title: PDAC_Flt3_YFPnegative_Macrophages_2

city: St. Louis

first: David

last: DeNardo

email: johnbaer@wustl.edu, ddenardo@wustl.edu

state: Missouri

address: 660 S Euclid Ave.

department: Internal Medicine

institute: Washington University in St. Louis

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.0.4b
Gene counts quantitated with Subread:featureCount 1.45 with CPM and RPKM transformations added with custom Rscripting.
Assembly: Ensembl GRCm38.76
Supplementary files format and content: Gene counts with CPM and RPKM in tab-delimitted text format

source_name: Mouse pancreas macrophages

extract_protocol:
Mice were sacrificed by cardiac perfusion with ~10-15mL PBS-heparin under isofluorane anesthesia. Pancreas or tumor tissue was then isolated, minced with scissors, and digested in ~15-25mL Dulbecco’s Modified Eagle Medium (DMEM) with 2mg/mL Collagenase A and 1x DNase I for either 15 minutes (steady-state pancreas and cerulein treated pancreas) or 25 minutes (tumor tissue) at 37°C with constant stirring. Digestion buffer was quenched with 3mL fetal bovine serum (FBS) and filtered through 100uM Nylon mesh, pelleted by centrifugation (2000rmp for 5 min) and resuspended in FACS buffer (1% BSA in PBS). Cells were then resuspended in FACS Buffer containing CD16/CD32 antibodies to block for 10 minutes on ice, pelleted by centrifugation, then resuspended in fluorophore-conjugated antibodies, stained for 25 minutes on ice, then washed with FACS Buffer. Cells were then immediately sorted on Aria-II (BD Biosciences).  For homeostatic pancreas, pancreatitis, and pancreatic tumors, live macrophages (CD45+CD11b+CD3-CD19-B220-SiglecF-Ly6G-Ly6C-7AAD-F4/80+MHCIIHI/Lo) were sorted. After cells were sorted into FACS Buffer, they were pelleted by centrifugation, resuspended in 0.04% BSA in PBS, and cell counts were obtained.
Clontech SMARTer v1

treatment_protocol: For steady-state samples, no treatment was done. For pancreatitis samples, mice were treated with by administering 6 hourly intraperitoneal injections (i.e. once per hour for six hours) of cerulein at a dose of 100ug/kg given every other day for one week. For PDAC samples, orthotopic pancreas KPC tumor models were established by implanting mice with 100,000 KPC-1 cells in 5uL serum-free DME/F-12 and 45uL Cultrex (Trevigen) by injecting cells directly into the pancreas.

value: pancreas

value: macrophages

value: Flt3-Cre;LSL-YFP (C57BL/6)


title: PDAC_Flt3_YFPnegative_Macrophages_1

status: Public on Jun 29 2023

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: cell type

tag: genotype


title: PDAC_Flt3_YFPpositive_Macrophages_3


title: ha-hht2-aa3spt16-rap020-x52

city: Rehovot

first: Naama

last: Barkai

state: --- Select a state ---

address: Herzl St 234

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

library_source: genomic

data_processing:
demultiplexing with bcl2fastq
paired end alignment to S288_R64 with bowtie2 (-p8 --local --very-sensitive )
readfiltering based on fragment size (keep 100-200 bp)
genome coverage with bedtools (-pc -d -fs 1)
Assembly: combined S. cerevisiae (GCA_000146045.2) and C. glabrata () genome
Supplementary files format and content: *.out.txt.gz file contains zipped genome coverage for all 12,157,105 bases in the S. cerevisiae genome (CHr 1-16+mitochondria); or 24,495,413 bases in the combined genome (first S.cerevisae then C. glabrata)

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: yeast cells were grown to saturation overnight in YPD and then dilute in fresh,pre-warmed YPD and incubated for at least 6 hours at 30deg before G1 arrest (alpha factor). After 3 hours in alpha facor, cells were released into HU and samples for ChIP taken in 10-20 minute intervals

extract_protocol:
ChIP was carried out as detailed in Gutin et all, Cell reports 2019, with following modifications. Cell pellets (each from 50 ml of cultures at OD600 0.4, 20 ODs total) were thawed on ice and washed in 10 ml 1M sorbitol. After complete liquid removal, pellets were resuspended in 600 ul RIPA buffer (10 mM Tris pH 8.0, 140 mM NaCl, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, EDTA-free protease inhibitor cocktail) and transferred to chilled LoBind Eppendorf microcentrifuge tubes containing ~500 ul of 0.5 mm zirconium oxide beads (Next Advance, ZrOB05). Cells were processed for 3 cycles in a Bullet Blender 24 (Next Advance) at level 8 for 1 min, with 1 minute on ice between cycles. Debris and lysate were transferred by piercing a hole in the bottom of the tube, placing a clean chilled tube under and centrifuging at 600xg for 5 seconds at 4C. The upper tube with the Zirconium beads was discarded and the lysate was hard spun at 17,000xg for 10 minutes at 4C. The supernatant containing cleaved solubilized 8xmyc tags was discarded, and the pellet was thoroughly resuspended in 100 ul NP buffer (10 mM Tris pH 7.4, 1 M sorbitol, 50 mM NaCl, 5 mM MgCl2, 1 mM CaCl2, and 0.075% NP-40, freshly supplemented with 1 mM β-mercaptoethanol, 500 μM spermidine, and EDTA-free protease inhibitor cocktail). Where indicated 10 ul of undiluted (HA,k9ac,k56ac) or 1:50 diluted (myc)  lysate of a C.Glabrata strain with myc-ha tagged H3 in  NP buffer were added to 110 ul of sample ( = 120 ul in total). SLIM-ChIP protocol was then continued as in Gutin et al.
SLIM-Chip, as per Gutin et al, Cell Reports 2019

value: yeast cells

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Hir1-FRB, Rtt106 & Asf1-FRB triple , spt16-FRB

tag: antibody

value: ha

tag: sensor

tag: experiment

tag: timepoint


title: WildType_2

city: Greenville

first: Kyle

middle: D.

last: Mansfield

state: NC

address: 600 Moye Blvd, MS622

department: Biochemistry and Molecular Biology

institute: East Carolina University, Brody School of Medicine

data_processing:
Sequences were basecalled using the high accuracy basecalling setting and default parameters for quality, barcode identification and trimming.
Passed reads were mapped using MinMap2 to Human Hg38 genome with the Oxford Nanopore read to reference mapping option enabled (minimap2 -x map-ont --q-occ-frac 0.01 -t 6 -a)
Reads were quantified using featureCounts and differential expression determined with DESeq2
Assembly: hg38
Supplementary files format and content: tab-delimited text file with normalized read counts for all genes in all samples/replicate

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: HEK293 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was isolated with TRIzol reagent (Ambion) according to manufacturer protocol.PolyA RNA was isolated total RNA using the Poly(A)Purist MAG Kit (Invitrogen) according to manufacturer protocol.
cDNA libraries were created with Nanopore Direct cDNA sequeuncing kit using  Native Barcoding according to manufacturer protocols

tag: cell line

value: Human Embryonic Kidney

value: Wild Type


title: PDAC_Flt3_YFPpositive_Macrophages_2


title: ha-hht2-aa3spt16-async-x52


title: WildType_1


title: PDAC_Flt3_YFPnegative_Macrophages_3


title: Pancreatitis_Flt3_YFPpositive_Macrophages_2


title: Pancreatitis_Flt3_YFPpositive_Macrophages_3


title: Pancreatitis_Flt3_YFPnegative_Macrophages_4


title: Pancreatitis_Flt3_YFPnegative_Macrophages_3


title: Pancreatitis_Flt3_YFPpositive_Macrophages_4


title: ha-h2b-aavps75-rap090-s46

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV, HTB2-GGS-HA-Fast-MYC, bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Vps75-FRB::KANMX


title: Pancreatitis_Flt3_YFPpositive_Macrophages_1


title: Pancreatitis_Flt3_YFPnegative_Macrophages_1


title: PDAC_Flt3_YFPpositive_Macrophages_1


title: Steady_state_pancreas_Flt3_YFPnegative_Macrophages_4


title: Pancreatitis_Flt3_YFPnegative_Macrophages_2


title: ha-h2b-aavps75-rap060-s46


title: ha-h2b-aavps75-rap040-s46


title: ha-h2b-aavps75-rap120-s46


title: Steady_state_pancreas_Flt3_YFPnegative_Macrophages_3


title: ha-hht2-aa3spt16-rap040-x52


title: ha-h2b-aavps75-rap020-s46


title: Steady_state_pancreas_Flt3_YFPnegative_Macrophages_2


title: ha-h2b-aavps75-rap000-s46


title: Steady_state_pancreas_Flt3_YFPnegative_Macrophages_1


title: Steady_state_pancreas_Flt3_YFPpositive_Macrophages_4


title: ha-h2b-aasth1-rap090-x52

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV, HTB2-GGS-HA-Fast-MYC, bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Sth1-FRB::KANMX


title: Steady_state_pancreas_Flt3_YFPpositive_Macrophages_3


title: Steady_state_pancreas_Flt3_YFPpositive_Macrophages_2


title: Steady_state_pancreas_Flt3_YFPpositive_Macrophages_1


title: ha-h2b-aasth1-rap060-x52


title: ha-h2b-aasth1-rap040-x52


title: USF2 KO, PMA/Ion 2

city: Vancouver

first: Ivan

last: Sadowski

state: British Columbia

address: 2350 Health Sciences Mall

country: Canada

institute: University of British Columbia

description: Galaxy936-[DESeq2_result_file_on_KB1_PMA_Ion_vs_RU2K5_PMA_Ion].tabular

data_processing:
De-multiplexed read sequences were  aligned to the reference sequence using STAR
featureCounts was used to count the number of reads per annotated genome
Counts were analyzed by DESeq2 analysis
Assembly: hg38
Supplementary files format and content: tab-delimited text files include DESeq2 results file

source_name: Jurkat Tat mHIV-Luciferase

growth_protocol: Jurkat Tat mHIV-Luciferase cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen) and used for the construction of sequencing libraries.
Qualifying samples were  prepped following the standard protocol for the NEBnext Ultra ii Stranded mRNA (New England Biolabs).

treatment_protocol: T cell activation was elicited by incubating with the combination of PMA and Ionomycin for 4 hrs

value: Jurkat Tat mHIV-Luciferase

value: T lymphocyte

value: USF2 Knockout

tag: treatment

value: PMA/Ionomycin

tag: time

value: 4 hrs


title: USF2 KO, PMA/Ion 3


title: ha-h2b-aasth1-async-x52


title: USF2 KO, PMA/Ion 1


title: ha-h2b-aaspt6-rap120-s42

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV, HTB2-GGS-HA-Fast-MYC, bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt6-FRB::KANMX


title: Liver of mouse subjected to IL1B #4

type: RNA

city: Lille

first: Jérôme

last: Eeckhoute

address: Bâtiment J&K, Faculté de Médecine de Lille-Pôle Recherche, Boulevard du Professeur Leclerc

country: France

institute: CNRS

description:
Transcriptomic liver mouse treated with IL1B
IL1B_4

hyb_protocol: Affymetrix GeneChip Hybridization Oven 640 for 16h at 45°C and 60 rpm on MoGene-2_0-st Chip. GeneChips were washed and stained in the Affymetrix Fluidics.

scan_protocol: Affymetrix GeneChip Scanner 7G and Affymetrix GeneChip Command Console software (AGCC).

data_processing: Normalization was performed using the apt-probeset-summarize tool of Affymetrix Power Tools (https://www.affymetrix.com/support/developer/powertools/changelog/index.html) using “gc correction+scale intensity+rma”. Normalization level was set to “Core genes”. The data obtained are log2-transformed.

label: biotin

source_name: C57BL/6 x CBA adult male mouse

label_protocol: RNA were processed using Affymetrix GeneChip® WT PLUS Reagent Kit.

growth_protocol: Mice were housed in a temperature-controlled room (22–24°C) with a 12h dark-light cycle. Animal studies were performed in compliance with European Community specifications regarding the use of laboratory animals and approved by the Nord-Pas de Calais Ethical Committee for animal use.

extract_protocol: RNA was extracted using Trizol and reverse transcribed using the High Capacity cDNA Reverse Transcription kit (Applied Biosystems, USA). Total RNA was checked for quantity and quality using the Agilent 2100 Bioanalyzer (Agilent Biotechnologies).

treatment_protocol: Mice were intraperitoneally injection of recombinant mouse IL1B using 0.5 µg/ mouse (BioLegend, 575102) or vehicle (PBS) for 3h

tag: strain background

value: C57BL/6 x CBA

tag: Sex

value: male

value: WT


title: USF2 KO 3

description: Galaxy932-[DESeq2_result_file_on_KB1_vs_RU2K5].tabular

value: Untreated


title: Liver of mouse subjected to IL1B #3

description:
Transcriptomic liver mouse treated with IL1B
IL1B_3


title: Liver of mouse subjected to IL1B #2

description:
Transcriptomic liver mouse treated with IL1B
IL1B_2


title: Liver of control mouse #4

description:
Transcriptomic liver control mouse
PBS_4

source_name: C57BL/6J adult male mouse

value: PBS


title: ha-h2b-aasth1-rap020-x52

value: yeast cells


title: USF2 KO 2


title: USF2 KO 1


title: ha-h2b-aaspt6-rap060-s42

value: ha


title: ha-h2b-aaspt6-rap040-s42


title: ha-h2b-aaspt6-rap090-s42


title: Liver of mouse subjected to IL1B #1

description:
Transcriptomic liver mouse treated with IL1B
IL1B_1


title: Liver of control mouse #2

description:
Transcriptomic liver control mouse
PBS_2


title: USF1 KO, PMA/Ion 2

description: Galaxy1101-[DESeq2_result_file_on_KB1_PMA_Ion_vs_RU1K23_PMA_Ion].tabular

value: USF1 Knockout


title: Liver of control mouse #1

description:
Transcriptomic liver control mouse
PBS_1


title: ha-h2b-aaspt6-rap020-s42


title: USF1 KO, PMA/Ion 1


title: ha-h2b-aaspt6-rap000-s42


title: USF1 KO, PMA/Ion 3


title: Liver of control mouse #3

description:
Transcriptomic liver control mouse
PBS_3


title: ha-h2b-aaspt6b-rap000-s41


title: IWR4, rep1, scRNA-seq

city: Houston

first: Jeffrey

middle: Andrew

last: How

state: TX

address: 1515 Holcombe Blvd. Unit 1362

department: Gyn Onc & Reproductive Med

institute: The University of Texas MD Anderson Cancer Center

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Quality check, data filtering, normalization, unsupervised clustering and dimensionality reduction were performed using “Seurat” R package (v3.1.5).
T cells were isolated based on the canonical lineage markers such as CD3D, CD3E, CD8A, CD8B, CD4.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files.

source_name: Brain Tumor

extract_protocol: scRNA-seq was performed using 10x Genomics Chromium Single Cell Controller. Sorted cells were washed with 1X PBS and suspended in PBS/0.04% BSA. Cells were double-checked for viability and cell number by using the countess II FL and microscope. All cells were diluted to a concentration of 500-1000 cells/μl in PBS/0.04% BSA before being used for single cell 10X 3’v3. Single cells were captured using the 10X Genomic controller according to the bead types and chip used for the experiments. The 10X Genomic Chromium Single cell 3’ GEM, library and Gel bead Kit ’v3 (Catalogue #1000075) and chromium chip B single cell kit (Part# 1000073) were used to capture cells on the controller; cell recovery targeted was in a range of 5000 - 10000 cells. Captured cells then undergo a GEM-RT, cDNA amplification, and all purification in accordance to the 10X protocol. Cleanup cDNA was checked via a tape station (Agilent 42000) HSD5000 (Catalogue# Part# 5067-5593) for cDNA traces. 25% of the cDNA was used to generate the library, and the Chromium i7 multiplex kit (Part# 120262) was used to identify each sample. Library cleanup was performed using AMPure beads and QC was done again with tape station D1000 tapes (Part # 5067-5583). Ten libraries of equal amount were pooled to give a final concentration of 10nM and submitted for sequencing with the NovaSeq6000 S2 sequencer, 28 cycles for read1, 8 cycles for i7 index, and 91 cycles for read 2 through the ATGC core at MD Anderson. Sequence data was then put through the 10X Genomic cell ranger 3.0 pipeline. QC and Fastq files were obtained and checked for data quality, and Fastq files were used to do further analysis.

value: Brain Tumor

value: Leukocytes

tag: diagnosis

value: Glioblastoma

value: IDH Wild Type

tag: primary/recurrent

value: Recurrent

value: Standard of care


title: IWR2, rep1, scRNA-seq

description: 10x Genomics

value: Glioblastoma/Gliosarcoma


title: IWR3, rep1, scRNA-seq

description: 10x Genomics


title: IWR1, rep1, scRNA-seq

description: 10x Genomics


title: ha-h2b-aaspt6-rap180-s41


title: USF1 KO 2

description: Galaxy1097-[DESeq2_result_file_on_KB1_vs_RU1K23].tabular

value: Jurkat Tat mHIV-Luciferase

value: T lymphocyte

value: 4 hrs


title: USF1 KO 3


title: USF1 KO 1


title: IWP3, rep1, scRNA-seq

description: 10x Genomics

value: Astrocytoma

value: Primary

value: Treatment Naive


title: IWP2, rep1, scRNA-seq

description: 10x Genomics


title: ha-h2b-aaspt6-rap120-s41

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV, HTB2-GGS-HA-Fast-MYC, bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt6-FRB::KANMX


title: Wildtype, PMA/Ion 3

description: Galaxy418-[DESeq2_KB1_vs_KB1_P_I].tabular

value: WT

value: PMA/Ionomycin


title: IMR3, rep1, scRNA-seq

description: 10x Genomics

value: Oligodendroglioma

value: IDH Mutant


title: ha-h2b-aaspt6-rap060-s41

value: yeast cells

value: ha


title: ha-h2b-aaspt6-rap090-s41


title: Wildtype, PMA/Ion 2


title: ha-h2b-aaspt6-rap040-s41


title: IMR1, rep1, scRNA-seq

description: 10x Genomics

value: Brain Tumor

value: Leukocytes


title: IMP3, rep1, scRNA-seq

description: 10x Genomics


title: ha-h2b-aaspt6-rap000-s41


title: Wildtype 3

value: Untreated


title: IMR4, rep1, scRNA-seq

description: 10x Genomics

value: Recurrent

value: Standard of care


title: IMP2, rep1, scRNA-seq

description: 10x Genomics


title: IMP1, rep1, scRNA-seq

description: 10x Genomics


title: Wildtype, PMA/Ion 1

value: Jurkat Tat mHIV-Luciferase

value: T lymphocyte


title: NGB2, rep1, scRNA-seq

description: 10x Genomics

source_name: Quasi-normal Brain

value: Quasi-normal Brain

value: Type IIIa focal cortical dysplasia

value: Not Applicable


title: Wildtype 2

value: 4 hrs


title: ha-h2b-aaspt16-ypd120-x40

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV, HTB2-GGS-HA-Fast-MYC, bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt16-FRB::KANMX


title: ha-h2b-aaspt16-ypd030-x40


title: Patient 10, lesion

type: genomic

city: Hasselt

first: Tim

last: Vanmierlo

address: Martelarenlaan 40

country: Belgium

institute: Universiteit Hasselt

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: R programming language

label: Cy3, Cy5

source_name: Brain lesion

label_protocol: Standard Illumina protocol

extract_protocol: gDNA isolation using standard chloroform-phenol extraction and ethanol precipitation method

tag: age

tag: seks

value: M

tag: pmi (minutes)

tag: sentrixid

tag: sentrixposition


title: hbca_c162,P121,replicate_1,contra,3hr_digestion

first: Nicholas

last: Navin

address: 6767 Bertner Ave

department: System Biology

institute: MD Anderson Cancer Center

description:
S4-200
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c162
surgical sample

data_processing:
Basecalls performed using CASAVA version 1.8.1
cellranger 10XRNA Vcellranger-3.1.0 mkfastq
cellranger 10XRNA Vcellranger-3.1.0 count
reads are mapped to hg38
UMI counts are summarized are gene expression levels
Assembly: hg38
Supplementary files format and content: Supplementary_files_format_and_content: H5

source_name: breast

extract_protocol:
RNAs are extracted from single cells suspensions
Single cell capture, barcoding and library preparation was performed by following the 10X Genomics Single Cell Chromium 3’ protocol (PN-1000075)

tag: tissue

value: breast

tag: paper participant_number

tag: assay

value: 10x Genomics Next GEM 3'v3.1


title: Patient 5, lesion

value: F


title: NGB1, rep1, scRNA-seq

description: 10x Genomics

tag: cell type

value: Dysembryoplastic neuroepithelial tumor

tag: genotype


title: Wildtype 1

tag: cell line

value: WT


title: hbca_c156,P115,replicate_1,contra,3hr_digestion

description:
S4-200
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c156
surgical sample


title: ha-h2b-aaspt16-rap120-x40

value: yeast cells

tag: antibody

value: ha

tag: sensor

tag: experiment

tag: timepoint


title: hbca_c157,P116,replicate_1,contra,3hr_digestion

description:
S4-200
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c157
surgical sample


title: Patient 6, lesion


title: Patient_P1959_Post_CART

city: Calgary

first: Nizar

last: Bahlis

state: Alberta

address: 3330 Hospital Dr NW HMRB328

department: Divisions of Hematology and Oncology

institute: University of Calgary

description: 10X Genomics Single Cell RNAseq v2 Chemistry

data_processing:
All raw FASTQs reads were aligned against the human reference genome GRCh38 with default parameters.
Assembly: Human referene genome GRCh38
Supplementary files format and content: Filtered feature - barcode HDF5 file output from CellRanger pipeline

source_name: Primary CD138+ MM cells

growth_protocol: Primary CD138+ MM cells were obtained from the BM aspirates of MM patients at the time of diagnostic procedure, using positive Primary CD138+ MM cells were obtained from the BM aspirates of MM patients at the time of diagnostic procedure, using positive selection with CD138 microbeads (Miltenyi Biotech, Auburn, CA) and accordingly to manufacturer’s instructions.  CD138+ fractions were subsequently analyzed by flow cytometry in order to confirm the sample’s purity.

extract_protocol: Single-cell library preparation for RNA-sequencing primary MM cells were processed according to 10X Genomics reagent Kits User Guide (CG00052 v2 Chemistry). Cells were partitioned into nanoliter-scale Gel Bead-In-Emulsions (GEMs) using 10X GemCode Technology. Primers containing (i) an Illumina R1 sequence, (ii) a 16 bp 10x barcode, (iii) a 10 bp Unique Molecular Identifier (UMI) and (iv) a poly-dT primer sequence were incubated with partitioned cells resulting in barcoded, full-length cDNA from poly-adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents/primers, then cDNA was amplified by PCR. Enzymatic Fragmentation and Size Selection was used to optimize cDNA amplicon size prior to library construction. R1 (read 1 primer sequence) were added during GEM incubation, whereas P5, P7, a sample index (i7), and R2 (read 2 primer sequence) were added during library construction via End Repair, A-tailing, Adaptor Ligation and PCR.

tag: disease state

value: Multiple myeloma

value: post


title: ha-h2b-aaspt16-rap030-x40


title: IWP1, rep1, scRNA-seq

description: 10x Genomics

value: Brain Tumor

value: Leukocytes

tag: diagnosis

value: Glioblastoma

value: IDH Wild Type

tag: primary/recurrent

value: Primary

tag: treatment

value: Treatment Naive


title: hbca_c167,P126,replicate_1,contra,3hr_digestion

description:
S4-200
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c167
surgical sample


title: Patient 7, NAWM

source_name: Brain NAWM

tag: age

tag: seks

tag: pmi (minutes)


title: Patient 9, lesion

tag: sentrixid

tag: sentrixposition


title: Patient_P1759_Pre_CART

value: pre


title: hbca_c161,P120,replicate_1,contra,3hr_digestion

description:
S4-200
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c161
surgical sample

tag: tissue

tag: paper participant_number

tag: assay


title: hbca_c164,P123,replicate_1,contra,3hr_digestion

description:
S4-200
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c164
surgical sample


title: Patient_3298_Post

description: 10X Genomics Single Cell Copy Number Variation

data_processing:
All raw FASTQs reads were aligned against the human reference genome GRCh38 with default parameters.
Assembly: Human referene genome GRCh38
Supplementary files format and content: Filtered feature - barcode HDF5 file output from cellranger-dna pipeline
Library strategy: CNV-Seq

source_name: Primary CD138+ MM

growth_protocol: Primary CD138+ MM cells were obtained from the BM aspirates of MM patients at the time of diagnostic procedure, using positive selection with CD138 microbeads (Miltenyi Biotech, Auburn, CA) and accordingly to manufacturer’s instructions.  CD138+ fractions were subsequently analyzed by flow cytometry in order to confirm the sample’s purity.

extract_protocol: For single-cell DNA library generation for CNV single-cell suspensions of primary MM cells were processed according to 10X Genomics Reagent Kits User Guide (CG000153). Single cells were partitioned in a hydrogel matrix by combining with a CB polymer to form Cell beads (CBs) using a microfluidic chip. Post a first encapsulation, CBs were treated to lyse the encapsulated cells and denature the genomic DNA (gDNA). The denatured gDNAs in the CB were then accessible to amplification and barcoding. A second microfluidic encapsulation step was then required to partition the CB with 10x barcode Gel Beads (GBs) to generate GEMs. Immediately after barcoding and amplification, 10x barcoded fragments were pooled and attached to standard Illumina adaptors. For all the single cell methods, quality control and quantification was performed using a Kapa Library Quantification qPCR kit (Kapa Biosystems) on a BioRad qPCR instrument prior to preparing a single pool containing equal amounts of each library. This pool was then subjected to on-board cluster formation and sequencing on an Illumina NextSeq 500 sequencer with a high-output v2.5 150 sequencing kit for RNA-seq  and 300 cycle sequencing kit for CNV-seq as per the standard Illumina protocols. After sequencing, the bcl data was converted to fastq data files using the Illumina BCL2FASTQ utility. Samples were processed with CellRanger suite v3.0 and downstream analyses were realized with Seurat and custom R packages.


title: Patient 10, NAWM

value: M


title: Patient 4, NAWM


title: hbca_c160,P119,replicate_1,contra,3hr_digestion

description:
S4-200
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c160
surgical sample

value: breast


title: hbca_c155,P114,replicate_1,contra,3hr_digestion

description:
S4-200
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c155
surgical sample

value: 10x Genomics Next GEM 3'v3.1


title: Patient 5, NAWM

value: F


title: Patient 1, NAWM


title: Patient 9, NAWM


title: ha-h2b-aaspt16-rap090-s42

tag: genotype

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV, HTB2-GGS-HA-Fast-MYC, bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt16-FRB::KANMX


title: hbca_c159,P118,replicate_1,contra,3hr_digestion

description:
S4-200
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c159
surgical sample


title: Patient 2, lesion


title: Patient_3239_Post


title: hbca_c158,P117,replicate_1,contra,3hr_digestion

description:
S4-200
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c158
surgical sample


title: ha-h2b-aaspt16-rap060-s42

tag: antibody


title: Patient_2969_Post


title: hbca_c163,P122,replicate_1,contra,3hr_digestion

description:
S4-200
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c163
surgical sample


title: Patient 7, lesion


title: Patient 3, lesion


title: ha-h2b-aaspt16-rap040-s42

tag: sensor


title: Patient 2, NAWM


title: Patient 4, lesion


title: IMR2, rep1, scRNA-seq

description: 10x Genomics

tag: cell type

value: IDH Mutant

value: Recurrent

value: Standard of care


title: Patient_2918_Post

value: Multiple myeloma

tag: timepoint


title: hbca_c154,P113,replicate_1,contra,3hr_digestion

description:
S4-200
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c154
surgical sample


title: Patient 3, NAWM


title: hbca_c165,P124,replicate_1,contra,3hr_digestion

description:
S4-200
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c165
surgical sample


title: Patient 1, lesion


title: Patient 6, NAWM


title: ha-h2b-aaspt16-rap020-s42

value: yeast cells

value: ha

tag: experiment


title: hbca_c48,P43,replicate_1,contra,3hr_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c48
surgical sample

value: 10x Genomics 3' V3


title: hbca_c49,P43,replicate_1,contra,overnight_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c49
surgical sample


title: Patient_2916_Post

tag: disease state

value: post


title: hbca_c47,P43,replicate_1,contra,short_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c47
surgical sample


title: ha-h2b-aaspt16-rap000-s42


title: hbca_c46,P42,replicate_1,contra,short_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c46
surgical sample


title: ha-h2b-aaspt16b-rap000-s41


title: Patient_2798_Post


title: hbca_c45,P36,replicate_1,contra,overnight_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c45
surgical sample


title: hbca_c44,P35,replicate_1,contra,overnight_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c44
surgical sample


title: ha-h2b-aaspt16-rap180-s41


title: Patient_2601_Pre


title: Patient_2510_Pre


title: hbca_c30,P23,replicate_2,contra,short_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c30
surgical sample


title: IMP4, rep1, scRNA-seq

description: 10x Genomics

value: Brain Tumor

value: Leukocytes

tag: diagnosis

value: Oligodendroglioma

tag: primary/recurrent


title: hbca_c29,P23,replicate_1,contra,short_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c29
surgical sample


title: hbca_c28,P22,replicate_1,contra,short_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c28
surgical sample


title: ha-h2b-aaspt16-rap120-s41


title: Patient_2289_Pre

description: 10X Genomics Single Cell Copy Number Variation

value: pre


title: Patient_2029_Pre


title: hbca_c42,P33,replicate_1,contra,overnight_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c42
surgical sample


title: hbca_c43,P34,replicate_1,contra,overnight_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c43
surgical sample


title: ha-h2b-aaspt16-rap090-s41


title: hbca_c41,P32,replicate_1,contra,overnight_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c41
surgical sample


title: ha-h2b-aaspt16-rap040-s41


title: ha-h2b-aaspt16-rap060-s41


title: ha-h2b-aaspt16-rap000-s41


title: Patient_2024_Pre


title: Patient_1966_Pre


title: hbca_c40,P37,replicate_1,contra,short_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c40
surgical sample


title: Patient_2015_Post


title: ha-h2b-aasnf2-rap090-x52

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV, HTB2-GGS-HA-Fast-MYC, bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Snf2-FRB::KANMX


title: hbca_c33,P25,replicate_1,contra,overnight_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c33
surgical sample

value: breast


title: Patient_1959_Post


title: ha-h2b-aasnf2-rap060-x52


title: Patient_1858_Post


title: hbca_c37,P29,replicate_1,contra,overnight_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c37
surgical sample


title: hbca_c27,P21,replicate_1,contra,overnight_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c27
surgical sample


title: Patient_1759_Pre


title: hbca_c36,P28,replicate_1,contra,overnight_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c36
surgical sample


title: hbca_c35,P27,replicate_1,contra,short_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c35
surgical sample


title: hbca_c34,P26,replicate_1,contra,overnight_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c34
surgical sample


title: ha-h2b-aasnf2-rap020-x52


title: Patient_1722_Pre


title: hbca_c166,P125,replicate_1,contra,3hr_digestion

description:
S4-200
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c166
surgical sample

value: 10x Genomics Next GEM 3'v3.1


title: hbca_c152,P111,replicate_1,left,3hr_digestion

description:
S4-200
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c152
surgical sample


title: hbca_c153,P112,replicate_1,left,3hr_digestion

description:
S4-200
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c153
surgical sample


title: Patient_1698_Pre


title: ha-h2b-aasnf2-async-x52


title: hbca_c151,P110,replicate_1,left,3hr_digestion

description:
S4-200
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c151
surgical sample


title: hbca_c150,P109,replicate_1,right,4hr_digestion

description:
S4-200
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c150
surgical sample


title: ha-h2b-aartt106-rap120-s46

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV, HTB2-GGS-HA-Fast-MYC, bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Rtt106-FRB::KANMX


title: Patient_1680_Pre


title: hbca_c149,P108,replicate_1,right,3hr_digestion

description:
S4-200
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c149
surgical sample


title: ha-h2b-aartt106-rap090-s46


title: hbca_c148,P107,replicate_1,right,3hr_digestion

description:
S4-200
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c148
surgical sample


title: hbca_c147,P106,replicate_1,right,3hr_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c147
surgical sample


title: Patient_1675_Pre

description: 10X Genomics Single Cell Copy Number Variation


title: ha-h2b-aartt106-rap060-s46


title: ha-h2b-aasnf2-rap040-x52


title: Patient_1643_Pre


title: hbca_c146,P105,replicate_1,left,3hr_digestion

description:
S4-200
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c146
surgical sample


title: hbca_c145,P104,replicate_1,right,2hr_digstion

description:
S4-200
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c145
surgical sample


title: ha-h2b-aartt106-rap040-s46


title: hbca_c144,P103,replicate_1,right,3hr_digestion

description:
S4-200
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c144
surgical sample


title: ha-h2b-aartt106-rap020-s46


title: Patient_1620_Pre


title: hbca_c138,P97,replicate_1,right,3hr_digestion

description:
S4-200
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c138
surgical sample


title: hbca_c141,P100,replicate_1,right,2hr_digstion

description:
S4-200
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c141
surgical sample


title: hbca_c142,P101,replicate_1,right,3hr_digestion

description:
S4-200
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c142
surgical sample


title: hbca_c137,P96,replicate_1,left,2hr_digstion

description:
S4-200
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c137
surgical sample


title: hbca_c143,P102,replicate_1,left,2hr_digstion

description:
S4-200
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c143
surgical sample


title: hbca_c140,P99,replicate_1,left,3hr_digestion

description:
S4-200
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c140
surgical sample


title: ha-h2b-aartt106-rap000-s46


title: ha-h2b-nofrb-rap000-s41

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV, HTB2-GGS-HA-Fast-MYC, bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12

value: aanofrb


title: Patient_1619_Pre


title: Patient_1576_Pre


title: hbca_c133,P92,replicate_1,right,2hr_digstion

description:
S4-200
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c133
surgical sample


title: ha-h2b-nofrb-rap120-s41


title: Patient_1627_Pre


title: hbca_c139,P98,replicate_1,left,3hr_digestion

description:
S4-200
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c139
surgical sample


title: ha-h2b-aaspt16-async-x40

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV, HTB2-GGS-HA-Fast-MYC, bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt16-FRB::KANMX


title: hbca_c136,P95,replicate_1,left,6hr_digestion

description:
S4-200
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c136
surgical sample


title: hbca_c135,P94,replicate_1,right,3hr_digestion

description:
S4-200
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c135
surgical sample


title: Patient_1608_Pre


title: hbca_c132,P91,replicate_1,left,6hr_digestion

description:
S4-200
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c132
surgical sample


title: hbca_c134,P93,replicate_1,right,2hr_digstion

description:
S4-200
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c134
surgical sample


title: hbca_c130,P89,replicate_1,right,2hr_digstion

description:
S4-200
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c130
surgical sample


title: Patient_1556_Pre

description: 10X Genomics Single Cell Copy Number Variation


title: Patient_1555_Pre


title: ha-h2b-aanap1-rap090-s46

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV, HTB2-GGS-HA-Fast-MYC, bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Nap1-FRB::KANMX


title: Patient_1498_Pre

value: Multiple myeloma


title: ha-h2b-aanap1-rap120-s46

value: yeast cells


title: hbca_c131,P90,replicate_1,right,3hr_digestion

description:
S4-200
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c131
surgical sample


title: hbca_c129,P88,replicate_1,right,3hr_digestion

description:
S4-200
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c129
surgical sample


title: ha-h2b-aanap1-rap060-s46

value: ha


title: Patient_1479_Pre


title: ha-h2b-aanap1-rap020-s46


title: hbca_c127,P86,replicate_1,right,2hr_digstion

description:
S4-200
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c127
surgical sample

value: 10x Genomics 3' V3


title: ha-h2b-aanap1-rap040-s46


title: Patient_1460_Pre


title: hbca_c125,P84,replicate_1,right,2hr_digstion

description:
S4-200
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c125
surgical sample


title: ha-h2b-aanap1-rap000-s46


title: hbca_c124,P83,replicate_1,right,3hr_digestion

description:
S4-200
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c124
surgical sample


title: hbca_c126,P85,replicate_1,right,2hr_digstion

description:
S4-200
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c126
surgical sample


title: hbca_c123,P82,replicate_1,right,3hr_digestion

description:
S4-200
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c123
surgical sample


title: hbca_c122,P81,replicate_1,right,2hr_digstion

description:
S4-200
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c122
surgical sample


title: ha-h2b-aaino80-rap090-x52

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV, HTB2-GGS-HA-Fast-MYC, bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Ino80-FRB::KANMX


title: hbca_c120,P79,replicate_1,left,3hr_digestion

description:
S4-200
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c120
surgical sample


title: hbca_c121,P80,replicate_1,right,2hr_digstion

description:
S4-200
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c121
surgical sample


title: hbca_c128,P87,replicate_1,right,3hr_digestion

description:
S4-200
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c128
surgical sample


title: hbca_c118,P77,replicate_1,left,3hr_digestion

description:
S4-200
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c118
surgical sample


title: ha-h2b-aaino80-rap040-x52


title: ha-h2b-aaino80-rap020-x52


title: hbca_c115,P74,replicate_1,right,2hr_digstion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c115
surgical sample


title: Patient_1438_Pre


title: hbca_c117,P76,replicate_1,left,3hr_digestion

description:
S4-200
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c117
surgical sample


title: Patient_1404_Pre


title: hbca_c119,P78,replicate_1,right,2hr_digstion

description:
S4-200
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c119
surgical sample


title: hbca_c114,P73,replicate_1,right,3hr_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c114
surgical sample


title: ha-h2b-aaino80-async-x52


title: Patient_1389_Pre

description: 10X Genomics Single Cell Copy Number Variation


title: Patient_1388_Pre


title: hbca_c116,P75,replicate_1,left,3hr_digestion

description:
S4-200
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c116
surgical sample


title: hbca_c111,P70,replicate_1,right,3hr_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c111
surgical sample


title: Patient_1426_Pre


title: ha-h2b-aaino80-rap060-x52


title: epicardium_14_2_S4

city: Leiden

first: Anke

last: Smits

address: Einthovenweg 20

department: Cell and Chemical Biology

country: Netherlands

institute: Leiden University Medical Center

description: SORT-seq

data_processing:
During sequencing, Read 1 was assigned 26 base pairs and was used to identify the Illumina library barcode, cell barcode, and UMI. Read 2 was assigned 60 base pairs and used to map to the human reference transcriptome (hg19) with BWA-MEM 0.7.15. Data was demultiplexed as described in Grün et al. 2014. Briefly,  Mapping and generation of count tables were automated using the MapAndGo script.
The count tables came in 3 types:
1. read counts (raw mapped reads)
2. barcode counts (UMI corrected version of 1)
3. transcript counts (poisson counting statistics corrected version of 2) This is the file used as input for downstream analysis. These files are included in this repository.
Assembly: hg19
Supplementary files format and content: Tab separated values

source_name: Human fetal epicardium

extract_protocol:
Fetal epicardial layers were isolated by separating the epicardium from the underlying myocardium of human hearts aged 14-15 weeks gestation. The tissue was processed into small pieces and gisteded during three round of Trypsin 0.25/EDTA incubation for a total of 30 minutes at 37 degrees Celsius. The suspension was subsequently passed through a series of syringes of decreasing size (19G to 21G). The cell suspsension was passed through a 70 micron cell strainer, collected and subsequently stained for 20 minutes using calcein AM at 100 nM in PBS at RT. Samples were kept on ice until sorting in 384-wells plates.
Using a Mosquito® HTS (TTP Labtech) 384 wells plates were filled with 50 nL lysis buffer containing CELseq2-primers, spike-ins and dinucleotide triphosphates and overlaid with mineral oil to prevent evaporation. Plates were stored at -80°C until sequencing. Viable cells were sorted one cell per well into these 384 wells plates using BD FACSAria III, fixed by lysis to preserve expression status, and immediately frozen at -80°C until further processing. cDNA was constructed using the SORT-seq protocol

value: Human fetal epicardium

value: Dissociated epicardial cells

tag: developmental stage

value: 14 weeks


title: hbca_c113,P72,replicate_1,right,2hr_digstion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c113
surgical sample


title: hbca_c108,P67,replicate_1,left,3hr_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c108
surgical sample


title: hbca_c110,P69,replicate_1,right,2hr_digstion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c110
surgical sample


title: ha-h2b-aahir1-rap090-s46

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV, HTB2-GGS-HA-Fast-MYC, bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Hir1-FRB::KANMX


title: ha-h2b-aahir1-rap040-s46


title: ha-h2b-aahir1-rap060-s46


title: hbca_c109,P68,replicate_1,left,2hr_digstion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c109
surgical sample


title: epicardium_14_1_S10

description: SORT-seq


title: hbca_c107,P66,replicate_1,right,3hr_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c107
surgical sample


title: hbca_c106,P65,replicate_1,right,2hr_digstion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c106
surgical sample


title: Patient_1217_Pre

value: pre


title: hbca_c103,P64,replicate_1,left,2hr_digstion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c103
surgical sample

value: breast


title: ha-h2b-aahir1-rap000-s46


title: hbca_c104,P64,replicate_1,right,2hr_digstion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c104
surgical sample


title: epicardium_15_2_S8

description: SORT-seq

value: 15 weeks


title: ha-h2b-aachz1-rap120-s46

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV, HTB2-GGS-HA-Fast-MYC, bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Chz1-FRB::KANMX


title: epicardium_14_2_S5

description: SORT-seq


title: hbca_c112,P71,replicate_1,left,3hr_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c112
surgical sample


title: hbca_c98,P62,replicate_1,left,2hr_digstion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c98
surgical sample


title: ha-h2b-aahir1-rap020-s46


title: hbca_c102,P63,replicate_1,right,3hr_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c102
surgical sample


title: ha-h2b-aahir1-rap120-s46


title: epicardium_15_2_S3

description: SORT-seq


title: hbca_c101,P63,replicate_1,left,3hr_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c101
surgical sample


title: epicardium_15_1

description: SORT-seq


title: hbca_c97,P61,replicate_1,right,4hr_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c97
surgical sample


title: h9_ko2_rep2

first: Marco

middle: A

last: Marra

state: BC

address: 675 W 10th Ave, 7th Floor

institute: Canada's Michael Smith Genome Sciences Centre

data_processing:
Raw sequencing data were demultiplexed using the CellRanger software (10X Genomics; cellranger mkfastq with default parameters; v1.2.1)
Alignment, filtering, barcode counting, and UMI counting were done using the CellRanger software (cellranger count with default parameters except --expect-cells set to 1000; v2.1.1). The CellRanger hg19-3.0.0 reference was used for alignment.
Data preprocessing was performed in R (v3.5.0), based on the filtered count matrices output by CellRanger. Counts for cells from all samples (7,735 cells) were combined into a single count matrix, and genes detected (UMI > 0) in at least two cells were retained. Normalization was then applied to all cells using the scran package in R (Lun et al. 2016) (v1.10.1). The quickCluster function was used to cluster cells for normalization (with min.mean = 0.1 as suggested for UMI data), and the resulting clusters were used as input to the computeSumFactors function (with min.mean = 0.1). These factors were then used in the normalize function of the scater R package (v1.10.0).
Genome_build: hg19
Supplementary_files_format_and_content: raw_counts_matrix.mtx and norm_counts_matrix.mtx are sparse matrices of raw and normalized UMI counts, respectively, for all cells identified by the CellRanger pipeline.
Supplementary_files_format_and_content: barcodes.tsv and genes.tsv are tab-delimited files that contain the count matrices' barcode (column) and gene (row) names, respectively.
Supplementary_files_format_and_content: metadata.csv is a comma-separated file that contains cell metadata (i.e. cell names, sample [cell line/replicate] from which they were derived, and cell cycle phase scores).

source_name: normal human astrocytes

growth_protocol: Cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% (v/v) heat-inactivated FBS (Thermo Fisher Scientific, Waltham, MA, USA).

extract_protocol: Single cell 3' RNA-seq libraries were generated using the Chromium Single Cell 3′ Library & Gel Bead Kit v1 (10X Genomics, Pleasanton CA) following the manufacturer's protocol. Briefly, the volume of cell suspension was determined based on a targeted cell recovery of 1,000 cells and mixed with the Single Cell Master Mix prior to loading onto the Single Cell 3' Chip. Following GEM generation in the Chromium Controller (10X Genomics), GEM-RT reaction was performed, GEMS were broken, and cDNA clean up was performed using Dynabeads MyOne Silane beads followed by a cleanup with SPRIselect beads  (Beckman Coulter, Indianapolis IN). cDNA amplification was performed with a total of 14 cDNA amplification cycles, followed by reaction clean up with SPRIselect beads. Total cDNA quantification was performed using the Agilent High Sensitivity DNA Kit (Santa Clara CA). cDNA shearing on the Covaris E220 Focused Ultrasonicator (Woburn MA), library construction (10 cycles for Sample Index PCR), and SPRIselect cleanups were performed to generate the final indexed libraries. Library quality was assessed using the Agilent High Sensitivity DNA Kit and quantified using the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific). Libraries were pooled (8 libraries/pool) and sequenced on one flowcell on the Illumina NextSeq500 platform (San Diego CA) using paired-end sequencing with dual indexing following Illumina protocols and 10X sequencing run parameters (98bp read1, 14bp i7 index, 8bp i5 index, and 98bp read2).

treatment_protocol: Cells were harvested using 0.05% Trypsin-EDTA, washed twice with 1x PBS + 0.04% BSA and passed through a 35µm strainer to generate a single-cell suspension.

tag: cell line

value: immortalized normal human astrocyte (NHA)

value: CIC knockout


title: h9_ko2_rep1


title: epicardium_14_1_S9

description: SORT-seq


title: hbca_c105,P65,replicate_1,left,2hr_digstion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c105
surgical sample


title: hbca_c99,P62,replicate_1,right,2hr_digstion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c99
surgical sample


title: ha-h2b-aachz1-rap060-s46


title: ha-h2b-aachz1-rap090-s46


title: ha-h2b-aachz1-rap040-s46


title: a2_ko1_rep2


title: hbca_c95,P60,replicate_1,right,3hr_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c95
surgical sample


title: a2_ko1_rep1


title: ha-h2b-aachz1-rap020-s46


title: ha-h2b-aachz1-rap000-s46


title: hbca_c94,P60,replicate_1,left,3hr_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c94
surgical sample


title: nha_wt_rep3

value: CIC wild type


title: hbca_c93,P59,replicate_1,right,3hr_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c93
surgical sample


title: nha_wt_rep2


title: ha-h2b-aachd1-rap090-x60

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV, HTB2-GGS-HA-Fast-MYC, bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Chd1-FRB::KANMX


title: nha_wt_rep1


title: hbca_c92,P59,replicate_1,left,3hr_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c92
surgical sample


title: hbca_c91,P41,replicate_1,right,4hr_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c91
surgical sample


title: ha-h2b-aachd1-rap060-x60


title: ha-h2b-aachd1-rap020-x60


title: hbca_c96,P61,replicate_1,left,4hr_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c96
surgical sample


title: ha-h2b-aachd1-async-x60


title: hbca_c88,P58,replicate_1,left,3hr_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c88
surgical sample


title: ha-h2b-aacac1-rap120-s46

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV, HTB2-GGS-HA-Fast-MYC, bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Cac1-FRB::KANMX


title: GFP+CV+ MDA-MB-231, day 28 (9 mice - pooled) - group S3

city: Leeds

first: Mihaela

last: Lorger

address: Woodhouse

country: United Kingdom

institute: University of Leeds

data_processing:
Raw data quality and integrity was assessed prior to processing by FastQC (v0.11.8)
Adaptor sequences were trimmed using Cutadapt
Primary assemblies and gene annotations (GRCh38.p12 and GRCm38.p6) were sourced from GENCODE
Human and mouse chromosomal identifiers were renamed for downstream disambiguation, and assemblies concatenated using Biostrings
Reads were mapped to concatenated assembly using STAR (v2.7), and quality control performed with Qualimap and Picard Tools
Read quantification, transcriptome merging and mapping of counts was performed using RSubread. Multi-mapping reads were included. Mouse-aligned reads were discarded from analysis.
Size factor normalization was performed on read counts using DESeq2, and gene expression values were calculated and annotated
Assembly: GRCh38.p12, GRCm38.p6 (concatenated prior to alignment)
Supplementary files format and content: Tab-delimited text file includes DESEq2-processed data with values for gene expression, complete abundance ("raw") and normalized abundance ("norm")

source_name: Mus musculus brain tumor xenograft

growth_protocol: MDA-MB-231GFP+ cells were maintained in EMEM supplemented with 10% FBS, L-glutamine, vitamin mix, non-essential amino acids, sodium pyruvate and antibiotics in a humidified environment at 37C and 5% CO2

extract_protocol:
Total RNA was extracted using Arcturus® PicoPure RNA Isolation Kit (Thermo Fisher); GFP+ (proliferating) and GFP+CV+ (cell cycle-inactive) cells were sorted directly into extraction buffer after isolation and dissociation of brain tissue.
Full length cDNA libraries were generated according to the published Smart-seq2 (Picelli et al., (2014). Nature Protocols. 9: 171-181), and with the Nextera XT DNA Library Prep kit (Illumina).

treatment_protocol: MDA-MB-231GFP+ cells were labelled with CV vital dye that is lost rapidly through cell proliferation, and used to generate mouse brain tumor xenografts (6-8wk old C.B-17 SCID, female) by internal carotid artery injection. Mice were euthanised by terminal perfusion 28-days post-injection.

value: Mus musculus brain tumor xenograft

value: Breast adenocarcinoma

value: GFP+

tag: treatment

value: CV-labelled; xenograft - mouse brain

tag: phenotype

value: cell cycle-inactive


title: hbca_c90,P41,replicate_1,left,4hr_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c90
surgical sample

value: 10x Genomics 3' V3


title: P60 Control biol rep2

city: SAFED

last: Enshell-Seijffers

address: Henrietta Szold 8

department: Azrieli Faculty of Medicine

institute: BAR ILAN UNIVERSITY

description: Ribosomal depletion was performed

data_processing:
trimmed and quality filtered using Trimmomatic
mapped to the mouse genome (NCBI38/mm10) using Tophat (version 2)
Mapped read for each annotated ENSEMBL gene (GRCm38.p4) were counted using HTSeq-count tool
Read count normalization and differential gene expression analysis was performed using DESeq2
Assembly: mm10

source_name: Hair follicle

extract_protocol:
Total RNA was purified from FACS-sorted cells utilizing the RNeasy Plus Micro kit (QIAGEN #74034)
Ribosomal depletion was performed on 100 ng of total RNA and libraries for Illumina sequencing were performed using the Nebnext Ultra Directional RNA kit (NEB, #E7420L)

value: Hair follicle

value: Dermal Papilla (DP) cells

value: Control

tag: time

value: 60 days Postnatal


title: P60 Control biol rep3

description: Ribosomal depletion was performed

tag: tissue


title: P60 Hdac1/Hdac2 double mutant biol rep1

description: Ribosomal depletion was performed

value: Hdac1/Hdac2 double mutant


title: P60 Hdac1/Hdac2 double mutant biol rep2

description: Ribosomal depletion was performed


title: hbca_c87,P40,replicate_1,right,3hr_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c87
surgical sample

value: breast

tag: paper participant_number


title: ha-h2b-aacac1-rap060-s46

value: yeast cells

value: ha


title: ha-h2b-aachd1-rap040-x60


title: hbca_c86,P40,replicate_1,left,3hr_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c86
surgical sample

tag: assay


title: P60 Control biol rep1

description: Ribosomal depletion was performed

tag: genotype


title: hbca_c100,P59,replicate_2,left,3hr_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c100
surgical sample


title: P60 Hdac1/Hdac2 double mutant biol rep3

description: Ribosomal depletion was performed


title: GFP+CV+ MDA-MB-231, day 28 (10 mice - pooled) - group S2


title: P28 Hdac1/Hdac2 double mutant biol rep3

description: Ribosomal depletion was performed

value: 28 days Postnatal


title: ha-h2b-aacac1-rap040-s46

tag: antibody


title: ha-h2b-aacac1-rap020-s46

tag: sensor


title: P28 Hdac1/Hdac2 double mutant biol rep2

description: Ribosomal depletion was performed

tag: cell type


title: GFP+CV- MDA-MB-231, day 28 (9 mice - pooled) - group S3

value: proliferating


title: hbca_c84,P39,replicate_1,left,3hr_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c84
surgical sample


title: GFP+CV+ MDA-MB-231, day 28 (10 mice - pooled) - group S1


title: hbca_c89,P58,replicate_1,right,3hr_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c89
surgical sample


title: ha-h2b-aacac1-rap090-s46

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV, HTB2-GGS-HA-Fast-MYC, bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Cac1-FRB::KANMX

tag: timepoint


title: P28 Hdac1/Hdac2 double mutant biol rep1

description: Ribosomal depletion was performed


title: hbca_c83,P38,replicate_1,right,3hr_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c83
surgical sample


title: GFP+CV- MDA-MB-231, day 28 (10 mice - pooled) - group S1

value: Mus musculus brain tumor xenograft


title: ha-h2b-aacac1-rap000-s46

tag: experiment


title: ha-h2b-aaasf1-rap120-s46

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV, HTB2-GGS-HA-Fast-MYC, bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Asf1-FRB::KANMX


title: P28 Control biol rep3

description: Ribosomal depletion was performed


title: hbca_c85,P39,replicate_1,right,3hr_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c85
surgical sample


title: hbca_c82,P38,replicate_1,left,3hr_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c82
surgical sample


title: ha-h2b-aaasf1-rap090-s46


title: X99, Mcm8-Ko, heart tissue, LCWE treatment

city: Guangzhou

first: Zhanghua

last: Chen

address: #9, Jinsui Road, Tianhe District

country: China

institute: Guangzhou Women and Children Medical Center

data_processing:
Libraries were sequenced on the Illumina HiSeq X Ten platform.
STAR (v2.7.8a) was applied to align sequencing reads to the mouse transcriptome (build GRCm38) and quantify gene counts.
The analysis of differentially expressed genes (DEGs) between Wt and Mcm8-/- mice was conducted using the R package limma v3.36.160. Signiﬁcant DEGs were identified using empirical Bayes moderated t-statistics (P value ≤ 0.05 and log2 fold change ≥ 0.5).
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text file containing raw count for each sample

source_name: Heart tissue

extract_protocol:
The extraction, reverse transcription, preamplification of total RNA from mice heart tissues (Wt and Mcm8-/-) were conducted using Discover-scTM WTA Kit V2 (Vazyme). The quantity and quality of RNA were assessed by the QubitRNA assay kit on Qubit3.0 Fluorometer (Life technologies, CA, USA) and RNA Nano 6000 Assay kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA), respectively
RNA libraries were constructed using Discover-scTM WTA Kit V2 (Vazyme) according to the manufacture‘s instructions.

value: Heart tissue

value: Mcm8 knockout

value: LCWE stimulation


title: ha-h2b-aaasf1-rap060-s46


title: P28 Control biol rep2

description: Ribosomal depletion was performed


title: GFP+CV- MDA-MB-231, day 28 (10 mice - pooled) - group S2

value: Breast adenocarcinoma

value: GFP+

value: CV-labelled; xenograft - mouse brain


title: P28 Control biol rep1

description: Ribosomal depletion was performed

value: Hair follicle

value: Dermal Papilla (DP) cells

value: Control


title: X134, Mcm8-Ko, heart tissue, LCWE treatment


title: hbca_c80,P57,replicate_1,left,3hr_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c80
surgical sample

value: breast

value: 10x Genomics 3' V3


title: P24 Hdac1/Hdac2 double mutant biol rep3

description: Ribosomal depletion was performed

value: Hdac1/Hdac2 double mutant

value: 24 days Postnatal


title: hbca_c78,P56,replicate_1,left,6hr_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c78
surgical sample


title: P24 Hdac1/Hdac2 double mutant biol rep2

description: Ribosomal depletion was performed


title: ha-h2b-aaasf1-rap020-s46

value: yeast cells

value: ha


title: hbca_c79,P56,replicate_1,right,6hr_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c79
surgical sample


title: X120, Mcm8-Ko, heart tissue, LCWE treatment


title: ha-h2b-aaasf1-rap000-s46


title: P24 Hdac1/Hdac2 double mutant biol rep1

description: Ribosomal depletion was performed


title: X117, Mcm8-Ko, heart tissue, LCWE treatment


title: hbca_c77,P55,replicate_1,right,3hr_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c77
surgical sample


title: X56, wild type, heart tissue, LCWE treatment

value: Wild type


title: P24 Control biol rep3

description: Ribosomal depletion was performed


title: HC2, 14dHC

city: Charlottesville

first: Joshua

last: Samuels

state: Virginia

address: 409 Lane Road

department: Neuroscience

institute: University of Virginia

data_processing:
CellRanger version 4.0 was used to demultiplex fastq files and matrix generation
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every sample

source_name: Brain

extract_protocol:
Sngle cells were obtained using a custom neurovascular cell isolation procedure. Antibody-conjugated microbeads, mechanical dissociation, and enzymatic dissociation (collogenase II) steps were used.
cDNA libraries were generated with Chromium Single Cell 3’ GEM, Library and Gel Bead Kit V3.1 (10x Genomics)

treatment_protocol:
An experimental C57BL/6 mouse was housed for 14 days in the home cage of a novel, aggressive CD-1 mouse. The mice were separated by a perforated, transparent acrylic partition allowing for continuous olfactory, visual, and auditory sensory exchange between the animals. The partition was removed for 5 minutes each day to allow for agonistic encounters between the mice.
Animals in the HC condition were pair-housed for 14 days in a novel cage permanently separated by a perforated, transparent acrylic partition.

tag: Sex

value: Male

value: Brain

value: Neurovascular Cells

value: WT

value: Home Cage


title: hbca_c81,P57,replicate_1,right,3hr_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c81
surgical sample


title: hbca_c76,P55,replicate_1,left,3hr_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c76
surgical sample


title: P24 Control biol rep2

description: Ribosomal depletion was performed


title: HC1, 14dHC


title: X314, wild type, heart tissue, LCWE treatment

value: Heart tissue

value: LCWE stimulation


title: hbca_c74,P54,replicate_1,left,3hr_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c74
surgical sample


title: ha-h2b-aaasf1-rap040-s46

source_name: yeast cells

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV, HTB2-GGS-HA-Fast-MYC, bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Asf1-FRB::KANMX


title: CSD2, 14dCSD

value: Chronic Social Defeat


title: hbca_c75,P54,replicate_1,right,3hr_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c75
surgical sample


title: P24 Control biol rep1

description: Ribosomal depletion was performed

value: Hair follicle

value: Dermal Papilla (DP) cells

value: Control


title: X54, Mcm8-Ko, heart tissue, LCWE treatment

value: Mcm8 knockout


title: X136, wild type, heart tissue, LCWE treatment


title: X121, wild type, heart tissue, LCWE treatment


title: CSD1, 14dCSD


title: P20 Hdac1/Hdac2 double mutant biol rep3

description: Ribosomal depletion was performed

value: Hdac1/Hdac2 double mutant

value: 20 days Postnatal


title: hbca_c73,P53,replicate_1,right,3hr_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c73
surgical sample

value: breast

value: 10x Genomics 3' V3


title: X108, wild type, heart tissue, LCWE treatment

value: Wild type


title: hbca_c72,P53,replicate_1,left,3hr_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c72
surgical sample


title: X42, Mcm8-Ko, heart tissue, PBS treatment

value: PBS


title: hbca_c70,P52,replicate_1,left,3hr_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c70
surgical sample


title: X107, Mcm8-Ko, heart tissue, PBS treatment


title: hbca_c71,P52,replicate_1,right,3hr_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c71
surgical sample


title: X516, Mcm8-Ko, heart tissue, PBS treatment


title: X47, wild type, heart tissue, LCWE treatment


title: hbca_c69,P51,replicate_1,right,3hr_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c69
surgical sample


title: P20 Control biol rep3

description: Ribosomal depletion was performed


title: P20 Hdac1/Hdac2 double mutant biol rep2

description: Ribosomal depletion was performed


title: P20 Hdac1/Hdac2 double mutant biol rep1

description: Ribosomal depletion was performed


title: sox1a_5dpf

city: Eggenstein-Leopoldshafen

first: sepand

last: Rastegar

address: Hermann-von-Helmholtz-Platz 1

department: Institute of Biological and Chemical Systems-Biological Information Processing (IBCS-BIP)

country: Germany

institute: Karlsruhe Institute of Technology (KIT)

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the 10x genomics' cellranger software version 6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/metrics)
The fastq files were aligned to zebrafish genome (GRCz11) and (ensemble transcripts from Ensembl Release 104) by using STAR. The BAM files were as input for Cell Ranger (10X genmoics) to generate processed data files that include gene names (row names) and cell names (column names) and counts. Further analysis done by using Seurat package in R.
Assembly: GRCz11
Supplementary files format and content: filtered_bc_matrix outputs from Cell Ranger

organism: Danio rerio

source_name: spinal cord

growth_protocol: Zebrafish were kept in the re-circulating system on a 14/10-h light/dark cycle, pH 7.5, at 28 °C (±1 °C) in groups of 20 animals per 2.8 L.

extract_protocol:
Cells from zebrafish spinla cord were dissociated, and sorted by FACS based on the reporter line. The library preparation was performed by 10X Genomics as per manufacture's protocol.
10X genomics

treatment_protocol: No treatment done.

value: spinal cord

tag: time point


title: P20 Control biol rep2

description: Ribosomal depletion was performed


title: hbca_c68,P51,replicate_2,right,3hr_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c68
surgical sample


title: OE_3

city: 上海

first: 玮玮

last: 代

state: 上海

address: 徐汇区东安路131号

institute: 复旦大学

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: U87MG cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: glioma cell lines

value: WT


title: OE_NC_2


title: NC_OE_3

value: IGF2BP3 overexpression


title: OE_2


title: NC_KO_3


title: hbca_c66,P51,replicate_2,left,3hr_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c66
surgical sample


title: OE_NC_3


title: OE_1


title: sox1a_3dpf

description: 10x Genomics


title: hbca_c67,P51,replicate_1,left,3hr_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c67
surgical sample


title: X156, wild type, heart tissue, PBS treatment

value: Heart tissue


title: P20 Control biol rep1

description: Ribosomal depletion was performed


title: X137, wild type, heart tissue, PBS treatment


title: hbca_c65,P50,replicate_2,right,3hr_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c65
surgical sample


title: X123, wild type, heart tissue, PBS treatment


title: sox1a_2dpf

description: 10x Genomics


title: KO_NC_2


title: sox1a_1dpf

description: 10x Genomics


title: KO_3

value: IGF2BP3 knockout


title: X560, wild type, heart tissue, PBS treatment


title: X110, wild type, heart tissue, PBS treatment


title: Pt24_sc

first: Guangshuai

last: Jia

address: Dongfengxi Rd, Yuexiu Campus

institute: Guangzhou Medical University

description:
GBM_recurrent_Neoadjuvant
Raw matrix for Pt24_sc

data_processing:
For data generated with 10x Genomics kits, the Cell Ranger toolkit (v3.0) with the GRCh38 (for human) and mm10 (for mouse) reference genomes was used to align and quantify the reads.
For data generated with Singleron kits, the reads were mapped to the GRCh38 genome using STAR, and gene counts and UMI counts were generated with ‘featureCounts’ software.
To identify the poor-quality/dead/stressed cells, we used the following thresholds: cells with few genes per cell (< 50) or many molecules (UMI counts) per cell (> 30,000) and cells with more than 20% of the counts derived from mitochondrial genes.
Such cells were removed prior to downstream analysis. After quality control, we used the standard analysis pipline of R package Seurat.
Assembly: GRCh38 (for human) and mm10 (for mouse)
Supplementary files format and content: Raw matrix
Supplementary files format and content: Processed Seurat object for scRNA-seq data of 24 GBM patients
Supplementary files format and content: Processed Seurat object for mouse scRNA-seq data

source_name: brain

extract_protocol:
For the samples from Pt1-Pt18 and mouse samples, scRNA-seq was performed using Chromium Single Cell Library Kits (10x Genomics). For the samples from Pt19-Pt24, scRNA-seq was performed with GEXSCOPE Single Cell RNA Library Kits
scRNA-seq was performed using Chromium Single  Cell Library Kits (10x Genomics).

value: brain

tag: age(year)

value: male

value: Neoadjuvant


title: hbca_c64,P50,replicate_1,right,3hr_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c64
surgical sample


title: Pt23_sc

description:
GBM_recurrent_Neoadjuvant
Raw matrix for Pt23_sc


title: KO_2


title: hbca_c63,P50,replicate_2,left,3hr_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c63
surgical sample


title: KO_NC_3


title: hbca_c62,P50,replicate_1,left,3hr_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c62
surgical sample


title: H524, CT2A subcutaneous tumor, WT

data_processing:
Raw reads were processed, and quantification and identification of differentially expressed genes were performed using DEseq2.
Trmmed secuence reads were mapped to mm10
Assembly: mm10
Supplementary files format and content: Processed count table for bulk RNA-seq

extract_protocol:
A total of 5000–20,000 CT2A cells were sampled
Bulk RNA-seq libraries were prepared using Smart-seq2 according to the manufacturer’s protocol

value: CT2A subcutaneous tumor

value: mouse GBM


title: H504, CT2A subcutaneous tumor, Siglece KO

value: Siglece KO


title: KO_1


title: Pt20_sc

description:
GBM_recurrent_Neoadjuvant
Raw matrix for Pt20_sc


title: hbca_c23,P18,replicate_2,both,overnight_digestion

description:
76PE
Read1 26cycles, i7: 8cycles, Read2: 98 cycles.
hbca_c23
surgical sample

value: 10x Genomics 3' end V2


title: Pt19_sc

description:
GBM_recurrent_Neoadjuvant
Raw matrix for Pt19_sc

value: female


title: Pt22_sc

description:
GBM_recurrent_Neoadjuvant
Raw matrix for Pt22_sc


title: Pt21_sc

description:
GBM_recurrent_Neoadjuvant
Raw matrix for Pt21_sc


title: hbca_c59,P49,replicate_2,right,4hr_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c59
surgical sample

value: breast

value: 10x Genomics 3' V3


title: hbca_c58,P48,replicate_1,right,2hr_digstion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c58
surgical sample


title: H511, CT2A subcutaneous tumor, WT


title: hbca_c61,P49,replicate_1,right,4hr_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c61
surgical sample


title: hbca_c24,P19,replicate_1,both,overnight_digestion

description:
76PE
Read1 26cycles, i7: 8cycles, Read2: 98 cycles.
hbca_c24
surgical sample


title: H884, CT2A subcutaneous tumor, Siglece KO


title: H507, CT2A subcutaneous tumor, Siglece KO


title: hbca_c60,P49,replicate_1,left,4hr_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c60
surgical sample


title: Pt18_sc

description:
GBM_recurrent_Neoadjuvant
Raw matrix for Pt18_sc


title: hbca_c22,P18,replicate_1,both,overnight_digestion

description:
76PE
Read1 26cycles, i7: 8cycles, Read2: 98 cycles.
hbca_c22
surgical sample


title: hbca_c15,P12,replicate_2,both,overnight_digestion

description:
76PE
Read1 26cycles, i7: 8cycles, Read2: 98 cycles.
hbca_c15
surgical sample


title: hbca_c57,P48,replicate_1,left,2hr_digstion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c57
surgical sample


title: Pt17_sc

description:
GBM_recurrent_Neoadjuvant
Raw matrix for Pt17_sc


title: hbca_c20,P16,replicate_1,both,overnight_digestion

description:
76PE
Read1 26cycles, i7: 8cycles, Read2: 98 cycles.
hbca_c20
surgical sample


title: hbca_c56,P47,replicate_1,right,2hr_digstion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c56
surgical sample


title: Pt15_sc

description:
GBM_recurrent_Neoadjuvant
Raw matrix for Pt15_sc


title: hbca_c54,P46,replicate_1,right,2hr_digstion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c54
surgical sample


title: H532, CT2A subcutaneous tumor, WT


title: hbca_c14,P12,replicate_1,both,overnight_digestion

description:
76PE
Read1 26cycles, i7: 8cycles, Read2: 98 cycles.
hbca_c14
surgical sample


title: hbca_c19,P15,replicate_1,both,overnight_digestion

description:
76PE
Read1 26cycles, i7: 8cycles, Read2: 98 cycles.
hbca_c19
surgical sample


title: mouse scRNA-seq


title: Pt16_sc

description:
GBM_recurrent_Neoadjuvant
Raw matrix for Pt16_sc


title: hbca_c53,P46,replicate_1,left,2hr_digstion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c53
surgical sample


title: hbca_c55,P47,replicate_1,left,2hr_digstion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c55
surgical sample


title: hbca_c16,P13,replicate_1,both,overnight_digestion

description:
76PE
Read1 26cycles, i7: 8cycles, Read2: 98 cycles.
hbca_c16
surgical sample


title: hbca_c51,P44,replicate_1,right,overnight_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c51
surgical sample


title: hbca_c21,P17,replicate_1,both,overnight_digestion

description:
76PE
Read1 26cycles, i7: 8cycles, Read2: 98 cycles.
hbca_c21
surgical sample


title: Pt11_sc

description:
GBM_recurrent_Neoadjuvant
Raw matrix for Pt11_sc


title: Pt14_sc

description:
GBM_newly_diagnosed
Raw matrix for Pt14_sc


title: Contra 12h

city: Lund

first: Robert

last: Carlsson

address: Sölvegatan 17

department: IKVL

country: Sweden

institute: Lund University

description: S2, Chromium™ Single Cell 3' GEM, Library & Gel Bead Kit v3.1 dual index

data_processing:
The cells from the sequenced data were counted with cell ranger v.5 set to default for contra- or IPSI - 1h, -12h or -24h samples. The individual .h5 - files were aggregated in cell ranger aggr
Assembly: mm10
Supplementary files format and content: Cell Ranger Aggr matrix. Aggregated Cell ranger file with all the conditions in the experiments, e.g,, 1h, 12h or 24h contra- or IPSI-lateral single cells from mouse brain cortex.
Supplementary files format and content: Order of files and cell indentifying suffixes in the matrix:
Supplementary files format and content: 1: Contra 1h
Supplementary files format and content: 2: IPSI 1h
Supplementary files format and content: 3: Contra 12h
Supplementary files format and content: 4: IPSI 12h
Supplementary files format and content: 5: Contra 24h
Supplementary files format and content: 6: IPSI 24h

extract_protocol:
Brain cortex from stroke (penumbra or stroke tissue ,IPSI) or contra (nonstroke corresponding brain cortex tissue area)
According to the 10x Library & Gel Bead Kit v3 single index or Library & Gel Bead Kit v3.1 dual index protocols, respectively

tag: age

value: Endothelial cells, Astrocytes, Oligodendrocytes, Microglia, Immune cells, Pericytes, Neuronal progenitors

value: RGS5::GFP het

value: Contra (stroke)


title: IPSI 1h

description: S2, Chromium™ Single Cell 3' GEM, Library & Gel Bead Kit v3 single index

value: IPSI (stroke)


title: IPSI 12h


title: Contra 1h


title: Pt13_sc

description:
GBM_newly_diagnosed
Raw matrix for Pt13_sc


title: hbca_c17,P13,replicate_2,both,overnight_digestion

description:
76PE
Read1 26cycles, i7: 8cycles, Read2: 98 cycles.
hbca_c17
surgical sample


title: Lung tumor with bleomycin treatment CAFs

first: David

last: DeNardo

address: 660 S Euclid Ave.

institute: Washington University in St. Louis

data_processing:
The generated libraries were sequenced by a NovaSeq 6000 sequencing system (Illumina, San Diego, CA, USA) to an average of 50,000 mean reads per cell. Cellranger mkfastq pipeline (10X Genomics) was used to demultiplex illumina base call files to FASTQ files. Afterward, fastq files from each sample were processed with Cellranger counts and aligned to the mouse mm10 reference genome (Cellranger v.4.0.0, 10X Genomics, mouse reference mm10-2020-A from https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-A.tar.gz) to generate feature barcode matrix.
Assembly: mouse reference mm10-2020-A from https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-A.tar.gz
Supplementary files format and content: Cell barcodes: TSV, features: TSV, expression matrix: MTX

source_name: Lung

extract_protocol:
Mice were euthanized by intracardiac perfusion with 15 mL of PBS-heparin under isoflurane anesthesia. Tissues were manually minced and digested in 20 mL of Hank’s Balanced Salt Solution (Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 2 mg/mL of collagenase A (Roche, Basel, Switzerland) and 1× DNase I (Sigma-Aldrich, St. Louis, MO, USA) for 30 min (20 min for normal tissue) at 37°C with agitation. After digestion, the cell suspensions were quenched with 5 mL of FBS and filtered through 40 μm nylon mesh. The filtered suspensions were then pelleted by centrifugation (1,800 rpm for 4 min at 4°C) and resuspended in flow cytometry buffer [PBS containing 1% bovine serum albumin (BSA) and 5 mM EDTA] as a single cell suspension. Following tissue digestion, single cell suspensions were blocked with rat anti-mouse CD16/CD32 antibodies (eBioscience, Waltham, MA, USA) for 10 min on ice, and pelleted by centrifugation. The cells were subsequently labeled with 100 µL of fluorophore-conjugated anti-mouse extracellular antibodies at recommended dilutions for 30 min on ice in flow cytometry buffer. Cells were then washed and immediately sorted for immune cells (CD45+) or mesenchymal/CAF cells (CD45-, CD31-, EpCAM-) on Aria-II (BD Biosciences). After cells were sorted into FACS buffer, the were pelleted by centrifugation, resuspended in 0.04% BSA in PBS, and cell counts were obtained.
Sorted cells from each sample were submitted to McDonnell Genome Institute at WUSM, where they were encapsulated into droplets and libraries were prepared using Chromium Single Cell 3’v3 Reagent kits according to the manufacturer’s protocol (10x Genomics, Pleasanton, CA, USA). The generated libraries were sequenced by a NovaSeq 6000 sequencing system (Illumina, San Diego, CA, USA) to an average of 50,000 mean reads per cell.

treatment_protocol: KPPL mice were generated by delivering adenovirus Cre-recombinase (University of Iowa, Viral Vector Core Facility) in to the trachea of KP (KrasLSL-G12D;Trp53fl/fl) mice. Single dose administration of either Bleo (1 mg/kg), FITC (3.5 mg/kg), or PBS was intratracheally administered in anesthetized (ketamine/xylazine cocktail) and intubated mice 4 weeks after the administration of adenovirus Cre-recombinase and at least 4 weeks prior to endpoints to allow for ample time for fibrosis to develop and limit the direct effect of these agents on the immune cells within the lung at the time of sacrifice.

value: Lung

value: Cancer-associated fibroblasts (CAFs)

value: KRAS-G12D;Trp53fl/fl; adeno-Cre

value: Lung tumor + bleomycin


title: hbca_c52,P45,replicate_1,right,3hr_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c52
surgical sample


title: Pt12_sc

description:
GBM_recurrent_TMZ+RT
Raw matrix for Pt12_sc

value: brain

value: male

value: TMZ+RT


title: Lung tumor CD45+ Immune cells

value: Immune (CD45+)

value: Lung tumor


title: Lung tumor with bleomycin treatment CD45+ Immune cells


title: hbca_c13,P11,replicate_1,contra,overnight_digestion

description:
76PE
Read1 26cycles, i7: 8cycles, Read2: 126 cycles.
hbca_c13
surgical sample

value: 10x Genomics 3' end V2


title: Pancreatitis CSF1R-CreER tdTomato-negative macrophages

data_processing:
The generated libraries were sequenced by a NovaSeq 6000 sequencing system (Illumina, San Diego, CA, USA) to an average of 50,000 mean reads per cell. Cellranger mkfastq pipeline (10X Genomics) was used to demultiplex illumine base call files to FASTQ files. Afterward, fastq files from each sample were processed with Cellranger counts and aligned to the mouse mm10 reference genome (Cellranger v.4.0.0, 10X Genomics, mouse reference mm10-2020-A from https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-A.tar.gz) to generate feature barcode matrix.
Assembly: mouse reference mm10-2020-A from https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-A.tar.gz
Supplementary files format and content: Cell barcodes: TSV, features: TSV, expression matrix: MTX

source_name: Pancreas

extract_protocol:
Mice were sacrificed by cardiac perfusion with ~10-15mL PBS-heparin under isofluorane anesthesia. Liver, lung, or pancreas tissue was then isolated, minced with scissors, and digested in ~15-25mL Dulbecco’s Modified Eagle Medium (DMEM) with 2mg/mL Collagenase A and 1x DNase I for 25 minutes (lung and liver tissue) at 37°C with constant stirring. Digestion buffer was quenched with 3mL fetal bovine serum (FBS) and filtered through 100uM Nylon mesh, pelleted by centrifugation (2000rmp for 5 min) and resuspended in FACS buffer (1% BSA in PBS). Cells were then resuspended in FACS Buffer containing CD16/CD32 antibodies to block for 10 minutes on ice, pelleted by centrifugation, then resuspended in fluorophore-conjugated antibodies, stained for 25 minutes on ice, then washed with FACS Buffer. Cells were then immediately sorted on Aria-II (BD Biosciences). After cells were sorted into FACS Buffer, they were pelleted by centrifugation, resuspended in 0.04% BSA in PBS, and cell counts were obtained.
Single-cell RNA-sequencing library preparation was then conducted by the Genome Technology Access Center at Washington University. Briefly, cells from each sample were encapsulated into droplets, and libraries were prepared using Chromium Single Cell 3’v3 Reagent kits according to the manufacturer’s protocol (10x Genomics, Pleasanton, CA, USA).

treatment_protocol: For liver metastasis of PDAC cells, hemispleen injection of 500,000 KPC-2 (aka “KP2”) tumor cells was performed using an adapted procedure from published studies. The KP2 cell line was derived from pancreatic tumors of a 6-month-old p48-CRE+/LSL-KRASG12D/p53flox/+ mouse, and tumor cells additionally were modified to express mCherry and click beetle red luciferase. To implant cells in the liver, the mice were anesthetized under continuously-monitored isoflurane, and the spleen was exteriorized from the peritoneal cavity under sterile conditions through a left flank laparotomy. The spleen was ligated using medium titanium Horizon ligation clips (Teleflex, Morrisville, NC) and divided in half. Tumor single-cell suspension in sterile PBS (100 uL), followed by 150uL of sterile PBS flush, was injected into the inferior pole of the spleen with a 30-gauge needle (BD, Franklin Lakes, NJ), monitoring for blanching of the spleen parenchyma and splenic vein to ensure injection efficacy. Once the cells and PBS flush were injected, the splenic vein was ligated, and the inferior pole of the spleen was excised. Once hemostasis was ensured, the peritoneum was closed with 5-0 ligature (Ethicon, Raritan, NJ), and the skin was closed with the AutoClip system (Braintree Scientific, Braintree, MA). Mice were post-operatively monitored and managed per IACUC guidelines for survival surgery. Livers were harvested at day 14 for cell sorting and single cell RNA sequencing analysis. For lung tumors, the KPL86 cell line was derived from lung tissues of the 9-month-old KrasLSL-G12D/p53flox/+ mouse treated with adenovirus-delivered Cre-recombinase. Cells were grown on collagen-coated tissue culture flasks for < 10 passages. To establish orthotopic NSCLC models, 1,000,000 KPL86 cells in 100 μL of phosphate-buffered saline (PBS, Trevigen, Gaithersburg, MD, USA) were retro-orbitally injected into 8–12-week-old Flt3-YFP mice. For steady-state pancreas samples, no treatment was done. For pancreatitis samples, mice were treated with either anti-IgG1 and PBS loaded liposomes, or anti-CSF1 and clodronate loaded liposomes, allowed to recover for 10 days, then pancreatitis was induced by administering 6 hourly intraperitoneal injections (i.e. once per hour for six hours) of cerulein at a dose of 100ug/kg given every other day for one week.  Csf1r-mer-iCre-mer;LSL-tdTomato mice were pulsed with tamoxifen (75mg/kg) dissolved in corn oil on five consecutive days. Mice were then allowed a chase period of 6 weeks, or until blood monocytes lost tdTomato labeling. Following chase period, mice were treated with acute cerulein, then sacrificed for FACS.

value: Pancreas

value: macrophages

value: Pulse-chase with tamoxifen then cerulein to induce pancreatitis


title: hbca_c50,P44,replicate_1,left,overnight_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c50
surgical sample

value: breast

value: 10x Genomics 3' V3


title: Pt9_sc

description:
GBM_newly_diagnosed
Raw matrix for Pt9_sc


title: hbca_c10,P09,replicate_1,contra,overnight_digestion

description:
76PE
Read1 26cycles, i7: 8cycles, Read2: 126 cycles.
hbca_c10
surgical sample


title: Lung tumor CAFs


title: Pt10_sc

description:
GBM_newly_diagnosed
Raw matrix for Pt10_sc

value: female


title: Pt8_sc

description:
GBM_recurrent_TMZ+RT
Raw matrix for Pt8_sc


title: hbca_c11,P10,replicate_1,contra,short_digestion

description:
76PE
Read1 26cycles, i7: 8cycles, Read2: 126 cycles.
hbca_c11
surgical sample


title: Pt6_sc

description:
GBM_recurrent_TMZ+RT
Raw matrix for Pt6_sc


title: hbca_c08,P08,replicate_1,contra,short_digestion

description:
76PE
Read1 26cycles, i7: 8cycles, Read2: 126 cycles.
hbca_c08
surgical sample


title: Pt7_sc

description:
GBM_recurrent_TMZ+RT
Raw matrix for Pt7_sc


title: Pt5_sc

description:
GBM_newly_diagnosed
Raw matrix for Pt5_sc


title: Pancreatitis CSF1R-CreER tdTomato-positive macrophages


title: hbca_c18,P14,replicate_1,both,overnight_digestion

description:
76PE
Read1 26cycles, i7: 8cycles, Read2: 98 cycles.
hbca_c18
surgical sample


title: hbca_c12,P11,replicate_1,contra,short_digestion

description:
76PE
Read1 26cycles, i7: 8cycles, Read2: 126 cycles.
hbca_c12
surgical sample


title: hbca_c07,P07,replicate_1,contra,short_digestion

description:
76PE
Read1 26cycles, i7: 8cycles, Read2: 126 cycles.
hbca_c07
surgical sample


title: Pt3_sc

description:
GBM_recurrent_TMZ+RT
Raw matrix for Pt3_sc


title: Pt4_sc

description:
GBM_newly_diagnosed
Raw matrix for Pt4_sc


title: Lung tumor Flt3-YFP-negative macrophages

value: Flt3-Cre;LSL-YFP (C57BL/6)

value: Lung tumor implantation


title: Pancreatitis fibroblasts with macrophage depletion

value: fibroblasts

value: FVB/NJ

value: aCSF1 + Clodronate loaded liposomes and cerulein to induce pancreatitis


title: hbca_c06,P06,replicate_1,contra,short_digestion

description:
76PE
Read1 26cycles, i7: 8cycles, Read2: 126 cycles.
hbca_c06
surgical sample


title: Steady-state pancreas fibroblasts


title: Pancreatitis fibroblasts

value: IgG + PBS loaded liposomes and cerulein to induce pancreatitis


title: Patient_23_D90_Med

city: Baltimore

first: Carrie

last: McCracken

state: MD

address: 670 W. Baltimore St

department: Institute for Genome Sciences

institute: Institute of Genome

data_processing:
Reads were assessed for quality, trimmed if PHRED scores fell below 20, and any remaining adapter sequences were removed
Processed paired-end reads were aligned to human reference genome GRCh38 using HISAT2, and counts were generated using the HTseq analysis package
Reads that successfully mapped to the reference genome were used for downstream analyses
Assembly: GRCh38
Supplementary files format and content: htseq output with gene counts for each sample

source_name: Peripheral Blood Mononuclear Cells

extract_protocol:
RNA was isolated using QIAzol and the Direct-zol RNA Mini Prep Plus Kit per manufacturer's instructions. RNA quality was assessed using the Agilent Bioanalyzer 2100, and only samples with RNA integrity numbers (RIN) greater than 7 or total RNA concentration greater than 100 ng were selected for RNA sequencing racted using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
PolyA-enriched, strand-specific RNA libraries were constructed and 100bp paired-end reads were sequenced on an Illumina NovaSeq 6000 platform

treatment_protocol: Samples were stimulated with Plasmodium falciparum schizonts, or SEB, or were left unstimulated.

tag: subject

value: Peripheral Blood Mononuclear Cells

value: Media


title: Patient_23_D150_SEB

tag: treatment

value: SEB


title: Patient_23_D150_Pfsz

value: P. falciparum schizonts


title: Patient_23_D150_Med


title: Patient_23_D90_Pfsz


title: Patient_23_D0_Pfsz


title: hbca_c05,P05,replicate_1,contra,short_digestion

description:
76PE
Read1 26cycles, i7: 8cycles, Read2: 126 cycles.
hbca_c05
surgical sample

data_processing:
Basecalls performed using CASAVA version 1.8.1
cellranger 10XRNA Vcellranger-3.1.0 mkfastq
cellranger 10XRNA Vcellranger-3.1.0 count
reads are mapped to hg38
UMI counts are summarized are gene expression levels
Assembly: hg38
Supplementary files format and content: Supplementary_files_format_and_content: H5

extract_protocol:
RNAs are extracted from single cells suspensions
Single cell capture, barcoding and library preparation was performed by following the 10X Genomics Single Cell Chromium 3’ protocol (PN-1000075)

value: 10x Genomics 3' end V2


title: Patient_23_D0_SEB


title: Patient_23_D0_Med


title: Pt1_sc

description:
GBM_newly_diagnosed
Raw matrix for Pt1_sc

value: brain

value: male


title: hbca_c04,P04,replicate_1,contra,short_digestion

description:
76PE
Read1 26cycles, i7: 8cycles, Read2: 126 cycles.
hbca_c04
surgical sample


title: Liver tumor Flt3-YFP-negative macrophages

city: St. Louis

source_name: Liver

value: Liver

value: macrophages

value: Hemispleen tumor implantation


title: hbca_c09,P09,replicate_1,contra,short_digestion

description:
76PE
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c09
surgical sample

source_name: breast

value: breast


title: Patient_26_D150_Pfsz


title: Lung tumor Flt3-YFP-positive macrophages

value: Lung

value: Flt3-Cre;LSL-YFP (C57BL/6)


title: hbca_c02,P02,replicate_1,contra,short_digestion

description:
76PE
Read1 26cycles, i7: 8cycles, Read2: 126 cycles.
hbca_c02
surgical sample


title: Tumor, RegressNP7

city: Iowa City

first: Michael

last: Chimenti

state: IA

address: 431 Newton Road

department: Iowa Institute of Human Genetics

institute: University of Iowa

data_processing:
Reads were processed with ‘bcbio-nextgen.py’ genomics pipeline run in “RNA-seq” mode with the ‘mm10’ key as the selected genome build (internally referencing Ensembl GRCm38.p6 v94, GENCODE M19).
The pipeline aligned reads to the GRCm38 genome using the splice-aware ‘hisat2’ aligner (2.2.1) and concurrently quantified reads to the GENCODE M19 transcriptome using ‘salmon’ (1.4.0) aligner.
Salmon-derived transcript quantifications (TPM) were imported and summarized to estimated counts at the gene level using ‘tximport’ (1.12.3).
Differential gene expression analysis was then conducted with DESeq2 (1.24.0) on estimated gene-level counts using a model conditioned on animal sex and tumor classification factor (‘vehicle’, ‘resistant’, or ‘sensitive’).
Assembly: GRCm38 / GENCODE M19
Supplementary files format and content: flat text, gene counts

source_name: Malignant Peripheral Nerve Sheath Tumor

growth_protocol: Tumors were generated via adenoviral delivery of a cas9 system targeting mouse Nf1 and Cdk2na

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen).
RNA libraries were prepared using TruSeq Stranded mRNA Library Prep (Illumina) kits in accordance with manufacturer guideliens

treatment_protocol: Mice were treated daily with 100 mg/kg Palbociclib + 1 mg/kg Mirdametinib or the vehicle control by oral gavage

value: Malignant Peripheral Nerve Sheath Tumor

tag: strain

value: WT

value: Palbociclib (100 mg/kg) + Mirdametinib (1 mg/kg)

tag: harvest time

value: During Regression


title: Liver tumor Flt3-YFP-positive macrophages

tag: tissue


title: hbca_c03,P03,replicate_1,contra,short_digestion

description:
76PE
Read1 26cycles, i7: 8cycles, Read2: 126 cycles.
hbca_c03
surgical sample

tag: paper participant_number


title: Patient_26_D150_SEB

tag: time

value: Peripheral Blood Mononuclear Cells


title: Patient_26_D150_Med

value: Media


title: ST_Pt18

description: Raw matrix for ST_Pt18

data_processing:
The Space Ranger toolkit (v1.2.1) with GRCh38 reference genomes was used to align and quantify the raw fastq files. Seurat was used to process the Space Ranger output files.
The ST data from individual patients and tumor/para-tumor regions were merged, and the function SCTransform implemented in Seurat was used to normalize the data. Because each ST spot contained several cells, we used the R package SPOTlight28 to deconvolute mixtures of cells using the scRNA-seq data as a reference.
The ST cell types were inferred from the scRNA-seq data, and the proportions of corresponding cell types for each spot were obtained with the NMF regression model.
Assembly: GRCh38 (for human)
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expresion count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json:scalefactors in ison format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png:low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: GBM.spatial.rds: Processed Seurat object for all ST data
Library strategy: Visium Spatial Transcriptomics

extract_protocol:
Cryosections of GBM tissues (10-μm thick) were embedded in OCT using the 2-methylbutane (isobutene) method. Tissue permeabilization for different times (8, 12, 16, or 20 min) was performed, and 16 min permeabilization resulted in the maximum fluorescence signal in both the tumor core and the para-tumor regions. The RNA quality of tissue sections was checked (RIN > 7.0).
ST experiment was performed using Visium Spatial Gene Expression Kits (10x Genomics) following standard manufacturer protocols. The libraries were sequenced on an Illumina HiSeq X Ten sequencer.

value: female

value: Neoadjuvant


title: Pt2_sc

description:
GBM_recurrent_Neoadjuvant
Raw matrix for Pt2_sc


title: ST_Pt17

description: Raw matrix for ST_Pt17


title: Tumor, Regress2L2

tag: genotype


title: Tumor, RegressLL8


title: hbca_c01,P01,replicate_1,contra,short_digestion

description:
76PE
Read1 26cycles, i7: 8cycles, Read2: 126 cycles.
hbca_c01
surgical sample

tag: assay

value: 10x Genomics 3' end V2


title: Tumor, ComboUR14

value: Terminal


title: Patient_26_D90_SEB

value: SEB


title: Patient_26_D90_Med


title: Patient_26_D90_Pfsz

value: P. falciparum schizonts


title: ST_Pt16

description: Raw matrix for ST_Pt16

value: brain

value: male


title: Patient_26_D0_SEB