 59EAT-07-19_S59


title: 58EAT-07-19_S58


title: 57EAT-07-19_S57


title: 54EAT-07-19_S54


title: 53EAT-07-19_S53


title: s0304_mouse1_MDAMB231_Metastases_0cells

description:
Fluidigm C1 platform
well304


title: s0303_mouse1_MDAMB231_Metastases_0cells

description:
Fluidigm C1 platform
well303


title: 55EAT-07-19_S55


title: s0302_mouse1_MDAMB231_Metastases_0cells

description:
Fluidigm C1 platform
well302


title: 50EAT-07-19_S50

value: WD+mmp12 inh1


title: 52EAT-07-19_S52


title: 44EAT-07-19_S44


title: 51EAT-07-19_S51


title: s0300_mouse1_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well300


title: s0301_mouse1_MDAMB231_Metastases_0cells

description:
Fluidigm C1 platform
well301


title: 49EAT-07-19_S49


title: 42EAT-07-19_S42


title: 43EAT-07-19_S43


title: 41EAT-07-19_S41


title: 75-3T3-07-19_S75

growth_protocol: 3T3-L1 cells were grown in DMEM (high glucose) media supplemented with 10% fetal bovine serum (FBS) in 5% CO2 incubator at 37 °C

extract_protocol:
RNA was extracted from cells in RLT buffer followed by Qiashredder and RNeasy kit (Qiagen) automated extraction according to the manufacturer’s specifications with DNase treatment (RNase-Free DNase Set, QIAGEN). Total RNA was quantified using Quant-iT RNA Assay Kit (Thermo Fisher Scientific).
RNA libraries were prepared with QuantSeq 3’mRNA-Seq Library Prep Kit (Lexogen) for the Apollo 324 NGS Library Prep System.

treatment_protocol: For differentiation, cells were seeded in 96 well plate at a density of 5000 cells/well. After 24 h, the medium was shifted to differentiation medium (90% DMEM, 10% FBS, 1.0 µM Dexamethasone, 0.5 mM Methylisobutylxanthine, 1.0 µg/mL Insulin). After 48 h, the medium was removed and the cells were cultured in adipocyte maintenance medium (90% DMEM, 10% FBS, 1.0 µg/mL Insulin) for 48 h. After that, the medium was changed to regular growth medium (90% DMEM, 10% FBS) and cells were cultured for another 48 h. Finally, cells were treated with insulin or vehicle for 12 h in DMEM (containing 1g/L glucose and 0.2% BSA).

tag: agent

value: insulin

value: 3t3l1+ insulin


title: s0296_mouse1_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well296

tag: tissue


title: s0297_mouse1_MDAMB231_Metastases_0cells

description:
Fluidigm C1 platform
well297

tag: cell line


title: s0299_mouse1_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well299

tag: cell type


title: 47EAT-07-19_S47


title: s0291_mouse1_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well291


title: 48EAT-07-19_S48


title: s0298_mouse1_MDAMB231_Metastases_0cells

description:
Fluidigm C1 platform
well298


title: 76-3T3-07-19_S76


title: 46EAT-07-19_S46


title: s0295_mouse1_MDAMB231_Metastases_0cells

description:
Fluidigm C1 platform
well295


title: 45EAT-07-19_S45


title: s0294_mouse1_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well294


title: s0292_mouse1_MDAMB231_Metastases_0cells

description:
Fluidigm C1 platform
well292


title: s0290_mouse1_MDAMB231_Metastases_0cells

description:
Fluidigm C1 platform
well290


title: s0293_mouse1_MDAMB231_Metastases_0cells

description:
Fluidigm C1 platform
well293


title: s0289_mouse1_MDAMB231_Metastases_0cells

description:
Fluidigm C1 platform
well289


title: s0288_mouse1_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well288


title: 73-3T3-07-19_S73

value: vehicle


title: s0286_mouse1_MDAMB231_Metastases_0cells

description:
Fluidigm C1 platform
well286


title: 71-3T3-07-19_S71


title: 467F

description:
467_GF_fat_1gf_WD
rnaseq_fat-2spf-1gf_rel_million_quantile.txt

data_processing:
De-multiplexed sequencing reads were generated using Illumina bcl2fastq (released version 2.18.0.12) allowing no mismatches in the index read.
Sequences were processed to remove adapter, polyA and low-quality bases by BBTools (https://jgi.doe.gov/data-and-tools/bbtools/)
Reads were aligned to mouse genome and transcriptome using Tophat (v2.1.1)
Per experiment, for each tissue from spf or germ status, number of reads assigned to mouse genes were counted using HTSeq (v 0.6.0) and relativised per million and quantile normalized.
Finally, the normalized tables are provided per tissue.
Genome_build: ENSEMBL NCBIM37
Supplementary_files_format_and_content: comma-delimited text files include relativized counts per million values for each Sample

extract_protocol:
RNA was extracted using an OMNI Bead Ruptor and 2.8 mm ceramic beads (OMNI International) in RLT buffer followed by Qiashredder and RNeasy kit using Qiacube (Qiagen) automated extraction according to manufacturer’s specifications. Total RNA was quantified using Quant-iT RNA Assay Kit (Thermo Fisher Scientific). Complementary DNA was prepared using qScript reverse transcription kit (Bio-Rad) and qPCR was performed using Perfecta SYBR mix (Quantabio) and StepOne Plus Real Time PCR system and software (Applied Biosystems).
RNA libraries were prepared with QuantSeq 3’mRNA-Seq Library Prep Kit (Lexogen) for the Apollo 324 NGS Library Prep System.
RNA-Seq (Illumina NextSeq 500; 75 bp single-end read)

tag: mouse id

tag: type

value: GF

value: fat

tag: genotype

value: C57Bl/6 WT

tag: diet

value: WD


title: 72-3T3-07-19_S72


title: 466F

description:
466_GF_fat_1gf_WD
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: s0285_mouse1_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well285


title: 74-3T3-07-19_S74


title: 465F

description:
465_GF_fat_1gf_WD
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: s0282_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well282

source_name: Tumor

value: Tumor


title: s0283_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well283


title: s0281_mouse3_MDAMB231_Tumor_0cells

description:
Fluidigm C1 platform
well281


title: 461F

description:
461_GF_fat_1gf_WD
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: 451F

description:
451_GF_fat_1gf_ND
rnaseq_fat-2spf-1gf_rel_million_quantile.txt

value: ND


title: s0287_mouse1_MDAMB231_Metastases_1cells

description:
Fluidigm C1 platform
well287


title: 460F

description:
460_GF_fat_1gf_WD
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: s0280_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well280


title: s0278_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well278


title: s0277_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well277


title: s0279_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well279


title: s0276_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well276


title: 453F

description:
453_GF_fat_1gf_ND
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: 472F

description:
472_GF_fat_1gf_ND
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: 454F

description:
454_GF_fat_1gf_ND
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: 473F

description:
473_GF_fat_1gf_ND
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: s0274_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well274


title: 467M

description:
467_GF_muscle_1gf_WD
rnaseq_fat-2spf-1gf_rel_million_quantile.txt

value: muscle


title: 465M

description:
465_GF_muscle_1gf_WD
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: s0272_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well272


title: s0275_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well275


title: 462M

description:
462_GF_muscle_1gf_WD
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: 462F

description:
462_GF_fat_1gf_WD
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: s0284_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well284


title: s0270_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well270


title: s0271_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well271


title: s0268_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well268


title: 466M

description:
466_GF_muscle_1gf_WD
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: s0267_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well267


title: 460M

description:
460_GF_muscle_1gf_WD
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: s0264_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well264


title: 461M

description:
461_GF_muscle_1gf_WD
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: s0263_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well263


title: s0269_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well269


title: 467i

description:
467_GF_ileum_1gf_WD
rnaseq_fat-2spf-1gf_rel_million_quantile.txt

value: ileum


title: 454M

description:
454_GF_muscle_1gf_ND
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: 466i

description:
466_GF_ileum_1gf_WD
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: s0266_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well266


title: 451M

description:
451_GF_muscle_1gf_ND
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: s0273_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well273


title: 462i

description:
462_GF_ileum_1gf_WD
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: 460i

description:
460_GF_ileum_1gf_WD
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: 473M

description:
473_GF_muscle_1gf_ND
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: 453M

description:
453_GF_muscle_1gf_ND
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: 472M

description:
472_GF_muscle_1gf_ND
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: 454i

description:
454_GF_ileum_1gf_ND
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: s0265_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well265


title: s0262_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well262


title: s0261_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well261


title: s0257_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well257


title: s0256_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well256


title: s0255_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well255


title: 451i

description:
451_GF_ileum_1gf_ND
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: 467L

description:
467_GF_liver_1gf_WD
rnaseq_fat-2spf-1gf_rel_million_quantile.txt

value: liver


title: s0253_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well253


title: 465i

description:
465_GF_ileum_1gf_WD
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: s0252_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well252


title: s0260_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well260


title: 466L

description:
466_GF_liver_1gf_WD
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: 465L

description:
465_GF_liver_1gf_WD
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: 461i

description:
461_GF_ileum_1gf_WD
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: 461L

description:
461_GF_liver_1gf_WD
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: s0259_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well259


title: s0258_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well258


title: s0247_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well247


title: 453i

description:
453_GF_ileum_1gf_ND
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: 473i

description:
473_GF_ileum_1gf_ND
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: s0254_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well254


title: 473L

description:
473_GF_liver_1gf_ND
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: 12rnaseqfa8

description:
1692_SPF_fat_abx3_WD
rnaseq_fat-2spf-1gf_rel_million_quantile.txt

value: SPF


title: 472L

description:
472_GF_liver_1gf_ND
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: 472i

description:
472_GF_ileum_1gf_ND
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: s0240_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well240


title: s0251_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well251


title: s0250_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well250


title: 462L

description:
462_GF_liver_1gf_WD
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: 12rnaseqfa6

description:
1690_SPF_fat_abx3_WD
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: 12rnaseqfa5

description:
1689_SPF_fat_abx3_ND
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: 460L

description:
460_GF_liver_1gf_WD
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: 454L

description:
454_GF_liver_1gf_ND
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: s0246_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well246


title: s0236_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well236


title: s0245_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well245


title: 453L

description:
453_GF_liver_1gf_ND
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: 451L

description:
451_GF_liver_1gf_ND
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: 12rnaseqfa3

description:
1687_SPF_fat_abx3_ND
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: 12rnaseqfa2

description:
1686_SPF_fat_abx3_ND
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: s0244_mouse3_MDAMB231_Tumor_2cells

description:
Fluidigm C1 platform
well244


title: s0243_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well243


title: s0235_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well235


title: s0238_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well238


title: s0242_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well242


title: 11rnaseqfa10

description:
1569_SPF_fat_abx2_WD
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: s0231_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well231


title: 12rnaseqfa10

description:
1694_SPF_fat_abx3_WD
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: s0241_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well241


title: s0249_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well249


title: s0248_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well248


title: s0233_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well233


title: s0230_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well230


title: 11rnaseqfa8

description:
1567_SPF_fat_abx2_WD
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: s0237_mouse3_MDAMB231_Tumor_2cells

description:
Fluidigm C1 platform
well237


title: 11rnaseqfa7

description:
1566_SPF_fat_abx2_WD
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: 12rnaseqfa9

description:
1693_SPF_fat_abx3_WD
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: 12rnaseqfa7

description:
1691_SPF_fat_abx3_WD
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: s0234_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well234


title: 11rnaseqfa3

description:
1562_SPF_fat_abx2_ND
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: 11rnaseqfa2

description:
1561_SPF_fat_abx2_ND
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: s0239_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well239


title: 12rnaseqmu10

description:
1694_SPF_muscle_abx3_WD
rnaseq_musc-2spf-1gf_rel_million_quantile.txt


title: 11rnaseqfa1

description:
1560_SPF_fat_abx2_ND
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: 11rnaseqfa6

description:
1565_SPF_fat_abx2_WD
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: s0228_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well228


title: s0227_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well227


title: s0221_mouse3_MDAMB231_Tumor_3cells

description:
Fluidigm C1 platform
well221


title: s0232_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well232


title: s0226_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well226


title: 11rnaseqfa9

description:
1568_SPF_fat_abx2_WD
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: 12rnaseqfa1

description:
1685_SPF_fat_abx3_ND
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: s0229_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well229


title: 11rnaseqfa5

description:
1564_SPF_fat_abx2_ND
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: s0225_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well225


title: 12rnaseqfa4

description:
1688_SPF_fat_abx3_ND
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: 11rnaseqfa4

description:
1563_SPF_fat_abx2_ND
rnaseq_fat-2spf-1gf_rel_million_quantile.txt


title: s0224_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well224


title: 12rnaseqmu6

description:
1690_SPF_muscle_abx3_WD
rnaseq_musc-2spf-1gf_rel_million_quantile.txt


title: 12rnaseqmu4

description:
1688_SPF_muscle_abx3_ND
rnaseq_musc-2spf-1gf_rel_million_quantile.txt


title: s0222_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well222


title: 12rnaseqmu7

description:
1691_SPF_muscle_abx3_WD
rnaseq_musc-2spf-1gf_rel_million_quantile.txt


title: 12rnaseqmu8

description:
1692_SPF_muscle_abx3_WD
rnaseq_musc-2spf-1gf_rel_million_quantile.txt


title: 12rnaseqmu1

description:
1685_SPF_muscle_abx3_ND
rnaseq_musc-2spf-1gf_rel_million_quantile.txt


title: s0216_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well216


title: s0210_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well210


title: 12rnaseqmu9

description:
1693_SPF_muscle_abx3_WD
rnaseq_musc-2spf-1gf_rel_million_quantile.txt


title: s0223_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well223


title: s0217_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well217


title: s0215_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well215


title: s0219_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well219


title: s0212_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well212


title: s0209_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well209


title: s0220_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well220


title: s0214_mouse3_MDAMB231_Tumor_2cells

description:
Fluidigm C1 platform
well214


title: 11rnaseqmu8

description:
1567_SPF_muscle_abx2_WD
rnaseq_musc-2spf-1gf_rel_million_quantile.txt


title: 11rnaseqmu6

description:
1565_SPF_muscle_abx2_WD
rnaseq_musc-2spf-1gf_rel_million_quantile.txt


title: s0218_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well218


title: 11rnaseqmu5

description:
1564_SPF_muscle_abx2_ND
rnaseq_musc-2spf-1gf_rel_million_quantile.txt


title: 12rnaseqmu3

description:
1687_SPF_muscle_abx3_ND
rnaseq_musc-2spf-1gf_rel_million_quantile.txt


title: 12rnaseqmu5

description:
1689_SPF_muscle_abx3_ND
rnaseq_musc-2spf-1gf_rel_million_quantile.txt


title: s0207_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well207


title: 11rnaseqmu4

description:
1563_SPF_muscle_abx2_ND
rnaseq_musc-2spf-1gf_rel_million_quantile.txt


title: 12rnaseqmu2

description:
1686_SPF_muscle_abx3_ND
rnaseq_musc-2spf-1gf_rel_million_quantile.txt


title: s0211_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well211


title: 11rnaseqmu3

description:
1562_SPF_muscle_abx2_ND
rnaseq_musc-2spf-1gf_rel_million_quantile.txt


title: 11rnaseqmu10

description:
1569_SPF_muscle_abx2_WD
rnaseq_musc-2spf-1gf_rel_million_quantile.txt


title: s0203_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well203


title: s0202_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well202


title: s0205_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well205


title: s0201_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well201


title: 12rnaseqil8

description:
1692_SPF_ileum_abx3_WD
rnaseq_ileum-2spf-1gf_rel_million_quantile.txt


title: 12rnaseqil9

description:
1693_SPF_ileum_abx3_WD
rnaseq_ileum-2spf-1gf_rel_million_quantile.txt


title: 11rnaseqmu1

description:
1560_SPF_muscle_abx2_ND
rnaseq_musc-2spf-1gf_rel_million_quantile.txt


title: s0208_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well208


title: s0213_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well213


title: 11rnaseqmu9

description:
1568_SPF_muscle_abx2_WD
rnaseq_musc-2spf-1gf_rel_million_quantile.txt


title: 11rnaseqmu7

description:
1566_SPF_muscle_abx2_WD
rnaseq_musc-2spf-1gf_rel_million_quantile.txt


title: s0206_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well206


title: s0204_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well204


title: s0198_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well198


title: s0197_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well197


title: s0199_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well199


title: s0195_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well195


title: s0200_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well200


title: 12rnaseqil10

description:
1694_SPF_ileum_abx3_WD
rnaseq_ileum-2spf-1gf_rel_million_quantile.txt


title: s0196_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well196


title: 12rnaseqil3

description:
1687_SPF_ileum_abx3_ND
rnaseq_ileum-2spf-1gf_rel_million_quantile.txt


title: 12rnaseqil1

description:
1685_SPF_ileum_abx3_ND
rnaseq_ileum-2spf-1gf_rel_million_quantile.txt


title: s0190_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well190


title: s0191_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well191


title: s0189_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well189


title: 12rnaseqil7

description:
1691_SPF_ileum_abx3_WD
rnaseq_ileum-2spf-1gf_rel_million_quantile.txt


title: 12rnaseqil6

description:
1690_SPF_ileum_abx3_WD
rnaseq_ileum-2spf-1gf_rel_million_quantile.txt


title: 11rnaseqmu2

description:
1561_SPF_muscle_abx2_ND
rnaseq_musc-2spf-1gf_rel_million_quantile.txt


title: s0193_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well193


title: 12rnaseqil5

description:
1689_SPF_ileum_abx3_ND
rnaseq_ileum-2spf-1gf_rel_million_quantile.txt


title: 11rnaseqil6

description:
1565_SPF_ileum_abx2_WD
rnaseq_ileum-2spf-1gf_rel_million_quantile.txt


title: 12rnaseqil2

description:
1686_SPF_ileum_abx3_ND
rnaseq_ileum-2spf-1gf_rel_million_quantile.txt


title: 11rnaseqil4

description:
1563_SPF_ileum_abx2_ND
rnaseq_ileum-2spf-1gf_rel_million_quantile.txt


title: 11rnaseqil8

description:
1567_SPF_ileum_abx2_WD
rnaseq_ileum-2spf-1gf_rel_million_quantile.txt


title: s0192_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well192


title: 11rnaseqil2

description:
1561_SPF_ileum_abx2_ND
rnaseq_ileum-2spf-1gf_rel_million_quantile.txt


title: s0185_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well185


title: 11rnaseqil9

description:
1568_SPF_ileum_abx2_WD
rnaseq_ileum-2spf-1gf_rel_million_quantile.txt


title: 12rnaseqli10

description:
1694_SPF_liver_abx3_WD
rnaseq_liv-2spf-1gf_rel_million_quantile.txt


title: 12rnaseqli9

description:
1693_SPF_liver_abx3_WD
rnaseq_liv-2spf-1gf_rel_million_quantile.txt


title: s0181_mouse2_MDAMB231_Tumor_0cells

description:
Fluidigm C1 platform
well181


title: s0194_mouse3_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well194


title: s0187_mouse2_MDAMB231_Tumor_0cells

description:
Fluidigm C1 platform
well187


title: 11rnaseqil10

description:
1569_SPF_ileum_abx2_WD
rnaseq_ileum-2spf-1gf_rel_million_quantile.txt


title: s0183_mouse2_MDAMB231_Tumor_5cells

description:
Fluidigm C1 platform
well183


title: 12rnaseqil4

description:
1688_SPF_ileum_abx3_ND
rnaseq_ileum-2spf-1gf_rel_million_quantile.txt


title: 12rnaseqli6

description:
1690_SPF_liver_abx3_WD
rnaseq_liv-2spf-1gf_rel_million_quantile.txt


title: s0184_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well184


title: s0178_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well178


title: 11rnaseqil3

description:
1562_SPF_ileum_abx2_ND
rnaseq_ileum-2spf-1gf_rel_million_quantile.txt


title: s0182_mouse2_MDAMB231_Tumor_0cells

description:
Fluidigm C1 platform
well182


title: s0186_mouse2_MDAMB231_Tumor_0cells

description:
Fluidigm C1 platform
well186


title: 11rnaseqil7

description:
1566_SPF_ileum_abx2_WD
rnaseq_ileum-2spf-1gf_rel_million_quantile.txt


title: s0188_mouse2_MDAMB231_Tumor_0cells

description:
Fluidigm C1 platform
well188


title: s0180_mouse2_MDAMB231_Tumor_0cells

description:
Fluidigm C1 platform
well180


title: 11rnaseqil1

description:
1560_SPF_ileum_abx2_ND
rnaseq_ileum-2spf-1gf_rel_million_quantile.txt


title: s0176_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well176


title: s0177_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well177


title: 11rnaseqil5

description:
1564_SPF_ileum_abx2_ND
rnaseq_ileum-2spf-1gf_rel_million_quantile.txt


title: s0179_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well179


title: 12rnaseqli7

description:
1691_SPF_liver_abx3_WD
rnaseq_liv-2spf-1gf_rel_million_quantile.txt


title: 12rnaseqli8

description:
1692_SPF_liver_abx3_WD
rnaseq_liv-2spf-1gf_rel_million_quantile.txt


title: s0174_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well174


title: 12rnaseqli4

description:
1688_SPF_liver_abx3_ND
rnaseq_liv-2spf-1gf_rel_million_quantile.txt


title: 12rnaseqli5

description:
1689_SPF_liver_abx3_ND
rnaseq_liv-2spf-1gf_rel_million_quantile.txt


title: s0173_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well173


title: 12rnaseqli3

description:
1687_SPF_liver_abx3_ND
rnaseq_liv-2spf-1gf_rel_million_quantile.txt


title: 12rnaseqli2

description:
1686_SPF_liver_abx3_ND
rnaseq_liv-2spf-1gf_rel_million_quantile.txt


title: 12rnaseqli1

description:
1685_SPF_liver_abx3_ND
rnaseq_liv-2spf-1gf_rel_million_quantile.txt


title: s0175_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well175


title: s0172_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well172


title: s0171_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well171


title: 11rnaseqli9

description:
1568_SPF_liver_abx2_WD
rnaseq_liv-2spf-1gf_rel_million_quantile.txt


title: s0170_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well170


title: 11rnaseqli7

description:
1566_SPF_liver_abx2_WD
rnaseq_liv-2spf-1gf_rel_million_quantile.txt


title: s0169_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well169


title: 11rnaseqli8

description:
1567_SPF_liver_abx2_WD
rnaseq_liv-2spf-1gf_rel_million_quantile.txt


title: s0168_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well168


title: 11rnaseqli10

description:
1569_SPF_liver_abx2_WD
rnaseq_liv-2spf-1gf_rel_million_quantile.txt


title: 11rnaseqli6

description:
1565_SPF_liver_abx2_WD
rnaseq_liv-2spf-1gf_rel_million_quantile.txt


title: s0165_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well165


title: 11rnaseqli5

description:
1564_SPF_liver_abx2_ND
rnaseq_liv-2spf-1gf_rel_million_quantile.txt


title: s0166_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well166


title: s0167_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well167


title: 11rnaseqli2

description:
1561_SPF_liver_abx2_ND
rnaseq_liv-2spf-1gf_rel_million_quantile.txt


title: s0164_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well164


title: 11rnaseqli3

description:
1562_SPF_liver_abx2_ND
rnaseq_liv-2spf-1gf_rel_million_quantile.txt


title: s0163_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well163


title: s0160_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well160


title: s0159_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well159


title: Cerebral organoid cells, Donor 24 Replicate 1, Day 46

city: Worcester

first: Elaine

last: Lim

state: MA

address: 366 Plantation Street, Paul J DiMare 5-1025

institute: UMass Chan Medical School

data_processing:
FastQC v0.10.0
Trimmomatic v0.32
TopHat v2.0.13, bowtie2 2.2.3
Cufflinks v2.2.1
STAR 2.4.0f1, GATK 3.3-0

source_name: Cerebral organoids

extract_protocol:
PureLink RNA Mini Kit
TruSeq Stranded Total RNA

value: Cerebral organoids

value: 16p11.2 deletion


title: Cerebral organoid cells, Donor 24 Replicate 2, Day 46


title: Cerebral organoid cells, Donor 25 Replicate 2, Day 46


title: Cerebral organoid cells, Donor 24 Replicate 3, Day 46


title: Cerebral organoid cells, Donor 25 Replicate 1, Day 46


title: Cerebral organoid cells, Donor 22 Replicate 3, Day 46


title: s0157_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well157

value: cancer cells


title: 11rnaseqli4

description:
1563_SPF_liver_abx2_ND
rnaseq_liv-2spf-1gf_rel_million_quantile.txt


title: s0154_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well154


title: s0156_mouse2_MDAMB231_Tumor_0cells

description:
Fluidigm C1 platform
well156


title: s0155_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well155


title: Cerebral organoid cells, Donor 22 Replicate 2, Day 46


title: Cerebral organoid cells, Donor 22 Replicate 1, Day 46


title: Cerebral organoid cells, Donor 21 Replicate 2, Day 46


title: s0162_mouse2_MDAMB231_Tumor_0cells

description:
Fluidigm C1 platform
well162


title: 11rnaseqli1

description:
1560_SPF_liver_abx2_ND
rnaseq_liv-2spf-1gf_rel_million_quantile.txt


title: Cerebral organoid cells, Donor 21 Replicate 1, Day 46


title: s0161_mouse2_MDAMB231_Tumor_2cells

description:
Fluidigm C1 platform
well161


title: s0151_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well151


title: Cerebral organoid cells, Donor 20 Replicate 3, Day 46


title: s0152_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well152


title: s0158_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well158


title: Cerebral organoid cells, Donor 20 Replicate 1, Day 46


title: s0149_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well149


title: s0150_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well150


title: Cerebral organoid cells, Donor 23 Replicate 1, Day 46


title: Cerebral organoid cells, Donor 19 Replicate 2, Day 46


title: s0153_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well153


title: Cerebral organoid cells, Donor 18 Replicate 3, Day 46


title: s0146_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well146


title: Cerebral organoid cells, Donor 19 Replicate 3, Day 46


title: s0147_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well147


title: Cerebral organoid cells, Donor 18 Replicate 1, Day 46


title: s0145_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well145


title: s0144_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well144


title: s0143_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well143


title: Cerebral organoid cells, Donor 17 Replicate 3, Day 46


title: s0142_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well142


title: Cerebral organoid cells, Donor 18 Replicate 2, Day 46


title: Cerebral organoid cells, Donor 19 Replicate 1, Day 46


title: s0140_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well140


title: s0141_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well141


title: Cerebral organoid cells, Donor 17 Replicate 1, Day 46


title: Cerebral organoid cells, Donor 20 Replicate 2, Day 46


title: Cerebral organoid cells, Donor 16 Replicate 2, Day 46

value: 15q11-13 duplication


title: s0148_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well148


title: s0139_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well139


title: Cerebral organoid cells, Donor 17 Replicate 2, Day 46


title: s0138_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well138


title: s0136_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well136


title: Cerebral organoid cells, Donor 16 Replicate 3, Day 46


title: s0137_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well137


title: Cerebral organoid cells, Donor 15 Replicate 3, Day 46


title: Cerebral organoid cells, Donor 15 Replicate 2, Day 46


title: s0135_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well135


title: s0134_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well134


title: Cerebral organoid cells, Donor 16 Replicate 1, Day 46


title: s0133_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well133


title: Cerebral organoid cells, Donor 14 Replicate 1, Day 46


title: Cerebral organoid cells, Donor 15 Replicate 1, Day 46


title: Cerebral organoid cells, Donor 14 Replicate 2, Day 46


title: s0132_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well132


title: s0129_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well129


title: Cerebral organoid cells, Donor 14 Replicate 3, Day 46


title: s0131_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well131


title: s0130_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well130


title: Cerebral organoid cells, Donor 12 Replicate 3, Day 46

value: Control


title: Cerebral organoid cells, Donor 13 Replicate 1, Day 46


title: Cerebral organoid cells, Donor 13 Replicate 3, Day 46


title: s0128_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well128


title: s0125_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well125


title: Cerebral organoid cells, Donor 13 Replicate 2, Day 46


title: Cerebral organoid cells, Donor 12 Replicate 1, Day 46


title: s0127_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well127


title: Cerebral organoid cells, Donor 11 Replicate 3, Day 46


title: s0126_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well126


title: Cerebral organoid cells, Donor 12 Replicate 2, Day 46


title: s0123_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well123


title: s0122_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well122


title: Cerebral organoid cells, Donor 11 Replicate 2, Day 46


title: Cerebral organoid cells, Donor 10 Replicate 3, Day 46


title: Cerebral organoid cells, Donor 11 Replicate 1, Day 46


title: s0121_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well121


title: CD4hiCD38hi PK Sabah Patient 6

type: RNA

city: Chermside

first: Simon

middle: H

last: Apte

state: QLD

address: Rode Rd

department: The Prince Charles Hospital

country: Australia

institute: Queensland Department of Health

hyb_protocol: nCounter codeset hybridization was performed as per manufacturer’s instructions using 5μl of cell lysate (10000 cells).

scan_protocol: Samples were processed using the NanoString GEN2 Prep Station and data acquired using the nCounter Digital Analyzer (NanoString Technologies).

data_processing: Data were normalized to the mean RPLP0 expression levels and the limit of detection was set as the average reading for the negative controls plus 2 SD and all values below this were raised to this value and all data were then Log2 normalized.

label: NanoString

source_name: Malaria

label_protocol: NanoString

extract_protocol: Following stimulation, the cells were washed and resuspended in RLT lysis buffer (2000 cells/ul) and stored at -70 C until use.

treatment_protocol: PBMCs isolated from adult patients with P. falciparum or P. knowlesi malaria in Papua or Sabah were sorted by flow cytometry into populations of CD4hiCD38hi T cells or CD4norm T cell populations. Immediately following the sort, the cells were   stimulated with PMA and Ionomycin for 3 hours.

tag: parasite

value: Plasmodium knowlesi

tag: locale

value: Sabah


title: s0119_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well119


title: CD4hiCD38hi PK Sabah Patient 4


title: CD4hiCD38hi PK Sabah Patient 5


title: Cerebral organoid cells, Donor 10 Replicate 2, Day 46


title: CD4hiCD38hi PK Sabah Patient 3


title: CD4hiCD38hi PK Sabah Patient 2


title: s0124_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well124


title: Cerebral organoid cells, Donor 9 Replicate 3, Day 46


title: CD4hiCD38hi PK Sabah Patient 1


title: Cerebral organoid cells, Donor 10 Replicate 1, Day 46


title: Cerebral organoid cells, Donor 9 Replicate 2, Day 46


title: Cerebral organoid cells, Donor 9 Replicate 1, Day 46


title: s0116_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well116


title: s0117_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well117


title: CD4norm PK Sabah Patient 5


title: CD4norm PK Sabah Patient 2


title: CD4norm PK Sabah Patient 1


title: CD4norm PK Sabah Patient 3


title: Cd4hiCD38hi PF Sabah Patient 6

value: Plasmodium falciparum


title: s0120_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well120


title: Cerebral organoid cells, Donor 8 Replicate 3, Day 46


title: s0115_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well115


title: Cd4hiCD38hi PF Sabah Patient 4


title: Cd4hiCD38hi PF Sabah Patient 5


title: s0114_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well114


title: CD4norm PK Sabah Patient 6


title: Cd4hiCD38hi PF Sabah Patient 3


title: Cerebral organoid cells, Donor 8 Replicate 2, Day 46


title: Cerebral organoid cells, Donor 7 Replicate 3, Day 46


title: s0112_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well112


title: s0118_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well118


title: Cd4hiCD38hi PF Papua Patient 4

value: Papua


title: Cd4hiCD38hi PF Sabah Patient 1


title: s0113_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well113


title: s0110_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well110


title: CD4norm PK Sabah Patient 4


title: Cd4hiCD38hi PF Papua Patient 6


title: iPSC_WT_TBX3_4C

city: Stanford

first: Howard

middle: Y

last: Chang

state: CA

address: CCSR 2130, 269 Campus Drive

department: Center for Personal Dynamic Regulomes

institute: Stanford University

data_processing:
4C-seq data was processed using pipe4C (PMID:31351925) and aligned to the hg38 genome
Genome_build: hg38
Supplementary_files_format_and_content: Bigwig (bw) files contain normalized, smoothened 4C-seq signal for visualization.

source_name: wild-type iPSC

growth_protocol: Cells were maintained in Essential 8 Flex medium (Thermo Fisher A2858501) on Vitronectin (Thermo Fisher A14700) coated plates.

extract_protocol:
4C-seq libraries were generated from fixed cells as described previously (PMID: 22929766). HindIII (6-bp cutter) was used as primary restriction enzyme. NlaIII was used as secondary restriction enzyme.
For each viewpoint, a total of 1.6 mg of each library was amplified by PCR.

value: human induced pluripotent stem cells (iPSCs)

tag: genotype/variation

value: wild type


title: Cerebral organoid cells, Donor 7 Replicate 2, Day 46


title: iPSC_MUT_PAX9_4C

source_name: RNA-binding deficient EZH2 mutant iPSC

value: RNA-binding deficient EZH2 mutant


title: s0107_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well107

value: Tumor


title: iPSC_MUT_TBX3_4C


title: s0108_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well108


title: s0111_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well111


title: CD4norm PF Sabah Patient 5


title: s0109_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well109


title: Cd4hiCD38hi PF Papua Patient 5


title: CD4norm PF Sabah Patient 6


title: Cerebral organoid cells, Donor 6 Replicate 3, Day 46


title: Cd4hiCD38hi PF Sabah Patient 2


title: Cd4hiCD38hi PF Papua Patient 2


title: Cerebral organoid cells, Donor 5 Replicate 3, Day 46


title: CD4norm PF Sabah Patient 4


title: Cerebral organoid cells, Donor 6 Replicate 2, Day 46


title: Cd4hiCD38hi PF Papua Patient 3


title: CD4norm PF Sabah Patient 1


title: Cerebral organoid cells, Donor 8 Replicate 1, Day 46


title: CD4norm PF Sabah Patient 3


title: CD4norm PF Papua Patient 6


title: CD4norm PF Papua Patient 5


title: Cerebral organoid cells, Donor 4 Replicate 2, Day 46


title: s0101_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well101


title: s0106_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well106


title: s0103_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well103


title: s0102_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well102


title: Cerebral organoid cells, Donor 7 Replicate 1, Day 46


title: Cerebral organoid cells, Donor 5 Replicate 1, Day 46


title: Cerebral organoid cells, Donor 6 Replicate 1, Day 46


title: Ventral spinal cord, C3-C6, Ovariectomized female, Rat 4

city: MINNEAPOLIS

first: Brendan

middle: J.

last: Dougherty

state: MN

address: 420 Delaware Street SE, MMC 388

department: Rehabilitation Medicine

institute: University of Minnesota - Twin Cities

data_processing:
Raw sequence that passed CASAV 1.8P/F filter were assessed by fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Read mapping was performed via Tophat (v2.0.13) using the rat (Rnor_6.0.98) as a reference.
Counts were quantified via Feature counts (Subread Package).
Differentially expressed genes were identified using the edgeR (negative binomial) feature in CLCGWB (Qiagen, Redwood city, CA) using raw read counts.
Assembly: Rattus noverticus (Rnor_6.0.98)
Supplementary files format and content: RawReadCounts_Dougherty002.txt

organism: Rattus norvegicus

source_name: ventral cervical spinal cord, C3-C6

extract_protocol:
Rats were deeply anesthetized with isoflurane in a closed container, transcardially perfused with ice-cold saline (pH 7.4), and the spinal cords immediately extracted from C3-C6 .  The dorsal half of the tissue segments were discarded to isolate only the ventral spinal cord. Samples were quickly transferred to ice-cold RNAlater solution and refrigerated at 4°C for 48 hours. Cords were subsequently removed from RNAlater solution, placed into fresh 1.5mL conical tubes and stored at -80°C. until processed for RNA extraction. RNA was isolated using the RNeasy mini kit (Qiagen) according to manufacturer's instructions.
RNA libraries were prepared for sequencing using Illumina Truseq protocols

value: ventral cervical spinal cord, C3-C6

tag: treatment

value: Ovaries removed


title: Ventral spinal cord, C3-C6, Ovariectomized female, Rat 5


title: iPSC_WT_PAX9_4C


title: Ventral spinal cord, C3-C6, Ovariectomized female, Rat 6


title: s0104_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well104


title: Cerebral organoid cells, Donor 5 Replicate 2, Day 46


title: Cerebral organoid cells, Donor 4 Replicate 1, Day 46


title: Cerebral organoid cells, Donor 4 Replicate 3, Day 46


title: CD4norm PF Sabah Patient 2


title: Cd4hiCD38hi PF Papua Patient 1


title: iPSC_MUT_NKX2_4C


title: iPSC_WT_NKX2_4C


title: Ventral spinal cord, C3-C6, Ovariectomized female, Rat 3


title: s0105_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well105


title: Cerebral organoid cells, Donor 3 Replicate 2, Day 46


title: CD4norm PF Papua Patient 4


title: s0100_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well100


title: Cerebral organoid cells, Donor 3 Replicate 1, Day 46


title: Ventral spinal cord, C3-C6, intact female, Rat 6

value: intact


title: Cerebral organoid cells, Donor 3 Replicate 3, Day 46


title: Ventral spinal cord, C3-C6, Ovariectomized female, Rat 2


title: Ventral spinal cord, C3-C6, intact female, Rat 5


title: s0097_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well97


title: Cerebral organoid cells, Donor 2 Replicate 3, Day 46


title: Ventral spinal cord, C3-C6, intact female, Rat 4


title: Cerebral organoid cells, Donor 2 Replicate 2, Day 46


title: CD4norm PF Papua Patient 3


title: s0098_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well98


title: s0095_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well95


title: CD4norm PF Papua Patient 2


title: s0094_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well94


title: s0099_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well99


title: CD4norm PF Papua Patient 1


title: Cerebral organoid cells, Donor 1 Replicate 3, Day 46


title: Ventral spinal cord, C3-C6, intact female, Rat 2


title: s0093_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well93


title: Cerebral organoid cells, Donor 1 Replicate 2, Day 46


title: Ventral spinal cord, C3-C6, Ovariectomized female, Rat 1


title: Ventral spinal cord, C3-C6, intact female, Rat 1


title: Cerebral organoid cells, Donor 1 Replicate 1, Day 46


title: s0096_mouse2_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well96


title: Ventral spinal cord, C3-C6, castrated male, Rat 6

value: Testes removed


title: s0091_mouse1_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well91


title: Cerebral organoid cells, Donor 2 Replicate 1, Day 46

value: Cerebral organoids


title: hCM-HAND1OE_HiChIP

data_processing:
Library strategy: HiChIP
Illumina Casava1.7 software used for basecalling.
HiChIP data were processed using HiC-Pro with default parameters with the exception of the LIGATION_SITE being set to GATCGATC, GANTGATC, GANTANTC, GATCANTC and the GENOME_FRAGMENT that was generated using digest_genome.py in HiC-Pro utilities. The following parameters were used: -r ^GATC G ^ANTC -o hg19_restriction sites.bed hg19.fasta. The raw reads were mapped to the hg19 reference genome and were assigned to restriction fragments. The raw reads were filtered for valid pairs (VI). 1D coverage files for the visualization in bigwig format were converted from bam format using deepTools and RPKM (Reads Per Kilobase per Million reads to normalize the number of reads per bin) normalization was used. The HiC files were generated using hicprotojuiebox.py utilities in HiC-Pro.
Genome_build: hg19
Supplementary_files_format_and_content: hic forrmat for visualization in Juicebox
Supplementary_files_format_and_content: bigwig format for visualization in IGV or washU Genome Browser

source_name: iPSC-derived cardiomyocyte

extract_protocol: H3K27ac HiChIP: biotin-labeled proximally-ligated chromatin was prepared using the Arima-HiC kit (Arima Genomics Cat # A510008). Briefly, the crosslinked chromatin was initially digested using a restriction enzyme (RE) cocktail. The 5’-overhangs were subsequently filled in and labeled with a biotinylated nucleotide. Subsequently, the spatially proximal digested ends of DNA were ligated. The resulting proximally-ligated chromatin was fragmented using the Diagenode Bioruptor Pico instrument, bound to an H3K27ac antibody (Abcam Cat # ab4729) overnight and immunoprecipitated on Protein A magnetic beads (Thermo Cat # 10002D). The immunoprecipitated chromatin was reverse crosslinked and purified using the Arima-HiC kit. Subsequently, the Illumina-compatible sequencing libraries were prepared by initial enrichment for biotin using C1 streptavidin beads (Thermo Cat # 65001). The samples were tagmented on-bead utilizing Tagment DNA Enzyme and Buffer (Illumina Cat # 20034197). Subsequently, DNA was PCR amplified utilizing NPM and the indexing primers from the Nextera XT DNA Library Prep kit (Illumina Cat # FC-131-1024). The PCR products were purified and size selected by 0.5X SPRI beads followed by 0.7X SPRI beads.

value: iPSC-derived cardiomyocyte

tag: method

value: HiChIP

tag: factor

tag: condition

value: Transfected with HAND1 overexpressing adenovirus


title: Ventral spinal cord, C3-C6, castrated male, Rat 5


title: s0090_mouse1_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well90

value: cancer cells


title: Ventral spinal cord, C3-C6, intact female, Rat 3


title: hCM-Ctrl_HiChIP

value: Transfected with control adenovirus


title: Ventral spinal cord, C3-C6, castrated male, Rat 4


title: s0089_mouse1_MDAMB231_Tumor_0cells

description:
Fluidigm C1 platform
well89


title: s0092_mouse1_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well92


title: MMI

city: Shanghai

first: Siyi

last: Shen

address: 320 Yueyang Road

country: China

institute: Shanghai Institution of Nutrition and Health, Chinese Academy of Sciences

data_processing:
The Cell Ranger Single Cell Software Suite v.3.0 was used to de-multiplex individual cells, process UMIs, and count UMIs per gene, following standard pipeline.
Genome_build: mm10
Supplementary_files_format_and_content: CellRanger Outputs including matrix.mtx, features.tsv and barcodes.tsv

source_name: MMI, iBAT, APCs

extract_protocol:
Cells of iBAT were isolated from MMI group and T3 group and sorted by FACS to obtain APCs (CD45-CD31-Sca1+ cells). Live cells were resuspended in 0.04% BSA and counted using the automated cell counter (Countess).
Single cell gel beads in emulsion (GEMs) generation, barcoding, post GEM-RT cleanup, cDNA amplification, and cDNA library construction were performed using Single Cell 3′ v3 chemistry (10X Genomics), according to manufacturer’s protocol. The libraries were sequenced on an Illumina HiSeq X Ten platform (Illumina).

treatment_protocol: Male C57BL/6 mice aged about 8 weeks were rendered hypothyroid by the addition of 0.1% methimazole (Sigma) and 1% NaClO4 (Sigma) in their drinking water for 25 days (MMI group). Some mice from MMI group were injected ip with T3 at 0.5X the standard dose (0.25 μg per gram body weight per day) for 4 days on day 21 of MMI/NaClO4 treatment (T3 group).

tag: strain

value: APCs of iBAT

value: MMI


title: NF-9_RNA

data_processing:
Illumina Casava1.7 software used for basecalling.
The reads were mapped to hg19 using STAR. The reads mapped to gene exon regions were counted using featureCounts. Differential expression was determined using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: hic forrmat for visualization in Juicebox
Supplementary_files_format_and_content: bigwig format for visualization in IGV or washU Genome Browser

source_name: heart tissue

extract_protocol: RNA-seq: Total RNA was extracted using Trizol (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions. Approximately 1 µg total RNA per sample was depleted from rRNA with the Ribo-Zero™ Magnetic Kit (Epicentre). The retrieved RNA was subjected to fragmentation by adding the First Strand Master Mix (Invitrogen). First-strand cDNA was generated using random primers and reverse transcription, followed by a second-strand cDNA synthesis. The synthesized cDNA was subjected to end-repair and was 3’ adenylated. The adapters were ligated to the ends of these 3’ adenylated cDNA fragments. A total of 10 rounds of PCR with PCR Primer Cocktail and PCR Master Mix were performed to amplify the cDNA fragments. The PCR products were purified and size selected by 0.5X SPRI beads followed by 0.9X SPRI beads. The identity of the final library was verified by the distribution of the fragments size using the Agilent 2100 bioanalyzer and quantified by the Qubit High sensitivity assay. The Qualified libraries were sequenced pair end on the Illumina HiSeq Xten (150 bp, pair-end).

value: heart

value: RNA-Seq

value: non-failing


title: Ventral spinal cord, C3-C6, castrated male, Rat 2


title: s0088_mouse1a_MDAMB231_Tumor_0cells

description:
Fluidigm C1 platform
well88

extract_protocol:
Primary tumors and lung metastases were mechanically and enzymatically digested with a collagenase/hyaluronidase solution (Stem Cell Technologies, 07912). Human cancer cells were recovered by FACS sorting, based CD298 or GFP expression.
Single cell isolation was performed on the Fluidigm C1 platform according to  manufacturer protocol. mRNA was isolated with the Takara SMART-Seq Ultra Low RNA kit (Takara Bio; 634833) . Libraries for Illumina sequencing were prepared with the Nextera XT DNA Library Preparation Kit (Illumina; FC-131-1096).


title: NF-6_RNA


title: Ventral spinal cord, C3-C6, intact male, Rat 6


title: NF-8_RNA


title: tMCAO_3

first: Xiangna

last: Guo

state: Guangdong

address: South Shatai Road, Baiyun District

institute: Southern Medical University

data_processing:
Cutadapt software (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9) was used to remove the reads that contained adaptor contamination,(command line: ~cutadapt -a ADAPT1 -A ADAPT2 -o out1.fastq -p out2.fastq in1.fastq in2.fastq -O 5 -m 100).
And After removed the low quality bases and undetermined bases ,we used HISAT2 software (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) to map reads to the genome (for example:Homo sapiens Ensembl v96),(command line: ~hisat2 -1 R1.fastq.gz -2 R1.fastq.gz -S sample_mapped.sam).
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d.Linux_x86_64) with default parameters (command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam). Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare
software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8.Linux_x86_64). After the final transcriptome was generated, StringTie and ballgown(http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]),(command line: ~stringtie -e -B -p 4 -G merged.gtf -o samples.gtf samples.bam).
The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and p value < 0.05 by R package edgeR(https://bioconductor.org/packages/release/bioc/html/edgeR.html) or DESeq2(http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html),and then analysis GO enrichment and KEGG enrichment to the differentially expressed mRNAs.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: hemisphere

growth_protocol: Male C57BL/6 mice (8–10 weeks old, 22–25 g) were kept in a temperature-controlled animal facility under normal light/dark cycle with free access to food and water. All animals adapted to the environment for 7 days before experiments.

extract_protocol:
The total RNA from the ischemic hemisphere or cells was isolated with the TRIzol Reagent according to the manufacturer’s instructions. A total of 5 µg RNA from ischemic hemisphere was utilized for each RNA sample.
Firstly, ribosomal RNA (rRNA) was depleted by Ribo-Zero Gold rRNA Removal Kit (Illumina, USA). Secondly, the left RNAs were fragmented into short fragments using divalent cations (NEBNext® Magnesium RNA Fragmentation Module, NEB, USA) under high temperature. The complementary DNA (cDNA) was synthesized and purified. Finally, the average insert size for the final cDNA library was 300 ± 50 bp. 2×150 bp paired-end sequencing was performed on Illumina Novaseq™6000 (LC-Bio Technology Co. Ltd., China) according to the recommended protocol.

treatment_protocol: To induce cerebral I/R injury, a transient middle cerebral artery occlusion (tMCAO) model was performed on the mice as previously described.Briefly, mice were anesthetized with sevoflurane (5% for induction and 2%–3% for maintenance). Following a midline cervical incision, the right common carotid artery (CCA), external carotid artery (ECA), and internal carotid artery (ICA) were carefully exposed under an operating microscope. Thereafter, a silicone rubber-coated nylon monofilament  was inserted into the ECA, and advanced to occlude the middle cerebral artery for 90 min. After 90 min occlusion, the monofilament was gently pulled out for reperfusion and the incision was sutured. Mice in sham group adopted a same surgery except the middle cerebral artery occlusion.Mice in cela group injected celastrol at the concentration of 4.5 mg/kg intraperitoneally at the onset of reperfusion.

value: hemisphere

tag: age

value: 8-10 weeks old

tag: Sex

value: Male

tag: mouse strain

value: tMCAO (transient middle cerebral artery occlusion) surgery


title: Ventral spinal cord, C3-C6, intact male, Rat 5

tag: tissue

value: ventral cervical spinal cord, C3-C6

value: intact


title: NF-7_RNA


title: Ventral spinal cord, C3-C6, castrated male, Rat 1

value: Testes removed


title: tMCAO_1


title: s0086_mouse1_MDAMB231_Tumor_0cells

description:
Fluidigm C1 platform
well86

data_processing:
Reads were aligned to human genom with STAR. Following observation under the microscope, wells containing more than 1 cell or debris were marked and removed from further analyses.
Following observation under the microscope, wells containing more than 1 cell or debris were marked and removed from further analyses.
Cell cycle of individual cells were inferred using sets of known cell cycle-regulated genes known to peak in transcription at given cell cycle stages obtained from (PMID: 12058064, PMID:11416145)
The cell cycle and library complexity (percentage of detected genes) were modeled as covariates and regressed out of the log-normalized counts using glm.fit (R package glm).
Differential gene expression between single cell clusters was performed using pairwise t-test implemented in FindMarkers function from R package scran.
Gene set enrichment was performed with bioconductor packages fgsea and msigdb
Assembly: hg38
Supplementary files format and content: counts_raw.csv is a matrix containing raw counts after alignment. counts_afterQC are counts for the cells passing QC. Cccorected_logcounts.csv contains logcounts  of the cells that passed QC after the cell-cycle correction. metadata.csv contains addition information on the column names of counts_raw.csv  and CCcorected_logcounts.csv.

value: Tumor

tag: cell line

tag: cell type


title: s0085_mouse1_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well85


title: tMCAO_2


title: T3

source_name: MMI+T3, iBAT, APCs

value: wild type


title: Sham_3

value: a same surgery except the middle cerebral artery occlusion


title: s0084_mouse1_MDAMB231_Tumor_0cells

description:
Fluidigm C1 platform
well84

value: cancer cells


title: Ventral spinal cord, C3-C6, intact male, Rat 3


title: NF-51_RNA


title: NF-50_RNA


title: Sham_2


title: s0087_mouse1_MDAMB231_Tumor_0cells

description:
Fluidigm C1 platform
well87


title: Sham_1


title: Ventral spinal cord, C3-C6, intact male, Rat 2


title: s0083_mouse1a_MDAMB231_Tumor_0cells

description:
Fluidigm C1 platform
well83


title: NF-5_RNA


title: Ventral spinal cord, C3-C6, intact male, Rat 1


title: Cela_3

value: celastrol treatmnt after tMCAO(transient middle cerebral artery occlusion) surgery


title: NF-49_RNA


title: s0082_mouse1_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well82


title: s0081_mouse1_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well81


title: Cela_2


title: NF-48_RNA


title: s0080_mouse1a_MDAMB231_Tumor_0cells

description:
Fluidigm C1 platform
well80


title: NF-47_RNA


title: s0079_mouse1_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well79


title: Cela_1


title: s0078_mouse1_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well78


title: NF-46_RNA


title: NF-45_RNA


title: s0077_mouse1_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well77


title: IL-15 expanded CD8+ T cells_1

city: Charlottesville

first: Pankaj

last: Kumar

state: VA

address: JPA, 1312A Pinn Hall

department: Bioinformatics Core

institute: University of Virginia

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and mapped to mm10 whole genome and transcriptome using STAR aligner. Count for each gene was generated using Htseq count.
Assembly: mm10
Supplementary files format and content: raw count

source_name: CD8+ Tcells

growth_protocol: CD8+ T cells were grwin in 24 well plate with 0.5 million cells/ well in RPMI-1640 complete media

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were expanded in respective cytokines throughout the entire length experiemnt

value: isolated from spleen

value: CD8+ Tcells

value: expanded for 14 days


title: IL-15 expanded CD8+ T cells_2


title: IL-2 expanded CD8+ T cells_4


title: IL-2 expanded CD8+ T cells_3


title: IL-15 expanded CD8+ T cells_3


title: IL-15 expanded CD8+ T cells_4


title: NF-44_RNA

value: heart

value: RNA-Seq


title: NF-43_RNA

value: non-failing


title: IL-2 expanded CD8+ T cells_2