title: Saline_M

status: Public on Jan 15 2023

data_processing:
Cell demultiplexing and genome alignment in Cell Ranger using Emsemble pre-mRNA reference assembly GTF file. Raw count data obtained in Cell Ranger.
Assembly: rn7
Supplementary files format and content: Cell Ranger output matrices for barcodes, features, and gene expression counts are provided for each sample.

source_name: Nucleus accumbens

extract_protocol:
1mm brain sections were taken at the level of the nucleus accumbens, and nucleus accumbens tissue was dissected using a 2mm punch tool centered on the nucleus accumbens core subregion. Frozen tissue punches were thawed slowly on ice prior to being chopped by scalpel 100 times in 2 orthogonal directions. Tissue from 4 animals in the same treatment condition was then combined and transferred to 5mL of chilled (4°C) Lysis Buffer (10mM Tris-HCl, 10mM NaCl, 3mM MgCl2 (Thermo Fisher, BP214-500), 0.1% Igepal in Nuclease-Free Water (Sigma, 18896-50ML)) for 15 min, mixing the tissue by inversion every 2 min. Lysis was quenched immediately at 15 min with 5mL of complete Hibernate-A (Thermo Fisher, A1247501) supplemented with B27 and Glutamax (Life Technologies, 35050-061)). Tissue was then triturated by fire-polished Pasteur pipette (2 pipettes of decreasing diameter; 8-10 passes per pipette) for 35 min and passed through a 40µm pre-wet filter. The samples were then pelleted at 500rcf for 10 min at 4°C followed by a wash in 10mL of Nuclei Wash & Resuspension Buffer (1X PBS, 1% BSA, 0.2U/ul NxGen RNase inhibitor (Lucigen, 30281-2)). Supernatant was then removed and the pellet was gently resuspended in a total volume of 800µl prior to 7-AAD (Thermo Fisher, 00-6993-50) staining and FACS to further purify the nuclei for sequencing. Immediately after FACS, nuclei were washed a final time at 200rcf in 10mL supplemented Hibernate-A containing 1% BSA for 10 minutes at 4°C to remove any remaining fine debris and nascent RNA. Nuclei were brought to a concentration of 1,500 nuclei/µl and an average total of 12,500 nuclei pooled from 4 rats were loaded per sex and treatment group.
FACS-sorted nuclei were subject to 10X GEM generation and barcoding, GEM-RT cleanup and cDNA amplification, and library construction using a Chromium Single Cell 3ʹ Reagent Kit (v3 chemistry). Libraries were quantified and underwent sequencing (~550M total 75bp paired-end reads) on an Illumina sequencing platform (NextSeq 500).

value: Sprague-Dawley

value: Saline

value: Male


title: KTPB20_IGO_11254_16_S16

status: Public on Sep 08 2022

type: SRA

city: New York

first: Yu-Jui

last: Ho

address: 1275 York Avenue

country: USA

institute: Memorial Sloan Kettering Cancer Center

library_source: transcriptomic

data_processing:
Illumina read quality was checked for each sample using FastQC v0.11.5.
Raw fastq files were analyzed by removing adaptor sequences using Trimmomatic (0.36), aligned to the mouse genome using STAR (2.5.3a), and quantified transcript counts using featureCounts (1.6.3).
Assembly: Reads were aligned to the mouse transcriptome (mm10, GRCm38.91)
Supplementary files format and content: Tab-delimited text file includes raw count table for each sample

molecule: total RNA

organism: Mus musculus

source_name: Pancreas tumor

growth_protocol: Mice undergo a survival surgery where the pancreas is exposed and 100.000 cells of the different genotypes are injected. Mice are then monitored and when they have overt disease assessed by palpation (~4 weeks after injection), the tumors are collected and a piece is flash frozen for total RNA extraction.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen)
PolyA mRNA was selected using beads coated with polyT oligonucleotides. Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation.
For sequencing, pooled multiplexed libraries were run on a HiSeq 2500 machine on RAPID mode. Approximately 10 million 76bp single-end reads were retrieved per replicate condition. Resulting RNA-Seq data was analyzed by removing adaptor sequences using Trimmomatic (29), aligning sequencing data to GRCh37.75(hg19) with STAR (30), and genome wide transcript counting using HTSeq (31) to generate a RPKM matrix of transcript counts.

treatment_protocol: Mice were pre-treated with either IgG or anti-IFNAR1 antibodies (200 ug i.p. 3 times a week) starting one week before injection of cells and kept until the end of the experiment.

tag: tissue

value: Pancreas tumor

value: Whole tissue

tag: treatment

value: IFNAR1 antibody

tag: genotype

value: KrasG12D; sgP53; dL


title: KTPB15_IGO_11254_12_S12

value: IgG antibody


title: KTPB14_IGO_11254_11_S11


title: In vitro_SEN_DMSO_1_(2days) [NSP_SEN_1]

status: Public on Jan 17 2023

organism: Mus

source_name: in vitro senescent (p53-restored) NSP cells

growth_protocol: NSP cells were cultured in DMEM supplemented with 10% FBS and 1% penicillin and streptomycin (GIBCO) on plates that were collagen-coated (PurCol, Advanced Biomatrix, 0.1 mg/ml) for 30’ at 37 C and maintained by the addition of 1 μg/ml doxycycline to suppress p53 expression. In order to restore p53 expression and therefore induce senescence, doxycycline-containing media was replaced with doxycycline-free media for 6 days and senescent cells were seeded and collected on day 8 after doxycycline withdrawal. For perturbing BRD4-dependent transcriptional programs, cells were treated with 500 nM of JQ1 (S7110, Selleck Chem) for 48 h prior to harvest, starting JQ1 at day 6 after restoring p53 (off-dox), when NSP cells are fully senescent. For drug-induced senescence experiments, p53-suppressed (on-dox) NSP cells were treated with trametinib + palbociclib, or cisplatin for 7 days. The concentration of DMSO corresponded to the drug treatment and does not exceed 1:1,000 dilution of total media volume, which shows no discernable toxicity to cultured cells. For IFN-γ of proliferating or senescent populations, the indicated doses of mouse recombinant IFN-γ was administrated to proliferating and senescent (p53-restored) NSP cells after 24 h of cell seeding and cells were harvested after 24 h of IFN-γ treatment.

extract_protocol:
Total RNA was extracted using using TRIzol (Thermo Fisher Scientific) following the manufacturer’s instructions.
PolyA mRNA was selected using beads coated with polyT oligonucleotides. Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation.
For sequencing, pooled multiplexed libraries were run on a HiSeq 2500 machine on RAPID mode. Approximately 10 million 76bp single-end reads were retrieved per replicate condition.

tag: sample type

value: Cell line

value: Doxycycline Off


title: KTPB12_IGO_11254_10_S10


title: In vivo NSP_51 [NSP_51]

source_name: in vivo bulk tumor (p53-restored)

growth_protocol: C57BL/6N female mice aged 8-9 weeks old were injected via hydrodynamic tail vein injection (HTVI) with a sterile 2 ml (or 1/10 of mouse body weight) 0.9% NaCl solution containing 5 μg of pT3-EF1a-NrasG12D-IRES-rtTA (Tet-On system) and 20 ug of pT3-TRE-tRFP-shp53 transposon vectors along with 5ug CMV-SB13 transposase (5:1 ratio) through the lateral tail vein. Doxycycline was administered to mice via 625 mg/kg doxycycline-containing food pellets (Harlan Teklad) at least 4 days before injection. The tumor was harvested at 5-7 weeks after injection for cell line isolation.

extract_protocol:
To extract tissue RNA, freshly isolated tumor chunk was first stored in RNA-later solution (AM7024, Thermo Scientific) to preserve RNA integrity until extraction and RNeasy kit (74106, Quiagen) was used to purified tissue RNA following the manufacturer instructions
PolyA mRNA was selected using beads coated with polyT oligonucleotides. Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation.
For sequencing, pooled multiplexed libraries were run on a HiSeq 2500 machine on RAPID mode. Approximately 10 million 76bp single-end reads were retrieved per replicate condition.


title: KTPB11_IGO_11254_9_S9


title: In vivo NSP_50 [NSP_50]

source_name: in vivo bulk tumor (p53-suppressed)

value: Doxycycline On


title: KTPB08_IGO_11254_8_S8

value: KrasG12D; sgP53; dS


title: KTPB06_IGO_11254_6_S6


title: KTPB05_IGO_11254_5_S5


title: Saline_F

city: Birmingham

first: Jeremy

last: Day

state: Alabama

address: 1825 University Blvd SHEL 910

department: Neurobiology

institute: University of Alabama at Birmingham

library_source: transcriptomic single cell

molecule: polyA RNA

organism: Rattus norvegicus

growth_protocol: Sprague-Dawley 90-120-day-old male or female rats were purchased from Charles River Laboratories. Male or female adult rats were co-housed in pairs in plastic filtered cages with nesting enrichment in an AAALAC-approved animal care facility maintained between 23-24°C on a 12-hour light/dark cycle with ad libitum food (Lab Diet Irradiated rat chow) and water. Bedding and enrichment were changed weekly by animal resources program staff. Animals were randomly assigned to experimental groups.

treatment_protocol: Rats were injected with either cocaine (20mg/kg, dissolved in physiological saline) intraperitoneally or equal volumes of physiological saline and placed in an open field for behavioral tracking. Injections occured daily across 7 consecutive days. Tissue was harvested 1hr after the final (7th) injection, when rats were sacrificed, the brain was blocked into 1mm sections, abd the NAc was harvested and flash frozen. A total of 16 rats (8 male, 8 female, 4 per GEMwell) were used for this experiment.

tag: strain

tag: age

tag: Sex

value: Female


title: KTPB18_IGO_11254_14_S14


title: KTPB02_IGO_11254_2_S2


title: KTPB01_IGO_11254_1_S1


title: IFNAR_A_HTO

description: polyA HTO

data_processing:
The data was processed using the tool SEQC wich was created by the Pe'er lab. It can be accessed on github: https://github.com/dpeerlab/seqc
The genome these samples were aligned against is a custom build that can be found (and is publicly available) here:s3://seqc-public/genomes/mm38_long_polya/
Supplementary files format and content: The output (the dense.csv files) is a filtered count matrix where: Rows are cells and columns are genes. Note that the first column may be called CLUSTER , which indicates clustering assignment of each cell and must not be treated as a gene.
Supplementary files format and content: For the HTO data: The data was processed using the tool SHARP, github link here: https://github.com/hisplan/sharp. The "final_classification" file is a gzipped tsv file that contains the cell barcode with its hashtag assignment on every row.

source_name: CD45+ cells from pancreas tumor

extract_protocol:
The single-cell RNA-Seq of FACS-sorted cell suspensions was performed on Chromium instrument (10X genomics) following the user guide manual for 3′ v3.1
Cells were captured in droplets. Following reverse transcription and cell barcoding in droplets, emulsions were broken and cDNA purified using Dynabeads MyOne SILANE followed by PCR amplification per manual instruction. Between 15,000 to 25,000 cells were targeted for each sample. Samples were multiplexed together on one lane of 10X Chromium following cell hashing protocol.
Final libraries were sequenced on Illumina NovaSeq S4 platform (R1 – 28 cycles, i7 – 8 cycles, R2 – 90 cycles). The cell-gene count matrix was constructed using the Sequence Quality Control (SEQC) package.

value: Sorted cells

value: IFNAR1 antiody


title: IgG_C_HTO

description: polyA HTO


title: IgG_A_HTO

description: polyA HTO


title: IFNAR_A

description: polyA RNA


title: IgG_C

description: polyA RNA


title: IgG_A

description: polyA RNA


title: input_3

status: Public on Aug 22 2022

first: Coen

last: van Solingen

state: NY

address: 435 E30th street SB 704

department: Medicine/Cardiology

institute: NYU Grossman School of Medicine

library_source: genomic

data_processing:
Library strategy: ChIRP-seq
trim adapters using Trimmomatic
map reads using bwa
call peaks relative to input using macs
perform differential binding analysis using DiffBind from BioConductor
Assembly: hg19
Supplementary files format and content: base mean data was calculated from reads of three replicate samples. ChIRP results were analyzed as % enrichment relative to input DNA of respective experimental conditions.

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: THP were cultivated in RPMI (ATCC) with 10% non-heat inactivated FBS and 1% P/S.

extract_protocol:
DNA was eluted from hybridized magnetic beads and subjected for Illumina sequencing. In short, beads were washed at room temperature with ChIRP wash buffer (EMD Millipore, #17-10494). Beads were subsequently captured using a DynaMag magnet (Thermo Fisher Scientific) and DNA was eluted by suspending beads in elution buffer (20 mM Tris pH 7.4, 1% SDS, 50 mM NaHCO3, 1 mM EDTA). ChIRP eluates were reverse cross-linked at 65C for 4h, digested with Proteinase K (EMD Millipore) at 55C followed by incubation with RNase cocktail (Ambion). ChIRP purified DNA was cleaned using PCR purification columns (Zymo Research) and subjected to Illumina sequencing.
Illumina

treatment_protocol: 100 ng/mL PMA to differentiate into THP1 macrophages

tag: cell line

value: monocytic cell line


title: input_2


title: Sample_9_KD_3, input

data_processing:
Reads were aligned to the human genome (hg38) using Bowtie2.
Alignments were sorted and indexed using Samtools for downstream processes. MACS2 was then used to identify significant peaks .
Peaks were annotated using the R package ChIPseeker [ref]. Peaks that overlapped a 4kb window centered at an annotated transcription start site were annotated as promoter peak
Differential enrichment analysis was performed using the R package DiffBind. Peaks with an FDR adjusted p-value of 0.1 or less were considered differentially enriched between the knockdown and control conditions
Motif enrichment analysis was performed on 3kb windows centered at the TSS of genes with differentially enriched promoter peaks using HOMER
Genome_build: hg38
Supplementary_files_format_and_content: peak text files

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit.

treatment_protocol: cells were tranfected with gapmers designed to target all variants of CHROME or a control gapmer.

tag: issue

value: transfection with gapmer targetting CHROME

tag: group

value: gapmer

tag: antibody

value: input


title: KTPB07_IGO_11254_7_S7


title: input_1


title: Sample_8_KD_2, input


title: KTPB04_IGO_11254_4_S4


title: odd_3

value: odd probes for CHROME


title: Sample_7_KD_1, input


title: odd_2


title: Sample_3_Control_3, input

value: transfection with control gapmer

value: control


title: KTPB03_IGO_11254_3_S3

value: Pancreas tumor

value: Whole tissue


title: odd_1


title: Sample_2_Control_2, input


title: even_3

value: even probes for CHROME


title: Sample_9_KD_3


title: NSP_PRO_No IFNG_2

status: Public on Jan 28 2023

source_name: in vitro proliferating NSP cells + no IFNg

growth_protocol: NSP cells were cultured in DMEM supplemented with 10% FBS and 1% penicillin and streptomycin (GIBCO) on plates that were collagen-coated (PurCol, Advanced Biomatrix, 0.1 mg/ml) for 30’ at 37 C and maintained by the addition of 1 μg/ml doxycycline to suppr

extract_protocol:
PolyA mRNA was selected using beads coated with polyT oligonucleotides. Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation.
For sequencing, pooled multiplexed libraries were run on a HiSeq 2500 machine on RAPID mode. Approximately 10 million 76bp single-end reads were retrieved per replicate  condition. Resulting RNA-Seq data was analyzed by removing adaptor sequences using Trimmomatic (29), aligning sequencing data to GRCh37.75(hg19) with STAR (30), and genome wide transcript counting using HTSeq (31) to generate a RPKM matrix of transcript counts.

value: Cell line


title: even_2


title: even_1


title: SC25_Dox_DMSO_1_(7_days) [NSP_PRO_DMSO_1]

source_name: in vitro proliferating (DMSO) NSP cells

value: Doxycycline Off


title: SC26_Dox_DMSO_2_(7_days) [NSP_PRO_DMSO_2]


title: Sample_8_KD_2


title: Sample_7_KD_1


title: Sample_3_Control_3


title: In vitro_SEN_JQ1_500nM_3_(2days) [NSP_SEN_JQ1_3]

source_name: in vitro senescent (p53-restored) NSP cells + JQ1


title: NSP_SEN_IFNg_IFNg_50pg_2 [NSP_SEN_IFNG_2]

source_name: in vitro senescent (p53-restored) NSP cells + IFNg


title: NSP_PRO_IFNg_50pg_1 [NSP_PRO_IFNG_1]

source_name: in vitro proliferating NSP cells + IFNg

value: Doxycycline On


title: NSP_SEN_IFNg_0pg_2 [NSP_SEN_UT_2]

source_name: in vitro senescent (p53-restored) NSP cells untreated


title: Sample_2_Control_2


title: NSP_SEN_IFNg_IFNg_50pg_1 [NSP_SEN_IFNG_1]


title: In vitro_SEN_JQ1_500nM_1_(2days) [NSP_SEN_JQ1_1]


title: gapCHROME_3_polyIC

data_processing:
 RNA-seq reads with aligned using the STAR, version 2.5, aligner against hg19 genome/transcriptome.
Gene counting was done using featureCounts , version 1.5.2, against hg19 annotations.
Raw counts were normalized and DE analysis was performed using DESeq2, version 3.4.
base mean data was calculated from reads of three replicate samples. Fold change was calculated as gapCHROME over gapctrl. P-values were calculated on these data. Data was used in manuscript for bioinformatics sections.
Genome_build: hg19
Supplementary_files_format_and_content: 2021_11_30_gapmer_poly_Counts_all.xlsx

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen) and Direct-zol RNA MiniPrep columns (Zymo Research).
Illumina TruSeq RNA sample preparation kit. Illumina HiSeq, 2x150bp configuration, single index, per lane

treatment_protocol: cells were tranfected with gapmers designed to target all variants of CHROME or a control gapmer and subsequent stimulated with polyIC (1000 ng/mL) or a control vehicle

tag: cell type

tag: modification

value: transfection with gapmer targeting CHROME

value: CHROME depletion

value: polyIC


title: gapCHROME_2_polyIC


title: SC30_Dox_Combo_3_(7_days) [NSP_SEN_COMBO_3]

source_name: in vitro senescent NSP (trametinib/palbociclib) cells


title: gapCHROME_1_polyIC


title: In vitro_PRO_JQ1_500nM_2_(2_days) [NSP_PRO_JQ1_2]

source_name: in vitro proliferating NSP cells + JQ1


title: In vitro_PRO_DMSO_2_(2_days) [NSP_PRO_2]

source_name: in vitro proliferating NSP cells


title: gapctrl_1_polyIC


title: gapCHROME_3_LPS

description:
gapmerCHROME_LPS_3_66_S66
processed data file: gapmerCHROME_vs_gapCTRL_LPS.csv

data_processing:
 RNA-seq reads with aligned using the STAR, version 2.5, aligner against hg19 genome/transcriptome.
Gene counting was done using featureCounts , version 1.5.2, against hg19 annotations.
Raw counts were normalized and DE analysis was performed using DESeq2, version 3.4.
Genome_build: hg19
Supplementary_files_format_and_content: base mean data was calculated from reads of three replicate samples. Fold change was calculated as gapCHROME over gapctrl. P-values were calculated on these data. Data was used in manuscript for bioinformatics sections.

treatment_protocol: cells were tranfected with gapmers designed to target all variants of CHROME or a control gapmer and subsequent stimulated with LPS (500 ng/mL) or a control vehicle


title: gapctrl_3_polyIC


title: In vivo NSP_49 [NSP_49]


title: gapCHROME_2_LPS

description:
gapmerCHROME_LPS_2_65_S65
processed data file: gapmerCHROME_vs_gapCTRL_LPS.csv


title: gapctrl_3_LPS

description:
gapctrl_LPS_3_63_S63
processed data file: gapmerCHROME_vs_gapCTRL_LPS.csv


title: gapctrl_1_LPS

description:
gapctrl_LPS_1_61_S61
processed data file: gapmerCHROME_vs_gapCTRL_LPS.csv


title: gapctrl_2_LPS

description:
gapctrl_LPS_2_62_S62
processed data file: gapmerCHROME_vs_gapCTRL_LPS.csv


title: gapCHROME_1_LPS

description:
gapmerCHROME_LPS_1_64_S64
processed data file: gapmerCHROME_vs_gapCTRL_LPS.csv


title: gapCHROME_2

description:
gapmerCHROME_2_59_S59
processed data file: gapmerCHROME_vs_gapCTRL.csv


title: gapCHROME_1


title: gapctrl_3

description:
gapctrl_3_57_S57
processed data file: gapmerCHROME_vs_gapCTRL.csv


title: gapctrl_2_polyIC


title: gapctrl_2

description:
gapctrl_2_56_S56
processed data file: gapmerCHROME_vs_gapCTRL.csv


title: gapctrl_1

description:
gapctrl_1_55_S55
processed data file: gapmerCHROME_vs_gapCTRL.csv


title: THR-432

data_processing:
Fastq qualtiy assessed via FastQC 0.11.7
Sample contamination assessed via fastqscreen v0.13.0
Fastq files trimmed via Trimmomatic v0.36
Fastq files aligned to the HG38 human genome via STAR v2.7.3a
Reads counted via featurecounts v1.6.3
Genome_build: hg38
Supplementary_files_format_and_content: Raw count table as a .txt file

source_name: whole blood

extract_protocol:
QIAsymphony PAXgene RNA isolation
Sequencing libraries were barcoded and prepared using the Clontech SMART-Seq HT with Nxt HT kit (Takara Bio USA) as per the manufacturer's instruction

value: whole blood

tag: cohort

value: Control

value: Male


title: THR-417


title: THR-428

value: Female


title: THR-399


title: THR-415


title: THR-303


title: THR-238


title: COV009

value: COVID

value: Alive


title: gapCHROME_3

description:
gapmerCHROME_3_60_S60
processed data file: gapmerCHROME_vs_gapCTRL.csv

value: monocytic cell line

value: transfection with gapmer targetting CHROME


title: COV008

value: Dead


title: COV004


title: COV005


title: COV002


title: COV007


title: COV010


title: Cocaine_M

value: Sprague-Dawley

value: Cocaine


title: COV001


title: Cocaine_F


title: motor_neuron_F21_FDQ_backfill

status: Public on Jul 29 2022

city: Basel

first: Patrick

last: Tschopp

address: Vesalgasse 1

department: Department of Environmental Sciences

country: Switzerland

institute: University of Basel

description:
F21
counts_MN_smartseq2.csv.gz

data_processing:
Raw reads were trimmed with Trimmomatic (v.0.39).
Trimmed reads were aligned with STAR (v.2.5.2) to the GRCg6a chicken genome.
Count tables were created with HTSeq (v.0.6.1).
Assembly: GRCg6a
Supplementary files format and content: Comma separated values file (.csv) . Count table created by HTSeq where genes are rows and cells are columns.

organism: Gallus gallus

source_name: spinal cord

extract_protocol:
Backfilled spinal cord was dissociated with Papain (0,25 mg/ml) and individual fluorescent cells were transferred to PCR strips.
SMART-seq2

tag: celltype

value: motor neuron

value: spinal cord

value: embryonic day 9


title: motor_neuron_F6_FDQ_backfill

description:
F6
counts_MN_smartseq2.csv.gz


title: motor_neuron_F19_FDQ_backfill

description:
F19
counts_MN_smartseq2.csv.gz


title: motor_neuron_F18_FDQ_backfill

description:
F18
counts_MN_smartseq2.csv.gz


title: motor_neuron_F10_FDQ_backfill

description:
F10
counts_MN_smartseq2.csv.gz


title: motor_neuron_F22_FDQ_backfill

description:
F22
counts_MN_smartseq2.csv.gz


title: liver tumor cells_Myc_p53_3

status: Public on Jul 20 2022

data_processing:
Trimmomatic (v0.36) was used to remove adaptor sequences. RNAseq reads were aligned to (GRCm38 - mm10) with STAR (v2.5.3a)
Genome wide transcript counting was performed by featureCounts (v1.6.3) to generate raw count table
Differential expression analysis was performed with DESeq2 (v1.20.0) package in R
Genome_build: GRCm38 - mm10
Supplementary_files_format_and_content: csv text file includes raw count value for each sample

source_name: liver cells

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen) and Rnase-Free Dnase Set (Qiagen) in accordance to manufacturer’s protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

value: primary liver cancer cell lines


title: motor_neuron_F16_FDQ_backfill

description:
F16
counts_MN_smartseq2.csv.gz


title: motor_neuron_F12_FDQ_backfill

description:
F12
counts_MN_smartseq2.csv.gz


title: KTPB19_IGO_11254_15_S15

source_name: Pancreas tumor

value: Pancreas tumor

value: Whole tissue

value: IFNAR1 antibody

value: KrasG12D; sgP53; dL


title: liver tumor cells_Myc_p53_1


title: liver tumor cells_Myc_Utx_2D


title: liver tumor cells_Myc_Utx_2A


title: liver tumor cells_Myc_Utx_2B


title: Tumor_CDK9_2

status: Public on Mar 30 2022

data_processing:
Illumina read quality was checked for each sample using FastQC v0.11.5.
Raw fastq files were analyzed by removing adaptor sequences using Trimmomatic (0.36), aligned to the mouse genome using STAR (2.5.3a), and quantified transcript counts using featureCounts (1.6.3).
Genome_build: Reads were aligned to the mouse transcriptome (mm10, GRCm38.91)
Supplementary_files_format_and_content: Tab-delimited text file includes raw count table for each sample

source_name: Myc;p53-/- Liver Tumor, shCdk9

growth_protocol: In preparation for the procedure, the mouse is carefully warmed with a heat lamp to cause vasodilation. The needle is directed into a lateral tail vein at an angle of approximately 20o. Once the vein has been penetrated (preferably midway down the tail), the needle will be directed cranially a distance of approximately 2mm. Sterile 0.9% NaCl solution containing 5 µg of DNA of pT3-EF1a-Myc and 20 µg of CRISPR plasmid px330 DNA expressing Cas9 and single guide RNA (sgRNA) targeting either p53 or Axin1 together with CMV-SB13 Transposase (1:5 ratio) for each injection is administered in 5-7 seconds. Pressure is applied over the injection site after the needle is withdrawn from the vein for approximately 30 seconds with gauze (or similar material).Tumor formation was assessed by ultrasound imaging and RNA was collected from whole tumor or healthy tissue.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen)
PolyA mRNA was selected using beads coated with polyT oligonucleotides. Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation.
For sequencing, pooled multiplexed libraries were run on a HiSeq 2500 machine on RAPID mode. Approximately 10 million 76bp single-end reads were retrieved per replicate  condition. Resulting RNA-Seq data was analyzed by removing adaptor sequences using Trimmomatic (29), aligning sequencing data to GRCh37.75(hg19) with STAR (30), and genome wide transcript counting using HTSeq (31) to generate a RPKM matrix of transcript counts.

treatment_protocol: Mice harboring tumors measuring 50-100 mm3 were fed with a Dox diet to systemically induce the Cdk9 shRNA and control shRNA.

value: Whole Liver

value: Doxycycline Diet

value: Myc;p53-/- , shCdk9


title: Tumor_CDK9_1


title: Tumor_Ren_1

source_name: Myc;p53-/- Liver Tumor, shRenilla

value: Myc;p53-/- , shRenilla


title: Normal_2

source_name: Normal Liver Tissue

value: Normal


title: Normal_1


title: 48h_1299_5_Scr_DMSO

status: Public on Feb 28 2022

city: London

first: Silvia

last: Marino

address: 4, Newark St

country: United Kingdom

institute: Queen Mary University of London

data_processing:
[trimming and alignment]  Quality control was performed with FastQC and adapter sequences were removed using Trimgalore v0.6.5. Reads were then aligned to the Ensembl  GRCh38 human reference genome using STAR v2.6.1 with gene count quantification mode, retaining only uniquely mapped reads.
[post-processing and filtering]  Lowly expressed genes (CPM < 1) were filtered out via a custom-made script in R and further biotype filtering was performed in R with the Bioconductor packages NOISeq and biomaRt, removing residual highly expressed mitochondrial and ribosomal RNA. Trimmed mean of M-values (TMM) normalization was applied to the dataset prior to differential expression (DE) analysis, performed using the Bioconductor package edgeR.
Genome_build: hg38
Supplementary_files_format_and_content: raw, unfiltered gene counts

source_name: Medulloblastoma

growth_protocol: ICb1299 were cultured in DMEM (high glucose, GlutaMAX™, ThermoFisher) supplemented with 10% foetal bovine serum (FBS, Gibco) and 1% Penicillin-Streptomycin (Gibco). CHLA-01-Med MB cells were grown in DMEM-F12 (Gibco) supplemented with B27 (Gibco), 20 ng/mL human epidermal growth factor (EGF, Peprotech) and 10 ng/mL human basic fibroblast growth factor (FGF, Peprotech)

extract_protocol:
Total RNA was extracted with RNA/DNA/Protein Purification Plus kit (Norgen), polyA mRNA was selected and library prepared using the NEBNext Ultra II Directional RNA Library Prep kit.
Libraries were size selected, multiplexed and 75bp paired-end sequences were obtained with HiSeq4000 (Illumina)

treatment_protocol: Cells were treated with 1uM PTC-209 (PTC, Tocris), 100nM PD325901 (PD, Tocris) or DMSO for the reported time.

tag: knockdown

value: Scramble

value: 48h of DMSO treatment


title: 48h_1299_5_shC_1uM_PTC

value: 48h of PTC-209 1uM treatment


title: 48h_1299_5_shC_DMSO


title: 24h_1299_5_shC_1uM_PTC

value: 24h of PTC-209 1uM treatment


title: 24h_1299_5_shC_DMSO

value: 24h of DMSO treatment


title: 24h_1299_5_Scr_100nM_PD

value: 24h of PD325901 100nM treatment


title: 24h_1299_5_Scr_DMSO


title: 48h_1299_4_Scr_DMSO


title: 48h_1299_4_shC_1uM_PTC


title: 48h_1299_4_shC_DMSO


title: 24h_1299_4_shC_100nM_PD


title: 24h_1299_4_shC_DMSO


title: liver tumor cells_Myc_p53_2


title: 24h_1299_4_Scr_100nM_PD


title: 24h_1299_4_Scr_1uM_PTC


title: 24h_1299_4_Scr_DMSO


title: Day_13_Non-T_P7_WT_3

status: Public on Feb 11 2022

data_processing:
Rnaseq reads were aligned to (GRCm38 - mm10) with STAR
Genome wide transcript counting was performed by HTSeq or featureCounts to generate FPKM matrix
Differential expression analysis was performed with DESeq2 package in R
Genome_build: GRCm38 - mm10
Supplementary_files_format_and_content: csv text file includes raw count value for each sample

source_name: CD45+CD8-CD4- sorted from B16-TME in WT mice

growth_protocol: B16 tumors were implanted in super p53 or WT mice. WT mice were treated with vehicle or APR-246  starting day 7 for 6 days and single cell suspensions of the tumors were obtained and antibody stained for CD45, CD8. CD4 and live/dead. CD45+ CD8+, CD45+CD8+ and CD45+CD4-CD8- sorted

extract_protocol:
RNA was extracted with the PAXgene RNA kit and purified in accordance with the manufacturer’s protocols
RNA sequencing libraries were generated using Illumina mRNA TruSeq kit with dual index barcoding.

tag: mouse

value: Mouse #1.5


title: Day_13_Non-T_P7_WT_2

treatment_protocol: WT mice were treated with vehicle or APR-246  starting day 7 for 6 day

value: Mouse #1.4


title: Day_13_Non-T_P7_WT_1

value: Mouse #1.3


title: Day_13_Non-T_P7_Apr246_5

source_name: CD45+CD8-CD4- sorted from B16-TME in APR246 treated WT mice

value: Mouse #2.1


title: Day_13_Non-T_P7_Apr246_2

value: Mouse #2.3


title: Day_13_Non-T_P7_Apr246_3

value: Mouse #2.4


title: Day_13_Non-T_P7_SuperP53_4

source_name: CD45+CD8-CD4- sorted from B16-TME in SuperP53 mice

value: Mouse #3.2


title: Day_13_Non-T_P7_SuperP53_3

value: Mouse #3.5


title: Day_13_Non-T_P7_SuperP53_1

value: Mouse #3.3


title: Day_13_CD8_WT_4

source_name: CD8 sorted from B16-TME in WT mice


title: Day_13_Non-T_P7_Apr246_1

value: Mouse #2.2


title: Day_13_Non-T_P7_Apr246_4

value: Mouse #2.5


title: Day_13_CD8_WT_1

value: Mouse #1.1


title: Day_13_CD8_Apr246_4

source_name: CD8 sorted from B16-TME in APR246 treated WT mice


title: Day_13_CD8_Apr246_2


title: Day_13_CD8_Apr246_3


title: Day_13_CD8_SuperP53_4

source_name: CD8 sorted from B16-TME in SuperP53 mice


title: Day_13_CD8_SuperP53_3

value: Mouse #3.4


title: Day_13_CD8_SuperP53_2


title: Day_13_CD8_SuperP53_1


title: Day_13_CD4_WT_4

source_name: CD4 sorted from B16-TME in WT mice


title: Day_13_CD4_WT_3

value: Mouse #1.2


title: Day_13_CD4_WT_1


title: Day_13_CD4_Apr246_5

source_name: CD4 sorted from B16-TME in APR246 treated WT mice


title: Day_13_CD4_Apr246_4


title: Day_13_CD4_Apr246_1


title: Day_13_CD4_SuperP53_1

source_name: CD4 sorted from B16-TME in SuperP53 mice

value: Mouse #3,2


title: MP10

status: Public on Dec 31 2021

source_name: Myc;p53-/- ovarian EPO-GEMM tumor

growth_protocol: 8-12 week old WT C57BL/6 female mice were anesthetized with isofluorane and the surgical site (pelvic region) scrubbed with a povidone-iodine scrub (Betadine) and rinsed with 70% alcohol. After opening the peritoneal cavity, the left ovary and oviduct were exteriorized. 25 μl of a plasmid mix (see table below) was injected into the ovary using a 27.5 gauge syringe and tweezer electrodes were tightly placed around the injection bubble. Two poring pulses of electrical current (50V) given for 30 ms lengths at 450 ms intervals and five transfer pulses (60V, 50 ms length, 450 ms intervals) were then applied using an in vivo electroporator (NEPAGENE NEPA21 Type II electroporator). After electroporation, the peritoneal cavity was rinsed with 0.5ml of pre-warmed saline. After the procedure the peritoneal cavity was sutured and the skin closed with skin staples. The mice were kept at 37˚C until they awoke and post-surgery pain management was done with injections of buprenorphine for the three following days. Tumor formation was assessed by ultrasound imaging. Mice were sacrificed at end point, and RNA collected from whole tumor tissue. Genome editing in EPO-GEMM tumors was confirmed by Sanger sequencing.

tag: tissue

value: ovarian tumor

value: Myc;p53-/- EPO-GEMM

value: non-treated


title: Day_13_CD4_SuperP53_2

value: Mouse #3,3


title: MP9

tag: treatment


title: MP8

tag: genotype


title: MP7


title: MP6


title: MP5


title: MP4


title: MP1


title: WT 3

source_name: WT ovary

value: ovary

value: WT


title: WT 2


title: CML3: BM Tregs isolated from CML mice_rep3

status: Public on Nov 03 2021

city: Bern

first: Ramin

last: Radpour

address: Murtenstrasse 35

department: Medical Oncology

institute: Bern University Hospital

description: BM Tregs isolated from CML mice_rep3

data_processing:
Primary data analysis was performed with the Illumina RTA v2.4.11 .
The  sequence assembly and alignment was performed using the SeqMan NGen software v.15 and analyzed using ArrayStar software v.15 (DNASTAR, USA).
The level of gene expression was assessed after Reads Per Kilobase Million (RPKM) normalization and log2 transformation.
Genome_build: GRCm38 - mm10
Supplementary_files_format_and_content: Tab-delimited text file includes linear total RPKM  normalized values.

source_name: BM Tregs

extract_protocol:
Total RNA was extracted from FACS-purified BM Tregs, using the RNeasy Micro Kit (QIAGEN AG, Switzerland).
Libraries were generated from  total RNA using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio, Japan).

treatment_protocol: FACS-purified LSKs were harvested and transduced twice with BCR-ABL1-GFP. Cells were injected intravenously (i.v.) into the non-irradiated syngeneic Foxp3-DTR-GFP recipients. BM Tregs from CML or naive mice were then isolated for RNA extraction.

value: Bone marrow derived Tregs

value: post natal week 8


title: Day_13_CD8_WT_2


title: CML2: BM Tregs isolated from CML mice_rep2

description: BM Tregs isolated from CML mice_rep2


title: CML1: BM Tregs isolated from CML mice_rep1

description: BM Tregs isolated from CML mice_rep1


title: Kras*+Injury_shBrd4_ATAC_3

status: Public on Jul 13 2021

description:
ATAC_T4_shBrd4_rep3_D15-5
T4_shBrd4_rep3_D15.5
PE-50

data_processing:
ATAC-seq reads were filtered for quality and 3' trimmed for adapter sequences using trimgalore.
Reads were aligned to mouse assembly mm9 using bowtie2 (v2.2.2) with default parameters.
Read count tables were created using featureCounts v1.6.0.
To create density files, the signal was normalised using the scalefactors from DESeq2 converted to BigWig using BEDTools.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: BigWig files containing read densities normalized using DESeq2.
Supplementary_files_format_and_content: Table of normalized counts over the union peak atlas.

source_name: sorted primary pancreatic epithelial cells

growth_protocol: 5-week-old KCsh (p48-Cre;RIK;LSLKrasG12D;CHC:TRE-GFP-shRNA) male mice were treated with 8 hourly intraperitoneal injections of 80 μg/kg caerulein (Bachem) for 2 consecutive days, and FACS-sorted cells were analyzed 2 days thereafter. 6 days prior to the caerulein treatment, mice were placed on doxycycline diet to induce the expression of GFP-linked shRNA targeting Brd4 or Ren (control).

extract_protocol:
Lysis Buffer 10mM Tris·Cl, pH 7.4; 10mM NaCl; 3mM MgCl2; 0.1% (v/v) Igepal CA-630 (Buenrostro et al., 2015 protocol).
Buenrostro et al., 2015 protocol

treatment_protocol: Pancretata were harvested from the indicated mouse models and processed for FACS sorting using Collagenase (1 mg/mL) & Dispase (2 U/mL) mix digestion solution and Gentle-MACS dissociator (mTDK_1 protocol), followed by a 0.05% Trypsin-EDTA step. Cell suspensions were incubated with Fc block and CD45-APC antibody to mark immune cells. Live pancreatic epithelial cells (marked as mKate2- or GFP-positive, CD45-negative and DAPI-negative) were sorted using Aria3 sorter, and collected in 2 % 1x PBS buffer containing 2% fetal bovine serum (FBS).

tag: experimental condition

tag: model

value: KC-shRNA GEMM

tag: alleles (gemm)

tag: oncotype (sorted cells)

value: KrasG12D (Brd4-knockdown)

value: Caerulein

tag: sample collection time point

value: Day 2 post-caerulein

value: pancreas

tag: sorting strategy

tag: age / stage (upon sample collection)

value: 5 - 6 weeks old

value: Male


title: Kras*+Injury_shRen_ATAC_3

description:
ATAC_T4_shRen_rep3_D16-4
T4_shRen_rep3_D16.4
PE-50

value: Kras*+Injury-shRen

value: KrasG12D (control)

tag: Sex


title: Kras*+Injury_shRen_ATAC_2

description:
ATAC_T4_shRen_rep2_D15-3
T4_shRen_rep2_D15.3
PE-50


title: Kras*+Injury_shBrd4_ATAC_1

description:
ATAC_T4_shBrd4_rep1_D4-1
T4_shBrd4_rep1_D4.1
PE-50


title: Kras*+Injury_shRen_ATAC_1

description:
ATAC_T4_shRen_rep1_D4-2
T4_shRen_rep1_D4.2
PE-50


title: Kras*+Injury_shBrd4_ATAC_2

description:
ATAC_T4_shBrd4_rep2_D15-4
T4_shBrd4_rep2_D15.4
PE-50


title: Kras*_rIL-33_ATAC_3

description:
B3_DACE116
KrasG12D_rIL33_t0_rep3_B3
PE-50

growth_protocol: 5-6 weeks-old KC (p48-Cre;RIK;LSLKrasG12D) mice were injected intraperitoneally once daily doses with 1 ug of murine recombinant IL-33 (#580504, R&D Systems) or vehicle (PBS) for 5 consecutive days.

treatment_protocol: Pancretata were harvested and processed for FACS sorting using Collagenase (1 mg/mL) & Dispase (2 U/mL) mix digestion solution and Gentle-MACS dissociator (mTDK_1 protocol), followed by a 0.05% Trypsin-EDTA step. Cell suspensions were incubated with Fc block and CD45-APC antibody to mark immune cells. Live pancreatic epithelial cells (marked as mKate2- or GFP-positive, CD45-negative and DAPI-negative) were sorted using Aria3 sorter, and collected in 2 % 1x PBS buffer containing 2 % fetal bovine serum (FBS).

value: KC + rIL-33

value: KC;RIK GEMM

value: Day 0 (last treatment day)

value: 5 weeks old


title: Tumor_Ren_2

tag: cell type

value: Whole Liver

value: Doxycycline Diet

value: Myc;p53-/- , shRenilla


title: Kras*_rIL-33_ATAC_2

description:
A8_DACE118
KrasG12D_rIL33_t0_rep2_A8
PE-50


title: Kras*_rIL-33_ATAC_1

description:
A3_DACE117
KrasG12D_rIL33_t0_rep1_A3
PE-50


title: 48h_1299_5_Scr_1uM_PTC

value: Scramble

tag: cell line

value: 48h of PTC-209 1uM treatment


title: 24h_1299_5_Scr_1uM_PTC

value: 24h of PTC-209 1uM treatment


title: 24h_1299_5_shC_100nM_PD

value: 24h of PD325901 100nM treatment


title: 48h_1299_4_Scr_1uM_PTC


title: 24h_1299_4_shC_1uM_PTC


title: Kras*_PBS_ATAC_3

description:
A6_DACE060
KrasG12D_PBS_t0_rep3_A6
PE-50

value: KC + Vehicle

value: PBS

value: 6 weeks old


title: Kras*_PBS_ATAC_2

description:
A4_DACE114
KrasG12D_PBS_t0_rep2_A4
PE-50

value: pancreas

value: Male


title: miRVana screen_3

status: Public on Jul 07 2021

type: other

description:
firefly_3
renilla_3

scan_protocol: Luciferase activity was read on a spectrophotometer (Envision).

data_processing:
PCSK9 3’UTR firefly luciferase values were normalized to those of control renilla luciferase values for each replicate
Raw data: Luciferase (firefly, renilla) activity in Relative Luciferase Units (RLU).  Six columns.
Normalized data: Ratio of average of firefly luciferase over average of renilla luciferase = ((firefly_1/renilla_1) + (firefly_2/renilla_2) + (firefly_3/renilla_3))/3.  One column.

molecule: other

growth_protocol: HEK293T cells  were maintained in Dulbecco’s Modified Eagle Medium (DMEM, Corning) containing 10% Fetal Bovine Serum (FBS, Life Technologies) and 1% penicillin-streptomycin (pen-strep, Life Technologies).

extract_protocol: Luciferase activity was assayed with the Dual-Glo Luciferase Assay® (Promega) according to the manufacturer’s instructions.

treatment_protocol: HEK293T cells were seeded in a 384-well, white solid bottom polystyrene TC-treated microplates and co-transfected with 1.5 pmol of miRNA mimic, and 10 ng of total DNA plasmids composed of a 2:1 ratio of PCSK9 3’-UTR firefly luciferase reporter plasmid (Switchgear Genomics) to renilla luciferase control plasmid using Lipofectamine 2000 (Invitrogen).

tag: luciferase

value: Firefly luciferase, Renilla luciferase


title: Kras*_PBS_ATAC_1

description:
A10_DACE115
KrasG12D_PBS_t0_rep1_A10
PE-50


title: miRVana screen_2

description:
firefly_2
renilla_2


title: miRVana screen_1

description:
firefly_1
renilla_1


title: AGM_E11.5_r2

status: Public on Jun 01 2021

data_processing:
Raw sequencing data was analyzed by first removing adaptor sequences using Trimmomatic (v0.36)
These RNA-seq reads were then aligned to mouse GRCm38/mm10 genome with STAR (v2.5.0a)
Expression count matrix was computed using featureCounts (v1.6.0)
Raw count matrix was processed using the R/Bioconductor package DESeq2 (v1.20.0), which is used to both normalize the full dataset and analyze differential expression between sample groups.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited file containing quantified counts

source_name: Embryonic AGM

extract_protocol:
tissue were removed, flash frozen on dry ice, and RNA was harvested using Qiagen Rneasy Micro Kit
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 100-500ng of total RNA underwent polyA selection and the library preparation according to instructions provided by Illumina or Kapa Biosystems.

tag: strain

value: Embryonic AGM

tag: age

value: wild type


title: AGM_E10.5_r2


title: AGM_E9.5_r2

value: Embryonic caudal half (including PsP)


title: Day_13_Non-T_P7_SuperP53_2

tag: mouse

value: Mouse #3.4


title: AGM_E11.5

description: Project_6708. (Sample_3_1_IGO_06708_3)

tag: tissue


title: Day_13_CD8_WT_3

value: Mouse #1.3


title: AGM_E10.5

description: Project_6708. (Sample_2_1_IGO_06708_2)


title: AGM_E9.5

description: Project_6708. (Sample_1_1_IGO_06708_1)


title: Day_13_CD8_Apr246_5

value: Mouse #2.3


title: ES14.5

description: Project_05996_D (Sample_ES_E14_5_2_IGO_05996_D_4)

source_name: Embryonic dosal skin cells

value: Embryonic dosal skin cells


title: ES12.5

description: Project_05996_D (Sample_ES_E12_5_2_IGO_05996_D_3)


title: Day_13_CD8_Apr246_1

value: Mouse #2.1


title: ES10.5

description: Project_05996_D (Sample_ES_E10_5_2_IGO_05996_D_2)


title: E14.5

description: Project_5996 (Sample_E14-5)


title: ES9.5

description: Project_05996_D (Sample_ES_E9_5_2_IGO_05996_D_1)


title: E12.5

description: Project_5996 (Sample_E12-5)


title: Day_13_CD4_WT_2

value: Mouse #1.5


title: E10.5

description: Project_5996 (Sample_E10-5)


title: E9.5

description: Project_5996 (Sample_E9-5)


title: ABC-imKO9 Cisplatin it AIBP rep3 line 1

status: Public on Apr 16 2021

city: Saint Louis

first: Juliana

last: Navia Pelaez

state: MISSOURI

address: 1500 S Grand Blvd, apt 201

institute: SLU

description:
ABC-imKO9 sample technical replicate 3.  fastq read- pairs from lane 1
Y54_L001

data_processing:
Illumina Casava1.7 software used for basecalling and Illumina bcl2fastq Conversion Software was then used to convert bcl files to fastq format
Splice aware alignment of FASTQ data was done using STAR (Dobin et al., 2013)
Quality control of sequenced data and alignment was performed by FASTQC v0.11.17,  QoRTs v1.3.0, and MultiQC v1.7 ( pmid: 27312411 )
Counting of genes associated with the reads was performed using STAR v2.6.0a (Dobin et al., 2013)
Comparisons of experimental groups were performed with DEseq2 binomial modeling using Wald test and accounting for an FDR of 10%. Volcano plots include genes significantly different with a fold change >1.5.
Pathway enrichment and GO analysis were performed in metascape.org using a minimum of 3 genes and P<0.05 (Zhou et al., 2019).
genome build: GRCm38 from ENSEMBL
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: table with normalized counts for expressed genes

source_name: Microglia

extract_protocol:
Microglia cells were sorted directtly into lysis buffer buffer containing Triton X-100, RNase Inhibitor, and Oligo(dT)30-VN and vortexed. Then lysates were hybridized with oligo(dT)+ to the poly(A) tails of the mRNA. Reagents for reverse transcription were added to construct cDNA libraries following addition of reagents for PCR amplification (qPCR was not performed at this point). Libraries were quantified and QC was performed using TapeStation high sensitivity D5000 screentape in addition to Qubit double stranded high sensitivity assay. All samples were adjusted to 1ng of cDNA for input into NexteraXT protocol. QC check was performed with TapeStation high sensitivity D1000 screen tape in addition to Qubit double stranded high sensitivity assay. The samples were subjected to qPCR and pooling and loaded onto the NovaSeq for paired-end 50x50 reads using NovaSeq S1 100 cycle kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cell suspentions from lumbar spinal cord were stained, filtered, and FACS-sorted to collect resident microglia

value: Spinal Cord

value: ABC-imKO (Abca1fl/fl Abcg1fl/fl Cx3cr1-CreERT2)

tag: treatment

value: i.p. injection of cisplatin on day1 and day3.  intrathecal (i.t.) injection of  AIBP on day7


title: ABC-imKO9 Cisplatin it AIBP rep3 line 2

description:
ABC-imKO9 sample technical replicate 3.  fastq read- pairs from lane 2
Y54_L002

tag: genotype


title: ABC-imKO9 Cisplatin it AIBP rep2 line 2

description:
ABC-imKO9 sample technical replicate 2.  fastq read- pairs from lane 2
Y53_L002


title: ABC-imKO9 Cisplatin it AIBP rep2 line 1

description:
ABC-imKO9 sample technical replicate 2.  fastq read- pairs from lane 1
Y53_L001


title: ABC-imKO9 Cisplatin it AIBP rep1 line 2

description:
ABC-imKO9 sample technical replicate 1.  fastq read- pairs from lane 2
Y52_L002


title: Day_13_CD4_Apr246_3

value: Mouse #2.2


title: Day_13_CD4_Apr246_2


title: ABC-imKO9 Cisplatin it AIBP rep1 line 1

description:
ABC-imKO9 sample technical replicate 1.  fastq read- pairs from lane 1
Y52_L001


title: ABC-imKO8 Cisplatin it AIBP rep2 line 2

description:
ABC-imKO8 sample technical replicate 2.  fastq read- pairs from lane 2
Y50_L002


title: ABC-imKO8 Cisplatin it AIBP rep3 line 1

description:
ABC-imKO8 sample technical replicate 3.  fastq read- pairs from lane 1
Y51_L001


title: Day_13_CD4_SuperP53_3

value: Mouse #3,4


title: ABC-imKO8 Cisplatin it AIBP rep2 line 1

description:
ABC-imKO8 sample technical replicate 2.  fastq read- pairs from lane 1
Y50_L001


title: ABC-imKO8 Cisplatin it AIBP rep1 line 1

description:
ABC-imKO8 sample technical replicate 1.  fastq read- pairs from lane 1
Y49_L001


title: ABC-imKO8 Cisplatin it AIBP rep3 line 2

description:
ABC-imKO8 sample technical replicate 3.  fastq read- pairs from lane 2
Y51_L002


title: ABC-imKO8 Cisplatin it AIBP rep1 line 2

description:
ABC-imKO8 sample technical replicate 1.  fastq read- pairs from lane 2
Y49_L002


title: ABC-imKO7 Cisplatin it AIBP rep3 line 2

description:
ABC-imKO7 sample technical replicate 3.  fastq read- pairs from lane 2
Y48_L002


title: ABC-imKO7 Cisplatin it AIBP rep2 line 1

description:
ABC-imKO7 sample technical replicate 2.  fastq read- pairs from lane 1
Y47_L001


title: ABC-imKO7 Cisplatin it AIBP rep3 line 1

description:
ABC-imKO7 sample technical replicate 3.  fastq read- pairs from lane 1
Y48_L001


title: ABC-imKO7 Cisplatin it AIBP rep2 line 2

description:
ABC-imKO7 sample technical replicate 2.  fastq read- pairs from lane 2
Y47_L002


title: ABC-imKO7 Cisplatin it AIBP rep1 line 2

description:
ABC-imKO7 sample technical replicate 1.  fastq read- pairs from lane 2
Y46_L002


title: ABC-imKO6 Cisplatin it Saline rep3 line 1

description:
ABC-imKO6 sample technical replicate 3.  fastq read- pairs from lane 1
Y45_L001

value: i.p. injection of cisplatin on day1 and day3.  intrathecal (i.t.) injection of  saline on day 7


title: ABC-imKO6 Cisplatin it Saline rep2 line 2

description:
ABC-imKO6 sample technical replicate 2.  fastq read- pairs from lane 2
Y44_L002


title: ABC-imKO6 Cisplatin it Saline rep2 line 1

description:
ABC-imKO6 sample technical replicate 2.  fastq read- pairs from lane 1
Y44_L001


title: ABC-imKO7 Cisplatin it AIBP rep1 line 1

description:
ABC-imKO7 sample technical replicate 1.  fastq read- pairs from lane 1
Y46_L001


title: ABC-imKO6 Cisplatin it saline rep1 line 1

description:
ABC-imKO6 sample technical replicate 1.  fastq read- pairs from lane 1
Y43_L001


title: ABC-imKO5 Cisplatin it Saline rep2 line 2

description:
ABC-imKO5 sample technical replicate 2.  fastq read- pairs from lane 2
Y41_L002


title: ABC-imKO5 Cisplatin it Saline rep3 line 1

description:
ABC-imKO5 sample technical replicate 3.  fastq read- pairs from lane 1
Y42_L001


title: ABC-imKO5 Cisplatin it Saline rep2 line 1

description:
ABC-imKO5 sample technical replicate 2.  fastq read- pairs from lane 1
Y41_L001


title: ABC-imKO6 Cisplatin it Saline rep1 line 2

description:
ABC-imKO6 sample technical replicate 1.  fastq read- pairs from lane 2
Y43_L002


title: ABC-imKO5 Cisplatin it Saline rep1 line 2

description:
ABC-imKO5 sample technical replicate 1.  fastq read- pairs from lane 2
Y40_L002


title: ABC-imKO5 Cisplatin it saline rep1 line 1

description:
ABC-imKO5 sample technical replicate 1.  fastq read- pairs from lane 1
Y40_L001


title: ABC-imKO4 Cisplatin it Saline rep3 line 2

description:
ABC-imKO4 sample technical replicate 3.  fastq read- pairs from lane 2
Y39_L002


title: ABC-imKO4 Cisplatin it Saline rep3 line 1

description:
ABC-imKO4 sample technical replicate 3.  fastq read- pairs from lane 1
Y39_L001


title: ABC-imKO4 Cisplatin it Saline rep2 line 2

description:
ABC-imKO4 sample technical replicate 2.  fastq read- pairs from lane 2
Y38_L002


title: ABC-imKO4 Cisplatin it Saline rep1 line 2

description:
ABC-imKO4 sample technical replicate 1.  fastq read- pairs from lane 2
Y37_L002


title: ABC-imKO3 Naïve rep3 line 2

description:
ABC-imKO3 sample technical replicate 3.  fastq read- pairs from lane 2
Y36_L002

value: naïve (no treatment)


title: ABC-imKO4 Cisplatin it Saline rep2 line 1

description:
ABC-imKO4 sample technical replicate 2.  fastq read- pairs from lane 1
Y38_L001


title: ABC-imKO4 Cisplatin it saline rep1 line 1

description:
ABC-imKO4 sample technical replicate 1.  fastq read- pairs from lane 1
Y37_L001


title: ABC-imKO3 Naïve rep3 line 1

description:
ABC-imKO3 sample technical replicate 3.  fastq read- pairs from lane 1
Y36_L001


title: ABC-imKO3 Naïve rep2 line 2

description:
ABC-imKO3 sample technical replicate 2.  fastq read- pairs from lane 2
Y35_L002


title: ABC-imKO3 Naïve rep1 line 2

description:
ABC-imKO3 sample technical replicate 1.  fastq read- pairs from lane 2
Y34_L002


title: ABC-imKO3 Naïve rep1 line 1

description:
ABC-imKO3 sample technical replicate 1.  fastq read- pairs from lane 1
Y34_L001


title: ABC-imKO2 Naïve rep3 line 2

description:
ABC-imKO2 sample technical replicate 3.  fastq read- pairs from lane 2
Y33_L002


title: ABC-imKO2 Naïve rep3 line 1

description:
ABC-imKO2 sample technical replicate 3.  fastq read- pairs from lane 1
Y33_L001


title: ABC-imKO2 Naïve rep2 line 2

description:
ABC-imKO2 sample technical replicate 2.  fastq read- pairs from lane 2
Y32_L002


title: ABC-imKO2 Naïve rep1 line 2

description:
ABC-imKO2 sample technical replicate 1.  fastq read- pairs from lane 2
Y31_L002


title: ABC-imKO2 Naïve rep1 line 1

description:
ABC-imKO2 sample technical replicate 1.  fastq read- pairs from lane 1
Y31_L001


title: ABC-imKO1 Naïve rep3 line 2

description:
ABC-imKO1 sample technical replicate 3.  fastq read- pairs from lane 2
Y30_L002


title: ABC-imKO1 Naïve rep3 line 1

description:
ABC-imKO1 sample technical replicate 3.  fastq read- pairs from lane 1
Y30_L001


title: ABC-imKO1 Naïve rep2 line 1

description:
ABC-imKO1 sample technical replicate 2.  fastq read- pairs from lane 1
Y29_L001


title: ABC-imKO1 Naïve rep1 line 2

description:
ABC-imKO1 sample technical replicate 1.  fastq read- pairs from lane 2
Y28_L002


title: ABC-imKO1 Naïve rep1 line 1

description:
ABC-imKO1 sample technical replicate 1.  fastq read- pairs from lane 1
Y28_L001


title: WT9 Cisplatin it AIBP rep3 line 2

description:
WT9 sample technical replicate 3.  fastq read- pairs from lane 2
Y27_L002

value: WT


title: WT9 Cisplatin it AIBP rep2 line 2

description:
WT9 sample technical replicate 2.  fastq read- pairs from lane 2
Y26_L002


title: WT9 Cisplatin it AIBP rep1 line 2

description:
WT9 sample technical replicate 1.  fastq read- pairs from lane 2
Y25_L002


title: WT7 Cisplatin it AIBP rep3 line 1

description:
WT7 sample technical replicate 3.  fastq read- pairs from lane 1
Y21_L001


title: WT7 Cisplatin it AIBP rep3 line 2

description:
WT7 sample technical replicate 3.  fastq read- pairs from lane 2
Y21_L002


title: WT7 Cisplatin it AIBP rep2 line 2

description:
WT7 sample technical replicate 2.  fastq read- pairs from lane 2
Y20_L002


title: WT7 Cisplatin it AIBP rep2 line 1

description:
WT7 sample technical replicate 2.  fastq read- pairs from lane 1
Y20_L001


title: WT7 Cisplatin it AIBP rep1 line 1

description:
WT7 sample technical replicate 1.  fastq read- pairs from lane 1
Y19_L001


title: WT6 Cisplatin it Saline rep3 line 2

description:
WT6 sample technical replicate 3.  fastq read- pairs from lane 2
Y18_L002


title: WT6 Cisplatin it Saline rep3 line 1

description:
WT6 sample technical replicate 3.  fastq read- pairs from lane 1
Y18_L001


title: WT6 Cisplatin it Saline rep2 line 2

description:
WT6 sample technical replicate 2.  fastq read- pairs from lane 2
Y17_L002


title: WT6 Cisplatin it Saline rep1 line 2

description:
WT6 sample technical replicate 1.  fastq read- pairs from lane 2
Y16_L002


title: WT6 Cisplatin it Saline rep1 line 1

description:
WT6 sample technical replicate 1.  fastq read- pairs from lane 1
Y16_L001


title: WT6 Cisplatin it Saline rep2 line 1

description:
WT6 sample technical replicate 2.  fastq read- pairs from lane 1
Y17_L001


title: WT5 Cisplatin it Saline rep3 line 2

description:
WT5 sample technical replicate 3.  fastq read- pairs from lane 2
Y15_L002


title: WT5 Cisplatin it Saline rep2 line 2

description:
WT5 sample technical replicate 2.  fastq read- pairs from lane 2
Y14_L002


title: WT5 Cisplatin it Saline rep3 line 1

description:
WT5 sample technical replicate 3.  fastq read- pairs from lane 1
Y15_L001


title: WT5 Cisplatin it Saline rep2 line 1

description:
WT5 sample technical replicate 2.  fastq read- pairs from lane 1
Y14_L001


title: WT5 Cisplatin it Saline rep1 line 2

description:
WT5 sample technical replicate 1.  fastq read- pairs from lane 2
Y13_L002


title: WT4 Cisplatin it Saline rep3 line 2

description:
WT4 sample technical replicate 3.  fastq read- pairs from lane 2
Y12_L002


title: WT4 Cisplatin it Saline rep3 line 1

description:
WT4 sample technical replicate 3.  fastq read- pairs from lane 1
Y12_L001


title: WT4 Cisplatin it Saline rep2 line 2

description:
WT4 sample technical replicate 2.  fastq read- pairs from lane 2
Y11_L002


title: WT4 Cisplatin it Saline rep2 line 1

description:
WT4 sample technical replicate 2.  fastq read- pairs from lane 1
Y11_L001


title: WT4 Cisplatin it Saline rep1 line 2

description:
WT4 sample technical replicate 1.  fastq read- pairs from lane 2
Y10_L002


title: WT4 Cisplatin it Saline rep1 line 1

description:
WT4 sample technical replicate 1.  fastq read- pairs from lane 1
Y10_L001


title: WT3 Naïve rep3 line 1

description:
WT3 sample technical replicate 3.  fastq read- pairs from lane 1
Y9_L001


title: WT3 Naïve rep3 line 2

description:
WT3 sample technical replicate 3.  fastq read- pairs from lane 2
Y9_L002


title: ABC-imKO2 Naïve rep2 line 1

description:
ABC-imKO2 sample technical replicate 2.  fastq read- pairs from lane 1
Y32_L001


title: WT3 Naïve rep2 line 1

description:
WT3 sample technical replicate 2.  fastq read- pairs from lane 1
Y8_L001


title: WT3 Naïve rep2 line 2

description:
WT3 sample technical replicate 2.  fastq read- pairs from lane 2
Y8_L002


title: WT3 Naïve rep1 line 2

description:
WT3 sample technical replicate 1.  fastq read- pairs from lane 2
Y7_L002


title: WT3 Naïve rep1 line 1

description:
WT3 sample technical replicate 1.  fastq read- pairs from lane 1
Y7_L001


title: ABC-imKO1 Naïve rep2 line 2

description:
ABC-imKO1 sample technical replicate 2.  fastq read- pairs from lane 2
Y29_L002


title: WT2 Naïve rep3 line 2

description:
WT2 sample technical replicate 3.  fastq read- pairs from lane 2
Y6_L002


title: WT9 Cisplatin it AIBP rep3 line 1

description:
WT9 sample technical replicate 3.  fastq read- pairs from lane 1
Y27_L001


title: WT2 Naïve rep3 line 1

description:
WT2 sample technical replicate 3.  fastq read- pairs from lane 1
Y6_L001


title: WT9 Cisplatin it AIBP rep2 line 1

description:
WT9 sample technical replicate 2.  fastq read- pairs from lane 1
Y26_L001


title: WT9 Cisplatin it AIBP rep1 line 1

description:
WT9 sample technical replicate 1.  fastq read- pairs from lane 1
Y25_L001


title: WT2 Naïve rep2 line 1

description:
WT2 sample technical replicate 2.  fastq read- pairs from lane 1
Y5_L001


title: WT2 Naïve rep2 line 2

description:
WT2 sample technical replicate 2.  fastq read- pairs from lane 2
Y5_L002


title: WT2 Naïve rep1 line 2

description:
WT2 sample technical replicate 1.  fastq read- pairs from lane 2
Y4_L002


title: WT2 Naïve rep1 line 1

description:
WT2 sample technical replicate 1.  fastq read- pairs from lane 1
Y4_L001


title: WT1 Naïve rep3 line 2

description:
WT1 sample technical replicate 3.  fastq read- pairs from lane 2
Y3_L002


title: WT1 Naïve rep3 line 1

description:
WT1 sample technical replicate 3.  fastq read- pairs from lane 1
Y3_L001


title: WT7 Cisplatin it AIBP rep1 line 2

description:
WT7 sample technical replicate 1.  fastq read- pairs from lane 2
Y19_L002


title: WT1 Naïve rep1 line 2

description:
WT1 sample technical replicate 1.  fastq read- pairs from lane 2
Y1_L002


title: WT1 Naïve rep2 line 2

description:
WT1 sample technical replicate 2.  fastq read- pairs from lane 2
Y2_L002


title: WT1 Naïve rep2 line 1

description:
WT1 sample technical replicate 2.  fastq read- pairs from lane 1
Y2_L001


title: WT1 Naïve rep1 line 1

description:
WT1 sample technical replicate 1.  fastq read- pairs from lane 1
Y1_L001


title: VTA_Female_1_snRNA-seq

status: Public on Mar 31 2021

data_processing:
Cell demultiplexing and genome alignment in Cell Ranger using Emsemble pre-mRNA (v95) reference assembly GTF file. Raw count data obtained in Cell Ranger.
Genome_build: rn6
Supplementary_files_format_and_content: Cell Ranger output matrices for barcodes, features, and gene expression counts are provided for each sample.

source_name: Ventral tegmental area

growth_protocol: Male and female Sprague-Dawley rats (200-250g) were purchased from Charles River Laboratories and individually housed for 1 week prior to tissue collection. Rats were maintained on a 12 h light/dark cycle with ad libitum access to food and water, and were briefly handled for 3 days prior to tissue collection (1-2min/day) to acclimate them to the experimenters. All experimental procedures were approved by the University of Alabama at Birmingham Institutional Animal Care and Use Committee, and were conducted in accordance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals.

extract_protocol:
Rats were euthanized by decapitation, and brains were rapidly removed and chilled in ice cold Hibernate A media without Ca2+ or Mg2+ (BrainBits, HACAMG500) for 30-60 sec. Chilled brains were then blocked into 1-mm-thick coronal sections on wet ice. Sections containing the VTA (ranging from -4.92 to -6.46mm AP relative to bregma) were transferred to glass petri dishes on dry ice, and the VTA was microdissected from neighboring brain regions (n = 6 rats per sex).  VTA tissue was then transferred to ice-cold centrifuge tubes, and stored at −80°C until the day of nuclei isolation and harvesting. To harvest nuclei, frozen VTA tissue was briefly thawed on wet ice before being chopped by scalpel 100 times in two orthogonal directions. Tissue from three rats per sex was combined and transferred to 5 ml of ice cold lysis buffer (10 mM tris-HCl, 10 mM NaCl, 3 mM MgCl2 and 0.1% Igepal in nuclease-free water (Sigma-Aldrich, 18896-50ML) for 15 min, mixing the tissue by inversion every 2 min. Lysis was quenched after 15 min with 5 ml of complete Hibernate A (Thermo Fisher Scientific, A1247501) supplemented with B27, GlutaMAX (Life Technologies, 35050-061), and NxGen RNase Inhibitor (0.2 U/μl; Lucigen, 30281-2). Tissue was then triturated by fire-polished Pasteur pipette (three pipettes of decreasing diameter; 8 to 10 passes per pipette) for 35 min and passed through a 40-μm prewet filter. The samples were then pelleted at 500 rcf for 10 min at 4°C followed by a wash in 10 ml of nuclei wash and resuspension buffer [1× phosphate-buffered saline (PBS), 1% bovine serum albumin (BSA), and NxGen RNase Inhibitor]. Supernatant was then removed, and the pellet was gently resuspended in 800 μl of wash buffer before 7-aminoactinomycin D (Thermo Fisher Scientific, 00-6993-50) staining and fluorescence-activated cell sorting (FACS) to further purify the nuclei for sequencing (BD FACS Aria, 70-μm nozzle, BD Biosciences). Immediately after FACS, nuclei were washed a final time at 250 rcf in 10 ml of supplemented Hibernate A containing 1% BSA for 10 min at 4°C to remove any remaining fine debris and nascent RNA. Nuclei were then brought to a concentration of 1400 nuclei/μl. A total of 11,367 nuclei pooled from three rats per sex and treatment group were loaded into a single well of the Chromium Single Cell B Chip using four of the eight available wells.
FACS-sorted nuclei were subject to 10X GEM generation and barcoding, GEM-RT cleanup and cDNA amplication, and library construction using a Chromium Single Cell 3ʹ Reagent Kit (v3 chemistry). Libraries were quantified and underwent sequencing (~500M total 75bp paired-end reads) on an Illumina sequencing platform (NextSeq 500).

treatment_protocol: Rats were experimentally naïve at the time of VTA sample collection.

value: Sprague-Dawley

value: Female

value: Ventral tegmental area


title: VTA_Male_1_snRNA-seq

value: Male


title: LSC isolated from BL/6 CML mice treated with Veh_rep3

status: Public on Feb 07 2021

source_name: LSK cells  treated with Veh

extract_protocol:
Total RNA was extracted from FACS-purified bone marrow BL/6 LSCs treated with MCP or Veh, using the RNeasy Micro Kit (QIAGEN AG, Switzerland).
Libraries were generated from  total RNA using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio, Japan).

treatment_protocol: FACS-purified BL/6 LSKs were harvested and transduced twice with BCR-ABL1-GFP. Cells were injected intravenously (i.v.) into the non-irradiated syngeneic BL/6 recipients. Upon CML development, mice were treated with MCP (10mg/kg) or Veh in vivo. LSCs from treated BL/6 mice of either group were then isolated for RNA extraction.

value: Bone marrow derived LSCs

value: post natal week 8

value: BL/6 (WT)


title: VTA_Male_2_snRNA-seq


title: LSC isolated from BL/6 CML mice treated with Veh_rep1


title: LSC isolated from BL/6 CML mice treated with Veh_rep2


title: LSC isolated from BL/6 CML mice treated with MCP_rep3

source_name: LSK cells  treated with MCP


title: LSC isolated from BL/6 CML mice treated with MCP_rep2


title: LSC isolated from BL/6 CML mice treated with MCP_rep1


title: CML LSC from CD93-/- (KO) rep2

description: CML LSC isolated from bone marrow of CD93-/- (KO) rep2

source_name: CML LSC cells

extract_protocol:
Total RNA was extracted from FACS-purified bone marrow BL/6 (WT) or CD93-/- (KO) LSKs and BL/6 (WT) or CD93-/- (KO) LSCs using the RNeasy Micro Kit (QIAGEN AG, Switzerland).
Libraries were generated from  total RNA using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio, Japan).

treatment_protocol: FACS-purified BL/6 and CD93-/- LSKs were harvested and transduced twice with BCR-ABL1-GFP. Cells were injected intravenously (i.v.) into the non-irradiated syngeneic BL/6 recipients (BL/6 and CD93-/- CML). Upon CML development, LSCs from BL/6 and CD93-/- CML mice were isolated. Naïve LSKs from BL/6 (WT) or CD93-/- (KO) mice were used as controls.

value: Bone marrow

tag: disease state

value: CML


title: CML LSC from BL/6 (WT) rep3

description: CML LSC isolated from bone marrow of BL/6 (WT) rep3


title: CML LSC from CD93-/- (KO) rep1

description: CML LSC isolated from bone marrow of CD93-/- (KO) rep1


title: CML LSC from BL/6 (WT) rep2

description: CML LSC isolated from bone marrow of BL/6 (WT) rep2


title: CML LSC from BL/6 (WT) rep1

description: CML LSC isolated from bone marrow of BL/6 (WT) rep1


title: naive LSK from CD93-/- (KO) rep2

description: naïve LSK isolated from bone marrow of CD93-/- (KO) rep2

source_name: LSK cells

value: Bone marrow derived LSKs

value: naive


title: naive LSK from CD93-/- (KO) rep1

description: naïve LSK isolated from bone marrow of CD93-/- (KO) rep1


title: WT5 Cisplatin it Saline rep1 line 1

description:
WT5 sample technical replicate 1.  fastq read- pairs from lane 1
Y13_L001

value: Spinal Cord


title: naive LSK from BL/6 (WT) rep2

description: naïve LSK isolated from bone marrow of BL/6 (WT) rep2


title: naive LSK from BL/6 (WT) rep1

description: naïve LSK isolated from bone marrow of BL/6 (WT)


title: Input for GST-fused AP2 domain of AP2-G

status: Public on Feb 01 2021

city: Tsu

first: Tsubasa

last: Nishi

state: Mie

address: Edobashi

country: Japan

institute: Mie university

data_processing:
PlasmoDB, version 3
Genome_build: Mapping data, bedgraph; Peak-calling, text.

organism: Plasmodium berghei ANKA

source_name: input

extract_protocol: Libraries were constructed using KAPA Hyperprep kit (KAPA Biosystems), and sequencing was performed with Illumina NEXTseq sequence (Single read - illumina NextSeq 500),

treatment_protocol: Recombinant GST-fused AP2 domain of AP2-G and genomic DNA fragments were incubated at RT for 30 min in 100 μL of binding/washing buffer (10 μM ZnSO4, 2 mM MgCl2, 2 mM Tris-HCl at pH 7.4, 100 mM KCl, and 10% glycerol). The mixture was then incubated with 50 μL glutathione sepharose resin at RT with rotation. Resin was washed three times with 150 μL of binding/washing buffer, and bound protein was eluted with 10 mM glutathione solution. Recovered DNA (5 ng) was sequenced using the same procedures as in ChIP-seq. Input genomic DNA fragments were also sequenced as a control.

value: input


title: Normal_rIL-33_d21_RNA3

status: Public on Nov 24 2020

description:
PE-101
DACE097_IGO_10855_25_S118

growth_protocol: 5-6 weeks-old KC (p48-Cre;RIK;LSLKrasG12D) mice were injected intraperitoneally once daily doses with 1 ug of murine recombinant IL-33 (#580504, R&D Systems) or vehicle (PBS) for 5 consecutive days, and cells were harvested at the indicated time-points.

extract_protocol:
Trizol RNA extraction protocol
Poly-A RNA-Seq / Paired-end 50

treatment_protocol: Pancretata were harvested from the indicated mouse models and processed for FACS sorting using Collagenase (1mg/mL) & Dispase (2U/mL) mix digestion solution and Gentle-MACS dissociator (mTDK_1 protocol), followed by a 0.05% Trypsin-EDTA step. Cell suspensions were incubated with Fc block and CD45-APC antibody to mark immune cells. Live pancreatic epithelial cells (marked as mKate2-positive, GFP-positive; CD45-negative and DAPI-negative) were sorted using Aria3 sorter, and collected directly into Trizol-LS.

tag: experimental condition

tag: model

value: C;RIK GEMM

tag: oncotype

value: KrasWT

tag: time point

value: Day 21

value: pancreas

tag: age (upon sample collection)

value: 8 weeks old


title: Normal_rIL-33_d21_RNA4

description:
PE-101
DACE111_IGO_10855_23_S116

tag: sorting strategy


title: VTA_Female_2_snRNA-seq

value: Sprague-Dawley

tag: Sex

value: Female


title: Normal_rIL-33_d21_RNA2

description:
PE-101
DACE068_IGO_10855_24_S117

value: 9 weeks old


title: Normal_rIL-33_d21_RNA1

description:
PE-101
DACD925_IGO_10855_6_S99


title: Normal_PBS_d21_RNA5

description:
PE-101
DACE110_IGO_10855_26_S119

value: C + Vehicle d21

value: PBS

value: Male


title: Normal_PBS_d21_RNA3

description:
PE-101
DACE069_IGO_10855_21_S114


title: Normal_PBS_d21_RNA4

description:
PE-101
DACE109_IGO_10855_22_S115


title: Normal_PBS_d21_RNA2

description:
PE-101
DACD926_IGO_10855_7_S100


title: CML LSC from CD93-/- (KO) rep3

description: CML LSC isolated from bone marrow of CD93-/- (KO) rep3

value: Bone marrow

tag: cell type

value: Bone marrow derived LSCs

value: post natal week 8


title: Normal_PBS_d21_RNA1

description:
PE-101
DACD921_IGO_10855_1_S94


title: Kras*_rIL-33_d21_RNA4

description:
PE-101
DACD912_IGO_10855_5_S98

value: KC + rIL-33 d21

value: KC;RIK GEMM


title: Kras*_rIL-33_d21_RNA3

description:
PE-101
DACE107_IGO_10855_20_S113


title: Kras*_rIL-33_d21_RNA2

description:
PE-101
DACE101_IGO_10855_17_S110


title: Kras*_rIL-33_d21_RNA1

description:
PE-101
DACD917_IGO_10855_3_S96


title: Kras*_PBS_d21_RNA3

description:
PE-101
DACE103_IGO_10855_19_S112

value: KC + Vehicle d21


title: Kras*_PBS_d21_RNA4

description:
PE-101
DACE120_IGO_10855_18_S111


title: Kras*_PBS_d21_RNA2

description:
PE-101
DACD928_IGO_10855_4_S97


title: Kras*_PBS_d21_RNA1

description:
PE-101
DACD923_IGO_10855_2_S95


title: Kras*_rIL-33_d0_RNA4

description:
PE-101
DACE118_IGO_10855_9_S102

value: KC + rIL-33 d0

value: Day 0 (last treatment day)

value: 5 weeks old


title: Kras*_rIL-33_d0_RNA3

description:
PE-101
DACE117_IGO_10855_8_S101

value: pancreas


title: Kras*_rIL-33_d0_RNA2

description:
PE-101
DACE116_IGO_10855_11_S104


title: Kras*_PBS_d0_RNA2

description:
PE-101
DACE114_IGO_10855_12_S105

value: KC + Vehicle d0


title: Kras*_PBS_d0_RNA3

description:
PE-101
DACE115_IGO_10855_10_S103


title: Kras*_rIL-33_d0_RNA1

description:
PE-101
DACE059_IGO_10855_13_S106

value: 6 weeks old


title: Kras*_PBS_d0_RNA1

description:
PE-101
DACE060_IGO_10855_14_S107


title: Kras*+Injury_KCshBrd4.552_RNA3

description:
PE-50
8_C270_NH_552_IGO_06389_B_8_S1_L001

growth_protocol: When indicated, 5 weeks-old mice were treated with 8 hourly intraperitoneal injections of 80 μg/kg caerulein (Bachem) for 2 consecutive days; and FACS-sorted cells were analyzed 2 days thereafter. 6 days prior to the caerulein treatment, mice were placed on doxycycline diet to induce the expression of GFP-linked shRNA targeting Brd4 or Ren (control).

value: KC-GEMM-ESC  derived from p48-9C ESCs (Saborowski et al., PNAS, 2013) targeted with the TRE-GFP-shRNA against Brd4 (sh552)

value: Doxycycline diet (6 days) + caerulein

value: Day 2 post-caerulein


title: Kras*+Injury_KCshBrd4.552_RNA2

description:
PE-50
5_C267_LH_552_IGO_06389_B_5_S8_L001


title: Kras*+Injury_KCshBrd4.552_RNA1

description:
PE-50
2_C266_RH_552_IGO_06389_B_2_S3_L001


title: Kras*+Injury_KCshBrd4.1448_RNA3

description:
PE-50
9_C261_2RH_1448_IGO_06389_B_9_S6_L001

value: KC-GEMM-ESC  derived from p48-9C ESCs (Saborowski et al., PNAS, 2013) targeted with the TRE-GFP-shRNA against Brd4 (sh1448)


title: Kras*+Injury_KCshBrd4.1448_RNA2

description:
PE-50
6_C260_LH_1448_IGO_06389_B_6_S7_L001

value: KC-GEMM-ESC derived from p48-9C ESCs (Saborowski et al., PNAS, 2013) targeted with the TRE-GFP-shRNA against Brd4 (sh1448)


title: Kras*+Injury_KCshRen.713_RNA3

description:
PE-50
7_C264_RH_REN_IGO_06389_B_7_S2_L001

value: Kras*+Injury-shRen

value: KC-GEMM-ESC derived from p48-9C ESCs (Saborowski et al., PNAS, 2013) targeted with the TRE-GFP-shRNA against Renilla (sh713)


title: Kras*+Injury_KCshRen.713_RNA2

description:
PE-50
4_C272_2LH_REN_IGO_06389_B_4_S9_L001


title: Kras*+Injury_KCshBrd4.1448_RNA1

description:
PE-50
3_C261_LH_1448_IGO_06389_B_3_S5_L001


title: Kras*+Injury_KCshRen.713_RNA1

description:
PE-50
1_C264_2RH_REN_IGO_06389_B_1_S4_L001


title: Injury_CshBrd4.1448_RNA3

description:
PE-50
DAC_B396_IGO_06389_C_15_S2

value: C-shRNA GEMM

value: KrasWT


title: Injury_CshBrd4.1448_RNA2

description:
PE-50
DAC_B094_IGO_06389_C_14_S17


title: Injury_CshBrd4.1448_RNA1

description:
PE-50
DAC_A940_IGO_06389_C_16_S11


title: Injury_CshRen.713_RNA3

description:
PE-50
DAC_B092_IGO_06389_C_5_S14

value: Injury-shRen


title: Injury_CshRen.713_RNA2

description:
PE-50
DAC_A682_IGO_06389_C_8_S6


title: Injury_CshRen.713_RNA1

description:
PE-50
DAC_A166_IGO_06389_C_9_S7


title: Normal_CshRen.713_RNA2

description:
PE-50
DACA604_IGO_06389_D_9_S8

value: Normal-shRen

value: Doxycycline diet (6 days)

value: Day 6 post-doxycycline


title: Normal_CshRen.713_RNA1

description:
PE-50
DACA603_IGO_06389_D_8_S16

value: 5 weeks old


title: Normal_CshRen.713_RNA3

description:
PE-50
DACA607_IGO_06389_D_10_S15

value: pancreas


title: PDAC_RNA2

description:
PE-50
C5_RenOff_1_PDAC_IGO_06389_C_38_S3

source_name: sorted PDAC cells

growth_protocol: For caerulein or PBS (control) treatments, 5 weeks-old KC;RIK (p48-Cre;RIK;LSLKrasG12D) or C;RIK (p48-Cre;RIK) littermate male mice were treated with 8 hourly intraperitoneal injections of 80 μg/kg caerulein (Bachem) or PBS for 2 consecutive days.

treatment_protocol: Pancretata were harvested from the indicated mouse models and processed for FACS sorting using Collagenase (1 mg/mL) & Dispase (2 U/mL) mix digestion solution and Gentle-MACS dissociator (mTDK_1 protocol), followed by a 0.05% Trypsin-EDTA step. Cell suspensions were incubated with Fc block and CD45-APC antibody to mark immune cells. Live pancreatic epithelial cells (marked as mKate2-positive, CD45-negative and DAPI-negative) were sorted using Aria3 sorter, and collected directly into Trizol-LS.

value: PDAC

value: KPflC;RIK GEMM

tag: alleles (gemm)

tag: oncotype (sorted cells)

tag: sample collection time point

value: PDAC lesion

tag: age / stage (upon sample collection)


title: PDAC_RNA1

description:
PE-50
C5_6_PDAC_1215_C5_1_IGO_06389_C_40_S33


title: Kras*+Injury_RNA4

description:
PE-50
DACC040_IGO_06389_E_9_S22

value: Kras*+Injury

value: KC;RIK GEMM

value: Caerulein

value: 5 - 6 weeks old


title: PDAC_RNA3

description:
PE-50
C5_RenOff_2_PDAC_IGO_06389_C_39_S4


title: Kras*+Injury_RNA2

description:
PE-50
DAC_A954_IGO_06389_C_29_S18

value: Day 2 post-caerulein


title: Kras*+Injury_RNA3

description:
PE-50
DAC_B612_IGO_06389_C_45_S6


title: Kras*+Injury_RNA1

description:
PE-50
DAC_A226_IGO_06389_C_34_S20


title: ABC-imKO6 Cisplatin it Saline rep3 line 2

description:
ABC-imKO6 sample technical replicate 3.  fastq read- pairs from lane 2
Y45_L002

value: Spinal Cord

value: ABC-imKO (Abca1fl/fl Abcg1fl/fl Cx3cr1-CreERT2)

value: i.p. injection of cisplatin on day1 and day3.  intrathecal (i.t.) injection of  saline on day 7


title: Kras*_RNA3

description:
PE-50
DAC_B837_IGO_06389_C_32_S1

value: Kras*

value: PBS

value: Day 2 post-PBS


title: Kras*_RNA1

description:
PE-50
DAC_A897_IGO_06389_C_44_S5


title: Kras*_RNA2

description:
PE-50
DAC_B098_IGO_06389_C_47_S8


title: Injury_RNA5

description:
PE-50
DAC_A999_IGO_06389_C_43_S35

value: Injury

value: C;RIK GEMM

value: KrasWT


title: Injury_RNA3

description:
PE-50
DAC_A950_IGO_06389_C_26_S31

value: pancreas


title: Injury_RNA4

description:
PE-50
DAC_A955_IGO_06389_C_27_S17


title: ABC-imKO5 Cisplatin it Saline rep3 line 2

description:
ABC-imKO5 sample technical replicate 3.  fastq read- pairs from lane 2
Y42_L002


title: Injury_RNA2

description:
PE-50
DAC_A756_IGO_06389_C_61_S12


title: Injury_RNA1

description:
PE-50
DAC_A224_IGO_06389_C_46_S7


title: Normal_RNA3

description:
PE-50
DAC_B097_IGO_06389_C_33_S19

value: Normal


title: Normal_RNA4

description:
PE-50
DAC_B873_IGO_06389_C_30_S32


title: Normal_RNA1

description:
PE-50
DAC_A946_IGO_06389_C_25_S16


title: Normal_RNA2

description:
PE-50
DAC_A962_IGO_06389_C_48_S9


title: Ly5.1 WT rep3

status: Public on Oct 23 2020

description: week 6 of mixed chimeras of Ltbr-/- and Ly5.1 BM LSKs, transplanted into lethally irradiated Ly5.1/Ly5.2 mice

data_processing:
Primary data analysis was performed with the Illumina RTA v2.4.11 .
The  sequence assembly and alignment was performed using the SeqMan NGen software v.16 and analyzed using ArrayStar software v.16 (DNASTAR, USA).
The level of gene expression was assessed using regularized logarithm (rlog) values from Bioconductor (DESeq2).
Genome_build: GRCm38 - mm10
Supplementary_files_format_and_content: Tab-delimited text file includes raw DESeq2 values.

source_name: LT/ST-HSCs

extract_protocol:
Total RNA was extracted from FACS-purified LT/ST-HSCs using the RNeasy Micro Kit (QIAGEN AG, Switzerland).
Libraries were generated from 20ng total RNA using the TruSeq Stranded mRNA Library Prep Kit High Throughput (Illumina, San Diego, CA, USA).

treatment_protocol: Ltbr-/- and Ly5.1 LT/ST-HSCs isolated from week 6 chimeric mice.

tag: donor strain

value: bone marrow

tag: donor age

value: 7-13 weeks


title: Ly5.1 WT rep2

tag: tissue


title: Ly5.1 WT rep1

tag: genotype


title: Ltbr KO  rep3

value: Ltbr KO

value: 10-13 weeks


title: Ltbr KO  rep2

value: 10 weeks


title: Ltbr KO  rep1

value: 13 weeks


title: Venus_positive_mouse_#3

status: Public on Sep 28 2020

data_processing:
Rnaseq reads were aligned to (GRCm38 - mm10) with STAR
Genome wide transcript counting was performed by HTSeq or featureCounts to generate FPKM matrix
Differential expression analysis was performed with DESeq2 package in R
Genome_build: GRCm38 - mm10
Supplementary_files_format_and_content: Raw count value for each sample

source_name: Isolated mouse hepatocytes

growth_protocol: Notch-Venus reporter mice were kept on NASH diet for 16 weeks, and subjected to hepatocyte isolation and FACS based on Venus signals.

extract_protocol:
RNA was extracted using the NucleoSpin RNA (Clontech) per manufacturer's instructions.
RNA integrity and concentration were assessed using a BioAnalyzer (Agilent).  RNA sequencing libraries were generated using Illumina mRNA TruSeq kit with dual index barcoding.

tag: notch-venus signal

value: Venus-positive

tag: mouse

value: Mouse #3

value: Isolated mouse hepatocytes


title: Venus_positive_mouse_#2

value: Mouse #2


title: Venus_positive_mouse_#1

value: Mouse #1


title: Venus_negative_mouse_#3

value: Venus-negative


title: ABC-imKO3 Naïve rep2 line 1

description:
ABC-imKO3 sample technical replicate 2.  fastq read- pairs from lane 1
Y35_L001

value: Spinal Cord

value: ABC-imKO (Abca1fl/fl Abcg1fl/fl Cx3cr1-CreERT2)

tag: treatment

value: naïve (no treatment)


title: Venus_negative_mouse_#2


title: Tumor_mouse_#3

source_name: Dissected mouse tissue

growth_protocol: L-NICD mice were kept on NASH diet for 16 weeks, and sacrificed for liver tissue harvest to separate surrounding non-tumor livers and tumors.

extract_protocol:
RNA was extracted using Trizol (ThermoFisher) per manufacturer's instructions.
RNA integrity and concentration were assessed using a BioAnalyzer (Agilent).  RNA sequencing libraries were generated using Illumina mRNA TruSeq kit with dual index barcoding.

value: Tumor

value: L-NICD Mouse #3


title: Venus_negative_mouse_#1


title: Tumor_mouse_#2

value: L-NICD Mouse #2


title: Non-tumor_mouse_#3

value: surrounding non-tumor liver


title: Non-tumor_mouse_#2


title: Non-tumor_mouse_#1

value: L-NICD Mouse #1


title: Tumor_mouse_#1


title: K4C ATAC-Seq

status: Public on Jul 28 2020

description: ATAC-seq

data_processing:
Low-quality bases (Phred <20) and Nextera adapters (5’-CTGTCTCTTATA-3’) were identified and trimmed using FastQC and TrimGalore (v0.4.5).
FASTQ files containing trimmed sequences were then aligned to Rn6 Ensembl genome assembly (v95) to generate binary alignment map (BAM) files with Bowtie2 (v.2.3.4.2) with custom options: `--local --very-sensitive-local`, and `-X 3000`
Post-trimming QC with FastQC
Sequences ordered by genomic position using Samtools (v.1.9)
BAM files for each brain region were merged to generate three metasamples that were used for downstream data analysis. Peaks for each region were called using macs2 (Zhang et al., 2008) callpeak with the options - -qvalue 0.00001 - -gsize 2729862089 - -format BAMPE, ignoring duplicates.
Within each brain region, peaks closer than 1000bps were merged with bedtools and peaks less than 146bp, the specific length of DNA wrapped around a single nucleosome, were removed in R. Finally, peaks from each brain region were merged with bedtools to create an additive peak set containing 192,830 peaks.
Genome_build: rn6
Supplementary_files_format_and_content: BED file cotaining ATAC-seq peaks (output of MACS2). Data are in BED format - columns are chromosome, start, end, and score for how many cell types (of 3) contained the ATAC peak.

source_name: Cortical neuron culture

growth_protocol: Neurons were removed from cortical, hippocampal, or striatal tissue at embryonic day 18, and maintained in vitro for 11 days prior to collection of RNA. Each culture well contained ~250,000 cells.

extract_protocol:
Following treatment, media containing KCl or Vehicle was aspirated, and cells were washed with 1x cold PBS. Then, 600 µl of Lysis Buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630, Molecular Grade H2O) was added to cell culture wells and incubated for 5 mins on ice. Lysed cells were then transferred to a 1.5 ml Eppendorf tube and centrifuged at 500 g for 10 mins in a swinging bucket centrifuge. Following removal of supernatant containing lysis buffer and cell debris, 500 µl of 1x cold PBS was added to each tube, and nuclei were counted using the Countess II (Life Technologies). The approximate volume needed to achieve 50,000 nuclei was then placed in new Eppendorf tube, and centrifuged at 500 g for 10 mins in a swinging bucket centrifuge.
The nuclei pellet was then resuspended in 22.5 µl of tagmentation reaction mix containing Molecular Grade H2O, 2x Tagment DNA Buffer (Illumina), 0.011% Digitonin, 0.1% Tween-20, followed by the addition of 2.5 µl TDE1 (Illumina) and incubated at 37°C for 1 hr. Following tagmentation, libraries were PCR amplified and purified using the Qiagen Minelute PCR purification kit (Qiagen). To remove primer dimers, libraries were bead purified using one round of 1.0X Ampure XP beads with 80% ethanol, followed by a second round of 0.8X Ampure beads with 80% ethanol. Libraries were sequenced (75-bp paired end reads) on the NextSeq500 platform (Illumina).

treatment_protocol: Neurons were treated as described with neurobasal media (vehicle) or potassium chloride (KCl; 25mM) for 1hr on DIV 11. 50,000 cells per sample were harvested for ATAC-seq.

tag: strain

value: Sprague-Dawley

tag: age

value: Embryonic day 18, 11 DIV

value: 25mM KCl


title: K3C ATAC-Seq

description: ATAC-seq


title: K3S ATAC-Seq

description: ATAC-seq

source_name: Striatal neuron culture


title: K4H ATAC-Seq

description: ATAC-seq

source_name: Hippocampal neuron culture


title: K2S ATAC-Seq

description: ATAC-seq


title: K2H ATAC-Seq

description: ATAC-seq


title: K1S ATAC-Seq

description: ATAC-seq


title: K2C ATAC-Seq

description: ATAC-seq


title: K1H ATAC-Seq

description: ATAC-seq


title: V4S ATAC-Seq

description: ATAC-seq

value: Vehicle


title: V3C ATAC-Seq

description: ATAC-seq


title: V2S ATAC-Seq

description: ATAC-seq


title: V2H ATAC-Seq

description: ATAC-seq


title: V4H ATAC-Seq

description: ATAC-seq


title: V2C ATAC-Seq

description: ATAC-seq


title: V1S ATAC-Seq

description: ATAC-seq


title: V1H ATAC-Seq

description: ATAC-seq


title: K5S

data_processing:
Pre-trimming QC with FastQC (version build within trim-galore v0.4.5)
Trimming of low quality bases (Phred score <20) and Illumina adapter with trim-galore v0.4.5
Post-trimming QC with FastQC
Splice-aware alignment to Rn6 genome reference with star v2.6.0c.
Merging of BAM files and index generation with samtools v1.9
Identification of transcriptionally active putative enhancers (TAPEs) with custom processing in Seqmonk v 1.46.0
Genome_build: rn6
Supplementary_files_format_and_content: Matrix with of transcriptionally active putative enhancer (TAPE) expression estimates, in counts per kilobase per million mapped reads for each sample. Columns are TAPE_ID, chromosome, start, end, type, distance, sample values (several columns), TAPE center, nearest gene, and information related to nearest gene.

extract_protocol:
Total RNA from was extracted, DNase-treated, and purified (RNeasy, Qiagen). 1µg of total RNA underwent quality control (Bioanalyzer; all RIN values > 7.0) and library construction for total RNA sequencing.
1 μg of total RNA underwent quality control (Bioanalyzer) and was prepared for directional RNA sequencing using NEBNext reagents (New England Biolabs) according to manufacturer’s recommendations. Specifically, the NEBnext rRNA depletion kit was used to remove ribosomal RNA to include both polyadenylated and non-polyadenylated RNA. RNA-seq libraries underwent sequencing (75 bp paired-end directional reads; ~12.6-20.4 M reads/sample) on an Illumina sequencing platform (NextSeq500)

treatment_protocol: Neurons were treated as described with neurobasal media (vehicle) or potassium chloride (KCl; 25mM) for 1hr on DIV 11. Media was removed and RNA was extracted.

value: Striatal neuron culture


title: V1C ATAC-Seq

description: ATAC-seq


title: K7S


title: K3H

value: Hippocampal neuron culture


title: K3C

value: Cortical neuron culture


title: K2C


title: K1S


title: K1H


title: K1C


title: V6S


title: V8S


title: V3C


title: V3H


title: V2H


title: V2C


title: V4S


title: V1C


title: Saline_M_S3

status: Public on Jun 24 2020

source_name: Nucleus accumbens

growth_protocol: Sprague-Dawley 90-120-day-old male or female rats were purchased from Charles River Laboratories. Male or female adult rats were co-housed in pairs in plastic filtered cages with nesting enrichment in an AAALAC-approved animal care facility maintained between 23-24°C on a 12-hour light/dark cycle with ad libitum food (Lab Diet Irradiated rat chow) and water. Bedding and enrichment were changed weekly by animal resources program staff. Animals were randomly assigned to experimental groups.

extract_protocol:
1mm brain sections were taken at the level of the nucleus accumbens, and nucleus accumbens tissue was dissected using a 1mm punch tool centered on the nucleus accumbens core subregion. Frozen tissue punches were thawed slowly on ice prior to being chopped by scalpel 100 times in 2 orthogonal directions. Tissue from 4 animals in the same treatment condition was then combined and transferred to 5mL of chilled (4°C) Lysis Buffer (10mM Tris-HCl, 10mM NaCl, 3mM MgCl2 (Thermo Fisher, BP214-500), 0.1% Igepal in Nuclease-Free Water (Sigma, 18896-50ML)) for 15 min, mixing the tissue by inversion every 2 min. Lysis was quenched immediately at 15 min with 5mL of complete Hibernate-A (Thermo Fisher, A1247501) supplemented with B27 and Glutamax (Life Technologies, 35050-061)). Tissue was then triturated by fire-polished Pasteur pipette (2 pipettes of decreasing diameter; 8-10 passes per pipette) for 35 min and passed through a 40µm pre-wet filter. The samples were then pelleted at 500rcf for 10 min at 4°C followed by a wash in 10mL of Nuclei Wash & Resuspension Buffer (1X PBS, 1% BSA, 0.2U/ul NxGen RNase inhibitor (Lucigen, 30281-2)). Supernatant was then removed and the pellet was gently resuspended in a total volume of 800µl prior to 7-AAD (Thermo Fisher, 00-6993-50) staining and FACS to further purify the nuclei for sequencing. Immediately after FACS, nuclei were washed a final time at 200rcf in 10mL supplemented Hibernate-A containing 1% BSA for 10 minutes at 4°C to remove any remaining fine debris and nascent RNA. Nuclei were brought to a concentration of 1,700 nuclei/µl and an average total of 2,400 nuclei pooled from 4 rats were loaded per sex and treatment group.
FACS-sorted nuclei were subject to 10X GEM generation and barcoding, GEM-RT cleanup and cDNA amplication, and library construction using a Chromium Single Cell 3ʹ Reagent Kit (v3 chemistry). Libraries were quantified and underwent sequencing (~500M total 75bp paired-end reads) on an Illumina sequencing platform (NextSeq 500).

treatment_protocol: Rats were injected with either cocaine (20mg/kg, dissolved in physiological saline) intraperitoneally or equal volumes of physiological saline and placed in an open field for behavioral tracking. 1hr after injections, rats were sacrificed and the brain was removed ad flash frozen.

value: Saline

value: Male


title: Cocaine_M_S4

value: Cocaine


title: Cocaine_F_S2

value: Female


title: Saline_F_S1


title: KCL_S4

growth_protocol: Neurons were removed from striatal tissue at embryonic day 18, and maintained in vitro for 11 days prior to collection of RNA. Each culture well contained ~250,000 cells.

extract_protocol:
Neurons were treated with described stimuli for 1hr, washed, and harvested in lysis buffer prior to isolation of nuclei via centrifugation and FACS sorting.
FACS-sorted nuclei were subject to 10X GEM generation and barcoding, GEM-RT cleanup and cDNA amplication, and library construction using a Chromium Single Cell 3ʹ Reagent Kit (v3 chemistry). Libraries were quantified and underwent sequencing (~500M total 75bp paired-end reads) on an Illumina sequencing platform (NextSeq 500).

treatment_protocol: DIV 11 rat primary striatal neurons were treated with vehicle (neurobasal media), dopamine (50µM), the Drd1 agonist SKF-38393 (1µM), and potassium chloride (25mM) for 1hr.

value: KCL


title: SKF_S3

value: SKF


title: Veh_S1

value: Veh


title: 106_7_S11

description: Experiment 2

data_processing:
Pre-trimming QC with FastQC (version build within trim-galore=0.4.5)
Trimming of low quality bases (Phred score <20) and Illumina adapter with trim-galore=0.4.5
Post-trimming QC with FastQC
Splice-aware alignment with star=2.6.0c. The genome utilized was: /data/project/daylab/Genome-Reference/Genomes/rn6-Ensembl/Rattus_norvegicus.Rnor_6.0.dna.toplevel.fa
Merging of BAM files and index generation with samtools=1.6
Count generation with bioconductor-rsubread=1.26.1 (R version: r-base=3.4.1). The GTF file utilized was: Rattus_norvegicus.Rnor_6.0.90.gtf
Genome_build: rn6
Supplementary_files_format_and_content: Matrix with of gene expression values (raw counts) for each gene in each sample. Genes are in rows, and columns contain the Ensembl ID, chromosome, start, end, and sample names.

extract_protocol:
Total RNA from was extracted, DNase-treated, and purified (RNeasy, Qiagen). 1µg of total RNA underwent quality control (Bioanalyzer; all RIN values > 7.0) and library construction for polyA+ RNA sequencing.
Directional polyA+ RNA llibraries were constructed at the UAB Helfin Genomics Core. Libraries were quantified and underwent sequencing (~25M total 75bp paired-end reads) on an Illumina sequencing platform (NextSeq 500).

treatment_protocol: Neurons were treated as described with CRISPR sgRNAs and dCas9-VPR fusion lentiviruses on DIV 4. Media was removed and RNA was extracted on DIV 11.

value: LacZ


title: 106_6_S10

description: Experiment 2

value: Dopaplex


title: DA_S2

value: DA


title: 106_5_S9

description: Experiment 2

value: Sprague-Dawley


title: 106_3_S8

description: Experiment 2

value: Embryonic day 18, 11 DIV


title: 103_5_S5

description: Experiment 1


title: 103_4_S4

description: Experiment 1


title: 106_2_S7

description: Experiment 2


title: 103_3_S3

description: Experiment 1


title: Striatal neuron culture, dopamine, S37-6

growth_protocol: Neurons were removed from striatal tissue at embryonic day 18, and maintained in vitro for 11 days prior to collection of RNA. Each culture well contained ~250,000 cells. Two culture wells were pooled at the time of extraction.

extract_protocol:
Total RNA from was extracted, DNase-treated, and purified (RNeasy, Qiagen). 1µg of total RNA underwent quality control (Bioanalyzer; all RIN values > 7.0) and library construction for polyA+ RNA sequencing.
Directional polyA+ RNA llibraries were constructed at HudsonAlpha Genomic Services Lab using NEBNext reagents (New England Biolabs) according to manufacturer's recommendations with minor modifications (including the use of custom library adapters and indexes). RNA libraries were quantified (Kapa Library Quant Kit, Kapa Biosystems), and underwent sequencing (25M total 50bp paired-end reads) on an Illumina sequencing platform (HiSeq v4).

treatment_protocol: Neurons were treated as described with neurobasal media (vehicle) or 1µM dopamine for 1hr on DIV 11. Media was removed and RNA was extracted.

value: Striatal neurons

value: Dopamine

tag: time


title: Striatal neuron culture, vehicle, S37-5

value: Vehicle


title: 103_1_S1

description: Experiment 1

value: Striatal neuron culture


title: Striatal neuron culture, dopamine, S37-4


title: Striatal neuron culture, vehicle, S37-3


title: Striatal neuron culture, dopamine, S37-2


title: Striatal neuron culture, vehicle, S37-1


title: MPten tumor 8

status: Public on Apr 28 2020

source_name: Myc;Pten-/- prostate EPO-GEMM tumor

growth_protocol: 8-12 week old WT C57BL/6 male mice were anesthetized with isofluorane and the surgical site (pelvic region) scrubbed with a povidone-iodine scrub (Betadine) and rinsed with 70% alcohol. After opening the peritoneal cavity, the left seminal vesicle is used as a landmark and the anterior lobe of the prostate is pulled out. 50 μl of a plasmid mix (see table below) was injected into the right anterior lobe of the prostate using a 27.5 gauge syringe and tweezer electrodes were tightly placed around the injection bubble. Two pulses of electrical current (60V) given for 35 ms lengths at 500 ms intervals were then applied using an in vivo electroporator (NEPAGENE NEPA21 Type II electroporator). After electroporation, the peritoneal cavity was rinsed with 0.5ml of pre-warmed saline. After the procedure the peritoneal cavity was sutured and the skin closed with skin staples. The mice were kept at 37˚C until they awoke and post-surgery pain management was done with injections of buprenorphine for the three following days. Tumor formation was assessed by ultrasound imaging. Mice were sacrificed at end point, and RNA collected from whole prostate tissue. Genome editing in EPO-GEMM tumors was confirmed by Sanger sequencing.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen)
PolyA mRNA was selected using beads coated with polyT oligonucleotides. Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation.
For sequencing, pooled multiplexed libraries were run on a HiSeq 2500 machine on RAPID mode. Approximately 10 million 76bp single-end reads were retrieved per replicate condition.

value: prostate tumors

value: Mpten

value: non-treated


title: MPten tumor 6


title: MPten tumor 7


title: MPten tumor 5


title: MPten tumor 4


title: MPten tumor 3


title: MPten tumor 2


title: MPten tumor 1


title: MP Wnt low tumor 5

source_name: Myc;p53-/- prostate EPO-GEMM tumor

value: MP Wnt low


title: MP Wnt low tumor 4


title: MP Wnt low tumor 3


title: MP Wnt low tumor 2


title: MP Wnt High tumor 5

value: MP Wnt High


title: MP Wnt low tumor 1


title: MP Wnt High tumor 4


title: MP Wnt High tumor 3


title: MP Wnt High tumor 2


title: WT prostate 6

source_name: WT prostate

value: normal prostate

value: WT


title: WT prostate 5


title: MP Wnt High tumor 1


title: WT prostate 3