title: Sample 1 Patient 110 [FLU013075]

value: Bone Marrow

value: Female

value: Normal

value: No

value: WT


title: Sample 1 Patient 112 [FLU014043]

status: Public on Nov 16 2022

type: SRA

city: Pamplona

first: Beñat

last: Ariceta

address: Av. de Pío XII, 55

department: Hemato-Oncology

country: Spain

institute: CIMA

library_source: transcriptomic

data_processing:
Fastq files generated by bcl2fastq v2.20.0
Fastq files aligned using STAR (v2.6.1)
Gene level quantification using Rsubread and Ensembl transcriptome (GRCh38 v92)
Normalization, processing and differential expression analyses were performed using DEseq2
Assembly: GRCh38
Supplementary files format and content: FLUGAZA_Counts.txt: File with raw counts after gene level quantification of all the samples included.

molecule: polyA RNA

organism: Homo sapiens

source_name: Bone Marrow

extract_protocol:
Co-Isolation protocol was performed to extract at the same time DNA and PolyA RNA from the same sample.
Poly-A RNA was selected with Dynabeads Oligo (dT) (Ambion) and reverse-transcribed with AffinityScript Multiple Temperature Reverse Transcriptase (Agilent) using poly-dT oligos carrying a 7 bp-index. Up to 8 samples with similar overall RNA content were pooled together and subjected to linear amplification by IVT using HiScribe T7 High Yield RNA Synthesis Kit (New England Biolabs). Next, aRNA was fragmented into 250-350 bp fragments with RNA Fragmentation Reagents (Ambion) and dephosphorylated with FastAP (Thermo) following manufacturer´s instructions. Partial Illumina adaptor sequences (Jaitin, 2014) were ligated with T4 RNA Ligase 1 (New England Biolabs), followed by a second RT reaction. Full Illumina adaptor sequences were added during final library amplification with KAPA HiFi DNA Polymerase (Kapa Biosystems). RNA-seq libraries quality controls consisted in quantification with Qubit 3.0 Fluorometer (Life Technologies) and size profiles examination with Agilent’s 4200 TapeStation System.

tag: tissue

tag: cell type

value: Leukemic blasts

tag: patient id

tag: age

tag: gender

value: Male

tag: karyotype

value: ND

tag: complex karyotype

value: Sí

tag: treatment

value: AZA


title: Sample 1 Patient 111 [FLU015060]


title: RRc17-RGo9, Day 4, BAL, Gene expression library

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

country: USA

institute: Yerkes National Primate Research Center

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
p21061-s013_RRc17-RGo9_D4_S5.filtered_feature_bc_matrix.h5

library_source: transcriptomic single cell

data_processing:
Sequence reads for each sample were demultiplexed and converted to a count matrix using Cellranger v3.1
Downstream analysis was carried out on Seurat v4.1
Assembly: mmul10
Supplementary files format and content: 10x genomics output of gene expression and HTO barcode counts in sparse matrix ".h5" format

organism: Macaca mulatta

source_name: Bronchoalveolar lavage (BAL)

extract_protocol:
Brochoalveolar lavage (BAL) fluid was collected at baseline (BL) before initiation of treatment or infection of animals, then collected at 2 days post infection (dpi), and, depending on necropsy date, at 4dpi and 7dpi. Lung samples were collected upon necropsy.
Library was prepared using Chromium Single Cell 5ʹ protocol (10x Genomics). Cellular mRNA and hashtag-antibody oligos were reverse-transcribed to generate both the mRNA-derived cDNA (>300bp) and the antibody-derived tagged cDNAs (180bp). These cDNAs were then each prepared for sequencing according to manufacturer instructions. Sequencing was performed on the Illumina NovaSeq 6000 targeting 50k reads/cell for the gene expression libraries and 5k reads/cell for the hashtag-antibody libraries.

treatment_protocol: One group of RMs received a four-day course of IFNmod  (1mg/day, intramuscularly) beginning 1 day prior to infection (day-1) and ending on day 2 post infection while the control group of animals remained untreated

value: Bronchoalveolar lavage (BAL)

tag: timepoint

value: Day 4 post-infection

tag: infection status

value: Untreated (RRc17), Untreated (RGo9)

tag: library type

value: RNA

tag: antibodies/tags


title: RMj8-KV31, Day 4, BAL, Gene expression library

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
p21061_s007_RMj8-KV31_D4_S7.filtered_feature_bc_matrix.h5

value: IFNant (RMj8), IFNant (KV31)


title: RNi17-RZs14, Day 2, BAL, Gene expression library

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
p21061-s019_RNi17-RZs14_D2_S11.filtered_feature_bc_matrix.h5

value: Day 2 post-infection

value: IFNant (RNi17), IFNant (RZs14)


title: RMs8-CD68, Day 4, BAL, Gene expression library

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
p21061_s006_RMs8-CD68_D4_S6.filtered_feature_bc_matrix.h5

value: Untreated (RMs8), Untreated (CD68)


title: LG92-LC10, Day 2, BAL, Gene expression library

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
p21061-s018_LG92-LC10_D2_S10.filtered_feature_bc_matrix.h5

value: Untreated (LG92), Untreated (LC10)


title: Sample 1 Patient 109 [FLU014057]

value: Bone Marrow

value: Female

value: Normal

value: Mutated

value: FLUGA


title: Sample 1 Patient 108 [FLU013018]

value: Leukemic blasts

value: Male

value: No

value: WT


title: RCk17-RRj11, Day 2, BAL, Gene expression library

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
p21061-s012_RCk17-RRj11_D2_S4.filtered_feature_bc_matrix.h5

value: Bronchoalveolar lavage (BAL)

value: IFNant (RCk17), IFNant (RRj11)


title: RRc17-RGo9, Day 2, BAL, Gene expression library

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
p21061-s011_RRc17-RGo9_D2_S3.filtered_feature_bc_matrix.h5

value: Untreated (RRc17), Untreated (RGo9)

value: RNA


title: WT-MA9_RNA_DMSO_d4_Rep3

city: New York

first: Douglas

last: Barrows

state: NY

address: 1230 York Ave

institute: Rockefeller University

data_processing:
Transcript abundance was computed from FASTQ files using Salmon (v0.8.2) and the GENCODE reference transcript sequences, transcript counts were imported into R with the tximport R Bioconductor package, and differential gene expression was determined with the DESeq2 R Bioconductor package
Genome_build: mm10/hg38
Supplementary_files_format_and_content: Counts tables contain the raw counts quantified by Salmon and DESeq2.

molecule: total RNA

organism: Mus musculus

source_name: WT-MA9 leukemia cells

growth_protocol: Cells were maintained in Iscove's Modified Dulbecco's Medium (IMDM,Gibco) supplemented with 15% fetal bovine serum (Sigma-Aldrich), Penicillin-Streptomycin, L-Glutamine, IL6, IL3, SCF. Cells were harvested four days after being treated with Menin-MLL inhibitor in this same media composition.

extract_protocol:
NEBNext Ultra II RNA
Leukemia cells were treated with either vehicle or Menin-MLL inhibitor for 4 days. Cells were harvested, washed with PBS, and flash frozen in liquid nitrogen. RNA was isolated using QIAGEN RNeasy kit. NEBNext Ultra II RNA Library Prep Kit was used with 1ug of total RNA for construction of sequencing libraries.

tag: cell line

value: Acute myeloid leukemia

tag: genotype

value: Stably expressing pMSCV-MLL-AF9-GFP

value: DMSO


title: WT-MA9_RNA_DMSO_d4_Rep2


title: Sample 1 Patient 107 [FLU014020]

value: Sí

value: AZA


title: RMj8-KV31, Day 2, BAL, Gene expression library

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
p21061_s005_RMj8-KV31_D2_S13.filtered_feature_bc_matrix.h5

value: Day 2 post-infection

value: IFNant (RMj8), IFNant (KV31)


title: WT-MA9_RNA_DMSO_d4_Rep1


title: WT-MA9_RNA_MI-503_d4_Rep3


title: LG92-LC10, Baseline, BAL, Gene expression library

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
p21061-s016_LG92-LC10_BL_S8.filtered_feature_bc_matrix.h5

value: Baseline

value: Uninfected

value: Untreated (LG92), Untreated (LC10)


title: RNi17-RZs14, Baseline, BAL, Gene expression library

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
p21061-s017_RNi17-RZs14_BL_S9.filtered_feature_bc_matrix.h5

value: IFNant (RNi17), IFNant (RZs14)


title: Sample 1 Patient 106 [FLU010043]

value: Bone Marrow

value: Leukemic blasts

value: Male

value: Normal

value: No

value: Mutated

value: FLUGA


title: WT-MA9_RNA_MI-503_d4_Rep2

value: Acute myeloid leukemia

value: Stably expressing pMSCV-MLL-AF9-GFP


title: RCk17-RRj11, Baseline, BAL, Gene expression library

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
p21061_s010_RCk17-RRj11_BL_S2.filtered_feature_bc_matrix.h5

value: Bronchoalveolar lavage (BAL)

value: IFNant (RCk17), IFNant (RRj11)

value: RNA


title: cDNA5253_SNPC69

city: Monrovia

first: Ajay

last: Goel

state: California

address: 1218 S. Fifth Avenue

department: Molecular Diagnostics and Experimental Therapeutics

institute: Beckman Research Institute of City of Hope

data_processing:
Illumina’s small RNA-seq 3' adapters were removed by Cutadapt software
Clean reads were aligned to hg38 dataset and annotated using “microRNA.subset.of.GENCODE.V24.gtf”.
The mapping of the sequenced reads and read count determination of the final miRNAs was undertaken using STARaligner algorithm.
Assembly: mm10
Supplementary files format and content: tab-delimited text files

source_name: surgical specimens

extract_protocol:
Total RNA was isolated using AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) as per the manufacturer’s recommendation.
Library construction for miRNAs was performed using the TruSeq Small RNA Kit (Illumina) with up to 200ng of total RNA input.

value: surgical specimens

value: female

tag: location

value: left

tag: differentiation

tag: t stage

tag: n stage

tag: Stage

tag: recurrence

value: no

tag: rfs month


title: WT-MA9_RNA_MI-503_d4_Rep1

tag: cell type


title: RRc17-RGo9, Baseline, BAL, Gene expression library

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
p21061_s009_RRc17-RGo9_BL_S1.filtered_feature_bc_matrix.h5

tag: tissue

value: Baseline

value: Uninfected

value: Untreated (RRc17), Untreated (RGo9)


title: Sample 1 Patient 105 [FLU016083]

value: Bone Marrow

value: Leukemic blasts

tag: patient id

tag: age

tag: gender

value: Female

tag: karyotype

value: ND

tag: complex karyotype

value: WT


title: cDNA5244_SNPC1


title: Sample 2 Patient 104 [FLU013067]

value: Male

value: Abnormal

value: No

value: Sí

tag: treatment

value: FLUGA


title: cDNA5043_SNPC65

value: surgical specimens

value: male


title: CD68, Baseline, BAL, Gene expression library

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
p21061_s002_CD68-GR1_BL_S10.filtered_feature_bc_matrix.h5

value: Bronchoalveolar lavage (BAL)

tag: timepoint

tag: infection status

value: Untreated

tag: library type

value: RNA

tag: antibodies/tags


title: RMs8, Baseline, BAL, Gene expression library

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
p21061_s001_RMs8-GR1_BL_S9.filtered_feature_bc_matrix.h5

value: Baseline

value: Uninfected


title: RMj8-KV31, Baseline, BAL, Gene expression library

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
p21061_s003_RMj8-KV31_BL_S11.filtered_feature_bc_matrix.h5

value: IFNant (RMj8), IFNant (KV31)


title: G059 LC10 G3 CTL 7

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

data_processing:
Read quality for each sample was first assessed with FASTQC
Globin and rRNA reads were filtered out using bowtie2v2.4.2
Remaining reads were alligned to the hg19 genome using STARv2.7.5a
Gene counts were calculated with HTSeqv0.13.5
Assembly: Mmu10 Ensembl v100

source_name: whole blood

extract_protocol:
Beckman RNAdvance Blood
mRNA Library Prep for RNA from Whole Blood Using KAPA HyperPrep Reagents

treatment_protocol: 18 RMs were infected with SARS-CoV-2 (USA-WA/2020 strain) intratracheally and intranasally. To investigate the role of type I IFN in SARS-CoV-2 pathogenesis, 9 of these RMs received a four-day course of IFNmod  (1mg/day, intramuscularly) beginning 1 day prior to infection (day-1) and ending on day 2 post infection while the remaining 9 control animals were untreated. Animals were necropsied at 2 days post infection (dpi), 4dpi, or 7dpi. 2.5mL whole blood was collected from the femoral veins of RMs into PAXgene RNA tubes (PreAnalytiX) at pre-infection baseline (-6dpi) and at days 1, 2, 4, 5 and 7dpi depending on necropsy date. PAXgene RNA Tubes were inverted multiple times to ensure adequate mixing, stored at -20C overnight, and transferred to -80C for long term storage.

value: Control

tag: animalid

tag: time

value: Day 7


title: Sample 1 Patient 104 [FLU013066]

value: Bone Marrow

value: Leukemic blasts


title: G060 LC10 G3 CTL 5

value: Day 5


title: Sample 1 Patient 103 [FLU017011]

value: Male

value: Abnormal

value: WT

value: Mutated


title: cDNA5041_SNPC54

value: surgical specimens

tag: location

value: left

tag: differentiation

tag: t stage

tag: n stage

tag: Stage

value: no


title: cDNA5042_SNPC6

tag: tissue

value: female

tag: recurrence

value: yes

tag: rfs month


title: RMs8-CD68, Day 2, BAL, Gene expression library

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
p21061_s004_RMs8-CD68_D2_S12.filtered_feature_bc_matrix.h5

value: Bronchoalveolar lavage (BAL)

value: Day 2 post-infection

value: Untreated (RMs8), Untreated (CD68)

value: RNA


title: G058 RZs14 G3 IFN 5

value: IFNmod


title: G057 RZs14 G3 IFN 7

value: Day 7


title: Sample 1 Patient 102 [FLU012032]

value: Bone Marrow

tag: cell type

value: Leukemic blasts

tag: patient id

tag: age

tag: gender

value: Female

tag: karyotype

value: Normal

value: No

value: Sí

value: AZA


title: G055 LC10 G3 CTL 4

tag: treatment

value: Control

value: Day 4


title: Sample 1 Patient 101 [FLU013047]

value: Male

value: ND

tag: complex karyotype

value: Mutated

value: WT

value: FLUGA


title: cDNA5039_SNPC389

value: surgical specimens

value: male

value: left

value: yes


title: G054 RNi17 G3 IFN 4

value: IFNmod

tag: animalid


title: G053 LG92 G3 CTL 4

tag: time


title: Sample 1 Patient 100 [FLU014073]

value: Bone Marrow

value: Leukemic blasts


title: G052 LG92 G3 CTL 2

value: Day 2


title: G051 RNi17 G3 IFN 2


title: cDNA5038_SNPC390

tag: location

value: right


title: G050 LC10 G3 CTL 2


title: G049 RZs14 G3 IFN 2


title: Sample 1 Patient 98 [FLU014064]


title: G056 RZs14 G3 IFN 4


title: Sample 1 Patient 96 [FLU016071]

value: Abnormal

value: Yes

value: AZA


title: Sample 1 Patient 97 [FLU012086]

value: Male

value: Normal

value: No


title: G047 LC10 G3 CTL D1

value: Control

value: Day 1


title: G048 RZs14 G3 IFN D1


title: cDNA5040_SNPC2

value: surgical specimens

tag: differentiation

value: no


title: Sample 1 Patient 95 [FLU013060]

value: Female

value: WT

value: FLUGA


title: cDNA5034_SNPC75

value: female

value: left

tag: t stage


title: cDNA5036_SNPC391

value: male

tag: n stage

value: yes


title: G043 LC10 G3 CTL BL

value: Baseline


title: G045 LG92 G3 CTL D1


title: cDNA5037_SNPC186

tag: Stage


title: cDNA5035_SNPC51

tag: tissue


title: G044 RZs14 G3 IFN BL

value: IFNmod


title: G046 RNi17 G3 IFN D1


title: cDNA5033_SNPC24

value: right

tag: recurrence


title: G042 RNi17 G3 IFN BL


title: G041 LG92 G3 CTL BL


title: Sample 1 Patient 94 [FLU010083]

value: Bone Marrow

value: Leukemic blasts

value: ND


title: G039 RGo9 G2 CTL 7

value: Control

value: Day 7


title: G040 RRj11 G2 IFN 7


title: Sample 1 Patient 93 [FLU013023]

value: Male

value: Normal

value: No

value: Mutated


title: cDNA5032_SNPC36

value: surgical specimens

value: no

tag: rfs month


title: G037 RGo9 G2 CTL 5

value: Day 5


title: Sample 1 Patient 92 [FLU013005]

tag: cell type

value: Female

value: Abnormal

value: WT

value: AZA


title: G038 RRj11 G2 IFN 5

value: IFNmod


title: Sample 1 Patient 99 [FLU013040]

value: Bone Marrow

tag: patient id

value: FLUGA


title: cDNA5030_SNPC61

tag: age

value: female

value: right


title: G034 RCk17 G2 IFN 4

value: Day 4


title: G036 RRj11 G2 IFN 4


title: G035 RGo9 G2 CTL 4

value: Control


title: cDNA5029_SNPC63

tag: gender

value: left


title: Sample 1 Patient 91 [FLU012014]

value: Leukemic blasts

tag: karyotype

value: No

value: Sí


title: G033 RRc17 G2 CTL 4

tag: treatment


title: G032 RRj11 G2 IFN 2

value: Day 2


title: G031 RGo9 G2 CTL 2


title: cDNA5028_SNPC12

value: surgical specimens

value: male

value: no


title: Sample 1 Patient 88 [FLU015090]

value: Male

value: ND

tag: complex karyotype

value: WT

value: Mutated


title: Sample 1 Patient 89 [FLU008076]

value: Bone Marrow

value: Normal

value: AZA


title: cDNA5026_SNPC40

value: right


title: G030 RCk17 G2 IFN 2

value: IFNmod

tag: animalid


title: cDNA5027_SNPC21

value: left


title: G027 RGo9 G2 CTL D1

value: Control

tag: time

value: Day 1


title: cDNA5025_SNPC62

value: female

tag: location


title: G026 RCk17 G2 IFN D1


title: Sample 1 Patient 87 [FLU012083]

value: Leukemic blasts

value: Female

value: Abnormal

value: Yes

value: FLUGA


title: G025 RRc17 G2 CTL D1


title: cDNA5031_SNPC386

value: surgical specimens

value: male

tag: differentiation

value: yes


title: G024 RRj11 G2 IFN BL

value: Baseline


title: G023 RGo9 G2 CTL BL


title: Sample 1 Patient 90 [FLU012041]

value: Bone Marrow

value: Normal

value: No

value: WT

value: Mutated


title: G021 RRc17 G2 CTL BL

value: Control


title: G022 RCk17 G2 IFN BL

value: IFNmod


title: Sample 1 Patient 85 [FLU012050]

value: ND


title: G020 KV31 G1 IFN 7

value: Day 5


title: Sample 1 Patient 86 [FLU014068]

value: Leukemic blasts

value: Male


title: G029 RRc17 G2 CTL 2

value: Day 2


title: Sample 2 Patient 87 [FLU012084]

value: Female

value: Abnormal

value: Yes

value: FLUGA


title: Sample 1 Patient 84 [FLU011085]

value: Sí

value: AZA


title: G019 CD68 G1 CTL 7


title: G028 RRj11 G2 IFN D1

value: Day 1


title: G017 CD68 G1 CTL 5


title: G018 KV31 G1 IFN 5


title: G016 KV31 G1 IFN 4

value: Day 4


title: cDNA5021_SNPC3

value: surgical specimens

value: male

value: left

tag: t stage

value: yes


title: cDNA5020_SNPC47

value: female

value: right

tag: n stage

value: no


title: Sample 1 Patient 83 [FLU011090]

value: Bone Marrow

value: Leukemic blasts

value: Male

value: Normal

value: No

value: ND


title: G015 CD68 G1 CTL 4

value: Control


title: cDNA5019_SNPC350

tag: Stage


title: Sample 1 Patient 82 [FLU011063]

tag: tissue

value: WT

value: Mutated

value: AZA


title: G014 RMj8 G1 IFN 4

value: IFNmod

value: Day 4


title: G013 RMs8 G1 CTL 4


title: Sample 2 Patient 81 [FLU010086]

value: Abnormal

value: FLUGA


title: cDNA5024_SNPC67

value: surgical specimens

value: female

value: left

tag: recurrence

value: yes


title: G012 KV31 G1 IFN 2

value: Day 2


title: cDNA5023_SNPC5

value: right

value: no

tag: rfs month


title: cDNA5018_SNPC37


title: G011 CD68 G1 CTL 2


title: cDNA5022_SNPC4


title: G010 RMj8 G1 IFN 2


title: G009 RMs8 G1 CTL 2


title: cDNA5017_SNPC185

value: male


title: Sample 1 Patient 80 [FLU008052]

value: Bone Marrow

tag: cell type

value: Leukemic blasts

value: Male

value: Normal

value: No


title: Sample 1 Patient 81 [FLU010085]

tag: patient id

value: WT

value: Mutated


title: G008 KV31 G1 IFN D1

value: IFNmod

value: Day 1


title: cDNA5016_SNPC362

value: surgical specimens

tag: age


title: G007 CD68 G1 CTL D1

value: Control


title: Sample 1 Patient 79 [FLU015065]

tag: gender

value: Abnormal

value: ND

value: FLUGA


title: cDNA5015_SNPC341

value: female

value: left


title: G006 RMj8 G1 IFN D1


title: G004 KV31 G1 IFN BL

value: Baseline


title: G003 CD68 G1 CTL BL


title: Sample 2 Patient 78 [FLU011050]

value: Bone Marrow

value: Female

tag: karyotype


title: Sample 1 Patient 78 [FLU011049]

value: Leukemic blasts

tag: treatment


title: cDNA5014_SNPC52

value: male

value: yes


title: cDNA5013_SNPC64

value: no


title: G001 RMs8 G1 CTL BL


title: G002 RMj8 G1 IFN BL


title: Sample 1 Patient 77 [FLU016060]

value: Normal

tag: complex karyotype

value: No

value: WT

value: Mutated

value: Sí

value: AZA


title: Sample 1 Patient 76 [FLU014001]

value: ND


title: p21258-s026_14D002_BAL_2021-10-22_D-4

data_processing:
Illumina bcl2fastq v2.20.0.422 was used for demultiplexing.
Reads were aligned using STAR v2.7.3a.(Dobin et al.)
Transcript abundance was estimated in STAR during alignment using the algorithm of htseq-count (Anders et al., 2015)
Assembly: Mmul_10/rheMac10
Supplementary files format and content: csv file with raw read counts per gene for each Sample

source_name: BAL

extract_protocol:
PBMCs: Whole blood was collected from the femoral vein in EDTA tubes. Peripheral blood mononuclear cells (PBMCs) were isolated from whole blood using a Ficoll-Paque Premium density gradient and resuspended in R10 media. For bulk RNAseq, 250,000 PBMCs were frozen in 700uL of QIAzol.; BAL: To collect BAL, a fiberoptic bronchoscope was used to administer 0.9% NaCl solution into the bronchus and re-aspirate the BAL fluid. BAL was then filtered through a 70μm cell strainer and centrifuged. Following centrifugation, BAL fluid supernatant was removed and the remaining cell pellet was lysed in ACK lysing buffer and resuspended in R10. For bulk RNAseq, 50,000 BAL cells were frozen in 700uL of QIAzol. For 10X, ~125,000 BAL cells from each animal were incubated with one of five TotalSeq-C anti human Hashtags. Following a 30 minute incubation, cells were washed with PBS, filtered with a 40uM cell filter, and resuspended in R10.
Ten nanograms of total RNA was used as input for cDNA synthesis using the Clontech SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio). Amplified cDNA was fragmented and appended with dual-indexed bar codes using the NexteraXT DNA Library Preparation kit (Illumina).

value: BAL

tag: day post infection

tag: day post treament

value: BL

tag: infection

value: Not-Infected

value: IFNmod


title: p21258-s027_14D002_BAL_2021-10-26_D0


title: p21258-s025_14D002_PBMC_2021-10-28_D2

source_name: PBMC

value: PBMC


title: Sample 1 Patient 75 [FLU009047]

value: Bone Marrow

value: Male

value: Abnormal


title: cDNA5010_SNPC56

value: surgical specimens

value: male

tag: location

value: left

tag: differentiation

value: yes


title: Sample 1 Patient 74 [FLU012023]

value: Leukemic blasts

value: Female

value: WT


title: p21258-s022_14D002_PBMC_2021-10-22_D-4


title: p21258-s024_14D002_PBMC_2021-10-27_D1


title: cDNA5009_SNPC377

value: right

tag: t stage

tag: n stage


title: p21258-s023_14D002_PBMC_2021-10-26_D0


title: p21258-s021_RUy14_BAL_2021-10-28_D2


title: Sample 2 Patient 73 [FLU011077]

tag: tissue

value: Yes

value: Mutated

value: AZA


title: G005 RMs8 G1 CTL D1

value: Control

tag: animalid

tag: time

value: Day 1


title: cDNA5008_SNPC72

tag: Stage

tag: recurrence

value: no

tag: rfs month


title: p21258-s020_RUy14_BAL_2021-10-26_D0

tag: cell type

value: BAL

value: Not-Infected

value: IFNmod


title: Sample 1 Patient 73 [FLU011076]

value: Bone Marrow

tag: patient id

tag: age

tag: gender

tag: karyotype

value: Abnormal


title: cDNA5006_SNPC18

value: surgical specimens

value: male

value: left


title: p21258-s018_RUy14_PBMC_2021-10-28_D2

value: PBMC

tag: day post infection

tag: day post treament

tag: treatment


title: p21258-s017_RUy14_PBMC_2021-10-27_D1

tag: infection


title: cDNA5012_SNPC68

tag: location

tag: differentiation

tag: t stage


title: cDNA5005_SNPC42

tag: tissue

tag: n stage


title: p21258-s016_RUy14_PBMC_2021-10-26_D0


title: p21258-s028_14D002_BAL_2021-10-28_D2


title: p21258-s015_RUy14_PBMC_2021-10-22_D-4

value: BL


title: p21258-s013_RCh15_BAL_2021-10-26_D0


title: cDNA5004_SNPC77

value: right

tag: Stage

value: yes


title: WT-MA9_UtxWT_RNA_MI-503_d4_Rep2

tag: cell line

value: Acute myeloid leukemia

tag: genotype

value: Stably expressing pMSCV-MLL-AF9-GFP, lenti-Cas9-Blast, pUSEPB-sgChr8


title: p21258-s019_RUy14_BAL_2021-10-22_D-4

tag: cell type


title: cDNA5011_SNPC71

value: female

tag: recurrence

tag: rfs month


title: cDNA5002_SNPC46

tag: age

tag: gender


title: p21258-s010_RCh15_PBMC_2021-10-27_D1

tag: day post infection


title: p21258-s012_RCh15_BAL_2021-10-22_D-4

tag: day post treament


title: Sample 1 Patient 70 [FLU011038]

value: Leukemic blasts

tag: patient id

value: Female

tag: karyotype

tag: complex karyotype

value: No

value: WT

value: Mutated

value: Sí

tag: treatment

value: AZA


title: p21258-s011_RCh15_PBMC_2021-10-28_D2

tag: infection

value: Not-Infected

value: IFNmod


title: Sample 1 Patient 71 [FLU009051]

tag: tissue

value: Bone Marrow

value: Male

value: Normal

value: FLUGA


title: Sample 1 Patient 69 [FLU013089]

value: ND


title: Sample 1 Patient 68 [FLU014047]


title: p21258-s008_RCh15_PBMC_2021-10-22_D-4

value: PBMC

value: BL


title: p21258-s009_RCh15_PBMC_2021-10-26_D0


title: cDNA5001_SNPC76

value: surgical specimens

value: male

tag: location

value: left

tag: differentiation

tag: t stage

tag: n stage

value: yes


title: p21258-s006_RLo15_BAL_2021-10-26_D0

tag: cell type

value: BAL


title: p21258-s004_RLo15_PBMC_2021-10-28_D2


title: p21258-s005_RLo15_BAL_2021-10-22_D-4


title: p21258-s003_RLo15_PBMC_2021-10-27_D1


title: p21258-s007_RLo15_BAL_2021-10-28_D2


title: Sample 1 Patient 66 [FLU008032]

value: Leukemic blasts

value: Female

value: WT


title: cDNA4999_SNPC57

tag: Stage

tag: recurrence

value: no


title: p21258-s014_RCh15_BAL_2021-10-28_D2

value: Not-Infected

value: IFNmod


title: Sample 1 Patient 67 [FLU012080]

value: Bone Marrow

tag: age

value: Male

value: Mutated

value: AZA


title: p21258-s002_RLo15_PBMC_2021-10-26_D0

value: PBMC


title: cDNA4998_SNPC73

tag: gender

tag: rfs month


title: p21258-s001_RLo15_PBMC_2021-10-22_D-4

tag: day post infection

tag: day post treament

value: BL


title: Sample 1 Patient 65 [FLU016057]

tag: patient id

tag: karyotype

value: Abnormal

value: No


title: cDNA5003_SNPC11

value: surgical specimens

value: female

value: right


title: p21232-s048-RAz8_BAL_D2

value: BAL

value: Infected

tag: treatment


title: p21232-s047-RAz8_BAL_D-11

tag: infection


title: cDNA4997_SNPC32

tag: tissue

value: poor

value: yes


title: p21232-s046-RAz8_PBMC_D2


title: p21232-s045-RAz8_PBMC_D1


title: cDNA5000_SNPC26

value: male

tag: location


title: p21232-s044-RAz8_PBMC_D0

value: IFNmod


title: p21232-s043-RAz8_PBMC_D-11


title: cDNA4996_SNPC81

tag: differentiation

value: no


title: cDNA4995_SNPC19

value: left

tag: t stage


title: Sample 1 Patient 63 [FLU011021]

value: Bone Marrow

value: Leukemic blasts

value: Male

value: ND

tag: complex karyotype


title: cDNA4994_SNPC44

tag: n stage


title: Sample 2 Patient 62 [FLU008012]

tag: cell type

value: Female

value: Normal

value: WT

value: Sí

value: Mutated

value: AZA


title: p21232-s042-RCd8_BAL_D2

value: BAL

value: Infected

value: Control


title: p21232-s041-RCd8_BAL_D-11

value: BL


title: p21232-s040-RCd8_PBMC_D2

value: PBMC


title: p21232-s039-RCd8_PBMC_D1


title: p21232-s038-RCd8_PBMC_D0


title: cDNA4993_SNPC60

value: surgical specimens

value: male

tag: Stage

tag: recurrence

value: no


title: cDNA4992_SNPC192

tag: age

tag: gender

value: left

value: yes


title: Sample 1 Patient 61 [FLU010079]

value: Bone Marrow

value: Leukemic blasts

value: Male

value: Abnormal

value: Yes


title: Sample 2 Patient 61 [FLU010080]

value: WT


title: p21232-s036-X17_BAL_D2

tag: day post infection

value: IFNmod


title: cDNA4991_SNPC366

value: female

tag: rfs month


title: Sample 1 Patient 64 [FLU011031]

tag: patient id

value: Female

value: Normal

value: No

value: ND

value: FLUGA


title: cDNA4990_SNPC98

value: surgical specimens


title: Sample 1 Patient 60 [FLU010047]

tag: karyotype


title: p21232-s034-X17_PBMC_D2

value: PBMC

tag: day post treament

value: Infected

tag: treatment


title: p21232-s033-X17_PBMC_D1

tag: infection


title: p21232-s032-X17_PBMC_D0


title: p21232-s031-X17_PBMC_D-10

value: BL


title: Sample 1 Patient 62 [FLU008011]

tag: tissue

value: Bone Marrow

value: Sí

value: Mutated

value: AZA


title: Sample 1 Patient 58 [FLU011048]

value: Leukemic blasts


title: cDNA4989_SNPC50

value: male

tag: location

value: left

tag: differentiation

value: yes


title: cDNA4988_SNPC369

value: female

tag: t stage


title: p21232-s030-RAa17_BAL_D2

value: BAL

value: Control


title: p21232-s037-RCd8_PBMC_D-11


title: Sample 1 Patient 57 [FLU010055]

value: Female

value: Normal

tag: complex karyotype

value: No

value: ND


title: p21232-s028-RAa17_PBMC_D2

tag: cell type

value: PBMC

value: Infected


title: p21232-s029-RAa17_BAL_D-10

value: BL


title: cDNA4987_SNPC393

value: surgical specimens

tag: n stage

tag: Stage

value: no


title: Sample 1 Patient 72 [FLU011046]

value: Bone Marrow

tag: age

value: Male

value: WT

value: AZA


title: p21232-s026-RAa17_PBMC_D0


title: cDNA4986_SNPC112

tag: gender

value: left

tag: recurrence

value: yes


title: Sample 1 Patient 56 [FLU008006]

value: Leukemic blasts

value: Abnormal

value: Mutated

value: FLUGA


title: p21232-s027-RAa17_PBMC_D1

tag: day post infection

value: Control


title: Sample 1 Patient 55 [FLU008031]

tag: patient id

value: Yes


title: cDNA4985_SNPC79

value: female

tag: rfs month


title: p21232-s024-LD22_BAL_D2

value: BAL

tag: day post treament

value: Infected

value: IFNmod


title: p21232-s023-LD22_BAL_D-6

value: BL

tag: treatment


title: cDNA4984_SNPC35

value: surgical specimens

value: no


title: p21232-s022-LD22_PBMC_D2

value: PBMC

tag: infection


title: Sample 1 Patient 59 [FLU016044]

tag: tissue

value: Bone Marrow

value: Male

tag: karyotype

value: Normal

value: No

value: WT

value: AZA


title: p21232-s035-X17_BAL_D-10


title: Sample 2 Patient 54 [FLU007037]

value: Leukemic blasts

value: Abnormal

value: Mutated


title: 2DCellLine-Control3

city: Lexington

first: Fan

last: Chen

state: Kentucky

address: 1095 V.A. Drive, HSRB 461

department: Toxicology and Cancer Biology

institute: University of Kentucky

data_processing:
Sequencing and base-calling were performed by University of Kentucky Genomics core and BGI (Beijing Genomics Institute), respectively.
Sequencing reads were trimmed and filtered using Trimmomatic (V0.39) to remove adapters and low quality reads. Reads from human and mouse samples were mapped to Ensembl GRCh38 and GRCm38 transcripts annotation (release 82), respectively, using RSEM (v1.3.2) and STAR (2.6.1d) with default settings.
Genome_build: GRCh38, GRCm38 release 82
Supplementary_files_format_and_content: tab-delimited text files including TPM, FPKM and expected_count for each gene

source_name: Mouse lung tumor

growth_protocol: Murine 2D lung tumor cells were propagated in 100-mm dishes with maintained in DMEM F-12 media with 10% fetal bovine serum, 1% Insulin-Transferrin-Selenium, 4mM L-glutamine and penicillin/streptomycin. Murine 3D lung tumor cells were propagated in DMEM/F12 media containing 1x penicillin/streptomycin, 4mM L-glutamine, 10% fetal bovine serum, 10µg/mL Insulin, 1x Insulin/transferrin/selenium mixture, 12.5µg/mL bovine pituitary extract, 0.1µg/mL cholera toxin, 25 ng/mL mEGF and 25 ng/mL rmFGF2, mixed 1:1 with growth factor-reduced Matrigel, and pipetted into a 24-well 0.4 µm Transwell insert. Human 2D cells H460, H2030 and BEAS2B were propagated in 100-mm dishes with maintained in RPMI-1640 media with 10% fetal bovine serum, 4mM L-glutamine and penicillin/streptomycin. Human 2D cells HBEC3KT were propagated in gelatin pre-coated 100-mm dishes with PneumaCult-Ex Basal media with 1X PneumaCult-Ex Supplement media, Hydrocortisone and penicillin/streptomycin.

extract_protocol:
RNA from treated cell lines was extracted using Absolutely RNA Microprep (2D cell and total tumor) or Nanoprep (sorted tumor and 3D spheroid) kits (Agilent).
RNA libraries were prepared for sequencing using BGI or TruSeq standard Illumina protocols or the Smart-SeqII low-input protocol (sorted tumors).

treatment_protocol: Murine in vivo allografts were treated with DMSO (vehicle) or 50mg/kg JQ1 i.p. for 10 consecutive days prior to harvest. Murine in vitro 3D spheroids and 2D cells were treated with DMSO (vehicle) or 25nM JQ1 for 10-12 days.

tag: model system

value: in vitro 2D cell

tag: genotype

value: Ezh2 null

value: DMSO

tag: donor mouse/cell line

tag: seq platform

value: BGI std/DNBSEQ


title: cDNA4983_SNPC15

value: female

tag: location

value: left

tag: differentiation

tag: t stage

tag: n stage


title: Sample 1 Patient 53 [FLU010074]

tag: cell type

tag: age

tag: gender

tag: complex karyotype

value: Sí


title: 2DCellLine-JQ1-treated3


title: 2DCellLine-JQ1-treated2

value: Ezh2 heterozygous


title: Sample 1 Patient 54 [FLU007036]

value: Bone Marrow

tag: patient id

value: Yes


title: p21232-s021-LD22_PBMC_D1

value: PBMC

tag: day post infection

tag: day post treament

value: Infected

tag: treatment

value: IFNmod


title: p21232-s020-LD22_PBMC_D0

tag: infection


title: p21232-s025-RAa17_PBMC_D-10

value: BL

value: Control


title: cDNA4982_SNPC49

tag: tissue

value: surgical specimens

value: male

tag: Stage

tag: recurrence

value: no

tag: rfs month


title: Sample 1 Patient 51 [FLU008023]

value: Leukemic blasts

value: Male

tag: karyotype

value: Abnormal

value: No

value: ND

value: WT

value: AZA


title: cDNA4981_SNPC191

value: female

tag: location

value: left

tag: differentiation


title: Sample 1 Patient 52 [FLU013010]

value: Bone Marrow

value: Mutated


title: cDNA4980_SNPC74

tag: t stage

tag: n stage


title: 2DCellLine-JQ1-treated1

tag: model system

value: in vitro 2D cell

tag: genotype

value: Ezh2 wild-type

tag: donor mouse/cell line

tag: seq platform

value: BGI std/DNBSEQ


title: p21232-s018-KV30_BAL_D2

tag: cell type

value: BAL

tag: day post infection

value: Infected

value: Control


title: 2DCellLine-Control1

tag: treatment

value: DMSO


title: cDNA4979_SNPC96

value: surgical specimens

tag: age

tag: gender

value: male

value: no


title: p21232-s017-KV30_BAL_D-6

value: BL

tag: day post treament

tag: infection


title: Sample 1 Patient 49 [FLU012089]

tag: tissue

value: Leukemic blasts

tag: patient id

value: Male

value: Abnormal

tag: complex karyotype

value: No

value: WT

value: FLUGA


title: 2DCellLine-Control2

value: in vitro 2D cell

value: Ezh2 heterozygous


title: 3DOrganoid-JQ1-treated3

value: in vitro 3D spheroid

value: Ezh2 null

value: BGI std/DNBSEQ


title: p21232-s016-KV30_PBMC_D2

value: PBMC

value: Infected

value: Control


title: Sample 1 Patient 48 [FLU007001]

value: Bone Marrow

value: Female

tag: karyotype

value: Yes

value: Mutated

value: AZA


title: Sample 1 Patient 50 [FLU009036]

value: Leukemic blasts

value: Male

value: ND


title: 3DOrganoid-Control3

value: DMSO


title: cDNA4977_SNPC365

value: surgical specimens

value: male

tag: location

value: left

tag: differentiation

tag: t stage

tag: Stage

tag: recurrence

value: yes

tag: rfs month


title: cDNA4978_SNPC372

value: right

tag: n stage


title: Sample 2 Patient 47 [FLU008089]

tag: cell type

value: Normal

value: No

value: WT


title: p21232-s015-KV30_PBMC_D1

value: PBMC

tag: day post infection

value: Infected

tag: treatment

value: Control


title: cDNA4976_SNPC7

tag: age

tag: gender

value: female


title: Sample 1 Patient 47 [FLU008088]

value: Bone Marrow

value: Mutated

value: AZA


title: p21232-s019-LD22_PBMC_D-6

value: BL

tag: day post treament

tag: infection

value: IFNmod


title: cDNA4975_SNPC78

tag: tissue

value: surgical specimens

value: no


title: 3DOrganoid-JQ1-treated2

tag: model system

value: in vitro 3D spheroid

tag: genotype

value: Ezh2 heterozygous

tag: donor mouse/cell line

tag: seq platform

value: BGI std/DNBSEQ


title: p21232-s013-KV30_PBMC_D-6


title: Sample 1 Patient 45 [FLU008001]

value: Leukemic blasts

tag: patient id

value: Male

tag: karyotype

value: Normal

tag: complex karyotype

value: Sí


title: 3DOrganoid-Control2

value: DMSO


title: cDNA4974_SNPC33

value: male

tag: location

value: left

tag: differentiation

tag: t stage

tag: Stage

tag: recurrence

tag: rfs month


title: Sample 1 Patient 44 [FLU008016]

value: Bone Marrow

tag: cell type

tag: age

tag: gender

value: Female

value: Abnormal

value: No

value: WT

tag: treatment

value: FLUGA


title: MP06-hVM-6wks

city: Lund

first: Petter

last: Storm

address: Sölvegatan 19, BMC A11

department: Developmental and Regenerative Neurobiology

country: Sweden

institute: Lund University

data_processing:
Basecalling using bcl2fastq 2.19
Cell Ranger pipeline (10x Genomics, Cellranger count v2) with default parameters  and GrCh38 as the reference genome
Seurat (v 3.1 and R version 3.6.1) was applied to the scRNA-data for downstream analysis of matrix files.
Genome_build: GrCH38
Supplementary_files_format_and_content: Count matrix, csv

source_name: human ventral midbrain, 6 weeks PC

growth_protocol: Human fetal tissues were collected from 6–11 week PC legally terminated embryos at Malmö Hospital (Malmö, Sweden) and Addenbrooke’s Hospital (Cambridge, U.K.). Ethical approval for the use of postmortem human fetal tissue was provided by the Swedish National Board of Health and Welfare under existing guidelines, including informed consent from women seeking abortions, and by the National Research Ethics Service Committee East of England - Cambridge Central (Local Research Ethics Committee, reference no. 96/085).

extract_protocol:
For 10x Genomics single cell RNA sequencing,  single cell suspensions were loaded onto 10x Genomics Single Cell 3′ Chips along with the mastermix as per the manufacturer’s protocol
According to 10X protocols.

treatment_protocol: Tissue from both Sweden and U.K. was dissected in HIBERNATE media (Thermo Fisher Scientifica). A narrow sub-dissection of the human VM was performed, and the tissue was washed in phosphate-buffered saline (PBS) solution. After 3 washes, the tissue was treated with Accutase (PAA Laboratories) for 20 min at 37°C degrees. After incubation, mechanical dissociation generated single-cell suspensions, and the cells were plated at a density of 70,000 cells/well (36,842 cells/cm2) in culture media. Culture media used was formulated as follows: Neurobasal Medium, 2 nM L-glutamine, 100 µg/mL pen/strep, 20 ng/ml BDNF, 10 ng/ml GDNF, 0.2 mM AA, 1/3 B27. The culture media was supplemented with Y-27632 (10 µM) to improve cell survival on the plating day. A total of 1% minimum essential medium-non essential amino acids (MEM-NEAA) and 0.1% 2-mercaptoethanol were added to the culture media from day 14. 3D cultures were generated using U-bottom-shaped ultra-low attachment 96-well plates (Corning). Droplets of Matrigel were applied to allow embedding at day 30 to sustain long-term cultures. At the time of embedding, 3D hVM cultures were transferred into ultra-low attachment 24-well plates (Corning). 3D cultured organoids used for calcium imaging were left attached on glass coverslips coated with polyornithine, fibronectin, and laminin at day 90.

tag: tissue

value: ventral midbrain

tag: culture condition

tag: time


title: p21232-s014-KV30_PBMC_D0

value: PBMC

tag: day post infection

tag: day post treament

tag: infection

value: Infected

value: Control


title: 3DOrganoid-Control1

tag: model system

value: in vitro 3D spheroid

tag: genotype

value: Ezh2 wild-type

tag: donor mouse/cell line

tag: seq platform

value: BGI std/DNBSEQ


title: 3DOrganoid-JQ1-treated1


title: p21232-s010-RZq10_PBMC_D2

value: IFNmod


title: Allograft-JQ1-treated1

value: in vivo allograft

value: Ezh2 null


title: p21232-s012-RZq10_BAL_D2

value: BAL


title: Sample 1 Patient 43 [FLU007014]

value: Bone Marrow

value: Leukemic blasts

tag: patient id

value: Male

tag: karyotype

value: Normal

tag: complex karyotype

value: Mutated

value: AZA


title: Allograft-Control1

value: DMSO


title: MP04-hVM-7wks-aggr-d14

source_name: human ventral midbrain, 14 days 3D culture

value: ventral midbrain

value: 14 days in culture


title: p21232-s009-RZq10_PBMC_D1

tag: cell type

value: PBMC

value: Infected


title: Sample 1 Patient 42 [FLU011016]

tag: age

value: Abnormal

value: No

value: WT


title: TotalTumor-null7

value: in vivo total tumor

value: BGI std/DNBSEQ


title: MP03-hVM-8wks

source_name: human ventral midbrain, 8 weeks PC


title: p21232-s008-RZq10_PBMC_D0

value: IFNmod


title: Sample 2 Patient 41 [FLU010024]

value: Bone Marrow

tag: gender

value: FLUGA


title: MP02-hVM-10-5wks

source_name: human ventral midbrain, 10.5 weeks PC


title: p21232-s007-RZq10_PBMC_D-6

value: BL

tag: treatment


title: TotalTumor-null5

value: Ezh2 null

value: TruSeq std/HiSeq


title: Sample 1 Patient 46 [FLU008028]

tag: tissue

value: Leukemic blasts

value: Female

value: Normal

value: Sí

value: Mutated


title: p21232-s011-RZq10_BAL_D-6

value: BAL

value: Infected


title: MP01-hVM-11-5wks

source_name: human ventral midbrain, 11.5 weeks PC

value: ventral midbrain

tag: culture condition


title: TotalTumor-null6


title: p21232-s006-RRo9_BAL_D2

value: Control


title: MP05-hVM-7wks-aggr-d30

source_name: human ventral midbrain, 30 days 3D culture

tag: time

value: 30 days in culture


title: hVM3Dday147weeks


title: TotalTumor-null4

value: in vivo total tumor

value: BGI std/DNBSEQ


title: Sample 2 Patient 39 [FLU009013]

value: Bone Marrow

value: Male

value: No

value: WT

value: AZA


title: p21232-s005-RRo9_BAL_D-6

tag: day post infection

value: BL


title: Sample 1 Patient 40 [FLU007006]

value: Leukemic blasts

value: Female

value: ND

value: FLUGA


title: hVM2Dday307weeks

source_name: human ventral midbrain, 30 days 2D culture


title: Sample 1 Patient 39 [FLU009012]

value: Normal

value: Mutated

value: Sí


title: TotalTumor-null2

value: Ezh2 null

value: TruSeq std/HiSeq


title: Sample 1 Patient 38 [FLU008084]


title: p21232-s004-RRo9_PBMC_D2

value: PBMC

tag: day post treament

value: Infected

value: Control


title: p21232-s003-RRo9_PBMC_D1

tag: infection


title: hVM2096d30

value: ventral midbrain

value: 30 days in culture


title: TotalTumor-null1

tag: model system

value: in vivo total tumor


title: Sample 1 Patient 37 [FLU007084]

value: Bone Marrow

value: Male

value: Abnormal

value: No

value: WT


title: p21232-s002-RRo9_PBMC_D0


title: TotalTumor-het6

tag: genotype

value: Ezh2 heterozygous

value: BGI std/DNBSEQ


title: Sample 2 Patient 36 [FLU006019]

value: Leukemic blasts

value: Normal

value: Mutated

value: FLUGA


title: hVM2096d14

source_name: human ventral midbrain, 14 days 2D culture

value: 14 days in culture


title: p21232-s001-RRo9_PBMC_D-6

value: PBMC

value: BL

value: Infected


title: hVM2096aggrd30

value: ventral midbrain

value: 30 days in culture


title: TotalTumor-het5

value: in vivo total tumor

tag: donor mouse/cell line


title: Sample 2 Patient 70 [FLU011039]

value: Bone Marrow

value: Female

value: Sí

value: AZA


title: Sample 1 Patient 36 [FLU006018]

value: Male

value: No

value: WT


title: Sample 1 Patient 41 [FLU010023]

value: Leukemic blasts

value: Normal


title: TotalTumor-null3

value: Ezh2 null

tag: seq platform

value: TruSeq std/HiSeq


title: hVM2015aggrd14

value: 14 days in culture


title: Sample 2 Patient 35 [FLU010066]

tag: patient id

value: Abnormal

value: Yes

value: Mutated


title: p21094-s113_RZs14-BAL-Day4-2021-04-16

value: BAL

value: Infected

value: IFNmod


title: TotalTumor-het4

value: in vivo total tumor

value: Ezh2 heterozygous

value: BGI std/DNBSEQ


title: TotalTumor-het3


title: Sample 1 Patient 35 [FLU010065]

value: Bone Marrow

value: Female

tag: karyotype

value: AZA


title: TotalTumor-het2


title: p21094-s112_RZs14-BAL-Day2-2021-04-14


title: p21094-s114_RZs14-BAL-Day7-2021-04-19


title: p21094-s111_RZs14-BAL-Day-7-2021-04-06

value: BL


title: Sample 1 Patient 34 [FLU009039]

value: Leukemic blasts

value: Male

tag: complex karyotype

value: No

value: WT

value: FLUGA


title: p21094-s110_LC10-BAL-Day7-2021-04-19

tag: cell type

value: Control


title: hVM2Dday147weeks

value: ventral midbrain

value: 14 days in culture


title: Sample 1 Patient 33 [FLU009005]

tag: age

value: Abnormal

value: Yes

value: Mutated


title: T24-NT4_S15

city: Yuseong-gu

first: Seung Woo

last: Baek

state: Daejeon

address: Gwahak-ro 125

country: South Korea

institute: Korea Research Institute Biology & Biotechnology

description: replicate 3

data_processing:
Reference genome indexing and read mapping of samples were performed using STAR software (ver. 2.6.1a).
FeatureCounsts (ver. 1.6.2) was used to calculate genereated binary alignment map (BAM) files.
The read counts per million fragments mapped (CPM) of each samples were used to estimate the expression level of each gene.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample

growth_protocol: T24 and Phase3, phase7, phase 15, gemcitabine-resistant T24 bladder cancer cells were cultured in DMEM supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin antibiotics solution. All of the cells were maintained at 37˚C with 5% CO2.

extract_protocol:
RNA samples for sequencing were isolated using the Qiagen RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol. Total RNA isolation was performed in a reverse transcription reaction with poly(dT) primers using PrimeScriptTM reverse transcriptase (TAKARA, Shiga, Japan) according to the manufacturer’s protocol. The library’s quality and quantity were measured by a Nanodrop spectrophotometer (ND-1000; Thermo Scientific, Waltham, MA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cell line

tag: phase

value: Bladder cancer


title: T24-NT3_S14

description: replicate 4

tag: tissue


title: T24-NT2_S13

description: replicate 1


title: p21094-s109_LC10-BAL-Day4-2021-04-16

value: BAL

value: Infected

tag: treatment


title: p21094-s108_LC10-BAL-Day2-2021-04-14


title: Sample 1 Patient 32 [FLU006087]

value: Bone Marrow

tag: gender

value: Female

value: ND


title: T24-1-P7-NT3_S10

description: replicate 4


title: TotalTumor-WT4

value: in vivo total tumor

value: Ezh2 wild-type

value: TruSeq std/HiSeq


title: TotalTumor-WT6

value: BGI std/DNBSEQ


title: p21094-s107_LC10-BAL-Day-7-2021-04-06

tag: day post infection

value: BL


title: T24-1-P7-NT4_S11

description: replicate 3


title: TotalTumor-WT5


title: TotalTumor-WT3


title: Sample 2 Patient 30 [FLU005001]

value: Leukemic blasts

value: Male

value: No

value: WT

value: FLUGA


title: T24-1-P7-NT1_S8

description: replicate 2


title: Sample 3 Patient 30 [FLU005002]

value: Abnormal


title: T24-1-P7-NT2_S9

description: replicate 1

value: Bladder cancer


title: p21094-s105_RNi17-BAL-Day2-2021-04-14

value: BAL

tag: day post treament

value: IFNmod


title: T24-NT1_S12

description: replicate 2


title: Sample 1 Patient 31 [FLU010031]

value: Bone Marrow

value: Yes

value: Mutated


title: TotalTumor-WT7

value: in vivo total tumor


title: T24-1-P3-NT3_S12

description: replicate 4


title: TotalTumor-het1

value: Ezh2 heterozygous


title: TotalTumor-WT2

value: Ezh2 wild-type

value: TruSeq std/HiSeq


title: Sample 2 Patient 29 [FLU008049]

value: Female

value: ND

value: AZA


title: Sample 1 Patient 30 [FLU004025]

value: Leukemic blasts

value: Male

value: No


title: TotalTumor-WT1


title: p21094-s103_LG92-BAL-Day4-2021-04-16

tag: infection

value: Infected

value: Control


title: p21094-s104_RNi17-BAL-Day-7-2021-04-06

value: BAL

value: BL


title: T24-1-P3-NT4_S13

description: replicate 3

value: Bladder cancer


title: Sample 1 Patient 29 [FLU008048]

value: Bone Marrow

value: WT


title: 2DCell-null3

tag: model system

value: in vitro 2D cell

value: Ezh2 null


title: Sample 2 Patient 28 [FLU005006]

value: Normal

value: Mutated


title: p21094-s102_LG92-BAL-Day2-2021-04-14


title: T24-1-P3-NT2_S11

description: replicate 1


title: 2DCell-null2

tag: genotype

value: TruSeq std/HiSeq


title: Sample 1 Patient 28 [FLU005005]

value: Female


title: 2DCell-null1

tag: donor mouse/cell line


title: p21094-s100_RRj11-BAL-Day7-2021-04-05

value: IFNmod


title: p21094-s101_LG92-BAL-Day-7-2021-04-06


title: p21094-s099_RRj11-BAL-Day4-2021-04-02


title: T24-1-P15-NT4_S9

description: replicate 3


title: T24-1-P15-NT2_S7

description: replicate 2


title: Sample 1 Patient 27 [FLU006048]

value: Leukemic blasts

value: FLUGA


title: 2DCell-null6

tag: seq platform

value: BGI std/DNBSEQ


title: Sample 2 Patient 26 [FLU009073]

tag: patient id

value: Male

value: Abnormal

value: No

value: Sí

value: AZA


title: p21094-s098_RRj11-BAL-Day2-2021-03-31

value: BAL

value: Infected


title: 2DCell-null5

value: in vitro 2D cell


title: T24-1-P15-NT1_S16

description: replicate 1

value: Bladder cancer


title: 2DCell-null4

value: Ezh2 null


title: T24-1-P3-NT1_S1

description: replicate 2


title: p21094-s097_RRj11-BAL-Day-7-2021-03-23

value: BL


title: MF3_unsorted_gray_matter

city: Los Angeles

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

data_processing:
Basecalls/demultiplexing performed using Illumina CASAVA 1.8.2
Aligned to Hg38 using STAR2.4.0
Count read using HT-seq0.6.1 using Hg38 RefSeq as reference
Normalization by FPKM
Genome_build: Hg38
Supplementary_files_format_and_content: excel file with raw and normalized counts for each sample

source_name: GBM

extract_protocol:
Trizol
Library was constructed using NuenOvation RNA Ultra Low Input kit and Illumina's TruSeq Nano.

value: GBM


title: Sample 1 Patient 25 [FLU009026]

source_name: Bone Marrow

value: Bone Marrow

value: Female

tag: karyotype

value: Yes

value: Mutated

value: WT


title: p21094-s096_RGo9-BAL-Day7-2021-04-05

value: Control


title: p21094-s106_RNi17-BAL-Day4-2021-04-16

value: IFNmod


title: 2DCell-null7

value: BGI std/DNBSEQ


title: T24-1-P15-NT3_S8

description: replicate 4


title: Sample 1 Patient 24 [FLU007068]

value: Leukemic blasts

value: Male

value: ND

tag: complex karyotype


title: p21094-s095_RGo9-BAL-Day4-2021-04-02

tag: cell type

value: BAL

value: Infected


title: 2DCell-het6

value: in vitro 2D cell

value: Ezh2 heterozygous


title: p21094-s094_RGo9-BAL-Day2-2021-03-31


title: Sample 2 Patient 23 [FLU007078]

tag: age

value: Abnormal

value: FLUGA


title: p21094-s093_RGo9-BAL-Day-7-2021-03-23

value: BL


title: MF2_unsorted_gray_matter

value: GBM


title: 2DCell-het4


title: Sample 1 Patient 23 [FLU007077]

value: Bone Marrow

value: Female

value: Yes


title: 2DCell-het5


title: Sample 1 Patient 26 [FLU009072]

value: No

value: WT

value: Sí

value: Mutated

value: AZA


title: Sample 2 Patient 22 [FLU004003]

value: Leukemic blasts

value: Normal


title: M4F1_unsorted_white_matter


title: MF3_unsorted_white_matter


title: p21094-s092_RCk17-BAL-Day4-2021-04-02

value: BAL

value: Infected

value: IFNmod


title: p21094-s091_RCk17-BAL-Day2-2021-03-31


title: M4F1_unsorted_gray_matter


title: 2DCell-het3

value: in vitro 2D cell

value: Ezh2 heterozygous

value: BGI std/DNBSEQ


title: 2DCell-het1

value: TruSeq std/HiSeq


title: M4_tumor_endothelial

value: GBM


title: p21094-s090_RCk17-BAL-Day-7-2021-03-23

value: BL


title: Sample 1 Patient 22 [FLU004002]

value: Bone Marrow

value: Female


title: 2DCell-het2


title: Sample 1 Patient 21 [FLU008039]

value: Male

value: No

value: WT


title: M2_tumor_endothelial


title: MF2_unsorted_white_matter


title: 2DCell-WT2

value: Ezh2 wild-type


title: Sample 2 Patient 27 [FLU006049]

value: Leukemic blasts

value: Mutated

value: FLUGA


title: M2_tumor_A2B5plus


title: 2DCell-WT3


title: p21094-s089_RRc17-BAL-Day4-2021-04-02

value: BAL

value: Infected

value: Control


title: 2DCell-WT9

value: in vitro 2D cell


title: p21094-s088_RRc17-BAL-Day2-2021-03-31


title: Sample 1 Patient 20 [FLU004022]

value: Normal

value: ND

value: AZA


title: Sample 1 Patient 19 [FLU006052]

value: Abnormal


title: p21094-s087_RRc17-BAL-Day-7-2021-03-23

value: BL


title: M1_tumor_endothelial

value: GBM


title: Sample 1 Patient 18 [FLU005023]

value: Bone Marrow

value: Female


title: 2DCell-WT1

value: BGI std/DNBSEQ


title: p21094-s085_KV31-BAL-Day4-2021-03-19

value: IFNmod


title: Sample 1 Patient 17 [FLU006032]

value: Leukemic blasts

value: Male

value: No

value: WT


title: 437_tumor_unsorted


title: p21094-s086_KV31-BAL-Day7-2021-03-22

value: BAL

value: Infected


title: Sample 2 Patient 16 [FLU002002]

value: Mutated

value: FLUGA


title: 437_tumor_endothelial


title: p21094-s084_KV31-BAL-Day2-2021-03-17


title: p21094-s083_KV31-BAL-Day-7-2021-03-08


title: Sample 1 Patient 16 [FLU002001]


title: 2DCell-WT8

value: in vitro 2D cell

value: Ezh2 wild-type


title: 2DCell-WT6


title: 2DCell-WT5


title: 427_tumor_endothelial


title: p21094-s082_CD68-BAL-Day7-2021-03-22

value: Control


title: Sample 1 Patient 14 [FLU007040]

value: Normal

value: ND

value: AZA


title: p21094-s081_CD68-BAL-Day4-2021-03-19


title: 427_tumor_A2B5plus

value: GBM


title: Sample 1 Patient 13 [FLU008070]

value: Bone Marrow

value: Sí


title: 425_tumor_unsorted


title: 2DCell-WT4

value: BGI std/DNBSEQ


title: p21094-s080_CD68-BAL-Day2-2021-03-17


title: Sample 1 Patient 12 [FLU006063]

value: Leukemic blasts

value: Male

value: Abnormal

value: Yes


title: 2DCell-WT7


title: M1_tumor_A2B5plus


title: p21094-s079_CD68-BAL-Day-7-2021-03-08

value: BAL

value: BL

value: Infected


title: 3DOrganoid-null-outlier2

value: in vitro 3D spheroid

value: Ezh2 null


title: 425_tumor_A2B5plus


title: Sample 1 Patient 15 [FLU002015]

value: WT


title: 3DOrganoid-null6


title: Sample 3 Patient 11 [FLU004007]

value: Mutated

value: FLUGA


title: 421_tumor_unsorted


title: Sample 2 Patient 11 [FLU004006]


title: 427_tumor_unsorted


title: Sample 1 Patient 11 [FLU004005]


title: 3DOrganoid-null5


title: 421_tumor_endothelial


title: p21094-s077_RMj8-BAL-Day2-2021-03-17

value: IFNmod


title: p21094-s078_RMj8-BAL-Day4-2021-03-19


title: p21094-s076_RMj8-BAL-Day-7-2021-03-08


title: 3DOrganoid-null4


title: 3DOrganoid-null-outlier1

value: UK1036 early passage


title: p21094-s075_RMs8-BAL-Day4-2021-03-19

value: Control


title: 3DOrganoid-null3


title: 3DOrganoid-null2


title: 419_tumor_endothelial

value: GBM


title: 419_tumor_unsorted


title: p21094-s074_RMs8-BAL-Day2-2021-03-17


title: Sample 2 Patient 10 [FLU003018]

value: Bone Marrow

value: Female

value: No

value: AZA


title: Sample 1 Patient 10 [FLU003017]

value: Leukemic blasts

value: Abnormal


title: Sample 1 Patient 9 [FLU004014]

value: Male

value: Sí


title: 425_tumor_endothelial


title: 409_tumor_unsorted


title: p21094-s073_RMs8-BAL-Day-7-2021-03-08

value: BAL

value: BL

value: Infected


title: 409_tumor_endothelial


title: Sample 1 Patient 8 [FLU008035]

value: Mutated

value: WT


title: 3DOrganoid-het6

value: in vitro 3D spheroid

value: Ezh2 heterozygous

value: BGI std/DNBSEQ


title: 409_tumor_A2B5plus

value: GBM


title: p21094-s072_RZs14-PBMC-Day7-2021-04-19

value: PBMC

value: IFNmod


title: Sample 1 Patient 7 [FLU001010]

value: Bone Marrow

value: Yes


title: p21094-s071_RZs14-PBMC-Day5-2021-04-17


title: 3DOrganoid-het5


title: Sample 3 Patient 6 [FLU001023]

value: Leukemic blasts

value: Normal

value: No

value: AZA


title: Sample 2 Patient 6 [FLU001021]

value: Male


title: 408_tumor_unsorted


title: p21094-s070_RZs14-PBMC-Day4-2021-04-16


title: 3DOrganoid-het3


title: p21094-s069_RZs14-PBMC-Day2-2021-04-14


title: Sample 1 Patient 6 [FLU001020]


title: 3DOrganoid-het2


title: 408_tumor_A2B5plus


title: p21094-s068_RZs14-PBMC-Day1-2021-04-13


title: 3DOrganoid-null1

value: Ezh2 null


title: Sample 2 Patient 5 [FLU006026]

value: Female

value: Abnormal

value: FLUGA


title: 407_tumor_unsorted


title: 3DOrganoid-het1

value: in vitro 3D spheroid


title: p21094-s067_RZs14-PBMC-Day0-2021-04-12

value: Infected


title: Sample 1 Patient 5 [FLU006025]

value: Mutated

value: WT


title: 407_tumor_endothelial

value: GBM


title: p21094-s066_RZs14-PBMC-Day-7-2021-04-06

value: PBMC

value: BL

value: IFNmod


title: 3DOrganoid-WT8

value: Ezh2 wild-type

value: BGI std/DNBSEQ


title: Sample 2 Patient 4 [FLU001017]

value: Bone Marrow

value: Leukemic blasts

value: Normal

value: No


title: 3DOrganoid-WT7


title: Sample 1 Patient 4 [FLU001016]

value: Female

value: AZA


title: 3DOrganoid-het4

value: Ezh2 heterozygous


title: p21094-s064_LC10-PBMC-Day5-2021-04-17

value: Control


title: 3DOrganoid-WT5

value: in vitro 3D spheroid


title: Sample 2 Patient 3 [FLU002011]

value: Male

value: Abnormal

value: Yes

value: Mutated


title: 408_tumor_endothelial

value: GBM


title: p21094-s063_LC10-PBMC-Day4-2021-04-16

value: PBMC

value: Infected


title: Sample 1 Patient 3 [FLU002010]

value: WT


title: 3DOrganoid-WT3

value: Ezh2 wild-type

value: BGI std/DNBSEQ


title: IL7 expanded B cell progenitors, IP,  Lin28b, biol rep 2

first: Joan

last: Yuan

address: Klinikgatan 17

description:
FPKM Input Lin28b#1,FPKM IP Lin28b#1,FPKM Input Lin28b#2,FPKM IP Lin28b#2,FPKM Input Littermate control,FPKM IP Littermate control
Lin28b_2 Input

data_processing:
Reads were aligned using STAR aligner v2.7.1 and counted using RSEM v.1.28.
Assembly: mm10
Supplementary files format and content: Gene FPKM (rows) for all samples of indicated sample type and genotype (columns)

source_name: Bone marrow

growth_protocol: Co-housed tet-Lin28b and a littermate control mouse was sacrificed for isolating bone marrow

extract_protocol:
Lin28b Lin28b and  co-immunoprecipitated  RNA  using  Magna  RIP  RNA-Binding  Protein Immunoprecipitation kit (Millipore,cat#17-700) according to the manufacturer’s instructions.
RNA was extracted using RNAzol  (Sigma-Aldrich,cat#R4533)  and  Direct-zol  RNA  MicroPrep  kit  (Zymo  Research, cat#R2060).
20ng of total RNA was used for the cDNA synthesis and amplification with the SMART-Seq v4 Ultra Low Input RNA   Kit   for   Sequencing   (Takara,   cat#634889)   in   accord   with   the   protocol.
Library agmentation and indexing was performed using Nextera XT DNA Kit (Illumina,cat#FC-121-1030) and Nextera XT v2 set A Indexing kit (Illumina,cat#15052163).

treatment_protocol: Bone marrow was isolated from back limbs and sternum, red blood cells were lysed (ACK lysis buffer), and resulting sample was plated to remove the adherent cell fraction before being plated in IL-7 (20 ng/mL) and doxycycline (0.1 mg/mL) containing whole RPMI medium.

value: Bone marrow

value: Ex vivo expanded B cell progenitors from adult mouse bone marrow

value: Doxycycline (0.1 mg/mL) and IL-7 (20 ng/mL) for 5 days


title: IL7 expanded B cell progenitors, input,  Littermate control, biol rep 1

description:
FPKM Input Lin28b#1,FPKM IP Lin28b#1,FPKM Input Lin28b#2,FPKM IP Lin28b#2,FPKM Input Littermate control,FPKM IP Littermate control
Littermate_1 IP

value: Littermate control


title: p21094-s062_LC10-PBMC-Day2-2021-04-14


title: p21094-s061_LC10-PBMC-Day1-2021-04-13


title: IL7 expanded B cell progenitors, IP,  Lin28b, biol rep 1

description:
FPKM Input Lin28b#1,FPKM IP Lin28b#1,FPKM Input Lin28b#2,FPKM IP Lin28b#2,FPKM Input Littermate control,FPKM IP Littermate control
Lin28b_1 Input


title: Sample 1 Patient 2 [FLU007019]

value: Bone Marrow

value: Leukemic blasts

value: Female

value: No

value: AZA


title: 407_tumor_A2B5plus


title: Sample 2 Patient 1 [FLU007032]

value: Abnormal

value: Yes


title: p21094-s065_LC10-PBMC-Day7-2021-04-19

value: Control


title: Sample 1 Patient 1 [FLU007031]

value: Mutated


title: 3DOrganoid-WT1

value: in vitro 3D spheroid


title: IL7 expanded B cell progenitors, input,  Lin28b, biol rep 1

description:
FPKM Input Lin28b#1,FPKM IP Lin28b#1,FPKM Input Lin28b#2,FPKM IP Lin28b#2,FPKM Input Littermate control,FPKM IP Littermate control
Lin28b_1 IP


title: p21094-s059_LC10-PBMC-Day-7-2021-04-06

value: PBMC

value: BL

value: Infected


title: Sortedtumors-null3

value: in vivo sorted tumor

value: Ezh2 null

value: Smart seqII/DNBSEQ


title: IL7 expanded B cell progenitors, IP,  Littermate control, biol rep 1

description:
FPKM Input Lin28b#1,FPKM IP Lin28b#1,FPKM Input Lin28b#2,FPKM IP Lin28b#2,FPKM Input Littermate control,FPKM IP Littermate control
Littermate_1 Input

value: Bone marrow

value: Ex vivo expanded B cell progenitors from adult mouse bone marrow

value: Littermate control

value: Doxycycline (0.1 mg/mL) and IL-7 (20 ng/mL) for 5 days


title: 3DOrganoid-WT2

value: Ezh2 wild-type

value: BGI std/DNBSEQ


title: s4.786O.DKO.c47.3

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: set 4, 786O cell line, double knockout clone c47, replicate 3

data_processing:
RNA-Seq data analysis was done with bowtie2 and rsem (ver. 1.2.3) using EBV genome version hg19
DESeq2 was used for differentail expression analysis
Assembly: hg19
Supplementary files format and content: Prosessed files contains the raw counts for all genes

source_name: 786O cell line

extract_protocol:
RNA was extracted with Trizol (Invitrogen) for all RNA preparations, then subsequently cleaned and DNase treated using RNeasy columns (Qiagen)
Sequencing library preparation was then completed using the QuantSeq 3’-mRNA kit (Lexogen) to generate Illumina-compatible sequencing libraries according to the manufacturer’s instructions

tag: set

tag: cell line

tag: knockout

value: DKO

tag: clone

tag: time

tag: replicate


title: p21094-s058_RNi17-PBMC-Day4-2021-04-16

tag: day post infection

tag: day post treament

tag: treatment

value: IFNmod


title: p21094-s057_RNi17-PBMC-Day2-2021-04-14

tag: infection


title: scRNA IL5466-N712-N507

city: Stanford

first: Helen

last: Blau

address: 3200 CCSR

institute: Stanford University

description: scRNA..musc.TPM

data_processing:
RNA sequences were aligned against the Mus musculus mm10 reference genome using the Spliced Transcripts Alignment to a Reference STAR software.
Assembly: mm10
Supplementary files format and content: TPM expression file

source_name: Muscle stem cell

growth_protocol: Following isolation, we resuspended MuSCs in myogenic cell culture medium containing DMEM/F10 50:50, 20% FBS, 2.5 ng·ml−1  fibroblast growth factor-2 FGF-2, also known as bFGF and 1% penicillin–streptomycin. We seeded MuSC suspensions at a density of 500 cells per cm2 surface area. We maintained cell cultures at 37°C in 5% CO2 and changed medium every other day.

extract_protocol:
RNA was isolated using Qiagen RNAEasy Micro kit from 5,000 -10,000 cells and cDNA generated and amplified using NuGEN Ovation RNA-Seq System v2 kit.
Libraries were constructed from cDNA with the TruSEQ RNA Library Preparation Kit v2 Illumina and sequenced to 30–40 × 106 1 × 75-bp reads per sample on a HiSEQ 2500

treatment_protocol: untreated

value: Muscle cell

tag: strain


title: s4.786O.DKO.c47.2

description: set 4, 786O cell line, double knockout clone c47, replicate 2


title: scRNA IL5466-N712-N508

description: scRNA..musc.TPM


title: Sortedtumors-null2

tag: model system

tag: genotype

tag: donor mouse/cell line

tag: seq platform


title: scRNA IL5466-N712-N506

description: scRNA..musc.TPM

tag: cell type


title: s4.786O.DKO.c47.1

description: set 4, 786O cell line, double knockout clone c47, replicate 1


title: 3DOrganoid-WT6


title: Sortedtumors-null1


title: IL7 expanded B cell progenitors, input,  Lin28b, biol rep 2

description:
FPKM Input Lin28b#1,FPKM IP Lin28b#1,FPKM Input Lin28b#2,FPKM IP Lin28b#2,FPKM Input Littermate control,FPKM IP Littermate control
Lin28b_2 IP

tag: tissue


title: p21094-s056_RNi17-PBMC-Day1-2021-04-13


title: Sortedtumors-het6

value: Ezh2 heterozygous


title: s4.786O.DKO.c5.3

description: set 4, 786O cell line, double knockout clone c5, replicate 3

tag: set


title: s4.786O.DKO.c5.2

description: set 4, 786O cell line, double knockout clone c5, replicate 2

tag: cell line


title: p21094-s055_RNi17-PBMC-Day0-2021-04-12


title: Sortedtumors-het5


title: scRNA IL5466-N712-N504

description: scRNA..musc.TPM

tag: age


title: p21094-s054_RNi17-PBMC-Day-7-2021-04-06


title: s4.786O.DKO.c5.1

description: set 4, 786O cell line, double knockout clone c5, replicate 1

tag: knockout

tag: clone


title: s4.786O.sgP.na.3

description: set 4, 786O cell line, PBRM1 knockout, replicate 3

value: sgP

tag: time

tag: replicate


title: p21094-s053_LG92-PBMC-Day4-2021-04-16

value: PBMC

tag: day post infection

tag: day post treament

value: Control


title: scRNA IL5466-N712-N503

description: scRNA..musc.TPM


title: Sortedtumors-het4

tag: treatment


title: Sortedtumors-het3


title: p21094-s052_LG92-PBMC-Day2-2021-04-14

tag: infection

value: Infected


title: s4.786O.sgP.na.2

description: set 4, 786O cell line, PBRM1 knockout, replicate 2


title: scRNA IL5466-N711-N508

description: scRNA..musc.TPM

tag: strain


title: p21094-s051_LG92-PBMC-Day1-2021-04-13


title: s4.786O.sgP.na.1

description: set 4, 786O cell line, PBRM1 knockout, replicate 1


title: Sortedtumors-het2

tag: model system

value: in vivo sorted tumor

tag: genotype


title: Sortedtumors-het1

tag: donor mouse/cell line

tag: seq platform


title: scRNA IL5466-N711-N507

description: scRNA..musc.TPM

tag: cell type


title: p21094-s050_LG92-PBMC-Day0-2021-04-12


title: s4.786O.sgA.c17.3

description: set 4, 786O cell line, ADIRF-AS1 knockout clone c17, replicate 3

tag: set

value: sgA


title: scRNA IL5466-N711-N506

description: scRNA..musc.TPM


title: p21094-s049_LG92-PBMC-Day-7-2021-04-06

value: BL


title: Sortedtumors-WT3

value: Smart seqII/DNBSEQ


title: s4.786O.sgA.c17.2

description: set 4, 786O cell line, ADIRF-AS1 knockout clone c17, replicate 2

tag: cell line


title: p21094-s048_RRj11-PBMC-Day7-2021-04-05


title: Sortedtumors-WT2


title: s4.786O.sgA.c17.1

description: set 4, 786O cell line, ADIRF-AS1 knockout clone c17, replicate 1


title: scRNA IL5466-N711-N504

description: scRNA..musc.TPM

tag: age


title: s4.786O.ctr.na.3

description: set 4, 786O cell line, control, replicate 3

tag: knockout

value: ctr


title: scRNA IL5466-N711-N505

description: scRNA..musc.TPM


title: scRNA IL5466-N711-N503

description: scRNA..musc.TPM


title: scRNA IL5466-N712-N502

description: scRNA..musc.TPM


title: Sortedtumors-WT1


title: p21094-s046_RRj11-PBMC-Day4-2021-04-02


title: scRNA IL5466-N711-N502

description: scRNA..musc.TPM


title: scRNA IL5466-N711-N501

description: scRNA..musc.TPM


title: p21094-s045_RRj11-PBMC-Day2-2021-03-31


title: p21094-s044_RRj11-PBMC-Day1-2021-03-30


title: s3.786O.sgA.c41.3

description: set 3, 786O cell line, ADIRF-AS1 knockout clone c41, replicate 3

tag: clone


title: scRNA IL5466-N710-N508

description: scRNA..musc.TPM


title: Mix culture_3

type: RNA

city: Noda-shi

first: Shunsuke

last: Kon

state: Chiba

address: 2669 Yamazaki

department: Research Institute for Biomedical Sciences

country: Japan

institute: Tokyo University of Science

description: Gene expression after 24h of tetracycline treatment

hyb_protocol: 1.65 µg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a Agilent fragmentation buffer and was hybridized at 65°C for 17 hr using Gene Expression Hybridization Kit.

scan_protocol: Microarray slides were scanned using an Agilent SureScan (G4900DA).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Canis lupus familiaris

source_name: MDCK-pTR GFP-RasV12 mCherry-β-catenin {delta}131 cells co-cultured with MDCK β-catenin {delta}131 cells at a ratio of 1:10

label_protocol: For cRNA amplification and labeling, Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) were used following the manufacter’s instructions.

growth_protocol: MDCK mCherry-β-catenin Δ131 and MDCK-pTR GFP-RasV12 mCherry-β-catenin Δ131 cells were cultured in Dulbecco's Modified Eagle Medium, High Glucose supplemented with 10% Fetal Bovine Serum and penicillin/Streptomycin at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was extracted from MDCK-pTR GFP-RasV12 mCherry-β-catenin Δ131 cells using ISOGEN II (NIPPON GENE Co., Ltd).

treatment_protocol: MDCK-pTR GFP-RasV12 mCherry-β-catenin Δ131 cells or a 10:1 mix culture of MDCK mCherry-β-catenin Δ131 and MDCK-pTR GFP-RasV12 mCherry-β-catenin Δ131 cells were cultured at a density of 1.2×10^7 cells on collagen-coated 10 cm dishes (CORNING). After incubation with tetracycline for 24 h at 37 ºC in a humidified incubator with 5% CO2, GFP-positive β-cat/RasV12 cells was separated with an analytical flow cytometer.

tag: culture condition

value: mix culture


title: p21094-s043_RRj11-PBMC-Day0-2021-03-29


title: s3.786O.sgA.c41.2

description: set 3, 786O cell line, ADIRF-AS1 knockout clone c41, replicate 2

tag: time

tag: replicate


title: scRNA IL5466-N710-N507

description: scRNA..musc.TPM


title: Mix culture_2

value: MDCK-pTR GFP-RasV12 mCherry-β-catenin {delta}131 cells co-cultured with MDCK β-catenin {delta}131 cells at a ratio of 1:10


title: p21094-s042_RRj11-PBMC-Day-7-2021-03-23

tag: day post infection

tag: day post treament


title: 3DOrganoid-WT4

value: in vitro 3D spheroid

value: Ezh2 wild-type

tag: treatment


title: Single culture_3

source_name: MDCK-pTR GFP-RasV12 mCherry-β-catenin {delta}131 cells culture alone

value: single culture


title: s3.786O.sgA.c41.1

description: set 3, 786O cell line, ADIRF-AS1 knockout clone c41, replicate 1


title: p21094-s041_RGo9-PBMC-Day7-2021-04-05

source_name: PBMC

tag: infection


title: s4.786O.ctr.na.2

description: set 4, 786O cell line, control, replicate 2


title: s3.786O.sgA.c36.3

description: set 3, 786O cell line, ADIRF-AS1 knockout clone c36, replicate 3


title: Mix culture_1


title: scRNA IL5466-N710-N506

description: scRNA..musc.TPM

tag: strain


title: s3.786O.sgA.c36.2

description: set 3, 786O cell line, ADIRF-AS1 knockout clone c36, replicate 2


title: p21094-s060_LC10-PBMC-Day0-2021-04-12


title: s4.786O.ctr.na.1

description: set 4, 786O cell line, control, replicate 1


title: scRNA IL5466-N710-N505

description: scRNA..musc.TPM


title: RIN14B scRNA-seq

city: Bethesda

first: Minh

middle: Q

last: Nguyen

state: MARYLAND

address: 9000, Rockville Pike

institute: NIDCR/NIH

description: rat pancreas cell line RIN14B

data_processing:
bcl2fastq (v2.17) was used for basecalling
Sequence reads from 10x libraries were processed using Cell Ranger 6.1.1 from 10x Genomics (https://www.10xgenomics.com/)
Reads were aligned using STAR (v 2.5.3a) to a pre-mRNA mm10 genome.
Seurat package (v2 and v3) was used for downstream data analysis in R as described by the Satija lab (http://satijalab.org/seurat/)
Assembly: rnor_6.0
Supplementary files format and content: rat.csv: csv file with genes and number of cells expressing that genes
Supplementary files format and content: rat_RIN14B.csv: csv file with cell barcodes and corresponding gene expression counts; only nuclei meeting minimum threshold of transcripts are included for analysis

molecule: nuclear RNA

organism: Rattus norvegicus

source_name: rat pancreas

growth_protocol: RIN14B cells were cultured in RPMI 1640 media with 10% FBS.

extract_protocol:
RIN14B cells were lysed and the resulting nuclei were stained with DRAQ5 and subjected to FAC sorting, selecting for DRAQ5.
Libraries construction were performed with method from 10x Genomics for 10x Chromium run.

treatment_protocol: Cells were collected at ~50% confluency for sequencing.

value: rat pancreas cell line


title: scRNA IL5466-N710-N504

description: scRNA..musc.TPM

value: Muscle cell


title: Single culture_2

value: MDCK-pTR GFP-RasV12 mCherry-β-catenin {delta}131 cells culture alone


title: p21094-s039_RGo9-PBMC-Day4-2021-04-02


title: Single culture_1


title: s3.786O.sgA.c36.1

description: set 3, 786O cell line, ADIRF-AS1 knockout clone c36, replicate 1


title: p21094-s047_RRj11-PBMC-Day5-2021-04-03

value: IFNmod


title: s3.786O.sgA.c23.3

description: set 3, 786O cell line, ADIRF-AS1 knockout clone c23, replicate 3


title: p21094-s038_RGo9-PBMC-Day2-2021-03-31

value: PBMC


title: scRNA IL5466-N710-N502

description: scRNA..musc.TPM


title: p21094-s037_RGo9-PBMC-Day1-2021-03-30

value: Control


title: scRNA IL5466-N710-N503

description: scRNA..musc.TPM


title: s3.786O.sgA.c23.2

description: set 3, 786O cell line, ADIRF-AS1 knockout clone c23, replicate 2


title: p21094-s040_RGo9-PBMC-Day5-2021-04-03

value: Infected


title: scRNA IL5466-N712-N505

description: scRNA..musc.TPM


title: p21094-s036_RGo9-PBMC-Day0-2021-03-29


title: s3.786O.sgA.c23.1

description: set 3, 786O cell line, ADIRF-AS1 knockout clone c23, replicate 1


title: p21094-s035_RGo9-PBMC-Day-7-2021-03-23


title: scRNA IL5466-N709-N508

description: scRNA..musc.TPM


title: s3.786O.ctr.na.3

description: set 3, 786O cell line, control, replicate 3


title: scRNA IL5466-N710-N501

description: scRNA..musc.TPM


title: scRNA IL5466-N709-N507

description: scRNA..musc.TPM


title: p21094-s034_RCk17-PBMC-Day4-2021-04-02


title: s3.786O.ctr.na.2

description: set 3, 786O cell line, control, replicate 2


title: scRNA IL5466-N709-N506

description: scRNA..musc.TPM


title: scRNA IL5466-N709-N505

description: scRNA..musc.TPM


title: p21094-s032_RCk17-PBMC-Day1-2021-03-30


title: s2.786O.sgA.c7.3

description: set 2, 786O cell line, ADIRF-AS1 knockout clone c7, replicate 3


title: scRNA IL5466-N709-N504

description: scRNA..musc.TPM


title: p21094-s031_RCk17-PBMC-Day0-2021-03-29


title: Sortedtumors-WT4

source_name: Mouse lung tumor

tag: model system

value: in vivo sorted tumor

tag: genotype


title: scRNA IL5466-N709-N503

description: scRNA..musc.TPM


title: s2.786O.sgA.c7.2

description: set 2, 786O cell line, ADIRF-AS1 knockout clone c7, replicate 2

value: sgA


title: p21094-s030_RCk17-PBMC-Day-7-2021-03-23

value: BL


title: s2.786O.sgA.c7.1

description: set 2, 786O cell line, ADIRF-AS1 knockout clone c7, replicate 1


title: p21094-s029_RRc17-PBMC-Day4-2021-04-02


title: s2.786O.sgA.c4.3

description: set 2, 786O cell line, ADIRF-AS1 knockout clone c4, replicate 3


title: s2.786O.sgA.c4.2

description: set 2, 786O cell line, ADIRF-AS1 knockout clone c4, replicate 2


title: p21094-s028_RRc17-PBMC-Day2-2021-03-31


title: s3.786O.ctr.na.1

description: set 3, 786O cell line, control, replicate 1


title: p21094-s033_RCk17-PBMC-Day2-2021-03-31


title: scRNA IL5466-N708-N508

description: scRNA..musc.TPM


title: scRNA IL5466-N709-N501

description: scRNA..musc.TPM


title: p21094-s027_RRc17-PBMC-Day1-2021-03-30


title: s2.786O.sgA.c4.1

description: set 2, 786O cell line, ADIRF-AS1 knockout clone c4, replicate 1


title: scRNA IL5466-N708-N507

description: scRNA..musc.TPM


title: p21094-s026_RRc17-PBMC-Day0-2021-03-29


title: scRNA IL5466-N709-N502

description: scRNA..musc.TPM


title: s2.786O.ctr.na.3

description: set 2, 786O cell line, control, replicate 3


title: scRNA IL5466-N708-N506

description: scRNA..musc.TPM


title: s2.786O.ctr.na.1

description: set 2, 786O cell line, control, replicate 1


title: p21094-s024_KV31-PBMC-Day7-2021-03-22


title: scRNA IL5466-N708-N505

description: scRNA..musc.TPM


title: scRNA IL5466-N708-N504

description: scRNA..musc.TPM


title: p21094-s025_RRc17-PBMC-Day-7-2021-03-23


title: s2.786O.ctr.na.2

description: set 2, 786O cell line, control, replicate 2


title: s1.U2OS.sgA.H9.48h.3

description: set 1, U2OS cell line, ADIRF-AS1 knockout clone H9, 48h hours, replicate 3

source_name: U2OS cell line


title: p21094-s022_KV31-PBMC-Day4-2021-03-19


title: scRNA IL5466-N708-N502

description: scRNA..musc.TPM


title: s1.U2OS.sgA.E2.48h.2

description: set 1, U2OS cell line, ADIRF-AS1 knockout clone E2, 48h hours, replicate 2


title: scRNA IL5466-N708-N503

description: scRNA..musc.TPM


title: s1.U2OS.ctr.na.48h.1

description: set 1, U2OS cell line, control, 48h hours, replicate 1


title: scRNA IL5466-N708-N501

description: scRNA..musc.TPM


title: p21094-s020_KV31-PBMC-Day1-2021-03-16


title: s1.U2OS.sgA.H9.44h.3

description: set 1, U2OS cell line, ADIRF-AS1 knockout clone H9, 44h hours, replicate 3


title: p21094-s021_KV31-PBMC-Day2-2021-03-17


title: p21094-s019_KV31-PBMC-Day0-2021-03-15


title: s1.U2OS.sgA.E2.44h.2

description: set 1, U2OS cell line, ADIRF-AS1 knockout clone E2, 44h hours, replicate 2


title: scRNA IL5466-N707-N507

description: scRNA..musc.TPM


title: scRNA IL5466-N707-N508

description: scRNA..musc.TPM


title: p21094-s023_KV31-PBMC-Day5-2021-03-20


title: s1.U2OS.ctr.na.44h.1

description: set 1, U2OS cell line, control, 44h hours, replicate 1


title: p21094-s018_KV31-PBMC-Day-7-2021-03-08


title: scRNA IL5466-N707-N506

description: scRNA..musc.TPM


title: p21094-s017_CD68-PBMC-Day7-2021-03-22


title: scRNA IL5466-N707-N505

description: scRNA..musc.TPM


title: p21094-s016_CD68-PBMC-Day5-2021-03-20


title: s1.U2OS.sgA.E2.40h.2

description: set 1, U2OS cell line, ADIRF-AS1 knockout clone E2, 40h hours, replicate 2


title: scRNA IL5466-N707-N504

description: scRNA..musc.TPM


title: scRNA IL5466-N707-N503

description: scRNA..musc.TPM


title: s1.U2OS.ctr.na.40h.1

description: set 1, U2OS cell line, control, 40h hours, replicate 1


title: p21094-s014_CD68-PBMC-Day2-2021-03-17


title: s1.U2OS.sgA.H9.36h.3

description: set 1, U2OS cell line, ADIRF-AS1 knockout clone H9, 36h hours, replicate 3


title: s1.U2OS.sgA.H9.40h.3

description: set 1, U2OS cell line, ADIRF-AS1 knockout clone H9, 40h hours, replicate 3


title: DURA52.N4.SORTED.OPC.B2

type: genomic

city: London

first: Silvia

last: Marino

address: Blizard Institute, 4 Newark Street

country: United Kingdom

institute: Queen Mary University of London

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Raw array data were first pre-processed using the ChAMP package in R to remove failed detections and probes with known design flaws, before normalisation using the SWAN algorithm

label: Cy3, Cy5

molecule: genomic DNA

source_name: Dura mater

label_protocol: Standard Illumina Protocol

growth_protocol: On Day 0 of our protocol (Day 8 of the Douvaras-Fossati et al protocol) Neural Expansion media was removed, and iNSCs cultured in N2 media with 100 nM RA and 1 µM Smoothened Agonist (SAG) added freshly each day. Media was then changed daily with fresh RA and SAG until Day 4, at which point cells became over-confluent and were detached and placed in N2B27 Media with freshly added RA and SAG. A series of scratches were made with a cell scraper vertically, horizontally, and diagonally across each well, and the contents of a single well transferred into eight wells of an ultra-low attachment 24-well plate (Corning Cat. #3473), with extra N2B27 media. Aggregates were then cultured in suspension for a further eight days, with media changed every 48 hours. On Day 12 of the protocol N2B27 media was replaced with PDGF media, and aggregates were cultured for a further 10 days, with media replaced every 48 hours. On Day 22 of the protocol aggregates were plated onto Poly-L-Ornithine and laminin coated plates and were cultured adherently until Day 67 of the protocol, with PDGF media changes every 48 hours.

extract_protocol: DNA was extracted using Norgen Biotek RNA/DNA/Protein Purification Plus Kit (Cat. #47700), which allows genomic DNA, total RNA, and protein to be isolated from a single sample.

tag: tissue type

value: Cell culture

value: Induced oligodendrocyte progenitor


title: DURA50.N12.SORTED.OPC.B2

tag: cell type


city: Santiago de Compostela

first: Angel

last: Diaz-Lagares

state: A Coruña

address: C/ Choupana s/n

department: ONCOMET

institute: Health Research Institute of Santiago (IDIS)

description:
cell-free DNA from luminal B breast cancer patient
25M

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to human Infinium MethylationEPIC BeadChip (Illumina) using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (HiScan) and standard recommended Illumina scanner setting

data_processing: RnBeads package in R environment (v4.1.1)

label: Cy5 and Cy3

source_name: luminal B breast cancer patient 25

extract_protocol: cell-free DNA was extracted from plasma samples using QIAamp Circulating Nucleic Acid Kit (Qiagen) according to standard instructions

tag: gender

value: Female

tag: sample type

value: plasma cell-free DNA

tag: disease state

value: Metastatic Luminal B Breast Cancer


title: s1.U2OS.sgA.E2.36h.2

description: set 1, U2OS cell line, ADIRF-AS1 knockout clone E2, 36h hours, replicate 2

tag: set

tag: cell line

tag: knockout


title: scRNA IL5466-N707-N502

description: scRNA..musc.TPM

tag: age


title: DURA050_OPC


title: scRNA IL5466-N707-N501

description: scRNA..musc.TPM


description:
cell-free DNA from luminal B breast cancer patient
70M 15

source_name: luminal B breast cancer patient 70


title: p21094-s012_CD68-PBMC-Day0-2021-03-15


title: s1.U2OS.ctr.na.36h.1

description: set 1, U2OS cell line, control, 36h hours, replicate 1

value: ctr

tag: clone

tag: time

tag: replicate


title: DURA44.N8.SORTED.OPC.B2


title: p21094-s015_CD68-PBMC-Day4-2021-03-19

tag: day post infection

tag: day post treament

tag: treatment


description:
cell-free DNA from luminal B breast cancer patient
47M

source_name: luminal B breast cancer patient 47


title: DURA31.N44B.SORTED.OPC.B2


title: DURA031_OPC


title: DURA052_OPC


title: scRNA IL5466-N706-N508

description: scRNA..musc.TPM

tag: strain


title: DURA019_OPC


title: p21094-s011_CD68-PBMC-Day-7-2021-03-08

tag: infection


description:
cell-free DNA from luminal B breast cancer patient
24M

source_name: luminal B breast cancer patient 24


title: p21094-s013_CD68-PBMC-Day1-2021-03-16


title: s1.U2OS.sgA.H9.32h.3

description: set 1, U2OS cell line, ADIRF-AS1 knockout clone H9, 32h hours, replicate 3


title: cell-free DNA from healthy control 20

description:
cell-free DNA from healthy control
CT20

source_name: healthy control 20

value: Healthy control


description:
cell-free DNA from luminal B breast cancer patient
28M

source_name: luminal B breast cancer patient 28


title: DURA044_OPC

tag: tissue type


title: GBM044_P8

source_name: Glioblastoma tumour

growth_protocol: Patient consent and ethical approval was available for the study (08/H0716/16 Amendment 1 17/10/2014). GIC were isolated from bulk tumour following a previously described protocol (Pollard et al 2009; doi:10.1016/j.stem.2009.03.014). Fresh GBM tissue was sliced and triturated with razor blade, dissociated with Accumax (Sigma, A7089) at 37˚C for 10 mins then filtered through a 70μm cell strainer. Dissociated cells were plated on laminin-coated 6-well plate in NeuroCult NS-A Proliferation kit media (STEMCELL, 05751), heparin (2 μg/ml; Gibco 12587-010), mEGF (20ng/ml, Prepro Tech, 315-09) and hFGF (10ng/ml; Prepro tech, AF-100-18B). Established cells were passaged when 70% confluent, frozen in Stem Cell Banker (Ambsio ZENOAQ, 11890) and stored in liquid nitrogen. Cell lines used in this study are primary lines derived from human tumours, they have been characterised by transcriptomic profiling and cultured according to current practice, including contamination assessment. Fibroblasts cultures were established from small strips of dura mater, collected at surgery. Tissue was minced with a scalpel then spun down and resuspended in trypsin for 5 minutes at 37 degrees. To stop the reaction fresh fibroblast media (DMEM, Glutamax, 10% Foetal calf serum, 2% L-Glutamin and 1% penicillin-streptomycin) was added. Samples were centrifuged and resuspended in fresh media, then plated in 6 well plates (Corning #BC010). Media was topped up frequently during the first week then changed every other day.

tag: cell type

value: Glioblastoma initiating cell


title: scRNA IL5466-N706-N507

description: scRNA..musc.TPM

value: Muscle cell


title: DURA19.N8C.SORTED.OPC.B2


title: p21094-s010_RMj8-PBMC-Day4-2021-03-19


title: s1.U2OS.sgA.E2.32h.2

description: set 1, U2OS cell line, ADIRF-AS1 knockout clone E2, 32h hours, replicate 2


title: scRNA IL5466-N706-N506

description: scRNA..musc.TPM


title: cell-free DNA from healthy control 17

description:
cell-free DNA from healthy control
CT17

source_name: healthy control 17

tag: gender


title: s1.U2OS.ctr.na.32h.1

description: set 1, U2OS cell line, control, 32h hours, replicate 1


title: p21094-s008_RMj8-PBMC-Day1-2021-03-16


title: p21094-s009_RMj8-PBMC-Day2-2021-03-17


title: s1.U2OS.sgA.H9.28h.3

description: set 1, U2OS cell line, ADIRF-AS1 knockout clone H9, 28h hours, replicate 3


title: scRNA IL5466-N706-N505

description: scRNA..musc.TPM


title: cell-free DNA from healthy control 14

description:
cell-free DNA from healthy control
CT14

source_name: healthy control 14

tag: sample type


description:
cell-free DNA from luminal B breast cancer patient
53M

source_name: luminal B breast cancer patient 53

tag: disease state


title: s1.U2OS.sgA.E2.28h.2

description: set 1, U2OS cell line, ADIRF-AS1 knockout clone E2, 28h hours, replicate 2

tag: set


title: DURA52.N4.NSC.P2

growth_protocol: EPSCs were then further differentiated into iNSCs with a Gibco commercially available kit (Gibco Cat. #A1647801). iNSCs were cultured on GelTrex (Gibco Cat. #A1413302) coated tissue culture plates and maintained in Neural Expansion media at 37°C, 5% CO2. iNSCs were passaged once they reached 80-90% confluence.

value: Induced neural stem cell


title: scRNA IL5466-N706-N504

description: scRNA..musc.TPM

source_name: Muscle stem cell


title: p21094-s007_RMj8-PBMC-Day0-2021-03-15

value: IFNmod


title: scRNA IL5466-N706-N503

description: scRNA..musc.TPM


title: s1.U2OS.ctr.na.28h.1

description: set 1, U2OS cell line, control, 28h hours, replicate 1

tag: cell line


title: p21094-s006_RMj8-PBMC-Day-7-2021-03-08

value: PBMC


title: scRNA IL5466-N706-N502

description: scRNA..musc.TPM


title: p21094-s005_RMs8-PBMC-Day4-2021-03-19

value: Control


title: GBM044_P4


title: p21094-s004_RMs8-PBMC-Day2-2021-03-17

value: Infected


title: scRNA IL5466-N706-N501

description: scRNA..musc.TPM


title: DURA50.N12.NSC.P4


title: s1.U2OS.sgA.E2.24h.2

description: set 1, U2OS cell line, ADIRF-AS1 knockout clone E2, 24h hours, replicate 2

tag: knockout


title: scRNA IL5466-N705-N508

description: scRNA..musc.TPM

tag: age


description:
cell-free DNA from luminal B breast cancer patient
17M

source_name: luminal B breast cancer patient 17


title: p21094-s003_RMs8-PBMC-Day1-2021-03-16

source_name: PBMC


title: s1.U2OS.sgA.H9.24h.3

description: set 1, U2OS cell line, ADIRF-AS1 knockout clone H9, 24h hours, replicate 3

tag: clone


title: s1.U2OS.ctr.na.24h.1

description: set 1, U2OS cell line, control, 24h hours, replicate 1

tag: time


title: cell-free DNA from healthy control 19

description:
cell-free DNA from healthy control
CT19

source_name: healthy control 19


title: cell-free DNA from healthy control 15

description:
cell-free DNA from healthy control
CT15

source_name: healthy control 15


title: p21094-s002_RMs8-PBMC-Day0-2021-03-15


title: s1.U2OS.sgA.H9.20h.3

description: set 1, U2OS cell line, ADIRF-AS1 knockout clone H9, 20h hours, replicate 3

source_name: U2OS cell line

tag: replicate


title: scRNA IL5466-N705-N506

description: scRNA..musc.TPM


title: s1.U2OS.sgA.E2.20h.2

description: set 1, U2OS cell line, ADIRF-AS1 knockout clone E2, 20h hours, replicate 2


title: s1.U2OS.ctr.na.20h.1

description: set 1, U2OS cell line, control, 20h hours, replicate 1


title: scRNA IL5466-N705-N505

description: scRNA..musc.TPM


title: scRNA IL5466-N705-N504

description: scRNA..musc.TPM


title: p21094-s001_RMs8-PBMC-Day-7-2021-03-08

tag: day post infection


title: DURA44.N8.NSC.P4

source_name: Dura mater


title: s1.U2OS.sgA.H9.16h.3

description: set 1, U2OS cell line, ADIRF-AS1 knockout clone H9, 16h hours, replicate 3


title: scRNA IL5466-N705-N503

description: scRNA..musc.TPM


title: DURA044_NSC_N8_P2


title: scRNA IL5466-N705-N502

description: scRNA..musc.TPM


title: s1.U2OS.ctr.na.16h.1

description: set 1, U2OS cell line, control, 16h hours, replicate 1


title: TRAMP-C1 tumors developed in HFD C57BL/6J mice, 2

city: Ciudad Autónoma de Buenos Aires

first: Cintia

middle: Lorena

last: Massillo

state: Buenos Aires

address: Vuelta de Obligado 2490

country: Argentina

institute: Instituto de Biología y Medicina Experimental

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C

scan_protocol: microarray were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing:
Data were processed using pd.mirna.4.0 and limma packages in R/Bioconductor environment. Background correction, normalization and gene level expreession were calcualted with RMA .
Mm_miRNA-4_0-st-v1.txt
Mm_miRNA-4_0-st-v1.GRCm38.txt

label: biotin

source_name: TRAMP-C1 tumor

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: Four-weeks-old C57BL/6J male mice were housed under pathogen-free conditions. Mice were randomized into two dietary groups and fed ad libitum during 27 weeks with CD (3,120 kcal/kg, 5% fat) or HFD (4,520 kcal/kg, 37% fat). After 15 weeks of diet, 3 ×106 TRAMP-C1 cells were subcutaneously injected. Animals were sacrificed in the 27th week and tumor samples were collected.

extract_protocol: RNA from TRAMP-C1 tumors was isolated using TriReagent (Molecular Research Center)

treatment_protocol: Tumors from control diet (CD) of high fat diet (HFD) fed mice were collected for RNA isolation followed by miRNA microarrays hybridization

value: 31 weeks

tag: Sex

value: male

tag: diet

value: high fat diet

value: TRAMP C1 cells

tag: genotype

value: wild-type


title: s1.U2OS.sgA.E2.16h.2

description: set 1, U2OS cell line, ADIRF-AS1 knockout clone E2, 16h hours, replicate 2

value: sgA


title: TRAMP-C1 tumors developed in HFD C57BL/6J mice, 1

tag: strain


title: DURA31.N44B.NSC.P3

tag: tissue type

value: Cell culture


title: scRNA IL5466-N705-N501

description: scRNA..musc.TPM

tag: cell type


title: TRAMP-C1 tumors developed in HFD C57BL/6J mice, 3


title: scRNA IL5466-N704-N508

description: scRNA..musc.TPM


title: s1.U2OS.sgA.H9.12h.3

description: set 1, U2OS cell line, ADIRF-AS1 knockout clone H9, 12h hours, replicate 3


title: TRAMP-C1 tumors developed in CD C57BL/6J mice, 3

value: control diet


title: s1.U2OS.sgA.E2.12h.2

description: set 1, U2OS cell line, ADIRF-AS1 knockout clone E2, 12h hours, replicate 2


title: scRNA IL5466-N704-N507

description: scRNA..musc.TPM


title: s1.U2OS.ctr.na.12h.1

description: set 1, U2OS cell line, control, 12h hours, replicate 1

value: ctr


title: TRAMP-C1 tumors developed in CD C57BL/6J mice, 1


title: TRAMP-C1 tumors developed in CD C57BL/6J mice, 2


title: s1.U2OS.sgA.H9.08h.3

description: set 1, U2OS cell line, ADIRF-AS1 knockout clone H9, 08h hours, replicate 3


title: s1.U2OS.sgA.E2.08h.2

description: set 1, U2OS cell line, ADIRF-AS1 knockout clone E2, 08h hours, replicate 2


title: scRNA IL5466-N704-N506

description: scRNA..musc.TPM


title: scRNA IL5466-N704-N504

description: scRNA..musc.TPM


title: SW480 cells, FM#1, 6 hrs

city: Xiamen

first: yongyou

last: zhang

state: Fujian

address: Xiang'an South Road

country: China

institute: Xiamen University

data_processing:
Illumina Novaseq platform
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Illumina Novaseq platform (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to hg38 using Illumina Novaseq platform (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 Illumina Novaseq platform
Supplementary files format and content: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: SW480 cells were maintained in 1640 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). A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each samples.

treatment_protocol: SW480 cells werecultured in the full medium (FM) or cystine-restriction medium (CR)

tag: tissue

value: colon cancer cell

value: WT

tag: treatment

value: complete medium for 6 hrs


title: scRNA IL5466-N704-N505

description: scRNA..musc.TPM

value: Muscle cell


title: DURA19.N8C.NSC.P7

value: Induced neural stem cell


title: SW480 cells, CR#2, 6 hrs

value: cystine-restriction medium for 6 hrs


title: DURA31.N44B.D20.ASTRO.B2

growth_protocol: Differentiation was initiated on Day -1, by seeding dissociated iNSCs at 1.5x10^4 cells/cm^2 density on GelTrex-coated plates in Neural Expansion media. On Day 0 Neural Expansion media was changed to Astrocyte media (ScienCell: Cat. #1801) supplemented with 2% FBS, Astrocyte Growth Supplement (AGS) and penicillin/streptomycin solution, provided with the media. From Day 2 onwards, media was changed every 48 hours for 20 – 30 days. At 80-90% confluence, the cells were passaged back to the starting seeding density (1.5 x 10^4 cells/cm^2), or at an approximate ratio of 1:6. Cells were detached using Accutase, and always cultured in the same Astrocyte media on GelTrex.

value: Induced astrocyte progenitor


title: scRNA IL5466-N704-N503

description: scRNA..musc.TPM


title: s1.U2OS.ctr.na.08h.1

description: set 1, U2OS cell line, control, 08h hours, replicate 1


title: s1.U2OS.sgA.H9.04h.3

description: set 1, U2OS cell line, ADIRF-AS1 knockout clone H9, 04h hours, replicate 3


title: scRNA IL5466-N704-N502

description: scRNA..musc.TPM


title: DURA50.N12.D20.ASTRO.B2


title: s1.U2OS.sgA.E2.04h.2

description: set 1, U2OS cell line, ADIRF-AS1 knockout clone E2, 04h hours, replicate 2


title: DURA44.N8.D20.ASTRO.B2


title: WT_SPG_3

city: Hangzhou

first: Heng-yu

last: Fan

state: Zhejiang

address: Yuhangtang Road

institute: Life Sciences  Institute

data_processing:
RNA-Seq was performed with biological replicates for all samples.
Raw reads were trimmed to 50 bp and mapped to the mouse genome (mm9) and ERCC spike-in sequences with Tophat v2.1.1.
Only uniquely mapped reads were subsequently assembled into transcripts guided by the reference annotation (UCSC gene models) with Cufflinks v2.2.1.
Raw counts were aquired by using htseq v0.11.2, and different expressional genes were analized by DEseq2 v=3.11.
Expression level  was further normalized with the ERCC spike-in.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include raw count values of all RNA-seq samples

source_name: Spermatogonia

extract_protocol:
Spermatogenic cells were collected with Fluorescence activated Cell Sorting (FACS) and Spermatocytes were flash frozen on dry ice, and RNA was harvested using Trizol reagent.
Sequencing libraries were constructed from 500 pg of amplified cDNA using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD503) according to manufacturer’s instructions. Barcoded libraries were pooled and sequenced on the Illumina HiSeq X Ten platform with 150 bp paired-end reads

value: spermatogonia

value: Wildtype


title: DURA52.N8.D20.ASTRO.B3


title: s1.U2OS.ctr.na.04h.1

description: set 1, U2OS cell line, control, 04h hours, replicate 1


title: scRNA IL5466-N705-N507

description: scRNA..musc.TPM


title: scRNA IL5466-N703-N508

description: scRNA..musc.TPM


title: WT_SPG_2


title: scRNA IL5466-N704-N501

description: scRNA..musc.TPM


title: DURA19.N8C.D20.ASTRO.B3


title: s1.U2OS.sgA.H9.00h.3

description: set 1, U2OS cell line, ADIRF-AS1 knockout clone H9, 00h hours, replicate 3