title: serum of DR patients2

city: Wuhan

first: Songtao

last: Yang

address: Jiefang Avenue 1277

department: Department of Endocrinology, Union Hospital

institute: Huazhong university of science and technology, Wuhan union hospital

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Assembly: ftp://ftp.ensembl.org/pub/release-101/fasta/homo_sapiens/dna/
Supplementary files format and content: excel,expression profiles

source_name: serum

extract_protocol:
Total RNA was extracted using Norgen51000 following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

value: serum


title: FPD_52.3

status: Public on Jul 12 2023

type: SRA

city: Philadelphia

first: Alexandra

last: Zezulin

address: 421 Curie Blvd 544 BRB II/III

country: USA

institute: University of Pennsylvania

library_source: genomic

data_processing:
Sequencing reads were demultiplexed using Bcl2Fastq v2.20 then trimmed and filtered for quality using Trim Galore v0.6.4 with the following settings: fastqc, paired, and trim1. Reads were then aligned to the human genome (hg38) using bowtie 2.3.5.1. Only uniquely mapped reads with fewer than 2 mismatches were used for downstream analyses. Samtools v.1.1 was used to convert SAM files to BAM files, and Sambamba v0.6.6 was used to filter out duplicates, multi-mappers, reads mapped to ChrM or blacklist regions, and unmapped reads. MACS2 2.2.7.1 was used for peak calling using the following parameters: BAMPE, q: 0.05. Peaks from the patient and control samples were called individually. For downstream analysis, we compared the patient and unaffected family members individually. The peaks from the patient sample and the corresponding control sample were merged for each comparison and RPKM per merged peak was calculated using BEDtools. Peaks with RPKM less than 0.5 in both control and patient were filtered from downstream analysis. Control or patient  specific peaks were called if the RPKM fold change between control and patient peaks was greater than 2. Individual samples were used to create bigwig files for visualization using Deeptools v3.3.0 and the  following parameters: normalized to Bins Per Million mapped reads (BPM), bin size: 50.
see SAMPLES section
Assembly: hg38
Supplementary files format and content: BigWig files provided are normalized tracks
Supplementary files format and content: Bed files provided are the output of merged MACS2 peak calling: the peaks from the patient sample and the corresponding control sample were merged for each comparison and RPKM per merged peak was calculated using BEDtools. Peaks with RPKM less than 0.5 in both control and patient were filtered from downstream analysis. Control or patient specific peaks were called if the RPKM fold change between control and patient peaks was greater than 2

molecule: genomic DNA

organism: Homo sapiens

source_name: PB Neutrophils

extract_protocol:
Neutrophils from human patient/control peripheral blood were isolated using the EasyStep Human Neutrophil Isolation Kit (Stem Cell). 50,000 cells were collected and washed with cold PBS. Cell pellets were resuspended in 50 µl of lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% Tween-20, 0.1% NP-40, 0.01% Digitonin, 1% BSA) and incubated on ice for 4 min. Lysis was halted with the addition of 50 uL of wash buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% Tween-20, 0.1%, 1% BSA). Samples were centrifuged at  500 x g, 4 °C for 5 min. Nuclei pellets were resuspended in 50 µl of wash buffer and centrifuged at  500 x g, 4 °C for 5 min.  Nuclei pellets were resuspended in 50 µl of transposition reaction mix (1× Tagment DNA Buffer, 2.5 µl of Tagment DNA Enzyme 1) and incubated for 30 min at 37 °C
Libraries were purified using SPRI-Select bead purification and the concentrations were measured using both Qubit and KAPA qPCR. 2100 Bioanalyzer was used to check the quality of libraries. Libraries were sequenced on the Illumina NextSeq 250, with 75-bp paired-end reads.

tag: disease state

value: FPDMM

tag: Sex

value: Male

tag: age

tag: organ

value: Peripheral Blood

tag: treatment protocol

value: PB was collected and neutrophils were isolated on the same day


title: FPD_52.2

value: Family Control

value: Female


title: IC-K064GBM-I-25195_S11

city: Cincinnati

first: Frank

last: Huang

state: OHIO

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

library_source: transcriptomic

data_processing:
Bowtie for reads alignment
HTSeq for mapping reads to each gene.
Assembly: hg38

molecule: total RNA

organism: Homo sapiens/Mus musculus xenograft

source_name: NOD SCID mouse

extract_protocol:
RNA was extracted using AllPrep DNA/RNA/Protein Mini Kit according to manufacturer's instructions (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Mus musculus Xenograft

tag: genotype

value: Tumor


title: RRBS Dentate Gyrus cells, Parental Group, Rep 6

city: Tallahassee

first: Nicholas

middle: James

last: Waddell

state: FL

address: 319 Stadium Dr

department: Biological Sciences

institute: Florida State University

data_processing:
Basecalls were performed using bcl2fastq for Novaseq output.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore (minimum quality 20, minimum length 20)
Sequences were aligned to the prairie vole genome using Bismark methylation alignment software.
Methylation calls were extracted using the built-in methylation extractor program provided in the Bismark suite.
Values were not normalized prior to import into DSS general for differential methylation analysis.
Assembly: MicOch1.0
Supplementary files format and content: files per sample are formatted for use in DSS-general for differential methylation analysis.  Columns are as follows: Chromosome, Position, N = number of reads covering this position, X = number of reads with methylation call at this position.

organism: Microtus ochrogaster

source_name: Dentate Gyrus

extract_protocol:
DNA and RNA were isolatted from the same tissue using the Qiagen AllPrep DNA/RNA Mircro Kit (Qiagen, #80284) according to the manufacturer's protocol.
100ng of genomic DNA was digested using MspI, and RRBS libraries were constructed using the Premium RRBS Kit (Diagenode, #C02030032)

treatment_protocol: Adult Voles were exposed to conspecific pups and their behavioral response was recorded. Samples were separated based on this response for virgin animals or based on sex for pair-bonded individuals.

value: Dentate Gyrus

value: WT

tag: behavioral group

value: Parental


title: IC-K060GBM-I-25195_S9


title: Exe_L6

city: Beijing

first: Jianxin

last: Wu

address: No. 2, Yabao Road, Chaoyang District

country: China

institute: Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics

description: chronic exercise, exercise model

data_processing:
To obtain clean reads from RNA-sequencing results, sequence with low quality including adapter sequences, sequences with quality score < 20, sequences with N base rate of raw reads >10% and sequence less than 25bp were removed.
HISAT was used to align clean reads with the reference genome GCF_000001635.27_GRCm39.
Bowtie2 was used to compare clean reads to the reference gene sequence and obtain the alignment results.
Assembly: mm10

organism: Mus musculus

source_name: liver

extract_protocol:
Total RNAs were isolated from liver tissue samples with TRIzol reagent.
Based on the DNBseq platform (PE150 strategy), sequencing was performed.

value: liver

tag: treatment

value: chronic exercise, running for 6 weeks


title: RRBS Dentate Gyrus cells, Attacker Group, Rep 4

value: Attacker


title: RRBS Dentate Gyrus cells, Father Group, Rep 2

value: Father


title: IC-K031GBM-I-15890_S15


title: IC-K045GBM-III-23561_S8


title: FPD_21.3

extract_protocol:
50,000 cells were collected and washed with cold PBS. Cell pellets were resuspended in 50 µl of lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% Tween-20, 0.1% NP-40, 0.01% Digitonin, 1% BSA) and incubated on ice for 4 min. Lysis was halted with the addition of 50 uL of wash buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% Tween-20, 0.1%, 1% BSA). Samples were centrifuged at  500 x g, 4 °C for 5 min. Nuclei pellets were resuspended in 50 µl of wash buffer and centrifuged at  500 x g, 4 °C for 5 min.  Nuclei pellets were resuspended in 50 µl of transposition reaction mix (1× Tagment DNA Buffer, 2.5 µl of Tagment DNA Enzyme 1) and incubated for 30 min at 37 °C
Libraries were purified using SPRI-Select bead purification and the concentrations were measured using both Qubit and KAPA qPCR. 2100 Bioanalyzer was used to check the quality of libraries. Libraries were sequenced on the Illumina NextSeq 250, with 75-bp paired-end reads.


title: RRBS Dentate Gyrus cells, Parental Group, Rep 5


title: IC-K038GBM-2093120833_S7


title: serum of DR patients3


title: RRBS Dentate Gyrus cells, Attacker Group, Rep 3


title: RRBS Dentate Gyrus cells, Attacker Group, Rep 2


title: Exe_L4

description: chronic exercise, exercise model


title: IC-K035GBM-III-19729_S4


title: serum of DM patients2


title: RRBS Dentate Gyrus cells, Attacker Group, Rep 1


title: serum of DR patients1


title: IC-K033GBM-III-23787_S5


title: serum of DM patients1


title: C-K023GBM-III-16823_S18


title: IC-K014GBM-III-18146_S17


title: IC-K012GBM-14875-Untreated-sur_S15


title: serum of DM patients3


title: Exe_L2

description: chronic exercise, exercise model


title: Exe_L5

description: chronic exercise, exercise model


title: RRBS Dentate Gyrus cells, Parental Group, Rep 4


title: Con_L5

description: control, sedentary mice

value: sedentary


title: HCT116 shUSP11-2

first: Daoyuan

address: 45 Changchun Street, Xicheng District

institute: Xuanwu Hospital Capital Medical University

data_processing:
Raw reads were subjected to quality control
Sequence reads were pre-processed to remove adaptors and filter low-quality reads
Transcript assembly and quantification with StringTie. Analysis of RNA-seq experiments requires accurate reconstructions of all the isoforms expressed from each gene, as well as estimates of the relative abundance of those isoforms. Use parameters as stringtie –e –B -p 8 -G -o.
Fragments per kilobase of transcript per million mapped reads (FPKM) were calculated using Ballgown from Pertea M et al., Nature Protocols, 2016. In short, differential expression analysis proceeds using a linear model. The FPKM values attached to transcripts are typically highly skewed; thus, to stabilize the variance, Ballgown’s builtin functions apply a log transformation and then fit standard linear models that can be used to test for differential expression.
Assembly: GRCH38
Supplementary files format and content: excel files include FPKM values for each Sample.

growth_protocol: HCT116 cells were obtained from ATCC and maintained at 37℃ and 5% CO2 in DMEM supplemented with 10% (v/v) FBS, 100 U/mL penicillin, and 100 mg/mL streptomycin. All cell lines were tested for mycoplasma contamination and authenticated utilizing short tandem repeat profiling.

extract_protocol:
HCT116 cells were harvested and RNA were extracted with Trizol reagent. RNA was amplified using the Smart-seq v4 (Takara) and library prep was performed using the NEBNext Ultra DNA Library prep kit (Illumina)
RNA libraries were prepared for sequencing using standard BGISEQ500 protocols

tag: cell line

tag: cell type

value: human colorectal carcinoma cell line

value: USP11 knockdown


title: IC-K024GBM-III-20112_S20


title: Con_L3

description: control, sedentary mice


title: Exe_L1

description: chronic exercise, exercise model


title: Exe_L3

description: chronic exercise, exercise model


title: RRBS Dentate Gyrus cells, Parental Group, Rep 3

value: Male


title: Con_L2

description: control, sedentary mice


title: HCT116 shUSP11-3


title: RNA-Seq Dentate Gyrus cells, Mother Group, Rep 6

data_processing:
Basecalls were performed using bcl2fastq for Novaseq output.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore (minimum quality 20, minimum length 20)
Trimmed sequences were aligned to the prairie vole genome MicOch1.0 using STAR (sjdb_overhang = maxReadLength - 1)
Read count extraction was performed by featureCounts, counting gene-level features.
Normalized values were calculated in R using programs included in the EdgeR library.
Assembly: MicOch1.0
Supplementary files format and content: tab-delimited text file, which includes raw RNAseq read counts for each annotated gene.

extract_protocol:
RNA was isolated using the Qiagen AllPrep DNA/RNA Micro Kit (Qiagen, #80284) according to the manufacturer's protocol.  150ng of RNA was used as input for subsequent library preparation.
Ribo-depleted RNA was prepared from extracted total RNA using NEBNext rRNA Depletion Kit (New England Biolabs, #E6310L). RNA-seq libraries were constructed using NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs, #E7765S)

value: Mother


title: HCT116 shLSH-3

value: LSH knockdown


title: RNA-Seq Dentate Gyrus cells, Mother Group, Rep 5


title: RRBS Dentate Gyrus cells, Parental Group, Rep 2


title: HCT116 shUSP11-1


title: Con_L1

description: control, sedentary mice


title: Con_L4

description: control, sedentary mice


title: RNA-Seq Dentate Gyrus cells, Mother Group, Rep 4


title: HCT116 shLSH-2


title: EORTC_26101_2023_376

type: genomic

city: Heidelberg

first: Tobias

last: Kessler

address: Im Neuenheimer Feld 280

country: Germany

institute: DKFZ

hyb_protocol: bisulphite conerted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450k Beadchip using standard Illumina protocol

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

data_processing:
BeadStudio software v3.2
Normalized Average Beta (BMIQ method)

label: Cy3 and Cy5

source_name: diffuse glioma

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and pruified from FFPE tissue according with the Maxwell 16 FFPE Plus LEV DNA Kit according to standard instructions

tag: gender

value: male


title: EORTC_26101_2023_380

value: female


title: EORTC_26101_2023_379


title: EORTC_26101_2023_377


title: EORTC_26101_2023_378


title: RNA-Seq Dentate Gyrus cells, Mother Group, Rep 3

value: Female


title: HCT116 shLSH-1


title: EORTC_26101_2023_375


title: EORTC_26101_2023_374


title: HCT116 shCtr-3


title: RRBS Dentate Gyrus cells, Parental Group, Rep 1


title: Con_L6

description: control, sedentary mice


title: EORTC_26101_2023_373


title: RNA-Seq Dentate Gyrus cells, Mother Group, Rep 2


title: EORTC_26101_2023_371


title: RNA-Seq Dentate Gyrus cells, Mother Group, Rep 1


title: HCT116 shCtr-2


title: EORTC_26101_2023_372


title: EORTC_26101_2023_370


title: RNA-Seq Dentate Gyrus cells, Father Group, Rep 5


title: HCT116 shCtr-1


title: EORTC_26101_2023_369


title: Pt-A128GBM_S9

source_name: human autopsy

value: GBM patient cerebrum (autopsy)

value: Tumor


title: EORTC_26101_2023_368


title: EORTC_26101_2023_367


title: RNA-Seq Dentate Gyrus cells, Father Group, Rep 4

value: Dentate Gyrus

value: WT


title: Pt-K064GBM_S8


title: EORTC_26101_2023_363


title: EORTC_26101_2023_362


title: Pt-K060GBM_S16


title: RNA-Seq Dentate Gyrus cells, Father Group, Rep 3


title: EORTC_26101_2023_364


title: RNA-Seq Dentate Gyrus cells, Father Group, Rep 2


title: RNA-Seq Dentate Gyrus cells, Father Group, Rep 1


title: Pt-K031GBM_S22


title: EORTC_26101_2023_360


title: EORTC_26101_2023_365


title: EORTC_26101_2023_361


title: EORTC_26101_2023_359


title: EORTC_26101_2023_358


title: RNA-Seq Dentate Gyrus cells, Attacker Group, Rep 6


title: Pt-K038GBM_S21


title: RRBS Dentate Gyrus cells, Father Group, Rep 4


title: RNA-Seq Dentate Gyrus cells, Attacker Group, Rep 5


title: EORTC_26101_2023_356


title: RNA-Seq Dentate Gyrus cells, Attacker Group, Rep 4


title: EORTC_26101_2023_355


title: EORTC_26101_2023_366


title: EORTC_26101_2023_357


title: Pt-K033GBM_S6


title: EORTC_26101_2023_354


title: EORTC_26101_2023_353


title: RNA-Seq Dentate Gyrus cells, Attacker Group, Rep 3


title: Pt-K035GBM_S3


title: RNA-Seq Dentate Gyrus cells, Attacker Group, Rep 2


title: EORTC_26101_2023_352


title: EORTC_26101_2023_350


title: EORTC_26101_2023_351


title: RNA-Seq Dentate Gyrus cells, Attacker Group, Rep 1


title: Pt-K012GBM_S16


title: Pt-K045GBM_S20


title: RNA-Seq Dentate Gyrus cells, Parental Group, Rep 6

value: Parental


title: EORTC_26101_2023_347


title: T0503-Normal cerebrum

value: Normal human cerebrum (autopsy)

value: normal


title: EORTC_26101_2023_346


title: D0322-Normal cerebrum


title: RNA-Seq Dentate Gyrus cells, Parental Group, Rep 5


title: EORTC_26101_2023_349


title: Pt-K024GBM_S19


title: PNAC-1 cells, RSL3, 12h, rep3

first: HENG

last: MA

address: NO.1 Shuaifu Gardern

department: Pothology

institute: Peking Union Medical College Hospital

data_processing:
Sequencing data contains a number of connectors, low-quality Reads, so we use Cutadapt (v1.15) software to filter the sequencing data to get high quality sequence（Clean）for further analysis .
The reference genome and gene annotation files were downloaded from genome website. The filtered reads were mapping to the reference genome using HISAT2 v2.0.5.
On the basis of the existing reference genome, using the software StringTie (http://ccb.jhu.edu/software/stringtie/) to assemble the mapped reads, and comparing the splicing results with the known transcripts to obtain no annotations Transcripts of information.
we used HTSeq(0.9.1) statistics to compare the Read Count values on each gene as the original expression of the gene, and then used FPKM to standardize the expression. Then difference expression of genes was analyzed by DESeq2 with screened conditions as follows: expression difference multiple |log2FoldChange| > 1, significant Q-value ≤ 0.05. At the same time, We used R language Pheatmap(1.0.8) software package to perform clustering analysis of all different genes of samples.
Assembly: mm10
Supplementary files format and content: tab-delimited text file and Excel files include FPKM values for each Sample

growth_protocol: The PANC-1 cells were maintained in DMEM (Corning, 10-013-CV) or RPMI 1640 (Corning, 10-040-CV) supplemented with 10% FBS. PANC-1 cells were cultured in 10 cm dishes.

extract_protocol:
The total RNA was extracted from PANC-1 cells treated with or without RSL3 (n=3 per group) using TRIzol (Invitrogen, 15596018). Purity and concentration of RNA were determined with NanoDrop spectrophotometer (Thermo Scientific), and integrity was determined by Agilent 2100 bioanalyzer (RNA 6000 Nano kit 5067-1511).
Sequencing libraries were generated using SMARTER mRNA-Seq Library Prep Kit according to manufacturer's protocols.

treatment_protocol: PANC-1 cells treated with or without 0.8 μM RSL3 (n=3 per group) for 12h

value: Human Pancreatic ductal adenocarcinoma cells


title: NC2-Normal cerebrum


title: PNAC-1 cells, RSL3, 12h, rep1


title: RNA-Seq Dentate Gyrus cells, Parental Group, Rep 4


title: RNA-Seq Dentate Gyrus cells, Parental Group, Rep 3


title: EORTC_26101_2023_344


title: EORTC_26101_2023_340


title: EORTC_26101_2023_343


title: EORTC_26101_2023_348


title: EORTC_26101_2023_345


title: EORTC_26101_2023_342


title: EORTC_26101_2023_341


title: RNA-Seq Dentate Gyrus cells, Parental Group, Rep 1


title: EORTC_26101_2023_339


title: PNAC-1 cells, vehicle, 12h, rep3

value: vehicle


title: RNA-Seq Dentate Gyrus cells, Parental Group, Rep 2


title: EORTC_26101_2023_334


title: EORTC_26101_2023_333


title: Ribosome_Footprint_seq_A549_nsp1_1

city: Bethesda

first: Markus

last: Hafner

state: MD

address: 50 South Drive

department: NIAMS

institute: NIH

description:
Ribosome footprinting of A549 cells after NSP1 expression 3' adapt: 5'-rAppNNAGTGTCTGGAATTCTCGGGTGCCAAGG-L
A549_RF_NSP1WTvsGFP_gene_exp.diff

data_processing:
bcl2fastq (version 2.20.0) was used to convert bcl sequencing files to fastq files demultiplexing by primer index
cutadapt (version 2.4 with Python 3.7.2) was used to demultiplex ribosome footprinting data and remove adapter sequences
STAR (version 2.7.2b) was used to aligned RNA-Seq and ChIP-Seq data to the human genome. tophat (version 2.1.1) was used to align ribosome footprinting data to the human transcriptome
cuffdiff (cufflinks version 2.2.1) was used to quantify and compare RNA abundance for RNA-Seq and ribosome footprinting data. bedtools (version 2.29.2)  was used to calculate coverage of aligned ChIP-Seq reads
Assembly: hg38

growth_protocol: A549 cells were cultured in DMEM medium (Gibco) supplemented with 10% (v/v) fetal bovine serum (FBS)

extract_protocol: RNA from transfected cells was isolated using the Direct-zol RNA Miniprep Kit (Zymo Research, Cat# R2050) according to the manufacturer’s instructions.

treatment_protocol: For transient transfection plasmids were transfected into cells using Lipofectamine 3000 (Invitrogen) according to manufacturer’s instructions. Poly I/C was transfected with the plasmid at 1/10 of the plasmid.

value: epithelial

value: FH-NSP1 expression


title: Ribosome_Footprint_seq_A549_nsp1_3

description:
Ribosome footprinting of A549 cells after  NSP1 expression 3' adapt: 5'-rAppNNGACATGTGGAATTCTCGGGTGCCAAGG-L
A549_RF_NSP1WTvsGFP_gene_exp.diff


title: EORTC_26101_2023_338


title: EORTC_26101_2023_336


title: EORTC_26101_2023_335


title: Ribosome_Footprint_seq_A549_nsp1_2

description:
Ribosome footprinting of A549 cells after  NSP1 expression 3' adapt: 5'-rAppNNATCGACTGGAATTCTCGGGTGCCAAGG-L
A549_RF_NSP1WTvsGFP_gene_exp.diff


title: Ribosome_Footprint_seq_A549_GFP_3

description:
Ribosome footprinting of A549 cells after GFP  expression 3' adapt: 5'-rAppNNTAGTCGTGGAATTCTCGGGTGCCAAGG-L
A549_RF_NSP1WTvsGFP_gene_exp.diff

value: GFP expression


title: PNAC-1 cells, vehicle, 12h, rep2


title: PNAC-1 cells, RSL3, 12h, rep2


title: EORTC_26101_2023_326


title: EORTC_26101_2023_324


title: A549_164165A_B

description:
RNA-seq of A549 cells with various expression constructs
A549_NSP1K164A/H165AvsGFP_gene_exp.diff

value: FH-NSP1 K164A/H165A expression


title: EORTC_26101_2023_323


title: 22PC_SE1

city: New York

first: Yingqian

middle: Ada

last: Zhan

state: New York

address: 430 East 67th Street

department: EPIGENETICS RESEARCH CENTER

institute: MSKCC

data_processing:
Transcript abundances were quantified using RNA-seq reads by Salmon v1.1.0.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file with TPM values over all genes for each sample.

source_name: Prostate

extract_protocol:
Frozen tissues were weighed and homogenized in RLT and nucleic acids were extracted using the AllPrep DNA/RNA Mini Kit (QIAGEN, #80204) according to the manufacturer’s instructions. RNA was eluted in nuclease-free water.
Fresh cell pellet or frozen tumor samples were shipped to GENEWIZ for RNA isolation, library preparation, and RNA sequencing. Total RNA was extracted using the RNeasy Plus Universal mini kit following manufacturer’s instructions (Qiagen, Hilden, Germany). RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). RNA samples and sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). Sequencing libraries were clustered on one flowcell lane and then loaded on the Illumina HiSeq instrument (4000 or equivalent) (RRID: SCR_020127) according to manufacturer’s instructions. Samples were sequenced using a 2x150bp paired end (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bclfiles) was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software (RRID: SCR_015058). One mismatch was allowed for index sequence identification.

value: Prostate

value: DKO 22PC

value: Prostate adenocarcinoma

value: TP53/RB1 KO

value: Enzalutamide+Selinexor


title: 22PC_SE2


title: EORTC_26101_2023_327

value: male


title: 22PC_S3

value: Selinexor


title: PNAC-1 cells, vehicle, 12h, rep1

value: WT


title: EORTC_26101_2023_331


title: 22PC_SE3


title: EORTC_26101_2023_330

value: female


title: EORTC_26101_2023_337


title: EORTC_26101_2023_332


title: EORTC_26101_2023_329


title: EORTC_26101_2023_328


title: EORTC_26101_2023_319


title: Ribosome_Footprint_seq_A549_GFP_2

description:
Ribosome footprinting of A549 cells after GFP  expression 3' adapt: 5'-rAppNNCTGTAGTGGAATTCTCGGGTGCCAAGG-L
A549_RF_NSP1WTvsGFP_gene_exp.diff


title: Ribosome_Footprint_seq_A549_GFP_1

description:
Ribosome footprinting of A549 cells after GFP expression 3' adapt: 5'-rAppNNTAGCGATGGAATTCTCGGGTGCCAAGG-L
A549_RF_NSP1WTvsGFP_gene_exp.diff


title: 22PC_S2


title: EORTC_26101_2023_322


title: EORTC_26101_2023_315


title: A549_H45A_B

description:
RNA-seq of A549 cells with various expression constructs
A549_NSP1H45AvsGFP_gene_exp.diff

value: FH-NSP1 H45A expression


title: EORTC_26101_2023_314


title: EORTC_26101_2023_321


title: 22PC_E1

value: Enzalutamide


title: 22PC_C4

value: Control


title: 22PC_E2


title: A549_nsp1wt_B

description:
RNA-seq of A549 cells with various expression constructs
A549_NSP1WTvsGFP_gene_exp.diff
A549_NSP1WTvsNSP1K164A/H165A_gene_exp.diff


title: EORTC_26101_2023_325


title: EORTC_26101_2023_320


title: 22PC_S1


title: 22PC_E3


title: EORTC_26101_2023_317


title: EORTC_26101_2023_316


title: EORTC_26101_2023_318


title: A549_GFP_A

description:
RNA-seq of A549 cells with various expression constructs
A549_NSP1WTvsGFP_gene_exp.diff
A549_NSP1K164A/H165AvsGFP_gene_exp.diff


title: A549_GFP_B


title: A549_nsp1_164165A_A


title: EORTC_26101_2023_309


title: EORTC_26101_2023_313


title: EORTC_26101_2023_308


title: EORTC_26101_2023_311


title: EORTC_26101_2023_312


title: EORTC_26101_2023_310


title: A549_nsp1wt_A


title: EORTC_26101_2023_307


title: A549_nsp1_H45A_A


title: 22PC_C1


title: Tc_1

city: Munich

first: Stefan

last: Engelhardt

address: Biedersteiner Str. 29

department: Institute of Pharmacology and Toxicology

institute: Technical University Munich

description: cell lysate

data_processing:
Single-end run (SE50) run was performed using a HiSeq2500, MiSeq or a NextSeq 500.
Most steps of this pipeline were performed using the Galaxy platform.
MirDeep2 2.0.0. was used for identification and quantification of microRNAs between samples.
Assembly: mm10
Supplementary files format and content: raw microRNA counts in txt.format

source_name: lung

extract_protocol:
Total RNA was prepared with Trizol reagent according to manufacturer's instructions or the cell lysate was used.
Libraries were generated using GenXPro TrueQuant SmallRNA Seq Kit for Ultra Low Input or using NEBNext® Small RNA Library Prep Set for Illumina according to manufacturer's instructions.

value: lung

tag: strain

value: T-cells

value: no treatment


title: Neut_1

description: cell lysate

value: Neutrophils


title: EORTC_26101_2023_304


title: H1563-DKO-r3

data_processing:
The reads were trimmed for both quality and Illumina adaptor sequences using trim_galore v0.4.4 in the pair-end mode.
Then the raw reads were aligned to human assembly hg38 using bowtie2 v2.3.4 using the default parameters.
Aligned reads with the same start site and orientation were removed using the Picard tool. Enriched regions in individual samples were called using MACS2 and then filtered against genomic ‘blacklisted’ regions. The filtered peaks within 500 bp were merged to create a union of peak atlas. Raw read counts were tabulated over this peak atlas using featureCounts v1.6.0. The read counts were then normalized with DESeq2.
The read density profile in the format of bigwig file for each sample was created using the BEDTools suite with the normalization factor from DESeq2.
All bigwig genome tracks on XPO1 gene region were generated using pyGenomeTracks v3.5
Assembly: hg38
Supplementary files format and content: bigWig for read coverage

source_name: Lung

extract_protocol:
Profiling of chromatin was performed by ATAC-Seq as described by Buenrostro, et al. Briefly, approximately 50,000 viably frozen cells were washed in cold PBS and lysed. The transposition reaction containing TDE1 Tagment DNA Enzyme (Illumina catalog # 20034198) was incubated at 37°C for 30 minutes.
The DNA was cleaned with the MinElute PCR Purification Kit (QIAGEN catalog # 28004) and material was amplified for 5 cycles using NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs catalog # M0541L). After evaluation by real-time PCR, 10-13 additional PCR cycles were done. The final product was cleaned by aMPure XP beads (Beckman Coulter catalog # A63882) at a 1X ratio, and size selection was performed at a 0.5X ratio. Libraries were sequenced using the Reagent Kit (200 Cycles) (Illumina).  An average of 76 million paired reads were generated per sample. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Buenrostro JD, Giresi PG, Zaba LC, Chang HY, Greenleaf WJ. Nat Methods. 2013 Dec;10(12):1213-8. doi: 10.1038/nmeth.2688. Epub 2013 Oct 6.

value: Lung

value: Lung adenocarcinoma

value: Untreated


title: EORTC_26101_2023_303


title: Fb_861

description: cell lysate

value: Fibroblasts


title: 22PC_C3

value: Prostate

value: DKO 22PC

value: Prostate adenocarcinoma

value: TP53/RB1 KO


title: H1563-DKO-r2


title: EORTC_26101_2023_302

value: male


title: Fb_441

description: cell lysate

value: WT


title: 22PC_C2


title: EORTC_26101_2023_300

value: female


title: H1563-DKO-r1


title: EORTC_26101_2023_301


title: EnC_33-8

description: cell lysate

value: Endothelial cells


title: H1563-RB1-r3

value: RB1 KO


title: EORTC_26101_2023_299


title: EORTC_26101_2023_296


title: EORTC_26101_2023_306


title: EORTC_26101_2023_305


title: E13_brainGFPpos_SNC42-4_Snip1CKO_H3K27ac

city: Doha

first: Mohamed Nadhir

last: Djekidel

state: Doha

address: Gharafa

department: Translational Medicine Department

country: Qatar

institute: Sidra Medicine

description: Brain E13 H3K27ac after Snip1KO

data_processing:
CUT&RUN libraries were sequenced on NovaSeq6000 sequencer and generated 50 bp paired-end reads
The reads were aligned to mouse mm10 genome reference and fruit fly dm6 genome reference by BWA (version 0.7.170.7.12, default parameter). Duplicated reads were marked by the bamsormadup from the biobambam tool (version 2.0.87) available at https://www.sanger.ac.uk/tool/biobambam/. Uniquely mapped reads were kept by samtools (parameter “-q 1 -F 1804,” version 1.14). Fragments < 2000 bp were kept for peak calling and bigwig files were generated for visualization.
SICER (PMID: 24743992) and macs2 (PMID: 18798982)   were bothwas used for peak calling, to identify both the narrow and broad peak correctly. With SICER, we assigned peaks that were at the top 1 percentile as the high-confidence peaks and the top 5 percentile as the low-confidence peaks. Two sets of peaks were generated: Strong peaks called with parameter ‘FDR < 0.05’ by at least one method (macs2 or SICER) and weak peaks called with parameter ‘FDR < 0.5’ by at least one method (macs2 or SICER). Peaks were considered reproducible if they were supported by a strong peak from all replicates or at least one strong peak and a weak peak in the other replicates.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

source_name: tissue

growth_protocol: embryos at an indicated embryonic day were dissected out from the uterus and visceral yolk sac. A part of the tail or limbs was collected for genotyping. Brains were dissected from embryos under the dissection microscope in cold 1x PBS. Then, 300 μL Dulbecco’s Modified Eagle’s Medium (DMEM) (ATCC 30-2002) and 150 μL of 10 mg/mL collagenase Type II (Worthington LS004176) were added to each brain and incubated for 5-10 min at 37 °C. After centrifugation at 1000 xg for 3 min, the tissue was incubated with 500 μL 0.25% Trypsin-EDTA (ThermoFisher 25200056) for 5 min at 37 °C. Trypsinization was quenched with 500 μL DMEM supplemented with 10% fetal bovine serum (FBS) and pelleted by centrifugation at 1000 xg for 3 min. Alternatively, cells were dissociated from the brain using the papain dissociation system (Worthington LK003153). Cells were then resuspended in 500 μL of NPC culture media (NeuroCult™ Proliferation Media; STEMCELL Technologies 05702) supplemented with 30 ng/mL human recombinant epidermal growth factor (rhEGF) (STEMCELL Technologies 78006) and filtered through a 40 μm filter (Fisherbrand™ 22-363-547) to obtain single cells. To collect NPCs, the dissociated brain cells were cultured in ultra-low attachment 6-well plates (Corning® Costar® CLS3471) in the NPC culture media at 37 °C. NPCs formed neurospheres in suspension. For passaging, neurospheres were incubated with Accutase™ (STEMCELL Technologies 07920) for 5 min at 37 °C and then dissociated by pipetting. After adding an equal volume of the NPC culture media, dissociated cells were centrifuged at 500 xg for 5 min. Cells were then grown in the NPC culture media either in suspension in the ultra-low attachment 6-well plates or on matrigel (Corning™ 354230) coated plates. The medium was changed every 2 to 3 days. For collecting uncultured NPCs, brain cells were sorted by fluorescence-activated cell sorting (FACS) using Sox2-eGFP or NeuroFluor™ CDr3 (STEMCELL Technologies 01800)

extract_protocol:
. DNA was released from the beads by incubating them for 30 min at 37 °C and collected by centrifugation at 16,000 x g for 5 min at 4 °C. DNA was then isolated by using a phenol/chloroform extraction method
We followed CUT&RUN described in Skene and Beniof (PMID:28079019), with minor variations.

treatment_protocol: Snip1-tm1a (Infrafrontier/EMMA 04224) were first crossed with Actin-FLPe to generate the Snip1-flox line. To genetically label NPCs, Snip1-flox; Nestin-Cre mice were crossed with Sox2-eGFP transgenic mice. Embryos were harvested at embryonic days as indicated in the figures or text

value: brain


title: H1563-RB1-r2


title: H1563-RB1-r1


title: EnC_162-8

description: cell lysate

value: lung


title: EORTC_26101_2023_295


title: EORTC_26101_2023_292


title: EORTC_26101_2023_293


title: E13_brainGFPpos_SNC42-7_Snip1WT_H3K27ac

description: Brain E13 H3K27ac WT


title: H1563-TP53-r3

value: TP53 KO


title: EORTC_26101_2023_294


title: EORTC_26101_2023_291


title: H1563-TP53-r2


title: EORTC_26101_2023_289


title: H1563-TP53-r1


title: Day3_Cre_Suz12_rep1

description: Day3, Suz12 CUT&RUN, Snip1 Cre

data_processing:
CUT&RUN libraries were sequenced on NovaSeq6000 sequencer and generated 50 bp paired-end reads
The reads were aligned to mouse mm10 genome reference and fruit fly dm6 genome reference by BWA (version 0.7.170.7.12, default parameter). Duplicated reads were marked by the bamsormadup from the biobambam tool (version 2.0.87) available at https://www.sanger.ac.uk/tool/biobambam/. Uniquely mapped reads were kept by samtools (parameter “-q 1 -F 1804,” version 1.14). Fragments < 2000 bp were kept for peak calling and bigwig files were generated for visualization.
SICER (PMID: 24743992) and macs2 (PMID: 18798982)   were bothwas used for peak calling, to identify both the narrow and broad peak correctly. With SICER, we assigned peaks that were at the top 1 percentile as the high-confidence peaks and the top 5 percentile as the low-confidence peaks. Two sets of peaks were generated: Strong peaks called with parameter ‘FDR < 0.05’ by at least one method (macs2 or SICER) and weak peaks called with parameter ‘FDR < 0.5’ by at least one method (macs2 or SICER). Peaks were considered reproducible if they were supported by a strong peak from all replicates or at least one strong peak and a weak peak in the other replicates.
Assembly: mm10
Supplementary files format and content: tsv, bed
Library strategy: CUT&RUN

source_name: mNPCs

value: Snip1 Cre


title: EORTC_26101_2023_290


title: Day3_Empty_Suz12_rep1

description: Day3, Suz12 CUT&RUN, Snip1 Empty


title: EORTC_26101_2023_298


title: EORTC_26101_2023_287


title: EORTC_26101_2023_297


title: Day2_Cre_Suz12_rep1

description: Day2, Suz12 CUT&RUN, Snip1 Cre


title: H1563-r3

value: Lung

value: Control


title: Day3_Empty_Ezh2_rep2

description: Day3, Ezh2 CUT&RUN, Snip1 Empty


title: EORTC_26101_2023_286


title: EORTC_26101_2023_285


title: H1563-r2

value: Lung adenocarcinoma

value: Untreated


title: EORTC_26101_2023_283


title: EORTC_26101_2023_284


title: EORTC_26101_2023_281


title: H1563-r1


title: Day3_Empty_Suz12_rep2

description: Day3, Suz12 CUT&RUN, Snip1 Empty


title: Day2_Cre_Ezh2_rep2

description: Day2, Ezh2 CUT&RUN, Snip1 Cre


title: EORTC_26101_2023_279


title: 22PC-DKO-r3

value: Prostate


title: EORTC_26101_2023_280


title: EORTC_26101_2023_278


title: 22PC-DKO-r2


title: Day3_Cre_Ezh2_rep2

description: Day3, Ezh2 CUT&RUN, Snip1 Cre


title: EORTC_26101_2023_277


title: Day2_Empty_Ezh2_rep2

description: Day2, Ezh2 CUT&RUN, Snip1 Empty


title: EORTC_26101_2023_276


title: EORTC_26101_2023_275


title: 22PC-DKO-r1


title: EORTC_26101_2023_288


title: Day2_Empty_Suz12_rep1

description: Day2, Suz12 CUT&RUN, Snip1 Empty


title: EORTC_26101_2023_274


title: EORTC_26101_2023_273


title: 22PC-RB1-r3


title: EORTC_26101_2023_272


title: Day2_Empty_Ezh2_rep1

description: Day2, Ezh2 CUT&RUN, Snip1 Empty


title: Day3_Empty_Ezh2_rep1

description: Day3, Ezh2 CUT&RUN, Snip1 Empty


title: EORTC_26101_2023_269


title: 22PC-RB1-r2


title: EORTC_26101_2023_282


title: 22PC-RB1-r1


title: EORTC_26101_2023_267


title: Day3_Cre_Suz12_rep2

description: Day3, Suz12 CUT&RUN, Snip1 Cre


title: 22PC-TP53-r2


title: EORTC_26101_2023_270


title: 22PC-TP53-r1


title: EORTC_26101_2023_266


title: EORTC_26101_2023_264


title: EORTC_26101_2023_265


title: EORTC_26101_2023_263


title: Day3_Cre_Ezh2_rep1

description: Day3, Ezh2 CUT&RUN, Snip1 Cre


title: EORTC_26101_2023_262


title: EORTC_26101_2023_261


title: Day2_Cre_Suz12_rep2

description: Day2, Suz12 CUT&RUN, Snip1 Cre


title: 22PC-r3


title: 22PC-r2


title: Day2_Cre_Ezh2_rep1

description: Day2, Ezh2 CUT&RUN, Snip1 Cre


title: EORTC_26101_2023_271


title: EORTC_26101_2023_260


title: EORTC_26101_2023_259


title: EORTC_26101_2023_268


title: Snip1TH_IP_Suz12_rep1

description: Suz12 Re-ChIP CUT&RUN


title: 22PC-TP53-r3


title: Day2_Empty_Suz12_rep2

description: Day2, Suz12 CUT&RUN, Snip1 Empty


title: Snip1TH_IP_IgG_rep2

description: IgG Re-ChIP CUT&RUN


title: 22PC-r1


title: EORTC_26101_2023_256


title: EORTC_26101_2023_258


title: EORTC_26101_2023_255


title: EORTC_26101_2023_257


title: EORTC_26101_2023_254


title: EORTC_26101_2023_253


title: Snip1TH_IP_Ezh2_rep2

description: Ezh2 Re-ChIP CUT&RUN


title: EORTC_26101_2023_252


title: EORTC_26101_2023_248


title: Snip1TH_IP_IgG_rep1

description: IgG Re-ChIP CUT&RUN


title: EORTC_26101_2023_250


title: EORTC_26101_2023_246


title: EORTC_26101_2023_249


title: Snip1TH_IP_H3K27me3_rep1

description: H3K27me3 Re-ChIP CUT&RUN


title: EORTC_26101_2023_251


title: EORTC_26101_2023_244


title: EORTC_26101_2023_247


title: Snip1TH_IP_Suz12_rep2

description: Suz12 Re-ChIP CUT&RUN


title: culturedmNPCs_IKK16_Snip1TH_rep1

description: IKK16 Treated cells


title: EORTC_26101_2023_242


title: EORTC_26101_2023_245


title: EORTC_26101_2023_243


title: EORTC_26101_2023_241


title: culturedmNPCs_IKK16_Snip1TH_rep2

description: IKK16 Treated cells


title: EORTC_26101_2023_240


title: culturedmNPCs_DMSO_IgG_rep2

value: DMSO


title: EORTC_26101_2023_238


title: EORTC_26101_2023_236


title: EORTC_26101_2023_237


title: Snip1TH_IP_Ezh2_rep1

description: Ezh2 Re-ChIP CUT&RUN


title: culturedmNPCs_JSH23_Snip1TH_rep1

description: JSH23 Treated cells


title: EORTC_26101_2023_235


title: EORTC_26101_2023_234


title: Snip1TH_IP_H3K27me3_rep2

description: H3K27me3 Re-ChIP CUT&RUN


title: culturedmNPCs_DMSO_Snip1TH_rep2

description: DMSO Treated cells


title: culturedmNPCs_Galunisertib_Snip1TH_rep1

description: Galunisertib Treated cells

value: Galunisertib


title: culturedmNPCs_LDN193189_Snip1TH_rep2

description: LDN193189 Treated cells


title: culturedmNPCs_BAY11_7082_Snip1TH_rep1

description: BAY11_7082 Treated cells


title: EORTC_26101_2023_232


title: EORTC_26101_2023_233


title: EORTC_26101_2023_227


title: EORTC_26101_2023_230


title: EORTC_26101_2023_226


title: EORTC_26101_2023_224


title: EORTC_26101_2023_225


title: EORTC_26101_2023_231


title: culturedmNPCs_K02288_Snip1TH_rep1

description: K02288 Treated cells


title: EORTC_26101_2023_223


title: EORTC_26101_2023_222


title: culturedmNPCs_DMSO_IgG_rep1


title: EORTC_26101_2023_239


title: culturedmNPCs_Galunisertib_Snip1TH_rep2

description: Galunisertib Treated cells


title: EORTC_26101_2023_221


title: EORTC_26101_2023_220


title: culturedmNPCs_JSH23_Snip1TH_rep2

description: JSH23 Treated cells


title: EORTC_26101_2023_219


title: EORTC_26101_2023_217


title: culturedmNPCs_DMSO_Snip1TH_rep1

description: DMSO Treated cells


title: EORTC_26101_2023_218


title: EORTC_26101_2023_216


title: EORTC_26101_2023_228


title: culturedmNPCs_LDN193189_Snip1TH_rep1

description: LDN193189 Treated cells


title: EORTC_26101_2023_229


title: culturedmNPCs_K02288_Snip1TH_rep2

description: K02288 Treated cells


title: EORTC_26101_2023_215


title: EORTC_26101_2023_212


title: EORTC_26101_2023_206


title: EORTC_26101_2023_205


title: EORTC_26101_2023_211


title: EORTC_26101_2023_214


title: NeuroD1_BMP2_rep2

city: La Jolla

first: Matthew

last: Wortham

state: CA

address: 2880 Torrey Pines Scenic Drive, Sanford Consortium for Regenerative Medicine, Room 3102

institute: University of California, San Diego

data_processing:
Data was mapped to the UCSC mouse genome NCBI37/mm10
Bowtie 2 was used to map data to the genome with the following settings: the seed length was set as 33 with a maximum number of 2 mismatches allowed in the seed region, and reads aligning to multiple locations were discarded.
Duplicate reads were removed using samtools.
Assembly: mm10
Supplementary files format and content: bigWig

source_name: pancreatic islets

growth_protocol: Isolated pancreatic islets were cultured in RPMI 1640 medium with 11mmol/l D-glucose supplemented with 2% human serum and 1 % penicillin/steptomycin. Medium and BMP2 were

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared using NEBNext® UltraTM DNA library Kit for Illumina

treatment_protocol: Islets were cultured in the absence or presence of 50ng/ml BMP2

value: pancreatic islets

value: 12 weeks

value: BMP2 10d

tag: chip antibody

value: NeuroD1 antibody (Cat#4373, Cell Signaling).


title: EORTC_26101_2023_213

value: male


title: EORTC_26101_2023_209


title: culturedmNPCs_BAY11_7082_Snip1TH_rep2

description: BAY11_7082 Treated cells


title: EORTC_26101_2023_210


title: EORTC_26101_2023_207


title: EORTC_26101_2023_204

value: female


title: NeuroD1_BMP2_rep1

value: Ctrl 10d


title: EORTC_26101_2023_208


title: EORTC_26101_2023_203


title: Men_KO3_d7_CD8T_biol_rep_3

city: Toon

first: Junpei

last: Suzuki

address: Shitukawa

department: Graduate School of Medicine

country: Japan

institute: Ehime University

data_processing:
CLC Genomics Workbench v22.0
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Splenic CD8 T cells

growth_protocol: WT and Menin KO naïve CD8 T (CD44low/CD62Lhigh) cells were prepared using a CD8+ T cell Isolation kit (BioLegend) with biotin anti-CD44 antibody (BioLegend).  Naïve CD8 T cells (0.75 × 10^6) were stimulated with immobilized anti-TCR-β mAb (3 μg/ml, BioLegend) and anti-CD28 mAb (1 μg/ml,BioLegend) for two days in the presence of IL-2 (10 ng/ml, BioLegend). Next, the cells were transferred to a new plate and further cultured in the presence of IL-2 (10 ng/ml).

extract_protocol:
RNA was extracted using RNeasy plus Micro plus kit (Qiagen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using QuantSeq 3'mRNA-Seq Library Prep Kit for illumina following manufacturer's protocols.

value: Splenic CD8 T cells

value: Menin knockout

tag: culture time

value: seven days


title: Men_KO2_d7_CD8T_biol_rep_2


title: NeuroD1_Ctrl_rep1


title: NeuroD1_Ctrl_rep2


title: WT3_d7_CD8T_biol_rep_3

value: WT


title: InputDNA_Ctrl_1

value: none (input)


title: Men_KO1_d7_CD8T_biol_rep_1


title: EORTC_26101_2023_195


title: EORTC_26101_2023_200


title: EORTC_26101_2023_196


title: EORTC_26101_2023_197


title: EORTC_26101_2023_199


title: EORTC_26101_2023_194


title: EORTC_26101_2023_192


title: WT2_d7_CD8T_biol_rep_2


title: EORTC_26101_2023_193


title: EORTC_26101_2023_198


title: EORTC_26101_2023_191


title: EORTC_26101_2023_188


title: EORTC_26101_2023_202


title: EORTC_26101_2023_187


title: EORTC_26101_2023_189


title: EORTC_26101_2023_186


title: Aged_CD8T_biol_rep_2

growth_protocol: Splenic CD8 T cells from young (6 weeks of age) and aged (around 65 weeks of age) mice were prepared using a CD8+ T cell Isolation kit (BioLegend).  Isolated CD8 T cells (0.75 × 10^6) were stimulated with immobilized anti-TCR-β mAb (3 μg/ml, BioLegend) and anti-CD28 mAb (1 μg/ml,BioLegend) for two days in the presence of IL-2 (10 ng/ml, BioLegend). Next, the cells were transferred to a new plate and further cultured in the presence of IL-2 (10 ng/ml) for five days.

value: around 65 weeks


title: Aged_CD8T_biol_rep_3


title: WT1_d7_CD8T_biol_rep_1


title: Aged_CD8T_biol_rep_1


title: EORTC_26101_2023_201


title: EORTC_26101_2023_185


title: EORTC_26101_2023_184


title: Leukemic blasts, 272

last: Herold

address: Marchioninistr. 15

department: Department of Internal Medicine III

institute: University Hospital Grosshadern, Ludwig-Maximilians-University (LMU)

data_processing:
Salmon (v0.9.1) was used for gene and transcript expression analysis.
Genome_build: GRCh37 release 87 reference genome
Supplementary_files_format_and_content: TPM quantified genes by salmon

source_name: leukemic blasts

extract_protocol:
Samples with <90% of human cells were enriched by Mouse Cell Depletion Kit (Miltenyi Biotec)
RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq Stranded mRNA library)

tag: disease

value: ALL

value: BCP

value: pediatric


title: Leukemic blasts, 265

value: relapse


title: Young_CD8T_biol_rep_3

value: 6 weeks


title: EORTC_26101_2023_183


title: EORTC_26101_2023_182


title: Leukemic blasts, 223

value: BCR-ABL

value: adult


title: EORTC_26101_2023_181


title: EORTC_26101_2023_180


title: Leukemic blasts, 202

value: T-ALL


title: Young_CD8T_biol_rep_2


title: EORTC_26101_2023_190

value: male


title: Young_CD8T_biol_rep_1

value: female


title: Leukemic blasts, 177


title: EORTC_26101_2023_179


title: EORTC_26101_2023_178


title: EORTC_26101_2023_177


title: Utx, KO, CD8T, biol rep 3

growth_protocol: WT and Utx KO naïve CD8 T (CD44lowCD62Lhigh) cells were prepared using a CD8+ T cell Isolation kit (BioLegend) with biotin anti-CD44 antibody (BioLegend).  Naïve CD8 T cells (0.75 × 10^6) were stimulated with immobilized anti-TCR-β mAb (3 μg/ml, BioLegend) and anti-CD28 mAb (1 μg/ml,BioLegend) for two days in the presence of IL-2 (10 ng/ml, BioLegend). Next, the cells were transferred to a new plate and further cultured in the presence of IL-2 (10 ng/ml) for three days.

extract_protocol:
RNA was extracted using RNeasy plus Micro plus kit (Qiagen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using QuabtSeq 3'mRNA-Seq Library Prep Kit for illumina following manufacturer's protocols.

value: Utx knockout


title: Leukemic blasts, 174


title: EORTC_26101_2023_175


title: Utx, KO, CD8T, biol rep 2

value: Splenic CD8 T cells


title: EORTC_26101_2023_174


title: Leukemic blasts, 707


title: Leukemic blasts, 677


title: Utx, KO, CD8T, biol rep 1


title: EORTC_26101_2023_172


title: EORTC_26101_2023_171


title: Leukemic blasts, 502


title: EORTC_26101_2023_169


title: WT, CD8T, biol rep 3


title: Leukemic blasts, 398


title: WT, CD8T, biol rep 2


title: EORTC_26101_2023_168


title: Leukemic blasts, 359


title: WT, CD8T, biol rep 1


title: E13_Sox2GFP_Snip1CKO_2830_2_Suz12AM

description: Suz12 CUT&RUN with Snip1_Nes_KO

data_processing:
CUT&RUN libraries were sequenced on NovaSeq6000 sequencer and generated 50 bp paired-end reads
The reads were aligned to mouse mm10 genome reference and fruit fly dm6 genome reference by BWA (version 0.7.170.7.12, default parameter). Duplicated reads were marked by the bamsormadup from the biobambam tool (version 2.0.87) available at https://www.sanger.ac.uk/tool/biobambam/. Uniquely mapped reads were kept by samtools (parameter “-q 1 -F 1804,” version 1.14). Fragments < 2000 bp were kept for peak calling and bigwig files were generated for visualization.
SICER (PMID: 24743992) and macs2 (PMID: 18798982)   were bothwas used for peak calling, to identify both the narrow and broad peak correctly. With SICER, we assigned peaks that were at the top 1 percentile as the high-confidence peaks and the top 5 percentile as the low-confidence peaks. Two sets of peaks were generated: Strong peaks called with parameter ‘FDR < 0.05’ by at least one method (macs2 or SICER) and weak peaks called with parameter ‘FDR < 0.5’ by at least one method (macs2 or SICER). Peaks were considered reproducible if they were supported by a strong peak from all replicates or at least one strong peak and a weak peak in the other replicates.
Assembly: mm10
Supplementary files format and content: bw, tsv, bed
Library strategy: CUT&RUN

source_name: brain

value: brain

tag: collection day

tag: antibody


title: EORTC_26101_2023_167


title: EORTC_26101_2023_176


title: EORTC_26101_2023_164


title: EORTC_26101_2023_166


title: EORTC_26101_2023_165


title: Leukemic blasts, 355

tag: Sex


title: EORTC_26101_2023_163


title: EORTC_26101_2023_173


title: Leukemic blasts, 271


title: E13_Sox2GFP_Snip1CKO_2830_1_Suz12AM

description: Suz12 CUT&RUN with Snip1_Nes_KO


title: EORTC_26101_2023_162


title: Leukemic blasts, 270


title: EORTC_26101_2023_161


title: E13_Sox2GFP_Snip1CKO_178_5_Ezh2

description: Ezh2 CUT&RUN with Snip1_Nes_KO


title: Leukemic blasts, 269


title: E13_Sox2GFP_Ctrl_1374_2_Suz12AM

description: Suz12 CUT&RUN in WT


title: EORTC_26101_2023_160


title: EORTC_26101_2023_157


title: Leukemic blasts, 268


title: EORTC_26101_2023_158


title: EORTC_26101_2023_170


title: EORTC_26101_2023_155


title: EORTC_26101_2023_159


title: EORTC_26101_2023_156


title: E13_Sox2GFP_Ctrl_1374_1_Ezh2

description: Ezh2 CUT&RUN in WT


title: Leukemic blasts, 267


description:
Snip1 CUT&RUN with Snip1_Nes_KO
2229288_E13_brainGFPpos_SNC72-6_Snip1CKO_Snip1TH


title: EORTC_26101_2023_154


title: Leukemic blasts, 236


title: Leukemic blasts, 266


title: E13_brainGFPpos_SNC176-6_Snip1WT_H3K27me3

description: H3K27me3 CUT&RUN in WT


title: MCF7, shPURA2, rep 1

city: yangzhou

first: Yu

last: Shiyi

state: Jiangsu

address: hanjiang district jiangyangzhonglu136, Hanjiang district, Jiangyangzhonglu 136

institute: yangzhou university

data_processing:
The sequencing data was filtered with SOAPnuke ( (v1.5.6))
The clean data were mapped to the GRCH38 whole genome using HISAT2 with default parameters.
The SAM files were processed with Samtools to generate BAM files.
The sorted BAM files were processed with featureCounts to calculate counts for each transcripts in GRCH38.
The differentially expressed genes were calculated by Deseq2.
Assembly: GRCH38
Supplementary files format and content: txt files with raw gene counts for every transcripts in each sample

growth_protocol: RPMI-1640 (Gibco) supplemented with 10% FBS (Hyclone)  was used to culture MCF7 cell lines in a humidified incubator at 37℃ with 5% CO2

extract_protocol:
Cells were directly subjected to RNA extraction using TRIzol reagent (Thermo Fisher Scientific). 1.0 ug of total RNA was used for the construction of sequencing libraries. The libraries was sequenced on DNBseq(PE150) platform.
DNBSEQ Eukaryotic Strand-specific mRNA library strategy was applied to establish libraries.

treatment_protocol: Cells were infected with lentivirus of control shRNA, PURA shRNA, AGPG shRNA, plvx or plvx-AGPG and were selected with puromycin

value: breast cancer cell line

value: PURA knockdown

value: infected with PURA shRNA2 lentivirus


title: MCF7, shPURA2, rep 2


title: E13_brainGFPpos_SNC176-4_Snip1WT_H3K27me3

description: H3K27me3 CUT&RUN in WT

value: WT


title: EORTC_26101_2023_152


title: EORTC_26101_2023_153


title: Leukemic blasts, 233

value: ALL


title: MCF7, shPURA1, rep 2

value: infected with PURA shRNA1 lentivirus


title: MCF7, shPURA1, rep 1


title: E13_Sox2GFP_Ctrl_1374_1_Suz12AM

description: Suz12 CUT&RUN in WT


title: EORTC_26101_2023_151


title: E13_brainGFPpos_SNC176-3_Snip1CKO_H3K27me3

description: H3K27me3 CUT&RUN with Snip1_Nes_KO


title: Leukemic blasts, 207

value: BCP

value: pediatric


title: Leukemic blasts, 179


title: MCF7, shCon_PURA, rep 1

value: control for PURA knockdown

value: infected with control shRNA lentivirus


title: E13_brainGFPpos_SNC176-2_Snip1CKO_H3K27me3

description: H3K27me3 CUT&RUN with Snip1_Nes_KO


description:
Snip1 CUT&RUN in WT
2229283_E13_brainGFPpos_SNC1250-3_Snip1WT_Snip1TH


title: EORTC_26101_2023_149


title: Leukemic blasts, 50


title: MCF7, plvx_AGPG, rep2

value: infected with plvx-AGPG lentivirus


title: EORTC_26101_2023_148


title: MCF7, plvx_AGPG, rep1


title: Leukemic blasts, 12


description:
Snip1 CUT&RUN with Snip1_Nes_KO
2252567_E13_brainGFPpos_SNC1250-1_Snip1CKO_Snip1TH


title: EORTC_26101_2023_147


title: Leukemic blasts, 763


title: MCF7, plvx, rep 1

value: control for AGPG_OE

value: infected with plvx lentivirus


title: E13_brainGFPpos_SNC1134-2_Snip1WT_H3K27ac

description: H3K27ac CUT&RUN in WT


title: MCF7, shAGPG2, rep2

value: AGPG knockdown

value: infected with AGPG shRNA2 lentivirus


title: EORTC_26101_2023_146

value: male


title: EORTC_26101_2023_145

value: female


title: E13_brainGFPpos_SNC1132-2_Snip1WT_H3K27ac

description: H3K27ac CUT&RUN in WT

value: brain


title: E13_brainGFPpos_SNC1134-1_Snip1CKO_H3K27ac

description: H3K27ac CUT&RUN with  Snip1_Nes_KO


title: EORTC_26101_2023_150


title: Leukemic blasts, 706


title: MCF7, shAGPG2, rep1

value: breast cancer cell line


title: MCF7, plvx, rep 2


title: Leukemic blasts, 387


title: EORTC_26101_2023_142


title: MCF7, shCon_PURA, rep 2


title: E13_Midbrain_Ctrl_rep3

data_processing:
Paired-end 100-cycle sequencing was performed on NovaSeq6000 sequencer following the manufacturer’s instructions (Illumina). Raw reads were first trimmed using TrimGalore (v0.6.3) with parameters ‘--paired --retain_unpaired’
Filtered reads were then mapped to the Homo sapiens reference genome GRCm37.p13 using STAR (v2.7.9a). Gene-level read quantification was done using RSEM (v1.3.1)on the Gencode annotation v19
To identify the differentially expressed genes, normalization factors are first estimated using the trimmed mean of M values (TMM) and genes with CPM < 1 in all samples were removed
Next, the TMM normalization factors and raw counts were then used for the Limma-voom analysis using the “voom”, “lmFit” and “eBayes” functtions from the limma R package
Assembly: mm10
Supplementary files format and content: tsv

source_name: Midbrain

extract_protocol:
Total RNA was extracted from FACS-sorted cells using TRIzol reagent (Invitrogen™ 15596026) and Direct-zol™ RNA Microprep (Zymo Research R2062) by following manufacturer’s instructions. DNA digestion with DNase I was also performed as part of the RNA extraction. cDNA was prepared with 500-1000 ng of total RNA using SuperScript™ IV VILO™ Master Mix (ThermoFisher 11766050) by following manufacturer’s instructions.
The QuantSeq 3’ RNA-Seq Library Prep Kit for Illumina (Lexogen) was used for library construction

value: Ctrl


description:
Snip1 CUT&RUN in WT
2252565_E13_brainGFPpos_SNC1250-2_Snip1WT_Snip1TH

value: WT


title: MCF7, shAGPG1, rep2

value: infected with AGPG shRNA1 lentivirus


title: E13_brainGFPpos_SNC1132-1_Snip1CKO_H3K27ac

description: H3K27ac CUT&RUN with Snip1_Nes_KO


title: EORTC_26101_2023_144


title: Leukemic blasts, 435

value: ALL


title: Leukemic blasts, 363

value: BCP

value: BCR-ABL

value: adult


title: EORTC_26101_2023_141


title: E13_Midbrain_Ctrl_rep2


title: Leukemic blasts, 352


title: MCF7, shCon, rep 2

value: control for AGPG knockdown

value: infected with control shRNA lentivirus


title: Leukemic blasts, 697

value: pediatric


title: E13_Midbrain_Snip1KO_rep3


title: EORTC_26101_2023_140


title: EORTC_26101_2023_139


title: MCF7, shCon, rep 1


title: Leukemic blasts, 247


title: EORTC_26101_2023_143


title: E13_Midbrain_Snip1EedKO_rep6


title: EORTC_26101_2023_138


title: E13_Midbrain_Snip1EedKO_rep5


title: Leukemic blasts, 241


title: EORTC_26101_2023_137


title: MCF7, shAGPG1, rep1


title: Leukemic blasts, 199


title: Leukemic blasts, 54


title: EORTC_26101_2023_135


title: EORTC_26101_2023_136


title: E13_Forebrain_Ctrl_rep1

source_name: Forebrain


title: mCRC73.T

type: RNA

city: Milan

first: Chiara

last: Balestrieri

address: Via Olgettina 58

department: Center for Omics Sciences

country: Italy

institute: IRCCS San Raffaele Scientific Institute

hyb_protocol: Nanostring

scan_protocol: Nanostring

data_processing:
nCounter PanCancer Immune Profiling Panel (NanoString Technologies, USA)
Raw counts were extracted from the nSolver analysis software 4.0 and raw RCC files were imported in ROSALIND (https://rosalind.onramp.bio/) and normalized using housekeeping genes.

label: Nanostring

source_name: liver metastasis from colorectal cancer

label_protocol: Nanostring

extract_protocol: Nanostring technology, total RNA was extracted from FFPE samples by using Maxwell RSC RNA FFPE Kit and Maxwell RSC Instrument (Promega), according to manufacturer’s instructions.

value: liver

tag: tissue type

value: tumor


title: E13_Forebrain_Snip1KO_rep2


title: mCRC73.P

value: peritumor


title: E13_Forebrain_Snip1EedKO_rep3


title: mouse glioma tumor, IDH1 R132H, rep1

first: Dr. Liang

last: Lei

state: NY

address: 1130 St. Nicholas Ave

department: Pathology and Cell Biology

institute: Columbia University

data_processing:
Raw reads were mapped to mm10 Illumina iGenomes annotation using Tophat 2
Cufflinks 2 was used to calculate expression levels for each gene as fpkm
Gene Set Enrichment Analysis was performed using the Broad Institute suite for comparing our samples to the TCGA database
GSEA focused on comparative expression of the Verhaak subtype classifier genes (Verhaak et al. 2010)
Assembly: mm10
Supplementary files format and content: tab-delimited text fastq. file includes raw data for each sample
Supplementary files format and content: tab-delimited text with fpkm from Cufflinks output includes processed data for each sample

source_name: adult mouse brain

extract_protocol:
total RNA was extracted with Rneasy kit (Qiagen)
We use poly-A pull-down to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>8 required) and proceed on library preparation by using Illumina TruSeq RNA prep kit.

value: adult mouse brain

value: Tp53fl/fl, stopfl/fl-luc

value: Male

tag: tumor stage

value: end-stage


title: mouse glioma tumor, IDH1 R132H, rep3


title: mouse glioma tumor, IDH1 R132H, rep4


title: EORTC_26101_2023_133

value: female


title: mouse glioma tumor, IDH1 R132H, rep2


title: EORTC_26101_2023_134


title: E13_Forebrain_Snip1EedKO_rep2

value: brain


title: Leukemic blasts, 248

value: male


title: mouse glioma tumor, IDH1 R132H, rep6


title: mCRC71.T


title: EORTC_26101_2023_132


title: E13_Midbrain_Snip1EedKO_rep4


title: mouse glioma tumor, IDH1 R132H, rep5


title: E13_Forebrain_Snip1KO_rep1


title: EORTC_26101_2023_131


title: mCRC65.T


title: mouse glioma tumor, IDH1 wildtype, rep4

value: Female

value: pQ-PDGFB-I-Cre


title: E13_Forebrain_Snip1EedKO_rep1


title: mouse glioma tumor, IDH1 wildtype, rep3


title: E13-brain-mNPC-GFPpos-Snip1wt_rep4

description: 2229436_E13-brain-mNPC-GFPpos-Snip1wt_rep5

source_name: brain-mNPC


title: mCRC65.P


title: mCRC62.T


title: EORTC_26101_2023_130


title: mCRC62.P


title: E13-brain-mNPC-GFPpos-Snip1wt_rep3

description: 2229435_E13-brain-mNPC-GFPpos-Snip1wt_rep4


title: mouse glioma tumor, IDH1 wildtype, rep2


title: EORTC_26101_2023_129


title: mouse glioma tumor, IDH1 wildtype, rep1


title: EORTC_26101_2023_128


title: E13-brain-mNPC-GFPpos-Snip1wt_rep2

description: 2145466_E13-brain-mNPC-GFPpos-Snip1wt_rep2


title: mCRC61.T


title: mCRC61.P


title: Vehicle 28 days post injury (dpi) above injury site 3

first: Jens

last: Hansen

address: 1425 Madison Ave

department: Department of Pharmacological Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Read alignment using Star (2.5.4b), supported by bowtie 2.2.1.0 and samtool 0.1.7
Mapping of aligned reads to gene regions using FeatureCounts (Rsubread 2.10.5)
Identification of differentially expressed genes using DESeq2 1.36.0
Assembly: GRCm38.p6
Supplementary files format and content: Toro_et_all_Feature_counts_matrix.txt: contains the number of reads mapping to each gene
Supplementary files format and content: Toto_et_all_DEGs.txt: Contains differentially expressed genes obtained between selected conditions

source_name: Spinal cord

extract_protocol:
TRIZOL reagent (ThermoFisher), manufacturer's instructions
Reverse transcription using Omniscript reverse transcriptase (Qiagen)TruSeq RNA Sample Prep Kit v2 protocol (Illumina)
random primed

treatment_protocol: A motor-incomplete contusion SCI was performed using an Infinite Horizons (IH) impactor (Precision Systems and Instrumentation). Starting at day 3 post injury, a daily administration of boldine (Millipore Sigma) dissolved in DMSO (Sigma) <2.5% and peanut oil (Sigma) was performed orally at a final concentration of 50mg/kg mixed in 1 g of peanut butter (PB). Control animals (laminectomy only) received DMSO/peanut oil in PB without boldine.

value: Spinal cord

tag: sacrifice time

value: 28 days post injury (dpi)

tag: injury

value: Spinal Cord Injury (SCI)

value: WT

value: Vehicle

tag: activity

value: no treadmill


title: EORTC_26101_2023_127

data_processing:
BeadStudio software v3.2
Normalized Average Beta (BMIQ method)

source_name: diffuse glioma


title: mouse glioma tumor, IDH1 wildtype, rep5

tag: tissue

tag: genotype


title: E13-brain-mNPC-GFPpos-Snip1cko_rep4

description: 2229437_E13-brain-mNPC-GFPpos-Snip1cko_rep4


title: E13-brain-mNPC-GFPpos-Snip1wt_rep1

description: 2145465_E13-brain-mNPC-GFPpos-Snip1wt_rep1


title: EORTC_26101_2023_126


title: mCRC60.T

value: liver

value: tumor


title: mCRC60.P

value: peritumor


title: EORTC_26101_2023_125


title: Vehicle 28 days post injury (dpi) above injury site 1

tag: treatment


title: E13-brain-mNPC-GFPpos-Snip1cko_rep3

description: 2145470_E13-brain-mNPC-GFPpos-Snip1cko_rep3


title: EORTC_26101_2023_124


title: Boldine 28 days post injury (dpi) above injury site 3

value: Boldine


title: E13-brain-mNPC-GFPpos-Snip1cko_rep2

description: 2145469_E13-brain-mNPC-GFPpos-Snip1cko_rep2


title: mCRC58.P


title: Boldine 28 days post injury (dpi) above injury site 2

value: Male


title: LEC, KO, Rep4

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

data_processing:
RTA version 2.11.3 running under NextSeq Control Software version 4.0.1.41 was used for basecalling.
Reads were aligned to GENCODE mouse genome (GRCm38) using STAR (2.7.7a) with argument “----quantMode TranscriptomeSAM GeneCounts".
Gene-based read counts were performed by STAR as well.
Assembly: GENCODE mouse genome (GRCm38)
Supplementary files format and content: csv file includes Gene counts for each Sample

source_name: Small intestine

extract_protocol:
Extract using Qiagen RNAeasy plus micro kit (Qiagen), Cells sorted into Qiagen RLT lysis buffer, snap frozen on dry ice and isolated using the kit as per manufacturers instructions.
Libraries prepared using NEBNext Single cell/low input RNA library prep kit for illumina (NEB) using 1ng total RNA, and sequenced with NextSeq500 with paired-end 40bp reads.

treatment_protocol: Following tamoxifen-mediated Cre induction (100mg/kg tamoxifen 5 doses every 2 days) in VeciCre x Ahr fl/fl x NuTRAP mice (experimental), or Veci Cre x NuTRAP (control), 2 weeks later mice were injected with 10mg/Kg 6-Formylindolo(3,2-b)carbazole (FICZ) or corn-oil vehicle control intraperitoneally, 3h prior to culling

tag: cell type

value: Small intestine lymphatic endothelial cells

value: VeciCre x AHRflfl x NuTRAP

value: Small intestine

tag: mean age

value: 11 wks

value: Ahr KO

value: FICZ


title: mCRC58.T


title: mCRC56.T


title: Vehicle 28 days post injury (dpi) below injury site 3

value: Spinal cord


title: Vehicle 28 days post injury (dpi) above injury site 2

value: 28 days post injury (dpi)


title: EORTC_26101_2023_121

extract_protocol: Genomic DNA was extracted and pruified from FFPE tissue according with the Maxwell 16 FFPE Plus LEV DNA Kit according to standard instructions

tag: gender

value: female


title: mCRC56.P


title: EORTC_26101_2023_120


title: Vehicle 28 days post injury (dpi) below injury site 2

value: Spinal Cord Injury (SCI)

value: WT


title: LEC, KO, Rep3

tag: strain

value: 8 wks


title: mCRC55.T

value: liver


title: LEC, KO, Rep2


title: LEC, WT, Rep4

value: VeciCre x NuTRAP

value: Ahr WT


title: EORTC_26101_2023_119

value: male


title: mCRC55.P

value: peritumor


title: EORTC_26101_2023_123


title: Boldine 28 days post injury (dpi) above injury site 1

value: Male

value: Boldine

value: no treadmill


title: E13-brain-mNPC-GFPpos-Snip1cko_rep1

description: 2145468_E13-brain-mNPC-GFPpos-Snip1cko_rep1

value: brain


title: Vehicle 28 days post injury (dpi) below injury site 1

value: Vehicle


title: Boldine 28 days post injury (dpi) below injury site 3


title: LEC, WT, Rep3

value: Small intestine lymphatic endothelial cells

value: Small intestine

value: FICZ


title: mCRC53.T

value: tumor


title: mCRC53.P


title: EORTC_26101_2023_117

value: female


title: Boldine 28 days post injury (dpi) below injury site 2

value: Spinal cord

value: 28 days post injury (dpi)

value: Spinal Cord Injury (SCI)

value: WT


title: EORTC_26101_2023_118


title: EORTC_26101_2023_122


title: LEC, WT, Rep1

value: VeciCre x NuTRAP

value: 8 wks

value: Ahr WT


title: mCRC51.T

value: liver


title: Boldine 28 days post injury (dpi) below injury site 1

value: Male

value: Boldine


title: BEC, KO, Rep4

source_name: Small intestine blood endothelial cells

value: Small intestine blood endothelial cells

value: VeciCre x AHRflfl x NuTRAP

value: 11 wks

value: Ahr KO


title: EORTC_26101_2023_116

value: male


title: BEC, KO, Rep3

value: Small intestine

value: FICZ


title: EORTC_26101_2023_115


title: mCRC51.P

value: peritumor


title: mCRC50.T

value: tumor


title: Vehicle 14 days post injury (dpi) above injury site 1

value: Spinal cord

value: 14 days post injury (dpi)

value: Spinal Cord Injury (SCI)

value: Vehicle

value: no treadmill


title: EORTC_26101_2023_114

value: female


title: BEC, KO, Rep2

value: 8 wks


title: Vehicle 14 days post injury (dpi) above injury site 2

value: Male

value: WT


title: Vehicle 14 days post injury (dpi) above injury site 3


title: EORTC_26101_2023_113


title: EORTC_26101_2023_112


title: BEC, WT, Rep3

value: Small intestine blood endothelial cells

value: VeciCre x NuTRAP

value: Ahr WT


title: Boldine 14 days post injury (dpi) above injury site 3

value: Boldine


title: EORTC_26101_2023_111

value: male


title: mCRC50.P

value: liver


title: mCRC49.T


title: BEC, WT, Rep1

value: Small intestine

value: FICZ


title: Boldine 14 days post injury (dpi) above injury site 2

value: Spinal cord


title: EORTC_26101_2023_110


title: mCRC49.P

value: peritumor


title: mCRC48.T

value: tumor


title: Vehicle 14 days post injury (dpi) below injury site 3

value: 14 days post injury (dpi)

value: Spinal Cord Injury (SCI)

value: Vehicle


title: EORTC_26101_2023_109

value: female


title: IMAC_2

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

data_processing:
Single-cell sequencing FASTQ files were processed using the Cell Ranger Single Cell Software Suite (v3.0.2) to perform quality control, sample de-multiplexing, barcode processing, alignment to mm10 genome with STAR (version 2.6.1a), and read counting on Ensembl 93 gene model (https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/3.0).
Default parameters were used for Cell Ranger, except for the STAR parameters outSAMmultNmax set to 1 and alignIntronMax set to 10000.
UMI were counted by extracting read counts from the .h5 files generated by Cell Ranger, using R (v3.6). The UMI matrix was filtered to keep only cells not likely to be empty droplets based on the emptyDrops function of the dropletUtils Bioconductor package (version 1.5.4). Additonal filtering was done using the cells library sizes, the nuumber of detected genes and the percenatge of reds mapping to mitochondrial genes. Eventually we retained a total of 12,182 genes for 943 high-quality cells. The UMI counts matrix for these cells is provided as file UMIsMatrix.txt.gz.
Further quality controls and analyses were performed using the scran (1.12) and scatter (1.12) Bioconductor packages, and following the simpleSingleCell  Bioconductor workflow.
Genome_build: mm10
Supplementary_files_format_and_content: TSV file (tab separated values) with raw UMI counts for ensembl release 93 gene models; columns correspond to: 1. ENSEMBL ID, 2. and remaining columns contain UMI counts for each cell; column headers include the cell barcode sequence and the sample ID separated by a dash (e.g., "AAAAAAAAAAAAAAAT-IMAC_2")

source_name: colon monocytes and macrophages from control (PBS-treated) mouse

growth_protocol: Mice were ordered from Charles River Laboratories (Germany) and kept in the animal facility of the Department of Biomedecine, University of Basel, Switzerland, under SPF conditions.

extract_protocol:
Single cells were extracted from suspensions of lamina propria of each individual mouse replicate.
Cells were sorted by flow cytometry (using a FACSAria III, BD Biosciences) and gated for Cd11b+, and Ly6c2+ or Cd64+ expression.
Sorted cell suspensions from each mouse were loaded into a single well of a 10× Genomics Chromium Single Cell Controller.
Single-cell capture and cDNA and library preparation were performed with a Single Cell 3’ v2 Reagent Kit (10× Genomics) according to manufacturer’s instructions.

treatment_protocol: Mice were orally gavaged 5 days a week for approximately 6 months with either 12ug diesel exhaust particles (DEP) disolved in 200uL PBS, or only PBS as control.

tag: strain background

value: control; PBS

value: monocytes and macrophages


title: IMAC_3


title: IMAC_15

source_name: colon monocytes and macrophages from DEP-treated mouse

value: diesel exhaust particles


title: EORTC_26101_2023_108


title: mCRC48.P


title: Vehicle 14 days post injury (dpi) below injury site 2

value: Male

value: WT

value: no treadmill


title: mCRC46.T


title: BEC, WT, Rep4

value: Small intestine blood endothelial cells

value: VeciCre x NuTRAP

value: 11 wks

value: Ahr WT


title: Vehicle 14 days post injury (dpi) below injury site 1

value: Spinal cord


title: IMAC_14

value: male


title: Boldine 14 days post injury (dpi) below injury site 3

value: Boldine


title: EORTC_26101_2023_106


title: A549_SARS2Inf_UNC0638_C_S12

description:
RNA-seq of A549 cells infected or not with SARS-CoV2 and with or without the H3K9 methyl transferases inhibitor UNC0638
A549_SARS-CoV2Inf_UNC0638vsDMSO_gene_exp.diff

data_processing:
bcl2fastq (version 2.20.0) was used to convert bcl sequencing files to fastq files demultiplexing by primer index
cutadapt (version 2.4 with Python 3.7.2) was used to demultiplex ribosome footprinting data and remove adapter sequences
STAR (version 2.7.2b) was used to aligned RNA-Seq and ChIP-Seq data to the human genome. tophat (version 2.1.1) was used to align ribosome footprinting data to the human transcriptome
cuffdiff (cufflinks version 2.2.1) was used to quantify and compare RNA abundance for RNA-Seq and ribosome footprinting data. bedtools (version 2.29.2)  was used to calculate coverage of aligned ChIP-Seq reads
Assembly: hg38

extract_protocol: RNA from transfected cells was isolated using the Direct-zol RNA Miniprep Kit (Zymo Research, Cat# R2050) according to the manufacturer’s instructions.

tag: cell line

value: epithelial

value: UNC0638, SARS-CoV2 infection


title: mCRC43.T

value: liver

value: tumor


title: A549_SARS2Inf_UNC0638_A_S10


title: Boldine 14 days post injury (dpi) below injury site 2

value: 14 days post injury (dpi)

value: Spinal Cord Injury (SCI)


title: A549_SARS2Inf_UNC0638_B_S11


title: Boldine 14 days post injury (dpi) above injury site 1


title: Boldine 14 days post injury (dpi) below injury site 1


title: EORTC_26101_2023_105

value: female


title: mCRC38.T


title: EORTC_26101_2023_103


title: A549_SARS2Inf_DMSO_C_S9

value: DMSO, SARS-CoV2 infection


title: mCRC42.P

value: peritumor


title: EORTC_26101_2023_104


title: mCRC34.T


title: COVID_M3

data_processing:
Single-end run (SE50) run was performed using a MiSeq or a NextSeq500.
Most steps of this pipeline were performed using the Galaxy platform.
MirDeep2 2.0.0. was used for identification and quantification of microRNAs between samples.
Assembly: hg38
Supplementary files format and content: raw microRNA counts in txt.format

source_name: lung

extract_protocol:
Total RNA was prepared with Trizol reagent according to manufacturer's instructions.
Libraries were generated using GenXPro TrueQuant SmallRNA Seq Kit for Ultra Low Input or using NEBNext® Small RNA Library Prep Set for Illumina according to manufacturer's instructions.

value: lung

value: total lung


title: COVID_M4


title: COVID_M5


title: A549_SARS2Inf_DMSO_B_S8

value: WT


title: A549_SARS2Inf_DMSO_A_S7


title: EORTC_26101_2023_107


title: mCRC34.P


title: EORTC_26101_2023_101


title: mCRC46.P


title: Control4_H


title: A549_NoInf_UNC0638_C_S6

description:
RNA-seq of A549 cells infected or not with SARS-CoV2 and with or without the H3K9 methyl transferases inhibitor UNC0638
A549_UNC0638vsDMSO_gene_exp.diff


title: mCRC32.T


title: A549_NoInf_UNC0638_B_S5


title: EORTC_26101_2023_099


title: mCRC43.P


title: Control2_H


title: mCRC30.T


title: EORTC_26101_2023_098


title: mCRC32.P


title: Control1_H


title: A549_NoInf_UNC0638_A_S4


title: ProDel3_c

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

data_processing:
Illumina Casava v1.8.2 software used for base-calling
All RNA-seq FastQ reads were aligned with the reference genome (danRer11) using TopHat2 default settings. The aligned BAM files sorted (SAMTools) and then processed using HTSeq-count to obtain the counts per gene
gene count measurements were obtained using HTSeq-count
Assembly: danRer11
Supplementary files format and content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count.

organism: Danio rerio

source_name: rhabdomyosarcoma tumors in zebrafish

growth_protocol: For expression of mutant human TP53 experiments, tumors were generated by injecting XhoI linearized rag2-kRASG12D and rag2-GFP along with Xmn1 linearized rag2-TP53-P153△, (35 ng/ml of rag2-kRASG12D, 15 ng/ml rag2-GFP or mutant TP53 and 10 ng/ml of rag2-GFP) into the one cell stage of syngeneic zebrafish CG1/tp53-/- embryos <1 hour post-fertilization (Ignatius et al., 2012). Animals were monitored for tumor onset beginning at 10 days post-fertilization by scoring for GFP fluorescence under an Olympus MVX10 stereomicroscope with an X-Cite series 120Q fluorescence illuminator. Scoring for tumor initiation was conducted for 60 days. 3 tumors each expressing kRASG12D/GFP/tp53-/-  or kRASG12D/GFP/tp53-/- +TP53-P153△ were transplanted into secondary CG1 recipients and engrafted tumors were isolated, prepared as single cell suspensions and sorted by flowcytometry. Tumor cells were then processed to isolate RNA which was then submitted for RNAseq analyses (Ignatius et al., 2012).

extract_protocol:
After tissue grinding and homogenization in RNA lysis buffer, total RNA was isolated from harvested tumors using the RNAeasy Kit (Qiagen; Valencia, CA) according to the manufacturer’s recommendation. After quantification with Nanodrop (Thermo Scientific; Rockford, IL), RNA was stored at -80ºC.
Total RNA was used for RNA-Seq library preparation by following the KAPA Stranded RNA-Seq Kit

value: zebrafish


title: EORTC_26101_2023_097


title: EORTC_26101_2023_102


title: A549_NoInf_DMSO_B_S2

value: DMSO


title: mCRC30.P


title: mCRC28.T


title: A549_NoInf_DMSO_C_S3


title: EORTC_26101_2023_095


title: A549_NoInf_DMSO_A_S1


title: EORTC_26101_2023_094


title: EORTC_26101_2023_096


title: ProDel2_b


title: p53LOF3_C

value: trunk tumor


title: ProDel1_a


title: mCRC27.P


title: EORTC_26101_2023_100

value: male


title: A549_nsp1_wt_UN_S2pol2_B

description: CHIP-seq of A549 cells expressing WT and mutant NSP1 and with or without the H3K9 methyl transferases inhibitor UNC0638

value: UNC0638, FH-NSP1 expression


title: p53LOF2_B

value: head tumor


title: A549_nsp1_wt_UN_S2pol2_A

value: epithelial


title: EORTC_26101_2023_093


title: EORTC_26101_2023_092


title: p53LOF1_A


title: A549_nsp1_wt_UN_H3K9me3_B


title: EORTC_26101_2023_091


title: mCRC21.P

value: liver


title: A549_nsp1_wt_UN_H3K9me3_A


title: EORTC_26101_2023_090


title: mCRC28.P


title: GSC456 treated, STAT5  CUT&Tag

city: Wuhan

first: Wei

last: Wang

state: Hubei

address: 13 Hangkong Road

institute: Huazhong University of Science and Technology Tongji Medical College

data_processing:
The paired-end reads from the sequencing data were trimmed and quality controlled using Fastp (v0.20.1) with default parameters.
The clean reads were aligned to the human reference genome (GRCh38) using bowtie2 (v2.3.5.1). The reads were also aligned to the E. coli genome for spike-in normalization.
BAM files were deduplicated using the MarkDuplicates function in picard (v2.18.29).
BigWig files were generated by the bamCoverage function in deepTools (v3.5.1) with CPM normalization.
Assembly: human reference genome (GRCh38)
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

growth_protocol: GSCs were cultured in DMEM/F12 media supplemented with B27, 20 ng/ml EGF, and 20 ng/ml basic fibroblast growth factor. Cells were incubated at 37 °C in a humidified 5% (v:v) CO2 incubator.

extract_protocol:
CUT&Tag was performed with Hyperactive® Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD903) according to the provided instructions.
ConA beads (concanavalin A-conjugated paramagnetic beads) were added to the cell pellet, and the mixed complexes were incubated overnight at 4°C with 5 µl of STAT5 (Cell Signaling Technology, #94205) or control Rabbit IgG (1 µg) antibodies. The cells were then incubated with a secondary antibody and subsequently linked by pA/G-Tnp. The complexes were sheared and the DNA were extracted. Sequencing libraries were constructed after 15 cycles of PCR amplification. The DNAs were purified using the VAHTS DNA Clean Beads and sequenced on the Novaseq PE150 platform.

value: GBM stem cell

value: erlotinib (1 µM, 12 hours)


title: GSC456 untreated, STAT5  CUT&Tag

value: untreated


title: A549_nsp1_wt_UN_H3K9me2_B


title: mCRC16.T

value: tumor


title: GSC456 untreated, IgG CUT&Tag


title: A549_nsp1_wt_UN_H3K9me2_A


title: mCRC16.P


title: EORTC_26101_2023_089

last: Kessler

address: Im Neuenheimer Feld 280

institute: DKFZ

value: female


title: mCRC10.T


title: EORTC_26101_2023_087


title: H9, MSL3KD RNA-seq Rep4

first: Pradeepa

middle: M

last: Madapura

state: UK

address: 4 Newark Street, Whitechapel

institute: Queen Mary University of London

data_processing:
The reads were processed and mapped using Lexogen Bluebee pipeline. The mapped data obtained as bam files were further used for extracting uniquely mapped reads and subjected to merging, sorting and indexing. The sorted bam files were converted to bigwigs via deepTools (version 3.5.1) bamCoverage tool with --skipNAs  ?normalizeUsing  RPKM --smoothLength 60  --centerReads options. Noramlised signal for Control (Scr) over MSL3KD was generated using bigwigCompare tool with options --skipZeroOverZero --binSize 20 with default noramlisation (log2 ratio).
Assembly: hg38
Supplementary files format and content: bigwig containing signal for RNAseq
H9_CT_merge_old_new.bw comprises data for H9, Scr RNA-seq Rep1-Rep4
H9_MSL3_sh1_merge_old_new.bw comprises data for H9, MSL3KD RNA-seq Rep1-Rep4
H9_CT_logFC_MSL3_merge_unq.bw contains the normalised signal as log2-ratio of H9_CT_merge_old_new.bw over H9_MSL3_sh1_merge_old_new.bw

growth_protocol: H9 hPSC (Control and MSL3 KD) lines were grown on geltrex coated plates (ThermoFisher Scientific, A1413302) in mTeSR™ Plus medium (StemCell Technologies, #100-0276) supplemented with 100 U/ml penicillin-streptomycin (Gibco, 15140122) and passaged every 3-4 days with ReLeSR™ (StemCell Technologies, 100-0484) according to manufacturer’s protocols. All the cell lines were tested for Mycoplasma contamination using EZ-PCR Kit (Geneflow, K1-0210).

extract_protocol:
RNA was isolated from RNeasy Plus Mini Kit (Qiagen, Cat. No. / ID: 74134 ), we spiked in equal amounts of The External RNA Controls Consortium (ERCC) Spike-in RNA Variant Control Sets (SIRV set 3, Lexogen) and 500 ng of RNA was used for depletion of rRNA using RiboCOP kit (Lexogen).
RNAseq library preparation using CORALL Total RNA-Seq Library Prep Kit (Lexogen). Libraries were sequenced as 150 bp paired-end reads using Novaseq 6000.

value: Human embryonic

value: expressing MSL3 knockdown (KD, two independent shRNAs)


title: H9, MSL3KD RNA-seq Rep3


title: A549_nsp1_wt_DMSO_pol2_A

last: Hafner

address: 50 South Drive

institute: NIH

value: DMSO, FH-NSP1 expression


title: A549_nsp1_wt_DMSO_pol2_B

value: WT


title: EORTC_26101_2023_088

first: Tobias


title: mCRC10.P

value: peritumor


title: EORTC_26101_2023_086


title: A549_nsp1_wt_DMSO_H3K9me3_B


title: mCRC24.T


title: mCRC08.T


title: H9, Scr RNA-seq Rep4

value: expressing non-targeting shRNA (control/Scr.)


title: A549_nsp1_wt_DMSO_H3K9me3_A


title: EORTC_26101_2023_085


title: mCRC24.P


title: H9, Scr RNA-seq Rep3


title: mCRC08.P


title: shIMP3_NT_2

city: Hershey

first: Irina

last: Elcheva

state: Pennsylvania

address: 500 University Drive, C7743

department: Pediatrics

institute: Penn State College of Medicine

description: NovaSeq_SP (100 cycles - SE 1x100, PE 2x50 ) (per flow cell)

data_processing:
Reads were mapped to hg38 genome assembly using STAR aligner version 2.7.3.
Unique reads were extracted with  samtools version 1.10.0 using "-q 255" flag.
Read counts were computed with featureCounts function in Rsubread package version 2.4.3 in R 4.0.3.
FPKM values were computed with cufflinks version 2.2.1 with gencode v38 annotation for hg38 genome assembly.
Assembly: hg38
Supplementary files format and content: tab-delimited text file including raw read counts
Supplementary files format and content: tab-delimited text file including FPKM values

source_name: human embryonic kidney (HEK)

growth_protocol: HEK293T cells growth was maintained on DMEM (high glucose) and 10% FBS. Cells were passaged (subcultured) 1:10 for maintanance, and 1:3 for IFN-beta treatments

extract_protocol:
Qiagen RNeasy mini kit, Qiagen DNAseI treatment on the column, and Invitorgen (Ambion) TURBO DNAseI treatment after total RNA isolation;
Illumina Stranded mRNA Prep, Ligation kit

treatment_protocol: hrIFN -beta was added to growth media to a final concentration 10ng/mL for 12 hours at 37C, 5% CO2 incubation

value: human embryonic kidney (HEK)

value: SV40 T large antigen transformed (T)

value: IMP3 knockdown

value: PBS


title: A549_nsp1_wt_DMSO_H3K9me2_B

first: Markus

value: epithelial


title: EORTC_26101_2023_084


title: mCRC07.P

value: liver


title: shIMP3_NT_1


title: A549_nsp1_wt_DMSO_H3K9me2_A


title: EORTC_26101_2023_083


title: shIMP3_INFbeta_2

value: INFbeta


title: EORTC_26101_2023_082

value: male


title: shIMP3_INFbeta_1


title: A549_nsp1_mut_UN_pol2_A

value: UNC0638, FH-NSP1 K164A/H165A expression


title: mCRC03.T

value: tumor


title: mCRC04.P


title: EORTC_26101_2023_081

value: female


title: mCRC05.P


title: EORTC_26101_2023_079


title: EORTC_26101_2023_080


title: A549_nsp1_mut_UN_H3K9me3_B


title: shIMP2_NT_1

value: IMP2 knockdown


title: mCRC03.P


title: EORTC_26101_2023_078


title: A549_nsp1_mut_UN_H3K9me2_B


title: A549_nsp1_mut_UN_H3K9me3_A


title: mCRC02.P


title: shIMP2_INFbeta_1


title: shIMP2_INFbeta_2


title: A549_nsp1_mut_UN_H3K9me2_A


title: EORTC_26101_2023_077


title: mCRC05.T


title: A549_nsp1_mut_UN_pol2_B


title: A549_nsp1_mut_DMSO_pol2_B

value: DMSO, FH-NSP1 K164A/H165A expression


title: shIMP1_NT_2

value: IMP1 knockdown


title: shIMP2_NT_2


title: EORTC_26101_2023_076


title: EORTC_26101_2023_075


title: A549_nsp1_mut_DMSO_pol2_A

value: WT


title: shIMP1_NT_1


title: shIMP1_INFbeta_2


title: EORTC_26101_2023_074


title: A549_nsp1_mut_DMSO_H3K9me3_B


title: shIMP1_INFbeta_1


title: shCntrl_NT_2

value: WT/non tareting shRNA control


title: A549_nsp1_mut_DMSO_H3K9me3_A


title: EORTC_26101_2023_072


title: shCntrl_NT_1


title: A549_nsp1_mut_DMSO_H3K9me2_B


title: A549_nsp1_mut_DMSO_H3K9me2_A


title: EORTC_26101_2023_071


title: Drosophila_F0-Poor_F1-Rich_F2-Poor_3

city: Aarhus C

first: Mads

middle: Fristrup

last: Schou

address: Nu Munkegade 114

department: Biology

country: Denmark

institute: Aarhus University

description:
Field collected lab stock
Gene expression data from Drosophila developed at poor or rich medium

hyb_protocol: Fifteen micrograms of cDNA were fragmented and loaded onto the Affymetrix probe array cartridge. Incubation, washing and staining procedures were performed in the Affymetrix Fluidics Station 450.

scan_protocol: The probe arrays were scanned at 560 nm using a confocal laser-scanning microscope (Affymetrix Scanner 3000 7G)

data_processing: The raw data was GC-RMA normalized and further analysed using several different approaches in R

label: biotin

organism: Drosophila melanogaster

label_protocol: The step was performed as described in Dyrskjot et al (2003) doi:10.1038/ng1061

growth_protocol: Flies developed on poor or rich food  in F0, F1 or F2

treatment_protocol: Frozen directly

tag: group


title: shCntrl_INFbeta_2


title: EORTC_26101_2023_070


title: shCntrl_INFbeta_1


title: Neut_861

first: Stefan

last: Engelhardt

address: Biedersteiner Str. 29

institute: Technical University Munich

description: cell lysate

data_processing:
Single-end run (SE50) run was performed using a HiSeq2500, MiSeq or a NextSeq 500.
Most steps of this pipeline were performed using the Galaxy platform.
MirDeep2 2.0.0. was used for identification and quantification of microRNAs between samples.
Assembly: mm10
Supplementary files format and content: raw microRNA counts in txt.format

extract_protocol:
Total RNA was prepared with Trizol reagent according to manufacturer's instructions or the cell lysate was used.
Libraries were generated using GenXPro TrueQuant SmallRNA Seq Kit for Ultra Low Input or using NEBNext® Small RNA Library Prep Set for Illumina according to manufacturer's instructions.

value: lung

value: Neutrophils

value: no treatment


title: Drosophila_F0-Poor_F1-Rich_F2-Poor_1

extract_protocol: The step was performed as described in Dyrskjot et al (2003) doi:10.1038/ng1061


title: EORTC_26101_2023_069


title: Drosophila_F0-Poor_F1-Rich_F2-Rich_3


title: Drosophila_F0-Poor_F1-Rich_F2-Rich_2


title: EpC_3

description: cell lysate

value: Epithelial cells


title: EpC_2

description: cell lysate


title: EORTC_26101_2023_073


title: Drosophila_F0-Poor_F1-Rich_F2-Poor_2


title: EORTC_26101_2023_068


title: EpC_1

description: cell lysate


title: Drosophila_F0-Poor_F1-Rich_F2-Rich_1


title: LUAD_08_NT

city: Kaohsiung City

first: Ying-Ming

last: Tsai

address: No.100, Shih-Chuan 1st Road, Sanmin Dist.

country: Taiwan

institute: Kaohsiung Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
The criteria for differentially expressed:mRNA by NGS analysis were fold change > 2 and fragments per kilobase million (FPKM) > 0.3.
Assembly: hg38
Supplementary files format and content: CSV files include normalized abundance measurements for each Sample

source_name: Lung organoid

extract_protocol:
The lung organoid specimens were extracted, rapidly frozen, and their RNA was collected using Trizol reagent. Subsequently, the Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was employed with 1 µg of total RNA to create sequencing libraries. Lastly, the RNA libraries were readied for sequencing following standard Illumina procedures.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: disease

value: Lung adenocarcinoma

value: Lung organoid

tag: type

value: Normal

tag: age

value: M

tag: Stage


title: EORTC_26101_2023_067


title: LUAD_07_PT

value: Tumor


title: Drosophila_F0-Poor_F1-Poor_3

tag: Sex

value: male


title: LT_D8_3

value: Bleomycin


title: EORTC_26101_2023_066

value: female


title: LUAD_07_NT


title: EORTC_26101_2023_065


title: Drosophila_F0-Poor_F1-Poor_2


title: LUAD_06_PT_Peripheral


title: Drosophila_F0-Poor_F1-Rich_3


title: LUAD_08_PT


title: EORTC_26101_2023_064


title: LUAD_06_NT


title: LT_D8_1


title: Drosophila_F0-Poor_F1-Poor_1


title: EORTC_26101_2023_063


title: CAL33 JQ1 24h

city: Boston

first: Srinivas Vinod

last: Saladi

state: Massachusetts

address: 20 Staniford St

institute: Harvard Medical School

data_processing:
Paired-end fastq files were trimmed of adapter sequence using NGMerge
mapped to the GRCh38 genome assembly using Bowtie2.3.4.3,using the following flags: --very-sensitive and -k20
For normalized bigwig pileup diagrams, aligned reads were normalized to CPM using the bamCoverage tool in deepTools with a binSize of 10
Differential peaks were identified using csaw v1.7.1, first by filtering for a log2 fold change of >2 using windows of 2000bp, and computing differential peaks using edgeR v3.32.1
Peaks were annotated by known genes within 3000 bp upstream of the TSS and 1000 bp downstream of the TES.
Assembly: Human GRCh38 genome assembly
Supplementary files format and content: bigWig

source_name: Squamous cell carcinoma of the oral tongue

growth_protocol: CAL33 was maintained in RPMI 1640 with 10% fetal bovine serum (FBS) and 100 units/ml antibiotic antimycotic solution at 37 °C in the presence of 5% CO2

extract_protocol:
The ATAC (Assay for Transposase-Accessible Chromatin) method was applied based on the published protocol (Buenrostro et al., 2013). CAL33 cells were plated at 5 x 10^6 cells into 10 cm plates, and treated the next day with DMSO or 1µM JQ1. Then the cells were trypsinized at 6 h and 24 h. After all samples were harvested, 50000 cells /sample were resuspended in 1 mL of cold PBS. Cells were centrifuged at 500g for 5 min in a pre-chilled (4ºC) fixed-angle centrifuge. After centrifugation, the supernatant was carefully completely aspirated. Cell pellets were then resuspended in 50 μL of ATAC-seq RSB containing 10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin by pipetting up and down three times. This cell lysis reaction was incubated on ice for 3 min. After lysis, 1 mL of ATAC-seq RSB containing 0.1% Tween-20 (without NP40 or digitonin) was added, and the tubes were inverted to mix. Nuclei were then centrifuged for 5 min at 500g in a pre-chilled (4ºC) fixed-angle centrifuge. The supernatant was removed and nuclei were resuspended in 50 μL of transposition reaction: 2.5 μL Tagment DNA Enzyme 1 (TDE1) (Cat#15027865, Illumina), Tagment DNA Buffer (Cat#15027866, Illumina), 16.5 μL PBS, 0.5 μL 1% digitonin, 0.5 μL 10% Tween-20, and 5 μL water by pipetting up and down five times. Transposition reactions were incubated at 37ºC for 30 min in a thermomixer with shaking at 1,000 r.p.m. Reactions were cleaned up with DNA Clean & Concentrator-5 Kit (Cat#D4013, Zymo research). Quality control of tagmented DNA was performed by TapeStation.
Libraries were amplified by PCR method based on the published protocol (Buenrostro et al., 2013). By using qPCR based methods to quantify ATAC-seq libraries. Quantifying libraries using the KAPA Library Quant Kit for Illumina Sequencing.

treatment_protocol: CAL33 was treated by DMSO or JQ1 (1µM)(Sigma-Aldrich) for 6 hrs and 24 hrs.

value: tongue squamous cell carcinoma

value: FAT1 mutant


title: CAL33 DMSO 24h

value: Squamous cell carcinoma of the oral tongue

value: DMSO


title: Drosophila_F0-Poor_3


title: LUAD_05_NT

value: F


title: EORTC_26101_2023_062

city: Heidelberg


title: EORTC_26101_2023_061


title: LUAD_04_PT


title: CAL33 JQ1 6h


title: CAL33 DMSO 6h


title: Drosophila_F0-Poor_2


title: EORTC_26101_2023_060


title: LT_D8_2

value: lung

value: WT


title: Drosophila_F0-Poor_1


title: Drosophila_F0-Poor_F1-Rich_2


title: LUAD_04_NT


title: Drosophila_F0-Poor_F1-Rich_1


title: EORTC_26101_2023_059