title: AT2_4_L

first: Kyungtae

last: Lim

email: kl492@cam.ac.uk, ktlim492@korea.ac.kr

address: Tennis Court Road

department: Gurdon Institute

description:
AT2_16402_L
AT2_merged.gene_counts_length_scaled.tsv

data_processing:
Raw RNA sequencing data was run by a bioinformatics pipeline, nf-core/rnaseq
According to the nf-core/rnaseq pipleline: Merge re-sequenced FastQ files (cat); Sub-sample FastQ files and auto-infer strandedness (fq, Salmon); Read QC (FastQC); UMI extraction (UMI-tools); Adapter and quality trimming (Trim Galore); Removal of genome contaminants (BBSplit); Removal of ribosomal RNA (SortMeRNA); Alignment and quantification; Sort and index alignments (SAMtools); UMI-based deduplication (UMI-tools); Duplicate read marking (picard MarkDuplicates); Transcript assembly and quantification (StringTie); Create bigWig coverage files (BEDTools, bedGraphToBigWig); Extensive quality control; Pseudo-alignment and quantification (Salmon); Present QC for raw read, alignment, gene biotype, sample similarity, and strand-specificity checks (MultiQC, R)
A comparison between the RNA sequencing data of AT2 organoids and publicly available data of fetal organoid types and other alveolar cell types was performed: fetal early tip progenitor organoids GSM5393370 and GSM5393371; fetal late tip progenitor organoids6 GSM5393372 and GSM5393373; PSC-iAT2s7 GSM5578511, GSM5578512 and GSM5578513; cultured adult AT2 cells7 GSM5578508, GSM5578509 and GSM5578510; freshly isolated adult AT2 cells8 GSM2537127, GSM2537128 and GSM2537129
A list of differentially expressed genes was extracted using the counted reads and R package edgeR10 version 3.40.2.
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: Expression matrix in tsv format.
Supplementary files format and content: Genes are represented in NCBI official gene symbols.

source_name: Fetal lung

growth_protocol: Cultured in alveolar type 2 differentiation medium (AT2 medium): Advanced DMEM/F12 supplemented with 1x GlutaMax, 1 mM HEPES and Penicillin/Streptomycin, 1X B27 supplement (without Vitamin A), 1X N2 supplement, 1.25 mM N-acetylcysteine, 50 nM Dexamethasone, 0.1 mM 8-Bromoadenosine 3’5’-cyclic monophosphate (cAMP), 0.1 mM 3-Isobutyl-1-methylxanthine (IBMX), 50 μM DAPT, 100 ng/ml recombinant human FGF7, 3 μM CHIR99021, 10 μM A83-01, and 10 μM Y-27632. Medium was replaced every 2 days and cultures maintained for 2 weeks until the initial AT2 organoid colonies formed in the matrigel droplet. Organoids were typically passaged at a 1 to 3 ratio weekly by gently breaking into small fragments.

extract_protocol:
RNA libraries of four biological lines of AT2 organoids at early (P1,4,6,7) and late (P12,13,16,17) passage were generated using an RNeasy kit (Qiagen, 74004) including the optional DNAse digestion step.
The quality of the RNA libraries was validated on Agilent 2200 Tapestation before sequencing on an Illumina NovaSeq 6000 at Novogene (novogene.com). RNA libraries were prepared for sequencing using standard Illumina protocols

value: Fetal lung

value: AT2 organoid

value: 20 post-conception week

value: Passage 13

value: AT2 medium


title: TgSPI1Fanca.ko  leukemic_39

status: Public on Aug 31 2023

type: SRA

city: VILLEJUIF

first: Christel

last: GUILLOUF

address: 114 rue Edouard vaillant

country: France

institute: Gustave Roussy

library_source: transcriptomic

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.17.1.14.
Sequence reads were mapped onto mm10/GRCm38 assembly of mouse genome using STAR v2.5.3a [1].
Gene expression was quantified using htseq-count v0.6.1p1 [2] with gene annotations from Ensembl release 98.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw count (htseq-count) for each Sample

molecule: polyA RNA

organism: Mus musculus

source_name: leukemic erythroid blasts

growth_protocol: cells were maintained in culture with EPO, diluted two days before RNA extraction

extract_protocol:
RNA was extracted using Qiagen Reasy Mini kit
Protocol1: RNA-Seq libraries were generated from 300 ng of total RNA using TruSeq Stranded mRNA Library Prep Kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.
Protocol2:  RNA-Seq libraries were generated from 400 ng of total RNA using TruSeq Stranded mRNA Library Prep Kit and IDT for Illumina - TruSeq RNA UD Indexes (96 Indexes, 96 Samples) (Illumina, San Diego, USA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 8 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using SPRI select beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

tag: genotype

tag: strain

tag: cell type

value: leukemic

tag: library protocol

value: Protocol 2


title: WT, biol rep 4

city: Pittsburgh

first: Rick

last: van der Geest

state: PA

address: 3459 Fifth Avenue

country: USA

institute: University of Pittsburgh

data_processing:
CLC Genomics Workbench (Qiagen)
Sequence reads were trimmed for adapter sequences and low quality sequences (limit = 0.01)
Trimmed sequences were mapped to GRCm38/mm10 v86 (mismatch cost: 2; insertion cost: 3; deletion cost: 3; length fraction: 0.8; similarity fraction 0.8)
Read count extraction was performed using CLC genomics workbench
Assembly: GRCm38/mm10 v86
Supplementary files format and content: tab-delimited excel file lists raw counts for each sample

molecule: total RNA

source_name: primary cells

growth_protocol: Alveolar macrophages were maintained in DMEM supplemented with 10% newborn calf serum, 100 units/mL penicillin and 100 ug/mL streptomycin in a cell culture incubator with 5% CO2 at 37C

extract_protocol:
RNA was isolated using RNeasy Plus Micro Kit (Qiagen)
Library preparation was performed using TruSeq Stranded mRNA Library Prep kit (Illumina) according to manufacturer instruction

treatment_protocol: M1-like macrophage polarization was induced by treating the cells with IFNg (10 ng/mL) for 4 hours, followed by stimulation with 20% K. pneumoniae supernatant for 6 hours

tag: cell line

value: primary cells

value: alveolar macrophages

value: WT

tag: treatment

value: IFNg + K. pneumoniae supernatant


title: Mo_BSA_rep3

city: Paris

first: Frederic

last: Blond

address: 17 rue Moreau

institute: Institut de la Vision

data_processing:
Raw reads were filtered with Trimmomatic to obatin Pass-filtered reads
Pass-filtered reads were mapped using HiSAT2 and aligned to human reference genome GRCh38.95
The count table of the gene features was obtained using HTSeq
Normalization and differential expression analysis values were computed with DESeq2
TPM were determined using Libinorm using htseq mode
Assembly: GRCh38
Supplementary files format and content: Tab-separated file including raw counts for all Samples
Supplementary files format and content: Tab-separated file containing all Samples metadata

organism: Homo sapiens

source_name: monocytes

extract_protocol:
Total RNA were extracted from hiMGCs and pMGCs using the Nucleospin RNA II kit (Macherey-Nagel) according to the manufacturer’s protocol, RNA quality and quantity were evaluated using BioAnalyzer 2100 (Agilent Technologies,) with the RNA 6000 Nano Kit (Agilent Technologies)
RNA sequencing libraries were constructed from 1 μg of total RNA using a modified TruSeq RNA Sample preparation kit protocol

tag: tissue

value: monocytes

value: healthy donor

value: 0,88% w/v of BSA in DMEM


title: TgSPI1Fanca.ko  leukemic_28


title: AT2_4_E

city: Cambridge

country: United Kingdom

institute: University of Cambridge

description:
AT2_16402_E
AT2_merged.gene_counts_length_scaled.tsv

value: Passage 4


title: TgSPI1Fanca.wt  preleukemic_138

source_name: preleukemic erythroid blasts

value: preleukemic


title: TgSPI1Fanca.ko preleukemic_77


title: Saccharomyces cerevisiae, mVCs, rep3

city: Tainan City

first: Hao-Jen

last: Huang

address: No. 1., University Road

country: Taiwan

institute: National Cheng Kung University

data_processing:
Reads were trimmed by Trimmomatic v3.6
Trimmed reads were mapped to reference genome by hisat2
Gene expression was calculated by stringtie
Assembly: Saccharomyces_cerevisiae.R64-1-1.109.gff3
Supplementary files format and content: tab-delimited text files include FPKM value for each sample

organism: Saccharomyces cerevisiae

source_name: whole cell

extract_protocol:
Total RNA from yeast cells was extracted using the RNeasy Plant Mini kit (Qiagen, Hilden, Germany) and treated with DNase I (Roche, Basel, Switzerland). The RNeasy MInElute Cleanup kit (Qiagen, Hilden, Germany) was used to purify RNA samples
RNA libraries were prepared in Illunima NovaSeq platform following manufacturer's protocols

treatment_protocol: We first sought to determine whether mVCs released by P. ureafaciens have the potential to inhibit growth of phytopathogenic fungi. Then, to assess how fungi respond to mVCs and how toxicity occurs, we performed bioassays on the S. cervisiae fungal model.

value: whole cell


title: 12-week HP Grin2b +/- Bulk RNA-seq Sample2

first: Ally

last: Nicolella

state: MA

address: 75 Ames St

department: Stanley Center for Psychiatric Research

institute: Broad Institute

data_processing:
Reads were aligned to RefSeq M25/GRCm38.p6 and gene and isoform level expression values were estimated using RSEM v1.3.0
Assembly: RefSeq M25
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Hippocampus

extract_protocol:
Brain dissection was performed in the cryostat using frozen brain tissues collected from Grin2a and Grin2b mutant mice. RNA was prepared from microdissected tissues using RNeasy Mini Kit (Qiagen). 200 ng of isolated total RNA from each sample was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using an Illumina TruSeq Stranded mRNA Kit (Illumina) following the manufacturer’s instructions.
rna

value: Hippocampus

value: Grin2b +/-

tag: age


title: WT, biol rep 2


title: AT2_3_L

description:
AT2_16392_L
AT2_merged.gene_counts_length_scaled.tsv

value: Fetal lung

value: AT2 organoid

value: 17 post-conception week

value: Passage 12


title: TgSPI1Fanca.ko preleukemic_40

value: Protocol 2


title: TgSPI1Fanca.ko preleukemic_224


title: AT2_3_E

description:
AT2_16392_E
AT2_merged.gene_counts_length_scaled.tsv

value: Passage 1

value: AT2 medium


title: 12-week HP Grin2b +/- Bulk RNA-seq Sample1


title: 4-week HP Grin2b WT Bulk RNA-seq Sample3

value: WT


title: TgSPI1Fanca.wt  preleukemic_445


title: sd_zt20_7

city: Seville

first: Francisco

middle: José

last: Romero-Campero

address: Americo Vespucio 49

department: Institute for Plant Biochemistry and Photosynthesis

country: Spain

institute: University of Sevilla

data_processing:
Quality control  was performed using the software packges FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Read mapping to the reference genome was performed using HISAT2 (http://daehwankimlab.github.io/hisat2/)
Transcript assembly was performed using Stringtie (http://ccb.jhu.edu/software/stringtie/)
Gene expression level measured in FPKM (fragments per kilobase of exon and million of mapped reads) was perfomed using Stringtie (http://ccb.jhu.edu/software/stringtie/)
Subsequent data analysis and visualization was performed using the R bioconductor package ballgown (https://www.bioconductor.org/packages/release/bioc/html/ballgown.html)
Genome_build: ostta4221 v3 available from https://mycocosm.jgi.doe.gov/Ostta4221_3/Ostta4221_3.home.html
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

organism: Ostreococcus tauri

source_name: liquid culture

growth_protocol: Ostreococcus tauri was grown in column photochemostats under long day, short day, continous light and continous darkness conditions.

extract_protocol:
Total RNA was extracted using E.Z.N.A.® Plant RNA Kit (Omega, R6827-01)
Libraries were prepared using 1 μg of total RNA with the VAHTSTM Total RNA-seq (H/M/R) Library Prep Kit for Illumina® (Vazyme, NR603) according to the manufacturer’s instructions.

treatment_protocol: Long day (16 hours light : 8 hours dark), short day (8 hours light : 16 hours dark), continous light, continous darkness.

tag: time point

tag: photoperiod

value: Continous darkness after short day


title: 4-week HP Grin2b WT Bulk RNA-seq Sample5


title: Saccharomyces cerevisiae, control, rep2


title: 4-week HP Grin2b WT Bulk RNA-seq Sample1


title: AT2_1_L

description:
AT2_15934_L
AT2_merged.gene_counts_length_scaled.tsv

value: Passage 16


title: TgSPI1Fanca.wt  preleukemic_451


title: Saccharomyces cerevisiae, control, rep1


title: AT2_1_E

description:
AT2_15934_E
AT2_merged.gene_counts_length_scaled.tsv

value: Passage 7


title: 4-week HP Grin2b +/- Bulk RNA-seq Sample4


title: 4-week HP Grin2b +/- Bulk RNA-seq Sample3


title: sd_zt16_6


title: 4-week HP Grin2b WT Bulk RNA-seq Sample4


title: Saccharomyces cerevisiae, mVCs, rep2


title: 34p RNA-Seq

city: Balice

first: Ewelina

last: Semik-Gurgul

address: Krakowska 1

department: Department of Animal Molecular Biology

country: Poland

institute: National Research Institute of Animal Production

data_processing:
Raw sequencing reads were first subjected to quality control using FastQC software (Babraham Bioinformatics, UK)
Low quality reads (phred-trimming set to 20, quality set to 20 and a minimum read length of 20 was required to pass the filter) and fragments containing adapter sequences were filtered with the use of FlexBar software (Dodt et al., 2012)
The mapping procedure was utilized using Tophat2 software (Trapnell et al., 2009), followed by counting of the reads to the gtf annotation file of Equus Caballus 3.0 assemble release v. 97 with the use of htseq-count software (Anders et al., 2015).
The differential expression analysis was performed with the use of Deseq2 software with the log transformation method (Love et al., 2014)
Genome_build: EquCab3.0
Supplementary_files_format_and_content: Files containing gene counts for every gene and every sample created with htseq-count software

organism: Equus caballus

source_name: lung

extract_protocol:
DNA was isolated from tissue using a PureLink RNA Mini Kit (Thermo Fisher Scientific)
The RNA-seq was performed using TruSeq RNA Library Prep Kit v2 (Illumina), according to the protocol. The libraries were ligated with different indexes,  pooled in one pool and sequenced in the 150 pair-end cycles on HiSeq 4000.

treatment_protocol: The collected material was transferred into tubes and stored at -80°C.

tag: individual

value: horse 4

value: lung


title: NK cells, ADSC secretome, 48h, 2

city: Seoul

first: Eunhee

last: Ko

state: Seoul

address: Avison Biomedical Research Center (ABMRC), Yonsei University Health System, 50-1 Yonsei-ro, Seodaemun-gu

country: South Korea

institute: Yonsei University College of Medicine

data_processing:
Before proceeding with the analysis of the raw sequence, a quality check is performed using the FastQC program v0.11.7 to ensure that there are no problems with the data.
Trimming for illumina paired-end was performed using the Trimmomatic 0.38 program.
Mapping to a known reference genome using the HISAT2 version 2.1.0, Bowtie2 2.3.4.1.
After read mapping, transcript assembly was performed using the StringTie version 2.1.3b.
Assembly: Genome Reference Consortium Human Build 37 (GRCh37) (annotation NCBI_105.20190906)

source_name: Peripheral blood

growth_protocol: Human primary NK cells were isolated from the human peripheral blood mononuclear cells of a healthy donor with negative selection using a human NK Cell Isolation Kit (Miltenyi Biotec.). Following isolation, purified NK cells (purity > 90%) were immediately cultured in alpha-MEM-based complete growth medium with 10 ng/mL rhIL-2 for their survival and activation. The cells were maintained in a cell incubator at 37 °C and 5% CO2.

extract_protocol:
Total RNA was isolated using RNeasy Micro Kit (Qiagen). 1ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA LT Sample Prep Kit following manufacturer's protocols.

treatment_protocol: Human primary NK cells isolated from PBMCs of a healthy donor were cultured for 48 h with 150 ug/ml ADSC secretome, or without in the presence of 10 ng/ml of rhIL-2.

value: Peripheral blood

value: Natural killer cell

value: IL-2 activation, ADSC secretome


title: TgSPI1Fanca.wt  preleukemic_479

value: preleukemic


title: Saccharomyces cerevisiae, mVCs, rep1

value: whole cell


title: AT2_2_L

description:
AT2_16011_L
AT2_merged.gene_counts_length_scaled.tsv

value: Fetal lung

value: AT2 organoid

value: 21 post-conception week

value: Passage 17


title: 4-week HP Grin2b WT Bulk RNA-seq Sample2

value: Hippocampus


title: 2-week HP Grin2b WT Bulk RNA-seq Sample5


title: NK cells, IL-2 Control, 48h, 2

value: IL-2 activation


title: 32p RNA-Seq

value: horse 3


title: Saccharomyces cerevisiae, control, rep3


title: sd_zt08_6

value: Continous darkness after short day


title: NK cells, IL-2 Control, 48h, 1


title: sd_zt20_6


title: 2-week HP Grin2b WT Bulk RNA-seq Sample3

value: WT


title: 4-week HP Grin2b +/- Bulk RNA-seq Sample5

value: Grin2b +/-


title: sd_zt16_7


title: 34w RNA-Seq

source_name: liver

value: horse 4

value: liver


title: sd_zt12_7


title: 32w RNA-Seq


title: AT2_2_E

description:
AT2_16011_E
AT2_merged.gene_counts_length_scaled.tsv

value: Passage 6

value: AT2 medium


title: 32s RNA-Seq

source_name: heart

value: heart


title: 4-week HP Grin2b +/- Bulk RNA-seq Sample2


title: 30s RNA-Seq

value: horse 2


title: 34s RNA-Seq


title: sd_zt12_6


title: 4-week HP Grin2b +/- Bulk RNA-seq Sample1


title: 2-week HP Grin2b +/- Bulk RNA-seq Sample5


title: AML3, AML patient

city: Shenzhen

first: Xuqiao

last: Hu

state: China

address: Buxin Road, Luohu District

country: China

institute: Shenzhen Center for Chronic Disease Control and Prevention

description: AML3, Raw files were not submitted due to patient privacy concerns

data_processing:
The raw scRNA-seq data were aligned to the human reference genome (GRCh38) and a digital gene expression matrix was built using STAR algorithm in CellRanger (‘count’ option; v3.1.0; 10x Genomics). The ‘filtered_feature_bc_matrix’ file folder generated by CellRanger was used for further analysis. Using the Seurat R package (v3.1.0; https://satijalab.org/seurat), cells that contained more than 5500 or fewer than 200 expressed genes, or more than 15% mitochondrial transcripts, or more than 5% hemoglobin transcripts were removed. Genes that were expressed in fewer than 3 cells were also removed. In addition, doublets identified by DoubletFinder (version 2.0.2; https://github.com/chris-mcginnis-ucsf/DoubletFinder) were also dropped.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every cell in each sample

source_name: Blood

extract_protocol:
Lymphoprep is added to the SepMate tubes (STEMCELL Technologies) by carefully pipetting it through the central hole of the SepMate insert, 10 mL fresh blood is diluted by two folds with PBS and layered on the top of Lymphoprep. The tubes were then centrifuged at 1200 × g for 10 minutes at room temperature, with the brake on. After the centrifugation, the plasma is at the top, followed by the PBMC/platelet layer, the Lymphoprep layer, the granulocyte layer, and finally the erythrocytes at the bottom of the centrifuge tube. The upper plasma layer was drawn into 15 mL centrifuge tube using a sterile pipette, the PBMC layer was transferred into a new 1.5 mL centrifuge tube, using another clean pipette. The PBMCs were washed by adding five volumes of PBS, centrifuged at 400  ×  g for 5 minutes at 4°C, and the supernatant was removed. 1.25 mL of red blood cell lysis buffer was then added to the pellet and mixed gently by slowly pipetting up and down for five times. The PBMCs were allowed to stand on ice for 8 minutes and then centrifuged at 300 × g for 5 minutes at 4°C. The supernatant was carefully removed without disturbing the pellet, followed by resuspension of pellet in 1 mL PBS by slowly pipetting up and down for five times to wash the cells. The cells were centrifuged at 300 × g for 5 min at 4°C, followed by another wash with PBS. The cells were then resuspended with PBS, and manually counted for three times by Trypan blue exclusion. Finally, the cells were centrifuged and resuspended at a concentration of 700-1200 cells/µl used for scRNA-seq.
Single-cell suspensions were loaded into Chromium microfluidic chips using the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (10X Genomics) according to the manufacturer’s instructions.

value: Blood

value: AML patient

value: PBMC


title: ld_zt20_7

value: Continous darkness after long day


title: AML3B, AML patient

description: AML3B, Raw files were not submitted due to patient privacy concerns


title: NK cells, IL-2 Control, 48h, 3

value: Peripheral blood

value: Natural killer cell


title: sd_zt08_7


title: 27p RNA-Seq

value: horse 1

value: lung


title: NK cells, ADSC secretome, 48h, 3

value: IL-2 activation, ADSC secretome


title: 2-week HP Grin2b +/- Bulk RNA-seq Sample3

value: Hippocampus


title: ld_zt20_6


title: sd_zt04_7

value: Continous darkness after short day


title: NK cells, ADSC secretome, 48h, 1


title: 2-week HP Grin2b +/- Bulk RNA-seq Sample4

value: Grin2b +/-


title: ld_zt16_6


title: 2-week HP Grin2b +/- Bulk RNA-seq Sample2


title: H7, healthy donor

description: H7, Raw files were not submitted due to patient privacy concerns

value: healthy donor


title: 30w RNA-Seq

value: liver


title: sd_zt04_6


title: 30p RNA-Seq


title: AML4, AML patient

description: AML4, Raw files were not submitted due to patient privacy concerns


title: 2-week HP Grin2b WT Bulk RNA-seq Sample2

value: WT


title: sd_zt00_7


title: 2-week HP Grin2b WT Bulk RNA-seq Sample4


title: ld_zt12_7


title: sd_zt00_6


title: Stat5CATim3-3

city: Philadelphia

first: E

middle: JOHN

last: WHERRY

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

institute: University of Pennsylvania

library_source: genomic

data_processing:
Raw ATACseq FASTQ files from paired-end sequencing were processed using the script available at the following repository (https://github.com/wherrylab/jogiles_ATAC).
Samples were aligned to the GRCm38/mm10 reference genome using Bowtie2.
We used samtools to remove unmapped, unpaired, mitochondrial reads and ENCODE blacklist regions were also removed
PCR duplicates were removed using Picard.
Peak calling was performed using MACS v2 (FDR q-value 0.01).
Normalization and differential accessibility analysis was done with DESeq2. For each experiment, peaks of all samples were merged to create a union peak list with BedTools merge.
The number of reads in each peak was determined using BedTools coverage.
Assembly: mm10
Supplementary files format and content: Raw and normalized open chromatin accessiblity counts files

molecule: genomic DNA

source_name: Sorted VEX+ P14 CD8 T cells

extract_protocol:
Transposed DNA fragments were purified using a Qiagen Reaction MiniElute Kit, barcoded with NEXTERA dual indexes (Illumina) and amplified by PCR for 11 cycles using NEBNext High Fidelity 2x PCR Master Mix (New England Biolabs)
PCR products were purified using a PCR Purification Kit (Qiagen) and amplified fragments size was verified on a 2200 TapeStation (Agilent Technologies) using High Sensitivity D1000 ScreenTapes (Agilent Technologies). Libraries were quantified by qPCR using a KAPA Library Quant Kit (KAPA Biosystems). Normalized libraries were pooled, diluted to 1.8pM, loaded onto a NextSeq 500/550 High Output Kit v2.5 (150 cycles, Illumina) and paired-end sequencing was performed on a NextSeq 550 (Illumina)

treatment_protocol: Sorted cells (2-to-5x104) were washed twice in cold PBS and resuspended in 50ml of cold lysis buffer (10mM Tris-HCl, pH 7.4, 10mM NaCl, 3mM MgCl2 and  0.1% IGEPAL CA-630),Lysates were centrifuge (750xg, 10min, 4oC) and nuclei were resuspended in 50l of transposition reaction mix (TD buffer [25l], Tn5 Transposase [2.5l], nuclease-free water [22.5l]; (Illumina)) and incubated for 30min at 37oC

value: Sorted VEX+ P14 CD8 T cells


title: AML2, AML patient

description: AML2, Raw files were not submitted due to patient privacy concerns


title: 27w RNA-Seq


title: 2-week HP Grin2b WT Bulk RNA-seq Sample1


title: AML5, AML patient

description: AML5, Raw files were not submitted due to patient privacy concerns


title: ld_zt16_7


title: Stat5CATim3-1


title: ld_zt12_6


title: 2-week HP Grin2b +/- Bulk RNA-seq Sample1


title: H4, healthy donor

description: H4, Raw files were not submitted due to patient privacy concerns


title: AML1, AML patient

description: AML1, Raw files were not submitted due to patient privacy concerns


title: H5, healthy donor

description: H5, Raw files were not submitted due to patient privacy concerns


title: 27s RNA-Seq

value: heart


title: EmptyTim3-4


title: Stat5CATim3-2


title: H6, healthy donor

description: H6, Raw files were not submitted due to patient privacy concerns

value: Blood


title: ld_zt08_7


title: H3, healthy donor

description: H3, Raw files were not submitted due to patient privacy concerns


title: EmptyTim3-3


title: ld_zt08_6


title: H2, healthy donor

description: H2, Raw files were not submitted due to patient privacy concerns


title: 20-week TH Grin2a WT Bulk RNA-seq Sample10

source_name: Thalamus

value: Thalamus


title: EmptyTim3-2


title: ld_zt04_6


title: 20-week TH Grin2a WT Bulk RNA-seq Sample7


title: 20-week TH Grin2a WT Bulk RNA-seq Sample6


title: EmptyLy108-4


title: 20-week TH Grin2a WT Bulk RNA-seq Sample5


title: 20-week TH Grin2a WT Bulk RNA-seq Sample9


title: RNA ref [RNA3]

city: Lyon

first: Virginie

last: MARCEL

address: 28 rue Laennec

institute: Cancer Research Center of Lyon

data_processing:
*library strategy: RiboMethSeq
We used the pipeline: ribomethseq-nf. fastQC was used to verify sequencing quality and adapter removal was performed using Trimmomatic. The trimmed reads were aligned by Bowtie2 on the 7.2 kb-long rRNA sequence of reference (NR_046235) and the 5’ read-ends were computed using bedtool genomcov utility
The C-score was calculated using a normalization against the median raw counts of neighbouring +/- 6 nucleotide window with the help of rRMSAnalyzer package
Assembly: NR_046235
Supplementary files format and content: Raw counts of 5' end reads on each position of each rRNA
Supplementary files format and content: CSV files. The C-score was calculated using a normalization against the median raw counts of neighbouring +/- 6 nucleotide window (Marcel et al, NAR Cancer 2020)

source_name: commercial RNA

extract_protocol: Total RNA was extracted using either the Maxwell RSC simplyRNA Tissue Kit (Promega) with Maxwell RSC Instrument (Promega) configured with Low Elution Volume (LEV) hardware according to the manufacturer’s protocol or TRIzol (Invitrogen) according to manufacturer’s instructions.  Total RNA was partially and randomly fragmented under alkaline conditions. Libraries of 24 samples were prepared simultaneously using NEBNext Multiplex Small RNA Library kit (New England Biolabs). A calibrated source of total RNA (Human Xpress Ref Universal Total RNA, Qiagen) was introduced in each library.

value: commercial RNA

tag: tissue type

value: RNA ref

tag: pfs

tag: os

tag: mitotic index

tag: cohort

value: validation-II

tag: rna extraction_method

value: Maxwell

tag: sequencing library


title: ld_zt00_7

tag: strain

value: Continous darkness after long day


title: 20-week TH Grin2a WT Bulk RNA-seq Sample4

tag: genotype


title: EmptyLy108-2

tag: cell type


title: Glioblastoma (G) [G-f]

source_name: brain

value: brain

value: Glioblastoma (G)


title: 20-week TH Grin2a WT Bulk RNA-seq Sample3


title: EmptyLy108-1


title: Glioblastoma (G) [G-g]


title: ld_zt00_6


title: 20-week TH Grin2a WT Bulk RNA-seq Sample8


title: sd_zt20_5

growth_protocol: Ostreococcus tauri was grown in column photochemostats under long day, short day and continous light conditions.

treatment_protocol: Long day (16 hours light : 8 hours dark), short day (8 hours light : 16 hours dark) and continous light.

value: Continous Light after Short Day


title: Glioblastoma (G) [G-d]


title: sd_zt20_4


title: Glioblastoma (G) [G-e]


title: 20-week TH Grin2a WT Bulk RNA-seq Sample2


title: Cl13Stat5CA_R2

data_processing:
Data qualities were checked using FastQC and MultiQC.
Paired-end reads were aligned to mm10 reference genome using Bowtie2 v2.3.5 with options suggested by Skene et al. 2018.79 Bam files containing uniquely mapped reads were kept using Samtools v1.1.
MarkDuplicates command from Picard tools v1.96 was used to remove presumed PCR duplicates.
Blacklist regions defined by ENCODE were removed, and filtered typical chromosomes were used for downstream analysis.
Read per million (RPM) normalized bigwig files to visualize binding signals were created using deepTools bamCoverage v3.3.2 with parameters --normalizeUsing CPM -bs 5 –smoothLength 20 –skipNAs.
Bigwig files of biological replicates were pooled using wiggletools with mean setting, median background were subtracted and bedGraphToBigWig was then applied to convert bedgraph to bigwig format.
Assembly: mm10
Library strategy: Cut&Run

source_name: CD8 T cell

extract_protocol:
Reaction was stopped by addition of 150microL of 2X stop Buffer (340mM NaCl, 20mM EDTA, 4mM EGTA, 0.02% Digitonin, 50microg/ml RNAseA and 50microg/ml Glycogen) followed by 10min incubation at 37oC to release target chromatin. Samples were then centrifuged 5min 16,000g 4oC and supernatants were transferred to new tubes. Chromatin fragments were incubated 10min at 70oC with 3microL of 10% SDS and 2.5microL of proteinase K (20mg/ml) followed by phenol/chloroform/isoamyl alcohol-based extraction according to original protocol (method B). Upper phase containing DNA was mixed with 1microL of glycogen (20mg/ml) and incubated with 750microL of cold 100% ethanol at -20oC O/N. Samples were centrifuged 30min 16,000g 4oC, rinsed once with 1ml of cold 100% ethanol and centrifuged again for 5min 16,000g 4oC to remove residual ethanol. Samples were air-dried, resuspended in 50microL of molecular grade water and stored at -20oC. DNA libraries were built using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NewEngland Biolabs) with the following modifications.2 NEBNext End Prep step was performed using 25microL of input material for a final volume of 30microL and the following adapted program (30min-20oC, 60min-50oC, Hold at 4oC). Adaptor was diluted at 1:25 and added at 1.5microL for ligation (15min-20oC) followed by addition of 1.5microL of Red USER Enzyme and additional 15min incubation at 37oC. Size selection was performed using 80microL of AMPure XP beads (Beckman Coulter) and purified DNA fragments were amplified for 14 cycles (annealing time changed to 10s). Libraries were cleaned-up with two rounds of size selection with AMPure XP beads (24microl/12microl; Beckman Coulter) eluted in 15microl of molecular grade water, and amplicons quality was assessed on a 2200 TapeStation (Agilent Technologies)
Libraries were quantified by qPCR using the NEBNext Library Quant kit for Illumina (NewEngland Biolabs) according to manufacturer’s protocol and pooled at equal molarity (1nM).  Denatured Libraries were diluted at 1.8pM, loaded into a NextSeq 500/550 High Output Kit (75 cycles, Illumina) and paired-end sequencing was performed on a NextSeq 550 (Illumina).

treatment_protocol: P14 Empty and P14 STAT5CA cells were sorted at d8p.i. with either LCMV Arm or Cl13 from recipients of two independent experiments and 0.5 to 3x105 cells were recovered in 1.5ml DNA LoBind Eppendorfs containing 650microl of 50%FBS RPMI. Samples were washed twice in 1ml of cold wash buffer (20mM HEPES-NaOH pH7.5, 150mM NaCl, 0.5mM Spermidine and protease inhibitor from Roche), re-suspended in 400microl (final) of wash buffer containing 20microl of BioMagplus Concanavalin A-coated magnetic beads (Bangs Laboratories) per reaction and rotated for 15min at 4oC to allow the cells to bind. Tubes were placed on a magnet stand and liquid was removed. Beads were then incubated O/N at 4oC in 250microl of antibody buffer (20mM HEPES-NaOH pH7.5, 150mM NaCl, 0.5mM Spermidine, 2mM EDTA, 0.1% digitonin and protease inhibitor from Roche) containing 2.5microl (1/100) of antibodies against H3K27ac (Active Motif) or IgG control (Cell Signalling Tech). Samples were then washed twice in 500microl of Digitonin Buffer (20mM HEPES-NaOH pH7.5, 150mM NaCl, 0.5mM Spermidine, 0.1% digitonin and protease inhibitor from Roche), resuspended in 250microl of cold Digitonin Buffer containing Protein-A micrococcal nuclease (pA-MN) and rotated at 4oC for 1h. Beads were washed twice in 1ml of cold Digitonin Buffer to remove unbound pA-MN, resuspended in 150microl of Digitonin Buffer, cooled down at 0oC on a pre-cooled metal block for 5min and incubated 30min at 0oC with CaCl2 (3microl of 0.1M per sample) to initiate pA-MN digestion

value: CD8 T cell

tag: chip antibody

value: Histone H3K27ac antibody pAb - Active Motif


title: 20-week TH Grin2a WT Bulk RNA-seq Sample1


title: Cl13Stat5CA_R1


title: EmptyLy108-3


title: sd_zt20_3

value: Short Day


title: sd_zt20_2


title: 20-week TH Grin2a -/- Bulk RNA-seq Sample4

value: Grin2a -/-


title: sd_zt16_5


title: ArmStat5CA_R1


title: Astrocytoma (A) [A-f]

value: Astrocytoma (A)


title: 20-week TH Grin2a -/- Bulk RNA-seq Sample3


title: 20-week TH Grin2a -/- Bulk RNA-seq Sample1


title: sd_zt20_1


title: ArmEmpty_R2


title: Oligodendroglioma (O) [O-h]

value: Oligodendroglioma (O)


title: Oligodendroglioma (O) [O-f]


title: sd_zt16_3


title: sd_zt16_4


title: Glioblastoma (G) [G-c]


title: ArmEmpty_R1


title: 20-week TH Grin2a +/- Bulk RNA-seq Sample4

value: Grin2a +/-


title: sd_zt16_2


title: Astrocytoma (A) [A-e]


title: Cl13Empty_R1


title: 20-week TH Grin2a -/- Bulk RNA-seq Sample2


title: Oligodendroglioma (O) [O-g]


title: Cl13Empty_R2


title: Naïve_R2


title: Oligodendroglioma (O) [O-e]


title: sd_zt16_1


title: 20-week TH Grin2a +/- Bulk RNA-seq Sample5


title: 20-week TH Grin2a +/- Bulk RNA-seq Sample3


title: IgG_Cl13Stat5CA_R1

value: Rabbit (DA1E) mAb IgG XP Isotype control - Cell Signaling Tech


title: Astrocytoma (A) [A-d]


title: sd_zt12_4


title: Oligodendroglioma (O) [O-d]


title: Naïve_R1


title: IgG_Cl13Stat5CA_R2


title: 12-week TH Grin2a WT Bulk RNA-seq Sample5

value: Thalamus

value: WT


title: IgG_Cl13Empty_R2


title: Oligodendroglioma (O) [O-c]


title: 20-week TH Grin2a +/- Bulk RNA-seq Sample1


title: sd_zt12_5


title: 12-week TH Grin2a WT Bulk RNA-seq Sample4


title: IgG_Cl13Empty_R1


title: Oligodendroglioma (O) [O-b]


title: sd_zt12_3


title: IgG_ArmStat5CA_R1


title: Astrocytoma (A) [A-c]


title: sd_zt12_2


title: 20-week TH Grin2a +/- Bulk RNA-seq Sample2


title: 12-week TH Grin2a -/- Bulk RNA-seq Sample5


title: Oligodendroglioma (O) [O-a]


title: 12-week TH Grin2a WT Bulk RNA-seq Sample3


title: 12-week TH Grin2a WT Bulk RNA-seq Sample2


title: 12-week TH Grin2a -/- Bulk RNA-seq Sample4


title: sd_zt12_1


title: IgG_Naive_R1


title: IgG_ArmEmpty_R2


title: IgG_ArmEmpty_R1


title: sd_zt08_5


title: Astrocytoma (A) [A-a]


title: sd_zt08_4


title: 12-week TH Grin2a -/- Bulk RNA-seq Sample3


title: EO771_BrM3_MVC19 Brain metastasis-associated microenviroment

city: Madrid

first: Santiago

middle: García

last: Martín

state: Madrid

address: Calle de Melchor Fernández Almagro, 3

department: Bioinformatics Unit

institute: Spanish National Cancer Research Centre

data_processing:
Raw images generated by the sequencer are submitted to analysis, per-cycle basecalling and quality score assignment with Illumina's Real Time Analysis integrated primary analysis software (RTA v2). Conversion of BCL (base calls) binary files to FASTQ format is subsequently performed with bcl2fastq2 (Illumina).
Fastq represents each sequence read by four lines (Sequence identifier, Sequence, Quality score identifier line and Quality score). Qscores are formatted in the standard Sanger encoding (ASCII with offset of 33).
Delivered sequences have passed Illumina quality filtering to remove least reliable reads (PF, for Passing Filter)
This instrument generates 4 files per sample with complementary information, with "L00?" (=Lane #) differing from "L001" to "L004"  in their name.  The contents of these 4 files have to be combined, or concatenated into a single file to include them all in the analysis.
[PF] read number is approximate
Assembly: GRCm39

source_name: Brain

growth_protocol: B16-F10-BrM4 and 482N1 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C. EO771 cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics and HEPES in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using Rneasy kit (Qiagen). 1ug of total RNA was used for the construction of sequencing libraries.
Total RNA samples [1µg] were converted into sequencing libraries with the "NEBNext Ultra II Directional RNA Library Prep Kit for Illumina" (NEB #E7760), as recommended by the manufacturer. Briefly, polyA+ fraction is purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters. Adapter-ligated library is completed by PCR with Illumina PE primers. {This kit generates directional libraries stranded in the antisense orientation [the read1 (the only read in single read format) has the antisense orientation (--library-type fr-firststrand in TopHat, --stranded=reverse in HTSeq]} The resulting purified cDNA libraries were applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument by following manufacturer's protocols.

value: Brain

tag: cell line

tag: treatment

value: SAC 10d post injection 40,000cells


title: 12-week TH Grin2a WT Bulk RNA-seq Sample1

tag: tissue

tag: age


title: IgG_Naive_R2


title: 12-week TH Grin2a -/- Bulk RNA-seq Sample2


title: sd_zt08_2

tag: time point

tag: photoperiod


title: Glioblastoma (G) [G-i]

tag: tissue type

value: validation-II

value: Maxwell


title: sd_zt08_1


title: Astrocytoma (A) [A-b]

value: brain

tag: pfs


title: EO771_BrM3_MVC18 Brain metastasis-associated microenviroment


title: Glioblastoma (G) [G-h]

value: Glioblastoma (G)

tag: os


title: Glioblastoma (G) [G-a]

tag: mitotic index


title: sd_zt04_5

value: Continous Light after Short Day


title: sd_zt08_3


title: 12-week TH Grin2a -/- Bulk RNA-seq Sample1


title: EO771_BrM3_MVC15 Brain metastasis-associated microenviroment


title: EO771_BrM3_MVC16 Brain metastasis-associated microenviroment


title: sd_zt04_3


title: EO771_BrM3_MVC17 Brain metastasis-associated microenviroment


title: 12-week TH Grin2a +/- Bulk RNA-seq Sample4


title: 12-week TH Grin2a +/- Bulk RNA-seq Sample5


title: sd_zt04_2


title: sd_zt04_4


title: EO771_BrM3_MVC14 Brain metastasis-associated microenviroment


title: sd_zt04_1


title: 12-week TH Grin2a +/- Bulk RNA-seq Sample2


title: 482N1_MVC13 Brain metastasis-associated microenviroment


title: sd_zt00_5


title: sd_zt00_3


title: 12-week TH Grin2a +/- Bulk RNA-seq Sample1


title: 4-week TH Grin2a WT Bulk RNA-seq Sample4


title: 482N1_MVC10 Brain metastasis-associated microenviroment


title: 482N1_MVC11 Brain metastasis-associated microenviroment


title: 12-week TH Grin2a +/- Bulk RNA-seq Sample3


title: sd_zt00_4


title: 4-week TH Grin2a WT Bulk RNA-seq Sample5


title: sd_zt00_2


title: 482N1_MVC09 Brain metastasis-associated microenviroment


title: sd_zt00_1


title: 4-week TH Grin2a WT Bulk RNA-seq Sample3


title: 482N1_MVC08 Brain metastasis-associated microenviroment


title: 4-week TH Grin2a WT Bulk RNA-seq Sample1


title: 4-week TH Grin2a WT Bulk RNA-seq Sample2


title: 482N1_MVC07 Brain metastasis-associated microenviroment


title: B16-F10-BrM4_MVC05 Brain metastasis-associated microenviroment


title: 4-week TH Grin2a -/- Bulk RNA-seq Sample5


title: ld_zt20_3

value: Long Day


title: B16-F10-BrM4_MVC06 Brain metastasis-associated microenviroment


title: ld_zt20_5

value: Continous Light after Long Day


title: 4-week TH Grin2a -/- Bulk RNA-seq Sample4


title: B16-F10-BrM4_MVC04 Brain metastasis-associated microenviroment


title: ld_zt20_2


title: B16-F10-BrM4_MVC03 Brain metastasis-associated microenviroment


title: ld_zt20_1


title: 4-week TH Grin2a -/- Bulk RNA-seq Sample2


title: 4-week TH Grin2a -/- Bulk RNA-seq Sample1


title: ld_zt16_4


title: ld_zt20_4


title: B16-F10-BrM4_MVC01 Brain metastasis-associated microenviroment


title: 4-week TH Grin2a +/- Bulk RNA-seq Sample5


title: 4-week TH Grin2a -/- Bulk RNA-seq Sample3


title: Glioblastoma (G) [G-b]

tag: cohort


title: B16-F10-BrM4_MVC02 Brain metastasis-associated microenviroment


title: ld_zt16_5


title: ld_zt16_3


title: ld_zt16_2


title: 4-week TH Grin2a +/- Bulk RNA-seq Sample3


title: 4-week TH Grin2a +/- Bulk RNA-seq Sample4


title: 4-week TH Grin2a +/- Bulk RNA-seq Sample2


title: SEM IKZF1 Knockout treated 3

city: Utrecht

first: Frank

middle: van

last: Leeuwen

address: Heidelberglaan 25

country: Netherlands

institute: Princess Maxima Center

data_processing:
Raw data (raw reads) of FASTQ format were processed through fastp
alignment to reference genome (hg38) using the HISAT2 v2.0.5 algorithm program
FeatureCounts v1.5.0-p3 was used to count the read numbers mapped of each gene.
FPKM of each gene was calculated
Assembly: Homo Sapiens(GRCh38/hg38)
Supplementary files format and content: .xslx file including FPKM values for each Sample

source_name: SEM

growth_protocol: Cells were grown in RPMI (Invitrogen, Thermo Fisher Scientific, Breda, the Netherlands), supplemented with 10% fetal bovine serum (FBS, Greiner Bio-One, Essen, Germany) and 1% penicillin/streptomycin solution (P/S) (Invitrogen) at a cell density between 0.25 and 3x106 cells per milliliter.

extract_protocol:
mRNA was purified from cell cultures using a RNeasy minikit (74106; Qiagen, Venlo, The Netherlands)
RNA sequencing and data analysis was performed by NovoGene (Cambridge, UK)

treatment_protocol: Cells were either treated or untreated with 1uM AraC  for 16 hours

value: SEM

value: BCP-ALL

value: IKZF1 Knockout

value: Cytarabine


title: ld_zt16_1


title: ld_zt12_3


title: ld_zt12_5


title: 4-week TH Grin2a +/- Bulk RNA-seq Sample1

value: Grin2a +/-


title: hiDP_direct_reprogramming_rep1

type: RNA

city: Daejeon

first: Minhyung

last: Lee

address: 125 Gwahak-ro

department: Stem Cell Convergence Research Center

institute: Korea Research Institute of Bioscience and Biotechnology

description:
Gene expression of reprogrammed hiDP cells
iDP-1

hyb_protocol: After checking labeling efficiency, fragmentation of cRNA was performed by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60oC for 30 min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Agilent’s Human Oligo Microarray (44K). The arrays hybridized at 65oC for 17 hours using Agilent Hybridization oven (Agilent Technology, USA). The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology, USA).

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).

data_processing: All data normalization and further analysis were performed using GeneSpringGX 7.3 (Agilent Technology, USA).

label_protocol: Amplified and labeled cRNA was purified on cRNA Cleanup Module (Agilent Technology) according to the manufacturer’s protocol. Labeled cRNA target was quantified using ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE).

growth_protocol: For hiDP reprogramming, the human fibroblasts were plated onto 24-well plates at 30,000 cells/well. The next day (0 days post transduction, dpt), the cells were transduced with Sendai virus (SeV) mixtures (CytoTune™-iPS 2.0 Sendai reprogramming kit; Thermo Fisher Scientific) at an appropriate multiplicity of infection (MOI; KOS:M:K = 4.2:4.2:2.5). After 24 h incubation, the SeV mixtures were replaced with RepM-Neural medium containing 3.0 μM CHIR99021, 0.5 μM A83-01, 50 µg/ml 2-phospho-L-ascorbic-acid (Sigma-Aldrich, St. Louis, MO, USA), 0.2 µM NaB (Sigma-Aldrich), 20 ng/ml epidermal growth factor (EGF; Peprotech), and 20 ng/ml fibroblast growth factor 2 (FGF2; Peprotech) for one week. The cells were dissociated by Accutase with 10 nM Y-27632 and re-plated onto a Geltrex-coated 6-well plate with the same medium containing 10 nM Y-27632 at 7 dpt. The next day, the culture media were replaced with RepM-Neural with 3.0 μM CHIR99021, 0.5 μM A83-01, 50 µg/ml 2-phospho-L-ascorbic-acid, 100 ng/ml FGF8 (Peprotech), and 800 ng/ml sonic hedgehog (SHH; R&D systems, Minneapolis, MN, USA). After 13–15 days, some colonies were manually isolated and maintained on Geltrex-coated plates with the same medium but a reduced SHH concentration (200 ng/ml)

extract_protocol: Total RNA was extracted from cells using an RNeasy mini kit with QiaShredder (Qiagen, Hilden, Germany) and DNase I (Qiagen).

treatment_protocol: All samples were treatred with growth media (differentiated and reprogrammed cell samples) or reprogramming media (reprogramming cell samples).

value: reprogrammed hiDP cells


title: hiDP_direct_reprogramming_day16_rep1

description:
Gene expression of reprogramming cells at day-16 of hiDP reprogramming
iDP_16day-1

value: Cells during hiDP reprogramming

tag: time


title: hiDP_direct_reprogramming_rep2

description:
Gene expression of reprogrammed hiDP cells
iDP-2


title: SEM IKZF1 Knockout treated 2


title: SEM IKZF1 Knockout untreated 3

value: Untreated


title: hiDP_direct_reprogramming_day8_rep1

description:
Gene expression of reprogramming cells at day-8 of hiDP reprogramming
iDP_8day-1


title: hiDP_direct_reprogramming_day8_rep2

description:
Gene expression of reprogramming cells at day-8 of hiDP reprogramming
iDP_8day-2


title: hiDP_direct_reprogramming_day16_rep2

description:
Gene expression of reprogramming cells at day-16 of hiDP reprogramming
iDP_16day-2


title: SEM IKZF1 Knockout untreated 2


title: 2-week TH Grin2a WT Bulk RNA-seq Sample5

value: Thalamus

value: WT


title: ld_zt12_1


title: hiDP_direct_reprogramming_day0_rep2

description:
Gene expression of reprogramming cells at day-0 of hiDP reprogramming
iDP_0day-2


title: ld_zt12_4


title: 2-week TH Grin2a WT Bulk RNA-seq Sample2


title: SEM IKZF1 Knockout untreated 1


title: ld_zt08_5


title: 2-week TH Grin2a WT Bulk RNA-seq Sample1


title: ld_zt08_3


title: SEM wildtype control treated 2


title: ld_zt08_2


title: 2-week TH Grin2a WT Bulk RNA-seq Sample4


title: SEM wildtype control treated 1


title: ld_zt12_2


title: hiDP_aged_donor-derived

description:
Gene expression of reprogrammed hiDP cells
A-hiDP

value: hiDP directly reprogrammed from aged donor


title: hiDP_direct_reprogramming_day0_rep1

description:
Gene expression of reprogramming cells at day-0 of hiDP reprogramming
iDP_0day-1


title: 2-week TH Grin2a WT Bulk RNA-seq Sample3


title: 2-week TH Grin2a -/- Bulk RNA-seq Sample3

value: Grin2a -/-


title: SEM IKZF1 Knockout treated 1


title: ld_zt08_4


title: 2-week TH Grin2a -/- Bulk RNA-seq Sample5


title: SEM wildtype control treated 3


title: PSC-derived_DP_rep1

description:
Gene expression of differentiated DP cells
PSC-DP1

value: DP differentiated from PSC


title: ld_zt08_1.


title: 2-week TH Grin2a -/- Bulk RNA-seq Sample4


title: SEM wiltdype control untreated 3


title: SEM wiltdype control untreated 1


title: ld_zt04_4.


title: ld_zt04_7

value: Continous darkness after long day


title: SEM wiltdype control untreated 2


title: C481_CART19_TP0903

city: Rochester

first: Saad

last: Kenderian

state: MN

address: 200 First Street SW

institute: Mayo Clinic

data_processing:
Binary base call data converted to fastq using Illumina bcl2fastq software
Check quality with FastQC, trim adapters with cutadapt, and re-check quality with FastQC
Latest human reference genome GRCh38 was downloaded from NCBI and indexed using STAR
Paired end reads were mapped to the genome, and HTSeq was used to generate expression counts for each gene
DeSeq2 was used to calculate differential expression
Assembly: CRCh38
Supplementary files format and content: tab-delimited text files contain the gene expression counts for each sample or DeSeq2 dataset

source_name: Healthy donor T cell

extract_protocol:
RNA was isolated using miRNeasy Micro kit (Qiagen, Gaithersburg, MD, USA) and treated with RNase-Free DNase Set (Qiagen, Gaithersburg, MD, USA).
TruSeq RNA Library Prep Kit v2
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Untransduced, CART19 treated with DMSO and CART19 treated with TP-0903 were produced on 3 biological replicates of normal donor T cells and total RNA was isolated.

value: Healthy donor T cell


title: 2-week TH Grin2a -/- Bulk RNA-seq Sample2


title: ld_zt04_5


title: C480_CART19_TP0903


title: BEAS2B cells, 3-miRNAs mixture -2

city: Songpa-gu

first: Dong Ha

last: Kim

address: 88, Olympic-ro 43-gil

department: Asan institute for life sciences

institute: ASAN Medical Center

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to GRCh38 whole genome using Tophat
FPKM calculation using Cufflink
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include Read count values for each Sample

growth_protocol: The human bronchial epithelial cell line BEAS2B were cultured in RPMI1640 medium, supplemented with 10% fetal bovine serum (FBS), 100-U/mL penicillin and 100-mg/mL streptomycin at 37 °C, 95% humidified air, and 5% CO2.

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

treatment_protocol: Transfection was performed using Lipofectamine 2000 according to the manufacturer’s instructions (Invitrogen)

value: Human bronchial epithelium, normal

value: miR-3124-5p and miR-200b-3p Overexpression, miR-92b Knockdown

value: Lipofectamine 2000


title: 2-week TH Grin2a +/- Bulk RNA-seq Sample4


title: C480_CART19_DMSO

value: DMSO


title: BEAS2B cells, miR-92b inhibitor  -2

value: miR-92b Knockdown


title: PSC-derived_DP_rep2

description:
Gene expression of differentiated DP cells
PSC-DP2


title: 2-week TH Grin2a +/- Bulk RNA-seq Sample3


title: ld_zt04_2

value: Long Day


title: ld_zt04_1


title: Injury Control, snRNA-seq

city: Baltimore

first: Pin

last: Lyu

address: 400 N Broadway

institute: JHU

description:
10x Genomics
muti_omic_injury_snRNAseq_mat.mtx
muti_omic_injury_snRNAseq_mat_cells.txt
muti_omic_injury_snRNAseq_mat_genes.txt

library_source: transcriptomic single cell

data_processing:
The multi-omic sequencing files were processed for demultiplexing and analyzed using Cell Ranger ARC v2.0. The genes were mapped and referenced using the zebrafish reference genome DanRer11.
To address potential ambient RNA contamination in the cell-by-gene expression matrix, we employed scAR module from scvi-tools with default parameters for further ambient RNA cleaning for each sample.
Assembly: DanRer11
Supplementary files format and content: Tab separated and matrix files

molecule: nuclear RNA

organism: Danio rerio

source_name: Retina

growth_protocol: All the zebrafish used in this study were adults between 6 and 12 months old. Prior to any experiments, the fish were anesthetized or euthanized using 1:1000 or 1:500 2-phenoxyethanol (Sigma), respectively.

extract_protocol:
Zebrafish retinas (4-6 retinas from 4-6 fish) were collected at different timepoints after NMDA and LD treatments, and flash-frozen in dry ice for ~15min before being transferred to a -800 C freezer for storage.
Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression (GEX) protocol (CGOOO338). Briefly, frozen retinal tissues were lysed in ice-cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged, washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of ~3000-5000 nuclei/ml. Nuclei (~15k) then were loaded onto 10x Genomic Chromium Controller, with a target number of ~10K nuclei per sample. RNA and ATAC libraries were prepared according to the 10xMultiome ATAC + Gene Expression protocol and subjected for Illumina NovaSeq sequencing at ~500 million reads per library

treatment_protocol: Phototoxic treatment that causes photoreceptor ablation was used to initiate a regenerative response in the zebrafish retina 2,53. All fish subjected to light damage were dark-adapted for two weeks and then placed adjacent to intense fluorescent lights for 96 hours. The temperature of the fish tanks was regularly monitored and maintained at 34ºC. After 96 hours, the fish were returned to the animal facility with a normal light/dark cycle and maintained for 7, 14, or 21 days recovery (DR). N-methyl-D-aspartate (NMDA, Sigma M3262) was administered to normal light/dark cycled fish via an intravitreal injection of 0.3µL 100mM NMDA solution in sterile PBS with a Hamilton syringe (Hamilton, 2.5µL Model 62 RN SYR, 87942), followed by placing the tanks in a dark incubator at 33ºC for 96 hours, after which the tanks were moved back into a normal light/dark cycle for 7 or 14 days recovery.  EdU (5-Ethynyl-2′-deoxyuridine, Life technologies A10044) was administered as previously described 53. Fish were anesthetized using 1:1000 2-phenoxyethanol and immobilized under a paper towel in a petri dish. Then, using an insulin syringe equipped with a 30-gauge needle, approximately 20 µL 1mg/mL EdU in water was injected intraperitoneally into each zebrafish at 60, 72, 84, 96 and 108 hours after damage. The retinal tissues were harvested at either 3, 7, 14, or 21 days recovery.

value: Retina

value: Control


title: 2-week TH Grin2a -/- Bulk RNA-seq Sample1


title: hiDP_young_donor-derived

description:
Gene expression of reprogrammed hiDP cells
Y-hiDP

value: hiDP directly reprogrammed from young donor


title: C481_CART19_DMSO


title: 2-week TH Grin2a +/- Bulk RNA-seq Sample5

value: Grin2a +/-


title: C375_CART19_DMSO


title: ld_zt04_3


title: BEAS2B cells, 3-miRNAs mixture -1


title: BEAS2B cells, miR-92b inhibitor  -1


title: 2-week TH Grin2a +/- Bulk RNA-seq Sample1

source_name: Striatum

value: Striatum


title: ld_zt00_5

value: Continous Light after Long Day


title: C375_CART19_TP0903

value: WT


title: BEAS2B cells, miR-200b-3p mimic -2

value: miR-200b-3p Overexpression


title: ld_zt00_4


title: shRNA3_2

city: Shiyan

first: Qin

last: Shanshan

address: Renmin Road 30, Maojian District

institute: Institute of Basic Medical Sciences, School of Basic Medical Sciences, Hubei University of Medicine

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to human genome assembly GRCh38 (ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz) using HISAT2 with default parameters.
HTSeq v0.11.2 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_29/gencode.v29.annotation.gtf.gz.
Assembly: GRCh38
Supplementary files format and content: FileincludeCount valuesforeachsample

growth_protocol: The human OSCC cancer cell line was purchased from the Shanghai Cell Bank of Chinese Academy of Sciences (Shanghai, China). The OSCC cells were cultured in DMEM medium containing 10% fetal bovine serum (FBS), 100 U/mL penicillin, 100 U/mL streptomycin and 0.03% glutamine at 37 oC in 5% CO2.

extract_protocol:
After 48 hours, remove the medium and directly add 800μL Trizol into the 6-well plate to harvest samples. Total RNA was extracted using Trizol reagent (Invitrogen, USA) according to the manufacturer’s instructions. The RNA purity and concentration was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA).
A total amount of 1.5 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: The negative conrtrol and FMOD-depletion OSCC cell lines  were grown as usual in 6-well plates. After 48 hours of treatment, the cells were digested for next studies.

value: oral squamous cell carcinoma


title: shRNA3_3


title: ld_zt00_3


title: BEAS2B cells, miR-200b-3p mimic -1


title: 20-week ST Grin2a WT Bulk RNA-seq Sample9


title: 20-week ST Grin2a WT Bulk RNA-seq Sample10


title: 2-week TH Grin2a +/- Bulk RNA-seq Sample2

value: Thalamus


title: shRNA2_3


title: BEAS2B cells, miR-3124-5p mimic -1

value: miR-3124-5p Overexpression


title: 20-week ST Grin2a WT Bulk RNA-seq Sample8


title: shRNA3_1


title: ld_zt00_2


title: ld_zt00_1


title: BEAS2B cells, miR-3124-5p mimic -2

value: Human bronchial epithelium, normal


title: shRNA2_1


title: BEAS2B cells, miRcontrol -2


title: shRNA2_2


title: 20-week ST Grin2a WT Bulk RNA-seq Sample7


title: 20-week ST Grin2a WT Bulk RNA-seq Sample6


title: cHCC-iCCA_Trp53 -/-, Rbpj -/- [ATR_5065T1]

city: Beijing

first: Qiongxuan

last: Fang

address: NO.11, Xizhimen South Street

department: Department of Internal Medicine I

institute: Peking University People's Hospital

description: combined hepatocellular and intrahepatic cholangiocarcinoma

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s protocol. On completion of the fragmentation reaction, 25 µl of 2x Agilent HiRPM hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse GE 8x60K Microarrays (G4852A) for 17 hours at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C prewarmed GE Wash buffer 2 (Agilent) and 30 seconds with Acetonitril.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA microarray Scanner G2505B (3micron) with the the Agilent Scan Control Version A.8.5.1 .

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent). Further processing (background correction, percentile shift normalization, summarization, log2 transformation, median shift) was done in Rstudio following Agilent's standardized method.

source_name: cHCC-iCCA

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's protocol, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with a NanoPhotometer

growth_protocol: mice were kept in a pathogen-free environment

extract_protocol: RNA was isolated using the RNeasy Mini Kit (Qiagen) following the manufacturer's protocol. RNA was quantified using a NanoPhotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: mice were treated with CCl4

value: tumor


title: cHCC-iCCA_Trp53 -/-, Rbpj -/- [ATR_5066T3]


title: cHCC-iCCA_Trp53 -/-, Rbpj -/- [ATR_5064T1]


title: 20-week ST Grin2a WT Bulk RNA-seq Sample5


title: shRNA1_3


title: shRNA1_2


title: 20-week ST Grin2a WT Bulk RNA-seq Sample4


title: HA844, oligodendrocyte co-cultured in direct with T cells (TCO), scRNAseq

city: Montreal

first: Haritha

last: Desu

state: Québec

address: 900 R. Saint-Denis

department: Neurosciences

country: Canada

institute: Centre de recherche du Centre Hospitalier de l'Université de Montréal

description: 10x Genomics

data_processing: The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0

growth_protocol: OLs were isolated from fresh non-pathological brain tissue from surgical resections for non-tumoral intractable focal epilepsy as previously published (Rone MB et al., 2016). OLs were harvested and plated on poly-L-lysine and extracellular matrix coated wells. During the first 4 days, OLs were allowed to grow in enriched cell medium containing 2ng/mL T3 , 1/50 N1 supplement , 1/50 B27 , 10ng/mL basic fibroblast growth factor  and 10ng/mL platelet derived growth factor – AA as previously published (Rone MB et al., 2016). After cell process extension, fresh medium without basic fibroblast growth factor and platelet derived growth factor – AA was used. Cells were treated with the experimental conditions after 8-10 days in vitro

extract_protocol:
In brief, media was collected and cells were treated with PBS-EDTA to detach the oligodendrocytes from the bottom of the well. Once cells were visibly detached, the suspension was combined with the collected media and the wells were washed twice with PBS to collect any residual cells and transferred to the same sample tube. The samples were centrifuged at 800rpm for 10min to pellet the live cells and then resuspended in PBS at a concentration of 350 thousand cells per milliliter. Approximately 10,000 cells were used for library construction.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).

value: Brain

tag: cell type_1

value: primary Oligodendrocytes

tag: cell type_2

value: T cells

value: Direct contact co-culture with T cells (TCO) for 12 hours


title: cHCC-iCCA_Trp53 -/-, Rbpj -/- [ATR_3654T3]

tag: genotype


title: cHCC-iCCA_Trp53 -/-, Rbpj -/- [ATR_3654T7]


title: HA844, oligodendrocyte only, scRNAseq

description: 10x Genomics

value: not applicable

value: Oligodendrocytes only


title: NC_3

tag: cell type

value: shRNA-NC


title: HA844, oligodendrocyte co-cultured with T cells separated by insert (TCM), scRNAseq

description: 10x Genomics

value: Co-culture with T cells separated by an insert (TCM) for 12 hours


title: cHCC-iCCA_Trp53 -/-, Rbpj -/- [ATR_3651T2]


title: HA843, oligodendrocyte co-cultured in direct with T cells (TCO), scRNAseq

description: 10x Genomics


title: shRNA1_1


title: 20-week ST Grin2a WT Bulk RNA-seq Sample3

city: Cambridge

data_processing:
Reads were aligned to RefSeq M25/GRCm38.p6 and gene and isoform level expression values were estimated using RSEM v1.3.0
Assembly: RefSeq M25
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
Brain dissection was performed in the cryostat using frozen brain tissues collected from Grin2a and Grin2b mutant mice. RNA was prepared from microdissected tissues using RNeasy Mini Kit (Qiagen). 200 ng of isolated total RNA from each sample was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using an Illumina TruSeq Stranded mRNA Kit (Illumina) following the manufacturer’s instructions.
rna

value: Striatum


title: BEAS2B cells, miRcontrol -1

value: Lipofectamine 2000


title: 20-week ST Grin2a WT Bulk RNA-seq Sample2

value: WT


title: NC_2


title: NC_1


title: iCCA_Trp53 -/-, Rbpj -/- [ATR_3649T1]

description: intrahepatic cholangiocarcinoma

source_name: iCCA


title: HA843, oligodendrocyte co-cultured with T cells separated by insert (TCM), scRNAseq

description: 10x Genomics


title: 20-week ST Grin2a -/- Bulk RNA-seq Sample4

value: Grin2a -/-


title: HCC_Trp53 -/-, Rbpj -/- [ATR_5075T1]

description: hepatocellular carcinoma

source_name: HCC


title: HCC_Trp53 -/-, Rbpj -/- [ATR_5066T1]

description: hepatocellular carcinoma


title: HA843, oligodendrocyte only, scRNAseq

description: 10x Genomics


title: 20-week ST Grin2a -/- Bulk RNA-seq Sample2


title: 20-week ST Grin2a -/- Bulk RNA-seq Sample3


title: CD4 T cells unstim_#5

city: Amsterdam

first: Chiara

last: Montironi

address: Meibergdreef 9

department: Experimental Immunology

institute: Amsterdam UMC

description:
b90_CD4.unstim
5_CD4 unstim

data_processing:
Sequence quality was assessed with FastQC, raw FASTq files were aligned with hisat2.1.0
Counts file is output of hisat
Assembly: GRCh38

source_name: Blood PBMCs

extract_protocol:
Total RNA was extracted with the Qiagen RNeasy kit
NEBNext Ultra II Directional RNA library prep kit for Illumina

value: Blood PBMCs

value: CD4 T cells

value: unstim


title: CD4 T cells stimulated in presence of PGA-1_#5

description:
b90_CD4.stimPGA
5_CD4 stimPGA

value: stimulated in presence of PGA-1


title: Whole intestine epithelial cells, dsRNA (K1) IP, control replicate 2

city: Piscataway

first: Michael

last: Verzi

state: NJ

address: 145 Bevier Road

department: Genetics

institute: Rutgers, The State University of New Jersey

description: D10-F530-K1_S10_L001_R1_001_count_nostrand.out

data_processing:
Quality checks were conducted with FastQC.
Tagging reads with UMIs: Unique molecular identifiers were added to raw reads using the umis package (version 1.0.3), followed by splice-aware alignment to the mm10 genome (from Gencode, GRCm38.p4) using STAR (version 2.7.10b).
Read alignment, deduplication, and raw counts: Reads were indexed with samtools (version 1.17), then deduplicated with UMI-tools (version 1.1.4) and counted with Htseq (version 2.0.2).
Read normalization: DESeq2 (version 1.40.1) was used to conduct differential analyses by calculating ratios of ratios. FPKM values were determined using edgeR (version 3.42.2) following the script provided by Gao et al (STAR Protocols, 2021).
Bigwig coverage: For bigwig files, bam files generated from STAR were processed with bamCoverage from deepTools (version 3.5.2).+
For analyzing repeating elements, RepeatMasker available from the UCSC Genome Browser was included during read alignment.
Assembly: mm10
Supplementary files format and content: Raw counts, bigwig, BAM, FPKM, and DESeq2 output files for each sample
Supplementary files format and content: Deduplicated raw counts were processed for differential enrichment by DESeq2 and outputted as a CSV table. FPKM table generated by edgeR from deduplicated raw counts was also outputted as a CSV table.

source_name: whole intestinal epithelial cells

extract_protocol:
Primary whole epithelial cells were isolated from the proximal half of the small intestine of adult mice (2 days after completing tamoxifen treatment) following incubation in EDTA for 50 minutes total at 4 C in tubes coated with 0.1% BSA in PBS. Isolated primary intestinal epithelial cells were resuspended in dsRIP buffer containing mammalian protease inhibitor and SUPERase RNase inhibitor for 5 minutes as previously described (Gao et al., 2021). After spin down, the supernatant was incubated with dsRNA J2 antibody (Cell Signaling Technology #76651) or dsRNA K1 antibody (Cell Signaling  Technology #28764) for 2 hours before adding to Protein G DynaBeads for 1 hour. RNA extraction was performed using Trizol and chloroform-based methodology, with two rounds of chloroform incubations to reduce phenol contamination. For pulldowns, RNA was extracted using an miRNeasy micro kit (Qiagen).
Library preparation included random hexamers and strand-specific rRNA depletion with UMIs (2x150 bp).

treatment_protocol: KAT2A/KAT2B DKO was induced with 100 mg/kg tamoxifen in 10% ethanol and 90% corn oil via intraperitoneal injections for 4 days daily. Controls received vehicle injections of 10% ethanol and 90% corn oil without tamoxifen.

value: 3 months

tag: Sex

value: Female

value: whole intestinal epithelial cells

value: Control

tag: antibody

value: dsRNA (K1), Cell Signaling Technology #28764

value: Vehicle injections IP


title: CD4 T cells stimulated_#5

description:
b90_CD4.stim
5_CD4 stim

tag: treatment

value: stimulated


title: Whole intestine epithelial cells, dsRNA (K1) IP, DKO replicate 1

description: D11-F551-K1_S11_L001_R1_001_count_nostrand.out

value: KAT2A/KAT2B DKO

value: Tamoxifen injections IP


title: HCC_Trp53 -/-, Rbpj -/- [ATR_5039T25]

description: hepatocellular carcinoma

tag: tissue

value: tumor


title: 20-week ST Grin2a +/- Bulk RNA-seq Sample5

first: Ally

last: Nicolella

address: 75 Ames St

institute: Broad Institute

value: Striatum

value: Grin2a +/-

tag: age


title: 20-week ST Grin2a WT Bulk RNA-seq Sample1

value: WT


title: CD4 T cells stimulated in presence of PGA-1_#4

description:
b89_CD4.stimPGA
4_CD4 stimPGA

value: Blood PBMCs


title: 20-week ST Grin2a +/- Bulk RNA-seq Sample4


title: HCC_Trp53 -/-, Rbpj -/- [ATR_3649T3]

description: hepatocellular carcinoma


title: Whole intestine epithelial cells, dsRNA (J2) IP, DKO replicate 2

description: D8-F554-J2_S8_L001_R1_001_count_nostrand.out

value: dsRNA (J2), Cell Signaling Technology #76651


title: CD4 T cells stimulated_#4

description:
b89_CD4.stim
4_CD4 stim

value: CD4 T cells


title: 20-week ST Grin2a +/- Bulk RNA-seq Sample3


title: HCC_Rbpj -/- [AR_5030T1]

description: hepatocellular carcinoma

value: Rbpj -/-


title: Whole intestine epithelial cells, dsRNA (K1) IP, DKO replicate 2

description: D12-F554-K1_S12_L001_R1_001_count_nostrand.out

value: 3 months


title: CD4 T cells unstim_#4

description:
b89_CD4.unstim
4_CD4 unstim

value: unstim


title: CD4 T cells stimulated in presence of PGA-1_#3

description:
b88_CD4.stimPGA
3_CD4 stimPGA

value: stimulated in presence of PGA-1


title: Whole intestine epithelial cells, dsRNA (J2) IP, control replicate 2

description: D6-F530-J2_S6_L001_R1_001_count_nostrand.out

value: Female

value: whole intestinal epithelial cells

value: Control


title: HCC_Rbpj -/- [AR_4162T2]

description: hepatocellular carcinoma


title: 20-week ST Grin2a +/- Bulk RNA-seq Sample2


title: 12-week ST Grin2a WT Bulk RNA-seq Sample4


title: 20-week ST Grin2a -/- Bulk RNA-seq Sample1

value: Grin2a -/-


title: Whole intestine epithelial cells, dsRNA (J2) IP, DKO replicate 1

description: D7-F551-J2_S7_L001_R1_001_count_nostrand.out

value: KAT2A/KAT2B DKO


title: CD4 T cells unstim_#3

description:
b88_CD4.unstim
3_CD4 unstim


title: Whole intestine epithelial cells, input, DKO replicate 2

description: D4-F554-input_S4_L001_R1_001_count_nostrand.out

value: Tamoxifen injections IP


title: HCC_Trp53 -/-, Rbpj -/- [ATR_3652T2]

description: hepatocellular carcinoma

value: tumor


title: HCC_Trp53 -/-, Rbpj -/- [ATR_3654T1]

description: hepatocellular carcinoma


title: CD4 T cells stimulated_#3

description:
b88_CD4.stim
3_CD4 stim

value: stimulated


title: CD4 T cells stimulated in presence of PGA-1_#2

description:
b87_CD4.stimPGA
2_CD4 stimPGA


title: CD4 T cells stimulated_#2

description:
b87_CD4.stim
2_CD4 stim


title: HCC_Rbpj -/- [AR_4162T1]

description: hepatocellular carcinoma


title: Whole intestine epithelial cells, dsRNA (K1) IP, control replicate 1

description: D9-F524-K1_S9_L001_R1_001_count_nostrand.out

value: dsRNA (K1), Cell Signaling Technology #28764

value: Vehicle injections IP


title: 12-week ST Grin2a WT Bulk RNA-seq Sample3

value: Striatum

value: WT


title: 20-week ST Grin2a +/- Bulk RNA-seq Sample1

value: Grin2a +/-


title: Whole intestine epithelial cells, input, control replicate 1

description: D1-F524-input_S1_L001_R1_001_count_nostrand.out


title: Whole intestine epithelial cells, dsRNA (J2) IP, control replicate 1

description: D5-F524-J2_S5_L001_R1_001_count_nostrand.out

value: dsRNA (J2), Cell Signaling Technology #76651


title: iCCA_Trp53 -/- [AT_3733T3]

description: intrahepatic cholangiocarcinoma


title: iCCA_Trp53 -/- [AT_3977T5]

description: intrahepatic cholangiocarcinoma


title: 12-week ST Grin2a WT Bulk RNA-seq Sample2


title: iCCA_Trp53 -/- [AT_3976T8]

description: intrahepatic cholangiocarcinoma


title: Whole intestine epithelial cells, input, control replicate 2

description: D2-F530-input_S2_L001_R1_001_count_nostrand.out

value: 3 months


title: CD4 T cells stimulated in presence of PGA-1_#1

description:
b83_CD4.stimPGA
1_CD4 stimPGA

value: Blood PBMCs

value: CD4 T cells


title: CD4 T cells unstim_#2

description:
b87_CD4.unstim
2_CD4 unstim

value: unstim


title: iCCA_Trp53 -/- [AT_5283T20]

description: intrahepatic cholangiocarcinoma


title: iCCA_Trp53 -/- [AT_3731T3]

description: intrahepatic cholangiocarcinoma


title: 12-week ST Grin2a -/- Bulk RNA-seq Sample5


title: CD4 T cells stimulated_#1

description:
b83_CD4.stim
1_CD4 stim


title: Whole intestine epithelial cells, input, DKO replicate 1

description: D3-F551-input_S3_L001_R1_001_count_nostrand.out

value: Female

value: whole intestinal epithelial cells


title: 12-week ST Grin2a -/- Bulk RNA-seq Sample2

value: Grin2a -/-


title: CD4 T cells unstim_#1

description:
b83_CD4.unstim
1_CD4 unstim


title: ImmatureB.1

city: Chicago

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

description: Primary flow purified WT small pre-B cells from mouse bone marrow

data_processing:
Hi-C processing was performed using Juicer 6 with default values, aligning to reference genome mm9; MboI fragment sizes were downloaded for mm9 from https://aryeelab.github.io/hichipper/RestrictionFragmentFiles/. Analysis was performed using the juicer.sh pipeline script.
Assembly: mm9
Supplementary files format and content: .hic file from JUICER

source_name: Immuture B cell

growth_protocol: No cultured cells were used. All cells used are primary small pre-B cells isolated from bone marrow of WT or BRWD knock out mice.

extract_protocol:
In situ Hi-C was performed as previously described (Rao Et. al. Cell 2014). Briefly, WT and Brwd1-/- small pre-B and WT immature B cells (5x10^6 for each stage) were crosslinked with 1% formaldehyde following a wash with ice cold PBS. Membranes were lysed to keep nuclei intact followed by restriction digestion with 100U of MboI (NEB R0147). The DNA ends were marked with biotin, ligated proximally and crosslinks were reversed. DNA shearing and size selection were then performed for fragments 300-500 bp. The amount of DNA was quantified with the Qubit dsDNA High Sensitivity Assay (Life technologies, Q32854), and biotin pull down was done to prepare the final in-situ Hi-C libraries (in duplicate).
Libraries were prepered  using Immumina Library preparation kit and sequenced on the Illumina NovaSeq 6000.

treatment_protocol: No treatment was performed

value: Immuture B cell


title: HCC_Trp53 -/- [AT_5283T7]

description: hepatocellular carcinoma


title: HCC_Trp53 -/- [AT_3977T2]

description: hepatocellular carcinoma


title: SetKO_3

city: 南京

first: lixia

last: dong

address: 学府路12号

department: 模式动物研究所

institute: 南京大学

data_processing:
TopHat (version2.1.1) software used for basecalling.
The sequencing data were mapped to mouse genome (Ensemble GRCm38.p5).
The expression levels of each gene was calculated by FPKM (fragments per kilobase of transcript per million fragments mapped) method. gene abundances and differential expression analysis were quantified by RSEM and R statistical package software EdgeR (Empirical analysis of Digital Gene Expression in R).
Assembly: The sequencing data were mapped to mouse genome (Ensemble GRCm38.p5).
Supplementary files format and content: The file provides the original expression of the gene, including the count value of each gene for each sample, the summary of the tpm value, and the diff. file after the comparison between the experimental group and the control group.

source_name: mouse embryonic stem cell

extract_protocol: RNA-seq transcriptome librariy was prepared using TruSeqTM RNA sample preparation Kit from Illumina.

treatment_protocol: ES cells were typsined and RNA was harvested using Trizol reagent (Invitrogen) following the manufacturer’s instructions

tag: strain

value: mouse embryonic stem cell


title: 12-week ST Grin2a -/- Bulk RNA-seq Sample1


title: 12-week ST Grin2a WT Bulk RNA-seq Sample1


title: SetKO_2


title: SpreB-WT.1


title: U251 shCD44 TMZ 2

city: Guangzhou

first: Chongxian

last: Hou

state: Guangdong

address: Industrial Road No.253

department: Neurosurgery

institute: Zhujiang Hospital, Southern Medical University

data_processing:
Reads were further filtered by fastp (version 0.18.0). The parameters were as follows: 1) removing reads containing adapters; 2) removing reads containing more than 10% of unknown nucleotides(N); 3) removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Assembly: The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach.
Supplementary files format and content: text file with raw counts
Supplementary files format and content: text file with FPKM values.

growth_protocol: Cells were cultured in high-glucose Dulbecco’s modified eagle medium (DMEM; ThermoFisher Biochemical Products Co., Ltd, Beijing, China) supplemented with 10% fetal bovine serum (FBS; Life Technologies Australia Pty Ltd, Thornton, Australia) at 37℃ under 5% CO2.

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis.
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads. Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA).The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).And polymerase chain reaction (PCR) amplified.The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).

treatment_protocol: Cells were treated with DMSO or 50 uM TMZ for 24 hours.

tag: cell line

value: human glioblastoma cells

value: CD44 knockdown

value: Temozolomide


title: U251 shCD44 TMZ 1


title: HCC_Trp53 -/- [AT_3733T1]

description: hepatocellular carcinoma

value: tumor


title: 12-week ST Grin2a -/- Bulk RNA-seq Sample4

value: Striatum


title: U251 shCD44 TMZ 3


title: 12-week ST Grin2a +/- Bulk RNA-seq Sample2


title: HCC_Trp53 -/- [AT_3975T4]

description: hepatocellular carcinoma


title: SpreB-Brwd1KO.1

description: Primary flow purified small pre-B cells from BRWD1 knock-out mouse bone marrow


title: HCC_Trp53 -/- [AT_3976T1]

description: hepatocellular carcinoma


title: SetKO_1


title: 12-week ST Grin2a +/- Bulk RNA-seq Sample4


title: HCC_Trp53 -/- [AT_3731T1]

description: hepatocellular carcinoma


title: U251 NC TMZ 2

value: WT


title: 12-week ST Grin2a +/- Bulk RNA-seq Sample3

value: Grin2a +/-


title: SetFF_3


title: 12-week ST Grin2a +/- Bulk RNA-seq Sample1


title: 12-week ST Grin2a -/- Bulk RNA-seq Sample3


title: SetFF_2


title: HCC_Trp53 +/+ [A_3717T1]

description: hepatocellular carcinoma


title: U251 shCD44 DMSO 3

value: DMSO


title: HCC_Trp53 +/+ [A_3717T2]

description: hepatocellular carcinoma


title: 4-week ST Grin2a WT Bulk RNA-seq Sample4


title: HCC_Trp53 +/+ [A_3716T1]

description: hepatocellular carcinoma


title: 4-week ST Grin2a WT Bulk RNA-seq Sample5


title: U251 NC TMZ 1


title: HCC_Trp53 +/+ [A_3715T2]

description: hepatocellular carcinoma


title: NK_3


title: U251 shCD44 DMSO 2


title: U251 NC TMZ 3


title: 4-week ST Grin2a WT Bulk RNA-seq Sample3


title: NK_1


title: U251 shCtrl DMSO 3


title: U251 shCD44 DMSO 1


title: 4-week ST Grin2a WT Bulk RNA-seq Sample2


title: WT_3


title: 4-week ST Grin2a WT Bulk RNA-seq Sample1


title: 4-week ST Grin2a -/- Bulk RNA-seq Sample4


title: SetFF_1


title: WT_1


title: U251 shCtrl DMSO 2


title: WT_2


title: U251 shCtrl DMSO 1


title: IMR90 cells, normal Proliferating conditions, replicate 2, control sample,RNA-seq

city: Athens

first: Vassilis

middle: George

last: Gorgoulis

state: Athens

address: Mikras Asias 75

department: Medicine

country: Greece

institute: University of Athens

data_processing:
Quality filtering for each library was performed with the FastQC tool (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
To detect over-represented Adapter and Kmer sequence files, the small utility program Minion was used (https://www.ebi.ac.uk/research/enright/software/kraken).
Adapter trimming was accomplished with Cutadapt, where the quality trimming threshold was set to 20 with a minimum read length set to 21 nt.
RNA-seq samples were mapped using STAR aligner using hg38 indexes.
Ribosome profiling data were aligned with TopHat aligner preferably using parameters bowtie1-g1.
For the downstream analysis of the Ribo-Seq data we used RiboTaper algorithm.
To estimate changes in mRNA abundance regarding the RNA-seq analysis we used featureCounts from the Rsubread package
To determine determine RNA abundance differences edgeR algorithm was used.
For translation efficiency changes, the Deseq2 pipeline was implemented after filtering the reads while excluding non-coding RNAs, tRNAs, rRNAs, miRNAs and snoRNAs.
Assembly: hg38
Supplementary files format and content: counts_RNA_Ribo.txt =Read count matrix for Ribo-Seq and RNA-Seq

growth_protocol: Human lung fibroblasts (IMR-90, ATCC) and Phoenix™-Ampho (ATCC) cells were maintained in Dulbecco′s High-Glucose Modified Eagle Medium (DMEM), containing 10% fetal bovine serum and 1% Penicillin-Streptomycin, and incubated at 37°C with 5% O2 and 5% CO2.

extract_protocol:
Cells were harvested 14 days post senescence induction. Growth media was removed, and the cells were washed with cold PBS containing 100 μg/ml of cycloheximide. Cells were subsequently scraped and pelleted, and later stored at -80°C until they were dispatched for sequencing. Stranded mRNA-seq libraries were generated from flash frozen cell pellets. Cell pellets were lysed in ice-cold polysome lysis buffer (20mM Tris pH 7.5, 150mM NaCl, 5mM MgCl2,1mM DTT, 1% Triton X-100) supplemented with cycloheximide (100µg/mL).  For stranded mRNA-seq, total RNA was extracted from 10% of lysate using TRIzol, before mRNA was poly(A)-enriched, fractionated, and converted into Illumina compatible cDNA libraries. Stranded mRNA-seq libraries were sequenced 150PE on Illumina’s Nova-seq 6000 platform to depths of 20 million raw read pairs per sample. For Ribo-seq, the remaining lysates which were not used for RNA-seq were RNase- treated before ribosomes were enriched by size exclusion chromatography using MicroSpin S-400 HR columns. Following RNA purification and size selection of ribosome protected mRNA fragments on 15% urea PAGE gels, contaminating rRNA was depleted from samples using EIRNA Bio’s custom biotinylated rRNA depletion oligos before the enriched fragments were converted into Illumina compatible cDNA libraries. Ribo-seq libraries were sequenced 150PE on Illumina’s Nova-seq 6000 platform to a depth of 100 million raw read pairs per sample.
The sequence structure of these reads is as follows: • UUUUUUUUUUUU - QQQQ - rpf sequence - NNNNN - BBBBB – AGATCGGAAGAGCACACGTCTGAA • The first 12nt are unique molecular identifiers (UMIs) (can be any 12 nt). • The next 4nt are untemplated additions (Usually C or G). • The read begins with the sequence of interest. • The next 5nt are unique molecular identifiers (UMIs) (can be any 5 nt). • The next 5nt are the Barcode used to demultiplex (the fastq files have already been demultiplexed). • The adapter sequence – AGATCGGAAGAGCACACGTCTGAA

treatment_protocol: Plasmids, retrovirus production and RAS transduction:Phoenix cells were seeded in T75 flasks one day prior to transfection, and were subsequently transfected with 1 ml of transfection mix in 6 ml of complete DMEM for 48 hours. The transfection mix was prepared with 1 µg of pLNCX2 ER:ras (Addgene #67844) per 100 µL of Opti-MEM™ (ThermoFisher Scientific) and 2% TurboFect™ (ThermoFisher Scientific).The retrovirus-containing medium was collected, filtered, and then used to transduce IMR-90 cells. After 24 hours of transduction, IMR-90 cells were incubated with a selection medium comprised of complete DMEM + G-418 (400 μg/mL). After 10 days of selection, IMR-90ER:RAS cells were maintained in complete DMEM + G-418 (200 μg/mL).Senescence induction: For replicative senescence, IMR-90 cells were continuously passaged to replicative exhaustion as previously described (DOI: 10.15252/msb.20209760 ). For H2O2-induced senescence, IMR-90 cells were treated with 600 μM H2O2 twice, as also described previously (DOI: 10.1007/978-1-62703-556-9_11 ). For oncogene-induced senescence, RAS was activated by treating the IMR-90ER:RAS cells with 100 nM of 4-hydroxy-tamoxifen (4-OHT) for 7 days. Senescence was verified seven days post induction.

value: IMR90 cells(fibroblasts isolated from normal lung tissue)

value: control

value: (normal Proliferating cells)


title: H35_2


title: NK_2


title: 4-week ST Grin2a -/- Bulk RNA-seq Sample2


title: H35_3


title: H35_1


title: HCC_Trp53 +/+ [A_3681T1]

description: hepatocellular carcinoma


title: H13_3


title: IMR90 cells, Oncogene Induced Senesence (OIS), replicate 2,RNA-seq

value: Oncogene Induced Senesence (OIS)


title: IMR90 cells, Oncogene Induced Senesence (OIS), replicate 1,RNA-seq


title: 4-week ST Grin2a +/- Bulk RNA-seq Sample5


title: H13_2


title: 4-week ST Grin2a +/- Bulk RNA-seq Sample4


title: H13_1


title: 4-week ST Grin2a -/- Bulk RNA-seq Sample5


title: IMR90 cells, H2O2 treatment (stress), replicate 1,RNA-seq

value: H2O2 treatment

value: Senescence (Replicative exhaustion) + H2O2 treatment


title: IMR90 cells, H2O2 treatment (stress), replicate 2,RNA-seq


title: HT_3


title: 4-week ST Grin2a +/- Bulk RNA-seq Sample3


title: 4-week ST Grin2a +/- Bulk RNA-seq Sample2


title: 4-week ST Grin2a -/- Bulk RNA-seq Sample3

value: Grin2a -/-


title: HT_2


title: IMR90 cells, normal Proliferating conditions, replicate 2, control sample,Ribo-seq


title: HT_1


title: IMR90 cells, normal Proliferating conditions, replicate 1, control sample,RNA-seq


title: IMR90  cells, Oncogene Induced Senesence (OIS), replicate 2


title: IMR90 cells, normal Proliferating conditions, replicate 1, control sample,Ribo-seq


title: 2-week ST Grin2a WT Bulk RNA-seq Sample5


title: H5_3


title: 2-week ST Grin2a WT Bulk RNA-seq Sample4


title: IMR90  cells, Oncogene Induced Senesence (OIS), replicate 1,Ribo-seq


title: H5_2


title: IMR90  cells, H2O2 treatment (stress), replicate 2,Ribo-seq


title: 4-week ST Grin2a -/- Bulk RNA-seq Sample1


title: Non-neoplastic (NT) [S11-2]

city: Lyon

first: Virginie

last: MARCEL

address: 28 rue Laennec

institute: Cancer Research Center of Lyon

data_processing:
We used the pipeline: RiboMethSeq-nf. fastQC was used to verify sequencing quality and adapter removal was performed using Trimmomatic. The trimmed reads were aligned by Bowtie2 on the 7.2 kb-long rRNA sequence of reference (NR_046235) and the 5’ read-ends were computed using bedtool genomcov utility
The C-score was calculated using a normalization against the median raw counts of neighbouring +/- 6 nucleotide window
Assembly: NR_046235
Supplementary files format and content: Raw counts of 5' end reads on each position of each rRNA
Supplementary files format and content: The C-score was calculated using a normalization against the median raw counts of neighbouring +/- 6 nucleotide window (Marcel et al, NAR Cancer 2020)
Library strategy: RiboMeth-Seq

extract_protocol: Total RNA was extracted using either the Maxwell RSC simplyRNA Tissue Kit (Promega) with Maxwell RSC Instrument (Promega) configured with Low Elution Volume (LEV) hardware according to the manufacturer’s protocol or TRIzol (Invitrogen) according to manufacturer’s instructions.   Total RNA was partially and randomly fragmented under alkaline conditions. Libraries of 24 samples were prepared simultaneously using NEBNext Multiplex Small RNA Library kit (New England Biolabs). A calibrated source of total RNA (Human Xpress Ref Universal Total RNA, Qiagen) was introduced in each library.

value: brain

tag: rna extraction_protocol

value: Trizol

value: validation

tag: sequencing library


title: IMR90 cells, H2O2 treatment (stress), replicate 1,Ribo-seq


title: 2-week ST Grin2a WT Bulk RNA-seq Sample2


title: H3_3

value: mouse embryonic stem cell


title: H3_2


title: 2-week ST Grin2a WT Bulk RNA-seq Sample1


title: 2-week ST Grin2a -/- Bulk RNA-seq Sample4


title: H1_3


title: 2-week ST Grin2a -/- Bulk RNA-seq Sample5


title: 4-week ST Grin2a +/- Bulk RNA-seq Sample1


title: 2-week ST Grin2a WT Bulk RNA-seq Sample3


title: H5_1


title: Non-neoplastic (NT) [S9-2]

tag: pfs

tag: os


title: 2-week ST Grin2a -/- Bulk RNA-seq Sample3


title: Glioblastoma (G) [S7-2]

tag: mitotic index

tag: cohort


title: H1_2


title: 2-week ST Grin2a -/- Bulk RNA-seq Sample2


title: Glioblastoma (G) [S6-2]


title: H1_1


title: 2-week ST Grin2a -/- Bulk RNA-seq Sample1


title: Non-neoplastic (NT) [S10-2]


title: C3_2


title: C3_1


title: Glioblastoma (G) [S5-2]


title: C3_3


title: 2-week ST Grin2a +/- Bulk RNA-seq Sample4


title: Glioblastoma (G) [S4-2]


title: Glioblastoma (G) [S8-2]


title: TgSPI1 leukemic_921

city: VILLEJUIF

first: Christel

last: GUILLOUF

address: 114 rue Edouard vaillant

institute: Gustave Roussy

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped onto mm10/GRCm38 assembly of mouse genome using STAR v2.5.3a [1].
Gene expression was quantified using htseq-count v0.6.1p1 [2] with gene annotations from Ensembl release 98.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw count (htseq-count) for each Sample

extract_protocol:
RNA was extracted using Qiagen Reasy Mini kit
RNA-Seq libraries were generated from 300 ng of total RNA using TruSeq Stranded mRNA Library Prep Kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

tag: strain background

tag: genotype/variation

tag: tumor stage

value: leukemic

value: erythroid blasts


title: Glioblastoma (G) [S2-2]


title: Glioblastoma (G) [S3-2]


title: Glioblastoma (G) [S1-2]


title: 2-week ST Grin2a +/- Bulk RNA-seq Sample3

value: Striatum

tag: genotype


title: TgSPI1 leukemic_601

tag: cell type


title: 2-week ST Grin2a +/- Bulk RNA-seq Sample2


title: 2-week ST Grin2a +/- Bulk RNA-seq Sample1


title: TgSPI1 leukemic_606


title: Non-neoplastic (NT) [S11-1]

value: Maxwell


title: 20-week SSC Grin2a WT Bulk RNA-seq Sample10

source_name: Somatosensory Cortex

value: Somatosensory Cortex

value: WT


title: 20-week SSC Grin2a WT Bulk RNA-seq Sample9


title: TgSPI1 preleukemic_837

value: preleukemic


title: Non-neoplastic (NT) [S10-1]


title: 20-week SSC Grin2a WT Bulk RNA-seq Sample8


title: TgSPI1 preleukemic_812


title: Non-neoplastic (NT) [S9-1]


title: 20-week SSC Grin2a WT Bulk RNA-seq Sample7


title: TgSPI1 preleukemic_663


title: Glioblastoma (G) [S8-1]


title: 20-week SSC Grin2a WT Bulk RNA-seq Sample6


title: TgSPI1 preleukemic_633


title: 20-week SSC Grin2a WT Bulk RNA-seq Sample4


title: 20-week SSC Grin2a WT Bulk RNA-seq Sample5


title: EF_12_3

city: Cleveland

first: Daniel

last: McGrail

state: Ohio

address: 9500 Euclid Avenue

department: Center for Immunotherapy and Precision Immuno-Oncology

institute: Cleveland Clinic

data_processing:
TPM determined using Kallisto v0.44.1
Genome_build: GRCm38
Supplementary_files_format_and_content: Files are given as TPM for each sample

source_name: ear

extract_protocol:
RNA was extracted using the Qiagen AllPrep DNA/RNA Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: condition

value: post-mortem

value: ear

value: fibroblast

tag: time point

value: 12 hr

tag: replicate