title: WTTCD8pCD45RCl (SMJ4)

city: Nantes

first: Victor

last: GOURAIN

address: 30 Bd Jean Monnet

country: France

institute: Centre de recherche en transplantation et immunologie

data_processing:
demultiplexing (python)
read trimming (cutadapt 1.18)
read mapping (bwa 0.7.17)
expression quantification (python)
Genome_build: rn6
Supplementary_files_format_and_content: raw count read per gene in tsv format

source_name: Spleen

extract_protocol:
Cell sorting in total spleen
Picarda et al., 2017
DGEseq

tag: rat lines model

value: Wild Type rat

value: Spleen

tag: egfp status

value: Negative

tag: expressed markers


title: WTTCD8pCD45RCl (SMI4)

status: Public on Nov 02 2022

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Rattus norvegicus

tag: strain

value: Sprague Dawley

tag: tissue

tag: cell type


title: WTTCD8pCD45RCh (SMI3)


title: WTTCD8pCD45RCh (SMH3)


title: WTTCD8pCD45RCh (SMJ3)


title: WTTCD4pCD25pCD127lTotal (SMH2)


title: WTTCD4pCD25pCD127lTotal (SMJ2)


title: WTTCD8pCD45RCl (SMH4)


title: WTTCD4pCD25pCD127lTotal (SMI2)


title: WTTCD4pCD25n (SMI1)


title: WTTCD4pCD25n (SMJ1)


title: d4_ko3a.6 [PBAT_capture_V1]

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

organism: Mus musculus

source_name: Cell Bank Riken BioResource Research Center)

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

value: DNMT3A_KO_Cell Bank Riken BioResource Research Center


title: d4_ko3a.5 [wgbs]


title: d4_ko3a.8 [PBAT_capture_V1]


title: d4_ko3a.7 [PBAT_capture_V1]


title: d4_ko3a.9 [PBAT_capture_V1]


title: d4_ko3a.3 [wgbs]


title: d3_wt.1 [PBAT_capture_V1]

source_name: J1 (SCRC1010, ATCC)

value: J1 (SCRC1010, ATCC)


title: d4_ko3a.4 [wgbs]


title: d4_ko3a.1 [PBAT_capture_V1]


title: d3_ko3b.1 [PBAT_capture_V1]

value: DNMT3B_KO_Cell Bank Riken BioResource Research Center


title: WTTCD4pCD25n (SMH1)


title: d3_tko.1 [PBAT_capture_V1]

value: TKO_Cell Bank Riken BioResource Research Center


title: d4_ko3a.2 [wgbs]


title: d2_wt.1 [PBAT_capture_V1]


title: d3_ko3a.1 [PBAT_capture_V1]


title: WTTCD8pCD45RCl (SMG4)


title: WTTCD8pCD45RCh (SMG3)


title: WTTCD4pCD25pCD127lTotal (SMG2)


title: d2_tko.1 [PBAT_capture_V1]


title: d2_ko3b.1 [PBAT_capture_V1]


title: WTTCD8pCD45RCl (SMF4)


title: WTTCD4pCD25n (SMF1)


title: d2_ko3a.1 [PBAT_capture_V1]


title: WTTCD4pCD25n (SMG1)


title: d1_wt.1 [PBAT_capture_V1]


title: d1_tko.1 [PBAT_capture_V1]


title: Foxp3TCD8pCD45RClGFPn (SME7)

value: rat Foxp3-EGFP


title: d0S_wt.5 [PBAT_capture_V1]


title: Foxp3TCD8pCD45RCh (SME5)


title: d1_ko3b.1 [PBAT_capture_V1]


title: d1_ko3a.1 [PBAT_capture_V1]


title: d0S_wt.3 [PBAT_capture_V1]


title: Foxp3TCD4pCD25pCD127lGFPn (SMD4)


title: Foxp3TCD4pCD25pCD127lGFPp (SME3)

value: Positive


title: Foxp3TCD8pCD45RClGFPp (SMD6)


title: Foxp3TCD4pCD25pCD127lGFPn (SME4)


title: Foxp3TCD8pCD45RCh (SMD5)


title: Foxp3TCD4pCD25n (SME1)


title: d0S_wt.2 [PBAT_capture_V1]


title: Foxp3TCD4pCD25pCD127lGFPp (SMD3)


title: d0S_tko.1 [PBAT_capture_V1]


title: d0S_ko3b.6 [PBAT_capture_V1]


title: d0S_ko3b.7 [PBAT_capture_V1]


title: d0S_ko3b.5 [PBAT_capture_V1]


title: Foxp3TCD8pCD45RClGFPp (SME6)


title: Foxp3TCD4pCD25pCD127lTotal (SMD2)

value: Positive/negative


title: d0S_wt.4 [PBAT_capture_V1]


title: WTTCD4pCD25pCD127lTotal (SMF2)


title: Foxp3TCD4pCD25n (SMD1)


title: d0S_wt.1 [PBAT_capture_V1]


title: d0S_ko3b.4 [wgbs]


title: d0S_ko3b.3 [wgbs]


title: Foxp3TCD8pCD45RClGFPp (SMC6)


title: Foxp3TCD8pCD45RCh (SMC5)


title: d0S_ko3b.1 [PBAT_capture_V1]


title: Foxp3TCD4pCD25n (SMC1)


title: d0S_ko3a.8 [PBAT_capture_V1]


title: Foxp3TCD8pCD45RClGFPn (SMB7)


title: d0S_ko3a.5 [wgbs]


title: d0S_ko3b.2 [wgbs]


title: d0S_ko3a.7 [PBAT_capture_V1]


title: Foxp3TCD4pCD25pCD127lGFPn (SMC4)


title: d0S_ko3a.4 [wgbs]


title: Foxp3TCD4pCD25pCD127lTotal (SMC2)


title: Foxp3TCD4pCD25pCD127lGFPp (SMC3)


title: d0S_ko3a.2 [wgbs]


title: Foxp3TCD4pCD25pCD127lGFPn (SMB4)


title: d0S_ko3a.3 [wgbs]


title: d0S_ko3a.6 [PBAT_capture_V1]


title: Foxp3TCD4pCD25pCD127lTotal (SMB2)


title: Foxp3TCD4pCD25pCD127lGFPp (SMB3)


title: Foxp3TCD4pCD25n (SMB1)


title: d0_wt.2 [PBAT_capture_V1]


title: d0S_ko3a.1 [PBAT_capture_V1]


title: Foxp3TCD8pCD45RClGFPn (SMA7)


title: d0_wt.1 [PBAT_capture_V1]


title: Foxp3TCD8pCD45RClGFPn (SMC7)


title: d0_tko.2 [PBAT_capture_V1]


title: Foxp3TCD8pCD45RCh (SMA5)


title: d0S_ko3a.9 [PBAT_capture_V1]


title: Foxp3TCD4pCD25pCD127lGFPn (SMA4)


title: d0_tko.1 [PBAT_capture_V1]


title: Foxp3TCD4pCD25pCD127lTotal (SMA2)


title: 20200618_A4-9_Luminal_CGDA7928_78_S56

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

country: USA

institute: Dana-Farber Cancer Institute

description: bulk sample from luminal sorted fraction of normal mammary glands from virgin tumor-bearing rats with estradiol (E2) pellets from the treatment arm (treated with drug)

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: old normal ACI +/- Estradiol luminal

value: ACI

value: normal mammary gland

value: luminal

tag: treatment

value: drug

tag: day

value: variable, after tumors developed

tag: animal

tag: tumor status

value: tumor-bearing

tag: parity

value: virgin

tag: estradiol pellet

value: with E2


title: 20200618_A4-9_CD45_CGDA7928_98_S76

description: bulk sample from CD45+ sorted fraction of normal mammary glands from virgin tumor-bearing rats with estradiol (E2) pellets from the treatment arm (treated with drug)

value: old normal ACI +/- Estradiol CD45


title: d0_ko3a.2 [PBAT_capture_V1]

value: DNMT3A_KO_Cell Bank Riken BioResource Research Center


title: Naive_3

city: Pamplona

first: Pablo

last: Sarobe

address: Avda. Pio XII, 55

country: Spain

institute: CIMA

description:
Low input RNA-seq (mars-seq)
cDNA

data_processing:
The quality of the samples was verified using FastQC v0.11.5 software.
FASTQ files were mapped to GRCm38 mouse assembly using STAR v2.5.3a with default parameters.
featureCounts v1.6.0 software and Gencode M20 release were used to obtain read counts at gene level considering only those genes aligned to exonic regions.
Obtained gene counts were normalized using edgeR and voom function of limma.
Assembly: GRCm38
Supplementary files format and content: .counts.txt: Tab-delimited text files include gene counts obtained with featureCounts for each sample.

source_name: Purified DCs

extract_protocol:
RNA was processed using Trizol and cleaned using Qiagen columns. RNA quality was analysed using Experion™ (Bio-Rad) and only RNAs with RQI>7 were included in the experiment.
Library construction was done as reported in Jaitin, D.A., et al., Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types. Science, 2014. 343(6172): p. 776-9.

treatment_protocol: Spleens of Vert-X mice were processed using Collagenase/DNase and CD11c+ cells were isolated using MagniSort™ Mouse CD11c Positive Selection Kit and autoMACS® Pro Separator. Next, cells were stained and IL-10+ and IL-10- CD11c+, I-Ab+ cells were sorted using FACSAria flow cytometer, after excluding CD3+, NKp46+ and CD19+ cells. Purified DC were lysed and stored in RLT buffer (Qiagen).

value: IL-10 reporter Vert-X (B6(Cg)-Il10tm1.1Karp/J)

tag: collection timing

value: 48h after vaccination

value: Dendritic cells


title: Poly_IC_3

description:
Low input RNA-seq (mars-seq)
cDNA


title: d0_ko3b.1 [PBAT_capture_V1]

value: DNMT3B_KO_Cell Bank Riken BioResource Research Center


title: Poly_IC_2

description:
Low input RNA-seq (mars-seq)
cDNA


title: Poly_IC_1

description:
Low input RNA-seq (mars-seq)
cDNA


title: 20200618_A4-8_Luminal_CGDA7928_73_S51

description: bulk sample from luminal sorted fraction of normal mammary glands from virgin tumor-free rats without estradiol (E2) pellets from the control arm (not treated with drug)

value: control

value: tumor-free

value: no E2


title: Naive_1

description:
Low input RNA-seq (mars-seq)
cDNA


title: Foxp3TCD4pCD25pCD127lGFPp (SMA3)

value: Sprague Dawley

value: rat Foxp3-EGFP

value: Spleen

value: Positive


title: 20200618_A4-8_CD45_CGDA7928_93_S71

description: bulk sample from CD45+ sorted fraction of normal mammary glands from virgin tumor-free rats without estradiol (E2) pellets from the control arm (not treated with drug)

value: ACI

value: normal mammary gland

value: variable, after tumors developed


title: 20200618_A4-4_Luminal_CGDA7928_77_S55

description: bulk sample from luminal sorted fraction of normal mammary glands from virgin tumor-free rats with estradiol (E2) pellets from the treatment arm (treated with drug)

value: old normal ACI +/- Estradiol luminal

value: luminal

value: drug

value: virgin

value: with E2


title: 20200618_A4-40_Luminal_CGDA7928_88_S66

description: bulk sample from luminal sorted fraction of normal mammary glands from virgin tumor-free rats without estradiol (E2) pellets from the treatment arm (treated with drug)


title: 20200618_A4-40_CD45_CGDA7928_108_S86

description: bulk sample from CD45+ sorted fraction of normal mammary glands from virgin tumor-free rats without estradiol (E2) pellets from the treatment arm (treated with drug)

value: old normal ACI +/- Estradiol CD45


title: 20200618_A4-3_Luminal_CGDA7928_70_S48

description: bulk sample from luminal sorted fraction of normal mammary glands from virgin tumor-bearing rats with estradiol (E2) pellets from the control arm (not treated with drug)

value: tumor-bearing


title: 20200618_A4-3_CD45_CGDA7928_90_S68

description: bulk sample from CD45+ sorted fraction of normal mammary glands from virgin tumor-bearing rats with estradiol (E2) pellets from the control arm (not treated with drug)

value: control


title: DC_IL10p_2

description:
Low input RNA-seq (mars-seq)
cDNA

value: IL-10 reporter Vert-X (B6(Cg)-Il10tm1.1Karp/J)

value: 48h after vaccination

value: Dendritic cells


title: DC_IL10p_1

description:
Low input RNA-seq (mars-seq)
cDNA


title: DC_IL10p_3

description:
Low input RNA-seq (mars-seq)
cDNA


title: DC_IL10n_3

description:
Low input RNA-seq (mars-seq)
cDNA


title: DC_IL10n_2

description:
Low input RNA-seq (mars-seq)
cDNA


title: DC_IL10n_1

description:
Low input RNA-seq (mars-seq)
cDNA


title: d0_ko3b.2 [PBAT_capture_V1]

value: DNMT3B_KO_Cell Bank Riken BioResource Research Center


title: 20200618_A4-38_CD45_CGDA7928_96_S74

value: tumor-free

value: no E2


title: Foxp3TCD4pCD25n (SMA1)

value: Sprague Dawley

value: rat Foxp3-EGFP

value: Spleen

value: Negative


title: 20200618_A4-37_Luminal_CGDA7928_72_S50

value: old normal ACI +/- Estradiol luminal

value: ACI

value: normal mammary gland

value: luminal

value: variable, after tumors developed


title: d0_ko3a.1 [PBAT_capture_V1]

value: DNMT3A_KO_Cell Bank Riken BioResource Research Center


title: 20200618_A4-37_CD45_CGDA7928_92_S70

value: old normal ACI +/- Estradiol CD45

value: control

value: tumor-bearing

value: virgin

value: with E2


title: poolD-94_S286

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 endothelial cells


title: poolD-96_S288


title: 20200618_A4-27_Luminal_CGDA7928_71_S49


title: poolD-93_S285


title: poolD-91_S283


title: 20200618_A4-28_CD45_CGDA7928_95_S73

value: tumor-free

value: no E2


title: poolD-92_S284


title: 20200618_A4-4_CD45_CGDA7928_97_S75

description: bulk sample from CD45+ sorted fraction of normal mammary glands from virgin tumor-free rats with estradiol (E2) pellets from the treatment arm (treated with drug)

value: drug


title: 20200618_A4-24_Luminal_CGDA7928_85_S63


title: 20200618_A4-38_Luminal_CGDA7928_76_S54


title: poolD-89_S281


title: 20200618_A4-28_Luminal_CGDA7928_75_S53


title: 20200618_A4-27_CD45_CGDA7928_91_S69


title: 20200618_A4-20_Luminal_CGDA7928_87_S65


title: 20200618_A4-24_CD45_CGDA7928_105_S83


title: poolD-88_S280


title: 20200618_A4-20_CD45_CGDA7928_107_S85


title: 20200618_A4-1_Luminal_CGDA7928_69_S47


title: poolD-84_S276


title: poolD-87_S279


title: poolD-86_S278


title: poolD-85_S277


title: 20200618_A4-18_Luminal_CGDA7928_74_S52


title: 20200618_A4-18_CD45_CGDA7928_94_S72


title: 20200618_A4-1_CD45_CGDA7928_89_S67


title: 20200618_A4-16_Luminal_CGDA7928_84_S62


title: poolD-83_S275


title: poolD-95_S287


title: poolD-81_S273


title: poolD-90_S282


title: poolD-78_S270


title: poolD-76_S268


title: poolD-74_S266


title: poolD-82_S274


title: poolD-77_S269


title: poolD-75_S267


title: poolD-73_S265


title: 20200618_A4-15pt2_Luminal_CGDA7928_81_S59


title: 20200618_A4-15pt4_CD45_CGDA7928_103_S81


title: 20200618_A4-15pt1_Luminal_CGDA7928_80_S58


title: 20200618_A4-15pt4_Luminal_CGDA7928_83_S61


title: poolD-70_S262


title: 20200618_A4-14_CD45_CGDA7928_99_S77


title: 20200618_A4-15pt3_Luminal_CGDA7928_82_S60


title: poolD-72_S264


title: 20200618_A4-15pt3_CD45_CGDA7928_102_S80


title: 20200618_A4-16_CD45_CGDA7928_104_S82


title: 20200618_D_P2R_Luminal_CGDA7928_31_S31

description: bulk sample from luminal normal mammary glands from parous (had previous pregnancy) old ACI rats from the treatement arm (treated with drug), collected at day 0 (right after treatment was stopped)

value: old ACI

value: parous


title: poolD-68_S260


title: 20200618_A4-10_CD45_CGDA7928_106_S84


title: poolD-79_S271


title: poolD-69_S261


title: poolD-71_S263


title: 20200618_A4-15pt1_CD45_CGDA7928_100_S78


title: 20200618_A4-15pt2_CD45_CGDA7928_101_S79


title: 20200618_A4-10_Luminal_CGDA7928_86_S64

description: bulk sample from luminal sorted fraction of normal mammary gland from virgin tumor-free rats without estradiol (E2) pellets from the treatment arm (treated with drug)

value: old normal ACI +/- Estradiol luminal


title: 20200618_A4-14_Luminal_CGDA7928_79_S57

value: ACI


title: poolD-67_S259


title: 20200618_D_P2R_Basal_CGDA7928_15_S15

description: bulk sample from basal normal mammary glands from parous (had previous pregnancy) old ACI rats from the treatement arm (treated with drug), collected at day 0 (right after treatment was stopped)

value: normal mammary gland

value: basal


title: 20200618_D_P2R_CD45_CGDA7928_47_S45

description: bulk sample from CD45+ sorted fraction from parous (had previous pregnancy) old ACI rats from the treatement arm (treated with drug), collected at day 0 (right after treatment was stopped)

value: old ACI CD45


title: 20200618_D_P2N_Luminal_CGDA7928_32_S32

value: luminal


title: poolD-65_S257


title: poolD-64_S256


title: 20200618_D_P2N_CD45_CGDA7928_48_S46


title: 20200618_D_P2N_Basal_CGDA7928_16_S16


title: poolD-63_S255


title: poolD-60_S252


title: poolD-59_S251


title: poolD-56_S248


title: poolD-61_S253


title: 20200618_D_P1R_Luminal_CGDA7928_29_S29


title: 20200618_D_P1N_Luminal_CGDA7928_30_S30


title: 20200618_D_P1N_CD45_CGDA7928_46_S44


title: poolD-58_S250


title: 20200618_D_P1R_CD45_CGDA7928_45_S43


title: 20200618_D_P1R_Basal_CGDA7928_13_S13


title: 20200618_D_P1N_Basal_CGDA7928_14_S14


title: poolD-62_S254


title: 20200618_D_N2R_Basal_CGDA7928_11_S11

description: bulk sample from basal normal mammary glands from virgin old ACI rats from the treatement arm (treated with drug), collected at day 0 (right after treatment was stopped)


title: poolD-54_S246


title: poolD-57_S249


title: poolD-55_S247


title: 20200618_D_N2N_Luminal_CGDA7928_28_S28

description: bulk sample from luminal normal mammary glands from virgin old ACI rats from the treatement arm (treated with drug), collected at day 0 (right after treatment was stopped)


title: poolD-66_S258


title: poolD-53_S245


title: poolD-52_S244


title: 20200618_D_N2N_Basal_CGDA7928_12_S12


title: 20200618_D_N1R_Luminal_CGDA7928_25_S25


title: poolD-50_S242


title: poolD-51_S243


title: 20200618_D_N2R_Luminal_CGDA7928_27_S27


title: 20200618_D_N2R_CD45_CGDA7928_43_S41

description: bulk sample from CD45+ sorted fraction from virgin old ACI rats from the treatement arm (treated with drug), collected at day 0 (right after treatment was stopped)


title: 20200618_D_N1R_CD45_CGDA7928_41_S39


title: 20200618_D_N1N_Luminal_CGDA7928_26_S26


title: 20200618_D_N1N_CD45_CGDA7928_42_S40


title: 20200618_C_P2R_Luminal_CGDA7928_23_S23

description: bulk sample from luminal normal mammary glands from parous (had previous pregnancy) old ACI rats from the control arm (not treated with drug), collected at day 0 (right after treatment was stopped for the treated arm)


title: poolD-44_S236


title: 20200618_C_P2R_CD45_CGDA7928_39_S37

description: bulk sample from CD45+ sorted fraction of normal mammary glands from parous (had previous pregnancy) old ACI rats from the control arm (not treated with drug), collected at day 0 (right after treatment was stopped for the treated arm)


title: poolD-45_S237


title: poolD-47_S239


title: 20200618_C_P2N_Luminal_CGDA7928_24_S24


title: poolD-46_S238


title: poolD-42_S234


title: 20200618_C_P2N_CD45_CGDA7928_40_S38


title: 20200618_C_P2R_Basal_CGDA7928_7_S7

description: bulk sample from basal normal mammary glands from parous (had previous pregnancy) old ACI rats from the control arm (not treated with drug), collected at day 0 (right after treatment was stopped for the treated arm)


title: poolD-41_S233


title: poolD-40_S232


title: 20200618_C_P2N_Basal_CGDA7928_8_S8


title: 20200618_C_P1R_Luminal_CGDA7928_21_S21


title: 20200618_C_P1R_Basal_CGDA7928_5_S5


title: 20200618_D_N1R_Basal_CGDA7928_9_S9


title: poolD-48_S240


title: 20200618_C_P1N_Basal_CGDA7928_6_S6


title: 20200618_C_P1N_Luminal_CGDA7928_22_S22


title: poolD-36_S228


title: 20200618_D_N1N_Basal_CGDA7928_10_S10


title: poolD-38_S230


title: poolD-43_S235


title: poolD-35_S227


title: 20200618_C_N2R_Luminal_CGDA7928_19_S19

description: bulk sample from luminal normal mammary glands from virgin old ACI rats from the control arm (not treated with drug), collected at day 0 (right after treatment was stopped for the treated arm)


title: poolD-34_S226


title: poolD-33_S225


title: poolD-32_S224


title: poolD-31_S223


title: 20200618_C_N2N_CD45_CGDA7928_36_S36

description: bulk sample from CD45+ sorted fraction of normal mammary glands from virgin old ACI rats from the control arm (not treated with drug), collected at day 0 (right after treatment was stopped for the treated arm)


title: 20200618_C_N2N_Luminal_CGDA7928_20_S20


title: 20200618_C_N2R_Basal_CGDA7928_3_S3

description: bulk sample from basal normal mammary glands from virgin old ACI rats from the control arm (not treated with drug), collected at day 0 (right after treatment was stopped for the treated arm)


title: 20200618_C_N2R_CD45_CGDA7928_35_S35


title: poolD-29_S221


title: 20200618_C_N1R_Luminal_CGDA7928_17_S17


title: poolD-30_S222


title: 20200618_C_N1R_CD45_CGDA7928_33_S33


title: poolD-49_S241


title: poolD-39_S231


title: 20200618_C_N2N_Basal_CGDA7928_4_S4


title: poolD-28_S220


title: poolD-37_S229


title: poolD-27_S219


title: 20200618_C_N1R_Basal_CGDA7928_1_S1


title: 20200618_C_N1N_Luminal_CGDA7928_18_S18


title: poolD-26_S218


title: poolD-25_S217


title: 20200618_C_N1N_CD45_CGDA7928_34_S34


title: 20200618_C_N1N_Basal_CGDA7928_2_S2


title: poolD-23_S215


title: poolD-24_S216


title: poolD-20_S212


title: poolD-18_S210


title: Patient61

city: Iowa City

first: Jesus

last: Gonzalez Bosquet

state: IA

address: 200 Hawkins Dr

institute: University of Iowa

data_processing:
STAR was used to align the RNA-seq reads to the human reference genome
The DESeq2 package was used to import, normalize, and prepare the gene counts for analysis
Fusion transcripts were determined using the STAR-Fusion suite from fastq files
BAM files for each sample were used for SNV discovery and base-calling against the human genome reference utilizing SAMtools and BCFtools for sorting and indexing
Assembly: hg38
Supplementary files format and content: CSV normalized, log2 transformed expresion data

organism: Homo sapiens

source_name: Endometrium

extract_protocol:
RNA was then isolated from these tumor specimens. Total cellular RNA was extracted from primary tumor tissue using the mirVana (Thermo Fisher, Waltham, USA) RNA purification kit. The RNA yield and quality were assessed with Trinean Dropsense 16 spectrophotometer and Agilent Model 2100 bioanalyzer. RNA quality was determined to be adequate if the sample had an RNA integrity number (RIN) of 7.0 or greater. Samples that were of adequate quality were then sequenced. 500ng of RNA was quantified by Qubit measurement (Thermo Fisher).
RNA was then converted to cDNA and ligated to sequencing adaptors with Illumina TriSeq stranded total RNA library preparation (Illumina, San Diego, CA, USA). cDNA samples were then sequenced with the Illumina HiSeq 4000 genome sequencing platform using 150 bp paired-end SBS chemistry. All sequencing was performed at the Genome Facility at the University of Iowa Institute of Human Genetics (IIHG).

value: Endometrium

tag: tumor type

value: Endometrioid endometrial cancer

tag: age

tag: bmi

tag: Stage


title: Patient58


title: Patient56


title: Patient57


title: poolD-17_S209


title: Patient55


title: Patient53


title: Patient52


title: Patient54


title: poolD-16_S208


title: Patient59


title: poolD-15_S207


title: poolD-21_S213


title: poolD-14_S206


title: Patient51


title: poolD-13_S205


title: poolD-12_S204


title: poolD-22_S214


title: Patient49


title: Patient60


title: poolD-11_S203


title: poolD-10_S202


title: Patient50


title: poolD-19_S211


title: Patient48


title: Patient47


title: poolD-09_S201


title: poolD-08_S200


title: Patient45


title: Patient46


title: poolD-07_S199


title: poolD-06_S198


title: Patient43


title: Patient41


title: poolD-02_S194


title: poolD-03_S195


title: poolD-04_S196


title: Patient44


title: poolD-01_S193


title: Patient38


title: poolC-96_S384


title: Patient37


title: poolC-95_S383


title: Patient36


title: poolD-80_S272


title: Patient35


title: poolC-94_S382


title: poolC-92_S380


title: Patient34


title: poolC-93_S381


title: Patient32


title: poolD-05_S197


title: Patient42


title: Patient33


title: poolC-91_S379


title: Patient31


title: Patient30


title: Patient40


title: poolC-89_S377


title: poolC-90_S378


title: poolC-88_S376


title: Patient39


title: Patient28


title: Patient29


title: poolC-87_S375


title: poolC-86_S374


title: Patient26


title: poolC-85_S373


title: poolC-84_S372


title: Patient27


title: Patient24


title: Patient23


title: poolC-81_S369


title: Patient22


title: poolC-83_S371


title: poolC-80_S368


title: Patient25


title: poolC-78_S366


title: poolC-82_S370


title: Patient21


title: Patient1


title: Patient19


title: poolC-77_S365


title: poolC-76_S364


title: poolC-75_S363


title: Patient17


title: Patient15


title: Patient18


title: poolC-74_S362


title: poolC-73_S361


title: poolC-72_S360


title: poolC-79_S367


title: Patient13


title: poolC-71_S359


title: Patient12


title: Patient11


title: poolC-69_S357


title: Patient14


title: Patient10


title: Patient9


title: poolC-67_S355


title: poolC-65_S353


title: poolC-66_S354


title: Patient8


title: Patient7


title: Patient16


title: Patient6


title: Patient4


title: Patient3


title: poolC-63_S351


title: poolC-61_S349


title: Patient5


title: poolC-64_S352


title: Patient2


title: poolC-70_S358


title: Patient20


title: Gata3-ChIPseq_2

city: Cambridge

first: Alastair

last: Crisp

address: Francis Crick Avenue

country: United Kingdom

institute: MRC Laboratory of Molecular Biology

data_processing:
Pooled libraries were sequenced using an Illumina Hiseq4000 running a single-read 50bp protocol
Sequenced reads were aligned to the mouse genome (GRCm38) using Bowtie2 (v2.3.5.1) with default parameters
reads that could not be uniquely mapped were removed from further analysis
Peak calling analysis was performed using Macs2 (v2.1.2)
Supplementary files format and content: GRCm38
Supplementary files format and content: macs2 output files with peak calling data

source_name: Splenic TH2 cell subsets expanded in vitro

extract_protocol:
Chromatin extracts from in vitro expanded ILC2 (10 million) were prepared using truChIP Chromatin Shearing kit (Covaris), with 5 min of crosslink and optimized shearing conditions (peak power 75, duty factor 10.0, cycles/burst 200, duration 300 sec) to obtain fragments of ~500bp
Chromatin-antibody-bead complexes were then subjected to tagmentation, followed by DNA elution, and libraries amplification and purification, as described previously (Schmidl et al., 2015)

tag: chip antibody

value: anti-GATA3 ((D13C9)


title: poolC-58_S346

tag: tissue


title: poolC-59_S347


title: poolC-60_S348


title: poolC-57_S345


title: poolC-56_S344


title: poolC-55_S343


title: ChIPseq WT LSK Isotype rep2

city: Nanjing

first: Xi

last: Wang

address: Longmian Avenue 101, Jiangning District

country: China

institute: Nanjing Medical University

data_processing:
Illumina HD.3.4.0/RTA 2.7.7 software used for sequencing and basecalling.
RNA-seq: adapter trimming and low-quality read filtering by flexbar (v2.5),  read mapping by Bowtie 2 (v2.2.9) and Tophat2 (v2.1.1), read counting by HTSeq-count (v 0.9.1).
scRNA-seq: 10x Genomics Cell Ranger v2.0.2/3.0.2 used for sequencing read alignment and UMI counting.
ChIP-seq: adapter trimming and low-quality read filtering by flexbar (v2.5), read mapping by Bowtie2 (v 2.2.9), duplicate read removal by Picard (v 2.17.3), peak calling by macs2 (v 2.1.1).
ATAC-seq: adapter trimming and low-quality read filtering by flexbar (v2.5), read mapping by Bowtie2 (v 2.2.9), duplicate read removal by Picard (v 2.17.3), peak calling by macs2 (v 2.1.1), heatmap by deeptoools (v3.4.3)
Assembly: mm10
Supplementary files format and content: RNA-seq: ; scRNA-seq; tar ball of mtx, tsv: UMI counts of individual genes in single cells; ChIP-seq:; ATAC-seq:

source_name: bone marrow

extract_protocol:
RNA-seq: RNA was extracted from sorted cells using the Arcturus PicoPure RNA Isolation Kit (Thermo Fisher Scientific).
ATAC-seq: 50,000 sorted LSK were lyzed and nuclei subjected to Tn5 mediated transposition for 30 minutes at 37°C. DNA was purified using Ampure XP beads and used for indexing PCR.
ChIP-seq: LSK were subjected to cross-linking in 1 % formaldehyde (in PBS) for 10 minutes at room temperature; chromatin was sheared to an average fragment size of 200-250 bp; pre-blocked magnetic Protein A beads were added; bead-bound chromatin fragments were separated on a magnetic tube rack and washed before they were subjected to tagmentation
scRNA-seq: Single cells were captured using the 10x Chromium system and further processed following the Chromium Single Cell 3’ Reagent Kit protocol.
RNA-seq: Sequencing libraries were prepared with the NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina according to the manufacturer’s instructions.
ATAC-seq: Purified DNA was used for indexing PCR; Amplified libraries were purified by two-sided Ampure XP bead purification
ChIP-seq: Purified DNA was used for indexing PCR; Amplified libraries were purified by two-sided Ampure XP bead purification
scRNA-seq: cDNA library were fragmented and the sequencing library was generated according to the Single Cell 3’ Reagent Kit protocol.

value: bone marrow

tag: cell type

value: LSK

tag: genotype

value: wild type

tag: replicate

value: isotype


title: poolC-54_S342

value: tumor endothelial cells


title: ChIPseq WT LSK Input rep1


title: poolC-68_S356


title: ChIPseq WT LSK Isotype rep1


title: ChIPseq WT LSK H2Bub1 rep2


title: poolC-62_S350


title: ChIPseq cKO LSK Input rep1

value: Usp22 cKO


title: poolC-53_S341


title: poolC-52_S340


title: poolC-51_S339


title: ChIPseq cKO LSK Isotype rep2


title: ChIPseq WT LSK H2Bub1 rep1


title: poolC-50_S338


title: ChIPseq cKO LSK Isotype rep1


title: poolC-48_S336


title: Gata3-ChIPseq_1

value: Splenic TH2 cell subsets expanded in vitro


title: ChIPseq cKO LSK H2Bub1 rep1


title: poolC-49_S337


title: poolC-47_S335


title: poolC-45_S333


title: ATACseq cKO LSK rep1


title: poolC-44_S332


title: ATACseq WT LSK rep2


title: ATACseq cKO LSK rep2


title: ATACseq WT LSK rep1


title: poolC-43_S331


title: scRNAseq WT TBM rep1

library_source: transcriptomic single cell

molecule: polyA RNA

value: Total bone marrow


title: scRNAseq WT MPP rep1

value: MPP


title: poolC-40_S328


title: poolC-41_S329


title: scRNAseq cKO MPP rep1


title: ChIPseq cKO LSK H2Bub1 rep2


title: poolC-38_S326


title: poolC-37_S325


title: poolC-39_S327


title: scRNAseq WT LT-HSC rep1

value: LT-HSC


title: poolC-36_S324


title: scRNAseq cKO ST-HSC rep1

value: ST-HSC


title: scRNAseq cKO LT-HSC rep1


title: RNAseq LSK WT test rep5

description: chimeras.count.matrix.tsv.gz


title: poolC-35_S323


title: poolC-34_S322


title: poolC-46_S334


title: poolC-42_S330


title: RNAseq LSK WT test rep4

description: chimeras.count.matrix.tsv.gz


title: RNAseq LSK WT test rep3

description: chimeras.count.matrix.tsv.gz


title: poolC-30_S318


title: poolC-33_S321


title: poolC-32_S320


title: poolC-29_S317


title: RNAseq LSK WT test rep2

description: chimeras.count.matrix.tsv.gz


title: RNAseq LSK WT test rep1

description: chimeras.count.matrix.tsv.gz


title: RNAseq LSK WT competitor rep4

description: chimeras.count.matrix.tsv.gz


title: scRNAseq cKO TBM rep1


title: poolC-31_S319


title: poolC-28_S316


title: RNAseq LSK WT competitor rep3

description: chimeras.count.matrix.tsv.gz


title: poolC-27_S315


title: scRNAseq WT ST-HSC rep1


title: RNAseq LSK WT competitor rep2

description: chimeras.count.matrix.tsv.gz


title: RNAseq LSK WT competitor rep1

description: chimeras.count.matrix.tsv.gz


title: poolC-26_S314


title: poolC-25_S313


title: RNAseq LSK cKO test rep4

description: chimeras.count.matrix.tsv.gz


title: RNAseq LSK cKO test rep3

description: chimeras.count.matrix.tsv.gz


title: poolC-24_S312


title: poolC-23_S311


title: RNAseq LSK cKO test rep2

description: chimeras.count.matrix.tsv.gz


title: poolC-22_S310


title: RNAseq LSK WT competitor rep5

description: chimeras.count.matrix.tsv.gz


title: RNAseq LSK cKO test rep1

description: chimeras.count.matrix.tsv.gz


title: poolC-21_S309


title: RNAseq LSK cKO competitor rep4

description: chimeras.count.matrix.tsv.gz


title: poolC-20_S308


title: poolC-17_S305


title: poolC-18_S306


title: RNAseq LSK cKO competitor rep2

description: chimeras.count.matrix.tsv.gz


title: poolC-15_S303


title: RNAseq LSK cKO competitor rep1

description: chimeras.count.matrix.tsv.gz


title: poolC-16_S304


title: RNAseq FrC WT rep3

description: FrC.count.matrix.tsv.gz

value: pre-B (fraction C)


title: RNAseq FrC WT rep2

description: FrC.count.matrix.tsv.gz


title: RNAseq FrC WT rep1

description: FrC.count.matrix.tsv.gz


title: RNAseq FrC cKO rep3

description: FrC.count.matrix.tsv.gz


title: poolC-14_S302


title: poolC-12_S300


title: poolC-11_S299


title: RNAseq FrC cKO rep2

description: FrC.count.matrix.tsv.gz


title: RNAseq LSK WT rep3

description: LSK.count.matrix.tsv.gz


title: RNAseq FrC cKO rep1

description: FrC.count.matrix.tsv.gz


title: RNAseq LSK WT rep2

description: LSK.count.matrix.tsv.gz


title: poolC-09_S297


title: poolC-10_S298


title: RNAseq LSK cKO competitor rep3

description: chimeras.count.matrix.tsv.gz


title: poolC-08_S296


title: poolC-19_S307


title: RNAseq LSK cKO rep3

description: LSK.count.matrix.tsv.gz


title: RNAseq LSK WT rep1

description: LSK.count.matrix.tsv.gz


title: poolC-06_S294


title: poolC-07_S295


title: poolC-05_S293


title: poolC-13_S301


title: RNAseq LSK cKO rep1

description: LSK.count.matrix.tsv.gz


title: RNAseq LSK cKO rep2

description: LSK.count.matrix.tsv.gz


title: poolC-03_S291


title: poolC-02_S290


title: poolC-01_S289


title: Adult forebrain wildtype replicate1 [P60-WT1]

city: Daejeon

first: Eunjoon

last: Kim

address: Kuseong-dong

department: Center for Synaptic Brain Dysfunctions/Department of Biological Sciences

country: South Korea

institute: IBS/KAIST

data_processing:
Transcript abundance was estimated with Salmon(v1.1.0) in Quasi-mapping-based mode onto the Mus musculus genome (GRCm38) with GC bias correction (--gcBias).
Quantified gene-level abundance data was imported to R (v.3.6.2) with tximport package and differential gene expression analysis was carried out using R/Bioconductor DEseq2 (v1.26.0).
The normalized read counts were computed by dividing the raw read counts by size factors and fit to a negative binomial distribution.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file include normalized read count metrix calculated by using DESeq2.

source_name: Brain

growth_protocol: Mice were fed ad libitum under a 12-h dark/light cycle. A mother mouse reared two to eight wild-type, heterozygous and knock-out mouse pups and two mother mice lived in one cage.

extract_protocol:
RNA samples were prepared for sequencing using a TruSeq RNA Sample Prep Kit v2 (Illumina) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: forebrain

tag: Sex

value: male

value: wildtype


title: Adult forebrain wildtype replicate2 [P60-WT2]


title: Adult forebrain wildtype replicate3 [P60-WT3]


title: Adult forebrain knock-out replicate2 [P60-KO2]

value: knock-out


title: poolB-96_S192


title: poolC-04_S292


title: Adult forebrain knock-out replicate1 [P60-KO1]


title: poolB-95_S191


title: Juvenile forebrain wildtype replicate3 [P25-WT3]


title: Juvenile forebrain wildtype replicate2 [P25-WT2]


title: Juvenile forebrain wildtype replicate1 [P25-WT1]


title: poolB-93_S189


title: poolB-92_S188


title: poolB-94_S190


title: Juvenile forebrain knock-out replicate3 [P25-KO3]


title: poolB-91_S187


title: poolB-90_S186


title: Juvenile forebrain knock-out replicate1 [P25-KO1]


title: poolB-89_S185


title: Adult forebrain knock-out replicate3 [P60-KO3]


title: NA_KCl_6h_rep2_RNA_seq

city: Blacksburg

first: Xiguang

last: Xu

state: VA

address: 1015 Life Science Circle

department: Department of Biomedical Sciences and Pathobiology

institute: Virginia Tech

data_processing:
Fastp v0.20 was used to remove adapter sequences, identify and remove low-quality reads and called bases.
After trimming, reads with length longer than 30nt were mapped to mm10 by RSEM (v1.3.0) with Bowtie2 (v2.2.9).
Assembly: mm10
Supplementary files format and content: tab-delimited files containing transcript abundance counts

source_name: E16.5 mouse cortical neurons

growth_protocol: E16.5 mouse cortex tissues were dissected and dissociated into single cell suspension, resuspended in neuronal culture media (Neurobasal medium containing 2% B27 supplement (Invitrogen), 1% Glutamax (ThermoFisher) and 1% penicillin-streptomycin (ThermoFisher)) and seeded on laminin and poly-ornithine coated 10-cm dishes. Neurons were grown in vitro for 7 days with fresh medium changed on DIV3 and DIV6.

extract_protocol:
Total RNA was extracted from the neuronal cultures using TRIzol reagent combined with RNeasy min kit (QIAGEN) with DNase I on-column digestion.
Two rounds of poly(A) selection was performed and RNA-seq libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: At DIV6, neuronal cells were silenced with 1 μM tetrodotoxin (TTX; Fisher) and 100 μM DL-2-amino-5-phosphopentanoic acid (DL-AP5; Fisher) overnight. The next morning, neuronal cells were depolarized with 55mM KCl for 0h, 2h, and 6h. At the end time point, the neuronal cells were harvested for RNA extraction.

tag: kcl treatment

value: 6 h

tag: developmental stage

tag: tissue/cell type

value: E16.5 mouse cortical neurons

value: WT

tag: gender

value: pooled male and female


title: poolB-88_S184


title: NA_KCl_6h_rep1_RNA_seq


title: poolB-86_S182


title: poolB-87_S183


title: NA_KCl_0h_rep1_RNA_seq

value: 0 h


title: NA_KCl_2h_rep1_RNA_seq

value: 2 h


title: NA_KCl_6h_rep2_RNA_BS_seq

data_processing:
Fastp v0.20 was used to remove adapter sequences, identify and remove low-quality reads and called bases
meRanGh v1.2.1 was used to map reads to C2T and G2A converted reference genomes
meRanCall was used to call m5C sites from mapped read files
In-house scripts using Python 3.9 and R 4.1.1 were used to further filter and process methylation calling files
Assembly: mm10
Supplementary files format and content: tab-delimited files containing methylation calling information for each called methylated site
Library strategy: RNA BS-Seq

extract_protocol:
Total RNA was extracted from the neuronal cultures using TRIzol reagent combined with RNeasy min kit (QIAGEN) with DNase I on-column digestion.
After two rounds of poly(A) selection, bisulfite conversion was performed and RNA-seq libraries were prepared for sequencing using standard Illumina protocols


title: poolB-85_S181

value: tumor endothelial cells


title: poolB-83_S179


title: NA_KCl_6h_rep1_RNA_BS_seq


title: NA_KCl_2h_rep2_RNA_seq


title: poolB-82_S178


title: poolB-80_S176


title: NA_KCl_0h_rep2_RNA_seq


title: Juvenile forebrain knock-out replicate2 [P25-KO2]


title: NA_KCl_0h_rep2_RNA_BS_seq


title: NA_KCl_2h_rep2_RNA_BS_seq


title: poolB-79_S175


title: poolB-77_S173


title: NA_KCl_0h_rep1_RNA_BS_seq


title: NA_KCl_2h_rep1_RNA_BS_seq


title: Striatum wildtype (Shank3) replicate5

extract_protocol:
RNA samples were prepared for sequencing using a TruSeq Stranded mRNA LT Sample Prep Kit (Illumina) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: striatum

value: 13 week


title: poolB-76_S172


title: Striatum wildtype (Shank3) replicate3


title: poolB-84_S180


title: poolB-74_S170


title: poolB-81_S177


title: Striatum wildtype (Shank3) replicate2


title: poolB-73_S169


title: poolB-72_S168


title: poolB-71_S167


title: Striatum wildtype (Shank3) replicate1


title: Striatum knock-out (Shank3) replicate5


title: Striatum knock-out (Shank3) replicate2


title: poolB-70_S166


title: poolB-78_S174


title: poolB-68_S164


title: Striatum heterozygous (Shank3) replicate5

value: heterozygous


title: poolB-66_S162


title: poolB-65_S161


title: poolB-69_S165


title: Striatum heterozygous (Shank3) replicate3


title: poolB-64_S160


title: Striatum wildtype (Shank3) replicate4


title: Striatum knock-out (Shank3) replicate1


title: Striatum heterozygous (Shank3) replicate2


title: poolB-63_S159


title: Striatum heterozygous (Shank3) replicate4


title: Striatum heterozygous (Shank3) replicate1


title: poolB-75_S171


title: poolB-62_S158


title: Hippocampus wildtype (Shank3) replicate5

value: hippocampus


title: poolB-61_S157


title: Striatum knock-out (Shank3) replicate4


title: Striatum knock-out (Shank3) replicate3


title: Hippocampus wildtype (Shank3) replicate4


title: Hippocampus wildtype (Shank3) replicate3


title: poolB-59_S155


title: poolB-58_S154


title: poolB-60_S156


title: Hippocampus wildtype (Shank3) replicate2


title: poolB-67_S163


title: Hippocampus wildtype (Shank3) replicate1


title: Hippocampus knock-out (Shank3) replicate5


title: poolB-57_S153


title: poolB-56_S152


title: Hippocampus knock-out (Shank3) replicate3


title: poolB-53_S149


title: Hippocampus knock-out (Shank3) replicate1


title: Hippocampus knock-out (Shank3) replicate2


title: poolB-52_S148


title: Hippocampus heterozygous (Shank3) replicate5


title: poolB-55_S151


title: poolB-51_S147


title: Hippocampus heterozygous (Shank3) replicate4


title: poolB-49_S145


title: Hippocampus heterozygous (Shank3) replicate3


title: poolB-48_S144


title: Hippocampus heterozygous (Shank3) replicate2


title: Hippocampus heterozygous (Shank3) replicate1


title: poolB-46_S142


title: Cortex wildtype (Shank3) replicate5

value: prefrontal cortex


title: poolB-47_S143


title: poolB-43_S139


title: Cortex wildtype (Shank3) replicate2


title: Cortex knock-out (Shank3) replicate5


title: Cortex wildtype (Shank3) replicate4


title: Hippocampus knock-out (Shank3) replicate4


title: Cortex wildtype (Shank3) replicate3


title: poolB-45_S141


title: poolB-50_S146


title: poolB-44_S140


title: poolB-54_S150


title: poolB-42_S138


title: Cortex wildtype (Shank3) replicate1


title: poolB-41_S137


title: poolB-40_S136


title: Cortex knock-out (Shank3) replicate3


title: poolB-38_S134


title: Cortex knock-out (Shank3) replicate2


title: Cortex knock-out (Shank3) replicate1


title: poolB-37_S133


title: poolB-36_S132


title: Cortex heterozygous (Shank3) replicate4


title: poolB-35_S131


title: Cortex heterozygous (Shank3) replicate3


title: poolB-34_S130


title: poolB-39_S135


title: Cortex heterozygous (Shank3) replicate2


title: Cortex heterozygous (Shank3) replicate1


title: poolB-33_S129


title: Cortex knock-out (Shank3) replicate4


title: poolB-31_S127


title: poolB-32_S128


title: poolB-30_S126


title: Hippocampus wildtype replicate4

growth_protocol: Mice were fed ad libitum under a 12-h dark/light cycle. A mother mouse reared two to eight wild-type, heterozygous and knock-out mouse pups in one cage.


title: Cortex heterozygous (Shank3) replicate5


title: poolB-29_S125


title: Hippocampus wildtype replicate2


title: Hippocampus wildtype replicate5


title: poolB-28_S124


title: Hippocampus wildtype replicate1


title: poolB-26_S122


title: poolB-27_S123


title: Hippocampus knock-out replicate1


title: poolB-24_S120


title: Hippocampus knock-out replicate3


title: Hippocampus knock-out replicate4


title: Hippocampus knock-out replicate2


title: poolB-25_S121


title: poolB-22_S118


title: poolB-21_S117


title: poolB-23_S119


title: Hippocampus heterozygous replicate4


title: Hippocampus heterozygous replicate5


title: Hippocampus heterozygous replicate3


title: poolB-19_S115


title: Hippocampus heterozygous replicate2


title: Hippocampus wildtype replicate3


title: poolB-18_S114


title: Hippocampus knock-out replicate5


title: Hippocampus heterozygous replicate1


title: Striatum wildtype replicate5


title: Striatum wildtype replicate3


title: poolB-17_S113


title: poolB-16_S112


title: Striatum wildtype replicate4


title: Striatum wildtype replicate2


title: Striatum wildtype replicate1


title: poolB-15_S111


title: poolB-13_S109


title: Striatum knock-out replicate4


title: poolB-12_S108


title: poolB-14_S110


title: Striatum knock-out replicate3


title: poolB-10_S106


title: Striatum knock-out replicate5


title: poolB-09_S105


title: poolB-11_S107


title: poolB-20_S116


title: poolB-07_S103


title: poolB-08_S104


title: Striatum knock-out replicate2


title: poolB-06_S102


title: Striatum heterozygous replicate5


title: Striatum heterozygous replicate4


title: poolB-05_S101


title: Striatum heterozygous replicate3


title: poolB-04_S100


title: Striatum heterozygous replicate2


title: poolB-02_S98


title: poolB-03_S99


title: poolB-01_S97


title: Striatum heterozygous replicate1


title: Cortex wildtype replicate5


title: poolA-96_S96


title: Striatum knock-out replicate1


title: Cortex wildtype replicate3


title: Cortex knock-out replicate5


title: Cortex wildtype replicate4


title: poolA-91_S91


title: poolA-94_S94


title: poolA-93_S93


title: poolA-95_S95


title: Cortex knock-out replicate4


title: Cortex knock-out replicate3


title: Cortex knock-out replicate1


title: Cortex heterozygous replicate5


title: poolA-87_S87


title: Cortex wildtype replicate2


title: poolA-89_S89


title: Cortex heterozygous replicate4


title: poolA-90_S90


title: poolA-86_S86


title: poolA-85_S85


title: Cortex heterozygous replicate3


title: Cortex heterozygous replicate2


title: Cortex wildtype replicate1


title: poolA-84_S84


title: poolA-83_S83


title: Cortex heterozygous replicate1


title: poolA-92_S92


title: Cortex knock-out replicate2


title: poolA-88_S88


title: poolA-80_S80


title: poolA-81_S81


title: poolA-82_S82


title: poolA-78_S78


title: poolA-76_S76


title: poolA-77_S77


title: Frontal_cortex_Day_Ctr0 3 [CH_DB_AI_055]

city: Berlin

first: Andranik

last: Ivanov

address: Chariteplatz 1

department: Core Unit Bioinformatics

country: Germany

institute: Berlin Institute of Health

data_processing:
Data were demultiplexed with blc2fastq2
Reads mapped to the mouse genome (GRCm38.p5) with STAR (v 2.7.3a)
Reads were assigned to genes with featureCounts (SUBREAD v2.0.0) using mouse Gencode annotation (GRCm38 vM12)
Assembly: GRCm38.p5
Supplementary files format and content: tab separated file with gene counts

extract_protocol:
Total RNA was extracted using the Lexogen SPLIT RNA Extraction kit (Cat. Nr. 008.48).
50 ng total RNA/sample were inputted for rRNA depletion with the NEBnext rRNA depletion kit V2 (Cat. Nr. E7400X) and total RNA library prep with the NEBnext Ultra II Library prep kit (Cat. Nr. E7770L).

value: Microglia


title: Frontal_cortex_Night_Soci 4 [CH_DB_AI_057]


title: Frontal_cortex_Night_Cogn 4 [CH_DB_AI_058]


title: Frontal_cortex_Day_Ctr0 4 [CH_DB_AI_063]


title: Frontal_cortex_Day_Ctr1 4 [CH_DB_AI_064]


title: Frontal_cortex_Night_Ctr0 4 [CH_DB_AI_059]


title: Frontal_cortex_Day_Ctr1 3 [CH_DB_AI_056]


title: Frontal_cortex_Day_Soci 4 [CH_DB_AI_061]


title: Frontal_cortex_Night_Ctr1 4 [CH_DB_AI_060]


title: poolA-74_S74


title: poolA-75_S75


title: Frontal_cortex_Day_Cogn 4 [CH_DB_AI_062]


title: poolA-72_S72


title: poolA-73_S73


title: Frontal_cortex_Day_Soci 3 [CH_DB_AI_053]


title: Frontal_cortex_Day_Cogn 3 [CH_DB_AI_054]


title: poolA-71_S71


title: poolA-70_S70


title: poolA-69_S69


title: poolA-79_S79


title: poolA-68_S68


title: Frontal_cortex_Night_Cogn 3 [CH_DB_AI_050]


title: Frontal_cortex_Day_Ctr1 2 [CH_DB_AI_048]


title: Frontal_cortex_Night_Soci 3 [CH_DB_AI_049]


title: poolA-67_S67


title: poolA-66_S66


title: poolA-65_S65


title: Frontal_cortex_Day_Ctr0 2 [CH_DB_AI_047]


title: poolA-64_S64


title: Frontal_cortex_Day_Cogn 2 [CH_DB_AI_046]


title: Frontal_cortex_Day_Soci 2 [CH_DB_AI_045]


title: poolA-62_S62


title: poolA-59_S59


title: Frontal_cortex_Night_Ctr1 2 [CH_DB_AI_044]


title: poolA-63_S63


title: Frontal_cortex_Night_Soci 2 [CH_DB_AI_041]


title: Frontal_cortex_Night_Ctr0 2 [CH_DB_AI_043]


title: Frontal_cortex_Night_Ctr1 3 [CH_DB_AI_052]


title: poolA-60_S60


title: Frontal_cortex_Night_Ctr0 3 [CH_DB_AI_051]


title: Frontal_cortex_Day_Ctr1 1 [CH_DB_AI_040]


title: Frontal_cortex_Day_Cogn 1 [CH_DB_AI_038]


title: poolA-58_S58


title: Frontal_cortex_Day_Soci 1 [CH_DB_AI_037]


title: poolA-57_S57


title: poolA-55_S55


title: poolA-56_S56


title: Frontal_cortex_Day_Ctr0 1 [CH_DB_AI_039]


title: Frontal_cortex_Night_Ctr1 1 [CH_DB_AI_036]


title: Frontal_cortex_Night_Cogn 2 [CH_DB_AI_042]


title: poolA-61_S61


title: Frontal_cortex_Night_Soci 1 [CH_DB_AI_033]


title: Frontal_cortex_Night_Cogn 1 [CH_DB_AI_034]


title: poolA-54_S54


title: Hippocampus_Day_Ctr1 4 [CH_DB_AI_032]

source_name: Hippocampus

value: Hippocampus


title: Hippocampus_Day_Cogn 4 [CH_DB_AI_030]


title: Hippocampus_Day_Soci 4 [CH_DB_AI_029]


title: Hippocampus_Night_Ctr1 4 [CH_DB_AI_028]


title: Hippocampus_Night_Ctr0 4 [CH_DB_AI_027]


title: Hippocampus_Night_Cogn 4 [CH_DB_AI_026]


title: poolA-53_S53


title: poolA-52_S52


title: poolA-51_S51


title: poolA-49_S49


title: poolA-48_S48


title: poolA-47_S47


title: poolA-46_S46


title: poolA-50_S50


title: poolA-44_S44


title: Hippocampus_Night_Soci 4 [CH_DB_AI_025]


title: Frontal_cortex_Night_Ctr0 1 [CH_DB_AI_035]


title: poolA-42_S42


title: poolA-43_S43


title: poolA-41_S41


title: Hippocampus_Day_Ctr0 3 [CH_DB_AI_023]


title: Hippocampus_Day_Ctr1 3 [CH_DB_AI_024]


title: poolA-45_S45


title: Hippocampus_Day_Soci 3 [CH_DB_AI_021]


title: Hippocampus_Day_Cogn 3 [CH_DB_AI_022]


title: Hippocampus_Day_Ctr0 4 [CH_DB_AI_031]


title: poolA-38_S38


title: poolA-39_S39


title: Hippocampus_Night_Ctr1 3 [CH_DB_AI_020]


title: Hippocampus_Night_Ctr0 3 [CH_DB_AI_019]


title: Hippocampus_Night_Cogn 3 [CH_DB_AI_018]


title: poolA-37_S37


title: poolA-40_S40


title: poolA-35_S35


title: Hippocampus_Night_Soci 3 [CH_DB_AI_017]


title: Hippocampus_Day_Ctr0 2 [CH_DB_AI_015]


title: poolA-33_S33


title: poolA-31_S31


title: Hippocampus_Day_Soci 2 [CH_DB_AI_013]


title: Hippocampus_Night_Ctr1 2 [CH_DB_AI_012]


title: poolA-32_S32


title: poolA-30_S30


title: Hippocampus_Day_Cogn 2 [CH_DB_AI_014]


title: Hippocampus_Night_Ctr0 2 [CH_DB_AI_011]


title: Hippocampus_Night_Cogn 2 [CH_DB_AI_010]


title: poolA-29_S29


title: Hippocampus_Night_Soci 2 [CH_DB_AI_009]


title: poolA-27_S27


title: Hippocampus_Day_Ctr1 1 [CH_DB_AI_008]


title: poolA-26_S26


title: poolA-28_S28


title: poolA-25_S25


title: Hippocampus_Day_Cogn 1 [CH_DB_AI_006]


title: Hippocampus_Day_Ctr0 1 [CH_DB_AI_007]


title: poolA-36_S36


title: poolA-24_S24


title: Hippocampus_Day_Soci 1 [CH_DB_AI_005]


title: Hippocampus_Day_Ctr1 2 [CH_DB_AI_016]


title: Hippocampus_Night_Ctr0 1 [CH_DB_AI_003]


title: poolA-21_S21


title: Hippocampus_Night_Cogn 1 [CH_DB_AI_002]


title: poolA-34_S34


title: Hippocampus_Night_Ctr1 1 [CH_DB_AI_004]


title: polysome_HF_rep2_RNA_seq

description: Polysome poly(A) RNA

source_name: adult mouse NSCs

growth_protocol: Adult mouse NSCs were seeded on poly-ornithine and laminin coated plates in DMEM/F12 medium (DMEM/F12, 2% B27, supplement, 2 mmol/L L-glutamine, 1x penicillin-streptomycin, 20 ng/ml epidermal growth factor (EGF, PeproTech), 20 ng/ml basic fibroblast growth factor (bFGF, PeproTech))containing LF, MF, HF folic acid for 4 days, with fresh medium change at day 2.

extract_protocol:
Total RNA was extracted from adult NSCs with TRIzol reagent. Polysome fractions were separated by sucrose gradient separation and polysome RNA was extracted from polysome fractions with TRIzol LS reagent following the manufacturer’s instructions. RNA samples were subject to turbo DNase digestion at 37℃ for 30min.
Two rounds of poly(A) selection was performed and RNA-seq libraries were prepared for sequencing using standard Illumina protocols

value: 6 to 8wk

value: adult neural stem cells from the subventricular zone (SVZ) of the lateral ventricles

value: male


title: Hippocampus_Night_Soci 1 [CH_DB_AI_001]


title: poolA-19_S19


title: polysome_MF_rep2_RNA_seq

description: Polysome poly(A) RNA


title: poolA-16_S16


title: polysome_HF_rep1_RNA_seq

description: Polysome poly(A) RNA


title: poolA-17_S17


title: poolA-18_S18


title: polysome_MF_rep1_RNA_seq

description: Polysome poly(A) RNA


title: poolA-15_S15


title: polysome_LF_rep2_RNA_seq

description: Polysome poly(A) RNA


title: poolA-22_S22


title: poolA-12_S12


title: polysome_LF_rep1_RNA_seq

description: Polysome poly(A) RNA


title: poolA-13_S13


title: poolA-11_S11


title: total_HF_rep1_RNA_seq

description: Total poly(A) RNA


title: total_MF_rep2_RNA_seq

description: Total poly(A) RNA


title: poolA-23_S23


title: total_LF_rep2_RNA_seq

description: Total poly(A) RNA


title: poolA-08_S8


title: poolA-07_S7


title: poolA-20_S20


title: poolA-09_S9


title: poolA-06_S6


title: poolA-05_S5


title: polysome_HF_rep2_RNA_BS_seq

description: Polysome poly(A) RNA

data_processing:
Fastp v0.20 was used to remove adapter sequences, identify and remove low-quality reads and called bases
meRanGh v1.2.1 was used to map reads to C2T and G2A converted reference genomes
meRanCall was used to call m5C sites from mapped read files
In-house scripts using Python 3.9 and R 4.1.1 were used to further filter and process methylation calling files
Assembly: mm10
Supplementary files format and content: tab-delimited files containing methylation calling information for each called methylated site

growth_protocol: Adult mouse NSCs were seeded on poly-ornithine and laminin coated plates in DMEM/F12 medium (DMEM/F12, 2% B27, supplement, 2 mmol/L L-glutamine, 1x penicillin-streptomycin, 20 ng/ml epidermal growth factor (EGF, PeproTech), 20 ng/ml basic fibroblast growth factor (bFGF, PeproTech))containing Low (1.5uM), Medium (10uM) and High (80uM) folic acid for 4 days, with fresh medium change at day 2.

extract_protocol:
Total RNA was extracted from adult NSCs with TRIzol reagent. Polysome fractions were separated by sucrose gradient separation and polysome RNA was extracted from polysome fractions with TRIzol LS reagent following the manufacturer’s instructions. RNA samples were subject to turbo DNase digestion at 37℃ for 30min.
After two rounds of poly(A) selection, bisulfite conversion was performed and RNA-seq libraries were prepared for sequencing using standard Illumina protocols
RNA BS-Seq


title: polysome_LF_rep1_RNA_BS_seq

description: Polysome poly(A) RNA


title: polysome_LF_rep2_RNA_BS_seq

description: Polysome poly(A) RNA


title: poolA-04_S4


title: polysome_MF_rep2_RNA_BS_seq

description: Polysome poly(A) RNA


title: polysome_MF_rep1_RNA_BS_seq

description: Polysome poly(A) RNA


title: total_MF_rep1_RNA_seq

description: Total poly(A) RNA


title: poolA-10_S10


title: total_HF_rep1_RNA_BS_seq

description: Total poly(A) RNA


title: total_HF_rep2_RNA_BS_seq

description: Total poly(A) RNA


title: total_MF_rep2_RNA_BS_seq

description: Total poly(A) RNA


title: total_MF_rep1_RNA_BS_seq

description: Total poly(A) RNA


title: total_LF_rep1_RNA_seq

description: Total poly(A) RNA


title: pool4-92_S380

value: tumor high-endothelial venules


title: poolA-01_S1


title: pool4-95_S383


title: pool4-96_S384


title: pool4-94_S382


title: poolA-03_S3


title: total_LF_rep2_RNA_BS_seq

description: Total poly(A) RNA


title: pool4-91_S379


title: poolA-02_S2


title: polysome_HF_rep1_RNA_BS_seq

description: Polysome poly(A) RNA


title: total_LF_rep1_RNA_BS_seq

description: Total poly(A) RNA


title: pool4-89_S377


title: pool4-90_S378


title: pool4-88_S376


title: pool4-93_S381


title: Gata3_sgRNA_Tomneg_replicate1 [S11]

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)
Genome_build: GRCm38
Supplementary_files_format_and_content: DEseq2 output file

source_name: In vitro differentiated TH2 cells

growth_protocol: Splenic CD4+ TN cells from Cas9xIl13Tom mice were flow-sorted, activated with a-CD3, a-CD28 and IL-2 for 24 hr and transduced with BFP/sgRNA-expressing retroviruses. Cells were maintained in IL-2 until day 6, and then differentiated into TH2 cells. At day 9, live BFP+ cells were flow purified for RNA extraction.

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)
and bar-coded using Ovation Ultralow Library Systems (Nugen)

value: In vitro differentiated TH2 cells

tag: sgrna

tag: sorted tom phenotype

value: neg


title: Nontargeting_sgRNA_Tompos_replicate3 [S10]

value: Nontargeting

value: pos


title: Gata3_sgRNA_Tomneg_replicate2 [S12]


title: Nontargeting_sgRNA_Tompos_replicate1 [S6]


title: Nontargeting_sgRNA_Tompos_replicate2 [S7]


title: Nontargeting_sgRNA_Tomneg_replicate3 [S5]


title: Gata3_sgRNA_Tomneg_replicate3 [S15]


title: pool4-84_S372

tag: facs gating


title: pool4-85_S373


title: Nontargeting_sgRNA_Tomneg_replicate2 [S2]


title: pool4-86_S374


title: pool4-80_S368


title: pool4-81_S369


title: pool4-79_S367


title: pool4-83_S371


title: pool4-78_S366


title: S32a_Tp

description:
processed data file:
S28_32ab_sec_lib_data.csv
S28_32ab_sec_screen_list.csv

data_processing:
Samples were sequenced using an Illumina Hiseq4000 running a single-read 50bp protocol
20 nt sgRNA sequences were trimmed from backbone sequences using Cutadapt version 1.4.1 (5’ GACGAAACACCG, 3’ GTTTTAGAGCTA).
sgRNA sequences were aligned to reference sgRNA libraries using Bowtie2 (version 1.2.3).
Supplementary_files_format_and_content: sgRNA count files (lib data) and pool information (screen list).

source_name: In vitro differentiated TH2 cells transduced with sgRNA-expressing retroviruses

growth_protocol: Splenic CD4+ TN cells from Cas9xIl13Tom mice were flow-sorted, activated with a-CD3, a-CD28 and IL-2 for 24 hr and transduced with BFP/sgRNA-expressing retroviral library. Cells were maintained in IL-2 until day 6, and then differentiated into TH2 cells. At day 9, live BFP+ Tom+ or Tom- cells were flow-purified for genomic DNA extraction

extract_protocol:
Cells were flow-sorted into 50% FCS PBS and genomic DNA from sorted cells were extracted using the QIAGEN DNeasy Blood & Tissue Kits following the manufacturer’s protocol, with the exception of DNA elution in water instead of buffer AE.
Illumina P7 barcodes; sgRNA-insert was first PCR-amplified using Herculase II Fusion DNA polymerase (Agilent) with primers (Forward) AATGGACTATCATATGCTTACCGTAACTTGAAAGTATTTCG and (Reverse) CTTTAGTTTGTATGTCTGTTGCTATTATGTCTACTATTCTTTCC, using up to 2 mg genomic DNA per 50 ml reaction. Equal volumes from each reaction were pooled and used for a further PCR amplification step to attach Illumina sequencing adaptors and Illumina P7 barcodes, using Herculase II Fusion DNA polymerase. The 330 bp library was gel purified and quantified using KAPA library quantification kit (Roche).

tag: screen

value: Secondary


title: S32a_Tn


title: S28_Tp


title: S32b_Tn


title: pool4-77_S365


title: S32b_Tp


title: S28_Tn


title: pool4-76_S364


title: pool4-87_S375


title: S16_Brie_Tp

description:
processed data file:
S16_Brie_lib_data.csv
S16_Brie_screen_list.csv

value: Brie


title: Nontargeting_sgRNA_Tomneg_replicate1 [S1]


title: S16_Brie_Tn


title: pool4-82_S370


title: S14_Brie_Tp

description:
processed data file:
S14_Brie_lib_data.csv
S14_Brie_screen_list.csv


title: pool4-75_S363


title: S14_Brie_Tn


title: pool4-72_S360


title: pool4-71_S359


title: pool4-74_S362


title: pool4-70_S358


title: pool4-69_S357


title: RBG26765_Young_AEC_083

city: Shanghai

first: Xiaonan

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: AEC

tag: age

value: Young


title: RBG26789_Old_AEC_081

value: Old


title: RBG26777_Young_AEC_084


title: RBG26801_Old_AEC_082


title: pool4-68_S356


title: RBG26729_Young_SEC_070

value: SEC


title: RBG26753_Old_SEC_071


title: pool4-66_S354


title: pool4-67_S355


title: RBG26800_Old_AEC_080


title: RBG26717_Young_SEC_069


title: pool4-65_S353


title: RBG26741_Old_SEC_070


title: pool4-64_S352


title: pool4-73_S361


title: pool4-63_S351


title: RBG26788_Old_AEC_079


title: pool4-62_S350


title: RBG26764_Young_AEC_081


title: RBG26776_Young_AEC_082


title: pool4-61_S349


title: RBG26752_Old_SEC_069


title: pool4-60_S348


title: pool4-59_S347


title: pool4-58_S346


title: RBG26728_Young_SEC_068


title: RBG26740_Old_SEC_068


title: RBG26716_Young_SEC_067


title: pool4-57_S345


title: pool4-55_S343


title: pool4-51_S339


title: pool4-54_S342


title: pool4-56_S344


title: RBG26751_Old_SEC_067


title: pool4-53_S341


title: RBG26739_Old_SEC_066


title: RBG26787_Old_AEC_077


title: pool4-50_S338


title: total_HF_rep2_RNA_seq

description: Total poly(A) RNA

value: WT


title: RBG26775_Young_AEC_080


title: pool4-49_S337


title: RBG26727_Young_SEC_066


title: RBG26763_Young_AEC_079


title: pool4-52_S340


title: RBG26715_Young_SEC_065


title: RBG26798_Old_AEC_076


title: RBG26786_Old_AEC_075


title: pool4-45_S333


title: pool4-48_S336


title: RBG26774_Young_AEC_078


title: pool4-46_S334


title: pool4-47_S335


title: pool4-44_S332


title: RBG26799_Old_AEC_078


title: pool4-43_S331


title: RBG26738_Old_SEC_064


title: RBG26750_Old_SEC_065


title: pool4-42_S330


title: pool4-41_S329


title: pool4-40_S328


title: pool4-37_S325


title: RBG26773_Young_AEC_076


title: RBG26785_Old_AEC_073


title: RBG26761_Young_AEC_075


title: RBG26797_Old_AEC_074


title: pool4-39_S327


title: RBG26737_Old_SEC_062


title: pool4-36_S324


title: RBG26714_Young_SEC_063


title: pool4-38_S326


title: RBG26762_Young_AEC_077


title: pool4-33_S321


title: RBG26725_Young_SEC_062


title: RBG26749_Old_SEC_063


title: RBG26713_Young_SEC_061


title: pool4-31_S319


title: RBG26796_Old_AEC_072


title: pool4-34_S322


title: pool4-32_S320


title: RBG26784_Old_AEC_071


title: pool4-30_S318


title: RBG26772_Young_AEC_074


title: RBG26726_Young_SEC_064


title: pool4-29_S317


title: RBG26760_Young_AEC_073


title: pool4-35_S323


title: poolA-14_S14

value: tumor endothelial cells


title: pool4-27_S315


title: pool4-25_S313


title: RBG26724_Young_SEC_060


title: RBG26712_Young_SEC_059


title: RBG26736_Old_SEC_060


title: pool4-22_S310


title: pool4-20_S308


title: RBG26783_Old_AEC_069


title: pool4-21_S309


title: pool4-19_S307


title: RBG26795_Old_AEC_070


title: pool4-23_S311


title: RBG26759_Young_AEC_071


title: RBG26771_Young_AEC_072


title: RBG26711_Young_SEC_057


title: RBG26735_Old_SEC_058


title: RBG26747_Old_SEC_059


title: pool4-18_S306


title: pool4-16_S304


title: pool4-17_S305


title: pool4-15_S303


title: RBG26794_Old_AEC_068


title: RBG26782_Old_AEC_067


title: pool4-28_S316


title: RBG26770_Young_AEC_070


title: pool4-14_S302


title: RBG26748_Old_SEC_061


title: pool4-26_S314


title: pool4-24_S312


title: RBG26758_Young_AEC_069


title: pool4-12_S300


title: pool4-13_S301


title: RBG26746_Old_SEC_057


title: pool4-11_S299


title: RBG26723_Young_SEC_058


title: pool4-10_S298


title: RBG26722_Young_SEC_056


title: pool4-09_S297


title: pool4-08_S296


title: RBG26793_Old_AEC_066


title: RBG26710_Young_SEC_055


title: pool4-06_S294


title: RBG26781_Old_AEC_065


title: pool4-07_S295


title: pool4-05_S293


title: RBG26757_Young_AEC_067


title: RBG26769_Young_AEC_068


title: RBG26745_Old_SEC_055


title: pool4-04_S292


title: O9-1 cells H3K4me3

city: Houston

first: Jun

state: TX

address: 6431 Fannin Street

institute: The University of Texas Health Science Center at Houston

data_processing:
The paired-end FASTQ format raw reads were aligned to mm10 by Bowtie2 using parameters “--end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700”, then the duplicates were removed by Picard, and the low-quality mapped reads were filtered by Samtools with the minimum quality score of 30.
To construct the UCSC visualization tracks, we converted alignment files into bigwig and bedgraph format with bamCoverage of deeptools
Then SEACR was used to call peaks with “stringent” and “norm” mode, the IgG alignment file was used as the control data.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: Cut&Tag

organism: Mus

extract_protocol:
CUT&Tag builds on the CUT&RUN protocol. It uses Tn5 transposase instead of MNase in CUT&RUN. CUT&Tag assay was performed according to the guidelines of Hatice S. Kaya-Okur’s protocol. Briefly, nucleus from O9-1 cells were incubated with concanavalin A (Con A)-coated magnetic beads (Bangs Laboratories, BP531) at room temperature for 10 min to immobilized nucleus on the Con A-coated magnetic beads. The bead-bound nuclei were then incubated with antibodies overnight at 4oC with rotation.  Guinea pig anti-rabbit second antibody (Antibodies-Online, ABIN101961, 1:100) was added into the nucleus to incubate for 30 min at room temperature. The pA-Tn5 adapter complex was incubated with nucleus at room temperature for 1 h. Nucleus were then resuspended in tagmentation buffer at 37oC for 1 h for DNA fragmentation. After 1 h, 0.5M EDTA, 10%SDS, and 20mg/mL Proteinase K were added to terminate tagmentation and incubate for 10 min at 70oC. DNA was then purified using phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation and dissolve in 21 μL 1 mM Tris-HCl at pH8 and 0.1 mM EDTA.
The libraries were prepared by add 2 uL of 10uM barcoded i5 primer, 2 uL of 10uM uniquely barcoded i7 primers and 25 uL NEBNext HiFi 2X PCR Master mix (Biolabs, M0541L), and PCR was performed according to the conditions in the protocol.  AMPure XP beads (Beckman Coulter, A63880) were used for DNA purification. Libraries were sequenced on NextSeq 550 (Illumina, USA) at UTHealth Cancer Genomics Center, and 75-bp paired-end reads were generated. Fastp software was used to remove adaptor and low-quality reads. All reads produced by CUT&Tag of H3K4me3 were aligned to the hg19 human genome using BWA (Burrows-Wheeler Aligner). MACS2 was used for peak calling. Genes with a peak within 3 kb of the transcription start site (TSS) were considered target genes. An area of 6 kb surrounding each TSS was selected to get CUT&Tag profiles of H3K4ac using deepTools software. Annotation of peaks was performed using ChIPseeker.

tag: cell line

tag: chip antibody

value: H3K4me3  (Active Motif, 39159)


title: O9-1 cells no antibody

value: No


title: pool4-02_S290

tag: tissue


title: RBG26733_Old_SEC_054


title: pool4-03_S291


title: RBG26721_Young_SEC_054


title: RBG26734_Old_SEC_056


title: RBG26709_Young_SEC_053


title: Cyt_48hr_2

type: RNA

city: Herlev

first: Joachim

last: Størling

address: Borgmester Ib Juuls Vej 83,

country: Denmark

institute: Steno Diabetes Center Copenhagen

description:
Sample11
human EndoC-βH1 cells, 48h, treated with IL-1β and IFNγ for 24 hours, replicate 2

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays V2 (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C. Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.

data_processing: Quantile normalization of raw data and subsequent data processing were performed using the R software limma package. After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least 3 out of 12 samples have flags in “P” or “M” (“All Targets Value”) were retained for further analyses.

label_protocol: Total RNA from each sample was treated with Rnase R to enrich circular RNA. The enriched circular RNA was then amplified and transcribed into fluorescent cRNA utilizing random primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.).

growth_protocol: Human insulin-producing EndoC-βH1 cells (Scharfmann et al., 2014) were grown on matrigel/fibronectin (100 and 2 μg/mL, respectively) coated plates and cultured in DMEM medium as previously described

extract_protocol: Total RNA was isolated using the RNeasy Mini kit (Qiagen, Venlo, The Netherlands) which favours purification of RNA molecules longer than 200 nucleotides.

treatment_protocol: EndoC-βH1 cells were exposed to the following cytokine concentrations: recombinant human IL-1β (R&D Systems, Abingdon, U.K.), 50 U/mL; and recombinant human IFN-γ (PeproTech, London, U.K.), 1,000 U/mL for 24 hours and 48 hours

value: human EndoC-βH1 cells (Human insulin producing cell line)

tag: treatment


title: Cyt_48hr_3

description:
Sample12
human EndoC-βH1 cells, 48h, treated with IL-1β and IFNγ for 24 hours, replicate 3


title: RBG26792_Old_AEC_064


title: pool3-94_S286

value: tumor high-endothelial venules


title: pool3-95_S287


title: RBG26768_Young_AEC_066


title: Control_48hr_1

description:
Sample7
human EndoC-βH1 cells, 48h, no treatment, replicate 1

value: no treatment


title: Cyt_48hr_1

description:
Sample10
human EndoC-βH1 cells, 48h, treated with IL-1β and IFNγ for 24 hours, replicate 1


title: O9-1 cells siCtrl-Yap


title: RBG26756_Young_AEC_065


title: Control_48hr_2

description:
Sample8
human EndoC-βH1 cells, 48h, no treatment, replicate 2


title: pool4-01_S289


title: pool3-93_S285


title: RBG26744_Old_SEC_053


title: Control_48hr_3

description:
Sample9
human EndoC-βH1 cells, 48h, no treatment, replicate 3


title: Cyt_24hr_3

description:
Sample6
human EndoC-βH1 cells, 24h, treated with IL-1β and IFNγ for 24 hours, replicate 3


title: primary rat microglia, LPS + Siponimod 3

city: Düsseldorf

first: Joel

last: Gruchot

address: Moorenstraße 5

department: Neurology

institute: Heinrich-Heine-University

data_processing:
The bcl2fastq tool (v2.20.0.422) was used to convert the bcl files to fastq files as well for adapter trimming and demultiplexing.
Data analyses on fastq files were conducted with CLC Genomics Workbench (version 22.0.2, QIAGEN, Venlo. NL). The reads of all probes were adapter trimmed (Illumina TruSeq) and quality trimmed (using the default parameters: bases below Q13 were trimmed from the end of the reads, ambiguous nucleotides maximal 2).
Mapping was done against the Rattus norvegicus (mRatBN7.2.106; July 05, 2022) genome sequence.

source_name: cortical

growth_protocol: Briefly, dissociated P1 Wister rat cortices were cultured on T-75 cell culture flasks in Dulbecco′s Modified Eagle′s Medium (DMEM) substituted with 10% fetal calf serum (FCS) and 4 mM L-glutamine, 50 U/ml penicillin/streptomycin. After 10 days, flasks were shaken at 180 rpm/min at 37 °C and microglia-containing supernatants were collected after 2 and 24 h. To further purify the primary rat microglia, cells were sorted using MACS against CD11b/c microbeads.

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen) and 150 ng of total RNA was used for the library construction
RNA libraries for RNA-Seq were prepared according to the manifacturers protocol using the VAHTS™ Universal RNA-Seq Library Prep Kit for Illumina® V6 with mRNA capture module

treatment_protocol: One day after microglial isolation, cells were stimulated with 50 µM siponimod or similar amounts of DMSO with or without 100 ng/ml LPS in microglia media (10% FCS, 2 mM L-glutamine, 50 U/ml penicillin/streptomycin in DMEM).

value: cortical

value: Postnatal day 1

tag: cell type

value: microglia

value: Wistar

value: LPS (100 ng/ml) + Siponimod 50 µM


title: primary rat microglia, LPS + Siponimod 2

tag: strain


title: Control_24hr_3

description:
Sample3
human EndoC-βH1 cells, 24h, no treatment, replicate 3


title: primary rat microglia, LPS + DMSO 2

value: LPS (100 ng/ml)


title: pool3-96_S288

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.


title: Cyt_24hr_2

description:
Sample5
human EndoC-βH1 cells, 24h, treated with IL-1β and IFNγ for 24 hours, replicate 2


title: Control_24hr_1

description:
Sample1
human EndoC-βH1 cells, 24h, no treatment, replicate 1


title: pool3-92_S284


title: pool3-91_S283


title: Control_24hr_2

description:
Sample2
human EndoC-βH1 cells, 24h, no treatment, replicate 2


title: pool3-89_S281


title: RBG26720_Young_SEC_052

value: mesenchymal and endothelial cells


title: Cyt_24hr_1

description:
Sample4
human EndoC-βH1 cells, 24h, treated with IL-1β and IFNγ for 24 hours, replicate 1


title: RBG26780_Old_AEC_063

value: AEC


title: pool3-90_S282


title: RBG26732_Old_SEC_052

value: Old


title: primary rat microglia, LPS + Siponimod 1


title: RBG26708_Young_SEC_051

value: SEC

value: Young


title: pool3-88_S280


title: primary rat microglia, LPS + DMSO 3


title: RBG26779_Old_AEC_062


title: primary rat microglia, LPS + DMSO 1


title: RBG26743_Old_SEC_051


title: pool3-85_S277


title: RBG26731_Old_SEC_050


title: RBG26719_Young_SEC_050


title: pool3-86_S278


title: RBG26767_Young_AEC_064


title: pool3-87_S279


title: RBG26755_Young_AEC_063


title: pool3-84_S276


title: Melanocyte-Keratinocyte_co-culture_PATIENT_R170015

city: Barcelona

first: Miriam

last: Potrony

address: Villarroel 170

institute: Hospital Clinic of Barcelona

hyb_protocol: According to Manufacturer recommendations

scan_protocol: Microarray Scanner G2565CA (Agilent). Feature Extraction Software (Agilent, Santa Clara, CA, US).

data_processing: Babelomics

source_name: Human Melanocyte-Keratinocyte co-culture derived from healthy skin biopsy

growth_protocol: Explained in Puig-Butille JA et al. Oncotarget 2014; 5:1439–51.

extract_protocol: Trizol extraction method (Invitrogen Life Technologies) an purification using the RNeasy kit (Qiagen)

value: F

tag: disease state

value: MELANOMA PATIENT

value: WT

value: Melanocyte-Keratinocyte co-culture


title: pool3-83_S275

value: tumor high-endothelial venules


title: Melanocyte-Keratinocyte_co-culture_PATIENT_R160273

label_protocol: According to Manufacturer recommendations

value: M


title: Melanocyte-Keratinocyte_co-culture_PATIENT_R160272

value: MUTATED


title: Melanocyte-Keratinocyte_co-culture_PATIENT_R170014


title: RBG26790_Old_AEC_061


title: Melanocyte-Keratinocyte_co-culture_PATIENT_R170001


title: Melanocyte-Keratinocyte_co-culture_PATIENT_R170016


title: pool3-82_S274


title: Melanocyte-Keratinocyte_co-culture_PATIENT_R160259


title: Melanocyte-Keratinocyte_co-culture_PATIENT_R160260


title: pool3-80_S272


title: Melanocyte-Keratinocyte_co-culture_PATIENT_R160277


title: RBG26707_Young_SEC_049


title: Melanocyte-Keratinocyte_co-culture_PATIENT_R160204


title: RBG26778_Old_AEC_060


title: RBG26766_Young_AEC_062


title: pool3-79_S271


title: pool3-77_S269


title: pool3-81_S273


title: Melanocyte-Keratinocyte_co-culture_PATIENT_R160195


title: RBG26754_Young_AEC_061


title: pool3-76_S268


title: RBG26730_Old_SEC_048


title: Melanocyte-Keratinocyte_co-culture_PATIENT_R160170


title: Melanocyte-Keratinocyte_co-culture_PATIENT_R160169


title: RBG26718_Young_SEC_048


title: RBG26706_Young_SEC_047


title: pool3-75_S267


title: pool3-74_S266


title: Melanocyte-Keratinocyte_co-culture_PATIENT_R160196


title: pool3-78_S270


title: Melanocyte-Keratinocyte_co-culture_PATIENT_R160194


title: pool3-73_S265


title: Melanocyte-Keratinocyte_co-culture_PATIENT_R160193


title: RBG26742_Old_SEC_049


title: M18(in vivo): WT GBS infected

city: New York

first: Itai

last: Yanai

state: NY

address: 435 East. 30th St.

institute: NYU Langone Health

description: in vivo

data_processing:
Basecalls was done using cellranger mkfastq V3.0.0
alignment, filtering, counting and umi counting was doe using cellranger count V3.0.0
Assembly: mm10-3.0.0
Supplementary files format and content: expression matrix of umi counts

source_name: mouse placental cells

growth_protocol: mouse placental cells were dissociated into suspension

extract_protocol:
mouse placental cells were dissociated and enzymatically digest, red blood cells were lysed and remaining cells were washed and run for scRNA-Seq
10x single cell RAN seq V3

treatment_protocol: mice were infected intravaginally with wild type of Bh/c KO GBS or PBS control. Placentas were harvested at different time points following infection and processed for scRNA-Seq

value: placenta

value: mouse placental cells

value: WT GBS infected


title: pool3-72_S264

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.


title: M19(in vivo): WT GBS infected

description: in vivo


title: Melanocyte-Keratinocyte_co-culture_CONTROL_R170012

value: CONTROL


title: M20(in vivo): WT GBS infected

description: in vivo


title: M15(in vivo): WT GBS infected

description: in vivo


title: RBG26693_Old_SEC_046


title: M17(in vivo): WT GBS infected

description: in vivo


title: Melanocyte-Keratinocyte_co-culture_CONTROL_R170018


title: Melanocyte-Keratinocyte_co-culture_CONTROL_R170008


title: Melanocyte-Keratinocyte_co-culture_CONTROL_R160209


title: Melanocyte-Keratinocyte_co-culture_CONTROL_R170011


title: Melanocyte-Keratinocyte_co-culture_CONTROL_R160174


title: M13(in vivo): WT GBS infected

description: in vivo


title: Melanocyte-Keratinocyte_co-culture_CONTROL_R170007


title: M12(in vivo): WT GBS infected

description: in vivo


title: RBG26681_Young_SEC_046


title: M11(in vivo): WT GBS infected

description: in vivo


title: RBG26705_Old_SEC_047


title: pool3-70_S262


title: RBG26657_Old_SEC_045


title: M10(in vivo): WT GBS infected

description: in vivo


title: M9(in vivo): WT GBS infected

description: in vivo


title: pool3-69_S261


title: pool3-68_S260


title: M7(in vivo): BH/c KO GBS infected

description: in vivo

value: BH/c KO GBS infected


title: M8(in vivo): BH/c KO GBS infected

description: in vivo


title: M4(in vivo): control

description: in vivo

value: control


title: pool3-67_S259


title: M3(in vivo): control

description: in vivo


title: RBG26621_Young_SEC_044

value: mesenchymal and endothelial cells


title: M2(in vivo): control

description: in vivo


title: RBG26704_Old_SEC_043

value: Old


title: M6(in vivo): BH/c KO GBS infected

description: in vivo


title: M5(in vivo): BH/c KO GBS infected

description: in vivo


title: RBG26645_Old_SEC_044

value: SEC


title: pool3-71_S263


title: RBG26633_Young_SEC_045

value: Young


title: pool3-66_S258


title: RBG26692_Old_SEC_042


title: M1(in vivo): control

description: in vivo


title: pool3-65_S257


title: SB204990_MC_scATAC-seq

city: Nashville

first: Dalton

middle: Lee

last: Greenwood

state: TN

address: 2201 West End Ave

department: PMI

institute: Vanderbilt University

description:
SB2_ATAC, replicate 1, scATACseq
10x Genomics

data_processing:
For scRNA-seq, The demultiplexing, barcode processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). For scATAC-seq, demultiplexing, barcode processing, peak calling, and aggregation were made using the Cell Ranger ATAC software v1.2.0. Files were imported into R using ArchR v1.0.0 (filterTSS = 8, filterFrags = 2819), with filterFrags value set based on the distribution of transcription start site (TSS) vs. the log transform of unique fragments generated by ArchR.
Assembly: mm10
Supplementary files format and content: Tab-separated values files, bed files for scATAC-seq, and matrix files

source_name: Bone marrow

extract_protocol:
For scRNA-seq extract protocol, For C57BL/6 Lineage-depleted BM cells were seeded at 1E3 cells per 35 mm dish in StemCell Technologies’ MethocultTM GF M3434 methylcellulose media and cultured for two weeks with either 30 uM SB204990 (Tocris Cat# 4962) or an equivalent volume of DMSO. Cells were harvested and resuspended in PBS alongside freshly isolated lineage-depleted BM cells from a C57BL/6 mouse. Cells were then stained for viability using eBioscience™ Fixable Viability Dye eFluor™ 780 (Thermo Fisher Scientific 65-0865-14) and flow-sorted for viable cells. For scATAC-seq extract protocol, C57BL/6 Lineage-depleted BM cells were seeded at 1E3 cells per 35 mm dish in StemCell Technologies’ MethocultTM GF M3434 methylcellulose media and cultured for two weeks with either 30 uM SB204990 (Tocris 4962) or an equivalent volume of DMSO. Cells were harvested and resuspended in PBS alongside freshly isolated lineage-depleted BM cells from a C57BL/6 mouse.
For scRNA-seq library construction, Cells were submitted to Vanderbilt University’s VANTAGE Core, where they were prepared for single-cell 5’ RNA sequencing using the 10x Genomics Chromium system. Libraries were prepared using P/N 1000014, 1000020, 1000080, and 120262 according to the manufacturer’s protocol. The libraries were sequenced using the NovaSeq 6000 with 150 bp paired-end reads. RTA (version 2.4.11; Illumina) was used for base calling. For scATAC-seq library construction, Nuclei were isolated and submitted to Vanderbilt University’s VANTAGE Core, where they were prepared for scATAC-seq following the manufacturer’s protocol using P/N 1000111, 1000086, and 1000084.

value: Methylcellulose-cultured Lin-, c-Kit+ HSPCs

value: Bone marrow

value: 6-8 weeks old


title: RBG26668_Young_SEC_042


title: pool3-63_S255


title: Fresh_Lin_Depleted_scRNA-seq

description:
FLD_RNA, replicate 1, scRNAseq
10x Genomics

value: Freshly isolated Lin-, c-Kit+ HSPCs


title: CB-389_MC_scATAC-seq

description:
CB839_ATAC, replicate 1, scATACseq
10x Genomics


title: Fresh_Lin_Depleted_scATAC-seq

description:
FLD_ATAC, replicate 1, scATACseq
10x Genomics


title: pool3-62_S254

value: tumor high-endothelial venules


title: SB204990_MC_scRNA-seq

description:
SB2_RNA, replicate 1, scRNAseq
10x Genomics


title: pool3-61_S253


title: M14(in vivo): WT GBS infected

description: in vivo


title: RBG26656_Old_SEC_041


title: CB-389_MC_scRNA-seq

description:
CB839_RNA, replicate 1, scRNAseq
10x Genomics


title: DMSO_MC_scRNA-seq

description:
DMSO_RNA, replicate 1, scRNAseq
10x Genomics


title: TH2_Itgav-KO_3

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 TH2 cells

tag: genotype


title: TH2_Itgav-KO_2


title: pool3-64_S256


title: RBG26644_Old_SEC_040


title: TH2_cont_1

value: Control


title: DMSO_MC_scATAC-seq

description:
DMSO_ATAC, replicate 1, scATACseq
10x Genomics


title: RBG26680_Young_SEC_043


title: pool3-58_S250


title: RBG26620_Young_SEC_041


title: pool3-60_S252


title: TH2_cont_2


title: pool3-59_S251


title: RBG26703_Old_SEC_039


title: TH1_Itgav-KO_2

value: Primary mouse TH1 cells


title: TH1_Itgav-KO_3


title: RBG26691_Old_SEC_038


title: RBG26679_Young_SEC_040


title: TH1_cont_3


title: pool3-56_S248


title: pool3-57_S249


title: TH1_Itgav-KO_1


title: TH1_cont_2


title: pool3-55_S247


title: TH2_cont_3


title: RBG26667_Young_SEC_039


title: RBG26655_Old_SEC_037


title: TH2_Itgav-KO_1


title: pool3-53_S245


title: pool3-54_S246