title: Post-challenge NK cells

city: Houston

first: DONGHAI

last: XIONG

state: TX

address: 6565 MD Anderson Blvd,

institute: The University of Texas MD Anderson Cancer Center

description:
Library name: PostChallenge_NK
10x Genomics Chromium Single Cell 3' v3.1; library SC295_scRNA_3_S5

data_processing:
Reads were processed with 10x Genomics Cell Ranger v9.0.1 using the count pipeline.
Reads from the first sample (human CAR-NK cells) were aligned to the GRCh38 reference (refdata-gex-GRCh38-2020-A). Reads from the second sample (human and mouse cells mixture) were aligned to the human and mouse hybrid reference genome (refdata-gex-GRCh38-and-mm10-2020-A).
Cell Ranger filtered feature-barcode matrices were exported in Market Exchange (MEX) format; file names were prefixed with the sample name to ensure uniqueness.
Assembly: GRCh38 (refdata-gex-GRCh38-2020-A) for PreInfusion_NK; GRCh38-and-mm10 hybrid (refdata-gex-GRCh38-and-mm10-2020-A) for PostChallenge_NK
Supplementary files format and content: Cell Ranger filtered feature-barcode matrix in Market Exchange (MEX) format: barcodes.tsv.gz (cell barcodes), features.tsv.gz (genes), matrix.mtx.gz (UMI counts per gene per cell). Files renamed with a sample prefix so every file name is unique.

source_name: umbilical cord blood

growth_protocol: Not applicable (cryopreserved CD5 CAR-NK cell product; see treatment protocol).

extract_protocol:
Single-cell suspensions were loaded onto the 10x Genomics Chromium Controller. Single-cell gel beads-in-emulsion (GEMs) were generated and total RNA captured per the Chromium Single Cell 3' v3.1 protocol.
cDNA libraries were prepared using the 10x Genomics Chromium Next GEM Single Cell 3' Reagent Kit v3.1 following the manufacturer's instructions.

treatment_protocol: Two samples were subjected to scRNA-seq. The first sample is the human CD5 CAR-NK cells product before being injected to the mouse model ('PreInfusion_NK'). The second sample is prepared as follows: The human CD5 CAR-NK cells were injected into the mouse model with CD5+ CCRF tumor cells, 100 days later rechallenged with tumor cells; then the sample was collected 4 weeks after tumor rechallenge.

value: umbilical cord blood

value: CD5 CAR-NK cells

value: post-challenge (CD5 CAR-NK cells recovered 4 weeks after in vivo tumor rechallenge)


title: Peripheral_Monocytes_HC06

status: Public on Jul 23 2026

type: SRA

city: London

first: Eve

last: Hornsby

address: 4 Newark St

department: Blizard Institue/CIB

country: United Kingdom

institute: QMUL

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Demultplexing, barcoded processing,  gene counting and aggregation were performed using 10x Genomics Cell Ranger pipeline (version 6.0.2).
Assembly: GRCh38 GENCODE v2/ Ensembl 98
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral Blood

extract_protocol:
Peripheral Blood Mononuclear Cells (PBMC) were obtained by centrifugation in Ficoll®Paque PLUS (GE Healthcare). Total monocytes were enriched from PBMC using negative magnetic selection (Pan-monocyte isolation kit, Miltenyi Biotech). Cells were then washed twice in Phosphate Buffered Saline(Ca2+ and Mg2+ -free) containing 0.04% Bovine Serum Albumin.
Samples were loaded to the Chromium Chip B Single Cell Kit (PN-1000074) using the Chromium Single Cell 3' GEM, Library & Gel Bead Kit v3 (PN-1000092) as described in the manufacturer’s user guide (10X Genomics, California, USA), aiming to capture 1000 cells per sample. 11 cycles of cDNA amplification were performed on the purified GEM-RT product, and cDNA was examined for quality using the Agilent 2200 Tapestation with the High-sensitivity D5000 screentape and reagents (Agilent Technologies, Waldbronn, Germany), and the Qubit® 2.0 Fluorometer and Qubit dsDNA HS Assay Kit (Life Technologies, California, USA). 10µL of cDNA was used to prepare the 10X 3’RNA library and 13 cycles were used for sample index PCR. Final cleaned libraries were quantified using the Qubit® 2.0 Fluorometer and Qubit dsDNA HS Assay Kit and average fragment size checked using the Agilent D1000 screentape and reagents.  An equimolar amount of each sample library was pooled for sequencing on one lane of an Illumina NovaSeq S4 flow cell at 150bp paired-end.

tag: tissue

value: Peripheral Blood

tag: diagnosis

value: Healthy Control

tag: cell type

value: Total monocytes


title: Peripheral_Monocytes_HC05

description: 10x Genomics


title: Peripheral_Monocytes_HC04

description: 10x Genomics


title: Peripheral_Monocytes_HC02

description: 10x Genomics


title: Peripheral_Monocytes_HC01

description: 10x Genomics


title: MDA-MB-231-D3H2LN (MDA231LN) rep 3

city: Chicago

first: Naiche

middle: L

last: Adler

address: 909 S Wolcott Ave, room 2160

country: USA

institute: University of Illinois Chicago

library_source: transcriptomic

data_processing:
Raw sequencing files (fq.gz) were aligned to the reference genome (Hs GrCh38) using STAR aligner. The output bam files were used to generate raw counts using FeatureCounts (Subread). The raw counts were normalized and processed to identify differentially expressed genes (DEGs) using DESeq2.
Assembly: Homo Sapiens GrCh38
Supplementary files format and content: txt files contain raw counts for each experiment
Supplementary files format and content: xlsx files contain a list of differentially expressed genes with corresponding Log fold changes, Padj and normalized counts for each experiment

source_name: MDA-MB-231-D3H2LN (MDA231LN)

growth_protocol: MDA-MB-231-D3H2LN human mammary tumor cell line (Perkin Elmer, further abbreviated MDA231-LN ) and parental MDA-MB-231 cells were maintained in high-glucose Dulbecco's Modified Eagle Medium(DMEM, Gibco) supplemented with 10% FBS

extract_protocol:
RNA was harvested by using a Rneasy mini plus kit (Qiagen).
Library prep was done using the services of Novogene and was sequenced at a depth of 20 million paired-ends with 150-based fragments

tag: cell line

value: MDA-MB-231-D3H2LN (MDA231LN)

value: Breast Cancer


title: WM-115-3

status: Public on Jul 24 2026

city: Kunming

first: Li

middle: Qiao

last: hua

state: Yunnan

address: No. 727, Jingming South Road, Chenggong District

country: China

institute: Kunming University of Science and Technology

description: Library name: Sample 24

data_processing:
Raw data were filtered using fastp software (v 0.23.2), and reads were mapped to GRCh38 using HISAT2 (v 2.1.0), featureCounts (v 2.0.1) is used to count the reads mapped to each gene
Differential expression analysis between the two comparison sets was performed using DESeq2 software (1.40.2)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: skin

extract_protocol:
RNA extraction using the phenol/chloroform method,1 ug total RNA of each sample was used as the starting material to construct a transcriptome sequencing library
According to the operating instructions of VAHTS Universal V6 RNA-Seq Library Prepkit for Illumina (NR 604-01/02)

value: skin

value: melanoma cell


title: MDA-MB-231-D3H2LN (MDA231LN) rep 2


title: MDA-MB-231 cells rep 3


title: MDA-MB-231-D3H2LN (MDA231LN) rep 1


title: MDA-MB-231 cells rep 2


title: MDA-MB-231 cells rep 1


title: HdLEC JAG1 stimulated 2

data_processing:
fastq files were aligned to human (ENSEMBL/GRCh38) using STAR (version 2.5.0a). Normalized read counts and analysis to generate a list of differentially expressed genes was done using DESeq2 (version 1.18.1)
Assembly: Human Genome (ENSEMBL/GRCh38)
Supplementary files format and content: Raw count files (.txt) were generated using FeatureCounts (v1.5.2) ; Normalized count files (.csv) were generated by DESeq2 (version 1.18.1)

source_name: Lymphatic Endothelial Cells

growth_protocol: Neonatal human dermal lymphatic endothelial cells (HdLECs)  were cultured on fibronectin-coated plates in EGM2-MV2 (Lonza; complete medium) supplemented with 10 ng/mL VEGF-C (R&D).

extract_protocol:
RNA was isolated from lysates (RLT+beta-mercaptoethanol) using RNEasy Mini Kit (Qiagen), as per the manufacturer's recommendation.
RNA libraries were prepared using standard protocols recommended by Illumina at NovogeneCorp.

treatment_protocol: Cells were detached by trypsinization and seeded on Fc (Control) or DLL4 coated plates for 6h from the time of seeding.

value: Lymphatic Endothelial Cells

value: Dermal LEC

tag: treatment

value: JAG1 ligand Stimulated


title: HdLEC JAG1 stimulated 3


title: HdLEC JAG1 stimulated 1


title: HdLEC Control 3

value: Control (Ig-Fc stimulated)


title: HdLEC Control 2


title: MDA-MB-231-D3H2LN with JAG1 KO + JAG1 OE (rescue) 3

growth_protocol: MDA-MB-231-D3H2LN human mammary tumor cell line (Perkin Elmer, further abbreviated MDA231-LN ) and was maintained in high-glucose Dulbecco's Modified Eagle Medium(DMEM, Gibco) supplemented with 10% FBS

treatment_protocol: JAG1 KO: Cas9 protein (IDT) and single-guide RNAs complex (RNP Complex) specific to two different locations of a Jag1 exon were assembled, then transfected into MDA231-LN cells. Knockout clones were first isolated by serial dilution to select single cell-derived clonal colonies. Then clonal, homozygous knockouts were confirmed via next generation amplicon sequencing (Illumina miniSeq 2x150) and western blotting.  JAG1 OE: HEK293T cells were grown to 70% confluence in high glucose 10%FBS DMEM and then transfected with 3μg of pVSVG, 5μg of pMDLg/pRRE, 2.5μg of pRSV-rev, and 10μg of pCCL lentiviral plasmids containing human JAGGED-1. To achieve transfection, calcium phosphate-based method was employed. 48 hours after transfection, the lentiviral particles were collected, filtered through a 0.45μm filter, and then used for transduction of target cells. 48 hours after transduction, cancer cells were subcultured. Shortly after, RNA and protein was collected for confirmation of successful cell line generation.

value: MDA-MB-231-D3H2LN with JAG1 KO cell line with lentiviral transduction with JAG1 -OE construct (pCCL.JAG1)


title: MDA-MB-231-D3H2LN with JAG1 KO + JAG1 OE (rescue) 2


title: MDA-MB-231-D3H2LN with JAG1 KO + JAG1 OE (rescue) 1


title: MDA-MB-231-D3H2LN with JAG1 KO 3

value: MDA-MB-231-D3H2LN with JAG1 KO cell line with lentiviral transduction with empty vector (pCCL.PKG-WPRE)


title: MDA-MB-231-D3H2LN with JAG1 KO 1


title: MDA-MB-231-D3H2LN cells with CRISPR/Cas9 JAG1 deletion - clone2 (F) rep3

description:
RvsFcounts.txt
F3

treatment_protocol: JAG1 KO: Cas9 protein (IDT) and single-guide RNAs complex (RNP Complex) specific to two different locations of a Jag1 exon were assembled, then transfected into MDA231-LN cells. Knockout clones were first isolated by serial dilution to select single cell-derived clonal colonies. Then clonal, homozygous knockouts were confirmed via next generation amplicon sequencing (Illumina miniSeq 2x150) and western blotting.

value: CRISPR/Cas9 JAG1 deletion - clone2


title: MDA-MB-231-D3H2LN cells with CRISPR/Cas9 JAG1 deletion - clone 2 (F) rep2

description:
RvsFcounts.txt
F2


title: MDA-MB-231-D3H2LN cells with CRISPR/Cas9 JAG1 deletion - clone 1 (E) rep3

description:
RvsEcounts.txt
E3

value: CRISPR/Cas9 JAG1 deletion - clone1


title: MDA-MB-231-D3H2LN cells with  CRISPR/Cas9 JAG1 deletion - clone 1 (E) rep2

description:
RvsEcounts.txt
E2


title: MDA-MB-231-D3H2LN cells with CRISPR/Cas9 JAG1 deletion - clone 1 (E) rep1

description:
RvsEcounts.txt
E1


title: MDA-MB-231-D3H2LN cells expressing JAG1 rep3

description:
RvsFcounts.txt
RvsEcounts.txt
R3

value: Control


title: MDA-MB-231-D3H2LN cells expressing JAG1 rep2

description:
RvsFcounts.txt
RvsEcounts.txt
R2


title: MDA-MB-231-D3H2LN cells expressing JAG1 rep1

description:
RvsFcounts.txt
RvsEcounts.txt
R1


title: NES tumours derived from inducing MYCN(T58A) in vivo, rep 5

first: Diego

last: Chillon Pino

address: Great Ormond Street Hospital for Children NHS

department: Cancer development and genomics

institute: UCL

description:
Library name: NESt_rep5
B5_1_Animal.DoxON_309484

data_processing:
Raw reads were filtered with SOAPnuke (BGI; -n 0.001 -l 20 -q 0.4 --adaMR 0.25 --ada_trim) to remove adapter sequences, low-quality reads and N-rich reads (Phred+33 output).
Read quality was assessed with FastQC. Reads were aligned to the human reference genome (GRCh38, GENCODE annotation) using STAR. Gene-level quantification was performed with RSEM, producing expected counts per gene.
RSEM expected counts were rounded to the nearest integer to meet the input requirements of DESeq2.
Differential expression was performed with DESeq2 in R (NES ON vs NES CTRL; significance: adjusted p < 0.05, |log2FC| > 1).
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file of RSEM gene-level expected counts (rows = Ensembl gene IDs with version, plus the constituent transcript IDs; one column per library). Values are RSEM expected counts and are non-integer by design.

molecule: polyA RNA

source_name: brain tumour (intracranial xenograft)

growth_protocol: Human embryonic hindbrain-derived NES cells (Sai2 line) were cultured in DMEM/F12 with 2 mM L-glutamine, N2 supplement, B27, penicillin-streptomycin (1:100), EGF (10 ng/mL) and FGF2 (10 ng/mL). Flasks were double-coated with poly-L-ornithine (0.1 mg/mL) then laminin (2 µg/mL). Cells were split ~1:3 every ~3 days with TrypLE Express; medium was refreshed daily. Maintained at 37 °C, 5% CO2.

extract_protocol:
Total RNA was extracted using the RNeasy Kit (Qiagen) per manufacturer's instructions (pelleted cells for in vitro samples; snap-frozen tumour for NESt). Samples passed QC: total RNA >= 200 ng, concentration >= 20 ng/µL, OD260/280 and OD260/230 >= 1.8, RIN >= 7.
Stranded mRNA libraries were prepared by BGI (DNBSEQ Eukaryotic Strand-specific mRNA library).

treatment_protocol: In vitro: MYCN(T58A) expression was induced in NES ON cultures by doxycycline; NES CTRL cultures were maintained without doxycycline. In vivo (NESt): recipient NSG mice received doxycycline feed (20 g/kg) from >=7 days before intracranial implantation and throughout tumour growth.

value: brain tumour (intracranial xenograft)

value: Sai2 (NES MYCN(T58A)-derived)

tag: genotype

value: MYCN(T58A), doxycycline-induced

value: doxycycline (in vivo dox diet)


title: NES tumours derived from inducing MYCN(T58A) in vivo, rep 4

description:
Library name: NESt_rep4
B4_1_Animal.DoxON_309483


title: NES tumours derived from inducing MYCN(T58A) in vivo, rep 3

description:
Library name: NESt_rep3
B3_1_Animal.DoxON_309481


title: NES tumours derived from inducing MYCN(T58A) in vivo, rep 2

description:
Library name: NESt_rep2
B2_1_Animal.DoxON_309479


title: NES cells, MYCN(T58A) uninduced (dox), rep 3

description:
Library name: NES_CTRL_rep3
B8_1_hbNES.Cell.DoxOFF_P58_3

value: hindbrain neuroepithelial stem cell

value: MYCN(T58A) doxycycline-inducible

value: untreated


title: NES cells, MYCN(T58A) uninduced (dox), rep 2

description:
Library name: NES_CTRL_rep2
B7_1_hbNES.Cell.DoxOFF_P58_2


title: NES cells, MYCN(T58A) uninduced (dox), rep 1

description:
Library name: NES_CTRL_rep1
B6_1_hbNES.Cell.DoxOFF_P58_1


title: NES cells, MYCN(T58A) induced (dox), rep 3

description:
Library name: NES_ON_rep3
B15_1_hbNES.Cell.DoxON_P58_3

value: doxycycline


title: NES cells, MYCN(T58A) induced (dox), rep 2

description:
Library name: NES_ON_rep2
B14_1_hbNES.Cell.DoxON_P58_2


title: NES cells, MYCN(T58A) induced (dox), rep 1

description:
Library name: NES_ON_rep1
B13_1_hbNES.Cell.DoxON_P58_1


title: Ag(aq), biological replicate 6

city: Austin

first: Jeffrey

middle: E.

last: Barrick

address: 2500 Speedway, Stop A4800

department: Molecular Biosciences

institute: The University of Texas at Austin

description: Library name: 38F

data_processing:
Adaptors were removed from reads using Trimmomatic (v0.38.0) in paired end mode. Trimmed read pairs and singletons were mapped to the P. aeruginosa PAO1 genome sequence (Genbank: NC_002516.2) using bowtie2 (v2.3.5.1). The number of sequenced fragments overlapping gene features were counted using HTseq (v0.12.4). Read count normalization and differential gene expression analysis were conducted using DEseq2 (v1.38.0).
Assembly: Pseudomonas aeruginosa PAO1 (NC_002516.2)
Supplementary files format and content: Read counts per gene (CSV)

organism: Pseudomonas aeruginosa PAO1

extract_protocol:
RNA was extracted from the membrane filters using the Qiagen RNeasy Kit with modifications to the manufacturer's protocol. Briefly, the tubes containing the filters were thawed on ice for 20 minutes, followed by the addition of 100 µL of 15 mg/mL lysozyme in Tris-EDTA (TE) buffer (10 mM Tris-Cl, 1 mM EDTA, pH 8.0). The tubes were vortexed at maximum speed for 10 minutes and then placed on ice for five minutes. Next, 350 µL of buffer RTL were added to each tube; the tubes were briefly vortexed and then centrifuged for 10 seconds at 5,000 xg. The supernatant was transferred to the Lysing Matrix E bead tubes (MP Biomedicals) and homogenized using a FastPrep-25 Classic homogenizer (MP Biomedicals) using three rounds of 50 seconds, with 5 minutes of cooling the tubes on ice between each round. The tubes were centrifuged at 17,000 xg, and the supernatant was transferred to new microcentrifuge tubes. Next, 220 µL of absolute ethanol was added, and the tubes were inverted five times to mix. The RNA was then captured on the spin columns from the kit per manufacturer’s instructions and eluted into 20 µL of RNase-free water. Extracted RNA was stored at -80°C for sequencing. Ribosomal RNA depletion was performed using the Ribo-Zero rRNA Removal Kit for bacteria (Illumina), and quality was assessed using a Bioanalyzer 2100 (Agilent).
Library construction was performed using the TruSeq Stranded Total RNA kit (Illumina).

value: Ag(aq)


title: Ag(aq), biological replicate 5

description: Library name: 38E


title: Ag(aq), biological replicate 4

description: Library name: 38D


title: Ag(aq), biological replicate 2

description: Library name: 34K


title: Ag(aq), biological replicate 1

description: Library name: 34J


title: AgNP, biological replicate 6

description: Library name: 38I

value: AgNP


title: V5_ACAP1

type: protein

city: Shanghai

first: Jiwei

last: Chen

address: 130 DongAn Road

institute: Fudan University

description: microarrays

hyb_protocol: The protein microrrays were incubated for 1 h at 4°C in Blocking Buffer I (PBS, 0.1% Tween-20, 1% BSA). The arrays were washed three times at 4°C in Blocking Buffer II (TBS supplemented with 0.5% Triton X-100, 1 mM β-mercaptoethanol, 5% Glycerol, 2 mM MgCl2, 1% BSA), and incubated for 1 h with 600 µl of immunopurified Flag-ACAP1-V5 fusion protein at room temperature. The arrays were washed three times in Blocking Buffer II and incubated with Alexa Fluor 647-conjugated anti-V5 antibody for 1 h at room temperature. The arrays were then washed three times in Blocking Buffer II, rinsed twice in water, and dried by spinning at 300 g for 5 min.

scan_protocol: Microarrays were scanned with a GenePix microarray scanner (Molecular Devices) at the Microarray Core Facility of UT Southwestern Medical Center.

data_processing: Fluorescence intensities were quantified using GenePix Pro software (version 7.0), and signal-to-noise ratios (SNRs) were calculated to ensure data quality. Data analyses, including the calculation of fold changes and Z-scores, were performed using R software.

label: Alexa Fluor 647

molecule: protein

source_name: V5-tagged ACAP1 protein purified from HEK293T cells

label_protocol: The purified protein was subjected to protein microarray using the ProtoArray Human Protein Microarray (v5.1, Invitrogen). Detection was carried out using an Alexa Fluor 647-conjugated anti-V5 antibody.

growth_protocol: HEK293T cells were cultured in DMEM medium supplemented with 10% FBS, 100 U/mL penicillin, and 100 μg/mL streptomycin.

extract_protocol: The Flag-ACAP1-V5 fusion protein was purified from the cell lysates using anti-Flag M2 Affinity Gel (Sigma-Aldrich) and subsequently eluted in 200 μl of TBS (50 mM Tris-HCl, pH 7.5, 137 mM NaCl) containing 150 μg/mL 3×Flag peptide (Sigma-Aldrich). The purity and concentration of the eluted protein were assessed by immunoblotting and silver staining.

treatment_protocol: Eight 150-mm dishes of HEK293T cells were transfected with a pcDNA6 vector encoding Flag-ACAP1-V5, a fusion protein bearing both Flag and V5 epitope tags.

tag: recombinant protein


title: AgNP, biological replicate 5

description: Library name: 38H


title: Peripheral_Monocytes_CD05

description: 10x Genomics

value: Peripheral Blood

value: Crohn's Disease

value: Total monocytes


title: AgNP, biological replicate 4

description: Library name: 38G


title: Peripheral_Monocytes_HC07

description: 10x Genomics

value: Healthy Control


title: AgNP, biological replicate 3

description: Library name: 34I


title: Ag(aq), biological replicate 3

description: Library name: 34L


title: Peripheral_Monocytes_HC03

description: 10x Genomics


title: AgNP, biological replicate 1

description: Library name: 34G


title: no-Ag control, biological replicate 6

description: Library name: 38C

value: no-Ag control


title: no-Ag control, biological replicate 5

description: Library name: 38B


title: no-Ag control, biological replicate 4

description: Library name: 38A


title: YUMM5.2 tumor cells from C57BL/6 mice treated with dabrafenib/trametinib (D/T)+nilotinib

city: Lexington

first: Rina

last: Plattner

state: KY

address: 760 Press Ave

department: Pharmacology & Nutritional Science

institute: University of Kentucky

description:
Library name: YUMM2-D/T+Nilo
10X Genomics

data_processing:
Single cell gene expression libraries were mapped to mm10 mouse reference (10X Genomics pre-built reference, mm10-2020-A) using Cell Ranger (v6.0.0, 10X Genomics).
Assembly: Mouse mm10
Supplementary files format and content: filtered cell by gene expression matrix in h5 format

organism: Mus musculus

source_name: tumor

extract_protocol:
Tumors (n=5/group) were pooled, dissociated with a MACS dissociator (mouse melanoma setting), red blood cells lysed and dead cells removed (Miltenyi kits). Viability was assessed on a Countess II FL.
Library preparation, sequencing, and analysis was performed by the Markey Cancer Center Oncogenommics Shared Resource. Live cells (D/T=10,251; D/T+nilotinib=15,947) were targeted for Gel Beads-in-emulsion (GEMs) formation on the 10X Genomics Chromium Controller. Library preparation was conducted according to the manufacturer's instructions using Chromium Next GEM Single Cell 3' Gene Expression Kit v3.1.

treatment_protocol: Mice were treated for 4 days with dabrafenib/trametinib (D/T) or dabrafenib+trametinib+nilotinib (D/T+nilo)

value: tumor

value: mouse melanoma

value: Braf V600E/WT; Trp53-/-


title: no-Ag control, biological replicate 3

description: Library name: 34C


title: YUMM5.2 tumor cells from C57BL/6 mice treated with dabrafenib/trametinib (D/T)

description:
Library name: YUMM1-D/T
10X Genomics

value: dabrafenib+trametinib (D/T)


title: no-Ag control, biological replicate 2

description: Library name: 34B


title: Del, ATAC

city: Tokorozawa-si

first: Noriko

last: Mizota

state: Saitama

address: 2-579-15 Mikajima

department: Faculty of Human Sciences

country: Japan

institute: Waseda University

library_source: genomic

data_processing:
Demultiplexing, barcode processing, gene counting, and aggregation were performed using the 10x Genomics Cell Ranger ARC (v2.0.0).
Downstream analysis was performed using the R packages seurat and signac.
Assembly: mm10
Supplementary files format and content: cellranger-arc output files (GEX): barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: cellranger-arc output files (ATAC): atac_fragments.tsv.gz
Library strategy: single cell multiome

molecule: genomic DNA

source_name: brain

extract_protocol:
Brain samples were isolated from embryonic day 14 (E14) mice. The samples were mechanically dissociated into single cells by gentle pipetting.
Library preparation was performed according to the manufacturer's instructions using the Chromium Next GEM Single Cell Multiome ATAC + GEX kit.

value: brain

tag: library type

value: ATAC


title: no-Ag control, biological replicate 1

description: Library name: 34A


title: HdLEC Control 1

value: Lymphatic Endothelial Cells

value: Dermal LEC

value: Control (Ig-Fc stimulated)


title: WT, ATAC

value: WT


title: Del, GEX

value: mRNA


title: HC1 sample long read RNA-Seq

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: Library name: bc08

library_source: other

data_processing:
Raw Illumina short-read RNA-seq data were processed using the ERVmancer pipeline for quantification of HERV expression at both the locus and clade levels. PacBio long-read RNA-seq reads were aligned to the hg38 human reference genome (UCSC) using minimap2 v2.28
Assembly: hg38 human reference genome (UCSC)
Supplementary files format and content: ervmancer_output_normalized.csv - short read based HERV quantification using ERVmancer, and minimap2_output_normalized.csv - long-read based HERV quantification using minimap2
Supplementary files format and content: Format is csv text files. The normalized counts (CPM) for each HERV and clade applying the ERVmancer tool to short read data: ervmancer_output_normalized.csv  and similar from long read, when applying minimap2 to the long read data: minimap2_output_normalized.csv

molecule: other

source_name: peripheral blood

extract_protocol:
Total RNA was isolated from 2 × 106 cells using the RNeasy Mini Kit (Qiagen, Germany) and treated with deoxyribonuclease (Qiagen, Hilden, Germany), following the manufacturer’s protocol. An RNA integrity number (RIN) value greater than 9.0 was determined by TapeStation (Agilent Technologies) for all samples prior to short paired-end and long-read RNA-seq.
For paired-end RNA-seq, sequencing library preparation for SLCLs was completed using the True-seq library preparation kit (Illumina, San Diego). For long-read RNA-seq isoform libraries were prepared with the PacBio Iso-Seq Express kit according to the manufacturer’s protocol, which included oligo(dT)-primed cDNA synthesis and SMRTbell adapter ligation.

value: peripheral blood

value: Spontaneous lymphoblastoid cell line

tag: sample group

value: HC


title: MDA-MB-231-D3H2LN with JAG1 KO 2

value: Breast Cancer

value: MDA-MB-231-D3H2LN with JAG1 KO cell line with lentiviral transduction with empty vector (pCCL.PKG-WPRE)


title: SMS5 sample long read RNA-Seq

description: Library name: bc06

value: SMS


title: WT, GEX


title: SMS6 sample long read RNA-Seq

description: Library name: bc07


title: MDA-MB-231-D3H2LN cells with  CRISPR/Cas9 JAG1 deletion - clone 2 (F) rep1

description:
RvsFcounts.txt
F1

value: CRISPR/Cas9 JAG1 deletion - clone2


title: TAMC NP-D@MP [N12]

city: Guangzhou

first: Dongbing

last: Ding

address: 600 Tianhe Road, Tianhe District, Guangzhou City, Guangdong Province

institute: The Third Affiliated Hospital of Sun Yat-sen University

data_processing:
Illumina Casava1.7 software used for basecalling.
Suquenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al. Nucleic Acids Research, 2009. In short exons from all isoforms.
Assembly: mm8
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: marrow

extract_protocol:
Retinas were removed, flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (cat#FC-122-1001) was used with 1 ug of total RNA for the construction.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: marrow

value: TAMC

value: Immune cell


title: SMS2 sample long read RNA-Seq

description: Library name: bc04


title: TAMC NP-D@MP [N11]


title: HC3 sample long read RNA-Seq

description: Library name: bc10


title: TAMC NP-D@MP [N10]


title: AMS5 sample long read RNA-Seq

description: Library name: bc03

value: AMS


title: TAMC NP-D@M [N9]


title: HC2 sample long read RNA-Seq

description: Library name: bc09


title: AMS3 sample long read RNA-Seq

description: Library name: bc02


title: AgNP, biological replicate 2

description: Library name: 34H

value: AgNP


title: TAMC NP-D@M [N8]


title: TAMC NP-D@M [N7]


title: SMS3 sample long read RNA-Seq

description: Library name: bc05


title: TAMC NP@M [N6]


title: TAMC NP@M [N5]


title: AMS2 sample long read RNA-Seq

description: Library name: bc01


title: Stereotaxic brain tumor biopsy, patient 237, Diffuse glioma

type: genomic

city: Frankfurt

first: Katharina

last: Weber

address: Heinrich-Hoffmann-Straße 7

department: Institute of Neurology

country: Germany

institute: University Hospital Frankfurt

hyb_protocol: Bisulfite-converted DNA was hybridized to Illumina Infinium MethylationEPIC BeadChip (v1) following the manufacturer's standard protocol.

scan_protocol: EPIC array BeadChips were scanned using an iScan system (Illumina, San Diego, California, USA) and raw intensity data (IDAT files) were obtained.

data_processing: IDAT files were uploaded to molecularpathology.org (Heidelberg brain tumor classifier v11b4) to obtain calibrated scores for DNA methylation classes and subclasses, copy number variation profiles and MGMT promoter methylation status. Additional classification was performed using the Bethesda brain tumor classifier (v2) and EpiDiP. IDAT files were processed using R packages RnBeads for quality control and normalization (dasen method from wateRmelon package), and MethylCIBERSORT for reference-based tumor deconvolution. Genome build: hg19.

label: Cy3, Cy5

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_237

label_protocol: DNA was further processed and hybridized to the Illumina Infinium MethylationEPIC BeadChip (v1) following protocols provided by the manufacturer.

growth_protocol: Not applicable (FFPE tissue from stereotaxic brain tumor biopsies)

extract_protocol: Selected FFPE tissue samples were transferred into Eppendorf tubes using biopsy punches.

treatment_protocol: Not applicable (tissue samples)

value: brain

tag: disease state

value: Diffuse glioma

tag: age

tag: Sex

value: female

tag: sample type

value: FFPE stereotaxic biopsy

tag: dna concentration (ng/ul)


title: TAMC PBS [N3]

value: PBS


title: TAMC NP@M [N4]


title: Stereotaxic brain tumor biopsy, patient 236, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_236


title: TAMC PBS [N2]


title: Stereotaxic brain tumor biopsy, patient 234, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_234

value: male


title: Stereotaxic brain tumor biopsy, patient 233, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_233


title: TAMC PBS [N1]


title: NES tumours derived from inducing MYCN(T58A) in vivo, rep 1

description:
Library name: NESt_rep1
B1_1_Animal.DoxON_309478

value: brain tumour (intracranial xenograft)

value: Sai2 (NES MYCN(T58A)-derived)

value: MYCN(T58A), doxycycline-induced

value: doxycycline (in vivo dox diet)


title: Peripheral blood serum, multiple myeloma group B 8

city: Brno

first: Sabina

last: Ševčíková

address: Kamenice 5

country: Czech Republic

institute: Masaryk University

description: Library name: MM.20.37

data_processing:
The miRge3 sequencing analysis pipeline, allowing processing Unique Molecular Identifiers (UMI), was applied for data processing. MiRBase database was used for miRNA reads alignment. Count-based miRNA expression data were further analyzed by R/Bioconductor packages.
Assembly: mirBase hg38
Supplementary files format and content: text file with raw reads for each sample

source_name: Peripheral blood serum

extract_protocol:
miRNeasy Serum/Plasma Kii
QIAseq miRNA Library Kit

value: Peripheral blood serum

tag: group

value: B


title: Stereotaxic brain tumor biopsy, patient 232, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_232

value: Glioblastoma


title: Peripheral blood serum, multiple myeloma group B 7

description:
Library name: MM.19.60
Samples MM.19.60 and MM.19.84 had very low read counts, so they were omitted from our analyses.


title: Stereotaxic brain tumor biopsy, patient 231, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_231


title: Peripheral blood serum, multiple myeloma group B 6

description: Library name: MM.18.27


title: Stereotaxic brain tumor biopsy, patient 230, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_230


title: Peripheral blood serum, multiple myeloma group B 5

description: Library name: MM.14.47


title: Stereotaxic brain tumor biopsy, patient 229, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_229


title: Peripheral blood serum, multiple myeloma group B 4

description: Library name: MM.13.68


title: Stereotaxic brain tumor biopsy, patient 228, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_228


title: Peripheral blood serum, multiple myeloma group B 3

description: Library name: MM.13.185


title: Peripheral blood serum, multiple myeloma group B 2

description: Library name: MM.13.104


title: Stereotaxic brain tumor biopsy, patient 227, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_227


title: Stereotaxic brain tumor biopsy, patient 226, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_226


title: Peripheral blood serum, multiple myeloma group B 1

description: Library name: MM.13.103


title: Peripheral blood serum, multiple myeloma group A 8

description: Library name: MM.11.112

value: A


title: Peripheral blood serum, multiple myeloma group A 7

description: Library name: MM.16.137


title: Stereotaxic brain tumor biopsy, patient 224, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_224


title: Stereotaxic brain tumor biopsy, patient 223, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_223


title: Peripheral blood serum, multiple myeloma group A 6

description: Library name: MM.19.108


title: siControl, DMSO control, 2

city: Vienna

first: Aleksandra

middle: S

last: Anisimova

address: Dr. Bohr Gasse 9

country: Austria

institute: Max Perutz Labs, Vienna BioCenter, University of Vienna, Medical University of Vienna

description: Library name: DMSO_siControl_2

data_processing:
The quality- and adapter-trimmed reads were aligned to human genome hg38 using GENCODE annotation (release 36) with STAR v2.7.5c allowing up to one or two mismatches. Gene read counts were obtained with featureCounts v2.0.1.
Assembly: hg38
Supplementary files format and content: csv, gene read count table

growth_protocol: HCT116 WT cells were a kind gift from Prof. Manuela Baccarini (MPL, University of Vienna). HCT116 cells were cultured in McCoy’s 5A (modified) medium (Sigma, M9309) supplemented with 10% fetal bovine serum (Gibco, 10437028), 2 mM L-Glutamine (Sigmam, G7513), 1% Pen/Step (Sigma, P0781) in a humidified incubator at 37°C and 5% CO2. For siRNA knockdown, cells were transfected with ON-TARGETplus Human IGF2BP2 (Dharmacon, L-017705-00-0005) or IGF2BP3 (Dharmacon, L-003976-00-0005) SMARTpool siRNAs  at 75 nM for 48 hours using DharmaFECT 2 (Dharmacon, T-2002-01). ON-TARGETplus nontargeting siRNA #1 (Dharmacon, D-001810-01-05) was used as a control.

extract_protocol:
One ~80% confluent well of a 6-well plate per condition (three biological replicates per condition) was washed with ice-cold PBS (Sigma) supplemented with 100 mg/mL cycloheximide, lysed on a plate on ice with 350 μL of ice-cold lysis buffer (20 mM HEPES pH 7.3, 150 mM KCl, 5 mM MgCl2, 1% Triton X-100, 100 mg/mL cycloheximide, 1 mM DTT, 1x EDTA-free protease inhibitor cocktail), scraped, and transferred to 1.5 mL RNase-free tube. Cell lysates were passed three times through the 27G needle, incubated on ice for 10 min with intermittent vortexing, and clarified on a table-top centrifuge at maximum speed (20,000 g) for 20 min at 4°C. Total RNA concentration in the lysate was estimated using OD A260 measurement on Nanodrop. The lysate concentrations were brought to 240 ng/μL, 15 μL aliquots were taken for matching RNA-Seq.
RNA-Seq libraries were prepared with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490L) and NEBNext Ultra II Directional RNA Library Prep Kit (NEB, E7765L) and sequenced on a NovaSeq SP on SR100 (Illumina) aiming for 30 million reads per sample on average.

treatment_protocol: Endoplasmic reticulum (ER) stress was induced with 5 µg/mL tunicamycin (TM) for 4 hours (1:1000 DMSO was used as a control).

value: human colorectal carcinoma

value: DMSO control


title: Peripheral blood serum, multiple myeloma group A 5

description: Library name: MM.16.80


title: Stereotaxic brain tumor biopsy, patient 222, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_222


title: Stereotaxic brain tumor biopsy, patient 221, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_221


title: Peripheral blood serum, multiple myeloma group A 4

description: Library name: MM.11.147


title: Peripheral blood serum, multiple myeloma group A 3

description: Library name: MM.20.146


title: Stereotaxic brain tumor biopsy, patient 220, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_220


title: Stereotaxic brain tumor biopsy, patient 219, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_219


title: Peripheral blood serum, multiple myeloma group A 2

description: Library name: EM.11.008


title: Stereotaxic brain tumor biopsy, patient 218, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_218


title: Stereotaxic brain tumor biopsy, patient 217, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_217


title: Peripheral blood serum, multiple myeloma group C 8

description: Library name: MM.6.67

value: C


title: Peripheral blood serum, multiple myeloma group A 1

description:
Library name: MM.19.84
Samples MM.19.60 and MM.19.84 had very low read counts, so they were omitted from our analyses.


title: Stereotaxic brain tumor biopsy, patient 216, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_216

value: brain


title: Peripheral blood serum, multiple myeloma group C 7

description: Library name: MM.9.143

source_name: Peripheral blood serum


title: Murine lung ILC2_IL-2_IL-7_IL-33+DTA-1_24h_rep2

city: Seoul

first: Young Gyun

last: Ko

address: 103, daehak-ro, Jongro-gu

country: South Korea

institute: Seuol National university

description: Library name: IL-33_DTA-1_2

data_processing:
Before starting analysis, Trim Galore (version 0.6.10) was used to remove adapter sequences and trim bases with base quality lower than three from both ends of the reads. Also using sliding window trim method, bases that does not qualify for window size=4, and mean quality=15 are filtered. Afterwards, reads less than 36 bp in length are excluded to produce high quality data.
The cleaned reads were aligned to the mouse genome (mm10) using Bowtie2 (version 2.5.1 parameter set --maxins 5000 --very-sensitive --no-discordant --no-mixed --no-unal --mm). Mapped data (SAM file format) were sorted and indexed using SAMtools (version 1.9). After removing reads aligned to the mitochondrial genome from the indexed BAM file, duplicate reads were removed using MarkDuplicates in Picard (version 0.118).
Peaks were called in the aligned sequence data using a model-based analysis of ATAC-seq (MACS2 version 2.1.1.20160309). The algorithm empirically models the length of ATAC-Seq fragments from the sequence data, considering local genomic biases in a distribution of mapped reads. The following parameters were used: macs2 callpeak -t ATAC-seq.bam -g hs --bdg --nolambda --keep-dup all --broad. Among the called peaks, the peaks overlapping with ENCODE blacklisted regions were removed.
ChIPseeker (version 1.22.1), a bioconductor package within R (version 4.2.2) to facilitate batch annotation of enriched peaks, was used to identify nearby genes and transcripts from the peaks obtained from MACS2
Assembly: mm10
Supplementary files format and content: bigWig

source_name: lung

growth_protocol: Murine primary lung ILC2 were maintained in RPMI 1640 supplemented with 10% FBS and gentamycin in humidified atomsphere with 5% CO2 at 37C

extract_protocol:
Prepare 100,000 cells. Cells were lysed using cold lysis buffer. Determine the nuclei concentration using LUNA-FL™ Automated Fluorescence Cell Counter (logos biosystems) and examine the nuclei morphology using microscopy.
Immediately after lysis, continue to transposition reaction using Tagment DNA TDE1 Enzyme and Buffer Kit (illumina). Resuspend nuclei (50,000 cells) in transposition reaction mix. Incubate the transposition reaction for 30min at 37°C. Immediately following transposition, purify using a Qiagen MinElute PCR purification Kit. Amplify transposed DNA fragment using Macrogen kit. To reduce GC and size bias in PCR, the appropriate number of cycles is determined using qPCR. Run a qPCR side reaction. Calculate the additional number of cycles needed, plot liner Rn versus cycle and determine the cycle number that corresponds to 1/4 of maximum fluorescent intensity. Run the remaining PCR reaction to the cycle number determined by qPCR. Purify amplified library. The libraries were sequenced using HiSeq X ten platform

treatment_protocol: isotype control antibody IgG2b and GITR agonist antibody DTA-1 were treated to ILC2 under 10 ng/ml IL-2, IL-7 and IL-33 stimulation condition for 24h

value: lung

value: primary lung ILC2

value: primary

value: WT


title: Stereotaxic brain tumor biopsy, patient 235, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_235

value: male

value: FFPE stereotaxic biopsy


title: MIAML-279-Dx

city: Ann Arbor

first: Qianyi

last: Ma

state: MI

address: 1141 E Catherine St

department: Human Genetics

institute: University of Michigan

description: human leukemic bone marrow mononuclear cells single cell Drop-seq

data_processing:
Two paired-end fastq files were converted to one query-sorted bam file using Picard tools v2.6.0 and samtools v1.2.
Sequence reads were tagged with cell and molecular barcodes, filtered for low base quality in cell or molecular barcodes, trimmed for starting sequence and polyA tail using Drop-seq tools v1.13.
The barcode-tagged, filtered and trimmed bam file is converted back to fastq file using Picard tools v2.6.0.
Alignment was performed using Star v2.5.2a.
Aligned reads were tagged with gene exons and cleaned for bead synthesis errors using Drop-seq tools v1.13.
Gene expression matrix was generated using Drop-seq tools v1.13.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include raw UMI counts for each cell (column) and each gene (row)

source_name: leukemic bone marrow (AML)

growth_protocol: Cryo-preserved bone marrow mononuclear cells or peripheral blood mononuclear cells from AML patients or healthy donors (STEMCELL Technologies) were thawed in a 37 °C water bath, dissociated by DNase I solution (New England Biolabs) treatment at a final concentration of 0.1 mg/mL and filtered through 40 μm cell strainers (Corning Life Sciences) to remove clumped cells. Isolated single cells were transferred into warm culture media (RPMI1640 supplemented with 10% FBS) and incubated at 37 °C for 2 hours. Then dead cells in the culture were eliminated using a dead cell removal kit from Miltenyi Biotec following the manufacturer’s protocol. The remaining viable single cells were counted and resuspended at 100 cells/ μl in a PBS-BSA solution.

extract_protocol:
Single-cell RNA sequencing was performed following the Drop-seq Online Protocol by Macosko et al (http://mccarrolllab.com/dropseq/) with minor modifications. Briefly, single cell suspension were loaded into the microfluidic device (FlowJEM) together with droplet-generating oil (Bio-Rad) and barcoded beads (MACOSKO-2011-10, Chemgenes) suspended in lysis buffer supplemented with RNase inhibitor (Lucigen) at a final concentration of 1 U/µL. Emulsions were incubated on ice for 30 minutes before droplet breakage and bead collection. Beads were subject to reverse transcription (Maxima H Minus Reverse Transcriptase: ThermoFisher; Template switch oligo: IDT) and Exo I (New England Biolabs) digestion. Next, 4000 beads were aliquoted into one PCR tube for amplification (KAPA HotStart ReadyMix: Kapa Biosystems). Products from multiple parallel PCRs were pooled together and purified using AMPure XP Beads (Beckman Coulter Life Sciences).
For each sample, 1 ng high quality cDNA was used for tagmentation and NGS library preparation using a Nextera XT kit (Illumina). High quality NGS libraries were sequenced on an Illumina NextSeq 550 (75-cycle kit) or NovaSeq 6000 (100-cycle kit) sequencers. All paired AML samples were processed and sequenced together to minimize batch effects.

tag: ex vivo treatment

value: untreated

value: bone marrow

value: AML

tag: time point

value: at diagnosis


title: Peripheral blood serum, multiple myeloma group C 6

description: Library name: MM.8.192

tag: tissue

value: Peripheral blood serum


title: Stereotaxic brain tumor biopsy, patient 215, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_215

value: Glioblastoma


title: Peripheral blood serum, multiple myeloma group C 5

description: Library name: MM.16.149


title: Murine lung ILC2_IL-2_IL-7_IL-33+DTA-1_24h_rep1

description: Library name: IL-33_DTA-1_1


title: Peripheral blood serum, multiple myeloma group C 4

description: Library name: MM.12.62


title: Stereotaxic brain tumor biopsy, patient 214, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_214

value: female


title: Peripheral blood serum, multiple myeloma group C 3

description: Library name: A.15.4


title: Murine lung ILC2_IL-2_IL-7_IL-33+IgG2b_24h_rep2

description: Library name: IL-33_IgG2b_2


title: Peripheral blood serum, multiple myeloma group C 2

description: Library name: MM.11.161


title: Stereotaxic brain tumor biopsy, patient 213, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_213


title: Murine lung ILC2_IL-2_IL-7_IL-33+IgG2b_24h_rep1

description: Library name: IL-33_IgG2b_1


title: SMS6 sample short read RNA-Seq

description: Library name: S6_2023-5-23_S6

source_name: peripheral blood

value: peripheral blood

value: Spontaneous lymphoblastoid cell line

value: SMS


title: Peripheral blood serum, multiple myeloma group C 1

description: Library name: MM.11.84

value: C


title: Stereotaxic brain tumor biopsy, patient 212, unclassified brain lesion

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_212

value: brain

value: unclassified brain lesion


title: SMS5 sample short read RNA-Seq

description: Library name: S5_2023-5-23_S5


title: exp07_memory_NupHox_LmOVA_D3_D5_Hashtag_Data

city: Prague

first: Juraj

last: Michalik

address: Vídeňská 1083

institute: Institute of Molecular Genetics of the Czech Academy of Sciences

description:
Library name: exp07-W1-CSP
Each sample has two hashtags: one from 1-6, one from 9-10. Samples are thus combination of Day/cell type and clone. Specifically: Mouse_Hashtag_1 and Mouse_Hashtag_9 = Taim progeny day 5 clone 12, Mouse_Hashtag_1 and Mouse_Hashtag_10 = Taim progeny day 5 clone 2, Mouse_Hashtag_2 and Mouse_Hashtag_9 = Tm progeny day 5 clone 12, Mouse_Hashtag_2 and Mouse_Hashtag_10 = Tm progeny day 5 clone 2, Mouse_Hashtag_3 and Mouse_Hashtag_9 = Tn progeny day 3 clone 12, Mouse_Hashtag_3 and Mouse_Hashtag_10 = Tn progeny day 3 clone 2, Mouse_Hashtag_4 and Mouse_Hashtag_9 = Tm progeny day 3 clone 12, Mouse_Hashtag_4 and Mouse_Hashtag_10 = Tm progeny day 3 clone 2, Mouse_Hashtag_5 and Mouse_Hashtag_9 = Taim progeny day 3 clone 12, Mouse_Hashtag_5 and Mouse_Hashtag_10 = Taim progeny day 3 clone 2, Mouse_Hashtag_6 and Mouse_Hashtag_9 = Tn progeny day 5 clone 12, Mouse_Hashtag_6 and Mouse_Hashtag_10 = Tn progeny day 5 clone 2.  Sample marked by Mouse_Hashtag_4 and Mouse_Hashtag_9  was not sorted and therefore was excluded along with remaining samples from clone 12 and day3 du to comparability issues.

data_processing:
Sequencing was performed on NovaSeq 6000 platform.
Base calling and FASTQ generation were performed using the Illumina BaseSpace GenerateFASTQ workflow v1.37.0.
The murine reference genome used for read alignment was obtained from Ensembl release 102 and prepared using the mkref tool from 10x Cell Ranger v5.0.1 (Zheng et al., 2017). Count matrices were generated using the count tool from either 10x Cell Ranger v5.0.1 using paired-end sequencing mode.
Subsequent analyses were performed in R v4.5.2 using the Seurat v5.3.0 package (Hao et al., 2024).
Assembly: GRCm38 v102 (Ensembl)
Supplementary files format and content: File containing specification of each hashtag and sample, in CSV format, used by 10X Cell Ranger to quantify each hashtag for each cell.
Supplementary files format and content: 10X Cell Ranger output: list of barcodes in TSV format
Supplementary files format and content: 10X Cell Ranger output: list of genes/features and their type in TSV format
Supplementary files format and content: 10X Cell Ranger output: sparse matrix quantifying results
Supplementary files format and content: RDS file containing Seurat object of processed samples from Day 3 (clone 2 only).
Supplementary files format and content: RDS file containing Seurat object of processed samples from Day 5.
Library strategy: CITE-seq

source_name: spleen

growth_protocol: Immortalized bone marrow hematopoietic stem cells from Vβ5 Rag2-/- mice were transduced with MSCV retroviral vectors encoding Clone 2 or Clone 12 TCRs and GFP or LNGFR selection markers as previously described {Ruedl et al., 2008; Drobek et al., 2018; Paprckova et al., 2022).

extract_protocol:
The progeny was FACS-isolated frrom the spleen.
Cells from all experiments were loaded onto a Chromium Controller (10x Genomics).cDNA libraries  were prepared using the Chromium Single Cell V(D)J Reagent Kits with Feature Barcode technology for Cell Surface Protein protocol (#CG000186 Rev D) and the Chromium Single Cell 5′ Library & Gel Bead Kit and Chromium Single Cell 5′ Feature Barcode Library Kit (10x Genomics; #PN-1000014, #PN-1000020, #PN-1000080, #PN-1000009, #PN-1000084).

treatment_protocol: FACS-sorted GFP+/LNGFR+ CD45.2+ cells were transplanted into irradiated (6 Gy) congenic CD45.1 recipient mice. At least 8 weeks after the transplantation, the GFP+ or LNGFR+ retrogenic T cells were FACS-sorted from the spleens and lymph nodes, FACS-sorted, and transferred into another congenic hosts followed by Lm-OVA infection day after.

value: spleen

value: CD8+ T cells

value: Progeny of Tn/Tm/Taim

value: Lm-OVA infection

tag: time

value: Day 3/ Day5


title: Stereotaxic brain tumor biopsy, patient 211, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_211

value: male

value: FFPE stereotaxic biopsy


title: SMS3 sample short read RNA-Seq

description: Library name: S3_2023-5-23_S3


title: SMS2 sample short read RNA-Seq

description: Library name: S2_2023-5-23_S2


title: exp07_memory_NupHox_LmOVA_D3_D5_GEX_Data

description: Library name: exp07-W1-GEX

data_processing:
Sequencing was performed on NovaSeq 6000 platform.
Base calling and FASTQ generation were performed using the Illumina BaseSpace GenerateFASTQ workflow v1.37.0.
The murine reference genome used for read alignment was obtained from Ensembl release 102 and prepared using the mkref tool from 10x Cell Ranger v5.0.1 (Zheng et al., 2017). Count matrices were generated using the count tool from either 10x Cell Ranger v5.0.1 using paired-end sequencing mode.
Subsequent analyses were performed in R v4.5.2 using the Seurat v5.3.0 package (Hao et al., 2024).
Assembly: GRCm38 v102 (Ensembl)
Supplementary files format and content: File containing specification of each hashtag and sample, in CSV format, used by 10X Cell Ranger to quantify each hashtag for each cell.
Supplementary files format and content: 10X Cell Ranger output: list of barcodes in TSV format
Supplementary files format and content: 10X Cell Ranger output: list of genes/features and their type in TSV format
Supplementary files format and content: 10X Cell Ranger output: sparse matrix quantifying results
Supplementary files format and content: RDS file containing Seurat object of processed samples from Day 3 (clone 2 only).
Supplementary files format and content: RDS file containing Seurat object of processed samples from Day 5.

tag: cell type


title: HC3 sample short read RNA-Seq

description: Library name: HC3_2023-5-23_S13

tag: cell line

value: HC


title: Stereotaxic brain tumor biopsy, patient 210, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_210

value: Diffuse glioma


title: HC1 sample short read RNA-Seq

description: Library name: HC1_2023-5-23_S11


title: KD_rep3

first: Jiexi

last: Li

address: 1881 East Road

institute: The University of Texas MD Anderson Cancer Center

description: Library name: Sample 12

data_processing:
The NextSeq RTA (version 2.4.11.0) was used for base calling. Bcl2fastq (version 2.20.0) was used to convert the .bcl files into .fastq files. Fastq files were aligned to the mouse reference genome (mm10) using HISAT2 software and assembled using StringTie. R package DESeq2 was used for data normalization and differential expression analysis.
Assembly: mm10
Supplementary files format and content: raw counts

source_name: Male

growth_protocol: OT-1 CD8+ T cells were cultured in complete T cell culture medium with mouse recombinant IL2.

extract_protocol:
RNA was harvested using the QIAGEN RNeasy Plus Universal Mini Total RNA protocol
Libraries were generated using Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus Kit following manufacturers protocol.

value: Male

value: OT-1 CD8+ T cells

value: KDM5D KD


title: HC2 sample short read RNA-Seq

description: Library name: HC2_2023-5-23_S12

value: peripheral blood

value: Spontaneous lymphoblastoid cell line


title: Stereotaxic brain tumor biopsy, patient 209, Circumscribed glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_209

value: Circumscribed glioma

value: female


title: AMS5 sample short read RNA-Seq

description: Library name: A5_2023-5-23_S10

value: AMS


title: AMS3 sample short read RNA-Seq

description: Library name: A3_2023-5-23_S8


title: KD_rep2

description: Library name: Sample 11


title: Stereotaxic brain tumor biopsy, patient 208, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_208

value: brain


title: Stereotaxic brain tumor biopsy, patient 225, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_225

value: Glioblastoma


title: AMS2 sample short read RNA-Seq

description: Library name: A2_2023-5-23_S7


title: Stereotaxic brain tumor biopsy, patient 206, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_206


title: EE_72h_Pituitary-83

type: RNA

city: Wuppertal

first: Mira

last: Pavkovic

address: Aprather Weg 18a

institute: Bayer AG

description: OECD-compliant uterotrophic assay using ethinyl estradiol (EE) in juvenile female rats

scan_protocol: fluorescent images of the GeneChips were captured with the Affymetrix GeneChip Scanner 3000

data_processing:
Using Affymetrix MicroarraySuite (MAS)5.0 the raw data image files (dat) were converted in to cel-files in which the scanned data were summarized as one intensity value per unit.
RAE230A.CDF

label: biotin

organism: Rattus norvegicus

source_name: pituitary gland

label_protocol: 5 µg total RNA was processed for Affymetrix RAE230A GenechipsR hybridization according to the manufacturer’s instructions

growth_protocol: OECD uterotrophic assay in immature rats

extract_protocol: total RNA isolation with the RNAeasy Mini kit (Qiagen; Hilden, Germany) according to the manufacturer’s instructions

tag: gender

tag: development stage

value: immature


title: WT_rep3

city: Houston

description: Library name: Sample 9

value: CD8+ T cells

tag: genotype

value: WT


title: WT_rep2

description: Library name: Sample 8


title: EE_72h_Pituitary-81

hyb_protocol: processed for Affymetrix RAE230A GenechipsR hybridization according to the manufacturer’s instructions


title: Stereotaxic brain tumor biopsy, patient 205, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_205


title: EE_72h_Pituitary-82


title: EE_48h_Pituitary-71


title: EE_48h_Pituitary-69


title: Control, IGF2BP3 KO, clone A3, 1

description: Library name: Control_IGF2BP3KO_A3_rep1

data_processing:
The quality- and adapter-trimmed reads were aligned to human genome hg38 using GENCODE annotation (release 36) with STAR v2.7.5c allowing up to two mismatches per read.
Assembly: hg38
Supplementary files format and content: csv, gene read count table

growth_protocol: HCT116 conditionally expressing doxycycline-inducible (tetON) OsTIR1 were obtained from the Masato Kanemaki lab (Natsume et al. 2016).  HCT116 cells were cultured in McCoy’s 5A (modified) medium (Sigma, M9309) supplemented with 10% fetal bovine serum (Gibco, 10437028), 2 mM L-Glutamine (Sigmam, G7513), 1% Pen/Step (Sigma, P0781) in a humidified incubator at 37°C and 5% CO2. For knockout cell line generation, gRNA sequences (IGF2BP3 KO clones E4 and A3: 5′TGGCACCGACTGATAGAGCT 3′; clone D12: 5′ACGCGTAGCCAGTCTTCACC 3′; IGF2BP2 KO clones F6 and B7: 5′GAGCTGCCGGAGGTCGTCGG 3′; clone G6: 5′AGGCGTAGCCGGACTTCAGC 3') were cloned into the pSpCas9 (BB)-2A-GFP (PX458) (plasmid #48138; Addgene) (Ran et al. 2013 ). HCT116 tetON OsTIR1 cells were transiently transfected using jetOPTIMUS reagent (Tamar, 101000051), and GFP-positive single-cell clones were FACS sorted at BD FACSAria IIIu at Max Perutz Labs BioOptics FACS Facility.

extract_protocol:
Total RNA was isolated using peqGOLD TriFast (Peqlab, VWR), treated with RNase-free DNase I (NEB), and re-purified with peqGOLD TriFast (Peqlab, VWR). RNA precipitation was done using isopropanol method.
Total RNA sequencing libraries were prepared with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490L) and NEBNext Ultra II Directional RNA Library Prep Kit (NEB, E7765L) by Vienna BioCenter NGS facility sequenced on a NovaSeq S4 on PE100 (Illumina) with 55 million reads per sample on average.

treatment_protocol: HCT116 tetON OsTIR1 IGF2BP3 KO clones E4, A3, and D12 (in duplicates) and parental cells (four replicates) were treated with 5 µg/mL tunicamycin (TM) for 4 hours (1:1000 DMSO was used as a control).

value: human colorectal carcinoma

value: IGF2BP3 KO, clone A3, Tet-OsTIR1-PURO

tag: treatment

value: DMSO control


title: EE_48h_Pituitary-68


title: WT_rep1

description: Library name: Sample 7


title: Stereotaxic brain tumor biopsy, patient 204, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_204

value: Diffuse glioma

value: male

value: FFPE stereotaxic biopsy


title: Male_rep3

description: Library name: Sample 6

value: Male

value: OT-1 CD8+ T cells


title: EE_24h_Pituitary-46


title: Stereotaxic brain tumor biopsy, patient 203, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_203


title: KD_rep1

description: Library name: Sample 10

value: KDM5D KD


title: Male_rep2

description: Library name: Sample 5


title: EE_24h_Pituitary-44


title: EE_8h_Pituitary-34


title: EE_24h_Pituitary-43


title: Stereotaxic brain tumor biopsy, patient 202, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_202


title: EE_8h_Pituitary-33


title: Male_rep1

description: Library name: Sample 4


title: Stereotaxic brain tumor biopsy, patient 201, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_201


title: Female_rep3

description: Library name: Sample 3

source_name: Female

value: Female


title: EE_8h_Pituitary-32

value: female


title: Stereotaxic brain tumor biopsy, patient 200, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_200


title: Female_rep2

description: Library name: Sample 2


title: EE_4h_Pituitary-23


title: EE_4h_Pituitary-20


title: EE_4h_Pituitary-21


title: Stereotaxic brain tumor biopsy, patient 199, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_199


title: Control_72h_Pituitary-76


title: Control_72h_Pituitary-75


title: Stereotaxic brain tumor biopsy, patient 198, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_198


title: Female_rep1

description: Library name: Sample 1


title: Control_72h_Pituitary-73


title: Control_48h_Pituitary-66


title: Brain Sample_female 2

city: hangzhou

first: kaiyuan

last: li

state: zhejiang

address: Zhejiang University School of Medicine, Hangzhou, 310058, China

department: Zhejiang University School of Medicine

institute: School of Brain Science and Brain Medicine

description:
Library name: Sample 4
10X Genomics

data_processing:
Libraries were sequenced on different lanes of an Illumina NovaSeq 6000 machine. Base calling was performed by Illumina software to generate FASTQ files, which were then processed through the Cell Ranger software pipeline (version 6.0.1) provided by 10×Genomics, aligning against the mm10 mouse genome. The resulting gene expression count matrix was processed and analyzed in Seurat V5.
Assembly: Mouse mm10
Supplementary files format and content: Seurat object containing good pSI neurons from all 4 samples.  rData file

source_name: brain

extract_protocol:
Single nucleus were suspended in calcium-, magnesium- and RNase-free PBS containing 0.04% weight/volume BSA. Then Cell nucleus were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads. Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed, and index adaptor ligated and library amplification.RNA libraries were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol. 10x Genomics Chromium Single Cell 3’ Reagents v3 snRNAseq
Library preparation was performed according to the manufacturer’s instructions (Single Cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate gel bead-in-emulsions (GEMs). Each GEM contained a single cell, a gel bead, and the necessary reagents for the reaction. The poly-A RNA released from the cell lysate within each GEM bound to primers on the gel bead and was reverse-transcribed into cDNA, which contained an Illumina R1 sequence, a Unique Molecular Identifier (UMI), and a 10x Barcode. Subsequently, the pooled barcoded cDNA was cleaned up with Silane DynaBeads, amplified by PCR, and appropriate-sized fragments were selected with SPRIselect reagent for subsequent library construction. During library construction, an Illumina R2 primer sequence, P5/P7 adapter sequences, and a sample index were added to generate a complete library ready for sequencing. The final library was assessed for concentration and fragment size distribution, and the qualified library was sequenced on the Illumina NovaSeq high-throughput sequencing platform.

value: wild type

tag: brain area

value: substantia innominata


title: Control_48h_Pituitary-64


title: Brain Sample_female 1

description:
Library name: Sample 3
10X Genomics

value: brain


title: Stereotaxic brain tumor biopsy, patient 197, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_197

tag: disease state

value: Glioblastoma


title: Stereotaxic brain tumor biopsy, patient 196, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_196

tag: age


title: Control_24h_Pituitary-42

value: immature


title: Control_48h_Pituitary-61


title: Control_24h_Pituitary-40


title: Brain Sample_male 2

description:
Library name: Sample 2
10X Genomics

tag: Sex


title: Liver from GalNAc-siRnf10-treated mouse 3

city: Tianjin

first: du

last: chunyuan

address: youyi road

institute: Tianjin Medical University

description:
Library name: GalNAc-siRnf10_3
Liver tissue from wild-type mouse treated with GalNAc-siRnf10

data_processing:
Raw sequencing reads were mapped to the Ensembl mouse reference genome using HISAT2.
Gene-level read counts were generated based on Ensembl gene annotation.
Differential gene expression analysis was performed using DESeq2.
Assembly: GRCm38/mm10
Supplementary files format and content: raw_counts_matrix.txt: Tab-delimited text file containing raw gene-level read counts for all samples. Rows represent genes and columns represent RNA-seq libraries.

source_name: Liver

growth_protocol: Wild-type mice were housed under specific pathogen-free conditions with free access to food and water and were maintained on a normal chow diet.

extract_protocol:
Total RNA was extracted from mouse liver tissues using TRIzol Reagent. RNA concentration and quality were assessed using a Nanodrop spectrophotometer.
RNA-seq libraries were prepared using the Illumina Stranded mRNA Prep, Ligation kit with 1 μg of total RNA. Paired-end cDNA libraries were sequenced on a DNBSEQ platform using the DNBSEQ reagent Kit (FCL PE150, version 3.0) with a read length of 150 bp.

treatment_protocol: Wild-type mice were treated with GalNAc-siNC or GalNAc-siRnf10 by subcutaneous injection at the indicated time points. Liver tissues were collected at 17 weeks of age for RNA extraction and RNA-seq analysis.

value: Liver

tag: batch

value: batch 1


title: Stereotaxic brain tumor biopsy, patient 195, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_195

tag: sample type


title: Liver from GalNAc-siRnf10-treated mouse 2

description:
Library name: GalNAc-siRnf10_2
Liver tissue from wild-type mouse treated with GalNAc-siRnf10


title: Control_24h_Pituitary-38


title: Stereotaxic brain tumor biopsy, patient 207, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_207

tag: dna concentration (ng/ul)


title: Brain Sample_male 1

description:
Library name: Sample 1
10X Genomics


title: Stereotaxic brain tumor biopsy, patient 194, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_194


title: Murine lung ILC2_IL-2_IL-7_IL-33+DTA-1_24h_rep3

description: Library name: SD4

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Tophat
FPKM calculation using Cufflink
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: lung

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the NEBNext Ultra II Directional RNA-Seq Kit standard protocols.

value: lung

value: primary lung ILC2

value: primary

value: WT


title: Liver from GalNAc-siRnf10-treated mouse 1

description:
Library name: GalNAc-siRnf10_1
Liver tissue from wild-type mouse treated with GalNAc-siRnf10


title: Stereotaxic brain tumor biopsy, patient 193, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_193

value: male

value: FFPE stereotaxic biopsy


title: Control_8h_Pituitary-26

source_name: pituitary gland


title: Liver from GalNAc-siNC-treated mouse 3

description:
Library name: GalNAc-siNC_3
Liver tissue from wild-type mouse treated with GalNAc-siNC

value: GalNAc-siNC


title: Control_8h_Pituitary-30


title: Murine lung ILC2_IL-2_IL-7_IL-33+DTA-1_24h_rep2

description: Library name: SD3


title: Liver from GalNAc-siNC-treated mouse 2

description:
Library name: GalNAc-siNC_2
Liver tissue from wild-type mouse treated with GalNAc-siNC


title: Stereotaxic brain tumor biopsy, patient 192, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_192


title: Murine lung ILC2_IL-2_IL-7_IL-33+DTA-1_24h_rep1

description: Library name: SD1


title: Stereotaxic brain tumor biopsy, patient 191, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_191


title: Control_8h_Pituitary-28


title: Liver from GalNAc-siNC-treated mouse 1

description:
Library name: GalNAc-siNC_1
Liver tissue from wild-type mouse treated with GalNAc-siNC


title: Murine lung ILC2_IL-2_IL-7_IL-33+IgG2b_24h_rep3

description: Library name: S4


title: Stereotaxic brain tumor biopsy, patient 190, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_190

value: Diffuse glioma


title: Control_4h_Pituitary-18


title: Input ChIP 3xFP-NES EtOH rep3

city: Zurich

first: Shin

last: Ohsawa

address: Otto-Stern-Weg 3

department: Institute of Biochemistry

country: Switzerland

institute: ETH Zurich

description:
Library name: input_3506_EtOH_3
Input control

data_processing:
Raw paired-end sequencing reads were processed using fastp (version 0.23.4) for automated adapter trimming and quality filtering (parameters: -q 30 --length_required 20 --detect_adapter_for_pe).
Cleaned reads were aligned to the standard Saccharomyces cerevisiae reference genome (R64-1-1) using STAR (version 2.7.11b) in basic two-pass mode (parameters: --twopassMode Basic --outFilterMismatchNmax 3 --chimSegmentMin 2 --alignIntronMax 299999 --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate).
Gene-level read quantification was performed using featureCounts from the Rsubread package (version 2.16.1). To accurately quantify transcripts from repetitive regions, multi-mapping reads (up to 10 alignments per read) and reads overlapping multiple features were retained and fractionally assigned (parameters: isPairedEnd = TRUE, countReadPairs = TRUE, countMultiMappingReads = TRUE, fraction = TRUE, allowMultiOverlap = TRUE).
Assembly: R64-1-1 (sacCer3)
Supplementary files format and content: raw_counts_Scerevisiae.csv is a comma-separated values (CSV) matrix containing raw read counts for all endogenous S. cerevisiae genes and exogenous constructs across all yeast RNA-seq samples, quantified via featureCounts.
Raw paired-end sequencing reads were trimmed and quality-filtered using fastp (version 0.23.4; parameters: -q 30 --length_required 20).
Cleaned reads were aligned to the human reference genome (GRCh38/hg38) using STAR (version 2.7.11b) in basic two-pass mode. To capture transcription from highly repetitive sequences and transposable elements (TEs), multi-mapping was permitted up to 100 locations per read (parameters: --outFilterMultimapNmax 100 --winAnchorMultimapNmax 100).
Aligned BAM files were name-sorted using multi-threaded samtools (version 1.19.2; samtools sort -n).
Simultaneous quantification of protein-coding genes (GENCODE v44 annotation) and transposable elements (RepeatMasker GTF) was executed using TEcount from the TEtranscripts package (version 2.2.4; in multi-mode: --mode multi).
Assembly: GRCh38 (hg38)
Supplementary files format and content: *.cntTable files (e.g., day2_r1.cntTable) are tab-delimited text tables containing raw read counts for both standard GENCODE protein-coding genes and repetitive transposable elements (TEs), generated via TEcount.
Raw paired-end sequencing reads were processed using fastp (version 0.23.4) for automated adapter trimming and quality filtering (-q 30 --length_required 20 --detect_adapter_for_pe).
leaned paired-end reads were aligned to the Saccharomyces cerevisiae reference genome (R64-1-1/sacCer3) using bowtie2 (version 2.5.2).
Alignments were converted, sorted by coordinate, and indexed using samtools (version 1.19.2). (Note: A single outlier replicate, 3xFP-NES mock replicate 2, exhibiting extreme technical variance on PCA was systematically excluded from downstream analytical quantification).
Genome-wide signal coverage tracks (BigWig format) were generated using bamCoverage from the deepTools suite (version 3.5.6) normalized to Counts Per Million (CPM) (parameters: --normalizeUsing CPM --centerReads --binSize 10).
Assembly: R64-1-1 (sacCer3)
Supplementary files format and content: *_CPM.bw files (e.g., IP_3225_EST_1_CPM.bw) are binary BigWig format tracks representing genome-wide ChIP or input control read coverage normalized to Counts Per Million (CPM), generated via deepTools bamCoverage.

organism: Saccharomyces cerevisiae

source_name: not applicable

growth_protocol:
Yeast cells (Saccharomyces cerevisiae) were cultured in standard growth media to logarithmic phase. For G1 arrest excessive cell expansion experiments, the temperature-sensitive cdc28-13 mutant strain was cultured at the restrictive temperature of 37°C.
Human retinal pigment epithelial (RPE1) cells were cultured under standard growth conditions as previously described (Manohar et al., 2023).
Yeast cells (Saccharomyces cerevisiae) were cultured in standard growth media to logarithmic phase.

extract_protocol:
Total RNA was extracted using a hot TES-phenol method followed by column-based cleanup. Cell pellets (mixed with Candida albicans reference pellets as a spike-in control) were resuspended in TES buffer (10 mM Tris pH 7.5, 10 mM EDTA pH 8.0, 0.5% SDS) and lysed with saturated phenol at 65°C under continuous agitation. After sequential re-extraction with phenol and chloroform, RNA was precipitated using 3 M sodium acetate (pH 5.2) and cold isopropanol at -20°C. Resuspended RNA was treated with DNase I in Buffer RDD (Qiagen, cat. no. 79254) at room temperature to eliminate genomic DNA. RNA was subsequently purified, concentrated, and eluted in RNase-free water using the RNeasy MinElute Cleanup Kit (Qiagen, cat. no. 74204). Quality and concentration were assessed using a Qubit Fluorometer (Thermo Fisher Scientific).
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Following fragmentation, first-strand cDNA was synthesized using random hexamer primers, followed by second-strand cDNA synthesis. The final cDNA library was completed through end repair, A-tailing, adapter ligation, size selection, amplification, and purification.
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, cat. no. 74104). Cell pellets were lysed in 400 µL Buffer RLT, vortexed, and homogenized by centrifugation through a QIAshredder spin column (Qiagen, cat. no. 79656). The lysate was mixed with ethanol, applied to an RNeasy spin column, and subjected to on-column DNase I digestion using the RNase-Free DNase Set (Qiagen, cat. no. 79254) to eliminate genomic DNA contamination. Following sequential washes, purified total RNA was eluted in RNase-free water and quantified via Qubit Fluorometer.
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Following fragmentation, first-strand cDNA was synthesized using random hexamer primers, followed by second-strand cDNA synthesis. The final cDNA library was completed through end repair, A-tailing, adapter ligation, size selection, amplification, and purification.
Harvested cell pellets (250–350 mg) were resuspended in FA lysis buffer (50 mM HEPES-KOH pH 8.0, 150 mM NaCl, 1 mM EDTA pH 8.0, 1% Triton X-100, 0.1% sodium deoxycholate) supplemented with 1 mM PMSF and protease inhibitor cocktail (Thermo Fisher Scientific, cat. no. 78429), and disrupted using ceramic beads in a FastPrep system (MP Biomedicals). Chromatin was sheared by Bioruptor (Diagenode) and clarified by centrifugation. Sheared chromatin was immunoprecipitated overnight at 4°C using Protein G Dynabeads (Thermo Fisher Scientific, cat. no. 10003D) pre-coated with Anti-RNA Polymerase II Antibody (Merck, clone 8WG16). Following sequential washes (FA lysis buffer, high-salt FA buffer, ChIP wash buffer, and TE buffer), chromatin was eluted in 1% SDS buffer at 65°C. Cross-links for both ChIP and input samples were reversed at 65°C overnight, followed by RNase A (Merck, cat. no. 10109169001) and Proteinase K (AppliChem, cat. no. A3830,0100) digestion. DNA was purified using the ChIP DNA Clean & Concentrator Kit (Zymo Research, cat. no. D5201).
ChIP DNA and input control DNA libraries were prepared using the NEBNext Ultra II Library Prep Kit for Illumina (New England Biolabs) according to the manufacturer's instructions. Library quality and fragment size distribution were verified using an Agilent TapeStation system with D1000 ScreenTapes (TapeStation Analysis Software v5.2).

treatment_protocol:
For compartment-specific protein accumulation experiments, cells expressing 3xFP-NLS, 3xFP-NES, or control constructs were treated with estradiol (induced condition) or ethanol (mock control) for 6 hours. For G1 arrest time-course experiments (cdc28-13 strain), cells were incubated at 37°C for 2, 4, or 6 hours with estradiol or ethanol mock treatment.
Cells were treated with the CDK4/6 inhibitor palbociclib to induce G1 arrest and excessive cell volume expansion. Cells were harvested at Day 2 (early arrest/reference size, using 1.5 × 10^6 cells) and Day 7 (extended arrest/enlarged size, using 0.5 × 10^6 cells) of palbociclib treatment.
Cells expressing inducible 3xFP-NLS, 3xFP-NES, or control constructs were treated with estradiol (induced) or ethanol (mock control) for 6 hours. Cells were subsequently cross-linked with 1% formaldehyde for 15 minutes at 30°C and quenched with 0.125 M glycine.

value: not applicable

value: whole cell

value: 6h ethanol mock


title: Murine lung ILC2_IL-2_IL-7_IL-33+IgG2b_24h_rep2

description: Library name: S3


title: Control_4h_Pituitary-17

value: female


title: Input ChIP 3xFP-NES EtOH rep2

description:
Library name: input_3506_EtOH_2
Input control


title: Murine lung ILC2_IL-2_IL-7_IL-33+IgG2b_24h_rep1

description: Library name: S2


title: Stereotaxic brain tumor biopsy, patient 189, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_189

value: brain


title: Stereotaxic brain tumor biopsy, patient 188, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_188


title: EE_72h_Uterus-84

source_name: uterus


title: Control_4h_Pituitary-16


title: Input ChIP 3xFP-NES EtOH rep1

description:
Library name: input_3506_EtOH_1
Input control


title: Sorted thymic  CD8negCD4neg  gamma delta T cells from WT and KO mice (cell hashing) 2

city: Montreal

first: Tarik

last: Moroy

state: QC

address: 110, West Pine Avenue, 597

country: Canada

institute: Institut de recherches cliniques de Montréal

description:
Library name: Thymus Tgd WT KO 2 CMO
10X Genomics

data_processing:
cellranger-8.0.1
Assembly: GRCm39
Supplementary files format and content: Cellranger output files filtered matrix: Spleen_Tgd_KO_1_barcodes.tsv.gz,Spleen_Tgd_KO_1_features.tsv.gz,Spleen_Tgd_KO_1_matrix.mtx.gz
Supplementary files format and content: Cellranger output files filtered matrix: Spleen_Tgd_WT_1_barcodes.tsv.gz,Spleen_Tgd_WT_1_features.tsv.gz,Spleen_Tgd_WT_1_matrix.mtx.gz
Supplementary files format and content: Cellranger output files filtered matrix: Spleen_Tgd_KO_2_barcodes.tsv.gz,Spleen_Tgd_KO_2_features.tsv.gz,Spleen_Tgd_KO_2_matrix.mtx.gz
Supplementary files format and content: Cellranger output files filtered matrix: Spleen_Tgd_WT_2_barcodes.tsv.gz,Spleen_Tgd_WT_2_features.tsv.gz,Spleen_Tgd_WT_2_matrix.mtx.gz
Supplementary files format and content: Cellranger output files filtered matrix: Thymus_DN_KO_1_barcodes.tsv.gz,Thymus_DN_KO_1_features.tsv.gz,Thymus_DN_KO_1_matrix.mtx.gz
Supplementary files format and content: Cellranger output files filtered matrix: Thymus_DN_WT_1_barcodes.tsv.gz,Thymus_DN_WT_1_features.tsv.gz,Thymus_DN_WT_1_matrix.mtx.gz
Supplementary files format and content: Cellranger output files filtered matrix: Thymus_DN_KO_2_barcodes.tsv.gz,Thymus_DN_KO_2_features.tsv.gz,Thymus_DN_KO_2_matrix.mtx.gz
Supplementary files format and content: Cellranger output files filtered matrix: Thymus_DN_WT_2_barcodes.tsv.gz,Thymus_DN_WT_2_features.tsv.gz,Thymus_DN_WT_2_matrix.mtx.gz
Supplementary files format and content: Cellranger output files filtered matrix: Thymus_Tgd_KO_1_barcodes.tsv.gz,Thymus_Tgd_KO_1_features.tsv.gz,Thymus_Tgd_KO_1_matrix.mtx.gz
Supplementary files format and content: Cellranger output files filtered matrix: Thymus_Tgd_WT_1_barcodes.tsv.gz,Thymus_Tgd_WT_1_features.tsv.gz,Thymus_Tgd_WT_1_matrix.mtx.gz
Supplementary files format and content: Cellranger output files filtered matrix: Thymus_Tgd_KO_2_barcodes.tsv.gz,Thymus_Tgd_KO_2_features.tsv.gz,Thymus_Tgd_KO_2_matrix.mtx.gz
Supplementary files format and content: Cellranger output files filtered matrix: Thymus_Tgd_WT_2_barcodes.tsv.gz,Thymus_Tgd_WT_2_features.tsv.gz,Thymus_Tgd_WT_2_matrix.mtx.gz

source_name: Thymus

extract_protocol:
Thymic or splenic T cells were sorted using FACS from WT and KO mice based on appropriate markers.
Single Cell 3' v3

value: Thymus

value: gamma delta T cells

value: WT and GFI1 KO

tag: library type

value: CMO

tag: cmo


title: Stereotaxic brain tumor biopsy, patient 187, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_187

tag: tissue

value: Glioblastoma


title: Sorted thymic  CD8negCD4neg  gamma delta T cells from WT and KO mice (cell hashing) 1

description:
Library name: Thymus Tgd WT KO 1 CMO
10X Genomics


title: Input ChIP 3xFP-NES EST rep3

description:
Library name: input_3506_EST_3
Input control

value: 6h estradiol


title: Stereotaxic brain tumor biopsy, patient 186, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_186


title: EE_72h_Uterus-82

value: immature


title: EE_72h_Uterus-83


title: Sorted thymic DN1-DN2-DN3 cells from WT and KO mice (cell hashing) 2

description:
Library name: Thymus DN WT KO 2 CMO
10X Genomics

value: Thymic DN1-DN2-DN3 cells


title: Input ChIP 3xFP-NES EST rep2

description:
Library name: input_3506_EST_2
Input control


title: Stereotaxic brain tumor biopsy, patient 185, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_185

value: male


title: Input ChIP 3xFP-NES EST rep1

description:
Library name: input_3506_EST_1
Input control


title: Sorted thymic DN1-DN2-DN3 cells from WT and KO mice (cell hashing) 1

description:
Library name: Thymus DN WT KO 1 CMO
10X Genomics


title: EE_72h_Uterus-81

description: OECD-compliant uterotrophic assay using ethinyl estradiol (EE) in juvenile female rats


title: EE_72h_Uterus-79


title: Stereotaxic brain tumor biopsy, patient 184, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_184

value: FFPE stereotaxic biopsy


title: Input ChIP empty EtOH rep3

description:
Library name: input_3229_EtOH_3
Input control

value: empty


title: Sorted splenic CD3+ CD4neg  gamma delta T cells from WT and KO mice (cell hashing) 2

description:
Library name: Spleen Tgd WT KO 2 CMO
10X Genomics

source_name: Spleen

value: Spleen


title: Sorted splenic CD3+ CD4neg  gamma delta T cells from WT and KO mice (cell hashing) 1

description:
Library name: Spleen Tgd WT KO 1 CMO
10X Genomics


title: Stereotaxic brain tumor biopsy, patient 183, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_183


title: Input ChIP empty EtOH rep2

description:
Library name: input_3229_EtOH_2
Input control

value: not applicable


title: Stereotaxic brain tumor biopsy, patient 182, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_182

value: Diffuse glioma


title: Sorted thymic  CD8negCD4neg  gamma delta T cells from WT and KO mice 2

description:
Library name: Thymus Tgd WT KO 2 GEX
10X Genomics

value: mRNA


title: Input ChIP empty EtOH rep1

description:
Library name: input_3229_EtOH_1
Input control

value: whole cell

value: 6h ethanol mock


title: EE_48h_Uterus-72

value: female


title: EE_48h_Uterus-71


title: Stereotaxic brain tumor biopsy, patient 181, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_181

value: brain


title: Input ChIP empty EST rep3

description:
Library name: input_3229_EST_3
Input control


title: Sorted thymic  CD8negCD4neg  gamma delta T cells from WT and KO mice  1

description:
Library name: Thymus Tgd WT KO 1 GEX
10X Genomics

value: Thymus

value: gamma delta T cells

value: WT and GFI1 KO


title: EE_48h_Uterus-69


title: Stereotaxic brain tumor biopsy, patient 180, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_180

value: Glioblastoma


title: Input ChIP empty EST rep2

description:
Library name: input_3229_EST_2
Input control

value: 6h estradiol


title: EE_48h_Uterus-68

value: immature


title: Sorted thymic DN1-DN2-DN3 cells from WT and KO mice  2

description:
Library name: Thymus DN WT KO 2 GEX
10X Genomics

value: Thymic DN1-DN2-DN3 cells


title: Stereotaxic brain tumor biopsy, patient 179, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_179

value: male

value: FFPE stereotaxic biopsy


title: Input ChIP empty EST rep1

description:
Library name: input_3229_EST_1
Input control

value: empty


title: EE_48h_Uterus-67


title: Sorted thymic DN1-DN2-DN3 cells from WT and KO mice 1

description:
Library name: Thymus DN WT KO 1 GEX
10X Genomics


title: Stereotaxic brain tumor biopsy, patient 178, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_178


title: EE_28h_Uterus-59


title: Input ChIP 3xFP-NLS EtOH rep3

description:
Library name: input_3225_EtOH_3
Input control

value: not applicable


title: Sorted splenic CD3+ CD4neg  gamma delta T cells from WT and KO mice  2

description:
Library name: Spleen Tgd WT KO 2 GEX
10X Genomics

value: Spleen


title: EE_28h_Uterus-58


title: Input ChIP 3xFP-NLS EtOH rep2

description:
Library name: input_3225_EtOH_2
Input control


title: Stereotaxic brain tumor biopsy, patient 177, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_177

value: Diffuse glioma


title: Sorted splenic CD3+ CD4neg  gamma delta T cells from WT and KO mice 1

description:
Library name: Spleen Tgd WT KO 1 GEX
10X Genomics

value: mRNA


title: Input ChIP 3xFP-NLS EtOH rep1

description:
Library name: input_3225_EtOH_1
Input control

source_name: not applicable

value: whole cell

value: 6h ethanol mock


title: Lung cells isolated from GFI1 WT mouse 1

description:
Library name: WT-ctrl_GEX
10X Genomics

data_processing:
cellranger-9.0.1 with GRCm39-2024-A reference transcriptome
Assembly: mm39
Supplementary files format and content: Cellranger output files filtered matrix: WT-ctrl_barcodes.tsv.gz WT-ctrl_features.tsv.gz WT-ctrl_matrix.mtx.gz  WT_cloupe.cloupe
Supplementary files format and content: Cellranger output files filtered matrix: KO-ctrl_barcodes.tsv.gz KO-ctrl_features.tsv.gz KO-ctrl_matrix.mtx.gz  KO_cloupe.cloupe

source_name: lung

extract_protocol:
Lungs from WT or GFI1 KO adult mice were enzymatically dissociated, before being washed and live lung cells were sorted using the ARIA III sorter. The sorted cells were used for gene expression (10x genomics).
Single Cell 3' v3

value: lung

value: Primary cells

value: Lung cells

value: GFI1 WT


title: EE_28h_Uterus-57

description: OECD-compliant uterotrophic assay using ethinyl estradiol (EE) in juvenile female rats

value: female


title: Stereotaxic brain tumor biopsy, patient 176, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_176

value: brain

value: Glioblastoma


title: Input ChIP 3xFP-NLS EST rep3

description:
Library name: input_3225_EST_3
Input control

value: 6h estradiol


title: Stereotaxic brain tumor biopsy, patient 175, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_175


title: EE_28h_Uterus-56

source_name: uterus

value: immature


title: Lung cells isolated from GFI1 KO mouse 1

description:
Library name: KO-ctrl_GEX
10X Genomics

value: GFI1 KO


title: Stereotaxic brain tumor biopsy, patient 174, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_174

value: male

value: FFPE stereotaxic biopsy


title: Input ChIP 3xFP-NLS EST rep2

description:
Library name: input_3225_EST_2
Input control

value: not applicable


title: EE_28h_Uterus-55


title: NESMYCNT58ADOXminusC

city: London

first: Diego

last: Chillon Pino

address: Great Ormond Street Hospital for Children NHS

institute: UCL

description: nCounter Human v3 miRNA Expression Assay (CodeSet CSO-MIR3-12). Hindbrain-derived NES cell line (Sai2) transduced with a doxycycline-inducible MYCN(T58A) construct.

hyb_protocol: Tag-ligated RNA (5 uL) was hybridised to the nCounter Human v3 miRNA Reporter CodeSet and Capture ProbeSet (CSO-MIR3-12) in a 30 uL reaction at 65 C for at least 12 h (not exceeding 30 h), per the manufacturer's instructions.

scan_protocol: Post-hybridisation processing (two-step magnetic bead purification and immobilisation on the cartridge) and digital counting of reporter barcodes were performed on the nCounter SPRINT Profiler, producing endpoint counts per target.

data_processing:
Endpoint digital counts were generated on the nCounter platform and exported. Counts were background-thresholded (values floored at 1) and normalised positive-control normalisation followed by housekeeping/top-100 normalisation, performed in nSolver; internal positive, negative and housekeeping control probes were removed after normalisation, leaving 798 miRNA targets. The submitted matrix contains these normalised values.
background-thresholded, normalised nCounter count (floored at 1). Values are non-integer as a result of normalisation; raw integer counts are not available.

source_name: NES cell line (MYCN(T58A) transduced)

label_protocol: nCounter miRNA Expression Assay (NanoString, MAN-C0009-07): mature miRNAs were annealed to miRNA-specific oligonucleotide tags (miRtags; nCounter miRNA Sample Preparation Kit, Hu-MIRTAG-12) and ligated, followed by enzymatic clean-up of unligated tags. Detection is by direct digital barcode counting; no fluorescent or radioactive labelling of target is performed.

growth_protocol: NES cells (Sai2, human embryonic hindbrain-derived) were cultured in DMEM/F12 with 2 mM L-glutamine, N2, B27, penicillin-streptomycin (1:100), EGF (10 ng/mL) and FGF2 (10 ng/mL) on poly-L-ornithine/laminin-coated flasks at 37 C, 5% CO2. NESt tumours were generated by intracranial implantation of Sai2 NES cells carrying doxycycline-inducible MYCN(T58A) into NSG mice and harvested at endpoint.

extract_protocol: Total RNA, with the small-RNA fraction preserved, was isolated from snap-frozen tumour material and cell pellets using QIAGEN miRNeasy. RNA quality was assessed spectrophotometrically; approximately 100 ng of total RNA per sample was used as input to the nCounter miRNA assay.

treatment_protocol: MYCN(T58A) expression was induced with doxycycline: in vitro for NES ON cultures [confirm concentration and duration]; in vivo by doxycycline feed (20 g/kg) for tumour-bearing mice. NES CTRL (DOXminus) cultures received no doxycycline.

value: hindbrain neuroepithelial stem cells


title: Stereotaxic brain tumor biopsy, patient 173, Glioblastoma

data_processing: IDAT files were uploaded to molecularpathology.org (Heidelberg brain tumor classifier v11b4) to obtain calibrated scores for DNA methylation classes and subclasses, copy number variation profiles and MGMT promoter methylation status. Additional classification was performed using the Bethesda brain tumor classifier (v2) and EpiDiP. IDAT files were processed using R packages RnBeads for quality control and normalization (dasen method from wateRmelon package), and MethylCIBERSORT for reference-based tumor deconvolution. Genome build: hg19.

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_173


title: EE_24h_Uterus-47


title: Input ChIP 3xFP-NLS EST rep1

description:
Library name: input_3225_EST_1
Input control


title: Stereotaxic brain tumor biopsy, patient 172, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_172

value: Diffuse glioma


title: NESMYCNT58ADOXminusB


title: PolII ChIP 3xFP-NES EtOH rep3

description:
Library name: IP_3506_EtOH_3
Anti-Pol II (8WG16) IP

value: whole cell


title: NESMYCNT58ADOXminusA


title: EE_24h_Uterus-46


title: Stereotaxic brain tumor biopsy, patient 171, unclassified brain lesion

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_171

value: unclassified brain lesion


title: PolII ChIP 3xFP-NES EtOH rep2

description:
Library name: IP_3506_EtOH_2
Anti-Pol II (8WG16) IP

value: 6h ethanol mock


title: EE_24h_Uterus-45


title: NESMYCNT58ADOXplusC


title: Stereotaxic brain tumor biopsy, patient 170, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_170


title: EE_24h_Uterus-44


title: PolII ChIP 3xFP-NES EtOH rep1

description:
Library name: IP_3506_EtOH_1
Anti-Pol II (8WG16) IP


title: Stereotaxic brain tumor biopsy, patient 169, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_169


title: NESMYCNT58ADOXplusB


title: PolII ChIP 3xFP-NES EST rep3

description:
Library name: IP_3506_EST_3
Anti-Pol II (8WG16) IP


title: EE_24h_Uterus-43


title: Stereotaxic brain tumor biopsy, patient 168, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_168


title: NESMYCNT58ADOXplusA


title: PolII ChIP 3xFP-NES EST rep2

description:
Library name: IP_3506_EST_2
Anti-Pol II (8WG16) IP


title: EE_8h_Uterus-35


title: Stereotaxic brain tumor biopsy, patient 167, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_167


title: 353490C

description: nCounter Human v3 miRNA Expression Assay (CodeSet CSO-MIR3-12). NESt xenograft tumour from Sai2 NES cells carrying doxycycline-inducible MYCN(T58A), implanted intracranially. NB: human miRNA panel applied to xenograft material; highly conserved miRNAs may also detect murine stroma.

source_name: NESt xenograft tumour (353490)

value: brain tumour (intracranial xenograft)


title: PolII ChIP 3xFP-NES EST rep1

description:
Library name: IP_3506_EST_1
Anti-Pol II (8WG16) IP


title: Stereotaxic brain tumor biopsy, patient 166, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_166


title: PolII ChIP empty EtOH rep3

description:
Library name: IP_3229_EtOH_3
Anti-Pol II (8WG16) IP

value: empty


title: EE_8h_Uterus-33


title: EE_8h_Uterus-34


title: 353490B


title: 353490A


title: Stereotaxic brain tumor biopsy, patient 165, unclassified brain lesion

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_165


title: PolII ChIP empty EtOH rep2

description:
Library name: IP_3229_EtOH_2
Anti-Pol II (8WG16) IP

source_name: not applicable


title: 353486C

source_name: NESt xenograft tumour (353486)


title: EE_8h_Uterus-32


title: Stereotaxic brain tumor biopsy, patient 164, Circumscribed glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_164

value: Circumscribed glioma


title: PolII ChIP empty EtOH rep1

description:
Library name: IP_3229_EtOH_1
Anti-Pol II (8WG16) IP


title: EE_8h_Uterus-31

value: female


title: 353486B


title: Stereotaxic brain tumor biopsy, patient 163, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_163

value: brain


title: PolII ChIP empty EST rep3

description:
Library name: IP_3229_EST_3
Anti-Pol II (8WG16) IP


title: 353486A


title: EE_4h_Uterus-24

source_name: uterus


title: PolII ChIP empty EST rep2

description:
Library name: IP_3229_EST_2
Anti-Pol II (8WG16) IP


title: Stereotaxic brain tumor biopsy, patient 162, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_162

value: Glioblastoma


title: Stereotaxic brain tumor biopsy, patient 161, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_161


title: EVs-EPM1-dCO_3

city: Planegg-Martinsried

first: Filippo M.

last: Cernilogar

address: Grosshaderner Strasse 9

department: Biomedical Center

institute: LMU Munich

data_processing:
RNA-seq reads were mapped to the human genome (hg38) using STAR (Dobin et al., 2013, PMID: 23104886). Expression of genes in TPM was calculated with RSEM (Li et al., 2011, PMID: 21816040).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: Neural progenitor cells

growth_protocol: NPCs were cultured in NPM medium according to Boyer et al., 2012. DMEM/F12 , 1× N2 supplement, 1× B27 supplement, Laminin (1 µg/ml), 1x Antibiotic mixture Anti-Anti

extract_protocol:
Trizol and RNA clean and concentrator kit (Zymo research)
Smarter ultra low input-v4 (Clontech 634888) and Microplex-v2 (Diagenode C05010012)

treatment_protocol: Acute treatment (12 hours) with dEVs or vEVs isolated from conditioned media of dorsally or ventrally patterned human spheroids originated from control iPSCs or EPM1 patients-iPSCs. Experiments were performed in biological triplicates.

value: iPScs-derived neural progenitor cells

value: NPCs acutely treated (12 hours) with Extracellular vesicles (EVs) purified by the conditioned medium of dorsally patterned human spheroids originated from EPM1 patients-iPSCs cells.


title: PolII ChIP empty EST rep1

description:
Library name: IP_3229_EST_1
Anti-Pol II (8WG16) IP

value: 6h estradiol


title: EE_4h_Uterus-23

description: OECD-compliant uterotrophic assay using ethinyl estradiol (EE) in juvenile female rats

value: immature