title: Sample 28_TH2

city: Yokohama

first: Kosuke

last: Miyauchi

state: Kanagawa

address: 1-7-22 Suehiro-sho

institute: RIKEN Center for Integrative Medical Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sample1-8; Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole mouse genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Sample9-30; Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole mouse genome using STAR 2.7.0c (command --runThreadN 60 --outSAMtype BAM SortedByCoordinate) Genome: mm10 GRCm38.p6 ENSEMBL GTF: GRCm38.97 ENSEMBL
Sample1-8; featurecounts v1.6.0 (command: -M -O -t exon -g gene_id -a) GTF: mm9 ENSEMBL release 67
Sample9-30; featurecounts v1.6.0 (command: -M -O -t exon -g gene_id -a) GTF: GRCm38.97 ENSEMBL
Genome_build: mm9 and mm10
Supplementary_files_format_and_content: tab-delimited text files include read counts for genes

extract_protocol:
Spleen were removed, stained TH cells were sorted using flow cytometer, and RNA was harvested using Trizol reagent. NEB Next Ultra RNA Library Prep Kit (Cat#E7530) for Sample1-8 or Lexogen 3'mRNA-seq library prep kit (Cat#015) for Sample9-30 was used with 10 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard NEB Ultra protocols or Lexogen 3'QuantSeq protocols
Sample1-Sample8, RNA-Seq; Sample9-Sample30, 3'QuantSeq

tag: strain background

tag: genotype/variation

value: OTII Tg IL-4BacTg x OTII Tg

tag: age

value: 8 weeks

value: spleen


title: Sample 30_Il4-/-

status: Public on Sep 26 2019

type: SRA

country: Japan

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

value: Il4-/- x OTII Tg

tag: tissue

tag: cell type


title: Sample 26_Bcl6KO

value: Bcl6f/fCd4cre x OTII Tg


title: Sample 25_TH2


title: Sample 27_Il4-/-


title: Sample 29_Bcl6KO


title: P115_B14 (scRNAseq)

city: Melbourne

first: Shian

last: Su

state: Victoria

address: 1G Royal Parade

department: Molecular Medicine

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
CelSeq2 RNA sequencing reads were mapped to the GRCm38 mouse genome and GRCh38 human genome using the Subread aligner and assigned to genes using scPipe with ENSEMBL v86 annotation. Gene counts were exported as a matrix by scPipe with UMI-aware counting and imported into R.
For 100 cell bulk samples, cells were removed from further analysis if they failed to achieve 5000 total counts. In single cell samples, cells were removed using the detect_outlier function from the scPipe. In 100 cell bulk samples, genes were filtered out if they failed to achieve 5 counts per million in 3 samples and in single cells genes were required to be expressed in at least 5 samples and an average of 2 or more counts in those samples.
Genome_build: GRCh38 and GRCm38
Supplementary_files_format_and_content: comma-separated files containing gene counts accounting for unique moleculat identifiers

molecule: polyA RNA

source_name: thymus

extract_protocol:
Single cell suspensions from mouse and human thymus were obtained by mechanically grinding the organs through a 70mm sieve. Single cell suspensions of mouse thymus were  stained with PE-mouse MR1-5-OP-RU tetramers prior to magnetic bead enrichment using anti-PE microbeads as per manufacturer’s instructions (Miltenyi Biotec). Single cell suspensions of human thymus were enriched for TRAV1.2+ cells by staining for TRAV1.2-PE antibody, followed by magnetic bead enrichment using anti-PE microbeads (Miltenyi Biotec). Human blood cell suspensions were obtained through Ficoll gradient separation. After staining with a panel of flow cytometry surface markers, cells were sorted into a chilled 384-well PCR plate (Greiner #785290) containing 1.2μl of primer/lysis mix.
RNA libraries were prepared and described fully in the methods section of the manuscript..

tag: sample index

value: CCGATATG

tag: plate number

tag: well position

tag: donor id

value: CD319+ Thymus Maits

tag: cell number


title: Sample 24_TFH

source_name: TFH

value: OTII Tg

value: CD4+CD45.2+CXCR5lo PD1+


title: P115_C11 (scRNAseq)

value: TCAGTGCA


title: Sample 23_TFH

value: CD4+CD45.2+CXCR5int PD1+


title: P115_B13 (scRNAseq)

value: TATCCAGG


title: P115_B11 (scRNAseq)

value: CAACGTAC


title: P115_B1 (scRNAseq)

value: GACTACTG


title: Sample 22_TFH

value: CD4+CD45.2+CXCR5hi PD1+


title: P115_B10 (scRNAseq)

value: GCACGTAT


title: Sample 21_TFH


title: Sample 20_TFH


title: Sample 19_TFH


title: P115_A7 (scRNAseq)

value: TCCAGTAG


title: P115_A9 (scRNAseq)

value: GATGCGTT


title: P115_B24 (scRNAseq)

value: CGCATGTA


title: P115_A5 (scRNAseq)

value: TAGTGCGT


title: P115_A4 (scRNAseq)

value: GTCCGAAT


title: Sample 16_TFH2

value: OTII Tg IL-4BacTg x OTII Tg

value: 8 weeks

value: spleen


title: P115_A3 (scRNAseq)

value: GGTCTATG

value: CD319+ Thymus Maits


title: Sample 15_TFH2


title: P115_A19 (scRNAseq)

value: CAACGCTA


title: P115_A21 (scRNAseq)

value: TAGGTCAC


title: Sample 12_TFH2

value: CD4+CD45.2+CXCR5int PD1+


title: Sample 17_TFH

value: OTII Tg


title: Sample 13_TFH2

value: CD4+CD45.2+CXCR5lo PD1+


title: P115_A16 (scRNAseq)

value: AGCTCTGA


title: Sample 14_TFH2

value: CD4+CD45.2+CXCR5hi PD1+


title: Sample 10_TH2


title: P115_A20 (scRNAseq)

value: GCATAGTC


title: Sample 9_TH2


title: P115_A15 (scRNAseq)

value: ACTTGTGG


title: Sample 8_TFH2

value: wild type IL-4BacTg x OTII Tg


title: P115_A12 (scRNAseq)

value: CTCCAAGA


title: Sample 18_TFH


title: Sample 6_TFH

value: wild type OTII Tg


title: P115_A10 (scRNAseq)

value: CCGTTAAG


title: Sample 4_Naïve CD4T

source_name: Naïve CD4T

value: wild type

value: 8 weeks


title: P115_A13 (scRNAseq)

value: CTGCGTAA


title: Sample 3_TFH

value: spleen


title: P115_A18 (scRNAseq)

value: CCTATGAG

value: CD319+ Thymus Maits


title: Sample 11_TFH2

value: OTII Tg IL-4BacTg x OTII Tg


title: Sample 2_TH2

value: wild type IL-4BacTg


title: N2 Spleen MAIT (bulk RNAseq)

data_processing:
CelSeq2 RNA sequencing reads were mapped to the GRCm38 mouse genome and GRCh38 human genome using the Subread aligner and assigned to genes using scPipe with ENSEMBL v86 annotation. Gene counts were exported as a matrix by scPipe with UMI-aware counting and imported into R.
Cells were removed from further analysis if they failed to achieve 5000 total counts. Genes were filtered out if they failed to achieve 5 counts per million in 3 samples and in single cells genes were required to be expressed in at least 5 samples and an average of 2 or more counts in those samples.
Genome_build: GRCh38 and GRCm38
Supplementary_files_format_and_content: comma-separated files containing gene counts accounting for unique moleculat identifiers

source_name: spleen

extract_protocol:
Single cell suspensions from mouse thymus, mouse spleen and human thymus were obtained by mechanically grinding the organs through a 70mm sieve. Single cell suspensions of mouse thymus were  stained with PE-mouse MR1-5-OP-RU tetramers prior to magnetic bead enrichment using anti-PE microbeads as per manufacturer’s instructions (Miltenyi Biotec). Single cell suspensions of human thymus were enriched for TRAV1.2+ cells by staining for TRAV1.2-PE antibody, followed by magnetic bead enrichment using anti-PE microbeads (Miltenyi Biotec). Human blood cell suspensions were obtained through Ficoll gradient separation. After staining with a panel of flow cytometry surface markers, cells were sorted into a chilled 384-well PCR plate (Greiner #785290) containing 1.2μl of primer/lysis mix.
RNA libraries were prepared and described fully in the methods section of the manuscript..

value: GTTACCGA

tag: strain

value: Spleen CD44+ MAIT cells

tag: umi position

value: 1 to 6 in R1

tag: index position

value: 7 to 14 in R1


title: N1 Spleen MAIT (bulk RNAseq)

value: GCGCTTAA


title: N3 Spleen MAIT (bulk RNAseq)

value: GGACTTGT


title: Sample 1_Naïve CD4T


title: M6 Thymus MAIT S3 (bulk RNAseq)

value: ATGTCCAG

value: Thymus stage 3 MAIT cells


title: M5 Thymus MAIT S3 (bulk RNAseq)

value: GGTATCGT


title: P115_A14 (scRNAseq)

value: GTCCAACA


title: M2 Thymus MAIT S1 (bulk RNAseq)

value: GGTACACT

value: Thymus stage 1 MAIT cells


title: M3 Thymus MAIT S1 (bulk RNAseq)

value: TCAAGCAC


title: M1 Thymus MAIT S1 (bulk RNAseq)

value: GTCATGCA


title: Sample 7_TH2

value: wild type IL-4BacTg x OTII Tg

value: 8 weeks

value: spleen


title: Sample 5_TH2

value: wild type IL-4BacTg


title: Cerebellum, Input_MEF2_H3K27ac_Ctrl (ChIP-seq)

city: st. louis

first: Naveen

last: Reddy

state: MO

address: 660 S Euclid Ave

country: USA

institute: Washington University In St. Louis

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie2 v2.3.4.2
Data were filtered using a map quality score of >10
Peaks were called using MACS2 on concatenated datasets. Mfold = (2,50); Bandwidth = 200; q-value 0.05
RNA-seq reads were aligned to mm10 genome assembly using RNA STAR 2.6
Genome_build: mm10
Supplementary_files_format_and_content: Text or excel workbooks containing raw read counts or CPM, histone enrichment, or fold change

molecule: genomic DNA

source_name: Cerebellum

growth_protocol: Brain tissue was taken from MEF2 conditional knockout and control mice maintained under standard housing conditions.

extract_protocol:
RNA was extracted from the cerebella of P22 mice using Trizol (Invitrogen) according to the manufacturer’s instructions. ChIP lysates clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions.

tag: genotype

value: MEF2AD Control

tag: Sex

value: Female

tag: chip antibody

value: H3K27ac (Abcam ab4729)

value: Cerebellum


title: P115_A11 (scRNAseq)

value: CAAGCCAT

value: CD319+ Thymus Maits


title: Cerebellum, MEF2AD_H3K27ac_cKO3 (ChIP-seq)

value: MEF2AD Conditional Knockout


title: Cerebellum, Input_MEF2_H3K27ac_cKO (ChIP-seq)


title: Cerebellum, MEF2AD_H3K27ac_cKO2 (ChIP-seq)


title: M4 Thymus MAIT S3 (bulk RNAseq)

value: GCAAGTTC

value: Thymus stage 3 MAIT cells

value: 1 to 6 in R1

value: 7 to 14 in R1


title: Cerebellum, MEF2AD_H3K27ac_Ctrl3 (ChIP-seq)


title: Cerebellum, MEF2AD_H3K27ac_Ctrl2 (ChIP-seq)


title: Cerebellum, MEF2AD_H3K27ac_cKO1 (ChIP-seq)


title: Cerebellum, MEF2D_H3K27ac_cKO3 (ChIP-seq)

value: MEF2D Conditional Knockout


title: EpiDerm FT (RHE), AZ, replicate 1

type: RNA

city: Ann Arbor

first: William

middle: R

last: Swindell

state: MI

address: 1500 E. Medical Center Drive

department: Dermatology

institute: University of Michigan

description:
Gene expression data from AZ-treated RHE cultures.
AZ_1

hyb_protocol: Arrays were hybridized using the Agilent Hybridization oven (Agilent Technology, USA). Hybridized microarrays were washed and processed following the manufacturer’s protocol (Agilent Technology, USA).

scan_protocol: Hybridizations were processed using Agilent’s microarray scanner and quantified using Agilent's Feature Extraction Software (Agilent Technology, Palo Alto, CA).

data_processing: Raw expression intensities were background corrected using the normal-exponential convolution model (R package: limma; function: backgroundCorrect) and subsequently standardized using quantile normalization (R package: limma; function: normalizeBetweenArrays).

organism: Homo sapiens

source_name: RHE tissue culture

label_protocol: 0.6 μg Cy3-labeled RNA was prepared following the Agilent protocol.

growth_protocol: EpiDerm FT (RHE) tissues prepared from neonatal keratinocytes and fibroblasts were obtained from Mattek (Ashland, MA; Cat. No. EFT-412; Lot No. 21452). EpiDerm FT tissues were handled according to the manufacturer’s instructions.

extract_protocol: RNA was then extracted and purified with NucleoSpin RNA II kit from Machery-Nagel (Bethleem, PA).

treatment_protocol: AZ was solubilized in DMSO at 20 mg/mL, diluted in water to 50 μg/mL and added on top of EpiDerm skin substitutes in duplicates for 24 hours (25 µL per sample). The solvent was the control (CTL). Tissues were equilibrated for 5 hours before test material incubation. At the end of the 24 hour incubation, tissues were observed through the Nikon Eclipse TS100 inverted microscope. No gross morphological changes were recorded.

tag: treatment

value: AZ

tag: tissue culture

value: EpiDerm FT (RHE)


title: EpiDerm FT (RHE), AZ, replicate 2

description:
Gene expression data from AZ-treated RHE cultures.
AZ_2


title: EpiDerm FT (RHE), CTL, replicate 2

description:
Gene expression data from CTL-treated RHE cultures.
CTL_2

value: CTL


title: Cerebellum, MEF2D_H3K27ac_cKO1 (ChIP-seq)


title: Cerebellum, MEF2D_H3K27ac_Ctrl3 (ChIP-seq)

value: MEF2D Control


title: Ler 4 DAG, bio rep3

city: Albany

first: Jennifer

middle: C

last: Fletcher

state: CA

address: 800 Buchanan Street

institute: Plant Gene Expression Center

description: Gene expression data from Ler 4 days after germination seedlings apices, biological replicate 3.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the GeneChip Arabidopsis ATH1 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

organism: Arabidopsis thaliana

source_name: Ler seedling apices

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Wild-type and mutant plants in Landsberg erecta background were grown in soil in constant light, 21C temperature conditions in a Percival growth chamber and watered daily with a dilute mixture of Miracle Grow 20-20-20 fertilizer.

extract_protocol: TRIzol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Shoot apices from Ler and ult1-3 4 day after germination (DAG) vegetative seedlings and from Ler, ult1-3, 35S:ULT1, and clf-2 mature reproductive plants at 1 cm bolt were collected and flash frozen on dry ice before storage at -80C.

value: Landsberg erecta


title: ult1 4 DAG, bio rep3

description: Gene expression data from ult1-3 4 days after germination seedlings apices, biological replicate 3.

source_name: ult1-3 seedling apices


title: Cerebellum, MEF2D_H3K27ac_Ctrl2 (ChIP-seq)


title: clf IFM, bio rep2

description: Gene expression data from clf-2 reproductive (inflorescence) apices, biological replicate 2.

source_name: clf-2 inflorescence apices

value: curly leaf-2


title: 35SU1 IFM, bio rep2

description: Gene expression data from 35S:ULT1 reproductive (inflorescence) apices, biological replicate 2.

source_name: 35S:ULT1 inflorescence apices

value: 35S:ULTRAPETALA1 Ler


title: EpiDerm FT (RHE), CTL, replicate 1

description:
Gene expression data from CTL-treated RHE cultures.
CTL_1


title: ult1 4 DAG, bio rep2

description: Gene expression data from ult1-3 4 days after germination seedlings apices, biological replicate 2.


title: ult1 IFM, bio rep2

description: Gene expression data from ult1-3 reproductive (inflorescence) apices, biological replicate 2.

source_name: ult1-3 inflorescence apices


title: Cerebellum, MEF2AD_H3K27ac_Ctrl1 (ChIP-seq)

value: MEF2AD Control

value: Female

value: H3K27ac (Abcam ab4729)


title: Cerebellum, MEF2D_H3K27ac_Ctrl1 (ChIP-seq)

value: Cerebellum


title: Cerebellum, MEF2A_H3K27ac_cKO3 (ChIP-seq)

value: MEF2A Conditional Knockout


title: Cerebellum, MEF2D_H3K27ac_cKO2 (ChIP-seq)


title: clf IFM, bio rep3

description: Gene expression data from clf-2 reproductive (inflorescence) apices, biological replicate 3.


title: 35SU1 IFM, bio rep3

description: Gene expression data from 35S:ULT1 reproductive (inflorescence) apices, biological replicate 3.


title: Ler IFM, bio rep3

description: Gene expression data from Ler reproductive (inflorescence) apices, biological replicate 3.

source_name: Ler inflorescence apices


title: Cerebellum, MEF2A_H3K27ac_cKO2 (ChIP-seq)


title: ult1 IFM, bio rep3

description: Gene expression data from ult1-3 reproductive (inflorescence) apices, biological replicate 3.


title: Cerebellum, MEF2A_H3K27ac_Ctrl3 (ChIP-seq)

value: MEF2A Control


title: Cerebellum, MEF2A_H3K27ac_cKO1 (ChIP-seq)


title: Ler IFM, bio rep2

description: Gene expression data from Ler reproductive (inflorescence) apices, biological replicate 2.


title: 35SU1 IFM, bio rep1

description: Gene expression data from 35S:ULT1 reproductive (inflorescence) apices, biological replicate 1.


title: Ler 4 DAG, bio rep2

description: Gene expression data from Ler 4 days after germination seedlings apices, biological replicate 2.


title: Ler 4 DAG, bio rep1

description: Gene expression data from Ler 4 days after germination seedlings apices, biological replicate 1.


title: ult1 4 DAG, bio rep1

description: Gene expression data from ult1-3 4 days after germination seedlings apices, biological replicate 1.


title: Cerebellum, MEF2A_H3K27ac_Ctrl2 (ChIP-seq)


title: clf IFM, bio rep1

description: Gene expression data from clf-2 reproductive (inflorescence) apices, biological replicate 1.


title: ult1 IFM, bio rep1

description: Gene expression data from ult1-3 reproductive (inflorescence) apices, biological replicate 1.


title: Ler IFM, bio rep1

description: Gene expression data from Ler reproductive (inflorescence) apices, biological replicate 1.


title: Cerebellum, Input_DCtrl (ChIP-seq)

value: None (Input)


title: Cerebellum, Input_AcKO (ChIP-seq)


title: Cerebellum, Input_ACtrl (ChIP-seq)


title: Cerebellum, D_DcKO (ChIP-seq)

value: MEF2D (Greenberg Lab)


title: Cerebellum, A_AcKO_M (ChIP-seq)

value: Male

value: MEF2A (Santa Cruz, C-21)


title: Cerebellum, A_AcKO_F (ChIP-seq)


title: Cerebellum, D_AcKO2 (ChIP-seq)


title: Cerebellum, MEF2A_H3K27ac_Ctrl1 (ChIP-seq)


title: Cerebellum, Input_DcKO (ChIP-seq)

value: MEF2D Conditional Knockout


title: Cerebellum, D_AcKO1 (ChIP-seq)


title: Cerebellum, D_Ctrl2 (ChIP-seq)


title: Cerebellum, D_Ctrl3 (ChIP-seq)


title: Cerebellum, D_Ctrl1 (ChIP-seq)


title: Cerebellum, A_DcKO4 (ChIP-seq)


title: Cerebellum, A_DcKO3 (ChIP-seq)


title: Cerebellum, D_AcKO3 (ChIP-seq)


title: Cerebellum, A_DcKO2 (ChIP-seq)


title: Cerebellum, A_Ctrl4 (ChIP-seq)


title: Cerebellum, A_DcKO1 (ChIP-seq)


title: Cerebellum, A_Ctrl3 (ChIP-seq)


title: T. ruminis_replicate 3, technical replicate

city: Woking

first: Kerry

middle: Louise

last: Newbrook

state: Surrey

address: Ash Road, Pirbright, Woking

department: Orbivirus Research

country: United Kingdom

institute: The Pirbright Institute

description:
processed data files:
SDE genes for all treatment groups
SDE genes summary for all treatment groups

data_processing:
FastQ sequence files were trimmed to exclude reads matching Illumina adaptor sequences of ≥3 bp at the 3’ end using option –O 3 in Cutadapt V1.2.1 (Martin, 2011). Sickle V1.200 (https://github.com/najoshi/sickle) was used to trim poor quality reads (minimum window quality score of 20) and those below 10 bp.
Trimmed reads were mapped to the Bos Taurus genome (UMD 3.1.1/bosTau8; GenBank Assembly Accession Number GCA_000003055.5) using TopHat2. Default mapping parameters were used, allowing up to two read mismatches, 160 bp ± 60 bp mean inner distance between mate pairs and a maximum one read alignment to genome.
Mapped reads were assembled into transcripts using Cufflinks.
A master transcriptome generated by Cuffmerge, using the annotated Bos Taurus genome (UMD 3.1.1/bosTau8) as a reference.
Differential gene expression profiles (mean FPKM gene expression) of each challenge vs control (media) group were generated using Cuffdiff. Mapped read (BAM) files for all replicates of challenge vs control groups were compared using the master transcriptome assembly. Default parameters were used; geometric library normalisation, pooled dispersion estimation, multi-read correct, bias correction and a false discovery rate (FDR) of 0.05. Differentially expressed genes with an adjusted p (q or FDR) value ≤ 0.05 were considered statistically significant, with a further log2 fold change cut-off (≥ 1 and ≤ -1) used to define biological significance; these criteria were used as a cut-off for SDE in all downstream analyses.
Genome_build: Bos Taurus genome (UMD 3.1.1/bosTau8; GenBank Assembly Accession Number GCA_000003055.5)
Supplementary_files_format_and_content: Microsoft Excel worksheet include RPKM values for each treatment pairing (LPS, T19, T320A, T3552B, Ru1), including some or all of the following; gene, gene locus, log2 (fold change), p value and q value.

organism: Bos taurus

source_name: Primary foot skin fibroblast cells

growth_protocol: Primary bovine dermal fibroblast cells were isolated from visibly healthy bovine foot skin tissue, as described previously (Evans et al 2014). Isolated cells were pelleted by centrifugation and seeded into tissue culture flasks at a density of 2x10^4 viable cells per ml growth media. Growth media was William's medium E supplemented with 100ug/ml neomycin, 50ug/ml gentamycin, 20%(v/v) foetal bovine serum (FBS), 2mM L-glutamine, 2.5ug/ml Fungizone antimycotic and 10ng/ml human recombinant epidermal growth factor. Cultures were maintained to 80% confluence prior to initial subculture within a humidified incubator (37 degrees, 5% CO2), with media replaced every 48 hours. T. medium phylogroup strain T19, T. phagedenis phylogroup strain T320A, T. pedis strain T3552B and T. ruminis strain Ru1 were all isolated and maintained as previous described (Evans et al. 2011; Evans et al. 2008). Stock cultures were initially thawed at room temperature and 10 to 15 drops of aspirated culture inoculated into 7 ml oral treponeme enrichment broth (OTEB) for resuscitation. T. medium cultures were additionally supplemented with 10% (v/v) rabbit serum and T. phagedenis and T. pedis cultures supplemented with 10% (v/v) FBS. Cultures were maintained within an anaerobic cabinet (36°C, 85% nitrogen, 10% hydrogen, 5% CO2) to late exponential growth phase prior to re-inoculation, after typically seven days (T. medium), five days (T. phagedenis), four days (T. pedis) and one day (T. ruminis) respectively. Either 300 µl T. medium, 120 µl T. phagedenis, 90 µl T. pedis or 450 µl T. rumunis aspirated cultures were inoculated into respective pre-warmed growth media, cultures were inverted five times to allow adequate mixing and then lids untightened to allow gaseous exchange with the anaerobic environment. Cultures were sonicated at late exponential growth phase (on ice; four minute continuous cycle of 10 sec sonication and resting) and diluted to 10ug/ml using control media (WME + 2mM L-glutamine).

extract_protocol:
Total RNA was extracted from cell pellets using an RNeasy® Plus Mini Kit (Qiagen) according to manufacturer instructions. Prior to elution, an extra 15 minute air-drying step was incorporated to prevent contamination of the spin column membrane. Total RNA was quantified using a Qubit® RNA Broad-Range Assay Kit and Qubit® 2.0 Fluorometer, according to manufacturer instructions. RNA integrity was assessed with a Eukaryote Total RNA 6000 Nano Electophoretic Assay and 2100 Bioanalyser (Agilent Technologies Inc), according to manufacturer instructions. RNA purity was measured by A260:A280 and A260:A230 ratios using a NanoDrop™ ND-2000 spectrophotometer, according to manufacturer instructions.
Total RNA preparations were submitted for RNA-Seq at the Centre for Genomic Research (University of Liverpool, UK). Total RNA (1000 ng) was depleted of rRNA using a Ribo-Zero™ Gold rRNA removal (human/mouse/rat) kit (Illumina®), as per manufacturer instructions. RNA-Seq (cDNA) libraries were then prepared using a NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (New England Biolabs), according to manufacturer instructions, and purified using AMPure XP beads. Libraries were diluted (1:4) in 0.1x Tris EDTA buffer and quantified using a Qubit® dsDNA High Sensitivity Assay Kit and Qubit® 2.0 Fluorometer, according to manufacturer instructions. Size distribution was assessed using an Agilent High Sensitivity DNA Kit and 2100 Bioanalyser. Libraries were pooled in equimolar amounts (n=10, two pools) and quality re-assessed as above. Libraries were quantified by qPCR (LightCycler® LC48011) with a KAPA Library Quantification Kit (Illumina®), according to manufacturer instructions. PhiX Control V3 (Illumina®) was used as a positive internal control library. Denatured template cDNA was loaded onto the flow cell for clustering using a HiSeq® 3000/4000 Paired-End Cluster Kit with a cBot™ Cluster Generation System (Illumina®), according to manufacturer instructions. Libraries were sequenced on a HiSeq™4000 (Illumina®) using version 1 chemistry (sequencing by synthesis) to generate 2 x 150 bp paired-end reads.

treatment_protocol: Primary bovine foot skin fibroblasts (1x10^5) were seeded into 25cm3 tissue culture flasks and maintained to 80% confluence. Monolayers were washed with 1x hanks balanced salt solution (HBSS) and then co-incubated (3 ml) for six hours with control media, 10 µg/ml purified LPS from Salmonella enterica serotype Typhimurium (positive control stimulant) or 10 µg/ml treponeme sonicate (either T. medium phylogroup strain T19, T. phagedenis phylogroup strain T320A, T. pedis strain T3552B or T. ruminis strain Ru1) in a humidified incubator (5% CO2, 37°C). Each treatment was performed in triplicate experimental replicates. Treatments were subsequently removed by washing and monolayers harvested for RNA extraction. To harvest, monolayers were washed with 1x HBSS and then detached by incubation (37°C, 5 minutes) with 0.025% (w/v) trypsin-ethylenediaminetetraacetic acid (trypsin-EDTA). Following neutralisation with WME containing 10% (v/v) FBS, cells were pelleted by centrifugation (180 g, 22°C, 10 minutes) and again washed with 1x HBSS.

tag: passage

value: foot skin fibroblast cells


title: T. pedis_replicate 3


title: T. ruminis_replicate 3


title: T. ruminis_replicate 2


title: T. ruminis_replicate 1


title: Cerebellum, A_Ctrl1 (ChIP-seq)


title: T. pedis_replicate 2


title: Vehicle control [15]

city: Trondheim

first: Hanna Maja

last: Tunset

state: Trondelag

address: Olav Kyrres gate 9

department: Dept of Circulation and Medical Imaging

country: Norway

institute: NTNU

description: quasi.gene.quant.txt

data_processing:
Basecalls performed using bcl2fast version 2.17
Demultiplexed fastq reads were quasi aligned to the GRCh38 genome assembly using Salmon version 0.12
Aggregation of transcript to gene expression TPM (Transcript Per Million) was performed using tximport (http://bioconductor.org/packages/release/bioc/html/tximport.html) version 1.8
Gene expression values with TPM  below one in more than three samples were filtered out
Genome_build: GRCh38
Supplementary_files_format_and_content: TPM

source_name: Spontaneous mammary carcinoma

growth_protocol: Cells were seeded in 10 % FBS/DMEM until 80 % confluency.

extract_protocol:
Qiagen RNeasy spin column, standard protocol
RNA Seq libraries were prepared using TruSeq Stranded mRNA kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions. Briefly, 500 ng total RNA was used as starting material. First, index barcodes were ligated for identification of individual samples. mRNA was purified from the total RNA using poly-T oligo-attached magnetic beads, follows by random fragmentation using divalent cations at 94°C for 4 min. First and second strand cDNAs were synthesized using random oligonucleotides and SuperScript II, followed by DNA polymerase I and RNase H. Exonuclease/polymerase was used to produce blunted overhangs. Illumina SR adapter oligonucleotides were ligated to the cDNA after 3' end adenylation. DNA fragments were enriched by 15 cycles of PCR reaction. The libraries were purified using the AMPure XP (Beckman Coulter, Inc., Indianapolis, IN, USA), quantitated by qPCR using KAPA Library Quantification Kit (Kapa Biosystems, Inc., Wilmington, MA, USA) and validated using Agilent High Sensitivity DNA Kit on a Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The size range of the DNA fragments were measured to be in the range of app. 200-1000 bp and peaked around 310 bp.
Libraries were normalized and pooled to 2.6 pM and subjected to clustering on one NextSeq 500 high output flowcell. Single end read sequencing was performed for 84 cycles on a NextSeq 500 instrument (Illumina, Inc. San Diego, CA, USA), according to the manufacturer's instructions.

treatment_protocol: Treatments were carried out in fresh 10 %FBS/DMEM, incubation for 24 h.

value: BALB/c

tag: cell line

value: Spontaneous mammary carcinoma

tag: metastatic potential

value: Metastatic

value: Vehicle control


title: T. pedis_replicate 1

tag: cell type


title: T. phagedenis_replicate 1, technical replicate


title: T. phagedenis_replicate 3


title: 15 uM CIX [14]

description: quasi.gene.quant.txt

value: Non-metastatic

value: 15 uM CIX


title: Isomorphic diffuse glioma, sample 13

type: genomic

city: Regensburg

first: Annika

middle: K

last: Wefers

address: Franz-Josef-Strauß-Allee 11

department: Neuropathology

country: Germany

institute: Regensburg University Hospital

description: Methylation data from brain tumor sample

hyb_protocol: Illumina protocol

scan_protocol: Illumina iScan System according to the manufacturer's protocol

data_processing: Bioconductor (Version 3.3) package minifi (Version 1.18) using function 'preprocessIllumina'  Average beta

label: Cy3 and Cy5

source_name: brain tumor

label_protocol: Illumina protocol

extract_protocol: Illumina protocol

treatment_protocol: An automated extraction was done with a Maxwell system (Promega, Fitchburg, WI, USA) and the Maxwell 16 FFPE Plus LEV DNA Purification Kit according to the manufacturer’s instructions.

tag: material

value: FFPE


title: 15 uM CIX [12]

description: quasi.gene.quant.txt


title: 15 uM CIX [16]

description: quasi.gene.quant.txt


title: Vehicle control [11]

description: quasi.gene.quant.txt


title: Isomorphic diffuse glioma, sample 24


title: Isomorphic diffuse glioma, sample 26


title: T. phagedenis_replicate 1


title: T. medium_replicate 2


title: T. medium_replicate 3


title: 15 uM CIX [10]

description: quasi.gene.quant.txt


title: T. phagedenis_replicate 2


title: Isomorphic diffuse glioma, sample 7


title: Isomorphic diffuse glioma, sample 21


title: Vehicle control [9]

description: quasi.gene.quant.txt


title: T. medium_replicate 1


title: LPS control_replicate 3


title: 15 uM CIX [8]

description: quasi.gene.quant.txt


title: Vehicle control [13]

description: quasi.gene.quant.txt


title: LPS control_replicate 2


title: Isomorphic diffuse glioma, sample 14


title: Isomorphic diffuse glioma, sample 15


title: LPS control_replicate 1


title: Isomorphic diffuse glioma, sample 8


title: 15 uM CIX [6]

description: quasi.gene.quant.txt


title: Isomorphic diffuse glioma, sample 6


title: Media control_replicate 3


title: Media control_replicate 2


title: Vehicle control [5]

description: quasi.gene.quant.txt


title: 15 uM CIX [4]

description: quasi.gene.quant.txt


title: Media control_replicate 1


title: Vehicle control [3]

description: quasi.gene.quant.txt


title: Isomorphic diffuse glioma, sample 1


title: Isomorphic diffuse glioma, sample 20


title: Isomorphic diffuse glioma, sample 11


title: 15 uM CIX [2]

description: quasi.gene.quant.txt


title: Vehicle control [1]

description: quasi.gene.quant.txt


title: Isomorphic diffuse glioma, sample 23


title: Isomorphic diffuse glioma, sample 10


title: Isomorphic diffuse glioma, sample 9


title: RNA_GMP_STAG2WT_rep2

city: New York

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

description: RNA_GMP_STAG2WT_rep2_Rs-A16-ACAGAT_ACAGAT_AHFYYYBCXY_L001_001

data_processing:
RNA-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned to human genome assembly mm9 using STAR (v2.4) with default parameters.
Read count tables were created using HTSeq v0.6.1.
Normalization and differential expression analysis was performed with DESeq2.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file with un-normalized read counts over all genes.

growth_protocol: Whole BM was negatively selected for lineage markers using antibodies conjugated to magnetic beads and separated using EasySep Mouse Hematopoietic Progenitor Cell Isolation Kit (STEMCELL Technologies).

extract_protocol:
RNA was isolated by TRIzol extraction from sorted cell populations.
RNA-sequencing libraries were generated by 3' sequencing and SMART-Seq2 amplification for GMP and CFU-E populations and by SMARTer amplification of full transcripts for LSK cells.

value: sorted GMP

tag: genotype/variation


title: Isomorphic diffuse glioma, sample 17


title: RNA_GMP_STAG2WT_rep3

description: RNA_GMP_STAG2WT_rep3_Rs-A16-ACACGC_ACACGC_AHFYYYBCXY_L001_001


title: RNA_GMP_STAG2WT_rep1

description: RNA_GMP_STAG2WT_rep1_Rs-A16-GTCAGG_GTCAGG_AHFYYYBCXY_L001_001


title: RNA_GMP_STAG2KO_rep2

description: RNA_GMP_STAG2KO_rep2_Rs-A16-GTGTAG_GTGTAG_AHFYYYBCXY_L001_001


title: Isomorphic diffuse glioma, sample 4


title: RNA_GMP_STAG2KO_rep4

description: RNA_GMP_STAG2KO_rep4_Rs-A16-GATTGT_GATTGT_AHFYYYBCXY_L001_001


title: RNA_GMP_STAG2KO_rep1

description: RNA_GMP_STAG2KO_rep1_Rs-A16-TGTGCA_TGTGCA_AHFYYYBCXY_L001_001


title: Isomorphic diffuse glioma, sample 5


title: RNA_CFU-E_STAG2WT_rep2

description: RNA_CFU-E_STAG2WT_rep2_Rs-A16-ACGTCT_ACGTCT_AHFYYYBCXY_L001_001

value: sorted CFU-E


title: RNA_CFU-E_STAG2WT_rep1

description: RNA_CFU-E_STAG2WT_rep1_Rs-A16-ACCGTG_ACCGTG_AHFYYYBCXY_L001_001


title: RNA_CFU-E_STAG2KO_rep3

description: RNA_CFU-E_STAG2KO_rep3_Rs-A16-ACTCTT_ACTCTT_BHG22CBCXY_L001_001


title: breast_cancer_primary_sample_762

city: Vancouver

first: Laura

last: Chang

state: BC

address: 1152 Mainland St, Suite 430

country: Canada

institute: PFS Genomics

description: breast cancer primary tumor

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials and protocols

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing: Data was normalized using SCAN (SCAN.UPC package from Bioconductor)

source_name: FFPE breast cancer

label_protocol: cDNA was amplified using the Ovation FFPE WTA system (NuGEN, San Carlos, CA). Amplified cDNA was fragmented and labeled using the Encore Biotin Module (NuGEN, San Carlos, CA).

extract_protocol: After pathologic review, FFPE tissue was harvested with a 1 mm punch. RNA was extracted from tissue punches using the RNeasy FFPE kit (Qiagen, Hilden, Germany).

tag: grade

tag: systemic therapy

tag: menopause

tag: tumor size (millimeters)

tag: age

value: female


title: breast_cancer_primary_sample_758

description: breast cancer primary tumor


title: RNA_CFU-E_STAG2KO_rep2

description: RNA_CFU-E_STAG2KO_rep2_Rs-A16-GTAGAA_GTAGAA_BHG22CBCXY_L001_001


title: breast_cancer_primary_sample_759

description: breast cancer primary tumor


title: breast_cancer_primary_sample_760

description: breast cancer primary tumor


title: breast_cancer_primary_sample_761

description: breast cancer primary tumor


title: RNA_GMP_STAG2KO_rep3

description: RNA_GMP_STAG2KO_rep3_Rs-A16-GGTATA_GGTATA_AHFYYYBCXY_L001_001


title: breast_cancer_primary_sample_757

description: breast cancer primary tumor


title: breast_cancer_primary_sample_756

description: breast cancer primary tumor


title: breast_cancer_primary_sample_765

description: breast cancer primary tumor


title: breast_cancer_primary_sample_755

description: breast cancer primary tumor


title: breast_cancer_primary_sample_754

description: breast cancer primary tumor


title: RNA_CFU-E_STAG2KO_rep4

description: RNA_CFU-E_STAG2KO_rep4_Rs-A16-TTCCGC_TTCCGC_BHG22CBCXY_L001_001


title: breast_cancer_primary_sample_753

description: breast cancer primary tumor


title: breast_cancer_primary_sample_763

description: breast cancer primary tumor


title: RNA_CFU-E_STAG2KO_rep1

description: RNA_CFU-E_STAG2KO_rep1_Rs-A16-GTGCCA_GTGCCA_AHFYYYBCXY_L001_001


title: RNA_CFU-E_STAG2WT_rep3

description: RNA_CFU-E_STAG2WT_rep3_Rs-A16-AGACCA_AGACCA_BHG22CBCXY_L001_001


title: Cerebellum, A_Ctrl2 (ChIP-seq)

value: MEF2A Control

value: Female

tag: strain

tag: tissue

value: Cerebellum


title: ATAC_GMP_Stag2WT_11936

data_processing:
ATAC-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned to mouse assembly mm9 using bowtie2 (v2.2.2) with default parameters.
To create density files, read overlap density was calculated with an extension of 0 bp, the signal was then normalized to ten million mapped reads and converted to BigWig using BEDTools.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files containing read densities normalized to 10 million reads

extract_protocol:
Cells (1e4) were lysed and incubated with transposition reaction mix containing PBS, 1% Digitonin, Tween-20, and Transposase (llumina). Samples were incubated for 30 minutes at 37C in a thermomixer at 1000rpm. Prior to amplification, samples were concentrated with the DNA Clean and Concentrator Kit-5 (Zymo).
Samples were eluted in 20uL of elution buffer and PCR-amplified using the NEBNext 2X Master Mix (NEB) for 10 cycles and sequenced on a NextSeq 500 for GMP and CFU-E populations and on the HiSeq 2500 for the LSK cells (Illumina).


title: breast_cancer_primary_sample_751

description: breast cancer primary tumor

tag: Sex


title: breast_cancer_primary_sample_752

description: breast cancer primary tumor


title: ATAC_GMP_Stag2WT_11735


title: Vehicle control [7]

description: quasi.gene.quant.txt


title: ATAC_GMP_Stag2KO_11843


title: breast_cancer_primary_sample_750

description: breast cancer primary tumor


title: ATAC_CFUE_Stag2WT_rep2


title: ATAC_GMP_Stag2KO_11840


title: ATAC_CFUE_Stag2WT_rep1


title: breast_cancer_primary_sample_747

description: breast cancer primary tumor


title: breast_cancer_primary_sample_748

description: breast cancer primary tumor


title: ATAC_CFUE_Stag2KO_rep2


title: breast_cancer_primary_sample_749

description: breast cancer primary tumor


title: breast_cancer_primary_sample_764

description: breast cancer primary tumor


title: ATAC_CFUE_Stag2KO_rep1


title: P131_F8 (scRNAseq)

tag: sample index

value: CGACGTAT

tag: plate number

tag: well position

tag: donor id

value: Thymus Maits stage 1

tag: cell number


title: P131_F9 (scRNAseq)

value: ACATGCCA


title: breast_cancer_primary_sample_746

description: breast cancer primary tumor


title: P131_F7 (scRNAseq)

value: ACACAGCT


title: P131_F6 (scRNAseq)

value: GAGAGGAA


title: P131_F4 (scRNAseq)

value: GTCGCTAA


title: P131_F5 (scRNAseq)

value: ATAGGCTC


title: P131_F3 (scRNAseq)

value: AGGAGGAA


title: P131_F14 (scRNAseq)

value: TACAGGCT


title: P131_F2 (scRNAseq)

value: TAACCGTG


title: P131_F13 (scRNAseq)

value: TACCGATG


title: P131_F12 (scRNAseq)

value: TGATGCTG


title: P131_F11 (scRNAseq)

value: GCGTGATT


title: breast_cancer_primary_sample_743

description: breast cancer primary tumor

value: female


title: P131_F10 (scRNAseq)

value: GTTCCAAG


title: breast_cancer_primary_sample_741

description: breast cancer primary tumor


title: P131_F1 (scRNAseq)

value: ATTCGCAG


title: breast_cancer_primary_sample_740

description: breast cancer primary tumor


title: P131_E9 (scRNAseq)

value: AGTGACTC


title: breast_cancer_primary_sample_742

description: breast cancer primary tumor


title: breast_cancer_primary_sample_737

description: breast cancer primary tumor


title: breast_cancer_primary_sample_745

description: breast cancer primary tumor


title: breast_cancer_primary_sample_744

description: breast cancer primary tumor


title: breast_cancer_primary_sample_735

description: breast cancer primary tumor


title: breast_cancer_primary_sample_739

description: breast cancer primary tumor


title: breast_cancer_primary_sample_738

description: breast cancer primary tumor


title: breast_cancer_primary_sample_732

description: breast cancer primary tumor


title: breast_cancer_primary_sample_736

description: breast cancer primary tumor


title: breast_cancer_primary_sample_733

description: breast cancer primary tumor


title: breast_cancer_primary_sample_729

description: breast cancer primary tumor


title: breast_cancer_primary_sample_730

description: breast cancer primary tumor


title: breast_cancer_primary_sample_726

description: breast cancer primary tumor


title: breast_cancer_primary_sample_731

description: breast cancer primary tumor


title: breast_cancer_primary_sample_728

description: breast cancer primary tumor


title: breast_cancer_primary_sample_727

description: breast cancer primary tumor


title: breast_cancer_primary_sample_725

description: breast cancer primary tumor


title: P131_E8 (scRNAseq)

value: AGCTTGCA


title: P131_E20 (scRNAseq)

value: TCGTTGGA

value: Thymus Maits stage 1


title: P131_E24 (scRNAseq)

value: ATCCGTAG


title: P131_E23 (scRNAseq)

value: CGACTACA


title: P131_E5 (scRNAseq)

value: ACGATGTC


title: P131_E18 (scRNAseq)

value: CACAAGTC


title: P131_E19 (scRNAseq)

value: CAACTGAC


title: P131_E2 (scRNAseq)

value: TGCGACTA


title: breast_cancer_primary_sample_724

description: breast cancer primary tumor


title: P131_E7 (scRNAseq)

value: TAGGTGCT


title: P131_E6 (scRNAseq)

value: GTACTTGG


title: P131_E17 (scRNAseq)

value: CGATTGTG


title: P131_E16 (scRNAseq)

value: GTACTGTG


title: P131_E15 (scRNAseq)

value: ATGGTGCT


title: P131_E14 (scRNAseq)

value: TCACGGTA


title: breast_cancer_primary_sample_721

description: breast cancer primary tumor

value: female


title: breast_cancer_primary_sample_719

description: breast cancer primary tumor


title: breast_cancer_primary_sample_723

description: breast cancer primary tumor


title: breast_cancer_primary_sample_722

description: breast cancer primary tumor


title: breast_cancer_primary_sample_720

description: breast cancer primary tumor


title: breast_cancer_primary_sample_718

description: breast cancer primary tumor


title: P131_E13 (scRNAseq)

value: TCGACTAG


title: breast_cancer_primary_sample_717

description: breast cancer primary tumor


title: breast_cancer_primary_sample_714

description: breast cancer primary tumor


title: P131_E11 (scRNAseq)

value: GTGCGTAT


title: P131_E12 (scRNAseq)

value: CGACACAT


title: P131_D9 (scRNAseq)

value: CAGTGCTA

value: Thymus Maits stage 1


title: P131_E1 (scRNAseq)

value: TGGTCGAT


title: P131_D8 (scRNAseq)

value: GACTACCA


title: P131_D7 (scRNAseq)

value: CATCCAGA


title: breast_cancer_primary_sample_713

description: breast cancer primary tumor


title: P131_D6 (scRNAseq)

value: ATGCCAGT


title: P131_E10 (scRNAseq)

value: TACGAGTC


title: P131_D5 (scRNAseq)

value: GCTAAGCT


title: P131_D4 (scRNAseq)

value: CTACGCAA


title: P131_D24 (scRNAseq)

value: GAAGGAAG


title: P131_D3 (scRNAseq)

value: ATTGCGTG


title: breast_cancer_primary_sample_715

description: breast cancer primary tumor


title: P131_D22 (scRNAseq)

value: TGGCGATT


title: P131_D21 (scRNAseq)

value: AGGTTCCA


title: breast_cancer_primary_sample_716

description: breast cancer primary tumor

value: female


title: breast_cancer_primary_sample_710

description: breast cancer primary tumor


title: P131_D20 (scRNAseq)

value: CAGCTTAG


title: breast_cancer_primary_sample_708

description: breast cancer primary tumor


title: P131_D2 (scRNAseq)

value: CCATCAAG


title: breast_cancer_primary_sample_711

description: breast cancer primary tumor


title: breast_cancer_primary_sample_707

description: breast cancer primary tumor


title: breast_cancer_primary_sample_712

description: breast cancer primary tumor


title: breast_cancer_primary_sample_705

description: breast cancer primary tumor


title: P131_D19 (scRNAseq)

value: CCTAGTAG


title: P131_D18 (scRNAseq)

value: TAGCGATC


title: breast_cancer_primary_sample_704

description: breast cancer primary tumor


title: breast_cancer_primary_sample_702

description: breast cancer primary tumor


title: P131_D16 (scRNAseq)

value: TCAGGTGT

value: Thymus Maits stage 1


title: breast_cancer_primary_sample_709

description: breast cancer primary tumor


title: P131_D15 (scRNAseq)

value: GGATGCTT


title: breast_cancer_primary_sample_706

description: breast cancer primary tumor


title: breast_cancer_primary_sample_701

description: breast cancer primary tumor


title: breast_cancer_primary_sample_699

description: breast cancer primary tumor


title: P131_D17 (scRNAseq)

value: TAGCTCAG


title: breast_cancer_primary_sample_703

description: breast cancer primary tumor


title: breast_cancer_primary_sample_700

description: breast cancer primary tumor


title: breast_cancer_primary_sample_698

description: breast cancer primary tumor


title: breast_cancer_primary_sample_695

description: breast cancer primary tumor


title: P131_D14 (scRNAseq)

value: GTGCGTTA


title: breast_cancer_primary_sample_734

description: breast cancer primary tumor


title: breast_cancer_primary_sample_697

description: breast cancer primary tumor


title: breast_cancer_primary_sample_696

description: breast cancer primary tumor


title: breast_cancer_primary_sample_693

description: breast cancer primary tumor


title: breast_cancer_primary_sample_692

description: breast cancer primary tumor


title: P131_D12 (scRNAseq)

value: CACTAGCA


title: P131_D11 (scRNAseq)

value: GGTAACTC


title: breast_cancer_primary_sample_691

description: breast cancer primary tumor


title: breast_cancer_primary_sample_694

description: breast cancer primary tumor


title: breast_cancer_primary_sample_690

description: breast cancer primary tumor


title: breast_cancer_primary_sample_688

description: breast cancer primary tumor


title: P131_D10 (scRNAseq)

value: CGTGAATC


title: P131_C6 (scRNAseq)

value: TACGCTGA


title: P131_C5 (scRNAseq)

value: ACGCGTTA


title: P131_C4 (scRNAseq)

value: CTATCGGA


title: breast_cancer_primary_sample_689

description: breast cancer primary tumor


title: breast_cancer_primary_sample_687

description: breast cancer primary tumor


title: P131_C3 (scRNAseq)

value: GGACTTAC


title: P131_D1 (scRNAseq)

value: ACAACGTC


title: breast_cancer_primary_sample_686

description: breast cancer primary tumor

value: female


title: P131_C23 (scRNAseq)

value: TCCTCTTC


title: P131_C24 (scRNAseq)

value: ACTGTGAC


title: breast_cancer_primary_sample_684

description: breast cancer primary tumor


title: breast_cancer_primary_sample_683

description: breast cancer primary tumor


title: P131_C8 (scRNAseq)

value: ATCACGAC


title: P131_C21 (scRNAseq)

value: TGACTCAG


title: breast_cancer_primary_sample_680

description: breast cancer primary tumor


title: breast_cancer_primary_sample_679

description: breast cancer primary tumor


title: P131_C2 (scRNAseq)

value: TGTCGCAA

value: Thymus Maits stage 1


title: P131_C19 (scRNAseq)

value: TGCACGTA


title: P131_C14 (scRNAseq)

value: GCTAGTGT


title: P131_C17 (scRNAseq)

value: CACGGTAT


title: P131_C15 (scRNAseq)

value: CTCACGAA


title: P131_C13 (scRNAseq)

value: TGCGTAGT


title: P131_C16 (scRNAseq)

value: AGTCACGT


title: P131_C12 (scRNAseq)

value: GCGATATC


title: P131_C11 (scRNAseq)

value: TCAGTGCA


title: P131_C10 (scRNAseq)

value: ACTGTTGG


title: P131_C18 (scRNAseq)

value: GGCACTTA


title: breast_cancer_primary_sample_678

description: breast cancer primary tumor

value: female


title: P131_B9 (scRNAseq)

value: GCCTTAAG

value: Thymus Maits stage 2


title: P131_B7 (scRNAseq)

value: CTCTCCTT


title: breast_cancer_primary_sample_685

description: breast cancer primary tumor


title: breast_cancer_primary_sample_682

description: breast cancer primary tumor


title: breast_cancer_primary_sample_673

description: breast cancer primary tumor


title: breast_cancer_primary_sample_677

description: breast cancer primary tumor


title: breast_cancer_primary_sample_668

description: breast cancer primary tumor


title: breast_cancer_primary_sample_681

description: breast cancer primary tumor


title: breast_cancer_primary_sample_669

description: breast cancer primary tumor


title: breast_cancer_primary_sample_675

description: breast cancer primary tumor


title: breast_cancer_primary_sample_674

description: breast cancer primary tumor


title: breast_cancer_primary_sample_670

description: breast cancer primary tumor


title: breast_cancer_primary_sample_676

description: breast cancer primary tumor


title: breast_cancer_primary_sample_672

description: breast cancer primary tumor


title: P131_B4 (scRNAseq)

value: TCACAGAC


title: P131_B3 (scRNAseq)

value: AGCAGCTT


title: P131_B22 (scRNAseq)

value: CAGTCATG


title: P131_B24 (scRNAseq)

value: CGCATGTA


title: P131_B21 (scRNAseq)

value: TACTGGCA


title: P131_B20 (scRNAseq)

value: ATGCTGAC


title: P131_B2 (scRNAseq)

value: AGTCTTGG


title: P131_B19 (scRNAseq)

value: ACCGACAT


title: breast_cancer_primary_sample_667

description: breast cancer primary tumor


title: breast_cancer_primary_sample_664

description: breast cancer primary tumor


title: P131_B16 (scRNAseq)

value: GTGGTTGT


title: P131_B12 (scRNAseq)

value: GCGTACAT


title: P131_B17 (scRNAseq)

value: GTTGCTGA


title: P131_B14 (scRNAseq)

value: CCGATATG


title: breast_cancer_primary_sample_671

description: breast cancer primary tumor


title: breast_cancer_primary_sample_661

description: breast cancer primary tumor


title: breast_cancer_primary_sample_665

description: breast cancer primary tumor


title: breast_cancer_primary_sample_658

description: breast cancer primary tumor


title: P131_B11 (scRNAseq)

value: CAACGTAC


title: breast_cancer_primary_sample_666

description: breast cancer primary tumor

value: female


title: breast_cancer_primary_sample_662

description: breast cancer primary tumor


title: P131_B10 (scRNAseq)

value: GCACGTAT


title: P131_B1 (scRNAseq)

value: GACTACTG

value: Thymus Maits stage 2


title: P131_B18 (scRNAseq)

value: CCTGGATA


title: breast_cancer_primary_sample_659

description: breast cancer primary tumor


title: breast_cancer_primary_sample_663

description: breast cancer primary tumor


title: P131_A9 (scRNAseq)

value: GATGCGTT


title: breast_cancer_primary_sample_660

description: breast cancer primary tumor


title: breast_cancer_primary_sample_657

description: breast cancer primary tumor


title: breast_cancer_primary_sample_655

description: breast cancer primary tumor


title: breast_cancer_primary_sample_654

description: breast cancer primary tumor


title: breast_cancer_primary_sample_649

description: breast cancer primary tumor


title: breast_cancer_primary_sample_651

description: breast cancer primary tumor


title: breast_cancer_primary_sample_650

description: breast cancer primary tumor


title: breast_cancer_primary_sample_653

description: breast cancer primary tumor


title: P131_A6 (scRNAseq)

value: GACTGTAC


title: P131_A8 (scRNAseq)

value: AGCGTTGT


title: P131_A7 (scRNAseq)

value: TCCAGTAG


title: breast_cancer_primary_sample_652

description: breast cancer primary tumor


title: breast_cancer_primary_sample_656

description: breast cancer primary tumor


title: P131_A20 (scRNAseq)

value: GCATAGTC


title: P131_A19 (scRNAseq)

value: CAACGCTA


title: P131_A4 (scRNAseq)

value: GTCCGAAT


title: P131_A18 (scRNAseq)

value: CCTATGAG


title: breast_cancer_primary_sample_645

description: breast cancer primary tumor


title: P131_A16 (scRNAseq)

value: AGCTCTGA


title: breast_cancer_primary_sample_648

description: breast cancer primary tumor


title: breast_cancer_primary_sample_646

description: breast cancer primary tumor


title: P131_A15 (scRNAseq)

value: ACTTGTGG


title: P131_A5 (scRNAseq)

value: TAGTGCGT


title: P131_A13 (scRNAseq)

value: CTGCGTAA


title: P131_A14 (scRNAseq)

value: GTCCAACA


title: P131_A12 (scRNAseq)

value: CTCCAAGA


title: breast_cancer_primary_sample_642

description: breast cancer primary tumor

value: female


title: P131_A11 (scRNAseq)

value: CAAGCCAT

value: Thymus Maits stage 2


title: breast_cancer_primary_sample_644

description: breast cancer primary tumor


title: breast_cancer_primary_sample_641

description: breast cancer primary tumor


title: breast_cancer_primary_sample_640

description: breast cancer primary tumor


title: P116_P9 (scRNAseq)

value: CTACGAAC

value: CD138+ Spleen Maits


title: breast_cancer_primary_sample_639

description: breast cancer primary tumor


title: breast_cancer_primary_sample_643

description: breast cancer primary tumor


title: breast_cancer_primary_sample_647

description: breast cancer primary tumor


title: P116_P7 (scRNAseq)

value: TGCAGACT


title: breast_cancer_primary_sample_638

description: breast cancer primary tumor


title: P116_P5 (scRNAseq)

value: GGTGATTC


title: P116_P4 (scRNAseq)

value: TACAGCGT


title: P131_A10 (scRNAseq)

value: CCGTTAAG


title: P116_P22 (scRNAseq)

value: ACGACTCA


title: P116_P3 (scRNAseq)

value: ACGCCATA


title: breast_cancer_primary_sample_637

description: breast cancer primary tumor


title: breast_cancer_primary_sample_636

description: breast cancer primary tumor


title: breast_cancer_primary_sample_634

description: breast cancer primary tumor


title: P116_P19 (scRNAseq)

value: TCAGCGTA


title: P116_P18 (scRNAseq)

value: ACGTGTGT


title: breast_cancer_primary_sample_631

description: breast cancer primary tumor


title: breast_cancer_primary_sample_630

description: breast cancer primary tumor


title: P116_P20 (scRNAseq)

value: AGAAGAGG


title: breast_cancer_primary_sample_627

description: breast cancer primary tumor


title: breast_cancer_primary_sample_633

description: breast cancer primary tumor


title: breast_cancer_primary_sample_635

description: breast cancer primary tumor


title: breast_cancer_primary_sample_632

description: breast cancer primary tumor


title: breast_cancer_primary_sample_628

description: breast cancer primary tumor


title: breast_cancer_primary_sample_624

description: breast cancer primary tumor


title: breast_cancer_primary_sample_626

description: breast cancer primary tumor


title: P116_P16 (scRNAseq)

value: CTGGTATG


title: breast_cancer_primary_sample_625

description: breast cancer primary tumor


title: P116_P15 (scRNAseq)

value: TCGAGACT


title: P116_P6 (scRNAseq)

value: TAGGCCAT


title: breast_cancer_primary_sample_622

description: breast cancer primary tumor

value: female


title: breast_cancer_primary_sample_621

description: breast cancer primary tumor


title: breast_cancer_primary_sample_619

description: breast cancer primary tumor


title: P116_P10 (scRNAseq)

value: AACACCAC


title: P116_O8 (scRNAseq)

value: GCCATCAA


title: P116_P14 (scRNAseq)

value: GCTTGATG


title: P116_O6 (scRNAseq)

value: CCACTAAG

value: CD138+ Spleen Maits


title: P116_O5 (scRNAseq)

value: TCACACGA


title: breast_cancer_primary_sample_620

description: breast cancer primary tumor


title: P116_O20 (scRNAseq)

value: CGCAATAC


title: P116_O18 (scRNAseq)

value: CGTCGATA


title: breast_cancer_primary_sample_623

description: breast cancer primary tumor


title: P116_O19 (scRNAseq)

value: TCCAGTGA


title: P116_O17 (scRNAseq)

value: GAATCCAC


title: P116_P8 (scRNAseq)

value: GAGAGAAG


title: P116_O16 (scRNAseq)

value: CTCACAGA


title: P116_O15 (scRNAseq)

value: AGCTCATG


title: P116_P12 (scRNAseq)

value: ACACTCGA


title: breast_cancer_primary_sample_617

description: breast cancer primary tumor


title: breast_cancer_primary_sample_618

description: breast cancer primary tumor


title: breast_cancer_primary_sample_615

description: breast cancer primary tumor


title: breast_cancer_primary_sample_614

description: breast cancer primary tumor


title: breast_cancer_primary_sample_611

description: breast cancer primary tumor


title: breast_cancer_primary_sample_609

description: breast cancer primary tumor


title: breast_cancer_primary_sample_608

description: breast cancer primary tumor


title: breast_cancer_primary_sample_613

description: breast cancer primary tumor


title: P116_O14 (scRNAseq)

value: GAGACCTT


title: P116_O13 (scRNAseq)

value: GGAAGAAG


title: breast_cancer_primary_sample_616

description: breast cancer primary tumor

value: female


title: breast_cancer_primary_sample_612

description: breast cancer primary tumor


title: P116_O2 (scRNAseq)

value: GCCATGAT


title: P116_O12 (scRNAseq)

value: ATGGTCCA


title: breast_cancer_primary_sample_605

description: breast cancer primary tumor


title: P116_O11 (scRNAseq)

value: GTGAGTTC


title: breast_cancer_primary_sample_607

description: breast cancer primary tumor


title: P116_N9 (scRNAseq)

value: TGGTTGCA


title: P116_N8 (scRNAseq)

value: AGGTTCAC

value: CD138+ Spleen Maits


title: P116_O10 (scRNAseq)

value: GGTCCAAT


title: breast_cancer_primary_sample_606

description: breast cancer primary tumor


title: breast_cancer_primary_sample_604

description: breast cancer primary tumor


title: breast_cancer_primary_sample_610

description: breast cancer primary tumor


title: P116_N5 (scRNAseq)

value: ACCGTGAT


title: P116_N4 (scRNAseq)

value: TGACCATG


title: breast_cancer_primary_sample_603

description: breast cancer primary tumor


title: P116_N3 (scRNAseq)

value: GGACTTGT


title: P116_N20 (scRNAseq)

value: GCATGTGT


title: breast_cancer_primary_sample_600

description: breast cancer primary tumor


title: breast_cancer_primary_sample_601

description: breast cancer primary tumor


title: breast_cancer_primary_sample_598

description: breast cancer primary tumor


title: P116_N19 (scRNAseq)

value: GCGTGTAT


title: P116_N21 (scRNAseq)

value: GTTGAGTC


title: P116_N17 (scRNAseq)

value: GTCAGTAC


title: breast_cancer_primary_sample_602

description: breast cancer primary tumor


title: P116_N15 (scRNAseq)

value: CCGATGTA


title: P116_N13 (scRNAseq)

value: TGCTAGGT


title: P116_N11 (scRNAseq)

value: CAGTACCA


title: P116_N16 (scRNAseq)

value: GGTTAGCT


title: P116_N14 (scRNAseq)

value: AACGTCAC


title: P116_N18 (scRNAseq)

value: CAATCGGT


title: breast_cancer_primary_sample_599

description: breast cancer primary tumor

value: female


title: P116_N10 (scRNAseq)

value: TAGCCGAT


title: P116_N1 (scRNAseq)

value: GCGCTTAA

value: CD138+ Spleen Maits


title: breast_cancer_primary_sample_597

description: breast cancer primary tumor


title: P116_M9 (scRNAseq)

value: CATTGTGG


title: breast_cancer_primary_sample_591

description: breast cancer primary tumor


title: P116_M8 (scRNAseq)

value: GGCCAATT


title: P116_M7 (scRNAseq)

value: ACTCTGAG


title: breast_cancer_primary_sample_592

description: breast cancer primary tumor


title: breast_cancer_primary_sample_595

description: breast cancer primary tumor


title: breast_cancer_primary_sample_596

description: breast cancer primary tumor


title: breast_cancer_primary_sample_589

description: breast cancer primary tumor


title: breast_cancer_primary_sample_593

description: breast cancer primary tumor


title: breast_cancer_primary_sample_594

description: breast cancer primary tumor


title: breast_cancer_primary_sample_590

description: breast cancer primary tumor


title: breast_cancer_primary_sample_587

description: breast cancer primary tumor


title: breast_cancer_primary_sample_586

description: breast cancer primary tumor


title: P116_M5 (scRNAseq)

value: GGTATCGT


title: breast_cancer_primary_sample_585

description: breast cancer primary tumor


title: breast_cancer_primary_sample_588

description: breast cancer primary tumor


title: P116_M4 (scRNAseq)

value: GCAAGTTC


title: breast_cancer_primary_sample_582

description: breast cancer primary tumor


title: P116_M3 (scRNAseq)

value: TCAAGCAC


title: P116_M21 (scRNAseq)

value: TGCCAGAT


title: P116_M24 (scRNAseq)

value: AGCATGTC


title: P116_M6 (scRNAseq)

value: ATGTCCAG


title: P116_M20 (scRNAseq)

value: GCCAATTG


title: P116_M2 (scRNAseq)

value: GGTACACT


title: breast_cancer_primary_sample_580

description: breast cancer primary tumor


title: P116_M22 (scRNAseq)

value: TAGCGTCA


title: breast_cancer_primary_sample_577

description: breast cancer primary tumor


title: breast_cancer_primary_sample_584

description: breast cancer primary tumor


title: P116_M19 (scRNAseq)

value: GCATCTAG


title: breast_cancer_primary_sample_581

description: breast cancer primary tumor

value: female


title: P116_M16 (scRNAseq)

value: ATTGCCGA


title: P116_M18 (scRNAseq)

value: TGGCAACT


title: P116_M13 (scRNAseq)

value: GACATGCT

value: CD138+ Spleen Maits


title: breast_cancer_primary_sample_583

description: breast cancer primary tumor


title: breast_cancer_primary_sample_578

description: breast cancer primary tumor


title: breast_cancer_primary_sample_573

description: breast cancer primary tumor


title: breast_cancer_primary_sample_579

description: breast cancer primary tumor


title: breast_cancer_primary_sample_572

description: breast cancer primary tumor


title: breast_cancer_primary_sample_574

description: breast cancer primary tumor


title: breast_cancer_primary_sample_629

description: breast cancer primary tumor


title: P116_M1 (scRNAseq)

value: GTCATGCA


title: P116_M11 (scRNAseq)

value: TCAGGCAT


title: breast_cancer_primary_sample_576

description: breast cancer primary tumor


title: breast_cancer_primary_sample_571

description: breast cancer primary tumor


title: breast_cancer_primary_sample_570

description: breast cancer primary tumor


title: breast_cancer_primary_sample_569

description: breast cancer primary tumor


title: breast_cancer_primary_sample_568

description: breast cancer primary tumor


title: breast_cancer_primary_sample_575

description: breast cancer primary tumor


title: P116_L24 (scRNAseq)

value: GTCATGTG


title: P116_L3 (scRNAseq)

value: TGCGGATT


title: P116_L23 (scRNAseq)

value: TGGTCTGA


title: P116_L5 (scRNAseq)

value: TCGCACAA


title: P116_L20 (scRNAseq)

value: CACACTAG


title: P116_L22 (scRNAseq)

value: GCAATGTC


title: breast_cancer_primary_sample_566

description: breast cancer primary tumor


title: breast_cancer_primary_sample_565

description: breast cancer primary tumor


title: breast_cancer_primary_sample_564

description: breast cancer primary tumor


title: breast_cancer_primary_sample_562

description: breast cancer primary tumor


title: P116_L2 (scRNAseq)

value: ACACGCAT


title: P116_L19 (scRNAseq)

value: ACCATGTG


title: P116_L17 (scRNAseq)

value: TCGAGTTG


title: P116_L12 (scRNAseq)

value: CGCAACAT


title: P116_L1 (scRNAseq)

value: CTAGGATC


title: P116_K8 (scRNAseq)

value: ACCACTGA

value: CD138- CD319- Spleen Maits


title: P116_K4 (scRNAseq)

value: TCTCAAGG


title: breast_cancer_primary_sample_563

description: breast cancer primary tumor

value: female


title: P116_L11 (scRNAseq)

value: CGCTAGTA

value: CD138+ Spleen Maits


title: breast_cancer_primary_sample_567

description: breast cancer primary tumor


title: P116_K3 (scRNAseq)

value: GTAGTGTC


title: P116_L18 (scRNAseq)

value: GCGCAATT


title: P116_K23 (scRNAseq)

value: CGTGATGT


title: breast_cancer_primary_sample_559

description: breast cancer primary tumor


title: P116_K22 (scRNAseq)

value: ACCAAGTC


title: breast_cancer_primary_sample_560

description: breast cancer primary tumor


title: breast_cancer_primary_sample_557

description: breast cancer primary tumor


title: breast_cancer_primary_sample_554

description: breast cancer primary tumor


title: breast_cancer_primary_sample_556

description: breast cancer primary tumor


title: breast_cancer_primary_sample_555

description: breast cancer primary tumor


title: P116_K21 (scRNAseq)

value: CGTAGCAT


title: breast_cancer_primary_sample_553

description: breast cancer primary tumor


title: breast_cancer_primary_sample_548

description: breast cancer primary tumor


title: breast_cancer_primary_sample_549

description: breast cancer primary tumor


title: P116_K20 (scRNAseq)

value: TATTGCGG


title: breast_cancer_primary_sample_558

description: breast cancer primary tumor


title: breast_cancer_primary_sample_561

description: breast cancer primary tumor


title: breast_cancer_primary_sample_551

description: breast cancer primary tumor


title: breast_cancer_primary_sample_552

description: breast cancer primary tumor


title: breast_cancer_primary_sample_550

description: breast cancer primary tumor


title: breast_cancer_primary_sample_547

description: breast cancer primary tumor


title: breast_cancer_primary_sample_546

description: breast cancer primary tumor


title: P116_K13 (scRNAseq)

value: ACTACGGT


title: P116_K2 (scRNAseq)

value: ACCAACGT


title: P116_K12 (scRNAseq)

value: GCAGTCAT


title: breast_cancer_primary_sample_543

description: breast cancer primary tumor


title: breast_cancer_primary_sample_544

description: breast cancer primary tumor


title: P116_K11 (scRNAseq)

value: TGCATGGT


title: breast_cancer_primary_sample_545

description: breast cancer primary tumor


title: breast_cancer_primary_sample_541

description: breast cancer primary tumor


title: P116_K10 (scRNAseq)

value: CAAGTGTC


title: breast_cancer_primary_sample_542

description: breast cancer primary tumor


title: P116_J9 (scRNAseq)

value: TACCGAAC


title: P116_K1 (scRNAseq)

value: TCTCCTCT

value: CD138- CD319- Spleen Maits


title: P116_J7 (scRNAseq)

value: TACTGTGG


title: P116_J8 (scRNAseq)

value: CTACGACA


title: P116_J6 (scRNAseq)

value: GCCAACTA


title: P116_K24 (scRNAseq)

value: CCATCGAA


title: P116_J4 (scRNAseq)

value: GGTGCATT


title: P116_J5 (scRNAseq)

value: GTGTGGTT


title: P116_J22 (scRNAseq)

value: GACCACTA


title: P116_M12 (scRNAseq)

value: TGCGGTTA

value: CD138+ Spleen Maits


title: P116_J20 (scRNAseq)

value: CTCCTCTT


title: breast_cancer_primary_sample_537

description: breast cancer primary tumor

value: female


title: breast_cancer_primary_sample_540

description: breast cancer primary tumor


title: breast_cancer_primary_sample_539

description: breast cancer primary tumor


title: P116_K18 (scRNAseq)

value: GTGGTCTA


title: breast_cancer_primary_sample_538

description: breast cancer primary tumor


title: breast_cancer_primary_sample_533

description: breast cancer primary tumor


title: breast_cancer_primary_sample_535

description: breast cancer primary tumor


title: breast_cancer_primary_sample_531

description: breast cancer primary tumor


title: breast_cancer_primary_sample_532

description: breast cancer primary tumor


title: breast_cancer_primary_sample_530

description: breast cancer primary tumor


title: P116_J3 (scRNAseq)

value: GTGCTCAA


title: breast_cancer_primary_sample_536

description: breast cancer primary tumor


title: breast_cancer_primary_sample_534

description: breast cancer primary tumor


title: breast_cancer_primary_sample_529

description: breast cancer primary tumor


title: breast_cancer_primary_sample_528

description: breast cancer primary tumor


title: P116_J19 (scRNAseq)

value: GCGTTAGT


title: P116_J14 (scRNAseq)

value: CGAATCCA


title: P116_J12 (scRNAseq)

value: CTGTGAGT


title: P116_J11 (scRNAseq)

value: CGACCTAA

value: CD138- CD319- Spleen Maits


title: breast_cancer_primary_sample_527

description: breast cancer primary tumor


title: P116_J10 (scRNAseq)

value: AGGCCATT


title: P116_J18 (scRNAseq)

value: TCTTCCTC


title: P116_J2 (scRNAseq)

value: CAAGACTC


title: P116_I8 (scRNAseq)

value: ATCTACGG


title: P116_I3 (scRNAseq)

value: CTAGACCA


title: P116_I4 (scRNAseq)

value: TACGGATC


title: P116_I5 (scRNAseq)

value: AGCAACTC


title: P116_I23 (scRNAseq)

value: TCGACCAA


title: P116_I21 (scRNAseq)

value: GTGACACT


title: P116_J1 (scRNAseq)

value: CACTGCAA


title: P116_I24 (scRNAseq)

value: CGTAACTG


title: P116_I7 (scRNAseq)

value: ACAGCACT


title: breast_cancer_primary_sample_526

description: breast cancer primary tumor

value: female


title: breast_cancer_primary_sample_525

description: breast cancer primary tumor


title: breast_cancer_primary_sample_523

description: breast cancer primary tumor


title: P116_I20 (scRNAseq)

value: ATGCACCA


title: breast_cancer_primary_sample_520

description: breast cancer primary tumor


title: P116_I19 (scRNAseq)

value: CACAGTAC


title: breast_cancer_primary_sample_517

description: breast cancer primary tumor


title: breast_cancer_primary_sample_518

description: breast cancer primary tumor


title: breast_cancer_primary_sample_524

description: breast cancer primary tumor


title: breast_cancer_primary_sample_515

description: breast cancer primary tumor


title: breast_cancer_primary_sample_522

description: breast cancer primary tumor


title: breast_cancer_primary_sample_516

description: breast cancer primary tumor


title: P116_I6 (scRNAseq)

value: AAGTCGCT


title: breast_cancer_primary_sample_513

description: breast cancer primary tumor


title: breast_cancer_primary_sample_514

description: breast cancer primary tumor


title: breast_cancer_primary_sample_521

description: breast cancer primary tumor


title: breast_cancer_primary_sample_519

description: breast cancer primary tumor


title: breast_cancer_primary_sample_509

description: breast cancer primary tumor


title: breast_cancer_primary_sample_511

description: breast cancer primary tumor


title: breast_cancer_primary_sample_512

description: breast cancer primary tumor


title: P116_I18 (scRNAseq)

value: GCAAGCTT

value: CD138- CD319- Spleen Maits


title: P116_I17 (scRNAseq)

value: AAGGAGGA


title: P116_I16 (scRNAseq)

value: CTAAGCCA


title: P116_I12 (scRNAseq)

value: ATGCAGCT


title: P116_I13 (scRNAseq)

value: AACCGTAC


title: P116_I14 (scRNAseq)

value: CTCTCTCT


title: P116_I10 (scRNAseq)

value: AAGCTCCA


title: P116_I1 (scRNAseq)

value: ATTGGCGT


title: P116_H9 (scRNAseq)

value: AGTCGTAC


title: P116_H7 (scRNAseq)

value: CGAACACT


title: P116_I11 (scRNAseq)

value: CAATCCAG


title: P116_H8 (scRNAseq)

value: GGAACTCT


title: P116_H6 (scRNAseq)

value: GTAACGCT


title: P116_H5 (scRNAseq)

value: AGTTGCTG


title: breast_cancer_primary_sample_508

description: breast cancer primary tumor

value: female


title: P116_H4 (scRNAseq)

value: GTGCATGT


title: P116_H3 (scRNAseq)

value: CGAATCGT


title: breast_cancer_primary_sample_507

description: breast cancer primary tumor


title: breast_cancer_primary_sample_510

description: breast cancer primary tumor


title: breast_cancer_primary_sample_504

description: breast cancer primary tumor


title: breast_cancer_primary_sample_506

description: breast cancer primary tumor


title: breast_cancer_primary_sample_505

description: breast cancer primary tumor


title: P116_H23 (scRNAseq)

value: CATACGTG

value: CD138- CD319- Spleen Maits


title: P116_H22 (scRNAseq)

value: CCTTCTTC


title: breast_cancer_primary_sample_496

description: breast cancer primary tumor


title: breast_cancer_primary_sample_503

description: breast cancer primary tumor


title: breast_cancer_primary_sample_502

description: breast cancer primary tumor


title: breast_cancer_primary_sample_501

description: breast cancer primary tumor


title: breast_cancer_primary_sample_500

description: breast cancer primary tumor


title: P116_H18 (scRNAseq)

value: GCGTTGTA


title: P116_H19 (scRNAseq)

value: GGAGTCTT


title: breast_cancer_primary_sample_499

description: breast cancer primary tumor


title: breast_cancer_primary_sample_495

description: breast cancer primary tumor


title: breast_cancer_primary_sample_498

description: breast cancer primary tumor


title: breast_cancer_primary_sample_497

description: breast cancer primary tumor


title: P116_H2 (scRNAseq)

value: GTTGCGAT


title: P116_H20 (scRNAseq)

value: AACGCTGT


title: breast_cancer_primary_sample_492

description: breast cancer primary tumor


title: breast_cancer_primary_sample_493

description: breast cancer primary tumor


title: breast_cancer_primary_sample_490

description: breast cancer primary tumor


title: breast_cancer_primary_sample_489

description: breast cancer primary tumor


title: breast_cancer_primary_sample_491

description: breast cancer primary tumor


title: breast_cancer_primary_sample_487

description: breast cancer primary tumor


title: breast_cancer_primary_sample_494

description: breast cancer primary tumor


title: breast_cancer_primary_sample_488

description: breast cancer primary tumor


title: breast_cancer_primary_sample_486

description: breast cancer primary tumor


title: P116_H17 (scRNAseq)

value: CATGGTTG


title: P116_H16 (scRNAseq)

value: GTTGTCAG


title: P116_H13 (scRNAseq)

value: TCCTTCTC


title: P116_H11 (scRNAseq)

value: ATTGGCAC


title: P116_H1 (scRNAseq)

value: TGCACTGA


title: P116_H10 (scRNAseq)

value: ACGGTTAC


title: P116_G9 (scRNAseq)

value: GATTCGGT


title: breast_cancer_primary_sample_484

description: breast cancer primary tumor

value: female


title: P116_G8 (scRNAseq)

value: GTAGGTCT


title: P116_G7 (scRNAseq)

value: GAATCGTC


title: P116_G6 (scRNAseq)

value: CCGATAGT


title: P116_H15 (scRNAseq)

value: ACGACATC

value: CD138- CD319- Spleen Maits


title: breast_cancer_primary_sample_482

description: breast cancer primary tumor


title: P116_G5 (scRNAseq)

value: ACCGTTAG


title: P116_G4 (scRNAseq)

value: GATTCGCA


title: breast_cancer_primary_sample_481

description: breast cancer primary tumor


title: breast_cancer_primary_sample_483

description: breast cancer primary tumor


title: breast_cancer_primary_sample_476

description: breast cancer primary tumor


title: breast_cancer_primary_sample_480

description: breast cancer primary tumor


title: breast_cancer_primary_sample_485

description: breast cancer primary tumor


title: P116_G21 (scRNAseq)

value: ATAGCGTC


title: P116_G20 (scRNAseq)

value: CGACATAC


title: P116_G2 (scRNAseq)

value: CACGAGTT


title: P116_G3 (scRNAseq)

value: CGAACTGT


title: P116_G18 (scRNAseq)

value: CGATTCAG


title: P116_G19 (scRNAseq)

value: GTACGACT


title: P116_G24 (scRNAseq)

value: ACAGCTAC


title: breast_cancer_primary_sample_474

description: breast cancer primary tumor


title: P116_G22 (scRNAseq)

value: AACCAGTC


title: breast_cancer_primary_sample_477

description: breast cancer primary tumor


title: breast_cancer_primary_sample_478

description: breast cancer primary tumor


title: breast_cancer_primary_sample_479

description: breast cancer primary tumor


title: P116_G15 (scRNAseq)

value: CCAACTAG


title: P116_G16 (scRNAseq)

value: AATCCGCA


title: breast_cancer_primary_sample_473

description: breast cancer primary tumor

value: female


title: breast_cancer_primary_sample_470

description: breast cancer primary tumor


title: breast_cancer_primary_sample_467

description: breast cancer primary tumor


title: breast_cancer_primary_sample_468

description: breast cancer primary tumor


title: breast_cancer_primary_sample_464

description: breast cancer primary tumor


title: breast_cancer_primary_sample_466

description: breast cancer primary tumor


title: breast_cancer_primary_sample_465

description: breast cancer primary tumor


title: breast_cancer_primary_sample_463

description: breast cancer primary tumor


title: P116_G13 (scRNAseq)

value: GGTCAATC


title: P116_G17 (scRNAseq)

value: GCTACAAC


title: breast_cancer_primary_sample_469

description: breast cancer primary tumor


title: P116_G12 (scRNAseq)

value: GTGTAGCT


title: breast_cancer_primary_sample_462

description: breast cancer primary tumor


title: breast_cancer_primary_sample_460

description: breast cancer primary tumor


title: P116_G11 (scRNAseq)

value: GTTGTGAC

value: CD138- CD319- Spleen Maits


title: P116_G10 (scRNAseq)

value: TGGCATCA


title: P116_G1 (scRNAseq)

value: GGCTAATC


title: P116_F9 (scRNAseq)

value: ACATGCCA

value: CD319+ Spleen Maits


title: P116_F7 (scRNAseq)

value: ACACAGCT


title: breast_cancer_primary_sample_459

description: breast cancer primary tumor


title: breast_cancer_primary_sample_461

description: breast cancer primary tumor


title: P116_F6 (scRNAseq)

value: GAGAGGAA


title: P116_F5 (scRNAseq)

value: ATAGGCTC


title: breast_cancer_primary_sample_458

description: breast cancer primary tumor


title: breast_cancer_primary_sample_456

description: breast cancer primary tumor


title: breast_cancer_primary_sample_455

description: breast cancer primary tumor


title: P116_F3 (scRNAseq)

value: AGGAGGAA


title: P116_F24 (scRNAseq)

value: GTAGTCCA


title: P116_F8 (scRNAseq)

value: CGACGTAT


title: P116_F21 (scRNAseq)

value: GTAGACCT


title: breast_cancer_primary_sample_472

description: breast cancer primary tumor

value: female


title: P116_F20 (scRNAseq)

value: CTGCAACA


title: P116_F2 (scRNAseq)

value: TAACCGTG


title: P116_F4 (scRNAseq)

value: GTCGCTAA


title: Hippocampus, ES-input

city: London

first: Shiva

middle: M

last: Singh

state: ON

address: 1151 Richmond Street

department: Biology

institute: Western University

data_processing:
Off-Line Basecaller (OLB V1.8) was used for base calling. Reads were aligned to the mouse genome (UCSC MM10) using HISAT2 (V2.1.0) after passing the Solexa CHASTITY quality filter and resulting BED files were used.
Aligned reads from HISAT2 were used for peak calling using MACS (V2), where enriched regions (peaks) for each sample were identified (q < 10‑5). MeDIP enriched regions were annotated to the nearest mRNA or lncRNA gene using UCSC RefSeq, with differentially methylated regions (DMRs) in the promoter of known genes identified by diffReps (cut‑off: log2FC = 1.0, p‑value = 10‑4).
Genome_build: mm10
Supplementary_files_format_and_content: wig files generated using MACS (V2); Excel files include peak annotations for each sample, including a peak identifier assigned by MACS (V2), chromosome, start/end position of peak, length of peak region, fold enrichment against input, q-value, and peak-associated gene information.

source_name: Hippocampus

extract_protocol:
Mice were sacrificed via carbon dioxide asphyxiation and cervical spinal dislocation. Hippocampus was dissected, snap-frozen in liquid nitrogen, and stored at -80°C. DNA was isolated using AllPrep DNA/RNA Mini Kit (Qiagen) and stored at -80°C.
DNA was fragmented to a range of 200-1500 bp using a Diagenode Bioruptor, end-repaired, and 3’ adenylated for ligation of genomic adapters. Fragments were immunoprecipitated by anti-5-methylcytosine antibody, then PCR amplified. AMPure XP beads were used to select fragments from 300-800 bp, then quantified by Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Following denaturation with 0.1 M NaOH, single-stranded DNA molecules were captured and amplified in situ on an Illumina flow cell. Libraries were sequenced on the Illumina HiSeq 4000 platform using the HiSeq 3000/4000 SBS Kit (300 cycles) protocol.

treatment_protocol: C57BL/6 mice were exposed to ethanol via voluntary maternal continuous preference drinking of 10% ethanol in water throughout gestation (ethanol) or water only (control). Pups then were either exposed to maternal separation stress via 3 hours of daily isolation from dam and littermates from postnatal days 2-14 (separation) or left undisturbed with the dam (control). This protocol produced 4 experimental groups - control mice that had neither exposure (CC), mice that had just the prenatal ethanol exposure (EC), mice with just the postnatal separation (CS), and mice that had both the prenatal ethanol exposure and the postnatal separation (ES).

value: postnatal day 70

tag: prenatal treatment

value: ethanol

tag: postnatal treatment

value: separation

tag: chip antibody


title: breast_cancer_primary_sample_450

description: breast cancer primary tumor


title: breast_cancer_primary_sample_452

description: breast cancer primary tumor


title: P116_F23 (scRNAseq)

value: AGCGTTAC

tag: cell type


title: P116_F19 (scRNAseq)

value: ACACACGT


title: breast_cancer_primary_sample_449

description: breast cancer primary tumor

tag: grade


title: breast_cancer_primary_sample_454

description: breast cancer primary tumor

tag: systemic therapy


title: breast_cancer_primary_sample_446

description: breast cancer primary tumor

tag: menopause


title: breast_cancer_primary_sample_448

description: breast cancer primary tumor

tag: tumor size (millimeters)


title: P116_F18 (scRNAseq)

value: TACCACGA

value: CD319+ Spleen Maits


title: breast_cancer_primary_sample_453

description: breast cancer primary tumor

tag: age


title: breast_cancer_primary_sample_445

description: breast cancer primary tumor


title: breast_cancer_primary_sample_457

description: breast cancer primary tumor


title: breast_cancer_primary_sample_447

description: breast cancer primary tumor


title: breast_cancer_primary_sample_451

description: breast cancer primary tumor


title: breast_cancer_primary_sample_444

description: breast cancer primary tumor


title: breast_cancer_primary_sample_443

description: breast cancer primary tumor


title: breast_cancer_primary_sample_442

description: breast cancer primary tumor


title: Hippocampus, ES2

tag: strain

value: Mouse monoclonal anti-5-methylcytosine antibody (Diagenode)


title: breast_cancer_primary_sample_441

description: breast cancer primary tumor


title: breast_cancer_primary_sample_440

description: breast cancer primary tumor


title: P116_F17 (scRNAseq)

value: GCTGCATA


title: P116_F16 (scRNAseq)

value: GAGTTCCA


title: Hippocampus, CS-input

value: control


title: P116_F14 (scRNAseq)

value: TACAGGCT


title: P116_F13 (scRNAseq)

value: TACCGATG


title: breast_cancer_primary_sample_438

description: breast cancer primary tumor

value: female


title: Hippocampus, CS2


title: Hippocampus, CS1


title: P116_F12 (scRNAseq)

value: TGATGCTG


title: Hippocampus, EC2


title: Hippocampus, EC-input


title: Hippocampus, EC1


title: Hippocampus, CC-input


title: P116_F11 (scRNAseq)

value: GCGTGATT


title: Hippocampus, CC2


title: P116_F10 (scRNAseq)

value: GTTCCAAG


title: breast_cancer_primary_sample_436

description: breast cancer primary tumor


title: P116_E8 (scRNAseq)

value: AGCTTGCA


title: P116_E9 (scRNAseq)

value: AGTGACTC


title: breast_cancer_primary_sample_433

description: breast cancer primary tumor


title: breast_cancer_primary_sample_430

description: breast cancer primary tumor


title: breast_cancer_primary_sample_427

description: breast cancer primary tumor


title: breast_cancer_primary_sample_437

description: breast cancer primary tumor


title: P116_E7 (scRNAseq)

value: TAGGTGCT


title: breast_cancer_primary_sample_431

description: breast cancer primary tumor


title: Hippocampus, CC1

value: postnatal day 70


title: breast_cancer_primary_sample_432

description: breast cancer primary tumor


title: breast_cancer_primary_sample_425

description: breast cancer primary tumor


title: breast_cancer_primary_sample_429

description: breast cancer primary tumor


title: breast_cancer_primary_sample_421

description: breast cancer primary tumor


title: breast_cancer_primary_sample_426

description: breast cancer primary tumor


title: breast_cancer_primary_sample_423

description: breast cancer primary tumor


title: breast_cancer_primary_sample_428

description: breast cancer primary tumor


title: P116_H21 (scRNAseq)

value: ACGAACTC

value: CD138- CD319- Spleen Maits


title: SC15

city: Chicago

first: Alexander

middle: V

last: Misharin

state: IL

address: 240 E Huron

department: Pulmonary and Critical Care

institute: Northwestern University

data_processing:
BaseCalls: HCS 3.4.0 Software for HiSeq 4000 and HiSeq 3000 Systems.
Fastq files were generated using bcl2fastq software (Illumina) as part of CellRanger V1.3 pipeline (10x Genomics) using mkfastq command.
Fastq files processed using CellRanger V1.3 pipeline (10x Genomics), mapping was done to mm10 version of mouse genome.
Genome_build: mm10
Supplementary_files_format_and_content: Filtered Gene-Barcode Matrices, containing the number of UMIs associated with a gene and barcode in Market Exchange Format (MEX). It also contains TSV files with genes and barcode sequences corresponding to row and column indices, respectively. Raw and filtered matrices in HDF5 format are provided as an alternative to MEX format.

source_name: Lung

growth_protocol: C57Bl/6J male mice, 3 months old were maintaned at the barier facility at the Center for Comparative Medicine at Northwestern University using standard rodent diet (Teklad LM-485 mouse diet, irradiated) and normal day-night cycle.

extract_protocol:
Mice were euthanized with sodium pentobarbital overdose. Chest cavity was opened and lungs were perfused through the right ventricle with 10 ml of HBSS. The lungs were removed and, using 30G needle, infused with 1 mL dispase (Corning) with DNase I (Sigma). Lungs were incubated at room temperature with gentle agitation for 45 minutes, followed by gentle teasing using forceps into small (1-2 mm) fragments and incubation in digestion buffer for another 15 minutes. Resulting suspension was passed through passed through 70 μm cell strainer (Falcon), washed with DMEM (Corning) supplemented with 5% FBS (Corning), pelleted by centrifugation and erythrocytes were lysed using BD Pharm Lyse (BD Biosciences). Resulting single cell suspension was kept in DMEM/FBS and passed through 40 μm cell strainer (Falcon) two times. Cells were counted using Cellometer K2 (Nexcelom) with nucleic acid binding dyes acridine orange (AO) to calculate total number of nucleated cells and propidium iodide (PI) to count dead cells. All manipulations were performed using wide bore tips (Axygen).
10x Genomics, 3' single-cell RNA-seq, V2 chemistry (Protocol CG00052 Rev B).
single-cell RNA-seq (10x Genomics)

treatment_protocol: Mice were anesthetised using isoflurane delivered via IMPAC6 instrument and 100 ug of TiO2 or crocidolite asbestos was administered intratracheally. Mice were harvested 14 days after the exposure.

tag: replicate

value: Fibrosis, Mouse #1

tag: mouse strain

value: C57Bl/6j (Jax stock 000664)

value: 3 months

value: Male


title: breast_cancer_primary_sample_424

description: breast cancer primary tumor

tag: Sex


title: breast_cancer_primary_sample_435

description: breast cancer primary tumor


title: breast_cancer_primary_sample_471

description: breast cancer primary tumor


title: SC14

value: Control, Mouse #1


title: breast_cancer_primary_sample_422

description: breast cancer primary tumor


title: P116_E6 (scRNAseq)

tag: sample index

value: GTACTTGG

tag: plate number

value: CD319+ Spleen Maits


title: P116_H12 (scRNAseq)

value: CAGTCCAA

tag: well position

tag: donor id


title: breast_cancer_primary_sample_434

description: breast cancer primary tumor

value: female


title: P116_E5 (scRNAseq)

value: ACGATGTC

tag: cell number


title: RNAseq_HDAC3ΔIEC_ZT20

city: Pittsburgh

first: Zheng

last: Kuang

state: PA

address: 4400 Fifth Avenue

department: Biological Sciences

institute: Carnegie Mellon University

data_processing:
Reads were mapped against mm10 using tophat with default parameters and FPKMs were caluclated using cuffdiff with default parameters
genome build: mm10
supplementary files format and content: Comma-delimited file with fpkm for each sample

source_name: ileum epithelial cells

extract_protocol:
RNA was extracted from intestinal epithelial cells isolated by laser capture microdissection. Extracted RNA was purified using PicoPure RNA Isolation Kit (Life Technology 12204-01).
Sequencing libraries were prepared using TruSeq RNA sample preparation kit v2 (Illumina)

tag: genotype

value: C57BL/6 Hdac3 {delta}IEC

tag: diet

value: Chow diet


title: P116_E4 (scRNAseq)

value: GGCATGTT

tag: cell type


title: breast_cancer_primary_sample_419

description: breast cancer primary tumor

tag: grade


title: RNAseq_HDAC3ΔIEC_ZT14


title: breast_cancer_primary_sample_418

description: breast cancer primary tumor

tag: systemic therapy


title: breast_cancer_primary_sample_417

description: breast cancer primary tumor

tag: menopause


title: breast_cancer_primary_sample_416

description: breast cancer primary tumor

tag: tumor size (millimeters)


title: P116_E24 (scRNAseq)

value: ATCCGTAG


title: breast_cancer_primary_sample_415

description: breast cancer primary tumor

tag: age


title: P116_E23 (scRNAseq)

value: CGACTACA


title: RNAseq_HDAC3ΔIEC_ZT2


title: RNAseq_HDAC3fl/fl_ZT14

value: C57BL/6 Hdac3 fl/fl


title: breast_cancer_primary_sample_475

description: breast cancer primary tumor


title: breast_cancer_primary_sample_413

description: breast cancer primary tumor


title: P116_E20 (scRNAseq)

value: TCGTTGGA


title: RNAseq_HDAC3fl/fl_ZT20


title: breast_cancer_primary_sample_414

description: breast cancer primary tumor


title: breast_cancer_primary_sample_411

description: breast cancer primary tumor


title: breast_cancer_primary_sample_410

description: breast cancer primary tumor


title: P116_E19 (scRNAseq)

value: CAACTGAC


title: RNAseq_HDAC3fl/fl_ZT8


title: breast_cancer_primary_sample_420

description: breast cancer primary tumor


title: P116_E18 (scRNAseq)

value: CACAAGTC


title: RNAseq_HDAC3ΔIEC_ZT8


title: RNAseq_HDAC3fl/fl_ZT2


title: P116_E2 (scRNAseq)

value: TGCGACTA


title: breast_cancer_primary_sample_412

description: breast cancer primary tumor


title: P116_E17 (scRNAseq)

value: CGATTGTG


title: breast_cancer_primary_sample_408

description: breast cancer primary tumor


title: breast_cancer_primary_sample_405

description: breast cancer primary tumor


title: breast_cancer_primary_sample_407

description: breast cancer primary tumor


title: breast_cancer_primary_sample_406

description: breast cancer primary tumor


title: ResA 10 nM DHT + 10 µM enz b2-rep3

city: Leuven

first: Frank

last: Claessens

address: Herestraat 49, box 901

department: Cellular and Molecular Medicine

country: Belgium

institute: KU Leuven

data_processing:
The reads were mapped to hg19 human reference genome using TopHat v1.3.3 with default settings.
The reads were counted with HTSeq.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *count.txt: Tab-delimited text files include mapped reads per gene counted with HTSeq.

source_name: LNCaP, enzalutamide resistant, subline ResA

growth_protocol: Cells were grown in RPMI 1640 with 4.5 g/l glucose, 10% FCS, 1% Penicillin/Streptomycin, 10 mM HEPES pH 7-7.6, and 1 mM sodium pyruvate, supplemented with 10 µM enzalutamide for the enzalutamide resistant cell lines.

extract_protocol:
RNA isolation was performed with the RNeasy plus mini kit according to the manufacturer's recommendation.
The libraries were generated with the TruSeq RNA Library Prep Kit according to the manufacturer’s recommendations.

treatment_protocol: Cells were plated in medium with 5% dextran-coated charcoal (DCC) treated FCS at a density of 1 million cells/well in 6-well plates. After 24 hours of steroid starvation the cells were treated with 10 nM DHT, 10 µM enzalutamide, a combination of the two, or vehicle (DMSO) for 18 hours.

tag: cell line

value: ResA

tag: treatment

value: 10 nM DHT + 10 uM enz

tag: batch


title: breast_cancer_primary_sample_409

description: breast cancer primary tumor

tag: Sex


title: breast_cancer_primary_sample_404

description: breast cancer primary tumor


title: P116_E16 (scRNAseq)

source_name: spleen

tag: sample index

value: GTACTGTG

value: CD319+ Spleen Maits


title: breast_cancer_primary_sample_401

description: breast cancer primary tumor

value: female


title: ResA 10 nM DHT + 10 µM enz b2-rep2


title: ResA 10 nM DHT + 10 µM enz b2-rep1


title: P116_E15 (scRNAseq)

value: ATGGTGCT

tag: plate number


title: ResA 10 nM DHT b2-rep3

value: 10 nM DHT


title: P116_E13 (scRNAseq)

value: TCGACTAG

tag: well position


title: breast_cancer_primary_sample_403

description: breast cancer primary tumor


title: ResA 10 nM DHT b2-rep2


title: P116_E11 (scRNAseq)

value: GTGCGTAT

tag: donor id


title: ResA 10 µM enz b2-rep3

value: 10 uM enz


title: P116_E12 (scRNAseq)

value: CGACACAT

tag: cell number


title: ResA 10 nM DHT b2-rep1


title: P116_E14 (scRNAseq)

value: TCACGGTA


title: breast_cancer_primary_sample_397

description: breast cancer primary tumor


title: P116_E1 (scRNAseq)

value: TGGTCGAT


title: breast_cancer_primary_sample_399

description: breast cancer primary tumor


title: breast_cancer_primary_sample_402

description: breast cancer primary tumor


title: breast_cancer_primary_sample_396

description: breast cancer primary tumor


title: ResA 10 µM enz b2-rep1


title: breast_cancer_primary_sample_393

description: breast cancer primary tumor


title: P116_D9 (scRNAseq)

value: CAGTGCTA


title: breast_cancer_primary_sample_400

description: breast cancer primary tumor


title: breast_cancer_primary_sample_395

description: breast cancer primary tumor


title: breast_cancer_primary_sample_394

description: breast cancer primary tumor


title: breast_cancer_primary_sample_398

description: breast cancer primary tumor


title: ResA DMSO b2-rep3

value: DMSO


title: ResA 10 µM enz b2-rep2


title: P116_D8 (scRNAseq)

value: GACTACCA


title: Hippocampus, ES1

tag: strain

value: postnatal day 70

tag: prenatal treatment

value: ethanol

tag: postnatal treatment

value: separation

tag: chip antibody

value: Mouse monoclonal anti-5-methylcytosine antibody (Diagenode)


title: breast_cancer_primary_sample_391

description: breast cancer primary tumor

tag: grade

tag: systemic therapy


title: breast_cancer_primary_sample_387

description: breast cancer primary tumor

tag: menopause

tag: tumor size (millimeters)


title: ResA DMSO b2-rep2

tag: cell line

value: ResA


title: breast_cancer_primary_sample_390

description: breast cancer primary tumor

tag: age

value: female


title: breast_cancer_primary_sample_392

description: breast cancer primary tumor


title: breast_cancer_primary_sample_384

description: breast cancer primary tumor


title: breast_cancer_primary_sample_388

description: breast cancer primary tumor


title: breast_cancer_primary_sample_389

description: breast cancer primary tumor


title: breast_cancer_primary_sample_386

description: breast cancer primary tumor


title: ResA DMSO b2-rep1

tag: treatment

tag: batch


title: breast_cancer_primary_sample_385

description: breast cancer primary tumor

tag: Sex


title: breast_cancer_primary_sample_383

description: breast cancer primary tumor


title: P116_D7 (scRNAseq)

tag: sample index

value: CATCCAGA

tag: plate number

tag: cell type

value: CD319+ Spleen Maits


title: breast_cancer_primary_sample_382

description: breast cancer primary tumor


title: P116_D6 (scRNAseq)

value: ATGCCAGT

tag: well position

tag: donor id

tag: cell number


title: P116_D5 (scRNAseq)

value: GCTAAGCT


title: ResB 10 µM enz b2-rep3

source_name: LNCaP, enzalutamide resistant, subline ResB

value: ResB

value: 10 uM enz


title: P116_D4 (scRNAseq)

value: CTACGCAA


title: breast_cancer_primary_sample_379

description: breast cancer primary tumor


title: breast_cancer_primary_sample_380

description: breast cancer primary tumor


title: breast_cancer_primary_sample_376

description: breast cancer primary tumor


title: ResB 10 µM enz b2-rep2


title: ResB 10 µM enz b2-rep1


title: breast_cancer_primary_sample_377

description: breast cancer primary tumor


title: breast_cancer_primary_sample_375

description: breast cancer primary tumor


title: breast_cancer_primary_sample_378

description: breast cancer primary tumor


title: breast_cancer_primary_sample_373

description: breast cancer primary tumor


title: P116_D3 (scRNAseq)

value: ATTGCGTG


title: ResB DMSO b2-rep3


title: P116_D22 (scRNAseq)

value: TGGCGATT


title: ResB DMSO b2-rep2

value: DMSO


title: ResB DMSO b2-rep1


title: P116_D24 (scRNAseq)

value: GAAGGAAG


title: P116_D21 (scRNAseq)

value: AGGTTCCA


title: P116_D20 (scRNAseq)

value: CAGCTTAG


title: LNCaP 10 µM enz b2-rep2

source_name: LNCaP

value: LNCaP


title: breast_cancer_primary_sample_367

description: breast cancer primary tumor


title: breast_cancer_primary_sample_369

description: breast cancer primary tumor


title: breast_cancer_primary_sample_370

description: breast cancer primary tumor


title: breast_cancer_primary_sample_368

description: breast cancer primary tumor


title: breast_cancer_primary_sample_374

description: breast cancer primary tumor


title: breast_cancer_primary_sample_365

description: breast cancer primary tumor


title: breast_cancer_primary_sample_439

description: breast cancer primary tumor


title: breast_cancer_primary_sample_372

description: breast cancer primary tumor


title: breast_cancer_primary_sample_371

description: breast cancer primary tumor


title: breast_cancer_primary_sample_363

description: breast cancer primary tumor


title: breast_cancer_primary_sample_366

description: breast cancer primary tumor


title: P116_D19 (scRNAseq)

value: CCTAGTAG


title: P116_D2 (scRNAseq)

value: CCATCAAG


title: LNCaP DMSO b2-rep3


title: P116_D18 (scRNAseq)

value: TAGCGATC


title: LNCaP 10 µM enz b2-rep1


title: breast_cancer_primary_sample_359

description: breast cancer primary tumor

value: female


title: LNCaP DMSO b2-rep2


title: LNCaP 10 µM enz b2-rep3


title: breast_cancer_primary_sample_361

description: breast cancer primary tumor


title: LNCaP DMSO b2-rep1


title: breast_cancer_primary_sample_362

description: breast cancer primary tumor


title: P116_D17 (scRNAseq)

value: TAGCTCAG

value: CD319+ Spleen Maits


title: breast_cancer_primary_sample_360

description: breast cancer primary tumor


title: breast_cancer_primary_sample_364

description: breast cancer primary tumor


title: ResB 10 nM DHT + 10 µM enz b1-rep3

value: 10 nM DHT + 10 uM enz


title: breast_cancer_primary_sample_358

description: breast cancer primary tumor


title: breast_cancer_primary_sample_357

description: breast cancer primary tumor


title: breast_cancer_primary_sample_354

description: breast cancer primary tumor


title: breast_cancer_primary_sample_356

description: breast cancer primary tumor


title: ResB 10 nM DHT + 10 µM enz b1-rep1

value: ResB


title: P116_D15 (scRNAseq)

value: GGATGCTT


title: ResB 10 nM DHT + 10 µM enz b1-rep2


title: breast_cancer_primary_sample_353

description: breast cancer primary tumor


title: breast_cancer_primary_sample_350

description: breast cancer primary tumor


title: P116_D10 (scRNAseq)

value: CGTGAATC


title: P116_D11 (scRNAseq)

value: GGTAACTC


title: P116_D16 (scRNAseq)

value: TCAGGTGT


title: P116_D14 (scRNAseq)

value: GTGCGTTA


title: P116_D12 (scRNAseq)

value: CACTAGCA