title: BCM-3887CR_110347, Basal-like triple-negative breast cancer patient-derived xenograft  [scRNA-seq]

description: Library name: BCM-3887CR_110347

data_processing:
Basecalling: BCL files were converted to fastq using bcl2fastq2 (v2.17.1.14)
QC: Fastq files containing the read were analyzed with FastQC >=v0.11.9 to identify any quality concerns with the raw data.
Alignment: Fastq files were aligned independently to the merged human/mouse hg19mm10 genome provided by 10X using CellRanger v8 "count" algorithm with the expected number of cells set to 5000.
Mouse Cell Removal: An in-house R script and the 10X-generated GEM file were used to identify and remove all mouse and multiplet cell barcodes from each PDX sample by using the CellRanger script "subset_bam".  The remaining reads were converted back to fastq files using the CellRanger script "bamtofastq".  These new filtered fastq files were then re-aligned independently to the GRCh38 human genome using the CellRanger "count" algorithm, however, this time the Force Cells option was set to the exact number of remaining human cells for each sample.
Assembly: GRCh38 (human) and mm10 (mouse)
Supplementary files format and content: The process data files include the 10X formatted features.tsv.gz, barcodes.tsv.gz, and matrix.mtx.gz files that can be imported directly into R using the Seurat package. These are provided as tar.gz files.

extract_protocol: 10x Genomics Chromium kit - Next GEM Single Cell 3' Reagent Kits v3.1

value: PDX mammary tumor

value: Carboplatin Resistant

value: WT

value: Untreated


title: Donor1, high TNF expression bin

status: Public on Apr 08 2026

type: SRA

city: San Francisco

first: Pascal

last: Devant

address: 1650 Owens Street

country: USA

institute: Gladstone Institutes

description:
Library name: TNF_D1_high
processed data file column name: D1_High
TNF.count.txt

library_source: genomic

data_processing:
Sequencing reads were demultiplexed using BCL Convert (v4.2.7) and aligned to the sgRNA reference library using the count function in MAGeCK (v0.5.9.5), generating a table of sgRNA read counts for each sample
Assembly: GRCh38
Supplementary files format and content: raw counts
Library strategy: CRISPR Screen

molecule: genomic DNA

organism: Homo sapiens

source_name: Peripheral blood

growth_protocol: Primary human monocytes were isolated from fresh peripheral blood Leukopaks (STEMCELL Technologies) with institutional review board-approved informed written consent. Leukopaks were washed twice with EasySep buffer (sterile PBS pH 7.4, 2% FCS, 1 mM EDTA pH 8.0) before isolation of monocytes using the Human Monocyte Enrichment kit without CD16 depletion (STEMCELL Technologies; 100-1525) according to manufacturer’s instruction. Briefly, PBMCs were diluted to 100x106 cells/ml in EasySep buffer, mixed with 100 µl of antibody cocktail per 100 million cells and incubated at RT for 5-10 mins. Magnetic beads were added and following 3 min of incubation at RT, tubes containing cells were placed in a magnetic field for 10 mins. Unbound cells (pure monocyte fraction) were removed, washed one more time with EasySep buffer. Cells were then counted and resuspended in Immunocult SF Macrophage media (STEMCELL technology; 10961) supplemented with differentiation cytokines (exact cytokines used are outlined below) at a density of 1x106 cells/ml and seeded in TC-treated 24-well plate (for most experiments; 0.5x10^6 cells per well) or 12-well plates (for pooled screens; 2.5x106 cells per well). For macrophage differentiation, media was supplemented with 20 ng/ml of M-CSF (Peprotech; 300-25). Media was replenished every 24-72 h by adding at least one half volume of fresh media and cytokines. All tissue culture was performed under sterile conditions and cells were cultured in temperature-controlled incubators at 37°C and 5% CO2.

extract_protocol:
Sorted cells were pelleted and resuspended at up to 5x10^6 cells per 400 µl of lysis buffer (1% SDS, 50 mM Tris, pH 8, 10 mM EDTA). The remaining protocol reflects additives/procedures performed per each 400 µl reaction. 16 µl of NaCl (5M; Fisher Scientific; AM9760G) was added, and the sample was incubated on a heat block overnight at 66°C. The next morning, 8 µl of RNAse A (10mg/ml; Thermo Fisher; FEREN0531) was added, and the sample was vortexed briefly, and incubated at 37°C for 1 hour. Next, after 8 µl of Proteinase K (20mg/ml; ThermoFisher; AM2548) was added, the sample was vortexed briefly and incubated at 55°C for 1 hour. Homemade phase lock tubes were prepared for each sample by spinning 200 µl sterilized high vacuum grease gel (DuPont; B0857KKVR8) to the bottom of a 1.5 ml tube at 20,000 g for 1 minute and then 400 µl of Phenol:Chloroform:Isoamyl Alcohol (25:24:1; Fisher Scientific; 15-593-031) was added to each tube. 400 µl of the sample was then added to the phase lock tube and the tube was shaken vigorously. The sample was centrifuged at maximum speed at room temperature for 5 minutes. The aqueous phase was transferred to a low-binding eppendorf tube (Eppendorf, Cat #022431021) and then 40 µl of Sodium Acetate (3M; VWR; 46-033-CI), 1µl GlycoBlue (Invitrogen; AM9515), and 600µl of room temperature isopropanol (Fisher Scientific; 32727-0010) was added. The sample was then vortexed and stored at -80°C for 30 minutes or until the sample had frozen solid. Next the sample was centrifuged at maximum speed at 4°C for 30 minutes, the pellet was washed with fresh 70% room temperature Ethanol, and allowed to air dry for 15 minutes. Pellets were then resuspended in Zymo DNA elution buffer (Zymo; D3004-4-10), and placed on the heat block at 65°C for 1 hour to completely dissolve the genomic DNA.
The sgRNA cassette was amplified and barcoded from the genomic DNA as initially described by Joung et al82. Up to 2.5 µg of genomic DNA were added to each 50 µL reaction, which included 25 µL of NEBNext Ultra II Q5 master mix (NEB; M0544L), 1.25 µL of the 10 µM forward primer and 1.25 µL of the 10 µM reverse primer, and H2O to 50 uL. Due to differences in sgRNA scaffold in the respective plasmid backbone, different reverse primer sets were used for CD80 and TNF screens. The following PCR cycling conditions were used: 98°C for 3 minutes, followed by 23 cycles at 98°C for 10 seconds, 63°C for 10 seconds, and 72°C for 25 seconds, and ending with 2 minutes at 72°C. Amplicons were purified using SPRIselect beads following manufacturer’s protocols (Beckman). The concentration of each sample was then measured using the Qubit dsDNA high sensitivity assay kit (Thermo Fisher Scientific, Cat #Q32854).

treatment_protocol: Pooled TNF screen: Primary monocytes from two healthy donors were isolated as described, and 360x106 cells from each donor were plated in 12-well plates (2.5x10^6 cells in 2 ml of media per well) in SF macrophage media + 20 ng/ml M-CSF. Additional culture media was either added or changed every 48 hours. 3 days after isolation, monocyte-derived macrophages were transduced with a sgRNA library packaged in a Vpx-containing lentiviral vector with a GFP marker at a pre-defined dose (7.5 ul of concentrated virus in 1 ml of media per well), resulting in ~65% and 90% transduction rate for either of the donors, respectively. 24 h after lentiviral transduction, the macrophages were treated with eVLP particles containing a scrambled/non-target sgRNA (50 ul of concentrated eVLP in 1 ml of media per well) and subsequently cultured in media with M-CSF as described above for another 5 days. Macrophages were stimulated with 50 ng/ml of ultrapure LPS isotype O:55 (Enzo) in the presence of GolgiPlug reagent for 5 h. Cells were then detached with Accutase for 30 min at 37°C, washed once with EasySep buffer and stained with Ghostdye Violet450 at 1:1000 dilution in EasySep buffer for 30 min on ice. Cells were then fixed using the CytoFix/Cytoperm kit (200 ul of Cytofix solution per 1 million cells) and stained with a APC-labeled human TNF-alpha. Cells were washed once with Perm/Wash buffer and resuspended at 20x10^6 cells/ml in EasySep buffer. Cell sorting was performed on a FACSARIA cell sorter at the UCSF Parnassus Flow Cytometry Core facility. We gated the population of single cells, which are GFP positive (transduced with lentivirus) and Ghostdye negative (viable) population and sorted the top and bottom 20% of TNF-alpha expressing cells. At least 12 million cells were sorted into each bin ensuring sufficient coverage. Pooled CD80 screen: Primary monocytes from four healthy donors were isolated as described, and 360x106 cells from each donor were plated in 12-well plates (2.5x10^6 cells in 2 ml of media per well) in SF macrophage media + 20 ng/ml M-CSF. Additional culture media was either added or changed every 48 hours. 3 or 4 days after isolation, monocyte-derived macrophages were transduced with the transcription factor and immunomodulator sgRNA library packaged in a Vpx-containing lentiviral vector with a GFP marker at a pre-defined dose (15 uL of  100x concentrated virus in 1 ml of media per well), resulting in at least ~70% transduction rate. 24 h after lentiviral transduction, the macrophages were treated with eVLP particles containing a scrambled/non-target sgRNA (35 ul of concentrated eVLP in 1 ml of media per well for Donor 1 and 2, 50 ul for Donor 3 and 4) and subsequently cultured in media with M-CSF as described above for another 5 days. Cells were then detached with Accutase for 30 min at 37°C, washed once with EasySep buffer and stained with Ghostdye Violet450 (1:1000) and APC anti-CD80 (Biolegend; 2 ul of antibody per 1 million cells) in EasySep buffer for 30 min on ice. Cells were washed once with Easysep buffer and resuspended at 20x106 cells/ml in EasySep buffer. Cell sorting was performed on a FACSARIA cell sorter at the UCSF Parnassus Flow Cytometry Core facility. We gated on single cells, which are GFP positive (transduced with lentivirus) and Ghostdye negative (viable) and sorted the top and bottom 20% of CD80 expressing cells. At least 10 million cells were sorted into each bin ensuring sufficient coverage.

tag: tissue

value: Peripheral blood

tag: cell type

value: monocyte-derived macrophages

tag: sample group

value: high TNF expression bin


title: Donor1, low TNF expression bin

description:
Library name: TNF_D1_Low
processed data file column name: D1_Low
TNF.count.txt

value: low TNF expression bin


title: Normal9

city: ShenZhen

first: Lin

last: Ma

state: Guangdong Province

address: Lihu Campus: Xueyuan Avenue, Nanshan District, Shenzhen

department: Medical School

country: China

institute: ShenZhen University

description: Library name: Sample 33

library_source: transcriptomic

data_processing:
Raw sequencing data were received in FASTQ format.
Read mapping was performed using Tophat 2.0.9 against the human reference genome.
The resulting BAM alignment files were processed using the HTSeq 0.6.1 python framework and respective GTF gene annotation.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for All Sample

molecule: total RNA

source_name: Oral squamous cell carcinoma

extract_protocol:
RNA was harvested using TRIzol reagent (Invitrogen) from fresh frozen tissues. 1 ug of total RNA was used for the construction of sequencing libraries.
The total RNA were first treated with Ribo-off rRNA Depletion Kit (Vazyme, N406), followed by library construction using VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme, NR605) according to the manufacturer’s guidelines.

value: Oral squamous cell carcinoma

tag: specimen type

value: tumor adjacent normal tissue

tag: batch


title: mRNA E18.5 lung Lrrc58 hom pup 2

city: Cambridge

first: Daniel

last: Lin

state: MA

address: 455 Main Street

institute: Whitehead Institute

description: Library name: Lrrc58_Lung_16_5_KO_M

data_processing:
Quality of the fastq files was assessed using FastQC v0.12.1. Reads were then quality filtered using fastp v0.24.0 with poly-X tail trimming, 3' quality-based tail trimming, a minimum Phred quality score of 15, and a minimum length requirement of 50 bp. Quality-filtered reads were aligned to the reference genome using STAR aligner v2.7.11 with non-canonical splice junction removal and output of unmapped reads, followed by coordinate sorting using samtools v1.22.1. PCR and optical duplicates were removed using UMI-based deduplication with UMIcollapse v1.1.0. Alignment quality metrics, strand specificity, and read distribution across genomic features were assessed using RSeQC v5.0.4 and Qualimap v2.3, with results aggregated into a comprehensive quality control report using MultiQC v1.32. Gene-level expression quantification was performed using featureCounts (subread package v2.1.1) with strand-specific counting, multi-mapping read fractional assignment, exons and three prime UTR as the feature identifiers, and grouped by gene_id. Gene counts were analyzed with DESeq2 v1.38.3 without use of the lfcShrink function.
Assembly: GRCm39v114
Supplementary files format and content: raw gene counts for all samples

organism: Mus musculus

source_name: Lung

extract_protocol:
Embryos were collected at E18.5 and dissected tissue was flash frozen in liquid nitrogen. Frozen tissue was transferred to a 50 mL conical tube, 1–2 mL of TRI Reagent was added, and the tissue was homogenized using a TissueRuptor and disposable probes (Qiagen). Following resuspension and/or homogenization, samples were phase separated with 100 μL 1-bromo-3-chloropropane (Sigma).
cDNA was prepared from total RNA using a poly(dT)VN primer. Following second strand synthesis, tagmentation, library indexing, and amplification, libraries were sequenced on the Illumina NovaSeq X Plus platform.

value: Lung

tag: genotype

value: Lrrc58 homozygous trigger site mutant


title: BCM-3887_110318, Basal-like triple-negative breast cancer patient-derived xenograft [scRNA-seq]

city: Richmond

first: Wright Center for Clinical and Translational Research

last: Bioinformatics Core

state: VA

address: 203 E Cary St

institute: Virginia Commonwealth University

description: Library name: BCM-3887_110318

library_source: transcriptomic single cell

source_name: PDX mammary tumor

growth_protocol: PDX tumors were grown orthotopically in NSG mice for 8 weeks.

treatment_protocol: Carboplatin Resistant:  Mice with PDXs were grown and treated three times spaced out every 4 days with 40mg/kg of carboplatin. Once the tumors regrew they were passaged to new recipient mice and then treated with another set of carboplatin. This proceeded until the tumors no longer responded to carboplatin; at this point they were termed carboplatin-resistant.

value: PDX

tag: treatment


title: Normal10

description: Library name: Sample 34


title: Normal8

description: Library name: Sample 32


title: PNF_sample8

city: Shanghai

first: Lingling

last: Ge

state: Shanghai

address: Ninth people's hospital

institute: Shanghai Jiao Tong University

description: Library name: PNF_sample8

data_processing:
We employed droplet-based scRNA-seq using the Chromium Single Cell 5’ solution from 10x Genomics to integrate transcriptome data from 9 PNF and 5 MPNST samples. Raw datasets were loaded using the Seurat (v5.0.1) in R.
Assembly: Huamn
Supplementary files format and content: barcodes, features, and matrix files
Supplementary files format and content: barcodes, features, and matrix files

source_name: tumor

extract_protocol:
Immediately following surgical excision, the tissue specimens were meticulously cleaned using Dulbecco’s Phosphate-Buffered Saline (DPBS) in a triple-wash protocol. Following this, the tissues were finely minced into fragments measuring 1 to 2 mm3. These tissue pieces were then subjected to enzymatic dissociation in a 37°C water bath for 45 minutes, with continuous agitation to enhance the process. The dissociation medium consisted of Collagenase I (Invitrogen, Carlsbad, CA, USA) and Dispase (Thermo Fisher Scientific, Waltham, MA, USA). Following digestion, a 40 μm sterile filter (Corning, NY, USA) was utilized to separate the dissociated cells from debris and other impurities. The filtered cell suspension was centrifuged at 1,000 rpm at 4°C for 10 minutes. After centrifugation, the cell pellets were gently resuspended in 1 mL of calcium- and magnesium-free PBS. The resuspended cells were adjusted to a concentration of 1,000-1,500 cells/μL, with a viability threshold exceeding 80% for subsequent sequencing analyses.
Single-cell gene expression libraries were constructed following the manufacturer’s guidelines, and single-cell RNA sequencing (scRNA-seq) was carried out on a NovaSeq 6000 sequencing platform.

value: tumor


title: Normal6

description: Library name: Sample 30


title: PNF_sample9

description: Library name: PNF_sample9


title: Normal7

description: Library name: Sample 31


title: mRNA E18.5 lung Lrrc58 WT pup 2

description: Library name: Lrrc58_Lung_16_1_WT_M

value: Lrrc58 WT


title: PNF_sample7

description: Library name: PNF_sample7


title: mRNA E18.5 lung Lrrc58 hom pup 1

description: Library name: Lrrc58_Lung_14_8_KO_F


title: Normal4

description: Library name: Sample 28


title: Normal5

description: Library name: Sample 29


title: PNF_sample5

description: Library name: PNF_sample5


title: mRNA E18.5 lung Lrrc58 WT pup 1

description: Library name: Lrrc58_Lung_14_1_WT_F


title: PNF_sample6

description: Library name: PNF_sample6


title: Normal2

description: Library name: Sample 26

value: normal tissue


title: mRNA E18.5 stomach Plagl1 mut(pat) pup 4

description: Library name: Plagl1_Stomach_L46_6_Het_F

source_name: Stomach

value: Stomach

value: Plagl1 mut(pat) trigger site mutant


title: Normal3

description: Library name: Sample 27


title: Normal1

description: Library name: Sample 25


title: PNF_sample4

description: Library name: PNF_sample4


title: PNF_sample3

description: Library name: PNF_sample3


title: Tumor22

description: Library name: Sample 22


title: mRNA E18.5 stomach Plagl1 WT pup 4

description: Library name: Plagl1_Stomach_L46_7_WT_F

value: Plagl1 WT


title: Tumor23

description: Library name: Sample 23


title: PNF_sample2

description: Library name: PNF_sample2


title: Tumor24

description: Library name: Sample 24


title: Tumor18

description: Library name: Sample 18


title: Tumor21

description: Library name: Sample 21


title: Tumor15

description: Library name: Sample 15


title: mRNA E18.5 stomach Plagl1 mut(pat) pup 3

description: Library name: Plagl1_Stomach_L19_2_Het_F


title: Tumor14

description: Library name: Sample 14


title: mRNA E18.5 stomach Plagl1 WT pup 3

description: Library name: Plagl1_Stomach_L19_3_WT_F


title: Tumor20

description: Library name: Sample 20


title: PNF_sample1

description: Library name: PNF_sample1


title: mRNA E18.5 stomach Plagl1 mut(pat) pup 2

description: Library name: Plagl1_Stomach_L46_1_Het_M


title: Tumor16

description: Library name: Sample 16


title: mRNA E18.5 stomach Plagl1 WT pup 2

description: Library name: Plagl1_Stomach_L46_2_WT_M


title: sRNA BJ-5ta CRISPRi control knockdown guide 2

description: Library name: BJ5ta_3B10_NT_2

data_processing:
Adaptor sequences (4 random nucleotides from the 5 prime end and the 3 prime adaptor (N{4}CTGTCTCTTATACACATCTCCGAGC) were trimmed from reads using cutadapt. Reads were filtered for quality using fastq_quality_filter with the parameters “–q 30 –p 100.” To assign processed sequencing reads to miRNAs, the first 19nt of each read was matched to a dictionary of miRNA sequences downloaded from TargetScan Release 8.0, requiring no mismatches between the read and the miRNA dictionary. Differential expression analysis was performed using DESeq2 v1.38.3 without use of the lfcShrink function.
Assembly: TargetScan Release 8.0 (human)
Supplementary files format and content: raw miRNA counts for all samples

growth_protocol: BJ-5ta CRISPRi cells were cultured in a 4:1 mixture of DMEM and Medium 199 supplemented with 0.01 mg/ml hygromycin B and 10% FBS. BJ-5ta CRISPRi cells were maintained between 10-75% confluency before harvesting.

extract_protocol:
Cultured cell lines were scraped from culture dishes into TRI Reagent and RNA was purified according to manufacturer's instructions.
Small-RNA sequencing libraries were prepared from 5 μg total RNA. 0.5 fmoles of miR-427-5p (X. tropicalis) and 0.5 fmoles of lsy-6-3p (C. elegans) were added to each sample as spike-ins. Small RNA species were isolated by excising the gel fragment migrating between 18-nt and 32nt radiolabeled internal standards on a 15% polyacrylamide urea gel. Size selected RNA was eluted from the gel, precipitated in ethanol, and ligated to a preadenylated 3¢ adapter (AppNNNNCTGTCTCTTATACACATCTCCGAGCddC) using T4 RNA Ligase 2 KQ mutant (NEB) in a reaction supplemented with 10% polyethylene glycol (PEG 8000, NEB). The 3¢ adapter had 4 random-sequence positions at its 5¢ end to reduce ligation bias. Ligated small RNAs were isolated on a 10% polyacrylamide urea gel, precipitated in ethanol, and ligated to a 5¢ adapter (CCUACACGACGCUCUUCCGAUCUNNNN) using T4 RNA Ligase I (NEB) in a reaction supplemented with 10% PEG. The 5¢ adapter had 4 random-sequence positions at its 3¢ end to reduce ligation bias. Ligated small RNAs were isolated on an 8% polyacrylamide urea gel, precipitated in ethanol, and reverse transcribed with SuperScript III (Invitrogen). Resulting cDNA was amplified using KAPA HiFi DNA polymerase (Kapa Biosystems). Amplified DNA was purified on a 90% formamide, 8% acrylamide gel and submitted for sequencing on the Illumina NovaSeq platform. A step-by-step protocol for constructing libraries for small-RNA sequencing is available at http://bartellab.wi.mit.edu/protocols.html.

tag: cell line

value: control


title: Tumor19

description: Library name: Sample 19


title: sRNA BJ-5ta CRISPRi PLAGL1 knockdown guide 2

description: Library name: BJ5ta_3B7_Plagl1_2

value: PLAGL1 knockdown


title: sRNA BJ-5ta CRISPRi control knockdown guide 1

description: Library name: BJ5ta_3B9_NT_1


title: Tumor17

description: Library name: Sample 17


title: mRNA E18.5 stomach Plagl1 mut(pat) pup 1

description: Library name: Plagl1_Stomach_L19_1_Het_M


title: sRNA BJ-5ta CRISPRi PLAGL1 knockdown guide 1

description: Library name: BJ5ta_3B6_Plagl1_1


title: sRNA BJ-5ta CRISPRi LRRC58 knockdown guide 2

description: Library name: BJ5ta_3B5_Lrrc58_2

value: LRRC58 knockdown


title: Tumor7

description: Library name: Sample 7


title: Tumor12

description: Library name: Sample 12


title: Tumor11

description: Library name: Sample 11


title: mRNA E18.5 stomach Plagl1 WT pup 1

description: Library name: Plagl1_Stomach_L19_6_WT_M


title: E14Tg2A, Nickel200 B, Day 6

city: New York

first: Suresh

last: Cuddapah

state: NY

address: 341 East 25th Street

institute: NYU School of Medicine

description:
Library name: 6d Ni200 B
E14Ni2006dB

data_processing:
Raw sequencing data were processed and analyzed using the Scientific Data Analysis Platform (SciDAP; Datirium, https://scidap.com/rna-seq.html). Briefly, quality-filtered FASTQ files were aligned to the mouse reference genome (GRCm38, NCBI RefSeq GCF_000001635.20) using STAR. Differentially expressed genes were identified using DESeq2. Genes exhibiting ≥1.5 fold up- or downregulation, along with an adjusted p-value <0.05 (Benjamini–Hochberg false discovery rate (FDR)) were considered significantly differentially expressed
Assembly: GRCm38
Supplementary files format and content: excel files including DESeq2 results for Nickel treated cells compared to time matched controls

growth_protocol: E14Tg2A Mouse embryonic stem cell (mESC) line was routinely cultured on 0.1% gelatin-coated plates (ES-006-B, MilliporeSigma) in ESGRO Complete PLUS Clonal Grade Medium (SF001-500P, MilliporeSigma). Cells were passaged every two days using 0.05% trypsin (25-052-CI, Corning).

extract_protocol:
Total RNA was isolated using QIAzol Lysis Reagent (79306, Qiagen) and RNeasy Mini kit (74106, Qiagen) according to the manufacturer’s instructions. cDNA was synthesized using SuperScript III Reverse Transcriptase (18080-044, Invitrogen).
RNA-Seq libraries were prepared using Illumina TruSeq Stranded mRNA Library Preparation Kit (20020595, Illumina) according to the manufacturer’s protocol.

treatment_protocol: For Ni exposure experiments, cells were maintained in DMEM (11965-092, Gibco) supplemented with 15% Stasis Stem Cell Qualified Fetal Bovine Serum (100-525, GeminiBio), 1% MEM Non-Essential Amino Acids (11140-050, Gibco), 1% GlutaMAX (35050-061, Gibco), 1% EmbryoMax Nucleosides (ES-008-D, Millipore Sigma), 1% Penicillin-Streptomycin Solution (30-002-CI, Corning), 0.147 mM 1-Thioglycerol (M6145, MilliporeSigma), and 0.01% Leukemia Inhibitory Factor (LIF; ESG1107, MilliporeSigma). E14Tg2A cells were treated with 100, 150, and 200 μM NiCl2 (N6136, Sigma) for six days, and the cells were collected on days 4 and 6. Cells were passaged every two days, and fresh NiCl2 was added to the culture medium after each passage. Time-matched untreated cells cultured under identical conditions served as controls. All cells were maintained at 37°C with 5% CO2.

value: embryonic stem cells

value: WT

tag: time

value: Day 6


title: E14Tg2A, Nickel200 A, Day 4

description:
Library name: 4d Ni200 A
E14Ni2004dA

value: Day 4


title: Tumor10

description: Library name: Sample 10

value: Oral squamous cell carcinoma


title: Tumor6

description: Library name: Sample 6


title: Tumor9

description: Library name: Sample 9


title: Tumor5

description: Library name: Sample 5


title: sRNA BJ-5ta CRISPRi LRRC58 knockdown guide 1

description: Library name: BJ5ta_3B4_Lrrc58_1


title: E14Tg2A, Nickel200 B, Day 4

description:
Library name: 4d Ni200 B
E14Ni2004dB


title: sRNA BJ-5ta CRISPRi ZSWIM8 knockdown guide 2

description: Library name: BJ5ta_3A2_Z8_2

value: ZSWIM8 knockdown


title: Tumor2

description: Library name: Sample 2


title: Tumor3

description: Library name: Sample 3


title: Tumor13

description: Library name: Sample 13


title: E14Tg2A, Nickel150 B, Day 6

description:
Library name: 6d Ni150 B
E14Ni1506dB


title: sRNA IMR90 control knockout guide 3

description: Library name: IMR90_CI_NegC

data_processing:
Adaptor sequences (4 random nucleotides from the 5 prime end and the 3 prime adaptor (N{4}CTGTCTCTTATACACATCTCCGAGC) were trimmed from reads using cutadapt. Reads were filtered for quality using fastq_quality_filter with the parameters “–q 30 –p 100.” To assign processed sequencing reads to miRNAs, the first 19nt of each read was matched to a dictionary of miRNA sequences downloaded from TargetScan Release 8.0, requiring no mismatches between the read and the miRNA dictionary. Differential expression analysis was performed using DESeq2 v1.38.3 without use of the lfcShrink function.
Assembly: TargetScan release 8.0 (human)
Supplementary files format and content: raw miRNA counts for all samples

growth_protocol: HFF-1 cells were cultured in DMEM supplemented with 15% FBS. IMR90 cells were cultured in EMEM supplemented with 10% FBS. BJ cells were cultured in EMEM supplemented with 10% FBS. Cells were grown to contact inhibition for at least 5 days before harvesting.


title: E14Tg2A, Nickel200 A, Day 6

description:
Library name: 6d Ni200 A
E14Ni2006dA


title: Tumor8

description: Library name: Sample 8


title: L36_TWEAK_48h_Rep3

city: Stuttgart

first: Steven

middle: A

last: Johnsen

address: Auerbachstrasse 112

country: Germany

institute: Robert Bosch Center for Tumor Diseases

description:
Library name: Sample030
RNA extracted from L3.6pl cells after 48 hour TWEAK treatment

data_processing:
Paired end sequencing reads were mapped to the reference genome assembly hg38 using STAR (star/2.7.9a). Reverse (sense strand) reads were quantified using htseq-count (htseq/0.9.1).
Assembly: hg39 (Human, GRCh38)
Supplementary files format and content: Comma-delimited and tab-delimited text file includes raw counts for each sample

source_name: cell line

growth_protocol: AsPC1 (RPMI, 10% FBS, 1% Pen-Strep) and L36pl (phenol red free MEM, 10% FBS, 1% Pen-Strep) were maintained in humidified 5% CO2 incubator at 37C.

extract_protocol:
Cells were washed twice with PBS after removing cell culture medium and total RNA was extracted from cells by adding 700 µL of QIAzol, incubated for 5 min on rocker, scraped and transferred to a new tube. 140 µL chloroform was added to the samples, vortexed for 15 sec, incubated for 3 min at room temperature, and centrifuged. Aqueous phase was transferred to a new tube and mixed with an equal volume of isopropanol. Samples were incubated at -20°C overnight and centrifuged. RNA pellet was washed twice with 70% ethanol and the pellet was air-dried at room temperature for 5-10 min. 50 µL of RNAse-free water was used to resuspend the pellet.
Before RNA-sequencing, RNA integrity was validated by gel electrophoresis and libraries were prepped using 500 ng following supplier’s protocol TruSeq Stranded mRNA Library Prep Kit (Illumina, 20020595). The library fragment size was determined by TapeStation.

value: cell line

value: PDAC

value: TWEAK


title: sRNA BJ-5ta CRISPRi ZSWIM8 knockdown guide 1

description: Library name: BJ5ta_3A1_Z8_1


title: E14Tg2A, Nickel150 B, Day 4

description:
Library name: 4d Ni150 B
E14Ni1504dB


title: Tumor1

description: Library name: Sample 1

value: tumor


title: E14Tg2A, Nickel150 A, Day 6

description:
Library name: 6d Ni150 A
E14Ni1506dA


title: sRNA IMR90 control knockout guide 1

description: Library name: IMR90_CI_NegA


title: L36_TWEAK_48h_Rep1

description:
Library name: Sample028
RNA extracted from L3.6pl cells after 48 hour TWEAK treatment


title: sRNA IMR90 control knockout guide 2

description: Library name: IMR90_CI_NegB


title: L36_TWEAK_48h_Rep2

description:
Library name: Sample029
RNA extracted from L3.6pl cells after 48 hour TWEAK treatment


title: Tumor4

description: Library name: Sample 4


title: L36_TWEAK_6h_Rep3

description:
Library name: Sample027
RNA extracted from L3.6pl cells after 6 hour TWEAK treatment


title: sRNA IMR90 ZSWIM8 knockout guide 3

description: Library name: IMR90_CI_Z8_10

value: Zswim8 knockout


title: L36_TWEAK_6h_Rep1

description:
Library name: Sample025
RNA extracted from L3.6pl cells after 6 hour TWEAK treatment


title: L36_TNFa_48h_Rep1

description:
Library name: Sample022
RNA extracted from L3.6pl cells after 48 hour TNFa treatment

value: TNFa


title: L36_TNFa_48h_Rep3

description:
Library name: Sample024
RNA extracted from L3.6pl cells after 48 hour TNFa treatment


title: L36_TNFa_6h_Rep3

description:
Library name: Sample021
RNA extracted from L3.6pl cells after 6 hour TNFa treatment


title: L36_TWEAK_6h_Rep2

description:
Library name: Sample026
RNA extracted from L3.6pl cells after 6 hour TWEAK treatment


title: sRNA BJ control knockout guide 3

description: Library name: BJ_CI_NegC

source_name: BJ

value: BJ


title: E14Tg2A, Nickel100 B, Day 6

description:
Library name: 6d Ni100 B
E14Ni1006dB


title: L36_Vehicle_Rep2

description:
Library name: Sample017
RNA extracted from L3.6pl cells after PBS treatment

value: Vehicle


title: E14Tg2A, Nickel100 A, Day 6

description:
Library name: 6d Ni100 A
E14Ni1006dA


title: sRNA IMR90 ZSWIM8 knockout guide 1

description: Library name: IMR90_CI_Z8_6


title: sRNA IMR90 ZSWIM8 knockout guide 2

description: Library name: IMR90_CI_Z8_9


title: E14Tg2A, control B, Day 6

description:
Library name: 6d control B
E14con6dB

value: control


title: L36_TNFa_48h_Rep2

description:
Library name: Sample023
RNA extracted from L3.6pl cells after 48 hour TNFa treatment


title: sRNA BJ control knockout guide 2

description: Library name: BJ_CI_NegB


title: AsPC1_TWEAK_48h_Rep3

description:
Library name: Sample015
RNA extracted from AsPC1 cells after 48 hour TWEAK treatment


title: E14Tg2A, Nickel100 A, Day 4

description:
Library name: 4d Ni100 A
E14Ni1004dA


title: sRNA BJ control knockout guide 1

description: Library name: BJ_CI_NegA


title: L36_TNFa_6h_Rep1

description:
Library name: Sample019
RNA extracted from L3.6pl cells after 6 hour TNFa treatment


title: L36_Vehicle_Rep3

description:
Library name: Sample018
RNA extracted from L3.6pl cells after PBS treatment


title: L36_Vehicle_Rep1

description:
Library name: Sample016
RNA extracted from L3.6pl cells after PBS treatment


title: E14Tg2A, control A, Day 6

description:
Library name: 6d control A
E14con6dA


title: E14Tg2A, Nickel100 B, Day 4

description:
Library name: 4d Ni100 B
E14Ni1004dB


title: AsPC1_TWEAK_48h_Rep2

description:
Library name: Sample014
RNA extracted from AsPC1 cells after 48 hour TWEAK treatment


title: sRNA BJ ZSWIM8 knockout guide 2

description: Library name: BJ_CI_Z8_9


title: AsPC1_TWEAK_48h_Rep1

description:
Library name: Sample013
RNA extracted from AsPC1 cells after 48 hour TWEAK treatment


title: Anableps ventral retina, biol rep3

city: Baton Rouge

first: Patricia

last: Schneider

state: Louisiana

address: LSU 131 Life Sciences Building

department: Biological Sciences

institute: Louisiana State University

description: Library name: Aa_V4

data_processing:
Adapter sequences were removed from the reads using NGmerge (version 0.3) (Gaspar, 2018). The trimmed reads were aligned to theTetraodon reference genome (tetNig2) using Bowtie2 (version 2.2.5). Alignments were output as a BAM file, which was indexed using Samtools (version 1.18) (Li et al., 2009). The fragment size distribution graph was created using the ATACseqQC package (version 1.24.0) (Ou et al., 2018) in RStudio (version 4.3.1). The trimmed reads were name-sorted using Samtools (version 1.18) (Li et al., 2009) and further processed with Genrich (version 0.6.1) to call narrow peaks using the parameters -j -y -r -v -m -e -a -f, to remove duplicate reads, multimapped reads, and reads mapped to mitochondrial chromosomes. Downstream analysis of the ATAC-seq data was performed using DiffBind.
Assembly: GCA_014839685.1
Supplementary files format and content: tab-delimited text file including differential chromatin accessibility peaks identified from ATAC-seq data

organism: Anableps anableps

source_name: Ventral retina

extract_protocol:
ATAC-seq libraries were prepared following the Active Motif ATAC seq protocol, which is based on a combination of the Buenrostro et al., 2013 and the Corces et al., 2017. Dorsal and ventral retinas were dissected and subsequently used for nuclei extraction.
All ATAC-seq libraries were performed from 50,000 cells and were amplified within 10 total PCR cycles. After PCR amplification, the libraries were purified with magnetic beads following the manufacturer’s protocol. Libraries were sequenced by Novogene Corporation Inc. The sequencing was performed using Nova-seq Paired-end 150.

value: Ventral retina


title: sRNA BJ ZSWIM8 knockout guide 1

description: Library name: BJ_CI_Z8_6


title: E14Tg2A, control A, Day 4

description:
Library name: 4d control A
E14con4dA


title: AsPC1_TWEAK_6h_Rep2

description:
Library name: Sample011
RNA extracted from AsPC1 cells after 6 hour TWEAK treatment


title: AsPC1_TWEAK_6h_Rep3

description:
Library name: Sample012
RNA extracted from AsPC1 cells after 6 hour TWEAK treatment


title: AsPC1_TWEAK_6h_Rep1

description:
Library name: Sample010
RNA extracted from AsPC1 cells after 6 hour TWEAK treatment


title: AsPC1_TNFa_48h_Rep2

description:
Library name: Sample008
RNA extracted from AsPC1 cells after 48 hour TNFa treatment


title: E14Tg2A, control B, Day 4

description:
Library name: 4d control B
E14con4dB


title: AsPC1_TNFa_48h_Rep3

description:
Library name: Sample009
RNA extracted from AsPC1 cells after 48 hour TNFa treatment


title: paipillary tumor, rep 10

city: Ithaca

first: Coulter

last: Ralston

address: 237 Tower Rd

department: Biomedical Engineering

institute: Cornell University

description:
Library name: DP_9322_17L
..alignments.DP_9322_17L

data_processing:
After quality analysis with FastQC and processing read lengths with trimmomatic (v0.39), reads were aligned to the GrCM38/mm10 reference genome with hisat2 (v2..2.1) and samtools (v1.21). Count matrices for each sample were generated using the subread (v.2.0.8) package.
Assembly: mm10
Supplementary files format and content: csv file containing raw counts for all samples. Each column represents a sample.

molecule: polyA RNA

growth_protocol: Targeted library preparation of tubal epithelial organoids with different mutated gene combinations was performed. Organoids of the same genotype were passaged and expanded until desired cell numbers were reached. Once desired cell numbers were reached, organoids were grown until day 14 prior to injections.

extract_protocol:
Tumor samples were collected and immediately flash frozen in liquid nitrogen. Pathological analysis of tumors was performed, and  tumors with papillary and mesenchymal phenotypes were collected for RNA-seq analysis. All RNA samples were prepared from tumors using the Zymo Quick RNA extraction kit (R1054).
mRNA library preparation with poly-A enrichment followed standard library construction procedures per Novogene. The sequencing platform and strategy was performed with the NovaSeq X Plus Series following the Novogene PE150 protocol.

treatment_protocol: Day 14 organoids were disrupted into single cells and 5x10^5 cells per combination were mixed with 100uL of 1X PBS (Gibco 10010023) and Matrigel (Corning #356231) at a 1:1 ratio and injected subcutaneously in the flanks of NSG mice. All mice received bilateral injections and were monitored weekly for tumor formation and growth of tumors. Mice were sacrificed when tumors reached 1 cm in diameter.

value: tubal epithelial organoids

value: subcutaneous flank injection


title: AsPC1_TNFa_6h_Rep1

description:
Library name: Sample004
RNA extracted from AsPC1 cells after 6 hour TNFa treatment


title: AsPC1_TNFa_48h_Rep1

description:
Library name: Sample007
RNA extracted from AsPC1 cells after 48 hour TNFa treatment


title: sRNA BJ ZSWIM8 knockout guide 3

description: Library name: BJ_CI_Z8_10


title: sRNA HFF1 control knockout guide 2

description: Library name: HFF1_CI_NegB


title: paipillary tumor, rep 8

description:
Library name: DP_9319_17R
..alignments.DP_9319_17R


title: sRNA HFF1 control knockout guide 3

description: Library name: HFF1_CI_NegC


title: AsPC1_Vehicle_Rep2

description:
Library name: Sample002
RNA extracted from AsPC1 cells after PBS treatment


title: AsPC1_TNFa_6h_Rep3

description:
Library name: Sample006
RNA extracted from AsPC1 cells after 6 hour TNFa treatment


title: L36_TNFa_6h_Rep2

description:
Library name: Sample020
RNA extracted from L3.6pl cells after 6 hour TNFa treatment


title: paipillary tumor, rep 9

description:
Library name: DP_9321_17L
..alignments.DP_9321_17L


title: sRNA HFF1 control knockout guide 1

description: Library name: HFF1_CI_NegA


title: AsPC1_TNFa_6h_Rep2

description:
Library name: Sample005
RNA extracted from AsPC1 cells after 6 hour TNFa treatment


title: paipillary tumor, rep 5

description:
Library name: DP_9277_17R
..alignments.DP_9277_17R


title: ChIP_L36pl_RELB_TWEAK_6h_Rep3

description:
Library name: Sample048
ChIP for RELB in L3.6pl cells after 6h TWEAK treatment

data_processing:
Paired end sequencing reads were mapped to the reference genome assembly hg38 using bowtie2/2.5.0. PCR duplicates were removed with samtools markdup and replicates were merged using samtools merge (samtools/1.18). Bigwig files for individual and merged bam files were generated removing blacklist regions using reads per genomic content (RPGC) normalization with bamCoverage (deeptools/3.3.2) . MACS2 callpeak (python/3.10.7) was used to call the significant peaks with --broad cutoff 0.05 for histone marks and non-broad cutoff of 0.05 for transcription factors while using input files from respective conditions as background.
Assembly: hg38 (Human, GRCh38)
Supplementary files format and content: The BED files are in narrowPeak and broadPeak format; please rename the extension to '.bed'

extract_protocol:
Chromatin immunoprecipitation was performed by crosslinking cells with 1% formaldehyde for 20 min and quenched by 1.25 M glycine for 5 min. Cells were lysed with lysis buffer (150 mM NaCl, 20 mM EDTA, 50 mM Tris-HCl, 0.5% v/v NP-40, 1% v/v Triton X-100, 10 mM NaF). Nuclear pellets were resuspended and sonicated in sonication buffer (150 mM NaCl, 20 mM EDTA, 50 mM Tris-HCl, 1% v/v NP-40, 0.5% v/v sodium deoxycholate, 10 mM NaF, 0.1% SDS) using a Bioruptor Pico (Diagenode) and a cycle setting of 30 sec on/off until fragment sizes around 200-500 bp was reached. Protease and phosphatase inhibitors were added to both lysis and sonication buffers. Samples were precleared by 50% slurry of sepharose resuspended in sonication buffer. Antibodies were added and incubated rotating overnight. Sepharose beads coupled with Protein A (rabbit antibodies) or Protein G (mouse or goat antibodies) were added to samples and incubated for 2 hr, washed, de-crosslinked, RNAse A and proteinase K treated, and DNA was extracted. For GATA6 and Pol II ChIP of PDX tumors, 5 mm3 samples were thawed on ice in a petri dish, washed three times with PBS, cut into small pieces and transferred to a 15 mL falcon. Samples were fixed with 1% formaldehyde rotating on wheel for 20 min and quenched with 1.25 M glycine for 5 min. Samples were washed three times with PBS, resuspended in RPMI 1640 with 210 µg liberase TH per sample and transferred to gentleMACS Octo Dissociator with Heaters (Miltenyi Biotec) and incubated (step 1: spin 50 rpm 20 min; step 2: spin 1000 rpm 30 min; step 3: spin -1000 rpm 30 min). Samples were centrifuged and transferred to a new tube and washed three times with lysis buffer, resuspending the nuclear pellet each time. ChIP was continues as described above for cell lines. For H3K27ac ChIP of PDX tumors, 5 mm3 samples were homogenized on dry ice using the Sciences BioMasher II Micro Tissue Homogenizer. ChIP was carried out for the powdered tissue as described for cell lines.
ChIP DNA was quantified with Qubit using the Qubit 1X dsDNA High Sensitivity Kit and libraries were prepped per supplier’s protocol using the MicroPlex Library Preparatioin Kit v3 (Diagenode, C05010001). The library fragment size was determined by TapeStation using the High Sensitivity D1000 Sample Buffer and High Sensitivity D1000 ScreenTape.

tag: antibody

value: RELB


title: ChIP_L36pl_RELB_TWEAK_30min_Rep3

description:
Library name: Sample045
ChIP for RELB in L3.6pl cells after 30min TWEAK treatment


title: E14Tg2A, Nickel150 A, Day 4

description:
Library name: 4d Ni150 A
E14Ni1504dA

value: embryonic stem cells

value: WT


title: ChIP_L36pl_RELB_TWEAK_30min_Rep2

description:
Library name: Sample044
ChIP for RELB in L3.6pl cells after 30min TWEAK treatment


title: paipillary tumor, rep 4

description:
Library name: DP_9267_17R
..alignments.DP_9267_17R


title: paipillary tumor, rep 7

description:
Library name: DP_9316_17L
..alignments.DP_9316_17L


title: AsPC1_Vehicle_Rep1

description:
Library name: Sample001
RNA extracted from AsPC1 cells after PBS treatment


title: AsPC1_Vehicle_Rep3

description:
Library name: Sample003
RNA extracted from AsPC1 cells after PBS treatment


title: Sequencing Lane 2,V(D)J

first: Jahan

last: Rahman

state: New York

address: 417 E 68th St

department: Center for Hematologic Malignancies

institute: Memorial Sloan Kettering

description: Library name: SD-4008_Pool_2_TCR_VDJ

library_source: other

data_processing:
Single-cell RNA FASTQ data were processed using the Cell Ranger version 9.0.0 ‘count’ workflow to generate gene expression count matrices.  Feature barcoding FASTQs were processed using Cite-Seq-Count v1.4.5 to construct count matrices for sample demultiplexing and the quantification of cell-surface protein expression.  TCR data were processed using Cell Ranger’s ‘vdj’ pipeline to generate cell clonotype annotations.
Assembly: Human reference, GRCh38 (GENCODE v32/Ensembl 98)
Supplementary files format and content: Raw count matrices:  RNA_counts.csv.gz, ADT_counts.csv.gz
Supplementary files format and content: Filtered contig annotations: filtered_contig_annotations.csv.gz
Supplementary files format and content: Cell-sample annotations: cell_sample_assign.csv.gz
Library strategy: TCR-Seq

molecule: other

source_name: Bone Marrow

extract_protocol:
Freshly isolated BMNCs from NSG-SGM3 mice engrafted with CD34⁺ cord blood–derived hematopoietic stem cells, collected from the femurs and tibias, were suspended in Human FcR Blocking Reagent (Miltenyi Biotec, catalog #130-059-901), diluted in Filtered DPBS (Corning, catalog #21-031-CM) + 0.5% BSA (Fisher, catalog #F2442-500ML) and incubated for 10 minutes at 4ºC.  Brilliant Staining Buffer (BD), TotalSeqTM Oligonucleotide anti-Human Hashtag antibodies (Biolegend; C0251 catalog # 394661, C0252 catalog # 394663, C0253 catalog # 394665, C0254 catalog # 394667, or C0258 catalog # 394675), surface antibody mix (including human anti-CD45 BV510, Biolegend) were added to the FcR Blocking solution and incubated at RT for 30 minutes in the dark. Cells were washed with filtered DPBS + 0.5% BSA, filtered using 30 µm filters (Sysmex), and resuspended in filtered DPBS + 2% BSA + DAPI. Cell populations were purified using Fluorescent Activated Cell Sorting (FACS), using the Aria3 Instrument (BD Biosciences). Upon purification and collection of cell populations in Protein Lo-Bind Eppendorf Tubes, samples were pooled together based off cell number  and washed with filtered Cell Staining Buffer (Biolegend, catalog # 420201). Cells were Fc Blocked using TruStain FcX (Biolegend) at 4ºC for 10 minutes and then stained with TotalseqTM Universal Cocktail (Biolegned, catalog #399905) for 30 minutes at 4ºC. The cells were washed once with Cell Staining Buffer and twice with DPBS + 0.04% BSA and then submitted to the MSKCC Integrative Genomics Core for sequencing.
Standard library construction was performed using a 10x Chromium Single Cell Immune Profiling Gel Bead Kit.

value: Bone Marrow

value: CD371 KO


title: ChIP_L36pl_RELB_TNFa_6h_Rep1

description:
Library name: Sample040
ChIP for RELB in L3.6pl cells after 6 hour TNFa treatment


title: paipillary tumor, rep 2

description:
Library name: DP_9258_17R
..alignments.DP_9258_17R


title: paipillary tumor, rep 6

description:
Library name: DP_9285_17R
..alignments.DP_9285_17R


title: ChIP_L36pl_RELB_TNFa_30min_Rep2

description:
Library name: Sample038
ChIP for RELB in L3.6pl cells after 30 min TNFa treatment


title: ChIP_L36pl_RELB_TWEAK_6h_Rep2

description:
Library name: Sample047
ChIP for RELB in L3.6pl cells after 6h TWEAK treatment


title: Sequencing Lane 2,Feature-barcoding

description: Library name: SD-4008_Pool_2_ADT_HTO

data_processing:
Single-cell RNA FASTQ data were processed using the Cell Ranger version 9.0.0 ‘count’ workflow to generate gene expression count matrices.  Feature barcoding FASTQs were processed using Cite-Seq-Count v1.4.5 to construct count matrices for sample demultiplexing and the quantification of cell-surface protein expression.  TCR data were processed using Cell Ranger’s ‘vdj’ pipeline to generate cell clonotype annotations.
Assembly: Human reference, GRCh38 (GENCODE v32/Ensembl 98)
Supplementary files format and content: Raw count matrices:  RNA_counts.csv.gz, ADT_counts.csv.gz
Supplementary files format and content: Filtered contig annotations: filtered_contig_annotations.csv.gz
Supplementary files format and content: Cell-sample annotations: cell_sample_assign.csv.gz
Library strategy: CITE-seq

molecule: protein


title: ChIP_L36pl_RELB_TNFa_30min_Rep3

description:
Library name: Sample039
ChIP for RELB in L3.6pl cells after 30 min TNFa treatment


title: ChIP_L36pl_RELB_TWEAK_6h_Rep1

description:
Library name: Sample046
ChIP for RELB in L3.6pl cells after 6h TWEAK treatment


title: sRNA HFF1 ZSWIM8 knockout guide 3

description: Library name: HFF1_CI_Z8_10


title: sRNA HFF1 ZSWIM8 knockout guide 2

description: Library name: HFF1_CI_Z8_9


title: sRNA HFF1 ZSWIM8 knockout guide 1

description: Library name: HFF1_CI_Z8_6


title: ChIP_L36pl_RELB_TNFa_6h_Rep3

description:
Library name: Sample042
ChIP for RELB in L3.6pl cells after 6 hour TNFa treatment


title: paipillary tumor, rep 3

description:
Library name: DP_9267_17L
..alignments.DP_9267_17L


title: ChIP_L36pl_RELB_TNFa_6h_Rep2

description:
Library name: Sample041
ChIP for RELB in L3.6pl cells after 6 hour TNFa treatment


title: ChIP_L36pl_RELB_TWEAK_30min_Rep1

description:
Library name: Sample043
ChIP for RELB in L3.6pl cells after 30min TWEAK treatment


title: ChIP_L36pl_RELB_Vehicle_Rep2

description:
Library name: Sample035
ChIP for RELB in L3.6pl cells after PBS treatment


title: GABI_24h3

city: Durham

first: Jialei

last: Sun

address: Stockton Road

department: Biosciences

country: United Kingdom

institute: Durham University

description: Library name: SAMPLE24

data_processing:
Original image data file from high-throughput sequencing platforms (like Illumina) is transformed to sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw data are stored in FASTQ(fq) format files, which contain sequences of reads and corresponding base quality. Each read has four descriptive lines, as indicated below:  Each read has four descriptive lines, as indicated below:  @A01426:11:H73WJDSX2:1:1101:2329:10161:N:0:GTGAGATC+GAACTAGC TCGCACGCGCTGCCGTATGTGACGCCGTCGCTGCCGCACACAGGATCGTAGAGGCTCGC + FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFF:FFFFFFFFFFF  Line 1: Begins with the at sign (@) followed by sequence identifiers and optional description (such as FASTA header). Line 2: Base sequences (raw read, A, G, C, and T). Line 3: Begins with the plus sign (+) optionally followed by the same Illumina sequence identifiers and description information as in Line 1. Line 4: The quality values for each base, corresponding to the data in Line 2.
Assembly: ncbi_arabidopsis_thaliana_gcf_000001735_4_tair10_1
Supplementary files format and content: Differential gene anaylsis, and GO & KEGG anaylsis

organism: Arabidopsis thaliana

source_name: Root

extract_protocol:
Total RNA was extracted using the ReliaPrep™ RNA Miniprep Systems Kit (Promega UK, Southampton, UK, Z6111) following the manufacturer’s instructions.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

value: Root

value: VAMP714 T-DNA insertion

value: 150 mM NaCl


title: Sequencing Lane 1,V(D)J

description: Library name: SD-4008_Pool_1_TCR_VDJ

value: Control


title: ChIP_L36pl_RELA_TWEAK_6h_Rep3

description:
Library name: Sample033
ChIP for RELA in L3.6pl cells after 6h TWEAK treatment

value: PDAC

value: TWEAK

value: RELA


title: ChIP_L36pl_RELA_TWEAK_30min_Rep3

description:
Library name: Sample030
ChIP for RELA in L3.6pl cells after 30min TWEAK treatment


title: HEPM, K139Q, 8h, rep3

first: Li

last: Meng

address: No. 639, Zhizaoju Road

institute: Shanghai jiao tong university

description: Library name: R157K_3

data_processing:
After quantified by Qubit 4.0, the sequencing library was performed on NovaSeq6000 platform using NovaSeq Reagent Kit.
Assembly: Tthe expression level of each transcript was calculated according to the transcripts per million reads (TPM) method. RSEM was used to quantify gene abundances.
Supplementary files format and content: xlsx files include FPKM values for each Sample

source_name: HEPM

growth_protocol: HEPM cells in α-MEM (Gibco, C12440500BT) supplemented with 10% FBS and 1% PS at 37°C and 5% CO2 in a humidified incubator.

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions.Then RNA quality was determined by 5300 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA samplewas used to construct sequencing library.
RNA purification, reverse transcription, library construction and sequencing were performed at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) according to the manufacturer’s instructions . The RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep, Ligation (San Diego, CA) using 1μg of total RNA. Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized with random hexamer primers. Then the synthesized cDNA was subjected to end-repair, phosphorylation and adapter addition according to library construction protocol. Libraries were size selected or cDNA target fragments of 300-400bp use magnetic beads followed by PCR amplified for 10-15 PCR cycles.

value: HEPM

value: Human embryonic palatal mesenchymal cells

value: MSX1 K139Q overexpression

value: plasmid transfection


title: Sequencing Lane 2,RNA

description: Library name: SD-4008_Pool_2_RNA

data_processing:
Single-cell RNA FASTQ data were processed using the Cell Ranger version 9.0.0 ‘count’ workflow to generate gene expression count matrices.  Feature barcoding FASTQs were processed using Cite-Seq-Count v1.4.5 to construct count matrices for sample demultiplexing and the quantification of cell-surface protein expression.  TCR data were processed using Cell Ranger’s ‘vdj’ pipeline to generate cell clonotype annotations.
Assembly: Human reference, GRCh38 (GENCODE v32/Ensembl 98)
Supplementary files format and content: Raw count matrices:  RNA_counts.csv.gz, ADT_counts.csv.gz
Supplementary files format and content: Filtered contig annotations: filtered_contig_annotations.csv.gz
Supplementary files format and content: Cell-sample annotations: cell_sample_assign.csv.gz


title: ChIP_L36pl_RELB_TNFa_30min_Rep1

description:
Library name: Sample037
ChIP for RELB in L3.6pl cells after 30 min TNFa treatment

value: TNFa


title: mesenchymal tumor, rep 3

description:
Library name: DP_9257_17R
..alignments.DP_9257_17R

value: tumor

value: tubal epithelial organoids

value: subcutaneous flank injection


title: ChIP_L36pl_RELA_TWEAK_30min_Rep1

description:
Library name: Sample028
ChIP for RELA in L3.6pl cells after 30min TWEAK treatment


title: ChIP_L36pl_RELB_Vehicle_Rep1

description:
Library name: Sample034
ChIP for RELB in L3.6pl cells after PBS treatment

value: Vehicle

value: RELB


title: ChIP_L36pl_RELB_Vehicle_Rep3

description:
Library name: Sample036
ChIP for RELB in L3.6pl cells after PBS treatment


title: mesenchymal tumor, rep 2

description:
Library name: DP_9257_17L
..alignments.DP_9257_17L


title: Sequencing Lane 1,Feature-barcoding

description: Library name: SD-4008_Pool_1_ADT_HTO

value: Bone Marrow


title: ChIP_L36pl_RELA_TNFa_6h_Rep3

description:
Library name: Sample027
ChIP for RELA in L3.6pl cells after 6 hour TNFa treatment


title: ChIP_L36pl_RELA_TNFa_30min_Rep3

description:
Library name: Sample024
ChIP for RELA in L3.6pl cells after 30 min TNFa treatment


title: HEPM, K139R, 8h, rep1

description: Library name: R157S_1

value: MSX1 K139R overexpression


title: ChIP_L36pl_RELA_TNFa_30min_Rep2

description:
Library name: Sample023
ChIP for RELA in L3.6pl cells after 30 min TNFa treatment


title: ChIP_L36pl_RELA_TWEAK_6h_Rep2

description:
Library name: Sample032
ChIP for RELA in L3.6pl cells after 6h TWEAK treatment


title: Sequencing Lane 1,RNA

description: Library name: SD-4008_Pool_1_RNA


title: paipillary tumor, rep 1

description:
Library name: DP_9258_17L
..alignments.DP_9258_17L


title: Mock_24h2

description: Library name: SAMPLE20

value: Root

value: WT (Col-0)

value: 150 mM NaCl


title: ChIP_L36pl_RELA_Vehicle_Rep3

description:
Library name: Sample021
ChIP for RELA in L3.6pl cells after PBS treatment

value: PDAC


title: HEPM, K139Q, 8h, rep2

description: Library name: R157K_2


title: mesenchymal tumor, rep 1

description:
Library name: DP_9252_17R
..alignments.DP_9252_17R


title: ChIP_L36pl_RELA_TWEAK_30min_Rep2

description:
Library name: Sample029
ChIP for RELA in L3.6pl cells after 30min TWEAK treatment

value: TWEAK

value: RELA


title: HEPM, MSX1, 8h, rep3

description: Library name: MSX1_3

value: HEPM

value: Human embryonic palatal mesenchymal cells

value: WT MSX1  overexpression


title: ChIP_L36pl_RELA_Vehicle_Rep1

description:
Library name: Sample019
ChIP for RELA in L3.6pl cells after PBS treatment


title: GABI_24h2

description: Library name: SAMPLE23

value: VAMP714 T-DNA insertion


title: ChIP_L36pl_FOSL1_Vehicle_Rep2

description:
Library name: Sample017
ChIP for FOSL1 in L3.6pl cells


title: Mock_24h1

description: Library name: SAMPLE19


title: ChIP_L36pl_RELA_TWEAK_6h_Rep1

description:
Library name: Sample031
ChIP for RELA in L3.6pl cells after 6h TWEAK treatment


title: ChIP_L36pl_RELA_Vehicle_Rep2

description:
Library name: Sample020
ChIP for RELA in L3.6pl cells after PBS treatment


title: HEPM, K139R, 8h, rep2

description: Library name: R157S_2

value: plasmid transfection


title: ChIP_L36pl_RELA_TNFa_6h_Rep2

description:
Library name: Sample026
ChIP for RELA in L3.6pl cells after 6 hour TNFa treatment

value: TNFa


title: HEPM, MSX1, 8h, rep1

description: Library name: MSX1_2


title: L36pl_FOSL1_Vehicle_Rep1

description:
Library name: Sample016
ChIP for FOSL1 in L3.6pl cells


title: HEPM, MSX1, 8h, rep2

description: Library name: MSX1_1


title: HEPM, K139R, 8h, rep3

description: Library name: R157S_3


title: ChIP_L36pl_H3K27ac_TWEAK_30min_Rep3

description:
Library name: Sample012
ChIP for H3K27ac in L3.6pl cells after 30 min TWEAK treatment


title: HEPM, K139Q, 8h, rep1

description: Library name: R157K_1

value: MSX1 K139Q overexpression


title: GABI_9h2

description: Library name: SAMPLE17


title: GABI_24h1

description: Library name: SAMPLE22


title: ChIP_L36pl_RELA_TNFa_6h_Rep1

description:
Library name: Sample025
ChIP for RELA in L3.6pl cells after 6 hour TNFa treatment


title: ChIP_L36pl_RELA_TNFa_30min_Rep1

description:
Library name: Sample022
ChIP for RELA in L3.6pl cells after 30 min TNFa treatment


title: Mock_9h3

description: Library name: SAMPLE15


title: ChIP_L36pl_H3K27ac_TWEAK_30min_Rep1

description:
Library name: Sample010
ChIP for H3K27ac in L3.6pl cells after 30 min TWEAK treatment


title: Mock_9h2

description: Library name: SAMPLE14


title: HEPM, Vector, 8h, rep3

description: Library name: Vector-3

value: Vector overexpression


title: ChIP_L36pl_FOSL1_Vehicle_Rep3

description:
Library name: Sample018
ChIP for FOSL1 in L3.6pl cells

value: Vehicle


title: Mock_24h3

description: Library name: SAMPLE21


title: GABI_9h3

description: Library name: SAMPLE18


title: HEPM, Vector, 8h, rep1

description: Library name: Vector-1


title: ChIP_L36pl_H3K27ac_TWEAK_6h_Rep3

description:
Library name: Sample015
ChIP for H3K27ac in L3.6pl cells after 6 hour TWEAKtreatment


title: ChIP_L36pl_H3K27ac_TNFa_6h_Rep2

description:
Library name: Sample008
ChIP for H3K27ac in L3.6pl cells after 6 hour TNFa treatment


title: Mock_9h1

description: Library name: SAMPLE13


title: HEPM, Vector, 8h, rep2

description: Library name: Vector-2


title: ChIP_L36pl_H3K27ac_TWEAK_30min_Rep2

description:
Library name: Sample011
ChIP for H3K27ac in L3.6pl cells after 30 min TWEAK treatment


title: ChIP_L36pl_H3K27ac_TNFa_30min_Rep3

description:
Library name: Sample006
ChIP for H3K27ac in L3.6pl cells after 30 min TNFa treatment


title: GABI_3h3

description: Library name: SAMPLE12


title: GABI_9h1

description: Library name: SAMPLE16


title: ChIP_L36pl_H3K27ac_TWEAK_6h_Rep2

description:
Library name: Sample014
ChIP for H3K27ac in L3.6pl cells after 6 hour TWEAKtreatment


title: shNEG_3

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

institute: University Medical Center Freiburg

description: Library name: Sample 3

data_processing:
Alignment to the hg38 genome was performed using STAR 2.7.11
Differential expression analysis was performed using DESeq2 1.40.0
Assembly: hg38
Supplementary files format and content: Tab-delimited text file depicting differential expression results

source_name: Fujioka

growth_protocol: The FUJIOKA cell line was obtained from the Japanese Collection of Research Bioresources Cell Bank, while KG1A cells were purchased from the American Type Culture Collection. The KO-52 cell line was a kind gift from Prof. Florian Grebien. FUJIOKA cells were cultured in RPMI-1640 medium supplemented with 10% foetal bovine serum (FBS), 50U/ml penicillin, 50µg/ml streptomycin, 2mM L-glutamine. KG1A cells were cultured in RPMI-1640 supplemented with 20% FBS, while KO-52 cells were grown in DMEM medium. Cells were kept at a concentration of 0.5 x 106 cells/ml at 37°C under normoxic conditions with 5% CO2 in a humidified incubator and were washed with PBS between passages. All cell lines were routinely screened for mycoplasma

extract_protocol:
RNA-seq library preparation was performed using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China) according to manufacturer’s instruction.
The generated DNA nanoballs were loaded in patterned nanoarray and PE150 base reads were generated by sequencing on a MGI G400 sequencing platform at MGI facility in Warsaw, Poland.

treatment_protocol: For the shRNA silencing work, stable shRNA expressing cell lines were generated. For this purpose, two SPINK2-targeting shRNA sequences were obtained from the GPP Web Portal (https://portals.broadinstitute.org/gpp/public/gene/search_clones) by selecting the two shRNAs which displayed the highest predicted silencing score: shRNA1, TCAGGGAAGGTGGTCATAATA (TRCN0000373635), and shRNA2, CGCCAAACTGCTCTCAGTATA (TRCN0000073496). Both shRNAs were cloned into the Tet-pLKO-puro vector (Addgene plasmid #21915) using AgeI/EcoRI restriction sites 24. The integrity of both shRNA inserts was confirmed by sequencing. A scrambled control shRNA plasmid (shCtr), Tet-pLKO-puro-Scrambled (Addgene plasmid #47541), was used as a non-targeting control 25. Recombinant lentiviral particles were generated by transient transfection of 293T cells as previously described . After induction of doxycycline (1µg/µl) cells were plated at a density of 106 cells/ml and viable cells were counted and passaged at a 1:2 ratio of day for four consecutive days to determine their growth rate. Cell cycle analysis was carried out by labelling cycling cells with 10µM BRDU (8811-6600-42, Thermofisher) for 1 hour, after which cells were co-stained with 7-AAD (IM3630c, Beckman-Coulter) according to manufacturer’s instructions, as previously described 3. Apoptosis analysis was performed using an Annexin V kit following manufacturer’s instruction. Myeloid maturation studies were performed using antibodies against CD14, CD35, CD64 and CD300E (Beckman Coulter). Acquisition of immunostaining data was carried out on a Cytoflex Instrument (Beckman Coulter) and the analysis was performed using a Flowjo software (Flowjo, LLC).

value: Fujioka


title: shSPINK2_3

description: Library name: Sample 6


title: shSPINK2_1

description: Library name: Sample 4


title: ChIP_L36pl_H3K27ac_TNFa_30min_Rep1

description:
Library name: Sample004
ChIP for H3K27ac in L3.6pl cells after 30 min TNFa treatment


title: ChIP_L36pl_H3K27ac_TWEAK_6h_Rep1

description:
Library name: Sample013
ChIP for H3K27ac in L3.6pl cells after 6 hour TWEAKtreatment


title: GABI_3h2

description: Library name: SAMPLE11


title: ChIP_L36pl_H3K27ac_Vehicle_Rep3

description:
Library name: Sample003
ChIP for H3K27ac in L3.6pl cells after PBS treatment


title: ChIP_L36pl_H3K27ac_Vehicle_Rep1

description:
Library name: Sample001
ChIP for H3K27ac in L3.6pl cells after PBS treatment


title: GABI_3h1

description: Library name: SAMPLE10


title: shNEG_2

description: Library name: Sample 2


title: Mock_3h3

description: Library name: SAMPLE9


title: shNEG_1

description: Library name: Sample 1


title: Neuro B3 | 030 | Full ROI

city: Woolloongabba

first: Fernando

last: Guimaraes

state: QLD

address: 37 Kent Street

country: Australia

institute: Frazer Institute - University of Queensland

data_processing:
Adapter trimming with trim galore,  trimGaloreOpts = " --hardtrim5 26 --dont_gzip"
If paired-end, merge overlapping R1 and R2 with flash2, flash2Opts = " -m 26 -e 26 -f 26 -s 1 -r 27”
Extract UMIs in bowtie2, umiExtractOpts = " --bc-pattern=NNNNNNNNNNNNNN"
Align RTS_IDs (probe barcodes) using bowtie2, bowtie2Opts = " --end-to-end -L 4 --trim5 0 --trim3 0 --norc"
Deduplication using UMI-tools, umiDedupOpts = " --edit-distance-threshold=1“
Assembly: sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform, see attached NanoString GeoMx Hs_R_NGS_WTA_v1.0 file
Supplementary files format and content: rawdata.csv: raw count data, normdata.csv: normalised count data (We performed quality control steps to all the samples, then removed samples with nuclei count < 200 and performed normalization of all samples that  passed the quality control steps.)
Library strategy: Spatial Transcriptomics

source_name: Neuroblastoma

extract_protocol:
Samples were incubated with DNA-oligo barcoded RNA-ISH probes which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with fluorescently labeled antibodies for visualization of morphological structures. Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)
Spatial transcriptome sequencing libraries were prepared with Nanostring GeoMx DSP WTA kit according to manufacture's construction

value: Neuroblastoma

value: Pre-treatment

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: roi

value: Tumor

tag: staging

value: Staging  I

tag: age dx_class

value: <12 months

tag: histology

value: Differentiating

tag: mycn amplification

value: non-amplified

tag: gender

value: F

tag: follow up_months

tag: overall survival_months

tag: overall survival_years

tag: death

value: Alive

tag: risk classification

value: Low


title: GABI_0h3

description: Library name: SAMPLE6

tag: tissue

value: Root

tag: genotype

value: VAMP714 T-DNA insertion

tag: treatment


title: MKL-2 shRNA delta catenin 3

city: Seattle

first: Joselyn

last: Landazuri Vinueza

state: WA

address: 4131 11th Ave NE

department: Microbiology

institute: University of Washington

description: Library name: JL6

data_processing:
Image analysis and basecalling was performed using Illumina's Real Time Analysis v3.10.30 software, followed by demultiplexing of indexed reads and generation of FASTQ files with Illumina's bcl2fastq-2.20 software.
Sequenced reads were aligned to a  custom GRCh38 reference (with an added contig for Merkel cell polyomavirus isolate MKL2) using STAR2 aligner v2.7.7a in the two-pass mode.
STAR2's internal quantification method was used to generate gene-level raw counts using edited gencode v38 gene definitions (with MKL2 ST and LT genes added)
Assembly: GRCh38 (custom, described in data processing step above)
Supplementary files format and content: tab-separated file containing raw gene counts

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (Qiagen) per manufacturer’s protocol
These libraries were prepped using the Illumina TruSeq Stranded mRNA Library Prep (Illumina, San Diego, CA; P/N 20020595).

tag: cell line

value: MKL-2 shRNA delta catenin


title: Mock_3h1

description: Library name: SAMPLE7

value: WT (Col-0)

value: 150 mM NaCl


title: ChIP_L36pl_H3K27ac_TNFa_30min_Rep2

description:
Library name: Sample005
ChIP for H3K27ac in L3.6pl cells after 30 min TNFa treatment

tag: cell type

value: PDAC

value: TNFa

tag: antibody


title: END3

city: Santiago

first: Gino

last: Nardocci

address: Av. Mons. Álvaro del Portillo 12.455

country: Chile

institute: Universidad de los Andes

description: Library name: Sample 6

data_processing:
Reads were aligned to the mouse genome (hg38) using bowtie2. Gene-level counts were generated with HTSeq. Differential expression analysis was performed using DESeq2 in the SARTools pipeline.
Assembly: hg38
Supplementary files format and content: Tab-delimited .txt files containing normalized gene counts

source_name: small extracellular vesicles from Menstrual Fluid

extract_protocol:
RNA was isolated from menstrual fluid plasma-derived sEV using TRIzol LS (Invitrogen, USA) on a 60 uL sEV sample volume. RNA concentration was assessed with a NanoDrop One (Thermo Fisher Scientific, USA). A minimum of 250 ng RNA was used for RNA sequencing (RNA-Seq).
RNA-Seq was performed by Azenta Life Sciences (South Plainfield, NJ, USA). Briefly, library preparation was performed with rRNA depletion, and sequencing was carried out on an Illumina next generation sequencing platform with paired-end 150 bp reads.


title: MKL-2 shRNA delta catenin 1

description: Library name: JL4


title: GABI_0h2

description: Library name: SAMPLE5


title: Mock_3h2

description: Library name: SAMPLE8


title: MKL-2 shRNA delta catenin 2

description: Library name: JL5


title: MKL-2 shRNA control 3

description: Library name: JL3

value: MKL-2 shRNA control


title: Neuro B3 | 026 | Full ROI

value: Neuroblastoma

value: Pre-treatment

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: roi

value: Staging  III

value: >18 months

value: M


title: ChIP_L36pl_H3K27ac_TNFa_6h_Rep3

description:
Library name: Sample009
ChIP for H3K27ac in L3.6pl cells after 6 hour TNFa treatment

tag: cell line

tag: treatment


title: ChIP_L36pl_H3K27ac_TNFa_6h_Rep1

description:
Library name: Sample007
ChIP for H3K27ac in L3.6pl cells after 6 hour TNFa treatment

tag: cell type

tag: antibody


title: Neuro B3 | 027 | Full ROI

tag: tissue

tag: aoisurfacearea

tag: aoinucleicount

value: Tumor

tag: staging

tag: age dx_class

tag: histology

value: Differentiating

tag: mycn amplification

value: non-amplified

tag: gender

tag: follow up_months

tag: overall survival_months

tag: overall survival_years

tag: death

tag: risk classification


title: shSPINK2_2

description: Library name: Sample 5

tag: cell line

value: Fujioka


title: Neuro B3 | 025 | Tumour

tag: treatment

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: roi

value: Staging  I

value: <12 months

value: F

value: Alive

value: Low


title: END1

description: Library name: Sample 4

tag: tissue

value: small extracellular vesicles from Menstrual Fluid


title: Neuro B3 | 021 | Tumour

tag: aoisurfacearea

tag: aoinucleicount

tag: staging

value: Staging  II

tag: age dx_class

tag: histology

tag: mycn amplification

tag: gender

tag: death


title: Mock_0h2

description: Library name: SAMPLE2

value: Root

tag: genotype

value: WT (Col-0)

tag: treatment


title: END2

description: Library name: Sample 5


title: MKL-2 shRNA control 2

description: Library name: JL2

tag: cell line

value: MKL-2 shRNA control


title: CTR2

description: Library name: Sample 2


title: MKL-2 shRNA control 1

description: Library name: JL1


title: Neuro B3 | 016 | Tumour

value: Neuroblastoma

value: Pre-treatment

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: risk classification


title: Neuro B3 | 029 | Full ROI

tag: tissue

tag: aoisurfacearea

tag: aoinucleicount

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: roi

tag: staging

tag: age dx_class

tag: follow up_months

tag: overall survival_months

tag: overall survival_years


title: GABI_0h1

description: Library name: SAMPLE4

tag: genotype

value: VAMP714 T-DNA insertion

tag: treatment


title: Neuro B3 | 024 | Tumour

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

value: Tumor

tag: histology

tag: mycn amplification

tag: gender

tag: death


title: Mock_0h3

description: Library name: SAMPLE3

tag: tissue


title: Neuro B3 | 022 | Tumour

tag: aoisurfacearea

tag: aoinucleicount

tag: sequencingsaturation

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: roi

tag: staging

tag: age dx_class

value: Differentiating

tag: risk classification


title: Neuro B3 | 018 | Tumour

tag: treatment

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

value: non-amplified


title: Mock_0h1

description: Library name: SAMPLE1

tag: tissue

tag: genotype


title: Neuro B3 | 014 | TME

tag: aoisurfacearea

tag: aoinucleicount

tag: stitchedreads

tag: sequencingsaturation

value: TME

tag: histology

tag: mycn amplification

tag: gender

tag: death


title: CTR1

description: Library name: Sample 1


title: CTR3

description: Library name: Sample 3


title: Neuro B3 | 011 | TME

tag: treatment

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: roi

tag: staging

tag: age dx_class

tag: risk classification


title: BIR_LUB_38

type: genomic

city: Nuthetal

first: Heike

last: Vogel

state: BRB

address: Arthur-Scheunert-Allee 114-116

department: Department of Experimental Diabetology

institute: German Institute of Human Nutrition Potsdam-Rehbruecke

hyb_protocol: The bisulfite treatment and hybridisation was carried out by Life & Brain GmbH

scan_protocol: iscan, carried out by Life & Brain GmbH

data_processing:
ChAMP package in R environment
processed value definition: combat normalised beta methylation values (linked as supplementary file on the Series record)

label: Cy3, Cy5

source_name: Blood cells

label_protocol: Labeling was carried out by Life & Brain GmbH

extract_protocol: precipitation with sodium acetate

treatment_protocol: Genomic DNA was extracted from blood cells.

tag: Sex

value: BIR

tag: tissue

value: Blood cells


title: Neuro B3 | 010 | TME

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

value: <12 months

value: F


title: BIR_LUB_35


title: Neuro B3 | 008 | Tumour

tag: treatment

tag: stitchedreads

tag: sequencingsaturation

tag: scanheight

tag: histology

tag: mycn amplification

tag: gender

tag: death

value: Alive

value: Low


title: BIR_LUB_39

tag: Sex

tag: tissue


title: Neuro B3 | 007 | TME

tag: aoisurfacearea

tag: aoinucleicount

tag: scanoffsetx

tag: scanoffsety

tag: roi

tag: staging

value: Staging  I

tag: age dx_class

value: M

tag: follow up_months

tag: overall survival_months

tag: overall survival_years

tag: risk classification


title: BIR_LUB_34


title: RRChIP GSC387 shNAT10 input

city: Chapel Hill

first: DONGHAI

last: WANG

state: North Carolina

address: 125 Mason Farm Rd

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina-Chapel Hill (UNC)

description: Library name: Sample16

data_processing:
Raw sequencing reads were aligned to the human genome (hg38) using Bowtie (v1.1.2) with default parameters. Read coverage was calculated using deepTools and normalized to reads per million. Data visualization was performed using the IGV genome browser. Peak calling was conducted with MACS2 (v2.1.2) using default settings and a p-value cutoff of 1 × 10⁻⁴. Peak annotation was performed using ChIPseeker (v1.28.3). Heatmaps and metagene profiles were generated using the computeMatrix command in deepTools.
Assembly: hg38
Supplementary files format and content: Bigwig

molecule: nuclear RNA

source_name: GBM tissue

extract_protocol:
Cells were lysed and nuclei isolated using lysis buffers on ice. Chromatin was sheared by sonication into 100–600 bp fragments, with 10% reserved as input. The remaining chromatin underwent overnight immunoprecipitation at 4 °C using an anti-V5 antibody, followed by capture with protein A/G magnetic beads. Beads were washed and R-loop-antibody complexes were eluted, then incubated overnight at 65 °C with NaCl and RNase inhibitor. After proteinase K digestion, DNA was extracted via phenol/chloroform and ethanol precipitation. R-loop RNA was isolated by DNase I digestion, heat denaturation, and purified using RNA Clean Beads.
Purified RNA was used for library preparation with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs). Libraries were sequenced on an Illumina NovaSeq 6000 platform.

value: GBM tissue

tag: cell line

tag: cell type

value: Glioblastoma stem cell

tag: treatment


title: Neuro B3 | 008 | TME

value: Neuroblastoma

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanheight

value: Staging  II

tag: histology

tag: mycn amplification

tag: gender

tag: death


title: Neuro B3 | 009 | TME

tag: tissue

value: Pre-treatment

tag: aoisurfacearea

tag: aoinucleicount

tag: scanoffsetx

tag: scanoffsety

tag: roi

tag: staging

tag: age dx_class

tag: risk classification


title: ChIP_L36pl_H3K27ac_Vehicle_Rep2

description:
Library name: Sample002
ChIP for H3K27ac in L3.6pl cells after PBS treatment

tag: cell line

tag: cell type

value: PDAC

tag: treatment

value: Vehicle

tag: antibody


title: RRChIP NSC11 input

description: Library name: Sample12

source_name: Brain

value: Brain

value: Neural stem cells


title: Neuro B3 | 013 | TME

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanheight

value: TME

tag: histology

value: Differentiating

value: non-amplified


title: RRChIP DGC23 input

description: Library name: Sample11

tag: tissue

value: Differentiated glioblastoma stem cell


title: BIR_LUB_37

tag: Sex

value: BIR

value: Blood cells


title: Neuro B3 | 015 | Tumour

tag: aoisurfacearea

tag: aoinucleicount

tag: scanoffsetx

tag: scanoffsety

tag: roi

value: Tumor

tag: staging

tag: age dx_class

value: <12 months

tag: mycn amplification

tag: gender

value: F

tag: death

value: Alive

tag: risk classification

value: Low


title: RRChIP GSC387 shCONT input

description: Library name: Sample15

value: GBM tissue

tag: cell line

tag: cell type

value: Glioblastoma stem cell

tag: treatment

value: shCONT


title: Neuro B3 | 012 | TME

value: Neuroblastoma

value: Pre-treatment

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanheight

value: Staging  II

tag: histology


title: Neuro B3 | 004 | Full ROI

tag: tissue

tag: aoisurfacearea

tag: aoinucleicount

tag: scanoffsetx

tag: scanoffsety

tag: roi

value: TME

tag: staging

value: Staging  I

tag: age dx_class

value: 12-18 months

tag: mycn amplification

value: M

tag: follow up_months

tag: overall survival_months

tag: overall survival_years


title: RRChIP GSC23 shCONT input

description: Library name: Sample13

tag: cell line

tag: cell type

tag: treatment


title: RRChIP GSC387 input

description: Library name: Sample10


title: Neuro B3 | 003 | Tumour

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanheight

value: Differentiating

value: non-amplified

tag: gender

tag: death

tag: risk classification


title: RRChIP GSC23 shNAT10 input

description: Library name: Sample14

tag: tissue


title: Neuro B3 | 005 | Full ROI

tag: aoisurfacearea

tag: aoinucleicount

tag: scanoffsetx

tag: scanoffsety

tag: roi

tag: staging

tag: age dx_class

tag: histology

tag: mycn amplification

tag: follow up_months

tag: overall survival_months

tag: overall survival_years


title: RRChIP GSC23 input

description: Library name: Sample9

tag: cell line

tag: cell type


title: BIS_LUB_31

tag: Sex

value: BIS

value: Blood cells


title: Neuro B3 | 006 | TME

tag: treatment

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanheight

value: <12 months

tag: gender

value: F

tag: death

tag: risk classification


title: Neuro B3 | 001 | Tumour

tag: tissue

tag: aoisurfacearea

tag: aoinucleicount

tag: scanoffsetx

tag: scanoffsety

tag: roi

value: Tumor

tag: staging

tag: age dx_class

tag: histology

tag: mycn amplification

tag: follow up_months

tag: overall survival_months

tag: overall survival_years

value: Alive

value: Low


title: BIS_LUB_33

tag: Sex


title: RRChIP GSC23 shNAT10

description: Library name: Sample6

value: GBM tissue

tag: cell line

tag: cell type

value: Glioblastoma stem cell

tag: treatment


title: Neuro B5 | 022 | Tumour

tag: tissue

value: Neuroblastoma

value: Post-treatment

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanheight

value: Staging  IV

value: Poorly diferentiated

value: amplified

tag: gender

tag: death

value: Death

tag: risk classification

value: High


title: Neuro B3 | 002 | Tumour

value: Pre-treatment

tag: aoisurfacearea

tag: aoinucleicount

tag: scanoffsetx

tag: scanoffsety

tag: roi

tag: staging

value: Staging  II

tag: age dx_class

tag: histology

value: Differentiating

tag: mycn amplification

value: non-amplified


title: Neuro B3 | 007 | Tumour

tag: tissue

tag: treatment

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

value: Staging  I

value: <12 months

value: M

tag: follow up_months

tag: overall survival_months

tag: overall survival_years


title: BIS_LUB_32

tag: Sex

value: BIS

value: Blood cells


title: BIS_LUB_26


title: RRChIP GSC23 shCONT

description: Library name: Sample5

value: GBM tissue

tag: cell line

tag: cell type

value: Glioblastoma stem cell

value: shCONT


title: Neuro B5 | 017 | Full ROI

value: Neuroblastoma

tag: aoisurfacearea

tag: aoinucleicount

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: roi

value: Tumor

tag: staging

value: Staging  IV

value: >18 months

value: unknown

tag: gender

value: F

tag: death

tag: risk classification


title: Neuro B5 | 015 | TME

tag: tissue

tag: treatment

value: Pre-treatment

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

value: TME

tag: age dx_class

tag: histology

value: Poorly diferentiated

tag: mycn amplification

tag: follow up_months

tag: overall survival_months

tag: overall survival_years

value: Death

value: High


title: BIS_LUB_30

tag: Sex


title: Neuro B5 | 019 | Full ROI

value: Post-treatment

tag: aoisurfacearea

tag: aoinucleicount

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: roi

value: Full ROI

tag: staging

value: Staging  III

value: <12 months

value: amplified

tag: gender

value: M


title: RRChIP GSC387 shNAT10

description: Library name: Sample8

tag: tissue

value: GBM tissue

tag: cell line

tag: cell type

value: Glioblastoma stem cell

tag: treatment


title: Neuro B5 | 014 | Tumour

value: Neuroblastoma

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

value: Tumor

tag: age dx_class

tag: histology

tag: mycn amplification

tag: follow up_months

tag: overall survival_months

tag: overall survival_years

tag: death

tag: risk classification


title: Neuro B5 | 020 | TME

tag: tissue

tag: aoisurfacearea

tag: aoinucleicount

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: roi

tag: staging

value: Staging  IV

tag: gender


title: BIR_LUB_28

tag: Sex

value: BIR

value: Blood cells


title: RRChIP GSC387 shCONT

description: Library name: Sample7

tag: cell line

tag: cell type

tag: treatment

value: shCONT


title: Neuro B5 | 018 | Tumour

value: Pre-treatment

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: age dx_class

tag: histology

value: Poorly diferentiated

tag: mycn amplification

tag: follow up_months

tag: overall survival_months

tag: overall survival_years

tag: death

tag: risk classification


title: BIS_LUB_25

tag: Sex

value: BIS

tag: tissue


title: BIS_LUB_22


title: Neuro B5 | 011 | Full ROI

tag: aoisurfacearea

tag: aoinucleicount

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: roi

tag: staging

value: >18 months

value: Differentiating

value: non-amplified

tag: gender

value: Alive

value: Low


title: BIS_LUB_21


title: Neuro B5 | 016 | TME

tag: treatment

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

value: TME

tag: age dx_class

tag: histology

tag: mycn amplification

value: unknown

value: F

tag: follow up_months

tag: overall survival_months

value: Death

value: High


title: Neuro B5 | 010 | Full ROI

tag: tissue

value: Neuroblastoma

value: Post-treatment

tag: aoisurfacearea

tag: aoinucleicount

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanheight

value: Tumor

value: Staging  IV

value: M

tag: overall survival_years

tag: death

tag: risk classification


title: Neuro B5 | 013 | Full ROI

tag: treatment

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: scanoffsetx

tag: scanoffsety

tag: roi

value: Full ROI

tag: staging

value: Staging  III

value: <12 months

value: Poorly diferentiated

value: amplified

tag: gender


title: RRChIP NSC11

description: Library name: Sample4

tag: tissue

value: Brain

tag: cell line

tag: cell type

value: Neural stem cells


title: Neuro B5 | 009 | Full ROI

tag: aoisurfacearea

tag: aoinucleicount

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanheight

tag: age dx_class

value: >18 months

tag: histology

tag: mycn amplification

value: non-amplified

tag: follow up_months

tag: overall survival_months


title: BIS_LUB_20

tag: Sex

value: BIS

value: Blood cells


title: RRChIP DGC23

description: Library name: Sample3

value: GBM tissue

value: Differentiated glioblastoma stem cell


title: RRChIP GSC387

description: Library name: Sample2

value: Glioblastoma stem cell


title: C_auris_co-culture 3.

city: Debrecen

first: Agnes

last: Jakab

address: Nagyerdei krt 98.

country: Hungary

institute: University of Debrecen

description: Library name: sample 6

data_processing:
The FastQC package (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) was used for quality control.
Sequencing reads were aligned to the C. auris B8441 reference genome (genome version GCA_002759435.2) using HISAT2 v2.1 and BAM files were generated.
The DESeq algorithm (StrandNGS software) was used to obtain normalized gene transcription values.
Differentially expressed genes were identified using a moderated t-test with Benjamini-Hochberg false discovery rate (FDR) correction for multiple testing.
Genes with a corrected p-value < 0.05 and a fold change (FC) > 1.5 or < −1.5 were considered upregulated or downregulated genes.
Assembly: C. auris genome version gca002759435.2 ; https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_002759435.2; accessed on 03/05/2024
Supplementary files format and content: Excel file includes normalized data for samples

organism: Candidozyma auris

source_name: fungal cells

growth_protocol: For monomicrobial growth, Candida auris was cultured on YPD agar for 24 h at 37 °C, inoculated into 5 mL YPD broth, and incubated at 30 °C for 18 h with shaking (140 rpm). Exponentially growing cells were diluted to an OD₆₄₀ of 0.1 in 20 mL fresh YPD broth and incubated at 37 °C with shaking (140 rpm). After 4 h of growth, cultures reached an OD₆₄₀ of 0.5 ± 0.04 (corresponding to 0.5 × 10⁷ ± 0.06 × 10⁷ cells/mL), at which point co-culture experiments were initiated. Pseudomonas aeruginosa was grown on Columbia agar supplemented with 5% sheep blood for 24 h at 37 °C. Bacterial cells were suspended in sterile physiological saline and adjusted to an OD₆₄₀ of 0.05 prior to addition to C. auris cultures. Dual-species cultures were generated by inoculating P. aeruginosa into exponentially growing C. auris cultures after 4 h of fungal incubation. For monoculture controls, P. aeruginosa was inoculated into YPD broth alone. The time of bacterial addition was designated as 0 h. Co-cultures were incubated for 2 h at 37 °C with shaking (140 rpm), unless otherwise indicated.

extract_protocol:
Total RNA was isolated from lyophilized samples with Trisol reagent.
RNA libraries for RNA-seq were prepared using TruSeq RNA Sample preparation kit (Illumina) following manufacturer's protocols. All samples had RNA integrity number (RIN) values between 8.2 and 9.0 and RNA concentrations of at least 1.7 µg/µL. RNA library preparation. RNA-seq sequencing were performed using Illumina NextSeq 2000 platform (Illumina, USA) and single-end 100 bp sequencing was performed. Approximately 17.7  to 29.3 million sequencing reads were generated per sample.

treatment_protocol: Bacterial cells were suspended in sterile physiological saline and adjusted to an OD₆₄₀ of 0.05 prior to addition to C. auris cultures. Dual-species cultures were generated by inoculating P. aeruginosa into exponentially growing C. auris cultures after 4 h of fungal incubation. Co-cultures were incubated for 2 h at 37 °C with shaking (140 rpm), unless otherwise indicated.

value: fungal cells

tag: genotype

value: Isolate 12

tag: treatment

value: Co-culture with P. aeruginosa


title: GSC387 shNAT10 rep2

description:
Library name: Sample8
GSC387KD1_2

data_processing:
Raw FASTQ reads were aligned to the human reference genome (hg38) using HISAT2 (v2.1.0). Read counts for the specified regions were quantified with HTSeq-count (v0.12.3) and analyzed for differential gene expression using DESeq2 (v1.32.0). P-value < 0.05 and |log₂ fold change| ≥ 0.5 were used to identify differentially expressed genes. GO enrichment analysis was performed using the ClusterProfiler package, and visualizations were generated with the ggplot2 package.
Assembly: hg38
Supplementary files format and content: txt

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Life Technologies, 15596018) following the manufacturer’s standard protocol.
mRNA was isolated from 1 µg of total RNA using mRNA Capture Beads and subsequently fragmented to a size range of 200–500 bp. cDNA synthesis and adaptor ligation were performed using the NEBNext Ultra RNA Library Prep Kit for Illumina. The resulting RNA-Seq libraries were sequenced using 150 bp paired-end reads on a NovaSeq 6000 platform.

tag: tissue

tag: cell line


title: Neuro B5 | 012 | Full ROI

value: Neuroblastoma

value: Pre-treatment

tag: aoisurfacearea

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: scanoffsetx

tag: scanoffsety

tag: roi

value: Tumor

tag: staging

value: Differentiating

tag: gender

value: M

tag: overall survival_years

tag: death

value: Alive

tag: risk classification

value: Low


title: Neuro B5 | 007 | Tumour

tag: aoinucleicount

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanheight

value: Staging  IV

tag: age dx_class

value: >18 months

tag: histology

value: Poorly diferentiated

tag: mycn amplification

tag: follow up_months

tag: overall survival_months

value: Death

value: High


title: Neuro B5 | 008 | TME

tag: tissue

tag: treatment

value: Post-treatment

tag: aoisurfacearea

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: scanoffsetx

tag: scanoffsety

tag: roi

value: TME

value: non-amplified

value: F


title: Neuro B5 | 006 | Tumour

tag: aoinucleicount

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: staging

tag: gender

tag: overall survival_years

tag: death

tag: risk classification


title: GSC387 shNAT10 rep1

description:
Library name: Sample7
GSC387KD1_1

tag: tissue

value: GBM tissue

tag: cell line

tag: cell type

value: Glioblastoma stem cell

tag: treatment


title: RRChIP GSC23

description: Library name: Sample1


title: BIS_LUB_18

tag: Sex

value: BIS

value: Blood cells


title: C_auris_Control-3.

description: Library name: sample 3

value: fungal cells

tag: genotype

value: Isolate 12

value: untreated


title: C_auris_co-culture 1.

description: Library name: sample 4

value: Co-culture with P. aeruginosa


title: BIS_LUB_13


title: Neuro B5 | 003 | TME

value: Neuroblastoma

value: Pre-treatment

tag: aoisurfacearea

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: roi

value: Staging  IV

tag: age dx_class

tag: histology

value: Differentiating

tag: mycn amplification

tag: follow up_months

tag: overall survival_months


title: BIS_LUB_12

tag: tissue


title: GSC387 shCONT rep2

description:
Library name: Sample6
GSC387NT_2

tag: cell line

tag: cell type

tag: treatment

value: shCONT


title: Neuro B5 | 005 | TME

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: staging

value: Staging  III

value: <12 months

value: Poorly diferentiated

value: amplified

tag: gender

value: M

tag: overall survival_years

tag: death

value: Death

tag: risk classification

value: High


title: BIR_LUB_10

tag: Sex

value: BIR

value: Blood cells


title: BIS_LUB_06

value: BIS

tag: tissue


title: Neuro B5 | 004 | TME

value: Post-treatment

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: roi

value: TME

tag: age dx_class

value: >18 months

tag: histology

tag: mycn amplification

value: non-amplified

value: F

tag: follow up_months

tag: overall survival_months


title: C_auris_co-culture 2.

description: Library name: sample 5

value: fungal cells

tag: genotype

value: Isolate 12

tag: treatment

value: Co-culture with P. aeruginosa


title: C_auris_Control-2.

description: Library name: sample 2

value: untreated


title: Neuro B5 | 002 | TME

value: Neuroblastoma

value: Pre-treatment

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: staging

value: Staging  IV

value: Differentiating

tag: gender

tag: overall survival_years

tag: death

tag: risk classification


title: RNA-Seq, Tetraodon ventral retina, biol rep4

description: Library name: Tn_V4

data_processing:
High quality sequencing reads were mapped to Tetraodon nigroviridis Genome Asselmby tetNig2 using STAR V2.7.10b. Read count extraction was performed using featureCounts v2.0.6. Read count normalization and DGE analysis were performed using DEseq2.
Assembly: tetNig2
Supplementary files format and content: tab-delimited text file including raw counts for each sample

organism: Tetraodon nigroviridis

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen_ThermoFIsher).
mRNA enriched librraies were preparaed and sequenced at Novogene (https://www.novogene.com/us-en). Briefly, for each sample, 1 µg RNA was used to generated RNA sequencing librarires using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB,USA), follwing the manufacturee's recommendation.

tag: tissue

value: Ventral retina

value: WT

tag: batch


title: GSC23 shNAT10 rep1

description:
Library name: Sample3
GSC23KD1_1

value: GBM tissue

tag: cell line

tag: cell type

value: Glioblastoma stem cell


title: BIR_LUB_07

tag: Sex

value: BIR

value: Blood cells


title: GSC23 shNAT10 rep2

description:
Library name: Sample4
GSC23KD1_2

tag: treatment


title: Neuro B1 | 018 | TME

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: roi

value: TME

value: Staging  I

tag: age dx_class

value: <12 months

tag: histology

value: Poorly diferentiated

tag: mycn amplification

value: M

tag: follow up_months

tag: overall survival_months

value: Alive

value: Low


title: GSC387 shCONT rep1

description:
Library name: Sample5
GSC387NT_1

tag: tissue

tag: cell line

tag: cell type

value: shCONT


title: BIR_LUB_02

tag: Sex


title: BIS_LUB_01

value: BIS


title: C_auris_Control-1.

description: Library name: sample 1

value: fungal cells

tag: genotype

value: Isolate 12

tag: treatment

value: untreated


title: GSC23 shCONT rep2

description:
Library name: Sample2
GSC23NT_2


title: Neuro B5 | 001 | Tumour

value: Neuroblastoma

value: Pre-treatment

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

value: Tumor

tag: staging

value: Staging  IV

value: >18 months

value: amplified

tag: gender

tag: overall survival_years

tag: death

value: Death

tag: risk classification

value: High


title: RNA-Seq, Tetraodon ventral retina, biol rep2

description: Library name: Tn_V2

tag: tissue

value: Ventral retina

value: WT

tag: batch


title: BIS_LUB_04

tag: Sex

value: Blood cells


title: Neuro B1 | 018 | Tumour

tag: treatment

tag: aoisurfacearea

tag: alignedreads

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: roi

value: Staging  I

tag: age dx_class

value: <12 months

tag: histology

value: Poorly diferentiated

tag: mycn amplification

value: non-amplified

value: M

tag: follow up_months

tag: overall survival_months

value: Alive

value: Low


title: RNA-Seq, Tetraodon ventral retina, biol rep3

description: Library name: Tn_V3

tag: genotype