title: TPEN1

city: Guangzhou

first: Jiahui

last: Tang

address: 7 Jinsui Road

institute: State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University

description: primary retinal ganglion cells, optic nerve crush+TPEN, day 3

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing.
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: primary retinal ganglion cell

extract_protocol:
Total RNAs were extracted from samples using TRIzol (Invitrogen). DNA digestion was carried out after RNA extraction by DNaseI. RNA quality was determined by examining A260/A280 with NanodropTM OneCspectrophotometer (Thermo Fisher Scientific Inc). RNA Integrity was confirmed by 1.5% agarose gel electrophoresis. Qualified RNAs were finally quantified by Qubit3.0 with QubitTM RNA Broad Range Assay kit (Life Technologies).
2 μg total RNAs were used for stranded RNA sequencing library preparation using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Seqhealth Technology Co., Ltd. Wuhan, China) following the manufacturer’s instruction.

value: primary retinal ganglion cell

value: WT

value: optic nerve crush+TPEN


title: miR-142 KO CML LSK, scRNAseq

status: Public on Nov 02 2022

type: SRA

city: Monrovia

first: Bin

last: Zhang

state: CA

address: 1218 S. Fifth Ave

department: Department of Hematological Malignancies Translational Science

country: USA

institute: City of Hope Beckman Research Institute

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, and gene counting were made using the Cell Ranger software v6.1.2.
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv, features.tsv, matrix.mtx.

molecule: total RNA

organism: Mus musculus

source_name: BM

extract_protocol:
~8000 cells were captured per sample on a 10x Genomics Chromium using a Next GEM Single Cell 3' GEM kit V3.1 (10xGenomics, Cat. PN- 1000121). All protocols were performed following the manufacture’s instruction. Final sequencing libraries were analyzed on a High Sensitivity DNA Chip (Agilent, Cat 5067-4626) and quantified with a Qubit high Sensitivity DNA assay Kit (Thermo, Cat. Q32854). The sequencing was performed on Illumina NovaSeq6000 with S4 Reagent v1.5 kit (Illumina, Cat 20028313) at Tgen with the sequencing length of 28+10+10+101. Real-time analysis (RTA) 3.4.4 software was used to process the image analysis.
Single cell 3’ gene expression library was prepared and final sequencing libraries were analyzed on a High Sensitivity DNA Chip (Agilent, Cat 5067-4626).

tag: cell type

value: Lin-Sca-1+c-Kit+ cells

tag: tissue

value: BM

tag: strain

value: Mir142 KO BCR-ABL+

tag: age

value: 8-10 weeks old


title: TPEN3

country: China

library_source: transcriptomic

tag: genotype

tag: treatment


title: ONC2

description: primary retinal ganglion cells, optic nerve crush+PBS, day 3

value: optic nerve crush+PBS


title: RBG26619_Young_SEC_037

city: Shanghai

first: Xiaonan

last: Wang

address: 227 Chongqing South Road

department: School of Public Health

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Reads were mapped to the Mus musculus genome (EMSEMBL GRCm38.p4 Release 81) and ERCC sequences using GSNAP (version 2015-09-29) with parameters: -A sam –B 5 –t 24 –n 1 –Q –N 1.
HTseq-count (PMID: 25260700) was used to count reads mapped to each gene, with parameters: –s no.
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: HT-Seq counts / gene counts (.txt)

source_name: endosteum and central marrow

extract_protocol:
Single endosteal and central marrow stromal cells were directly sorted into individual wells of a 96-well PCR plate containing 2.3 µl of 0.2% Triton-X100 (Sigma-Aldrich, 93443) and 1U of Superase-In RNase Inhibitor (Ambion). Of note, information regarding expression of surface markers was recorded for each cell. Cells were frozen immediately at -80C until further processing. After thawing on ice, 2 µl of annealing mixture (1 µM oligodT –IDT-, 5mM each dNTPs and a dilution 1:6,000,000 of ERCC RNA Spike-In Mix -Invitrogen-) was added followed by incubation at 72C for 3 minutes. Then 5.7 µl of Reverse Transcription mix (3.5 U/µl of Maxima H minus retrotranscriptase –ThermoFisher-, 0.88 U/µl of Superase-In RNase Inhibitor, 1.75X Maxima RT Buffer, 3.5 µM TSO – Qiagen- and 13.15% PEG 8000 –Sigma-Aldrich-) was added and the mixture was incubated at 42 C for 90 min, followed by 70 C for 15 min. cDNA was further amplified by adding 40 µl of PCR mix (0.03 U/µl of Terra PCR direct polymerase –Takara Bio-, 1.25X Terra PCR Direct Buffer, 0.25 µM IS PCR primer –IDT-). PCR was as follows: 3 min at 98 °C for initial denaturation followed by 21 cycles of 15 s at 98 °C, 30 s at 65 °C, 4 min at 68 °C. Final elongation was performed for 10 min at 72 °C.  Sequences of oligodT, TSO and IS PCR primers were as previously described (PMID: 24385147).
Following preamplification, all samples were purified using Ampure XP beads (Beckman Coulter) at a ratio of 1:0.6 with a final elution in 25 µl of EB Buffer (Qiagen). The cDNA was then quantified using the Quant-iT PicoGreen dsDNA Assay Kit (Thermo Fisher). Size distributions were checked on high-sensitivity DNA chips (Agilent Bioanalyzer). Samples were used to construct Nextera XT libraries (Illumina) from 100 pg of preamplified cDNA. Libraries were purified and size selected (0.5X-0.7X) using Ampure XP beads. Then, libraries were quantified using KAPA qPCR quantification kit (KAPA Biosystems), pooled and sequenced in an Illumina HiSeq 4000 instrument.

tag: cell population

value: mesenchymal and endothelial cells

value: SEC

value: Young


title: miR-142 WT CML LSK, scRNAseq

description: 10x Genomics

value: BCR-ABL+


title: pool3-52_S244

city: Leuven

first: Gabriele

last: Bergers

address: Herestraat 49

department: Department of Oncology

country: Belgium

institute: KU Leuven-VIB CCB

data_processing:
BAM files were converted to merged, demultiplexed FASTQ files, cleaned using fastq-mcf (ea-utils r819), and QC checked with FastQC (0.11.4). Reads were then mapped to the mouse genome (mm10) using STAR (2.4.1b) and quantified with Subread (1.4.6-p2). Cells with less than 1000 genes expressed, more than 30% mitochondrial reads were discarded. 538 cells passed these stringent quality criteria.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.csv: Comma-separated text files include raw count matrices. Genes are in rows, and cells are in columns.

source_name: PyMT tumor

extract_protocol:
For the isolation of ECs, tumors were minced and incubated with enzymes A, D and R (Tumor Dissociation Kit, Miltenyi) in combination with mechanical dissociation by gentleMACS™ Dissociator (Miltenyi). Tumor endothelial cells were enriched by removing immune cells and tumor cells using the positive selection anti-mouse CD45 (TIL) MicroBeads (Miltenyi) and the positive selection anti-mouse CD326 (EpCAM) MicroBeads (Miltenyi). The negative fraction that contained the remaining endothelial cells was collected and washed with PBS before flow cytometry staining. CD45-CD31+MECA79+ cells (TU_HEV and LN_HEV), or CD45-CD31+MECA79- (TU_EC) cells were sorted (BD FACSAria III) in 96 well plates (VWR, DNase, RNase free) containing 2 μL of lysis buffer (0.2% Triton X-100, 4U of RNase inhibitor, Takara) per well. Plates were properly sealed and spun down at 2000 g for 1 min before storing at −80°C. Whole transcriptome amplification was performed with a modified SMART-seq2 protocol as described previously (Picelli et al., 2014), using 23 instead of 18 cycles of cDNA amplification. PCR purification was realized with a 0.8:1 ratio (ampureXP beads:DNA). Amplified cDNA quality was monitored with a high sensitivity DNA chip (Agilent) using the Bioanalyzer (Agilent).
Sequencing libraries were performed using the Nextera XT kit (Illumina) as described previously (Picelli et al., 2014), using 1/4th of the recommended reagent volumes and 1/5th of input DNA with a tagmentation time of 9 min. Library quality was monitored with a high sensitivity DNA chip (Agilent) using the Bioanalyzer (Agilent). Indexing was performed with the Nextera XT index Kit V2 (A-D). Up to 4x96 single cells were pooled per sequencing lane. Samples were sequenced on the Illumina NextSeq 500 platform using 75bp single-end reads.

tag: facs gating

value: tumor high-endothelial venules


title: pool3-50_S242


title: RBG26631_Young_SEC_038


title: ctrl3

description: primary retinal ganglion cells, normal control

value: normal


title: TPEN2


title: ONC3


title: Lung, 7 weeks, 3 pooled experimental animals

city: Cambridge

first: Alastair

last: Crisp

address: Francis Crick Avenue

country: United Kingdom

institute: MRC Laboratory of Molecular Biology

data_processing:
Alignment using Cellranger v6.0.1
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: aceNKP_cloupe.cloupe

source_name: Lung

extract_protocol: Single cell RNA-seq (10X Chromium 3'), according to manufacturer's instructions.

value: Lung

value: lymphocytes

value: Id2+/BFP, Gata3+/hCD2, Rora+/Teal, Bcl11b+/tdTomato, or Rorc+/Katushka in 5x polychromILC mouse

value: aceNKP-derived progeny


title: TH1_cont_1

data_processing:
Samples were sequenced using an Illumina Hiseq4000 running a single-read 50bp protocol
Sequence data were trimmed to remove adaptors and sequences with a quality score below 30 using Trim Galore (v0.50, Babraham Bioinformatics)
sequences were aligned to the mouse genome (GRCm38) using STAR (v2.6.0a, Spliced Transcripts Alignment to a Reference, Alexander Dobin)
differential expression calculated using DEseq2 (v1.18.1)
Supplementary files format and content: GRCm38
Supplementary files format and content: DEseq2 output file

source_name: Spleen

growth_protocol: Splenic CD4+ TN cells from Cd4 CreERT2 control or alpha-v conditional knockout mice were flow-purified and cultured in vitro in TH1 or TH2 conditions for 5 days. On day 5, live CD4+ cells were flow-sorted for RNA analyses.

extract_protocol:
Cells were flow sorted into PBS 50% FCS and RNA was extracted using RNeasy Plus micro kit (Qiagen). After assessment using a Bioanalyser (Agilent), RNA was processed for RNA-sequencing using an Ovation RNA-seq System V2 (Nugen), fragmented using the Covaris M220,
and bar-coded using Ovation Ultralow Library Systems (Nugen)

value: Spleen

value: Primary mouse TH1 cells

value: Control


title: pool3-51_S243


title: RBG26643_Old_SEC_036

value: Old


title: ONC1

value: primary retinal ganglion cell

value: WT


title: ctrl2


title: pool3-49_S241


title: RBG26690_Old_SEC_034


title: ctrl1


title: d6_dko.2 [PBAT_capture_V2]

city: Rehovot

first: Amos

last: Tanay

address: Herzl

country: Israel

institute: Weizmann Institute of Science

library_source: genomic

data_processing: PE 150bp or 300bp reads were aligned to the mm9 reference genome  using an in-house script based on Bowtie2. In cases where the two reads ends were not aligned in a concordant manner, the reads were discarded. Reads that were mapped to the same genome coordinates where marked as duplicates and were used only once. We subsample methylation of single-cells to have only one methylation call per CpG.

molecule: genomic DNA

source_name: Dr. Masaki Okano

growth_protocol: Mouse embryonic stem cells (mESCs) were maintained under standard conditions. Cells were fed with fresh medium every day and were split every 2 days.

extract_protocol:
whole-genome single-cell PBAT DNA methlyation profiling: single cells were FACS sorted into 2 μl lysis buffer in  384-wells plates, before bisulfite-conversion and processing by the scPBAT protocol.Cells were lysed at 65C for 30 min and were subjected in to sequential process, performed by Bravo Automated Liquid Handling Platform (Agilent) combining with modified scaled down version of EZ-96 DNA Methylation-Lightning MagPerp kit (D5046, Zymo).
For PBAT in a  bulk Samples of 80 ng gDNA were suspended in 12 μl Tris pH 8 and bisulfate conversion was performed according to the EZ-96 DNA Methylation-Lightning MagPerp kit manufacture protocol with the following slight modifications. Mainly, half of the recommended amount of each reagent was used. CT reagent volume was reduced to 65 ml and 90 μl M-Binding buffer plus 10 μl MagBinding beads were added in to each sample. Bisulfate converted DNA samples were eluted in 38 ml elution buffer and were subjected the slightly modified PBAT protocol(Miura et al., 2012).
In solution sequence capture-PBAT:Pool of barcoded libraries (same molarity of each library), was concentrated by 0.7X beads to a volume of 10 μl and was subjected into Mybait capture reaction (MYcroarray Ann Arbor, Michigan, USA) https://arborbiosci.com/genomics/targeted-sequencing/mybaits/mybaits-custom/) according to the manufacture instructions with the following modifications.The amount of baits mix in the hybridization mix was changed to 2 μl and as a consequence the hybridization mix was in aliquot of 16 μl. The volume of the DNA library (125 ng to 2 μg) in the blockers mix was changed to 10 μl and the captured libraries were washed 4 times for 10 min with washing buffer 2.2. Following amplification the product was purify by 0.7X Agencourt Ampure XP beads, eluted in 10 μl elution buffer and was subjected to additional round of capture, four washes and 14 cycles of amplification. Libraries were pooled and sequenced on an iIllumina Nextseq or Navaseq system using the 150 bp high output sequencing kits or 300 bp SP1 kits respectively.

treatment_protocol: For the epigenetic reset, mESC were cultured in Neurobasal and DMEM-F12 (WITHOUT HEPES) medium (1:1), supplemented with N2B27, 20 ng/ml recombinant human LIF and 2i for two to three passages. Embryoid bodies were established in 25 μl hanging drops on a cover of low-adherent bacterial culture dish, allowing 500 cells/drop to aggregate for 48 hours. After two days 48-56 EBs were pooled into 10 cm low adherent bacterial culture dish.

tag: cell line/mouse line


title: d6_dko.1 [PBAT_capture_V2]


title: d5_dko.2 [PBAT_capture_V2]


title: pool3-48_S240


title: pool3-47_S239


title: RBG26678_Young_SEC_036


title: sc_mouse_e7.5.9 [sc_PBAT: plate_32]


title: RBG26666_Young_SEC_035


title: sc_mouse_e7.5.6 [sc_PBAT: plate_29]


title: pool3-43_S235


title: sc_wt_d5.9 [sc_PBAT: plate_26]

source_name: J1 (SCRC1010, ATCC)

value: J1 (SCRC1010, ATCC)


title: d5_dko.1 [PBAT_capture_V2]


title: RBG26654_Old_SEC_033

value: mesenchymal and endothelial cells


title: RBG26702_Old_SEC_035

value: SEC


title: sc_mouse_e7.5.8 [sc_PBAT: plate_31]


title: pool3-46_S238


title: sc_mouse_e7.5.7 [sc_PBAT: plate_30]


title: RBG26642_Old_SEC_032


title: RBG26701_Old_SEC_031


title: pool3-45_S237


title: sc_ko3b_d5.7 [sc_PBAT: plate_28]

source_name: Cell Bank Riken BioResource Research Center)

value: DNMT3B_KO_Cell Bank Riken BioResource Research Center


title: RBG26630_Young_SEC_034

value: Young


title: pool3-41_S233

value: tumor high-endothelial venules


title: sc_ko3a_d5.7 [sc_PBAT: plate_27]

value: DNMT3A_KO_Cell Bank Riken BioResource Research Center


title: RBG26677_Young_SEC_032


title: RBG26618_Young_SEC_033


title: sc_ko3b_d5.6 [sc_PBAT: plate_25]


title: pool3-44_S236


title: sc_wt_d5.7 [sc_PBAT: plate_20]


title: sc_wt_d5.8 [sc_PBAT: plate_23]


title: sc_ko3b_d5.3 [sc_PBAT: plate_18]


title: sc_ko3b_d5.5 [sc_PBAT: plate_22]


title: pool3-42_S234


title: sc_ko3a_d5.6 [sc_PBAT: plate_24]


title: RBG26689_Old_SEC_030


title: RBG26653_Old_SEC_029


title: sc_ko3a_d5.3 [sc_PBAT: plate_16]


title: sc_wt_d5.6 [sc_PBAT: plate_15]


title: sc_ko3a_d5.5 [sc_PBAT: plate_21]


title: sc_wt_d5.5 [sc_PBAT: plate_14]


title: sc_ko3b_d5.4 [sc_PBAT: plate_19]


title: pool3-38_S230


title: pool3-40_S232


title: RBG26641_Old_SEC_028


title: sc_ko3b_d5.1 [sc_PBAT: plate_12]


title: sc_ko3a_d5.2 [sc_PBAT: plate_11]


title: sc_ko3a_d5.4 [sc_PBAT: plate_17]


title: pool3-37_S229


title: sc_ko3b_d5.2 [sc_PBAT: plate_13]


title: sc_wt_d5.4 [sc_PBAT: plate_09]


title: sc_wt_d5.3 [sc_PBAT: plate_08]


title: RBG26629_Young_SEC_030


title: pool3-36_S228


title: sc_ko3a_d5.1 [sc_PBAT: plate_10]


title: RBG26665_Young_SEC_031


title: RBG26688_Old_SEC_026


title: pool3-33_S225


title: pool3-39_S231


title: sc_wt_d5.1 [sc_PBAT: plate_06]


title: sc_mouse_e7.5.2 [sc_PBAT: plate_02]


title: sc_mouse_e7.5.5 [sc_PBAT: plate_05]


title: RBG26664_Young_SEC_027


title: sc_wt_d5.2 [sc_PBAT: plate_07]


title: RBG26700_Old_SEC_027


title: pool3-35_S227


title: RBG26676_Young_SEC_028


title: sc_mouse_e7.5.4 [sc_PBAT: plate_04]


title: pool3-34_S226


title: ABZM01172: J1P6P2_sdEB7_2 [MARS_scRNA]

data_processing:
Read-1 files were mapped to the mm9 genome assembly using Bowtie2 (default parameters)
Demultiplexing and UMI counting were based on 8bp of UMI and 7bp of cell-barcodes in Read-2, and performed using the pipeline described in Jaitin et al. 2014

extract_protocol:
RNA capture for scRNA MARSseq: single-cells were FACS-sorted directly into barcoded lysis solution in 384-well MARS-seq plates, which were immediately transfered and kep at -80C. lysis solution contained UPW, 2nM poly-dT barcodes,  0.1%triton and RNAse inhibitors.
cDNA MARS-seq library preparation: scRNA MARS-seq library prepartion was performed as described in Jaitin et al. 2014. For bulk MARS-seq, only differences were were using set of 348 barcoded oligos, which allowed to pool the 384 well plate into VBLOCK KIT reservoir by centrifuge, later in the process. The step of klenow heat inactivation was removed. The volumes of the first RT and Exonuclease I reaction mix were scaled down to 1 and 0.5 μl respectively. Each reaction mix was dispensed by MANTISR (FORMULATRIX).

tag: batch index

value: CGGT


title: RBG26640_Old_SEC_024


title: sc_mouse_e7.5.1 [sc_PBAT: plate_01]


title: pool3-32_S224


title: RBG26617_Young_SEC_029


title: ABZM01173: J1P6P2_sdEB7_3 [MARS_scRNA]

value: GCAT


title: ABZM01171: J1P6P2_sdEB7_1 [MARS_scRNA]

value: TAGA


title: sc_mouse_e7.5.3 [sc_PBAT: plate_03]


title: pool3-30_S222


title: pool3-29_S221


title: ABZM01167: J1P6P2_sdEB6_5 [MARS_scRNA]

value: GCCA


title: pool3-28_S220


title: ABZM01170: J1P6P2_sdEB6_8 [MARS_scRNA]

value: AAGT


title: ABZM01168: J1P6P2_sdEB6_6 [MARS_scRNA]

value: AGCT


title: RBG26652_Old_SEC_025


title: ABZM01169: J1P6P2_sdEB6_7 [MARS_scRNA]

value: GCTG


title: RBG26616_Young_SEC_025


title: RBG26628_Young_SEC_026


title: ABZM01166: J1P6P2_sdEB6_4 [MARS_scRNA]

value: TAAG


title: pool3-31_S223


title: ABZM01164: J1P6P2_sdEB6_2 [MARS_scRNA]

value: CGAG


title: ABZM01163: J1P6P2_sdEB6_1 [MARS_scRNA]

value: CTGA


title: ABZM01162: J1P6P2_sdEB5_8 [MARS_scRNA]

value: J1 (SCRC1010, ATCC)

value: AGGG


title: RBG26687_Old_SEC_022

value: mesenchymal and endothelial cells

value: SEC

value: Old


title: pool3-25_S217

value: tumor high-endothelial venules


title: ABZM01161: J1P6P2_sdEB5_7 [MARS_scRNA]

value: TCCG


title: RBG26675_Young_SEC_024

value: Young


title: ABZM01160: J1P6P2_sdEB5_6 [MARS_scRNA]

value: GGTA


title: pool3-26_S218


title: ABZM01159: J1P6P2_sdEB5_5 [MARS_scRNA]

value: TTTC


title: pool3-27_S219


title: RBG26663_Young_SEC_023


title: pool3-24_S216


title: ABZM01158: J1P6P2_sdEB5_4 [MARS_scRNA]

value: GCGC


title: ABZM01165: J1P6P2_sdEB6_3 [MARS_scRNA]

value: GTAG


title: RBG26699_Old_SEC_023


title: ABZM01157: J1P6P2_sdEB5_3 [MARS_scRNA]

value: AAAC


title: RBG26651_Old_SEC_021


title: ABZM01156: J1P6P2_sdEB5_2 [MARS_scRNA]

value: CGCC


title: pool3-22_S214


title: ABZM01155: J1P6P2_sdEB5_1 [MARS_scRNA]

value: ACTT


title: ABZM01154: J1P6P2_sdEB45_8 [MARS_scRNA]

value: TCTA


title: ABZM01153: J1P6P2_sdEB45_7 [MARS_scRNA]

value: TGAT


title: pool3-21_S213


title: ABZM01152: J1P6P2_sdEB45_6 [MARS_scRNA]

value: J1 (SCRC1010, ATCC)

value: ATCA


title: pool3-20_S212


title: RBG26627_Young_SEC_022

value: mesenchymal and endothelial cells


title: RBG26639_Old_SEC_020

value: SEC


title: ABZM01151: J1P6P2_sdEB45_5 [MARS_scRNA]

value: CTAC


title: RBG26615_Young_SEC_021


title: RBG26698_Old_SEC_019

value: Old


title: ABZM01149: J1P6P2_sdEB45_3 [MARS_scRNA]

value: TTGG


title: ABZM01148: J1P6P2_sdEB45_2 [MARS_scRNA]

value: CATG


title: pool3-18_S210

value: tumor high-endothelial venules


title: ABZM01147: J1P6P2_sdEB45_1 [MARS_scRNA]

value: AGTC


title: ABZM01146: J1P11P2_sdEB6_12 [MARS_scRNA]

value: GCGC


title: pool3-23_S215


title: RBG26686_Old_SEC_018


title: pool3-17_S209


title: ABZM01145: J1P11P2_sdEB6_11 [MARS_scRNA]


title: ABZM01143: J1P11P2_sdEB6_9 [MARS_scRNA]


title: RBG26662_Young_SEC_019

value: Young


title: pool3-16_S208


title: ABZM01144: J1P11P2_sdEB6_10 [MARS_scRNA]


title: ABZM01141: J1P11P2_sdEB6_7 [MARS_scRNA]


title: ABZM01142: J1P11P2_sdEB6_8 [MARS_scRNA]


title: ABZM01139: J1P11P2_sdEB6_5 [MARS_scRNA]


title: ABZM01150: J1P6P2_sdEB45_4 [MARS_scRNA]

value: ACAG


title: ABZM01137: J1P11P2_sdEB6_3 [MARS_scRNA]


title: pool3-14_S206


title: pool3-15_S207


title: ABZM01140: J1P11P2_sdEB6_6 [MARS_scRNA]


title: RBG26650_Old_SEC_017


title: RBG26638_Old_SEC_016


title: ABZM01138: J1P11P2_sdEB6_4 [MARS_scRNA]


title: pool3-13_S205


title: pool3-19_S211


title: pool3-12_S204


title: ABZM01135: J1P11P2_sdEB6_1 [MARS_scRNA]


title: RBG26614_Young_SEC_017


title: ABZM01136: J1P11P2_sdEB6_2 [MARS_scRNA]


title: RBG26674_Young_SEC_020


title: pool3-11_S203


title: RBG26626_Young_SEC_018


title: ABZM01133: J1P11P2_sdEB55_7 [MARS_scRNA]

value: CTCG


title: pool3-10_S202


title: RBG26685_Old_SEC_015


title: RBG26673_Young_SEC_016


title: ABZM01130: J1P11P2_sdEB55_4 [MARS_scRNA]

value: GATC


title: ABZM01129: J1P11P2_sdEB55_3 [MARS_scRNA]

value: GCAT


title: ABZM01131: J1P11P2_sdEB55_5 [MARS_scRNA]

value: GTCC


title: pool3-09_S201


title: RBG26661_Young_SEC_015


title: ABZM01128: J1P11P2_sdEB55_2 [MARS_scRNA]

value: J1 (SCRC1010, ATCC)

value: CGGT


title: pool3-08_S200


title: ABZM01126: J1P11P2_sdEB53_5_ab [MARS_scRNA]

value: AAGT


title: pool3-07_S199


title: ABZM01134: J1P11P2_sdEB55_8 [MARS_scRNA]

value: ATGC


title: RBG26649_Old_SEC_014

value: mesenchymal and endothelial cells

value: SEC


title: pool3-06_S198


title: ABZM01125: J1P11P2_sdEB53_4_ab [MARS_scRNA]

value: GCTG


title: RBG26637_Old_SEC_013

value: Old


title: ABZM01127: J1P11P2_sdEB55_1 [MARS_scRNA]

value: TAGA


title: ABZM01122: J1P11P2_sdEB53_1_ab [MARS_scRNA]

value: TAAG


title: RBG26625_Young_SEC_014


title: ABZM01123: J1P11P2_sdEB53_2_ab [MARS_scRNA]

value: GCCA


title: ABZM01132: J1P11P2_sdEB55_6 [MARS_scRNA]

value: GGAC


title: ABZM01120: J1P11P2_sdEB5_6_ab [MARS_scRNA]

value: CGAG


title: pool3-04_S196

value: tumor high-endothelial venules


title: ABZM01121: J1P11P2_sdEB5_7_ab [MARS_scRNA]

value: GTAG


title: pool3-05_S197


title: RBG26696_Old_SEC_012


title: RBG26613_Young_SEC_013

value: Young


title: ABZM01119: J1P11P2_sdEB5_5_ab [MARS_scRNA]

value: CTGA


title: ABZM01118: J1P11P2_sdEB5_4_ab [MARS_scRNA]

value: J1 (SCRC1010, ATCC)

value: AGGG


title: pool3-03_S195


title: RBG26684_Old_SEC_011


title: pool3-02_S194


title: ABZM01117: J1P11P2_sdEB5_3_ab [MARS_scRNA]

value: TCCG


title: RBG26672_Young_SEC_012


title: ABZM01115: J1P11P2_sdEB5_1_ab [MARS_scRNA]

value: TTTC


title: ABZM01116: J1P11P2_sdEB5_2_ab [MARS_scRNA]

value: GGTA


title: ABZM01124: J1P11P2_sdEB53_3_ab [MARS_scRNA]

value: AGCT


title: pool3-01_S193


title: ABZM01114: J1P11P2_sdEB43_4_ab [MARS_scRNA]

value: GCGC


title: ABZM01113: J1P11P2_sdEB43_3_ab [MARS_scRNA]

value: AAAC


title: pool2-96_S192

source_name: lymph node

value: lymph node high-endothelial venules


title: RBG26660_Young_SEC_011

value: mesenchymal and endothelial cells

value: SEC


title: ABZM01111: J1P11P2_sdEB43_1_ab [MARS_scRNA]

value: ACTT


title: RBG26648_Old_SEC_010

value: Old


title: pool2-9_S105


title: pool2-95_S191


title: RBG26636_Old_SEC_009


title: ABZM01112: J1P11P2_sdEB43_2_ab [MARS_scRNA]

value: CGCC


title: RBG26612_Young_SEC_009


title: ABZM01108: J1P11P2_sdEB4_6_ab [MARS_scRNA]

value: ATCA


title: ABZM01109: J1P11P2_sdEB4_7_ab [MARS_scRNA]

value: TGAT


title: pool2-93_S189


title: ABZM01107: J1P11P2_sdEB4_5_ab [MARS_scRNA]

value: CTAC


title: RBG26695_Old_SEC_008


title: Liver_ADREX_Ozone_84

city: Research Triangle Park

first: Thomas

last: Jackson

state: NC

address: 109 TW Alexander Dr

department: CPHEA

institute: United States Environmental Protection Agency

data_processing:
Partek Allignment to Rat Genome
Partek Quantification (Gene) using EM
Genes with < 2 counts across all samples removed
Genes rounded to integers in preparation for DESEQ2
Normalized Counts from DESEQ2
Genome_build: rn6 ensemble release 83
Supplementary_files_format_and_content: Data Matrix of 22587 Genes by 16 Samples (columns) as .CSV

organism: Rattus norvegicus

source_name: Liver

extract_protocol:
Livers were removed, flash frozen on dry ice, and RNA was harvested using Direct-Zol RNA MiniPrep kit from Zymo Research (Irvine, CA, USA). Total mRnA was isolated (Wafergen Biosystems, Fremont, CA, USA) and run in Apollo324 automated sample processing system for mRNA selection. RNA-Seq library was prepared with Wafergen's PrepX mRNA 48 protocol. cDNA libraries were amplified and dsDNA from each library were quality checked by Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Each library was sequenced according to Illumina NextSeq 500 protocols (1.8 pM + 5% PhiX from Illumina Inc., San Diego, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Wistar-Wyoto

value: Liver

tag: Sex

value: Male

tag: condition

value: Total Bilateral Adrenalectomy

value: Ozone (0.8 ppm, 4 hours)

value: 13 weeks old


title: pool2-92_S188


title: Liver_ADREX_Ozone_83


title: pool2-91_S187


title: ABZM01105: J1P11P2_sdEB4_3_ab [MARS_scRNA]

value: J1 (SCRC1010, ATCC)

value: TTGG


title: RBG26683_Old_SEC_007


title: ABZM01110: J1P11P2_sdEB4_8_ab [MARS_scRNA]

value: TCTA


title: RBG26671_Young_SEC_008

value: mesenchymal and endothelial cells

value: Young


title: Liver_ADREX_Ozone_82


title: RBG26624_Young_SEC_010

value: SEC


title: pool2-90_S186

value: lymph node high-endothelial venules


title: RBG26659_Young_SEC_007


title: pool2-94_S190


title: ABZM01103: J1P11P2_sdEB4_1_ab [MARS_scRNA]

value: AGTC


title: pool2-8_S104


title: RBG26647_Old_SEC_006

value: Old


title: Liver_ADREX_Ozone_81


title: Liver_ADREX_Air_68


title: pool2-89_S185


title: ABZM00965: N15_DNMT3A_4.7 [MARS_scRNA]

source_name: Dr. Masaki Yagi

value: GCGC


title: RBG26635_Old_SEC_005


title: pool2-88_S184


title: ABZM01106: J1P11P2_sdEB4_4_ab [MARS_scRNA]

value: ACAG


title: Liver_ADREX_Air_67

value: Wistar-Wyoto


title: ABZM00964: N15_WT_4.7 [MARS_scRNA]

value: N15_Masaki Yagi

value: AAAC


title: RBG26623_Young_SEC_006


title: Liver_ADREX_Air_66

value: Liver

value: Male

value: Total Bilateral Adrenalectomy


title: RBG26611_Young_SEC_005


title: Liver_ADREX_Air_65

value: Ozone (0.8 ppm, 4 hours)

value: 13 weeks old


title: pool2-86_S182


title: ABZM00963: N15_DNMT3B_6.7 [MARS_scRNA]

value: CGCC


title: RBG26694_Old_SEC_004

value: mesenchymal and endothelial cells


title: ABZM01104: J1P11P2_sdEB4_2_ab [MARS_scRNA]

value: J1 (SCRC1010, ATCC)

value: CATG


title: ABZM00962: N15_DNMT3B_6.6 [MARS_scRNA]

value: ACTT


title: Liver_SHAM_Ozone_20

value: SHAM


title: Liver_SHAM_Ozone_19


title: ABZM00961: N15_DNMT3A_6.7 [MARS_scRNA]

value: TCTA


title: Liver_SHAM_Ozone_18


title: ABZM00960: N15_DNMT3A_6.6 [MARS_scRNA]

value: TGAT


title: RBG26682_Old_SEC_003

value: SEC

value: Old


title: pool2-84_S180

value: lymph node high-endothelial venules


title: pool2-85_S181


title: ABZM00959: N15_WT_6.7 [MARS_scRNA]

value: N15_Masaki Yagi

value: ATCA


title: DNAmethylation_RMCpatient2

type: genomic

city: Augsburg

first: Victoria

last: Fincke

state: Bayern

address: Stenglinstraße 2

department: pediatric oncology

country: Germany

institute: University hospital Augsburg

hyb_protocol: strandard protocol

scan_protocol: strandard protocol

data_processing: Data was processed as described in PMID: 26923874

label: cy3, cy5

organism: Homo sapiens

source_name: tumor sample 2

label_protocol: strandard protocol

extract_protocol: DNA was isolated from FFPE tumor samples, purification and bisulfite conversion were performed as described in  PMID: 33331994.

value: formalin-fixed paraffin-embedded tumor sample

tag: tumor grade

value: RMC grade 4


title: pool2-87_S183


title: RBG26658_Young_SEC_003

value: Young


title: RBG26670_Young_SEC_004


title: DNAmethylation_RMCpatient3

source_name: tumor sample 3


title: pool2-83_S179


title: RBG26646_Old_SEC_002


title: DNAmethylation_RMCpatient1

source_name: tumor sample 1


title: ABZM00958: N15_WT_6.6 [MARS_scRNA]

value: CTAC


title: pool2-82_S178


title: Liver_SHAM_Ozone_17

value: Wistar-Wyoto

value: Liver

value: Male

value: Ozone (0.8 ppm, 4 hours)

value: 13 weeks old


title: DNAmethylation_RMCpatient4

source_name: tumor sample 4


title: Liver_SHAM_Air_4

value: SHAM

value: Air (4 hours)


title: ABZM00957: N15_DNMT3B_5.7 [MARS_scRNA]

value: ACAG


title: pool2-80_S176


title: pool2-81_S177


title: RBG26622_Young_SEC_002

value: mesenchymal and endothelial cells

value: SEC


title: Liver_SHAM_Air_3


title: pool2-7_S103

value: lymph node high-endothelial venules


title: RBG26634_Old_SEC_001

value: Old


title: Liver_SHAM_Air_1


title: RBG20353_Old_MSC-S_059

value: MSC-S


title: RBG26610_Young_SEC_001


title: TGFBRi_CD45_D8R

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: bulk sample CD45+ from normal mammary glands of young SD rats from a treated strong responder animal, collected at day 0 (right after treatment was stopped for the treatment arm)

data_processing:
single cell: Sequenced reads were aligned to the rat reference genome rn6 using 10x Genomics Cell Ranger 4.0.0.
single cell: The filtered reads assigned to cell barcodes were analyzed with the R package Seurat, version 4.0.0 (21,763 cells for ACI and 68,492 cells for SD). In an initial quality control step, only genes expressed in at least 10 cells and only cells expressing at least 100 genes were retained. In a second step, cells with more than 15% mitochondrial genes were removed, and, in a third step, cells with either i) any read aligned to PTPRC (CD45+) or ii) less than 2 reads aligned to any cytokeratin were removed. For the analyses and plots done on unfiltered data presented in the manuscript, only the first two filtering steps were performed. For all the other analyses, all three steps were included.
single cell: The data were normalized separately for each rat strain using SCTransform and decomposed using PCA. UMAP embeddings were then computed using the first 30 PCA dimensions as input.
single cell: Following clustering and dimensionality reduction, the two main sorted cell types (basal and luminal) were well segregated in the UMAP space. For this reason, the few cells of a sorted cell type that were part of a cluster that was at least 95% the other sorted cell type were considered to be mislabeled by sorting and were removed (85 basal and 32 luminal cells for ACI, and 349 basal and 31 luminal cells for SD). This amounted to retaining 16,762 ACI cells (9,835 basal: 5,479 control and 4,356 treated; 48 secretory basal: 11 control and 37 drug; 3,306 luminal progenitors: 1,474 control and 1,832 treated; and 3,573 mature luminal: 1,517 control and 2,056 treated) and 39,766 SD cells (15,142 basal: 3,172 control and 11,970 treated; 849 secretory: 68 control and 781 treated; 15,951 luminal progenitors: 4,528 control and 11,423 treated; 7,824 mature luminal: 1,737 control and 6,087 treated). The cleaned data was reanalyzed with all cell types together, and further analyzed separately for each cell type.
single cell: For identifying matching cell type clusters between control and treated conditions, cells from each different rat were integrated using canonical correlation analysis as implemented in Seurat. For the separate analysis of SD luminal progenitor cells, animal 2 could not be integrated because it had too few cells (158), therefore those cells were removed only in this analysis. Cell type clusters were identified by examining the expression of representative cellular markers, as well as of top differentially expressed genes characterizing each cluster.
bulk: the bulk RNASeq samples were preprocessed together within experiments (as indicated in the annotation above), as follows: normal ACI; normal SD D0 and normal SD D87 NMU; tumor SD EPCAM; tumor SD CD45; normal ACI CD45; normal SD CD45 D87 NMU and normal SD CD45 D0; old ACI; old ACI CD45, old normal ACI +/- Estradiol CD45
bulk: Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq500 with Single-End 75bp (SE75) reads by the Dana-Farber Cancer Institute Molecular Biology Core Facilities. RNA-seq datasets were aligned to the rat reference rn6 genome using the STAR RNA-Seq aligner (version STAR_2.5.1b). Two-pass mapping was performed using the following modified parameters: --outSAMstrandField intronMotif, --outFilterMultimapNmax 20, -- alignSJoverhangMin 8, --alignSJDBoverhangMin 1, --outFilterMismatchNmax 999, -- outFilterMismatchNoverLmax 0.1, --alignIntronMin 20, --alignIntronMax 1000000, -- alignMatesGapMax 1000000, --outFilterType BySJout, --outFilterScoreMinOverLread 0.33, -- outFilterMatchNminOverLread 0.33, --limitSjdbInsertNsj 1200000, --chimSegmentMin 15, -- chimJunctionOverhangMin 15, --twopassMode Basic.
bulk: The read counts for individual genes were generated using the htseq-count script of the HTSeq framework (version 0.6.1p1) using modified parameters (--stranded no) and the rn6 refGene annotation file available at the UCSC Genome Browser. Genes were filtered to retain only those with at least 10 counts across all samples, then differentially expressed genes were identified by using DESeq2 version 1.30.1 with a cutoff of padj ≤ 0.05.
Genome_build: rn6
Supplementary_files_format_and_content: expression text files

source_name: normal mammary gland

extract_protocol:
single cell: mammary gland single-cell suspensions were stained with Live/Dead aqua stain the following markers: CD24, CD29, CD31, and CD45 in PBE (PBS with 0.5% BSA and 2 mM EDTA, for 30 min at 4oC). Basal, luminal cells, and leukocytes were sorted into lysis buffer and RNA was extracted using teh AllPrep DNA/RNA mini kit (Qiagen)  Total RNA was extracted using the RNeasy Mini Kit (Qiagen).
bulk: The total RNA was measured using the Agilent 2100 Bioanalyzer. RNA-seq libraries were prepared using Clontech Low Input mRNA Library (Clontech SMARTer) v4 kit from less than 10ng of purified total RNA according to the manufacturer’s protocol. The concentrations of finished dsDNA library were measured using the Qubit Fluorometer, the size of library fragment was measured by Agilent TapeStation 2200, and RT-qPCR for adapted library molar concentration measurement according to manufacturer’s protocols. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq500 with Single-End 75bp (SE75) reads by the Dana-Farber Cancer Institute Molecular Biology Core Facilities.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Rats were treated with vehicle or 75mg/kg of LY22157299 by oral gavage twice daily (8-16 hours between doses) for 10 consecutive days for all experiments except for the tumor prevention experiment in ACI ratswhere rats were treated for 21 days.

tag: experiment

value: normal SD CD45 D0

value: SD

value: normal mammary gland

value: drug

tag: day

tag: animal

tag: tumor status

tag: parity

value: virgin

tag: estradiol pellet


title: ABZM00955: N15_DNMT3A_5.7 [MARS_scRNA]

value: CATG


title: ABZM00954: N15_DNMT3A_5.6 [MARS_scRNA]

value: AGTC


title: pool2-79_S175

tag: tissue


title: TGFBRi_CD45_D8N

tag: strain

tag: cell type


title: pool2-77_S173


title: TGFBRi_CD45_D7R

description: bulk sample CD45+ from normal mammary glands of young SD rats from a treated weak responder animal, collected at day 0 (right after treatment was stopped for the treatment arm)

tag: treatment


title: ABZM00951: N15_DNMT3B_4.6 [MARS_scRNA]

value: GGAC


title: ABZM00956: N15_DNMT3B_5.6 [MARS_scRNA]

value: TTGG


title: RBG20352_Old_MSC-S_058

tag: cell population

tag: age


title: TGFBRi_CD45_D7N


title: RBG20350_Old_MSC-S_056


title: ABZM00953: N15_WT_5.7 [MARS_scRNA]

tag: cell line/mouse line

value: N15_Masaki Yagi

value: ATGC


title: pool2-75_S171

tag: facs gating


title: pool2-76_S172


title: RBG20351_Old_MSC-S_057


title: RBG20349_Old_MSC-S_055


title: ABZM00949: N15_DNMT3A_4.6 [MARS_scRNA]

tag: batch index

value: GATC


title: TGFBRi_CD45_D4R

description: bulk sample CD45+ from normal mammary glands of a tumor-bearing SD rat exposed to the carcinogen NMU right after drug treatment was ended (drug animal), collected at Day 87 after exposure

value: normal SD CD45 D87 NMU

value: tumor-bearing


title: pool2-74_S170

value: lymph node high-endothelial venules


title: ABZM00950: N15_DNMT3B_4.5 [MARS_scRNA]

value: GTCC


title: RBG20348_Old_MSC-S_054

value: mesenchymal and endothelial cells

value: MSC-S

value: Old


title: pool2-78_S174


title: ABZM00952: N15_WT_5.6 [MARS_scRNA]

value: CTCG


title: ABZM00948: N15_DNMT3A_4.5 [MARS_scRNA]

value: GCAT


title: TGFBRi_CD45_D3R

value: SD

value: normal mammary gland

value: drug

value: virgin


title: pool2-73_S169


title: Liver_SHAM_Air_2

value: Wistar-Wyoto

value: Liver

tag: Sex

value: Male

tag: condition

value: SHAM

value: Air (4 hours)

value: 13 weeks old


title: TGFBRi_CD45_D2R

description: bulk sample CD45+ from normal mammary glands of a tumor-free SD rat exposed to the carcinogen NMU right after drug treatment was ended (drug animal), collected at Day 87 after exposure

tag: experiment

value: normal SD CD45 D87 NMU

value: tumor-free


title: ABZM00947: N15_WT_4.6 [MARS_scRNA]

value: N15_Masaki Yagi

value: CGGT


title: pool2-72_S168

value: lymph node high-endothelial venules


title: TGFBRi_CD45_D2N

tag: day

value: tumor-bearing


title: RBG20346_Old_MSC-S_052

value: mesenchymal and endothelial cells

value: MSC-S

value: Old


title: pool2-71_S167


title: ABZM00946: N15_WT_4.5 [MARS_scRNA]

value: TAGA


title: pool2-6_S102


title: RBG20344_Old_MSC-S_050


title: TGFBRi_CD45_D1N

value: SD

value: normal mammary gland

value: drug

tag: animal

value: virgin


title: pool2-70_S166


title: ABZM00944: N15_DNMT3B_6.4 [MARS_scRNA]

value: GCTG


title: RBG20342_Old_MSC-S_048


title: RBG20347_Old_MSC-S_053


title: pool2-69_S165


title: ABZM00945: N15_DNMT3B_6.5 [MARS_scRNA]

value: AAGT


title: TGFBRi_CD45_C7N

description: bulk sample CD45+ from normal mammary glands of young SD rats from a control (untreated animal), collected at day 0 (right after treatment was stopped for the treated arm)

value: normal SD CD45 D0

value: control

tag: tumor status


title: TGFBRi_CD45_D1R

value: normal SD CD45 D87 NMU

value: tumor-free

tag: parity


title: RBG20343_Old_MSC-S_049


title: TGFBRi_CD45_C7R

tag: estradiol pellet


title: ABZM00943: N15_DNMT3A_6.5 [MARS_scRNA]

value: AGCT


title: pool2-68_S164

tag: tissue

value: lymph node high-endothelial venules


title: ABZM00941: N15_WT_6.5 [MARS_scRNA]

value: N15_Masaki Yagi

value: TAAG


title: TGFBRi_CD45_C6R

tag: strain


title: TGFBRi_CD45_C6N

tag: cell type


title: pool2-67_S163


title: ABZM00942: N15_DNMT3A_6.4 [MARS_scRNA]

value: GCCA


title: pool2-66_S162


title: TGFBRi_CD45_C5R

description: bulk sample CD45+ from normal mammary glands of a tumor-bearing SD rat exposed to the carcinogen NMU, and not to the drug (control animal), collected at Day 87 after exposure

tag: treatment

value: tumor-bearing


title: ABZM00940: N15_WT_6.4 [MARS_scRNA]

value: GTAG


title: RBG20345_Old_MSC-S_051

tag: cell population

value: mesenchymal and endothelial cells

value: MSC-S

value: Old


title: pool2-65_S161


title: RBG20340_Old_MSC-S_046

tag: age


title: ABZM00939: N15_DNMT3B_5.5 [MARS_scRNA]

tag: cell line/mouse line

value: CGAG


title: RBG20339_Old_MSC-S_045


title: RBG20341_Old_MSC-S_047


title: RBG20338_Old_MSC-S_044


title: RBG20337_Old_MSC-S_043


title: pool2-63_S159

tag: facs gating


title: pool2-64_S160


title: TGFBRi_CD45_C2N

value: SD

value: normal mammary gland

value: virgin


title: ABZM00938: N15_DNMT3B_5.4 [MARS_scRNA]

tag: batch index

value: CTGA


title: TFGBRi_CD45_Drug_Day_9_LD9R

description: bulk sample CD45+ from normal mammary glands of young ACI rats, collected at Day 7 (7 days after treatment was stopped) from a treated animal

value: normal ACI CD45

value: ACI

value: drug


title: ABZM00936: N15_DNMT3A_5.4 [MARS_scRNA]

value: TCCG


title: RBG20336_Old_MSC-S_042


title: pool2-61_S157

value: lymph node high-endothelial venules


title: ABZM00937: N15_DNMT3A_5.5 [MARS_scRNA]

value: AGGG


title: TFGBRi_CD45_Drug_Day_7_LD9L


title: pool2-62_S158


title: ABZM00935: N15_WT_5.5 [MARS_scRNA]

value: N15_Masaki Yagi

value: GGTA


title: RBG20335_Old_MSC-S_041


title: RBG20334_Old_MSC-S_040


title: pool2-60_S156


title: ABZM00934: N15_WT_5.4 [MARS_scRNA]

value: TTTC


title: TFGBRi_CD45_Drug_Day_7_LD6R


title: RBG20333_Old_AEC_059

value: mesenchymal and endothelial cells

value: AEC


title: pool2-5_S101


title: RBG20332_Old_AEC_058

value: Old


title: TFGBRi_CD45_Drug_Day_14_LD16NP

description: bulk sample CD45+ from normal mammary glands of young ACI rats, collected at Day 14 (14 days after treatment was stopped) from a treated animal


title: ABZM00933: N15_DNMT3B_4.4 [MARS_scRNA]

value: GCGC


title: pool2-59_S155


title: ABZM00932: N15_DNMT3B_4.3 [MARS_scRNA]

value: AAAC


title: RBG20331_Old_AEC_057


title: TFGBRi_CD45_Drug_Day_14_LD16L

value: normal mammary gland


title: TGFBRi_CD45_C2R

value: normal SD CD45 D87 NMU

value: SD

value: control

value: tumor-bearing

value: virgin


title: ABZM00931: N15_DNMT3A_4.4 [MARS_scRNA]

value: CGCC


title: pool2-58_S154

value: lymph node high-endothelial venules


title: RBG20330_Old_AEC_056


title: TFGBRi_CD45_Drug_Day_0_LD7R

description: bulk sample CD45+ from normal mammary glands of young ACI rats, collected at Day 0 (when treatment was stopped) from a treated animal

value: normal ACI CD45

value: ACI

value: drug


title: pool2-57_S153


title: RBG20329_Old_AEC_055


title: ABZM00930: N15_DNMT3A_4.3 [MARS_scRNA]

value: ACTT


title: TFGBRi_CD45_Drug_Day_0_LD7L


title: RBG20328_Old_AEC_054

value: mesenchymal and endothelial cells


title: TFGBRi_CD45_Drug_Day_0_LD10R


title: TFGBRi_CD45_Drug_Day_14_LD20L


title: ABZM00929: N15_WT_4.4 [MARS_scRNA]

value: N15_Masaki Yagi

value: TCTA


title: RBG20327_Old_AEC_053

value: AEC

value: Old


title: pool2-55_S151


title: ABZM00927: J1_WT_1.6 [MARS_scRNA]

value: J1 (SCRC1010, ATCC)

value: ATCA


title: RBG20326_Old_AEC_052


title: TFGBRi_CD45_Control_Day_7_LD5R

description: bulk sample CD45+ from normal mammary glands of young ACI rats, collected at Day 7 (7 days after treatment was stopped) from a control animal

value: normal mammary gland


title: TFGBRi_CD45_Control_Day_7_LD2LR

value: control


title: pool2-54_S150


title: pool2-53_S149


title: RBG20325_Old_AEC_051


title: TFGBRi_CD45_Control_Day_7_LD2L


title: ABZM00926: J1_WT_1.5 [MARS_scRNA]

value: CTAC


title: ABZM00925: J1_WT_8h.6 [MARS_scRNA]

value: ACAG


title: RBG20324_Old_AEC_050


title: pool2-52_S148


title: pool2-51_S147


title: TFGBRi_CD45_Control_Day_14_LD12R

description: bulk sample CD45+ from normal mammary glands of young ACI rats, collected at Day 14 (14 days after treatment was stopped) from a control animal

value: virgin


title: ABZM00924: J1_WT_8h.5 [MARS_scRNA]

value: TTGG


title: RBG20323_Old_AEC_049


title: pool2-50_S146

value: lymph node high-endothelial venules


title: pool2-56_S152


title: ABZM00923: J1_WT_0.6 [MARS_scRNA]

value: CATG


title: TFGBRi_CD45_Control_Day_14_LD11R

value: normal ACI CD45

value: ACI


title: RBG20322_Old_AEC_048

value: mesenchymal and endothelial cells


title: ABZM00928: N15_WT_4.3 [MARS_scRNA]

value: N15_Masaki Yagi

value: TGAT


title: TFGBRi_CD45_Control_Day_14_LD11L


title: ABZM00922: J1_WT_0.5 [MARS_scRNA]

value: AGTC


title: RBG20321_Old_AEC_047

value: AEC

value: Old


title: TFGBRi_CD45_Control_Day_0_LD4R

description: bulk sample CD45+ from normal mammary glands of young ACI rats, collected at Day 0 (when treatment was stopped) from a control animal


title: pool2-49_S145


title: ABZM00921: N15_DNMT3B_6.3 [MARS_scRNA]

value: CGAG


title: TFGBRi_CD45_Control_Day_0_LD3R

value: normal mammary gland


title: pool2-48_S144


title: RBG20319_Old_AEC_045


title: TFGBRi_CD45_Control_Day_0_LD3L

value: control


title: ABZM00920: N15_DNMT3B_6.2 [MARS_scRNA]

value: CTGA


title: pool2-46_S142


title: pool2-47_S143


title: ABZM00919: N15_DNMT3B_6.1 [MARS_scRNA]

value: AGGG


title: ABZM00918: N15_DNMT3A_6.3 [MARS_scRNA]

value: TCCG


title: RBG20318_Old_AEC_044


title: D4R_Tumor_CD45plus

description: bulk sample CD45+ from breast tumors of SD rats exposed to the carcinogen NMU right after drug treatment was stopped, collected at day 87 after exposure

source_name: breast tumor

value: tumor SD CD45

value: SD

value: breast tumor

value: drug

value: tumor-bearing

value: virgin


title: D4R_Tumor_Epcamplus

description: bulk sample EPCAM+ from breast tumors of SD rats exposed to the carcinogen NMU right after drug treatment was stopped, collected at day 87 after exposure

value: tumor SD EPCAM

value: EPCAM


title: pool2-44_S140

value: lymph node high-endothelial venules


title: ABZM00917: N15_DNMT3A_6.2 [MARS_scRNA]

value: GGTA


title: pool2-4_S100


title: pool2-45_S141


title: RBG20316_Old_AEC_042

value: mesenchymal and endothelial cells

value: AEC

value: Old


title: RBG20315_Old_AEC_041


title: D4R_BAS

description: bulk sample from basal normal mammary gland from tumor-bearing SD rats exposed to the carcinogen NMU right after drug treatment was stopped, collected at day 87 after exposure

value: normal SD D87 NMU

value: normal mammary gland

value: basal


title: RBG20313_Young_MSC-S_059

value: MSC-S

value: Young


title: pool2-43_S139


title: ABZM00916: N15_DNMT3A_6.1 [MARS_scRNA]

value: TTTC


title: ABZM00915: N15_WT_6.3 [MARS_scRNA]

value: N15_Masaki Yagi

value: GCGC


title: pool2-42_S138


title: D3R_Tumor_CD45plus

value: tumor SD CD45

value: SD

value: breast tumor

value: drug

value: tumor-bearing


title: RBG20320_Old_AEC_046


title: ABZM00914: N15_WT_6.2 [MARS_scRNA]

value: AAAC


title: D3R_Tumor_Epcamplus

value: tumor SD EPCAM

value: EPCAM

value: virgin


title: RBG20317_Old_AEC_043

value: mesenchymal and endothelial cells

value: AEC

value: Old


title: ABZM00913: N15_WT_6.1 [MARS_scRNA]

value: CGCC


title: pool2-3_S99

value: lymph node high-endothelial venules


title: pool2-41_S137


title: RBG20309_Young_MSC-S_056

value: MSC-S

value: Young


title: RBG20310_Young_MSC-S_057


title: D4R_LUM

description: bulk sample from luminal normal mammary gland from tumor-bearing SD rats exposed to the carcinogen NMU right after drug treatment was stopped, collected at day 87 after exposure

value: normal SD D87 NMU

value: normal mammary gland

value: luminal


title: ABZM00909: N15_DNMT3B_5.2 [MARS_scRNA]

value: ATCA


title: D3R_LUM

value: SD

value: drug


title: RBG20308_Young_MSC-S_055


title: ABZM00908: N15_DNMT3B_5.1 [MARS_scRNA]

value: CTAC


title: pool2-39_S135


title: RBG20307_Young_MSC-S_054


title: pool2-38_S134


title: ABZM00907: N15_DNMT3A_5.3 [MARS_scRNA]

value: ACAG


title: D2N_Tumor_Epcamplus

value: tumor SD EPCAM

value: breast tumor

value: EPCAM

value: tumor-bearing


title: D2N_LUM

value: virgin


title: pool2-37_S133


title: RBG20312_Young_MSC-S_058

value: mesenchymal and endothelial cells


title: D2N_Tumor_CD45plus

value: tumor SD CD45


title: RBG20306_Young_MSC-S_053

value: MSC-S


title: ABZM00906: N15_DNMT3A_5.2 [MARS_scRNA]

value: TTGG


title: RBG20305_Young_MSC-S_052

value: Young


title: ABZM00905: N15_DNMT3A_5.1 [MARS_scRNA]

value: CATG


title: pool2-40_S136

value: lymph node high-endothelial venules


title: ABZM00910: N15_DNMT3B_5.3 [MARS_scRNA]

value: TGAT


title: pool2-36_S132


title: D3R_BAS

value: normal SD D87 NMU

value: SD

value: normal mammary gland

value: basal


title: pool2-35_S131


title: D2N_BAS

value: drug


title: D2R_LUM

description: bulk sample from luminal normal mammary gland from tumor-free SD rats exposed to the carcinogen NMU right after drug treatment was stopped, collected at day 87 after exposure

value: luminal

value: tumor-free


title: D2R_BAS

description: bulk sample from basal normal mammary gland from tumor-free SD rats exposed to the carcinogen NMU right after drug treatment was stopped, collected at day 87 after exposure


title: pool2-34_S130


title: ABZM00903: N15_WT_5.2 [MARS_scRNA]

value: N15_Masaki Yagi

value: ATGC


title: D1R_LUM

value: virgin


title: ABZM00902: N15_WT_5.1 [MARS_scRNA]

value: CTCG


title: RBG20302_Young_MSC-S_049

value: mesenchymal and endothelial cells

value: MSC-S


title: RBG20301_Young_MSC-S_048

value: Young


title: pool2-33_S129


title: ABZM00901: N15_DNMT3B_4.2 [MARS_scRNA]

value: GGAC


title: D1N_LUM


title: pool2-31_S127

value: lymph node high-endothelial venules


title: RBG20299_Young_MSC-S_046


title: ABZM00900: N15_DNMT3B_4.1 [MARS_scRNA]

value: GTCC


title: D1N_BAS

value: normal SD D87 NMU


title: RBG20300_Young_MSC-S_047


title: pool2-30_S126


title: ABZM00899: N15_DNMT3A_4.2 [MARS_scRNA]

value: GATC


title: C5R_Tumor_CD45plus

description: bulk sample CD45+ from breast tumors of SD rats exposed to the carcinogen NMU and no drug (control), collected at day 87 after exposure

value: tumor SD CD45

value: SD

value: breast tumor

value: control

value: tumor-bearing


title: ABZM00904: N15_WT_5.3 [MARS_scRNA]

value: N15_Masaki Yagi

value: AGTC


title: D1R_BAS

value: normal mammary gland

value: basal

value: drug

value: tumor-free

value: virgin


title: RBG20298_Young_MSC-S_045

value: mesenchymal and endothelial cells

value: MSC-S

value: Young


title: RBG20297_Young_MSC-S_044


title: RBG20304_Young_MSC-S_051


title: ABZM00898: N15_DNMT3A_4.1 [MARS_scRNA]

value: GCAT


title: pool2-2_S98

value: lymph node high-endothelial venules


title: C5R_Tumor_Epcamplus

description: bulk sample EPCAM+ from breast tumors of SD rats exposed to the carcinogen NMU and no drug (control), collected at day 87 after exposure

value: tumor SD EPCAM

value: EPCAM


title: RBG20303_Young_MSC-S_050


title: ABZM00897: N15_WT_4.2 [MARS_scRNA]

value: CGGT


title: pool2-29_S125


title: pool2-28_S124


title: RBG20296_Young_MSC-S_043


title: C5R_LUM

description: bulk sample from luminal normal mammary gland from tumor-bearing SD rats exposed to the carcinogen NMU and no drug (control), collected at day 87 after exposure

value: normal SD D87 NMU

value: SD

value: luminal

value: control


title: ABZM00896: N15_WT_4.1 [MARS_scRNA]

value: N15_Masaki Yagi

value: TAGA


title: pool2-32_S128


title: C5R_BAS

description: bulk sample from basal normal mammary gland from tumor-bearing SD rats exposed to the carcinogen NMU and no drug (control), collected at day 87 after exposure

value: normal mammary gland

value: basal

value: tumor-bearing


title: RBG20294_Young_MSC-S_041

value: mesenchymal and endothelial cells


title: RBG20295_Young_MSC-S_042

value: MSC-S


title: ABZM00895: N15S_DNMT3B_6.2 [MARS_scRNA]

value: AAGT


title: pool2-26_S122


title: pool2-27_S123


title: C2R_Tumor_CD45plus

value: tumor SD CD45

value: breast tumor

value: virgin


title: RBG20293_Young_AEC_060

value: AEC

value: Young


title: RBG20292_Young_AEC_059


title: ABZM00894: N15S_DNMT3B_6.1 [MARS_scRNA]

value: GCTG


title: pool2-25_S121

value: lymph node high-endothelial venules


title: ABZM00893: N15S_DNMT3B_5.2 [MARS_scRNA]

value: AGCT


title: pool2-24_S120


title: C2R_Tumor_Epcamplus

value: tumor SD EPCAM

value: SD

value: EPCAM

value: control


title: RBG20291_Young_AEC_058


title: C2R_LUM

value: normal SD D87 NMU

value: normal mammary gland

value: luminal


title: ABZM00892: N15S_DNMT3B_5.1 [MARS_scRNA]

value: GCCA


title: C2R_BAS

value: basal

value: tumor-bearing


title: RBG20290_Young_AEC_057

value: mesenchymal and endothelial cells


title: pool2-23_S119


title: ABZM00891: N15S_DNMT3A_6.2 [MARS_scRNA]

value: TAAG


title: RBG20289_Young_AEC_056

value: AEC


title: ABZM00890: N15S_DNMT3A_6.1 [MARS_scRNA]

value: GTAG


title: pool2-22_S118


title: ABZM00889: N15S_DNMT3A_5.2 [MARS_scRNA]

value: CGAG


title: C2N_Tumor_CD45plus

value: tumor SD CD45

value: breast tumor

value: virgin


title: C2N_LUM

value: SD


title: pool2-20_S116

value: lymph node high-endothelial venules


title: ABZM00888: N15S_DNMT3A_5.1 [MARS_scRNA]

value: CTGA


title: C2N_BAS

value: normal SD D87 NMU

value: control


title: RBG20287_Young_AEC_054

value: Young


title: pool2-1_S97


title: ABZM00887: N15S_WT_5.3 [MARS_scRNA]

value: N15_Masaki Yagi

value: AGGG


title: pool2-19_S115


title: ABZM00886: N15S_WT_5.2 [MARS_scRNA]

value: TCCG


title: C2N_Tumor_Epcamplus

value: tumor SD EPCAM

value: EPCAM

value: tumor-bearing


title: RBG20285_Young_AEC_052

value: mesenchymal and endothelial cells

value: AEC


title: pool2-18_S114


title: pool2-17_S113


title: RBG20286_Young_AEC_053


title: D8N_LUM

description: bulk sample from luminal normal mammary glands from young SD rats, collected at Day 0 (when treatment was stopped) from a strong responder animal

value: normal SD D0

value: normal mammary gland

value: luminal

value: drug


title: RBG20283_Young_AEC_050


title: RBG20288_Young_AEC_055


title: ABZM00885: N15S_WT_4.2 [MARS_scRNA]

value: GGTA


title: ABZM00884: N15S_WT_4.1 [MARS_scRNA]

value: TTTC


title: pool2-21_S117

value: lymph node high-endothelial venules


title: D8N_BAS

description: bulk sample from basal normal mammary glands from young SD rats, collected at Day 0 (when treatment was stopped) from a strong responder animal

value: SD

value: basal

value: virgin


title: RBG20282_Young_AEC_049

value: Young


title: pool2-16_S112


title: D7R_LUM

description: bulk sample from luminal normal mammary glands from young SD rats, collected at Day 0 (when treatment was stopped) from a weak responder animal


title: pool2-15_S111


title: ABZM00882: N15S_WT_6.3 [MARS_scRNA]

value: N15_Masaki Yagi

value: AAAC


title: ABZM00883: N15S_WT_5.1 [MARS_scRNA]

value: GCGC


title: RBG20281_Young_AEC_048


title: D7R_BAS

description: bulk sample from basal normal mammary glands from young SD rats, collected at Day 0 (when treatment was stopped) from a weak responder animal


title: RBG20284_Young_AEC_051


title: D8R_LUM


title: RBG20279_Young_AEC_046


title: D8R_BAS


title: pool2-13_S109


title: D7N_BAS


title: RBG20278_Young_AEC_045


title: RBG20280_Young_AEC_047


title: C7R_LUM

description: bulk sample from luminal normal mammary glands from young SD rats, collected at Day 0 (when treatment was stopped) from a control animal

value: control


title: pool2-10_S106


title: pool2-11_S107


title: pool1-96_S96


title: C7N_LUM


title: D7N_LUM


title: C7N_BAS

description: bulk sample from basal normal mammary glands from young SD rats, collected at Day 0 (when treatment was stopped) from a control animal


title: pool2-12_S108


title: C6R_LUM


title: RBG20274_Young_AEC_041

value: mesenchymal and endothelial cells


title: RBG20277_Young_AEC_044

value: AEC


title: RBG20276_Young_AEC_043


title: RBG20275_Young_AEC_042


title: RBG20273_Old_MSC-L_058

value: MSC-L

value: Old


title: pool2-14_S110


title: pool1-93_S93


title: RBG20272_Old_MSC-L_057


title: C7R_BAS

value: normal SD D0

value: normal mammary gland


title: pool1-92_S92


title: ABZM00876: J1_WT_6.9 [MARS_scRNA]

value: J1 (SCRC1010, ATCC)

value: CTAC


title: ABZM00877: J1_WT_6.10 [MARS_scRNA]

value: ATCA


title: ABZM00873: J1_WT_4.10 [MARS_scRNA]

value: CATG


title: ABZM00875: J1_WT_5.9 [MARS_scRNA]

value: ACAG


title: ABZM00880: N15S_WT_6.1 [MARS_scRNA]

value: ACTT


title: ABZM00872: J1_WT_4.9 [MARS_scRNA]

value: AGTC


title: ABZM00874: J1_WT_5.8 [MARS_scRNA]

value: TTGG


title: ABZM00870: J1_WT_7.6 [MARS_scRNA]

value: CGAG


title: C6N_LUM

value: SD

value: luminal

value: virgin


title: pool1-95_S95

value: lymph node high-endothelial venules


title: pool1-94_S94


title: C6N_BAS

value: basal

value: control


title: RBG20271_Old_MSC-L_056

value: mesenchymal and endothelial cells

value: MSC-L

value: Old


title: pool1-91_S91


title: ABZM00881: N15S_WT_6.2 [MARS_scRNA]

value: N15_Masaki Yagi

value: CGCC


title: ABZM00871: J1_WT_7.7 [MARS_scRNA]

value: J1 (SCRC1010, ATCC)

value: GTAG


title: ABZM00869: J1_WT_7.5 [MARS_scRNA]

value: CTGA


title: C6R_BAS

value: normal SD D0

value: normal mammary gland


title: pool1-90_S90


title: Drug_D7_LD9R_Luminal

description: bulk sample from luminal normal mammary glands from young ACI rats, collected at Day 7 (7 days after the treatment was stopped) from a treated animal

value: normal ACI

value: ACI

value: drug


title: RBG20270_Old_MSC-L_055


title: ABZM00868: J1_WT_7.4 [MARS_scRNA]

value: AGGG


title: RBG20269_Old_MSC-L_054


title: pool1-89_S89

value: lymph node high-endothelial venules


title: ABZM00867: J1_WT_6.8 [MARS_scRNA]

value: TCCG


title: Ctlr_D7_LD2LR_Luminal

value: luminal

value: control

value: virgin


title: pool1-88_S88


title: ABZM00866: J1_WT_6.7 [MARS_scRNA]

value: GGTA


title: RBG20268_Old_MSC-L_053

value: mesenchymal and endothelial cells

value: MSC-L

value: Old


title: pool1-84_S84


title: Ctlr_D7_LD2LR_Basal

description: bulk sample from basal normal mammary glands from young ACI rats, collected at Day 7 (7 days after the treatment was stopped) from a treated animal

value: basal


title: Drug_D0_LD10R_Basal

description: bulk sample from basal normal mammary glands from young ACI rats, collected at Day 0 (when treatment was stopped) from a treated animal


title: pool1-85_S85


title: ABZM00865: J1_WT_6.6 [MARS_scRNA]

value: J1 (SCRC1010, ATCC)

value: TTTC


title: Drug_D0_LD10R_Luminal

description: bulk sample from luminal normal mammary glands from young ACI rats, collected at Day 0 (when treatment was stopped) from a treated animal

value: normal mammary gland


title: RBG20266_Old_MSC-L_051


title: pool1-87_S87


title: RBG20267_Old_MSC-L_052


title: RBG20265_Old_MSC-L_050


title: pool1-86_S86


title: ABZM00863: J1_WT_7.2 [MARS_scRNA]

value: AAAC


title: RBG20264_Old_MSC-L_049


title: RBG20263_Old_MSC-L_048


title: Drug_D14_LD20L_Luminal

description: bulk sample from luminal normal mammary glands from young ACI rats, collected at Day 14 (14 days after the treatment was stopped) from a treated animal

value: normal ACI

value: ACI


title: pool1-82_S82


title: ABZM00864: J1_WT_7.3 [MARS_scRNA]

value: GCGC


title: Drug_D14_LD20L_Basal

description: bulk sample from basal normal mammary glands from young ACI rats, collected at Day 14 (14 days after the treatment was stopped) from a treated animal

value: drug


title: ABZM00861: J1_WT_3.5 [MARS_scRNA]

value: ACTT


title: ABZM00860: J1_WT_3.4 [MARS_scRNA]

value: TCTA


title: Drug_D14_LD16NP_Luminal

value: luminal


title: RBG20261_Old_MSC-L_046


title: RBG20262_Old_MSC-L_047


title: Drug_D14_LD16NP_Basal

value: virgin


title: Drug_D7_LD9R_Basal


title: ABZM00859: J1_WT_2.4 [MARS_scRNA]

value: TGAT


title: RBG20260_Old_MSC-L_045

value: mesenchymal and endothelial cells


title: ABZM00862: J1_WT_7.1 [MARS_scRNA]

value: CGCC


title: pool1-83_S83

value: lymph node high-endothelial venules


title: ABZM00858: J1_WT_2.3 [MARS_scRNA]

value: ATCA


title: pool1-80_S80


title: Ctlr_D14_LD12R_Luminal

description: bulk sample from luminal normal mammary glands from young ACI rats, collected at Day 14 (14 days after the treatment was stopped) from a control animal

value: control


title: RBG20258_Old_MSC-L_043

value: MSC-L

value: Old


title: RBG20259_Old_MSC-L_044


title: Drug_D14_LD16L_Basal

value: normal mammary gland

value: basal


title: ABZM00857: J1_WT_2.2 [MARS_scRNA]

value: J1 (SCRC1010, ATCC)

value: CTAC


title: pool1-79_S79


title: pool1-78_S78


title: Drug_D14_LD16L_Luminal

value: normal ACI

value: ACI

value: drug


title: RBG20257_Old_MSC-L_042


title: pool1-77_S77


title: pool1-81_S81


title: ABZM00855: J1_WT_1.4 [MARS_scRNA]

value: TTGG


title: RBG20256_Old_MSC-L_041


title: ABZM00856: J1_WT_2.1 [MARS_scRNA]

value: ACAG


title: Ctlr_D14_LD11R_Luminal

value: luminal

value: virgin


title: pool1-75_S75


title: Ctlr_D14_LD12R_Basal

description: bulk sample from basal normal mammary glands from young ACI rats, collected at Day 14 (14 days after the treatment was stopped) from a control animal


title: RBG20255_Old_MSC-L_040

value: mesenchymal and endothelial cells


title: Ctlr_D14_LD11R_Basal


title: Ctlr_D14_LD11L_Luminal


title: pool1-76_S76

value: lymph node high-endothelial venules


title: ABZM00854: J1_WT_1.3 [MARS_scRNA]

value: CATG


title: ABZM00853: J1_WT_1.2 [MARS_scRNA]

value: AGTC


title: pool1-74_S74


title: ABZM00852: J1_WT_1.1 [MARS_scRNA]

value: ATGC


title: RBG20254_Old_MSC-L_039

value: MSC-L

value: Old


title: RBG20233_Young_MSC-L_053

value: Young


title: Ctlr_D14_LD11L_Basal

value: normal mammary gland

value: basal

value: control


title: RBG20232_Young_MSC-L_052


title: ABZM00851: J1_WT_8h.4 [MARS_scRNA]

value: J1 (SCRC1010, ATCC)

value: CTCG


title: pool1-72_S72


title: pool1-73_S73


title: pool1-71_S71


title: RBG20231_Young_MSC-L_051


title: ABZM00850: J1_WT_8h.3 [MARS_scRNA]

value: GGAC


title: Drug_D7_LD9L_Luminal

value: normal ACI

value: ACI

value: drug


title: pool1-70_S70


title: pool1-69_S69


title: RBG20229_Young_MSC-L_049

value: mesenchymal and endothelial cells


title: ABZM00847: J1_WT_0.4 [MARS_scRNA]

value: GCAT


title: RBG20230_Young_MSC-L_050


title: ABZM00848: J1_WT_8h.1 [MARS_scRNA]

value: GATC


title: Drug_D0_LD7R_Luminal

value: luminal

value: virgin


title: pool1-68_S68

value: lymph node high-endothelial venules


title: Drug_D7_LD9L_Basal


title: ABZM00846: J1_WT_0.3 [MARS_scRNA]

value: CGGT


title: Drug_D0_LD7L_Luminal


title: pool1-67_S67


title: Drug_D0_LD7L_Basal


title: ABZM00849: J1_WT_8h.2 [MARS_scRNA]

value: GTCC


title: RBG20227_Young_MSC-L_047

value: MSC-L

value: Young


title: RBG20226_Young_MSC-L_046


title: ABZM00845: J1_WT_0.2 [MARS_scRNA]

value: TAGA


title: Drug_D7_LD6R_Luminal

value: normal mammary gland


title: pool1-66_S66


title: Drug_D0_LD7R_Basal

value: basal


title: ABZM00844: J1_WT_0.1 [MARS_scRNA]

value: J1 (SCRC1010, ATCC)

value: AAGT


title: RBG20225_Young_MSC-L_045


title: ABZM00843: DKO16_5.3 [MARS_scRNA]

value: GCTG


title: pool1-65_S65


title: Drug_D7_LD6R_Basal

value: normal ACI

value: ACI

value: drug


title: pool1-64_S64


title: ABZM00842: DKO16_5_EPCAMneg_CXCRposandEPCAMpos_CXCRpos [MARS_scRNA]

value: AGCT


title: Ctlr_D7_LD5R_Basal

description: bulk sample from basal normal mammary glands from young ACI rats, collected at Day 7 (7 days after the treatment was stopped) from a control animal

value: control


title: RBG20223_Young_MSC-L_043

value: mesenchymal and endothelial cells


title: RBG20222_Young_MSC-L_042


title: ABZM00840: DKO16_5_EPCAMpos_CXCRneg.1 [MARS_scRNA]

value: TAAG


title: ABZM00841: DKO16_5_EPCAMpos_CXCRneg.2 [MARS_scRNA]

value: GCCA


title: pool1-61_S61

value: lymph node high-endothelial venules


title: pool1-60_S60


title: Ctlr_D0_LD4R_Basal

description: bulk sample from basal normal mammary glands from young ACI rats, collected at Day 0 (when treatment was stopped) from a control animal

value: virgin


title: RBG20220_Young_MSC-L_040

value: MSC-L

value: Young


title: pool1-63_S63


title: Ctlr_D0_LD4R_Luminal

description: bulk sample from luminal normal mammary glands from young ACI rats, collected at Day 0 (when treatment was stopped) from a control animal

value: normal mammary gland

value: luminal


title: ABZM00839: DKO16_5.2 [MARS_scRNA]

value: GTAG


title: pool1-59_S59


title: ABZM00837: DKO_5_EPCAMneg_CXCRposandEPCAMpos_CXCRpos [MARS_scRNA]

value: CTGA


title: pool1-62_S62


title: RBG20224_Young_MSC-L_044


title: ABZM00838: DKO16_5.1 [MARS_scRNA]

value: CGAG


title: Ctlr_D0_LD3L_Luminal

value: normal ACI


title: Ctlr_D7_LD5R_Luminal

description: bulk sample from luminal normal mammary glands from young ACI rats, collected at Day 7 (7 days after the treatment was stopped) from a control animal

value: ACI


title: pool1-58_S58


title: RBG20219_Young_MSC-L_039


title: RBG20218_Young_MSC-L_038


title: RBG20221_Young_MSC-L_041


title: RBG20217_Young_MSC-L_037


title: pool1-57_S57


title: ABZM00836: DKO_5_EPCAMpos_CXCRneg.2 [MARS_scRNA]

value: TCCG


title: RBG20216_Young_MSC-L_036


title: pool1-56_S56


title: ABZM00835: DKO_5_EPCAMpos_CXCRneg.1 [MARS_scRNA]

value: GGTA


title: Ctlr_D0_LD3R_Luminal

value: control


title: Ctlr_D0_LD3R_Basal

value: basal


title: Ctlr_D0_LD3L_Basal


title: ABZM00834: DKO_5.7 [MARS_scRNA]

value: TTTC


title: RBG20214_Young_MSC-L_034

value: mesenchymal and endothelial cells


title: Ctlr_D7_LD2L_Basal


title: SD-Lum9

description: single cell sample from a sorted luminal fraction from mammary glands from young SD rats, collected at Day 0 (when treatment was stopped) from a drug-treated animal

value: single cell normal SD

value: SD

value: drug


title: RBG20215_Young_MSC-L_035

value: MSC-L

value: Young


title: ABZM00833: DKO_5.6 [MARS_scRNA]

value: GCGC


title: ABZM00832: J1_WT_5_EPCAMneg_CXCRposandEPCAMpos_CXCRpos [MARS_scRNA]

value: J1 (SCRC1010, ATCC)

value: AAAC


title: RBG20193_Old_mOPr_026

value: mOPr

value: Old


title: pool1-53_S53

value: lymph node high-endothelial venules


title: ABZM00831: J1_WT_5_EPCAMpos_CXCRneg.2 [MARS_scRNA]

value: CGCC


title: SD-Lum2

description: single cell sample from a sorted luminal fraction from mammary glands from young SD rats, collected at Day 0 (when treatment was stopped) from a control animal

value: normal mammary gland

value: luminal

value: virgin


title: RBG20192_Old_mOPr_025


title: pool1-54_S54


title: pool1-52_S52


title: RBG20191_Old_mOPr_024


title: Ctlr_D7_LD2L_Luminal

value: normal ACI

value: ACI

value: control


title: SD-Lum1

value: single cell normal SD

value: SD


title: SD-Lum14

value: drug


title: RBG20190_Old_mOPr_023

value: mesenchymal and endothelial cells


title: pool1-50_S50


title: pool1-51_S51


title: RBG20189_Old_mOPr_022


title: ABZM00829: J1_WT_5.7 [MARS_scRNA]

value: TCTA


title: SD-Lum13


title: pool1-55_S55


title: SD-Lum12


title: pool1-49_S49


title: SD-Lum3


title: pool1-48_S48


title: ABZM00820: DKO16_4.3 [MARS_scRNA]

value: CTGA


title: RBG20188_Old_mOPr_021


title: ABZM00819: DKO16_4.2 [MARS_scRNA]

value: AGGG


title: RBG20187_Old_mOPr_020

value: mOPr


title: SD-Lum11


title: ABZM00818: DKO16_4.1 [MARS_scRNA]

value: TCCG


title: ABZM00830: J1_WT_5_EPCAMpos_CXCRneg.1 [MARS_scRNA]

value: J1 (SCRC1010, ATCC)

value: ACTT


title: SD-Lum10

value: normal mammary gland


title: RBG20185_Old_mOPr_019

value: Old


title: pool1-47_S47

value: lymph node high-endothelial venules


title: RBG20184_Old_mOPr_018


title: ABZM00817: DKO_4.8 [MARS_scRNA]

value: GGTA


title: pool1-45_S45


title: ABZM00816: DKO_4.7 [MARS_scRNA]

value: TTTC


title: ABZM00821: J1_WT_5.6 [MARS_scRNA]

value: CGAG


title: ABZM00815: DKO_4.6 [MARS_scRNA]

value: GCGC


title: pool1-44_S44


title: RBG20183_Old_mOPr_017


title: SD-Bas9

description: single cell sample from a sorted basal fraction from mammary glands from young SD rats, collected at Day 0 (when treatment was stopped) from a drug-treated animal

value: single cell normal SD

value: SD

value: basal

value: virgin


title: pool1-43_S43


title: RBG20182_Old_mOPr_016

value: mesenchymal and endothelial cells


title: SD-Bas2

description: single cell sample from a sorted basal fraction from mammary glands from young SD rats, collected at Day 0 (when treatment was stopped) from a control animal

value: control


title: ABZM00814: J1_WT_4.8 [MARS_scRNA]

value: AAAC


title: pool1-42_S42


title: RBG20180_Old_mOPr_014

value: mOPr


title: SD-Bas1


title: pool1-46_S46


title: RBG20181_Old_mOPr_015


title: RBG20178_Old_OPr_029

value: OPr


title: ABZM00813: J1_WT_4.7 [MARS_scRNA]

value: J1 (SCRC1010, ATCC)

value: CGCC


title: pool1-41_S41


title: RBG20167_Old_OPr_028

value: Old


title: SD-Bas13

value: normal mammary gland

value: drug


title: RBG20166_Old_OPr_027


title: pool1-40_S40

value: lymph node high-endothelial venules


title: ABZM00811: DKO16_3.3 [MARS_scRNA]

value: TCTA


title: ABZM00810: DKO16_3.2 [MARS_scRNA]

value: TGAT


title: SD-Bas3

value: single cell normal SD


title: ABZM00812: J1_WT_4.6 [MARS_scRNA]

value: ACTT


title: SD-Bas12

value: SD

value: basal


title: pool1-39_S39


title: RBG20158_Young_mOPr_026

value: mesenchymal and endothelial cells

value: Young


title: pool1-38_S38


title: SD-Bas11

value: virgin


title: pool1-37_S37


title: ABZM00805: DKO_3.3 [MARS_scRNA]

value: CATG


title: RBG20157_Young_mOPr_025

value: mOPr


title: pool1-36_S36


title: SD-Bas14


title: pool1-35_S35


title: ACI-Lum8

description: single cell sample from a sorted luminal fraction from mammary glands from young ACI rats, collected at Day 0 (when treatment was stopped) from a control animal

value: single cell normal ACI

value: ACI

value: luminal

value: control


title: SD-Bas10

value: normal mammary gland

value: drug


title: ACI-Lum7


title: ABZM00803: DKO_3.1 [MARS_scRNA]

value: GGAC


title: RBG20155_Young_mOPr_023


title: pool1-34_S34

value: lymph node high-endothelial venules


title: RBG20156_Young_mOPr_024


title: pool1-33_S33


title: RBG20152_Young_mOPr_021


title: ABZM00809: DKO16_3.1 [MARS_scRNA]

value: ATCA


title: ABZM00801: J1_WT_3.2 [MARS_scRNA]

value: J1 (SCRC1010, ATCC)

value: GATC


title: ABZM00804: DKO_3.2 [MARS_scRNA]

value: AGTC


title: pool1-32_S32


title: RBG20154_Young_mOPr_022

value: mesenchymal and endothelial cells


title: ACI-Lum9


title: RBG20151_Young_mOPr_020

value: Young


title: ACI-Lum16

description: single cell sample from a sorted luminal fraction from mammary glands from young ACI rats, collected at Day 0 (when treatment was stopped) from a drug-treated animal

value: virgin


title: ACI-Lum15


title: pool1-31_S31


title: RBG20150_Young_mOPr_019


title: ABZM00799: DNMT3b_dEB6_P7 [MARS_scRNA]

value: DNMT3B_KO_Cell Bank Riken BioResource Research Center

value: CGGT


title: ABZM00798: DNMT3b_dEB6_P5 [MARS_scRNA]

value: TAGA


title: pool1-30_S30


title: ACI-Bas9

description: single cell sample from a sorted basal fraction from mammary glands from young ACI rats, collected at Day 0 (when treatment was stopped) from a control animal

value: single cell normal ACI

value: ACI

value: basal


title: RBG20148_Young_OPr_044

value: OPr


title: ACI-Bas8

value: normal mammary gland

value: control


title: pool1-29_S29

value: lymph node high-endothelial venules


title: ABZM00802: J1_WT_3.3 [MARS_scRNA]

value: GTCC


title: RBG20147_Young_OPr_043


title: pool1-28_S28


title: ACI-Bas7


title: ABZM00797: DNMT3a_dEB6_P7 [MARS_scRNA]

value: DNMT3A_KO_Cell Bank Riken BioResource Research Center

value: AAGT


title: ACI-Bas16

description: single cell sample from a sorted basal fraction from mammary glands from young ACI rats, collected at Day 0 (when treatment was stopped) from a drug-treated animal

value: drug


title: ABZM00800: J1_WT_3.1 [MARS_scRNA]

value: J1 (SCRC1010, ATCC)

value: GCAT


title: ACI-Bas15

value: virgin


title: RBG20145_Young_OPr_042

value: mesenchymal and endothelial cells

value: Young


title: RBG20228_Young_MSC-L_048

value: MSC-L


title: pool1-27_S27


title: RBG20143_Young_OPr_041


title: ABZM00794: J1_P9P2_dEB6_P7.1 [MARS_scRNA]

value: GCCA


title: ABZM00795: J1_P9P2_dEB6_P7.2 [MARS_scRNA]

value: AGCT


title: RBG20141_Young_OPr_040


title: ABZM00793: J1_P9P2dEB6_P5 [MARS_scRNA]

value: TAAG


title: ACI-Bas12

value: single cell normal ACI

value: ACI

value: basal


title: pool1-25_S25

value: lymph node high-endothelial venules


title: ACI-Lum12

value: normal mammary gland

value: luminal


title: RBG20139_Young_OPr_039

value: OPr


title: pool1-23_S23


title: Ch1 HL 4 h, rep2

city: Singapore

first: Eugene

last: Koh

address: 1 Research Link

country: Singapore

institute: Temasek Life Sciences Laboratories

data_processing:
Bcl files were converted into fastq by bcl2fastq. Demultiplexing is done using the sample barcode found on R2, the UMI found on R2 is inserted in the read name (in R1 fastq).  R1 Fastq data submitted. MARS-seq analysis was done using the UTAP transcriptome analysis pipeline (Kohen et al., 2019). Reads were trimmed using Cutadapt and mapped to the Arabidopsis thaliana genome (Araport11) using STAR v2.4.2a. The pipeline quantifies the genes annotated in Araport11 (that have expanded with 1000 bases toward 5’ edge and 100 bases toward 3’ bases). Counting was done using htseq-count (union mode). Genes having minimum 5 UMI-corrected reads in at least one sample, were considered. Normalization of the counts and differential expression analysis was performed using DESeq2 package.
Assembly: Araport11
Supplementary files format and content: Tab-delimited text file contains raw and normalized counts, and DESeq2 analysis for genes after filtering based on expression levels (sum normalized count in all samples greater than 5)

organism: Arabidopsis thaliana

source_name: Ch1 whole seedlings

growth_protocol: Plants were grown on standing square Petri dishes on 1/2MS + 1% sucrose, pH5.8. Growth room with a 16h light/8h dark cycle, and temperature of 22oC

extract_protocol:
Standard Trizol RNA extraction
Total RNA was eluted with 50ul of UPW and stored at -80C. For library preparation RNA was used for the bulk MARS-seq protocol (Jaitin et al. 2014 Science.343:776-9). MARS-seq libraries were sequenced using Illumina NextSeq 500 High Output v2 Kit (75 cycles).

treatment_protocol: Plants were equilibrated for at least 1hour in ddw in petri dishes, then sorted into a set of 12-well plates with ddw in preparation for treatment. Samples were shifted from these holding plates to plates containing DDW, and incubated under low light (30 µE) or high light (1000 µE) for 0, 1, 2, 4 h

value: Ch1 whole seedlings

tag: time point

value: high light (1000 uE)

value: 2 week old

tag: ecotype


title: ABZM00796: DNMT3a_dEB6_P5 [MARS_scRNA]

value: DNMT3A_KO_Cell Bank Riken BioResource Research Center

value: GCTG


title: ABZM00792: J1_P9P2_dEB6_P5 [MARS_scRNA]

value: J1 (SCRC1010, ATCC)

value: GTAG


title: Ch1 HL 4 h, rep3


title: ABZM00791: J1_P9P2_dEB4_P5 [MARS_scRNA]

value: CGAG


title: RBG20138_Young_OPr_038

source_name: endosteum and central marrow

value: mesenchymal and endothelial cells

value: Young


title: pool1-24_S24


title: ABZM00790: TKO_6.2 [MARS_scRNA]

value: TKO_Cell Bank Riken BioResource Research Center

value: CTGA


title: RBG20133_Young_OPr_036


title: Ch1 HL 4 h, rep1


title: Ch1 HL 2 h, rep3


title: pool1-26_S26


title: ABZM00789: TKO_6.1 [MARS_scRNA]

value: AGGG


title: RBG20131_Young_OPr_035


title: pool1-20_S20

value: lymph node high-endothelial venules


title: RBG20130_Young_OPr_034


title: pool1-18_S18


title: pool1-21_S21


title: Ch1 HL 2 h, rep1


title: pool1-19_S19


title: ABZM00787: DKO_6.4 [MARS_scRNA]

value: GGTA


title: ABZM00786: J1_WT_6.5 [MARS_scRNA]

value: TTTC


title: RBG20128_Old_OPr_026

value: OPr

value: Old


title: RBG20135_Young_OPr_037


title: pool1-22_S22


title: Ch1 HL 1 h, rep2

value: Ch1 whole seedlings

value: high light (1000 uE)


title: RBG20129_Young_OPr_033


title: pool1-17_S17


title: Ch1 HL 1 h, rep1

value: 2 week old


title: ABZM00785: J1_WT_6.4 [MARS_scRNA]

value: GCGC


title: RBG20126_Old_OPr_024


title: RBG20127_Old_OPr_025


title: RBG20125_Old_OPr_023


title: Ch1 HL 2 h, rep2


title: pool1-16_S16


title: ABZM00783: TKO_5.1 [MARS_scRNA]

value: CGCC


title: Ch1 HL 0 h, rep3


title: Ch1 HL 0 h, rep2


title: ABZM00788: DKO_6.5 [MARS_scRNA]

value: TCCG


title: ABZM00782: DKO_5.5 [MARS_scRNA]

value: ACTT


title: ABZM00784: TKO_5.2 [MARS_scRNA]

value: AAAC


title: Ch1 HL 1 h, rep3


title: pool1-14_S14


title: pool1-13_S13


title: Ch1 LL 4 h, rep3

value: low light (30 uE)


title: pool1-12_S12


title: ABZM00780: J1_WT_5.5 [MARS_scRNA]

value: J1 (SCRC1010, ATCC)

value: TGAT


title: Ch1 HL 0 h, rep1


title: ABZM00781: DKO_5.4 [MARS_scRNA]

value: TCTA


title: pool1-11_S11

value: lymph node high-endothelial venules


title: ABZM00779: J1_WT_5.4 [MARS_scRNA]

value: ATCA


title: Ch1 LL 4 h, rep1


title: RBG20122_Old_OPr_020

value: mesenchymal and endothelial cells


title: pool1-15_S15


title: RBG20121_Old_OPr_019

value: OPr


title: RBG20123_Old_OPr_021

value: Old


title: Ch1 LL 4 h, rep2

value: Ch1 whole seedlings


title: Ch1 LL 2 h, rep3


title: ABZM00778: TKO_4.2 [MARS_scRNA]

value: TKO_Cell Bank Riken BioResource Research Center

value: CTAC


title: ABZM00777: TKO_4.1 [MARS_scRNA]

value: ACAG


title: pool1-09_S9


title: RBG20124_Old_OPr_022


title: RBG20120_Old_OPr_018


title: Ch1 LL 2 h, rep2

value: 2 week old


title: ABZM00776: DKO_4.5 [MARS_scRNA]

value: TTGG


title: pool1-10_S10


title: RBG20118_Old_OPr_016


title: Ch1 LL 2 h, rep1


title: pool1-07_S7


title: pool1-06_S6


title: RBG20116_Old_OPr_015


title: Ch1 LL 1 h, rep3


title: RBG20114_Old_OPr_014


title: RBG20119_Old_OPr_017


title: Ch1 LL 1 h, rep2


title: pool1-05_S5


title: ABZM00774: J1_WT_4.5 [MARS_scRNA]

value: AGTC


title: ABZM00773: J1_WT_4.4 [MARS_scRNA]

value: ATGC


title: Ch1 LL 1 h, rep1

value: low light (30 uE)


title: pool1-04_S4


title: RBG20112_Old_OPr_013


title: ABZM00775: DKO_4.4 [MARS_scRNA]

value: CATG


title: pool1-08_S8


title: Ch1 LL 0 h, rep3


title: RBG20110_Old_OPr_012


title: pool1-03_S3


title: Ch1 LL 0 h, rep2


title: RBG20091_Young_mOPr_018

value: mOPr

value: Young


title: ABZM00770: DKO_7_g.2 [MARS_scRNA]

value: GTCC


title: ABZM00772: DKO_7_g.4 [MARS_scRNA]

value: CTCG


title: RBG20109_Old_OPr_011

value: mesenchymal and endothelial cells


title: Ch1 LL 0 h, rep1


title: pool1-01_S1

value: lymph node high-endothelial venules


title: RBG20090_Young_mOPr_017


title: RBG20089_Young_mOPr_016


title: VPM28210630_S24_R1_001_VP24_B6

city: Amsterdam

first: Mattia

last: Falcone

address: Plesmanlaan 121

department: Oncogenomics

country: Netherlands

institute: NKI

description: irradiated cultured in media without Ser/Gly

data_processing:
Libraries were run on an Illumina NextSeq500 using the High Output 75 cycles kit (2x36 cycles, paired end reads, single index).
Quality checks on the raw RNA-Seq data files were done using FastQC and Fastq Screen
Alignment of the RNA-Seq paired-end reads was to the GRCm38 version of the mouse genome and annotation using HiSat2 and TopHat
Gene expression levels were quantified using the featureCounts tool available on Galaxy.org
Genome_build: GRCm38
Supplementary_files_format_and_content: Gene expression levels were quantified using the featureCounts tool available on Galaxy.org and then nomalised with DESeq2 in R version 3.3.1 in R-Studio (version 0.99.903).

source_name: 4T1 cells

growth_protocol: RPMI (Invitrogen, 31870025) supplemented with 10% FBS, 1% penicillin-streptomycin, 0.2% amphotericin B and glutamine (2mM)

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (Qiagen)
Libraries were prepared using the TruSeq stranded totalRNA with RiboZero kit (Illumina). Quality and quantity of the cDNA libraries was assessed on an Agilent 2200 Tapestation (D1000 screentape).

treatment_protocol: 4T1 cells were cultured with media containing either serine and glycine (+SG) or not (-SG) and subsequently irradiated with a final dose of radiations 5 Gy (IR) for 24h before RNA extraction

tag: radiation

tag: serine/glycine

value: -Ser/Gly

tag: origin

value: murine breast cancer line


title: ABZM00768: DNMT3B_7_g.4 [MARS_scRNA]

value: DNMT3B_KO_Cell Bank Riken BioResource Research Center

value: GCAT


title: VPM28210630_S23_R1_001_VP23_B5


title: pool1-02_S2


title: ABZM00771: DKO_7_g.3 [MARS_scRNA]

value: GGAC


title: RBG20088_Young_OPr_032

value: OPr


title: VPM28210630_S22_R1_001_VP22_B4


title: ABZM00766: DNMT3B_7_g.2 [MARS_scRNA]

value: TAGA


title: ABZM00767: DNMT3B_7_g.3 [MARS_scRNA]

value: CGGT


title: ABZM00769: DKO_7_g.1 [MARS_scRNA]

value: GATC


title: RBG20087_Young_OPr_031


title: VPM28210630_S21_R1_001_VP21_B3

description: irradiated cultured in media with Ser/Gly

value: +Ser/Gly


title: RBG20086_Young_OPr_030


title: ABZM00765: DNMT3B_7_g.1 [MARS_scRNA]

value: AAGT


title: ABZM00764: DNMT3A_7_g.4 [MARS_scRNA]

value: DNMT3A_KO_Cell Bank Riken BioResource Research Center

value: GCTG


title: MPP4-old-3

type: RNA

city: New York

first: Emmanuelle

last: Passegue

state: NY

department: Columbia Stem Cell Initiative

institute: Columbia University Irving Medical Center

description: Gene expression data from mouse bone marrow hematopoietic progenitor populations

hyb_protocol: Labeled cRNA were hybridized following the GeneChip Expression Analysis Technical Manual 702232 Rev. 3.

scan_protocol: Microarray chips were scanned using an Affymetrix GCS 3000 Scanner.

data_processing: Gene expression microarray data were normalized using RMA followed by quantile normalization as implemented in the 2.15.1 R package.

label: biotin

label_protocol: Sense-strand RNA was transcribed from amplified RNA with the NuGen WT-Ovation Exon Module, purified using Qiagen QIAquick columns and subsequently fragmented and biotinylated using the NuGen Encore Biotin module according to manufacturers' instructions. All samples were  checked for proper amplification and fragmentation on an Agilent 2100 Bioanalyzer using RNA pico chips according to manufacturer's instructions. Amplified products were quantified using a NanoDrop spectrophotometer.

extract_protocol: Total RNA was isolated using the Arcturus PicoPure kit according to manufacturer's instructions, and included an in-column Dnase I digest using Qiagen DNase I. Resulting RNA was amplified using the NuGen Pico WTA kit. Amplified products were purified using Qiagen QIAquick columns according to the NuGen protocol.

treatment_protocol: MPP populations were isolated from bone marrow by flow cytometry. cKit-enriched cells were stained on ice in HBSS supplemented with 2% FBS and dead cells were excluded using 1 μg/ml propidium iodide. Cells were double-sorted on a BD FACSAria II cell sorter to ensure maximum purity, and 20,000 cells from each population were sorted directly into Trizol LS for RNA extraction.

tag: genotype

value: wild-type

value: bone marrow

value: Old


title: VPM28210630_S20_R1_001_VP20_B2


title: RBG20085_Young_OPr_029

value: mesenchymal and endothelial cells

value: Young


title: ABZM00763: DNMT3A_7_g.3 [MARS_scRNA]

value: AGCT


title: RBG20084_Young_OPr_028


title: VPM28210630_S18_R1_001_VP18_A6

description: non-irradiated cultured in media without Ser/Gly

value: IR-CTRL

value: -Ser/Gly

value: murine breast cancer line


title: VPM28210630_S19_R1_001_VP19_B1


title: RBG20083_Young_OPr_027

value: OPr


title: MPP4-old-1


title: ABZM00762: DNMT3A_7_g.2 [MARS_scRNA]

value: GCCA


title: MPP4-old-2


title: RBG20082_Young_OPr_026


title: MPP4-young-4


title: MPP4-young-3


title: MPP4-young-5


title: ABZM00761: DNMT3A_7_g.1 [MARS_scRNA]

value: TAAG


title: ABZM00760: J1_WT_7_g.4 [MARS_scRNA]

value: J1 (SCRC1010, ATCC)

value: GTAG


title: RBG20081_Young_OPr_025


title: VPM28210630_S15_R1_001_VP15_A3

description: non-irradiated cultured in media with Ser/Gly

value: +Ser/Gly


title: VPM28210630_S16_R1_001_VP16_A4


title: RBG20080_Young_OPr_024


title: VPM28210630_S14_R1_001_VP14_A2


title: MPP4-young-2


title: VPM28210630_S17_R1_001_VP17_A5


title: MPP4-young-1


title: RBG20078_Young_OPr_022


title: ABZM00759: J1_WT_7_g.3 [MARS_scRNA]

value: CGAG


title: RBG20079_Young_OPr_023


title: ABZM00758: J1_WT_7_g.2 [MARS_scRNA]

value: CTGA


title: VPM28210630_S13_R1_001_VP13_A1


title: ABZM00756: DKO_6.3 [MARS_scRNA]

value: TCCG


title: ABZM00757: J1_WT_7_g.1 [MARS_scRNA]

value: AGGG


title: RBG20077_Young_OPr_021


title: EO047: Old_IL1R1-/-_LK

data_processing:
Raw fastq files were aligned and processed to count matrices using Cell Ranger v5.0.1.
We performed QC and kept: cells with number of detected genes > 150, cells with number of counts < 100,000, those genes where at least 1 UMI is detected in at least 1 cell, and only those cells with less than 20% of UMIs corresponding to mitochondrial genes.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: tar archives include barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, and h5 files; contain a matrix of selected cellular barcodes, Ensembl IDs, official gene symbols and read counts.

molecule: polyA RNA

source_name: Bone marrow

growth_protocol: Mice were maintained in CUIMC animal facilities under SPF conditions.

extract_protocol:
For stromal samples, bone chips (endosteum) were harvested by crushing bones and washing away marrow with ice-cold HBSS. Marrow plugs (central marrow) were harvested by flushing intact plugs with ice-cold HBSS. All samples were subjected to collagenase digestion as indicated in the manuscript to liberate stromal cells, filtered through 100 micron mesh, treated with red blood cell lysis buffer, and stained for surface protein expression. Live Ter119-/CD45- cells from each compartment were directly sorted into filter-sterilized alphaMEM supplemented with 10% FBS. For bone marrow samples, marrow was liberated by crushing bones, resuspended in ice-cold HBSS, filtered through 40 micron mesh, treated with red blood cell lysis buffer and stained for surface protein expression. Live Lineage-/cKit+ (LK) and Lineage-/cKit+/Sca-1+ (LSK) cells were sorted directly into HBSS supplemented with 2% FBS. For all samples, purity was confirmed to be >95% by running freshly sorted cells on the same sorter.
Libraries were constructed following manufacturer's instructions for Chromium Single Cell 3' Library & Bead Kit v3 (10X Genomics). 5,000 cells were loaded for each sample and samples were sequenced in a NextSeq 550 sequencer (Illumina).

value: Bone marrow

value: Hematopoietic stem and progenitor cells

value: 24 months


title: EO048: Old_IL1R1-/-_LSK


title: MPP3-old-3

value: wild-type

value: bone marrow

value: Old


title: MPP3-old-2


title: ABZM00754: DKO_6.1 [MARS_scRNA]

value: TTTC


title: ABZM00755: DKO_6.2 [MARS_scRNA]

value: GGTA


title: MPP3-old-1


title: RBG20075_Young_OPr_020

value: mesenchymal and endothelial cells

value: OPr

value: Young


title: MPP3-young-3


title: RBG20074_Young_OPr_019


title: MPP3-young-2


title: EO046: Old_WT_LSK

value: Wild type


title: 48_B F ATG HYP

city: Sheridan

first: Kenneth

middle: L

last: Jones

state: Wyoming

address: 1309 Coffeen Avenue STE 10090

institute: Bioinformatic Solutions LLC

description:
Group P
sample name: 48

data_processing:
Quality trim to a minimum of Q15
Map to the mm10 genome using GSNAP version 2012-07-20 using the commandline: gsnap -d mm10_total -v mm10_total.snp138 --use-splicing=mm10_total.ensembl.splicesites --max-mismatches=0.06 -i2 -n2 -Q --gunzip --force-xs-dir --nofails -B5 -t${num_processors} --read-group-id=$j --read-group-name=$j --read-group-library=$j --read-group-platform=illumina -A sam $outfile_R1 $outfile_R2 | samtools view -bS -@ ${num_processors} - | samtools sort -@ ${num_processors} -o ./Illumina_data/${j}.sorted.bam -; samtools index ./Illumina_data/${j}.sorted.bam
sort and index using SAMTOOLS
call FPKM using CUFFLINKS
Assembly: mm10
Supplementary files format and content: Excel file containing FPKM values

source_name: Lung Tissue

extract_protocol:
Total RNA was extracted with Qiagen Rneasy Mini Kit
Illumina directional mRNA prep; HiSeq2000 using 2x150bp format

treatment_protocol: Adult mice were exposued to either a single I.P injection of saline or 25mg/kg of ATG. Mice were these placed in either room air or hyperoxia (>95%) oxygen for 96hrs. Following exposure mice were dosed with ketamine/xylazine for euthanazia; and lung tissue was collected. ~20ug of tissue was collected for transcriptomics, which was snap frozen at the time of colelction. Stored in -70C until time of processing for RNA-sequencing.

value: lung

tag: Sex

value: Female

tag: atg treatment

value: Aurothioglucose

tag: air treatment

value: Hyperoxia


title: EO045: Old_WT_LK

tag: tissue


title: RBG20073_Young_OPr_018


title: 46_B F ATG HYP

description:
Group P
sample name: 46

tag: strain


title: 47_B F ATG HYP

description:
Group P
sample name: 47


title: EO044: Old_IL1R1-/-_CentralMarrow

source_name: Central marrow stroma

value: Central marrow stroma

tag: cell type

value: Bone marrow stromal cells


title: ABZM00752: DNMT3B_6.2 [MARS_scRNA]

value: DNMT3B_KO_Cell Bank Riken BioResource Research Center

value: AAAC


title: 45_B F SAL HYP

description:
Group O
sample name: 45

value: Saline


title: ABZM00751: DNMT3B_6.1 [MARS_scRNA]

value: CGCC


title: RBG20071_Young_OPr_016

tag: cell population


title: 44_B F SAL HYP

description:
Group O
sample name: 44


title: RBG20070_Young_OPr_015

tag: age


title: EO042: Old_WT_CentralMarrow

value: 24 months


title: EO041: Old_WT_Endosteum

source_name: Endosteal stroma

value: Endosteal stroma


title: RBG20072_Young_OPr_017


title: ABZM00749: DNMT3A_6.2 [MARS_scRNA]

source_name: Cell Bank Riken BioResource Research Center)

tag: cell line/mouse line

value: DNMT3A_KO_Cell Bank Riken BioResource Research Center

value: TCTA


title: ABZM00750: DNMT3A_6.3 [MARS_scRNA]

value: ACTT


title: RBG20069_Young_OPr_014

value: mesenchymal and endothelial cells

value: OPr

value: Young


title: ABZM00748: DNMT3A_6.1 [MARS_scRNA]

value: TGAT


title: 42_B F ATG RA

description:
Group N
sample name: 42

value: lung

value: Female

value: Aurothioglucose

value: Room Air


title: EO036: Young_WT_LSK

value: Central marrow stroma

value: Hematopoietic stem and progenitor cells

value: 10 weeks

value: Wild type


title: 41_B F ATG RA

description:
Group N
sample name: 41


title: EO035: Young_WT_LK

value: Bone marrow


title: 43_B F SAL HYP

description:
Group O
sample name: 43

value: Saline

value: Hyperoxia


title: EO043: Old_IL1R1-/-_Endosteum

value: Endosteal stroma

value: Bone marrow stromal cells

value: 24 months


title: RBG20047_Old_MSC-L_037

value: mesenchymal and endothelial cells

value: MSC-L

value: Old


title: ABZM00746: J1_WT_6.2 [MARS_scRNA]

source_name: J1 (SCRC1010, ATCC)

value: J1 (SCRC1010, ATCC)

value: CTAC


title: RBG20046_Old_MSC-L_036


title: ABZM00753: DNMT3B_6.3 [MARS_scRNA]

value: DNMT3B_KO_Cell Bank Riken BioResource Research Center

value: GCGC


title: ABZM00747: J1_WT_6.3 [MARS_scRNA]

value: ATCA


title: 39_B F SAL RA

description:
Group M
sample name: 39

value: lung

value: Female

value: Room Air


title: RBG20044_Old_MSC-L_035


title: ABZM00745: J1_WT_6.1 [MARS_scRNA]

value: ACAG


title: PP_STm_4

first: Ziv

last: Shulman

address: Herzl St 234

department: Department of Immunology

data_processing:
Reads were trimmed using Cutadapt
Reads were aligned to the genome using STAR
Quantification was done using htseq-count as previously described in R. Kohen, BMC Bioinformatics, 2019.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file with Deseq2 output

source_name: Peyer's patch

growth_protocol: Fresh cells were sorted for RNA preparation

extract_protocol:
mRNA was extracted from sorted cells using mRNA direct kit (Invitrogen) and mRNA from each sample was barcoded during reverse transcription and pooled.
Libraries were prepared using a bulk adaptation of the previously described protocol (Keren-Shaul et al. Nat. Protoc, 2019 and Jaitin et al. Science, 2014).Following Agencourt Ampure XP bead cleanup (Beckman Coulter), the pooled samples underwent second strand synthesis and were linearly amplified by T7 in vitro transcription. The resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with Illumina sequences during ligation, RT, and PCR.  Libraries were quantified by Qubit and TapeStation as well as by qPCR for the ACTB gene as previously described. Sequencing was done using a Nextseq 75 cycle high output kit (Illumina; paired end sequencing).

treatment_protocol: Mice were orally infected with Salmonella Typhimurium for 3 days or injected with 50 microgram LPS twice and analysed on day 3. Peyer's patches were harvested and cells were sorted into lysis buffer (invitrogen Dynabeads kit) for RNA extraction.

value: Whole tissue extract

tag: mouse strain

value: wild type

tag: treatment

value: STm infected


title: 38_B F SAL RA

description:
Group M
sample name: 38

value: Saline


title: PP_STm_3


title: PP_STm_5


title: ABZM00744: DKO_5.3 [MARS_scRNA]

source_name: Dr. Masaki Okano

tag: batch index

value: TTGG


title: RBG20043_Old_MSC-L_034

value: mesenchymal and endothelial cells


title: PP_STm_2


title: RBG20048_Old_MSC-L_038

value: MSC-L


title: 37_B F SAL RA

description:
Group M
sample name: 37


title: RBG20042_Old_MSC-L_033

value: Old


title: 36_H F ATG HYP

description:
Group L
sample name: 36

value: Aurothioglucose

value: Hyperoxia


title: 40_B F ATG RA

description:
Group N
sample name: 40


title: PP_STm_1


title: RBG20041_Old_MSC-L_032


title: PP_Control_4

value: untreated


title: ABZM00742: DKO_5.1 [MARS_scRNA]

value: AGTC


title: ABZM00716: DNMT3B_5.3 [MARS_scRNA]

value: DNMT3B_KO_Cell Bank Riken BioResource Research Center

value: AAAC


title: MPP3-young-1

value: wild-type

value: bone marrow

value: Young


title: 34_H F ATG HYP

description:
Group L
sample name: 34

value: lung

value: Female


title: 35_H F ATG HYP

description:
Group L
sample name: 35


title: PP_Control_2

value: Whole tissue extract

value: wild type


title: ABZM00715: DNMT3B_5.2 [MARS_scRNA]

value: CGCC


title: PP_Control_3


title: ABZM00714: DNMT3B_5.1 [MARS_scRNA]

value: ACTT


title: 33_H F SAL HYP

description:
Group K
sample name: 33

value: Saline


title: 31_H F SAL HYP

description:
Group K
sample name: 31


title: RBG20039_Old_MSC-L_030

value: mesenchymal and endothelial cells

value: MSC-L

value: Old


title: 32_H F SAL HYP

description:
Group K
sample name: 32

value: Hyperoxia


title: GCB2_STm_IFNg_4

source_name: B cells

value: PP GC B cell (B220+, CD138-, FAS+, CD38-)

value: STm infected


title: ABZM00743: DKO_5.2 [MARS_scRNA]

value: CATG


title: RBG20037_Old_MSC-L_028


title: RBG20038_Old_MSC-L_029


title: 30_H F ATG RA

description:
Group J
sample name: 30

value: Aurothioglucose

value: Room Air


title: ABZM00711: DNMT3A_5.1 [MARS_scRNA]

value: DNMT3A_KO_Cell Bank Riken BioResource Research Center

value: ATCA


title: RBG20036_Old_MSC-L_027


title: GCB2_STm_IFNg_3


title: RBG20035_Old_MSC-L_026


title: RBG20040_Old_MSC-L_031


title: 29_H F ATG RA

description:
Group J
sample name: 29

value: lung

value: Female


title: ABZM00710: J1_WT_5.3 [MARS_scRNA]

value: J1 (SCRC1010, ATCC)

value: CTAC


title: GCB2_STm_IFNg_2

value: wild type


title: GCB2_STm_IFNg_1


title: ABZM00709: J1_WT_5.2 [MARS_scRNA]

value: ACAG


title: 28_H F ATG RA

description:
Group J
sample name: 28


title: RBG20034_Old_MSC-L_025

value: mesenchymal and endothelial cells


title: PP_Control_1

value: Whole tissue extract

value: untreated


title: 27_H F SAL RA

description:
Group I
sample name: 27

value: Saline


title: ABZM00712: DNMT3A_5.2 [MARS_scRNA]

value: TGAT


title: 26_H F SAL RA

description:
Group I
sample name: 26


title: ABZM00713: DNMT3A_5.3 [MARS_scRNA]

value: TCTA


title: GCB_STm_2

value: PP GC B cell (B220+, CD138-, FAS+, CD38-)

value: STm infected


title: ABZM00707: DKO_4.3 [MARS_scRNA]

value: CATG


title: RBG20030_Old_MSC-L_022

value: MSC-L

value: Old


title: ABZM00706: DKO_4.2 [MARS_scRNA]

value: AGTC


title: GCB_STm_1


title: RBG20033_Old_MSC-L_024


title: 24_B M ATG HYP

description:
Group H
sample name: 24

value: lung

value: Male

value: Aurothioglucose

value: Hyperoxia


title: GCB2_Control_3

value: wild type


title: GCB_STm_3


title: RBG20029_Old_MSC-L_021

value: mesenchymal and endothelial cells


title: ABZM00705: DKO_4.1 [MARS_scRNA]

value: TAGA


title: RBG20008_Young_MSC-L_033

value: Young


title: 23_B M ATG HYP

description:
Group H
sample name: 23


title: RBG20007_Young_MSC-L_032


title: GCB2_Control_2

value: untreated


title: ABZM00704: DNMT3B_4.3 [MARS_scRNA]

value: DNMT3B_KO_Cell Bank Riken BioResource Research Center

value: AAGT


title: 22_B M ATG HYP

description:
Group H
sample name: 22


title: 21_B M SAL HYP

description:
Group G
sample name: 21

value: Saline


title: ABZM00708: J1_WT_5.1 [MARS_scRNA]

value: J1 (SCRC1010, ATCC)

value: TTGG


title: RBG20031_Old_MSC-L_023

value: MSC-L


title: RBG20006_Young_MSC-L_031


title: ABZM00700: DNMT3B_4.1 [MARS_scRNA]

value: GCAT


title: RBG20005_Young_MSC-L_030


title: Monocytes_STm_IFNg_4

source_name: Monocytes

value: Ly6G- CD11b+ Ly6Chi

value: STm infected


title: 20_B M SAL HYP

description:
Group G
sample name: 20

value: lung

value: Male


title: 19_B M SAL HYP

description:
Group G
sample name: 19

value: Hyperoxia


title: RBG20004_Young_MSC-L_029


title: Monocytes_STm_IFNg_3

value: wild type


title: ABZM00656: DNMT3A_4.3 [MARS_scRNA]

value: DNMT3A_KO_Cell Bank Riken BioResource Research Center

value: TTTC


title: ABZM00655: DNMT3A_4.2 [MARS_scRNA]

value: GCGC


title: 18_B M ATG RA

description:
Group F
sample name: 18

value: Aurothioglucose

value: Room Air


title: RBG20003_Young_MSC-L_028

value: mesenchymal and endothelial cells

value: Young


title: Monocytes_STm_IFNg_2


title: RBG20000_Young_MSC-L_027


title: Monocytes_STm_IFNg_1


title: 17_B M ATG RA

description:
Group F
sample name: 17


title: Monocytes_STm_IFNg_5


title: ABZM00651: J1_WT_4.2 [MARS_scRNA]

value: J1 (SCRC1010, ATCC)

value: CTAC


title: 25_H F SAL RA

description:
Group I
sample name: 25

value: Female

value: Saline


title: ABZM00652: J1_WT_4.3 [MARS_scRNA]

value: ATCA


title: GCB2_Control_1

value: Ly6G- CD11b+ Ly6Chi

value: untreated