title: P217

city: York

first: Ethan

middle: James

last: Redmond

address: Wentworth Way

department: Department of Biology

country: United Kingdom

institute: University of York

description: 4 days of stratification at 4C; 10 days grown on plates (16h light / 8h dark); 10 days grown in soil (same photoperiod); then sampled

data_processing:
Before analysis of the raw sequencing data, FastQC v0.11.7(Andrews et al. 2012) was used to assess read quality.
Illumina adapters were trimmed using CutAdapt v3.4 (Martin 2011). (parameters: -a AGATCGGAAGAG -A AGATCGGAAGAG -j 0 -q 10,10 -m 30 -u 10 -U 10)
Reads were quantified using Salmon v1.6.0 (Patro et al. 2017) and the TAIR10 transcriptome (Berardini et al. 2015). (parameters: -l A  --validateMappings)
To analyse genetic variation within the population, we followed GATK guidelines for short variant discovery from RNA-seq data.
We used STAR (v2.7.10b; two-pass mode) to align reads to TAIR10 genome, revision 56 (Dobin et al. 2013). (parameters: --runThreadN 20 --readFilesIn ${file}_1.fq.gz ${file}_2.fq.gz --readFilesCommand "gunzip -c" --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 5000000000 --twopassMode Basic --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 0 --outFilterMismatchNmax 1)
We then pre-processed the aligned reads using the commands ‘MarkDuplicates’ (parameters: gatk --java-options '-Xmx28G' MarkDuplicates -ASO coordinate --VERBOSITY DEBUG --MAX_RECORDS_IN_RAM 5000000) and ‘SplitNCigarReads’ (parameters: gatk --java-options '-Xmx28G' SplitNCigarReads --verbosity DEBUG) from GATK (v4.3.0.0) (Poplin et al. 2018).
We used the command ‘HaplotypeCaller’ (parameters: -ERC GVCF --dont-use-soft-clipped-bases true --standard-min-confidence-threshold-for-calling 20) to produce genomic variant calling format (gVCF) files per sample.
Finally, we combined GVCF files using 'CombineGVCFs' (parameters: gatk --java-options '-Xmx60G' CombineGVCFs) produced identified single-nucleotide variants (SNVs) and insertions / deletions (indels) which were confidently called across the whole population, using ‘GenotypeGVCFs’ (parameters: gatk --java-options "-Xmx60g" GenotypeGVCFs).
For further processing of these initial SNVs and indels, we followed the filtering guidelines suggested by ref. (Cruz et al. 2020). Specifically, we selected only biallelic variants with a minimum genotype quality of 40, and which were called in at least 80% of all samples, using VCFtools (v0.1.16) (Danecek et al. 2011). (parameters: --minGQ 40 --max-missing 0.8 --out joint_genotyping/all_genotyped_filtered.vcf --recode)
We then imputed missing genotypes using Beagle (v5.4, 22Jul22, 46e) on default settings (Browning, Zhou, and Browning 2018). Note, due to pre-processing by Beagle, the variant calling format (VCF) file includes two versions of the same heterozygous haplotype (‘0|1’ and ‘1|0’). (parameters: java -Xmx10240m -jar beagle.22Jul22.46e.jar  nthreads=2)
Finally, we selected variants with a minor allele frequency (MAF) of at least 0.05, using VCFtools. (vcftools --maf 0.05 --recode)
Assembly: TAIR10
Supplementary files format and content: Salmon quantification folder for each sample, included as a .tar file
Supplementary files format and content: A final VCF file for all samples

source_name: 3rd and 4th rosette leaves

growth_protocol: The Arabidopsis thaliana ecotype Wassilewskija Ws-2 seeds were surface sterilized and then grown in MS-agar, 1% sucrose plates. These were cold treated at 4C in the dark for 4 days before being grown in 16h light/ 8h dark cycles at a constant temperature of 21C. Seedlings were transferred to soil (with 5% sand) after 10 days and the 3rd and 4th true rosette leaves were tracked for future reference. After 10 days in soil conditions, 75 plants were selected from the total of 225 plants grown, with plants selected to ensure a diversity of bolting statuses. At ZT4 (4h after lights on) the following day, the 3rd and 4th rosette leaves for each individual plant were pooled and flash frozen in liquid nitrogen.

extract_protocol:
Total RNA was isolated from these samples using the Qiagen RNeasy Plant Mini Kit (Cat no. 74904). Residual genomic DNA was removed using the Invitrogen Turbo DNA-free kit (Cat no. AM1907), according to the manufacturer’s protocol.
Libraries were prepared with the NEBNext Ultra II Directional Library Prep Kit for Illumina (Cat no. E7765), using the NEBNext poly(A) magnetic isolation module (Cat no. E7490). Quality control was performed with the Agilent 2100 Bioanalyzer instrument (Part no. G2939BA). Finally, a total of 70 libraries were pooled and sequenced, via Novagene, using one lane on an Illumina NovaSeq system.

value: 3rd and 4th rosette leaves


title: P219

status: Public on Sep 11 2023

type: SRA

library_source: transcriptomic

molecule: polyA RNA

organism: Arabidopsis thaliana

tag: tissue

tag: genotype


title: OVE4_p53.3 [JP-15]

city: Ottawa

first: David

last: Cook

state: ON

address: 501 Smyth Rd

department: Cancer Therapeutics Program

country: Canada

institute: Ottawa Hospital Research Institute

description:
mouse_sample_annotation.csv
txi_mouse.rds
tpm_matrix._mouse.csv

data_processing:
Pseudoalignment and transcript quantification for each sample was performed using Kallisto (v0.45.0) with the GRCm38 build of the mouse genome. The R package tximport (v1.24.0) was used to load transcript quantifications, converting to gene-level transcript estimates.
Assembly: GRCm38
Supplementary files format and content: mouse_sample_annotation.csv - Annotation table providing metadata for each sample
Supplementary files format and content: txi_mouse.rds - R object containing raw counts and tpm matrices for each sample following import with tximport
Supplementary files format and content: tpm_matrix._mouse.csv - Transcripts per million (TPM) count matrix for all genes and samples

organism: Mus musculus

source_name: cell line

extract_protocol:
Total RNA was extracted according to the manufacturer’s instructions with the RNeasy Plus Mini Kit (Qiagen) for the majority of samples. IP tumours collected from mice injected with ID8-Trp53-/-, ID8-Trp53-/-; Brca1-/-, ID8-Trp53-/-; Brca2-/-, ID8-Trp53-/-; Nf1-/-, and ID8-Trp53-/-; Pten-/- cells were isolated at endpoint using the total RNA Purification Kit (Norgen Biotek Corporation, ON, Canada) as per the manufacturer’s instructions.
RNA-Seq libraries were generated from 250 ng of total RNA as following: mRNA enrichment was performed using the NEBNext Poly(A) Magnetic Isolation Module (New England BioLabs). cDNA synthesis was achieved with the NEBNext RNA First Strand Synthesis and NEBNext Ultra Directional RNA Second Strand Synthesis Modules (New England BioLabs). The remaining steps of library preparation were done using and the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs). Adapters and PCR primers were purchased from New England BioLabs.
The pool was loaded at 200pM on a Illumina NovaSeq S4 lane using Xp protocol as per the manufacturer’s recommendations. The run was performed for 2x100 cycles (paired-end mode). A phiX library was used as a control and mixed with libraries at 1% level. Base calling was performed with RTA v3. Program bcl2fastq2 v2.20 was then used to demultiplex samples and generate fastq reads

value: cell line

tag: model


title: P213


title: ASCL1 ChIP E13.5 BG WT 2

city: Davis

first: Alex

middle: S.

last: Nord

state: CA

address: 1544 Newton Court

department: Center for Neuroscience

country: USA

institute: University of California Davis

library_source: genomic

data_processing:
We applied the MAPS pipeline to detect statistically significant H3K4me3-centric long-range chromatin interactions from PLAC-seq data. We only analyzed intra-chromosomal interactions for autosomal chromosomes, and identified chromatin interactions at 10-kb bin resolution between 20 kb and 1 Mb. We first mapped the raw paired-end reads (i.e. FASTQ file) to the mm10 reference genome using BWA mem. Next, we applied filtering steps to remove PCR duplicates, low-quality reads (MAPQ <= 30) and chimeric reads. We then split the remaining mapped reads into short-range (distance between pair ends within 1 kb) and long-range reads (distance between pair ends between 1 kb and 1 Mb). We used the short-range and long-range reads to measure protein immunoprecipitation (IP) efficiency and detect long-range chromatin interactions, respectively.
For ChIP-seq, quality-controlled FASTQ files containing the reads were further cleaned-up from the remaining adapter sequences using Trim Galore version 0.4.5. The resulting reads were aligned to the mouse (mm10) genome using BWA version 0.7.9a, and duplicates removed with Samtools version 1.8. Peaks of enriched binding regions against both negative binding and input DNA control were called using MACS version 2.1 with p-value cutoffs of 10E-4.
Assembly: mm10
Supplementary files format and content: PLAC-seq: interaction bed files
Supplementary files format and content: ChIP-seq: narrow peaks

molecule: genomic DNA

source_name: brain

extract_protocol:
ChIP was performed using antibodies against SP9, ARX, ASCL1, GSX2, and NR2F1. Basal ganglia were dissected in cold PBS from CD1 embryos (2 L/Ab for NR2F1; 3 L/Ab for ARX, ASCL1, and GSX2). The basal ganglia consisted of the LGE, MGE and CGE progenitor and mantle zones. The dissected basal ganglia were either fixed in 1% formaldehyde at RT for 10 min (SP9, ASCL1, GSX2, NR2F1) or fixed in 1.5% formaldehyde at RT for 20 min (ARX), neutralized with glycine, and washed gently in PBS. The fixed cells were lysed with a hypotonic buffer (50 mM Tris pH 7.5 / 0.5% NP40 / 0.25% sodium deoxycholate / 0.1% SDS / 150 mM NaCl) to obtain the nuclei; these were then lysed in 1% SDS buffer and the chromatin was sheared into 300-1000 bp fragments by sonicating for 40 cycles (30 sec on and 45 sec off) using a bioruptor (Diagenode). Immunoprecipitation (IP) reactions were performed with the sheared chromatin diluted 1/10 times with “dilution buffer” (0.01% SDS, 1.1% Triton X- 100, 1.2 mM EDTA, 16.7 mM Tris-HCl, pH 8.1, 167mM NaCl, usually in 6 ml. Antibody was then added to either 5 µg (ARX, SP9, NR2F1) or 8 µg (ACSL1, GSX2) specific antibodies. Negative control ChIP reactions used either IgG (5µg) or blocking peptide (ARX, 400x molar excess). Antibody/chromatin complexes were purified using Dynabeads (Invitrogen) and washed extensively in “wash buffer” (low salt, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl, pH 8.1, 150 mM NaCl; high salt, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl, pH 8.1, 500 mM NaCl; LiCl, 0.25 M LiCl, 1% IGEPAL CA630, 1% deoxycholic acid (sodium salt), 1mM EDTA, 10mM Tris, pH 8.1 and TE). Complexes were eluted with 1% SDS, 10 mM sodium bicarbonate buffer at 65 ºC for 10 min. Eluted chromatin was reverse-crosslinked overnight at 65 ºC in the presence of 500 mM NaCl, then subsequently treated with RNase (10 µg/200 µL reaction, 15 min at 37 ºC) and Proteinase K (10 µg/200 µL reaction, 60 min at 55 ºC) and cleaned using a ChIP DNA Clean & Concentrator kit (Zymo Research). The chromatin was quality-controlled (QC) using qPCR to check for enrichment of genomic DNA fragments that were expected, and not expected, to have the different TF binding.
For ChIP-seq, libraries were prepared using an Ovation Ultralow DR Multiplex System (Nugen), size- selected in the range of 300 bp on a chip from BluePippin (Sage Science) and lastly QC tested on a Bioanalyzer (Agilent). The libraries were sequenced as single-end 50-bp reads on a HiSeq 4000 (Illumina) at the Center for Advanced Technology (UCSF). PLAC-seq libraries for E13.5 basal ganglia were prepared similar to a previously published protocol61. 3 to 7 million cells were used for each library. If the cells appeared aggregated, they were dissociated with gentle MACS dissociator or Dounce homogenizer. Each PLAC-seq library was prepared using DpnII as the restriction enzyme and Dynabeads M-280 sheep anti-rabbit IgG (Invitrogen #11203D) mixed with 5 µg of H3K4me3 (04-745, Millipore) for the chromatin immunoprecipitation step. Finally, libraries were prepared with the Illumina TruSeq adaptors and the final libraries were sent for paired-end sequencing on the HiSeq X Ten (150-bp reads) equipment.
ChIP-seq, PLAC-seq

value: brain

tag: cell line

value: basal ganglia

tag: cell type

value: wild-type

tag: chip antibody


title: P205


title: P214


title: OVE4_p53.2 [JP-14]


title: VSG2_8 - E0771 tumor excised from C57BL6Ncrl mouse_DIO-HFD

type: RNA

city: chapel hill

first: michael

middle: francis

last: coleman

state: North Carolina

address: 235 dauer drive

institute: UNC

hyb_protocol: Labeled cDNA was hybridized to the plate using GeneTitan Hybridization Wash and Stain Kit for WT Arrays (Affymetrix)

scan_protocol: arrays were scanned using GeneTitan

data_processing: Quality control and differential gene expression was conducted using TAC4 software (Affymetrix)

label: biotin

molecule: total RNA

source_name: Obese - no weight loss

label_protocol: The GeneChip® WT PLUS Reagent Kit (Affymetrix, Santa Clara, CA) was used to prepare the samples

growth_protocol: C57BL/6N mice were randomized to receive a control diet D12450J, or a 60% high fat diet (D12492) to promote diet induced obesity. Once obese, mice were randomized to either remain obese or undergo weight loss via 1) vertical sleeve gastrectomy with low-fat diet, 2) intermittent calorie restriction, or 3) chronic calorie restriction.

extract_protocol: RNA was isolated by bead beating in TRIzol reagent, followed by isolation with EZNA HP Total RNA kit (omega bio-tek)

treatment_protocol: All mice received either sham surgery or vertical sleeve gastrectomy. 25 weeks after initial randomization mice were orthotopically injected with E0771 cells into the 4th mammary fat pad and tumors were allowed to grow till endpoint. At endpoint the tumor was removed and used for nucleic acid extraction.

value: tumor

tag: group

value: DIO-HFD


title: P204


title: P203


title: OVE16.3 [JP-18]


title: P202


title: OVE4_p53.1 [JP-13]


title: P199


title: OVE4_p53_mut.3 [JP-12]


title: P158_rerun

description: Resequencing of plant P158. Used in further analysis.


title: OVE4_p53_mut.2 [JP-11]


title: VSG2_85 - E0771 tumor excised from C57BL6Ncrl mouse_CON-LFD

source_name: Control  - never obese

value: CON-LFD


title: VSG2_4 - E0771 tumor excised from C57BL6Ncrl mouse_DIO-HFD


title: VSG2_40 - E0771 tumor excised from C57BL6Ncrl mouse_CON-LFD


title: OVE4_p53_mut.1 [JP-10]


title: P183


title: VSG2_106 - E0771 tumor excised from C57BL6Ncrl mouse_CON-LFD


title: VSG2_34 - E0771 tumor excised from C57BL6Ncrl mouse_CON-LFD


title: P174


title: P181


title: VSG2_24 - E0771 tumor excised from C57BL6Ncrl mouse_CON-LFD


title: VSG2_3 - E0771 tumor excised from C57BL6Ncrl mouse_CON-LFD


title: OVE4.2 [JP-8]


title: OVE4.3 [JP-9]


title: P200


title: P158


title: P159


title: OVE4.1 [JP-7]


title: P196


title: P155


title: x30_2.3 [JP-6]


title: E0771 tumor excised from C57BL6Ncrl mouse_DIO-VSG6

source_name: Obese - vertical sleeve gastrectomy

growth_protocol: C57BL/6N mice were randomized to receive a control diet D12450J, or a 60% high fat diet (D12492) to promote diet induced obesity. Once obese, mice were randomized to either remain obese or undergo weight loss via 1) vertical sleeve gastrectomy with low-fat diet, 2) or low fat diet.

treatment_protocol: All mice received either sham surgery or vertical sleeve gastrectomy. 22 weeks after initial randomization mice were orthotopically injected with E0771 cells into the 4th mammary fat pad and tumors were allowed to grow till endpoint. At endpoint the tumor was removed and used for nucleic acid extraction.

value: DIO-VSG


title: E0771 tumor excised from C57BL6Ncrl mouse_DIO-VSG5


title: P188


title: P152


title: P144


title: x30_2.2 [JP-5]


title: E0771 tumor excised from C57BL6Ncrl mouse_DIO-VSG4


title: P142


title: P143


title: x30_2.1 [JP-4]


title: E0771 tumor excised from C57BL6Ncrl mouse_DIO-VSG3


title: P169


title: P138


title: P130


title: P128


title: x28_2.3 [JP-3]


title: E0771 tumor excised from C57BL6Ncrl mouse_DIO-LFD5

source_name: Obese - low fat diet

value: DIO-LFD


title: P154


title: E0771 tumor excised from C57BL6Ncrl mouse_DIO-VSG1


title: P127


title: E0771 tumor excised from C57BL6Ncrl mouse_DIO-VSG2


title: x28_2.1 [JP-1]


title: Hobit-1

city: Copenhagen

first: William

middle: Winston

last: Agace

address: Blegdamsvej 3B

department: Skin Immunology Research Center

country: Denmark

institute: Copenhagen University

description: tpm.txt

data_processing:
Abundances of transcripts from the bulk RNA sequencing reads were quantified using kallisto v0.46.0
Differential gene expression analysis was performed using DESeq2 v1.22.2
Assembly: gencode.v37.transcripts
Supplementary files format and content: Normalized counts (TPMs)

organism: Homo sapiens

source_name: Jurkat

growth_protocol: RPMI 10% FCS.

extract_protocol:
Qiagen Rneasy
NEBNext single-cell/low input library Prep Kit

treatment_protocol: grown with or without 1 ug/uL of doxycycline

value: Jurkat

value: Dox-induced ZNF683


title: P122


title: E0771 tumor excised from C57BL6Ncrl mouse_DIO-LFD4


title: Hobit-3

description: tpm.txt


title: STOSE.4 [BV-60]

value: STOSE


title: P114


title: Mock-2

description: tpm.txt

value: Mock


title: E0771 tumor excised from C57BL6Ncrl mouse_DIO-LFD3


title: E0771 tumor excised from C57BL6Ncrl mouse_DIO-LFD2


title: Mock-1

description: tpm.txt


title: P170


title: P140


title: P112


title: STOSE_A2.1 [BV-58]


title: P111


title: Mock-3

description: tpm.txt


title: Hobit-2

description: tpm.txt


title: STOSE_A4.2 [BV-57]


title: P110


title: P109


title: active TA-TMA serum [TSSA20]

city: Cincinnati

first: Stella

last: Davies

state: OH

address: 3333 Burnet Ave

department: Cancer & Blood Disease Institute

institute: Cincinnati Children's Hospital

description: controlTSSA11121314_vs_comparisonTSSA1617181920.genes.deseq.counts

data_processing:
sequencing setting is PE 2x61 bp
Demultiplexing is performed under Illumina BaseSpace default setting. AdapterRead1: AGATCGGAAGAGCACACGTC; AdapterRead2: AGATCGGAAGAGCGTCGTGT
General bioinformatic analysis was performed via BaseSpace SEQUECNCE HUB app RNA-Seq Alignment v2.0.2 followed by RNA-Seq Differential Expression version 1.0.1.
The analysis used STAR for alignment and Salmon for quantification (Transcripts Per Million, TPM), followed by DESeq2 to identify differentially expressed genes.
RNA-seq Alignment setting is Mark Duplicates unchecked (ref: PMID 27156886)
Assembly: UCSC hg19

source_name: Primary

growth_protocol: Primary human glomerular endothelial cells were maintained in endothelial cell media supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was isolated according to manufacture's protocol using the MagMAX mirVana Total RNA Isolation Kit
NEBNext Ultra II Directional RNA Library Prep kit for RNA-seq library preparation

treatment_protocol: 70% confluent primary glomerular endothelial cells were incubated for 72 hr in media with 10% human serum from patients with active TA-TMA (n=5), timepoint-matched patients with no TA-TMA (n=4) or complete media control (n=1).

value: Primary

value: Glomerular Endothelial Cells

tag: treatment

value: active TA-TMA serum

value: 72 hr


title: STOSE_A4.1 [BV-56]

value: cell line


title: active TA-TMA serum [TSSA19]


title: P100

value: 3rd and 4th rosette leaves


title: active TA-TMA serum [TSSA18]


title: STOSE_A2.2 [BV-59]


title: P098


title: E0771 tumor excised from C57BL6Ncrl mouse_DIO-HFD4


title: STOSE_A3.1 [BV-54]


title: E0771 tumor excised from C57BL6Ncrl mouse_DIO-HFD5


title: active TA-TMA serum [TSSA17]


title: ID8.2 [BV-53]

source_name: IB tumour

value: IB tumour


title: P097


title: E0771 tumor excised from C57BL6Ncrl mouse_DIO-HFD6


title: E0771 tumor excised from C57BL6Ncrl mouse_DIO-HFD2


title: P095


title: active TA-TMA serum [TSSA16]


title: ID8.1 [BV-52]


title: E0771 tumor excised from C57BL6Ncrl mouse_DIO-LFD1


title: E0771 tumor excised from C57BL6Ncrl mouse_DIO-HFD1


title: P094


title: ID8_p53.3 [BV-51]


title: STOSE_A3.2 [BV-55]


title: P092


title: ID8_p53.2 [BV-50]


title: No TA-TMA control [TSSA13]

value: No TA-TMA control


title: No TA-TMA control [TSSA12]


title: E0771 tumor excised from C57BL6Ncrl mouse_DIO-HFD3

value: tumor


title: P085


title: No TA-TMA control [TSSA11]


title: ID8_p53.1 [BV-49]


title: active TA-TMA serum [TSSA10]

description: controlTSSA1234_vs_comparisonTSSA678910.genes.deseq.counts

value: 24 hr


title: E0771 tumor excised from C57BL6Ncrl mouse_CON-LFD3

value: CON-LFD


title: ID8_C3.3 [BV-48]


title: P080


title: E0771 tumor excised from C57BL6Ncrl mouse_CON-LFD6


title: P079


title: E0771 tumor excised from C57BL6Ncrl mouse_CON-LFD4


title: ID8_C3.1 [BV-46]


title: No TA-TMA control [TSSA14]


title: ID8_C3.2 [BV-47]


title: P077


title: active TA-TMA serum [TSSA8]


title: M6_6-8h_csRNA

city: Ramat Gan

first: Tamar

last: Juven-Gershon

address: Life Sciences Building (212) Room 102

country: Israel

institute: Bar-Ilan University

data_processing:
Sequencing data was analyzed using HOMER csRNAseq module (http://homer.ucsd.edu/homer/ngs/csRNAseq/index.html(http://homer.ucsd.edu/homer/ngs/csRNAseq/index.html)) and R custom scripts. 3′ adapter sequences of the reads were trimmed using HOMER (Heinz et al. 2010) and aligned to dm6 genome using STAR (version 2.7.10a) (Dobin et al. 2013). Reads were visualized as strand-specific bedGraph using HOMER makeUCSCfile command with -style tss parameter. Peak calling was performed using the findcsRNATSS.pl function in HOMER (Duttke et al. 2019), with inputusing the small RNA- seq used(csInput) as background to eliminate transcripts from degraded and high-abundance RNAssmall and miRNAs in csRNA-seq libraries. HOMER annotatePeaks.pl command was used with -rlog parameter for calculating the normalized expression values for each peak used in downstream analyses. It was also used for generating transcription profile plots, for example annotatePeaks.pl tss dm6 -size 400 -hist 10 -pc 3. For differential expression, getDiffExpression.pl -edgeR -simpleNorm -dispersion 0.05 -AvsA was used on raw counts. ComplexHeatmap R package (Gu et al. 2016) was used for hierarchal clustering. HOMER analyzeClusters.pl was used for motifs and GO terms enrichment analysis in the identified cluster.
Assembly: dm6
Supplementary files format and content: .bedGraph.gz contains the analyzed peaks file, separately for each strand
Supplementary files format and content: all.merged.tss.txt.gz contains all annotated TSS by all time points merged into single file
Supplementary files format and content: all.rlog.byTime.txt.gz contains the normalized rlog counts for all samples and timepoints
Library strategy: capped short RNA-seq (csRNA-seq)

organism: Drosophila melanogaster

source_name: embryo

growth_protocol: F3, M6 and Cas9 embryos were aged at 25oC and collected at 0-2h, 2-4h, 4-6h and 6-8h time points.

extract_protocol:
Total RNA was extracted from dechorionated embryos using TRI Reagent (Sigma-Merck) according to the manufacturer’s protocol, followed by ethanol precipitation for further purification.
csRNA-seq v. 5.2 (Duttke et al. 2019). Total RNA was heat denatured and short RNAs (18-65 nt) purified by 15% UREA-PAGE. 5% of these short RNAs are used to generate input libraries (input RNA-seq) and the remainder cap-selected with 5´ monophosphate-dependent exonuclease (TER51020) followed by two phosphatase (CIP) treatments. Sequencing libraries for input-RNAseqsmall RNA-seq (csInput) and csRNAseqcsRNA-seq were generated using the NEB sRNA kit but with addition of RppH forby decapping the RNA using RppH (Hetzel et al. 2016). ) followed by library preparation using the NEB sRNA kit.

tag: strain

value: embryo

value: tinmDPE

tag: time


title: M6_6-8h_csInp

data_processing:
Sequencing data was analyzed using HOMER csRNAseq module (http://homer.ucsd.edu/homer/ngs/csRNAseq/index.html(http://homer.ucsd.edu/homer/ngs/csRNAseq/index.html)) and R custom scripts. 3′ adapter sequences of the reads were trimmed using HOMER (Heinz et al. 2010) and aligned to dm6 genome using STAR (version 2.7.10a) (Dobin et al. 2013). Reads were visualized as strand-specific bedGraph using HOMER makeUCSCfile command with -style tss parameter. Peak calling was performed using the findcsRNATSS.pl function in HOMER (Duttke et al. 2019), with inputusing the small RNA- seq used(csInput) as background to eliminate transcripts from degraded and high-abundance RNAssmall and miRNAs in csRNA-seq libraries. HOMER annotatePeaks.pl command was used with -rlog parameter for calculating the normalized expression values for each peak used in downstream analyses. It was also used for generating transcription profile plots, for example annotatePeaks.pl tss dm6 -size 400 -hist 10 -pc 3. For differential expression, getDiffExpression.pl -edgeR -simpleNorm -dispersion 0.05 -AvsA was used on raw counts. ComplexHeatmap R package (Gu et al. 2016) was used for hierarchal clustering. HOMER analyzeClusters.pl was used for motifs and GO terms enrichment analysis in the identified cluster.
Assembly: dm6
Supplementary files format and content: .bedGraph.gz contains the analyzed peaks file, separately for each strand
Supplementary files format and content: all.merged.tss.txt.gz contains all annotated TSS by all time points merged into single file
Supplementary files format and content: all.rlog.byTime.txt.gz contains the normalized rlog counts for all samples and timepoints


title: M6_4-6h_csRNA


title: E0771 tumor excised from C57BL6Ncrl mouse_CON-LFD2


title: P068


title: E0771 tumor excised from C57BL6Ncrl mouse_CON-LFD5


title: E0771 tumor excised from C57BL6Ncrl mouse_CON-LFD1


title: ID8.3 [BV-45]


title: active TA-TMA serum [TSSA7]


title: M6_4-6h_csInp


title: P064


title: ID8.2 [BV-44]


title: active TA-TMA serum [TSSA9]


title: active TA-TMA serum [TSSA6]


title: ID8.1 [BV-43]


title: No TA-TMA control [TSSA4]


title: P059


title: M6_2-4h_csRNA


title: M6_2-4h_csInp


title: MOE_PTEN_KRAS.3 [BV-42]


title: P054


title: P053


title: MOE_PTEN_KRAS.2 [BV-41]


title: P052


title: No TA-TMA control [TSSA3]


title: M6_0-2h_csInp


title: P051


title: No TA-TMA control [TSSA1]


title: MOE_PTEN_P53.3 [BV-39]


title: MOE_PTEN_KRAS.1 [BV-40]


title: No TA-TMA control [TSSA2]


title: P050


title: x28_2.2 [JP-2]


title: F3_6-8h_csRNA


title: MOE_PTEN_P53.2 [BV-38]


title: STOSE.5 [BV-61]


title: 92-1,FHT-1015, 4h,ATACseq, biol rep 2

city: Cambridge

first: Salih

last: Topal

address: 500 Technology Square Suite 700

institute: Foghorn Therapeutics

data_processing:
Reads were trimmed for adapter sequences using  cutdapt3 and aligned to version hg38 of the human genome using bowtie2 (parameters -k 4, -X2000, --local ,--mm)
Multimapping alignments were removed and only the the alignment with the highest score for each read pair was kept
Duplicate reads were removed using Picard Tookit and alignments mapping to mitochondrial genome were excluded
Alignments were filtered for size smaller than 120 bp and read ends shifted +4 or -5 nucleotides depending on the direction of the read
Peak calling was performed using MACS2.0 with a shift parameter of -75 and an extension size of 150 without modelling
Signal tracks were created using the fold enrichment option
Consistent peaks among replicates were obtained using IDR using a soft idr threshold of 0.1
Differential genome accessibility calculation was performed using limma package
Motif enrichment was performed using Meme suite tools (MEME-chip)7 and CISBP transcription motif data from MEME motif database version 12.19
Ridge regression analysis was performed using glmnet R package with coefficients calculated using the minimum estimated lambda
Genomic context annotation was performed using the annotatePeaks function of HOMER package using hg38 version of the human genome
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak

extract_protocol:
DNA extraction was performed as described in Buenrostro et al., 2013
ATAC-seq library was generated as described in Buenrostro et al., 2013. Following library generation, left- and right- size selection was performed with SPRIselect beads (Beckman Coulter) according to the manufacturer’s recommendations.

value: uveal melanoma

value: WT

value: dual SMARCA4/SMARCA2 inhibition


title: AMPK B1 KO, PF, S23

city: Hamilton

first: Dongdong

last: Wang

state: Ontario

address: 1200 Main Street West

department: Department of Medicine

institute: McMaster University

data_processing:
Trim Galore was used to automate quality and adapter trimming as well as quality control.
We quantified the expression of transcripts using RNA-seq data through Salmon.
Salmon’s transcript-level quantifications DESeq2 was applied for detection of differentially expressed genes (DEG).

source_name: Primary Bone Marrow Dervied Macrophages

growth_protocol: BMDMs were generated by isolating marrow from the tibia and femur of each leg by centrifugation. Marrow was then suspended in DMEM supplemented with 10% FBS and 1% antibiotic-antimycotic. After 5 hours L929 media (a source of M-CSF) was added and cells were plated in 10cm tissue culture dishes. Cells were then allowed to differentiate for 7 days before reseeding for experiments as described.

extract_protocol:
Cells were lysed in TRIzol reagent. After centrifuging, the supernatant (aqueous phase) was used to extract total RNA using the RNeasy kit (Qiagen, 74106) according to its protocols.
RNA libraries for RNA-seq were prepared using the NEBNext® Ultra™ II Directional RNA Library kit following manufacturer's protocols.

treatment_protocol: Cells were treated with Vehicle (DMSO 0.1%) or 10uM PF-06409577

value: Primary Bone Marrow Dervied Macrophages

value: AMPK B1 Knockout


title: AMPK B1 KO, PF, S24


title: P049


title: F3_4-6h_csRNA


title: P039


title: AMPK B1 KO, Vehicle, S21

value: Vehicle


title: F3_4-6h_csInp


title: AMPK B1 KO, PF, S22


title: M6_0-2h_csRNA


title: P038


title: STOSE.2 [BV-35]

value: STOSE


title: MOE_PTEN_P53.1 [BV-37]


title: AMPK B1 KO, Vehicle, S20


title: P037


title: F3_2-4h_csRNA


title: F3_2-4h_csInp


title: STOSE.1 [BV-34]


title: F3_6-8h_csInp


title: AMPK B1 KO, Vehicle, S19


title: F3_0-2h_csRNA


title: P035


title: ID8_p53_PTEN.3 [BV-33]


title: F3_0-2h_csInp


title: WT, PF, S18

value: Wildtype


title: P024


title: WT, PF, S17


title: cas9_6-8h_csRNA

value: tinWT


title: ID8_p53_PTEN.1 [BV-31]

value: cell line


title: WT, PF, S16


title: STOSE.3 [BV-36]

value: IB tumour


title: P023

value: 3rd and 4th rosette leaves


title: cas9_6-8h_csInp


title: P017


title: ID8_p53_Nf1.3 [BV-30]


title: cas9_4-6h_csRNA


title: ID8_p53_Nf1.2 [BV-29]


title: WT, Vehilce, S14


title: P016


title: ID8_p53_Nf1.1 [BV-28]


title: WT, Vehilce, S13


title: cas9_4-6h_csInp


title: ID8_p53_BRCA2.3 [BV-27]


title: cas9_2-4h_csRNA


title: ID8_p53_PTEN.2 [BV-32]


title: cas9_2-4h_csInp


title: ID8_p53_BRCA2.2 [BV-26]


title: Mesenchymal chondrosarcoma, Runx3 on Runx2 KO

city: Tokyo

first: Takuro

last: Nakamura

address: 3-8-31 Ariake, Koto-ku

department: The Cancer Institute

country: Japan

institute: Japanese Foundation for Cancer Research

data_processing:
Base calls were performed using Bowtie 1.1.1.
ChIP-seq reads were aligned to the mm9 genome assembly using samtools 1.2.
Peak call was performed using MACS1.4.
Assembly: mm9
Supplementary files format and content: For every 300 bp window, the mapped tag count for ChIP, Cc and that for Input, Ci were used for calculation. Ec and Ei indicates the estimate count for 300 bp window for ChIP and Input. Signal ratio of ‘target TF’ was calculated as, Cc/Ec + 1 ÷ Max (1, Ci/Ei + 1).

source_name: Mesenchymal chondrosarcoma

growth_protocol: Sarcoma cells were maintained in IMDM supplemented with 10% FBS

extract_protocol:
Lysates were clarified from sonicated nuclei and immunoprecipitated with each antibodies
Libraries were prepared according to Illumina's instructions accompanying the ThruPLEX DNA-seq 6S (12) Kit (R400523). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: HEY1-NCOA2 was introduced by retrovirus-mediated gene transfer

value: Balb/c

value: HEY1-NCOA2-expressing murine mesenchymal chondrosarcoma cells

value: RUNX3 (Cell Signaling, 9647, lot 2)


title: P009


title: P010


title: cas9_0-2h_csRNA

value: embryo


title: Mesenchymal chondrosarcoma, K27Ac on Runx2 KO

value: Histone H3K27ac (Active Motif, 39133, lot 16119013)


title: cas9_0-2h_csInp


title: P007


title: Mesenchymal chondrosarcoma, Runx3


title: Mesenchymal chondrosarcoma, HEY1-NCOA2 on Runx2 KO

value: FLAG (Sigma, F7425, lot 085M4774V)


title: ID8_p53_BRCA2.1 [BV-25]


title: WT, Vehilce, S15


title: P020


title: ID8_p53_BRCA1.3 [BV-24]


title: P004


title: Mesenchymal chondrosarcoma, Input

data_processing:
Base calls were performed using Bowtie 1.1.1.
ChIP-seq reads were aligned to the mm9 genome assembly using samtools 1.2.
Peak call was performed using MACS1.4.
Genome_build: mm9
Supplementary_files_format_and_content: For every 300 bp window, the mapped tag count for ChIP, Cc and that for Input, Ci were used for calculation. Ec and Ei indicates the estimate count for 300 bp window for ChIP and Input. Signal ratio of ‘target TF’ was calculated as, Cc/Ec + 1 ÷ Max (1, Ci/Ei + 1).

extract_protocol:
Lysates were clarified from sonicated nuclei and immunoprecipitated with each antibodies
Libraries were prepared according to Illumina's instructions accompanying the ThruPLEX DNA-seq 6S (12) Kit (R400523). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina MiSeq following the manufacturer's protocols.


title: P002


title: ID8_p53_BRCA1.1 [BV-22]


title: ID8_p53_BRCA1.2 [BV-23]


title: Kidney transplant nephrectomy, G22, scTCR

city: Rotterdam

first: Hector

last: Tejeda Mora

address: Doctor Molewaterplein 40

department: Developmental Biology

country: Netherlands

institute: Erasmus MC

data_processing:
The raw data were processed into FASTQ files. Raw sequences were inspected for quality using FastQC (version 0.11.5, Babraham Bioinformatics, Cambridge, UK)
Reads containing sequence information were mapped to the GRCh38 human genome.
The generation of BAM files and filtered gene-barcode matrices was accomplished using Cell Ranger Software (version 6.0 10X Genomics, Pleasanton, CA, USA).
VCF files were generated using Strelka2 and used for individual identification (donor/recipient).
Using Seurat (version 4.3.0) standard pre-processing was done. Selection and filtration of cells was done (genes that were expressed in fewer than three cells, and cells with fewer than 200 distinct transcripts were removed). Data was normalized and scaled, followed by the detection of highly variable genes. Datasets were integrated with rPCR. scTCR data was added based on cell barcodes.
From the generated Seurat-Object, scale RNA data was exported as a comma separated table in an unique CSV files (processed_data_integrated.csv)
Assembly: GRCh38
Supplementary files format and content: Comma separated values files and matrix files for the scRNA; comma separated values files for the scTCR
Library strategy: scTCR-seq

source_name: kidney

growth_protocol: Mononuclear cells from four chimeric kidney explant samples were used for the single-cell transcriptomic analysis.

extract_protocol:
Isolation of CD4 TRM and CD8 TRM cells was performed using a FACS Aria II cell sorter, using the following fluorescent antibodies (CD45, CD3, CD4, CD19, CD69, CD103, CD49a, CD11b, CD16 and CD127).
Libraries were prepared on a Chromium Controller using the Chromium Next GEM Single Cell 5’ Reagent Kit V2 in combination with the Chromium Single Cell Human TCR Amplification Kit (10x Genomics, Pleasanton, CA, USA). In this way, single-cell transcriptomes and immune profiles were generated from the same sample. Next-generation sequencing (26-10-10-90 cycles) of both libraries (transcriptome and TCR-enriched) was performed on an Illumina NovaSeq 6000 platform.

treatment_protocol: Mononuclear cells were thawed.

value: kidney

value: CD4 CD8 TRM cells

value: sorted


title: Mesenchymal chondrosarcoma, Hey1

value: HEY1 (Proteintech, 19929-1-AP, lot 1)


title: Kidney transplant nephrectomy, G10, scTCR


title: Mesenchymal chondrosarcoma, Runx2

value: RUNX2 (Cell Signaling, 12554S, lot 2)


title: P008


title: Mesenchymal chondrosarcoma, K4Me3

value: Histon H3K4Me3 (Abcam, ab8580, lot GR3263891-1)


title: ID8_p53.3 [BV-21]


title: Mesenchymal chondrosarcoma, K27Me3

value: Histone H3K27me3 (Abcam, ab6002, lot GR3232152-1)


title: ID8_p53.2 [BV-20]


title: ID8_p53.1 [BV-19]


title: ID8_C3.3 [BV-18]


title: rat antrum scRNA-seq

city: Beijing

first: Ye-guang

last: Chen

address: Tsinghua Road, Medical Building

department: School of life science

country: China

institute: Tsinghua University

library_source: transcriptomic single cell

data_processing:
Raw reads were aligned to the different species genome (Human: GRCh38/hg38, Pig: Sscrofa11.1, Rat: Rnor_6.0, Mouse: GRCm38/mm10), and Cell Ranger (v3.1.0) was used to estimate unique molecular identifiers (UMIs).
Raw aligned features were loaded and processed using the Seurat package (v4.0.2)
Low-quality cells were filtered if they expressed no more than 200 genes or with more than 20% of mitochondrial genes
Assembly: Human: hg38, Pig: Sscrofa11.1, Rat: Rnor_6.0, Mouse: mm10
Supplementary files format and content: text files

organism: Rattus norvegicus

source_name: antral epithelium

extract_protocol:
Gastric glands were isolated and digested with EDTA and Tryple, alive cells were sorted by flow cytometry. Single cell suspensions were captured using the 10X Genomics Chromium
ScRNA-seq libraries were generated using the Chromium Single Cell 3’ Reagent Ki V3 (10X Genomics). The libraries were sequenced as paired-end with Illumina Novaseq 6000.

value: antral epithelium

tag: strategy

value: scRNA-seq

value: Wild type

value: Untreated


title: WT rat gastric antral organoids-2

description: rat-TNFa-con.csv

data_processing:
RNA-seq reads were aligned to the human, pig, rat or mouse genome available in Ensembl (release 95) with HISAT2 (v2.1.0)
StringTie (v1.3.3b) for transcript assembly
The quantitative gene expression (FPKM) was obtained with Ballgown
Assembly: Human: hg38, Pig: Sscrofa11.1, Rat: Rnor_6.0, Mouse: mm10
Supplementary files format and content: csv

source_name: Gastric antral organoids

growth_protocol: Organoids were embedded in Matrigel and seeded on 48- or 24- well plate. After Matrigel polymerization, the CM medium (Advanced DMEM/F12 supplemented with Penicillin/Streptomycin, GlutaMAX, N2, B27, and N-acetylcysteine containing 50 ng/mL EGF, 100 ng/mL Noggin, 500 ng/mL R-spondin1, 5 μM CHIR, 10 nM Gastrin, 10 μM SB431542, 100 ng/mL FGF10 and 10 μM Y27632) was added and refreshed every 2 days.

extract_protocol:
Organoids were digested with Tryple and alive cells were sorted by flow cytometry. Total RNA was extracted with RNeasy Mini Kit (QIAGEN) according to the manufacturer’s instructions.
The library were prepared for sequecing using NEBNext Ultra RNA library Prep Kit for Illumina.

treatment_protocol: Organoids derived from antral glands of 4 kinds of species were treated with Tnfa 10 ng/ml for 2 days.

value: RNA-Seq


title: TNFa treated rat gastric antral organoids-2

description: rat-TNFa-con.csv

value: Treated with TNFa 2 days


title: ID8_C3.2 [BV-17]

value: cell line


title: TNFa treated rat gastric antral organoids-1

description: rat-TNFa-con.csv


title: Mesenchymal chondrosarcoma, K27Ac

value: Balb/c

value: HEY1-NCOA2-expressing murine mesenchymal chondrosarcoma cells


title: WT rat gastric antral organoids-1

description: rat-TNFa-con.csv


title: Mesenchymal chondrosarcoma, HEY1-NCOA2

value: FLAG (Sigma, F7425, lot 085M4774V)


title: MP41 Resistant 9

data_processing:
Reads were aligned with BWA MEM using default options, duplicated alignments were removed using picard MarkDuplitcates
GATK IndelRealigner was used for indel realignment
GATK HaplotypeCaller was used in discovery mode for variant calling using the following parameters: -dontUseSoftClippedBases -stand_call_conf 20.0
Variants were filtered for QD<2, FS>60 and MQ<40. Variants remaining after filtering were annotated using snpEFF
Assembly: hg38
Supplementary files format and content: vcf files
Library strategy: WES

extract_protocol: Whole exome analysis was performed on genomic DNA processed using Agilent SureSelectXT2 Human All Exon V6 Kit and sequenced to 6G of 150bp paired end reads.

value: uveal melanoma


title: CLL-Rat-Stat1

city: Nantong

first: Yun

last: Gu

state: Jiangsu

address: 19 Qixiu Road

institute: Nantong University

data_processing:
Basecalls were performed using Illumina Casava1.8.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp.
ChIP-seq reads were aligned to the UCSC rn6 genome using Bowtie2 version 2.3.5.1. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called using MACS v2 (Modelbased Analysis of ChIP-seq) with the significance cut-off q-value <=0.01.
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: rn6
Supplementary files format and content: bigWig, narrowPeak

source_name: Sciatic nerve

growth_protocol: Schwann cells (SCs) were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), 5 μM forskolin, 2 ng/ml Nrg1 and 1x penicillin/streptomycin, and cultured in humidified atmosphere with 5% CO2 at 37ºC.

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris). Sonicated chromatin (~300 µg) was used for immunoprecipitation by incubation with Stat1 antibody (5 μg, Cell Signaling, #14994) overnight at 4 °C. ChIP Grade Protein A/G plus Agarose (20 μl, Thermo Fisher Scientific, #26156) were added to each ChIP reaction and reactions were incubated for 1 h at 4 °C. The beads were then incubated in 150 μl elution buffer at 65 °C for 40 min to elute immunoprecipitated materials.
ChIP-seq libraries were prepared using the NEBNext ChIP-seq Library Prep Master Mix Set for Illumina (NEB catalogue number E6240L) and then run on the Illumina sequencer NovaSeq 6000. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

treatment_protocol: To induce SC differentiation, cells were cultured in DMEM/F12 supplemented with 1% fetal bovine serum, 1 mM dibutyryl cyclic AMP, 20 ng/ml Nrg1 and 1x penicillin/streptomycin for 2 days.

value: Sciatic nerve

value: Primary cultured Schwann cells

tag: condition

value: differentiation

value: WT

value: Stat1, Cell Signaling, #14994


title: ID8_C3.1 [BV-16]


title: Sample 6_day40

city: Ann Arbor

first: Xufeng

last: Xue

state: MI

address: 2350 Hayward Street

department: Mechanical Engineering

institute: University of Michigan

data_processing:
Illumina NovaSeq-6000 for basecalling
10x Genomics Cell Ranger pipeline (version 3.1.0) for barcoding, alignment, filtering
Assembly: GRCh38
Supplementary files format and content: TSV and MTX files are generated by Cell Ranger pipeline, including barcodes, features and matrix. RDS file is generated using Seurat, including integrated data of day4, day9 and day21 from batch 1.

source_name: hESC-derived forebrain-like structure

extract_protocol:
microfluidic neural tube-like structures were dissociated into single cells using accutase. Dissociated cells were then lysed and barcoded with 10x Chromium Controller Instrument (10x Genomics).
cDNA library was constructed according to the standard 10x Genomics scRNA-seq library construction protocol (Single Cell 3' v2). The libraries were sequenced on Illumina NovaSeq-6000 with paired-end sequencing (One sample per flow cell).

tag: timepoint

tag: batch


title: Sample 5_day11

source_name: hESC-derived neural tube-like structure


title: Kidney transplant nephrectomy, G1, scRNA

description:
10xGenomics
processed_data_integrated.csv

data_processing:
The raw data were processed into FASTQ files. Raw sequences were inspected for quality using FastQC (version 0.11.5, Babraham Bioinformatics, Cambridge, UK)
Reads containing sequence information were mapped to the GRCh38 human genome.
The generation of BAM files and filtered gene-barcode matrices was accomplished using Cell Ranger Software (version 6.0 10X Genomics, Pleasanton, CA, USA).
VCF files were generated using Strelka2 and used for individual identification (donor/recipient).
Using Seurat (version 4.3.0) standard pre-processing was done. Selection and filtration of cells was done (genes that were expressed in fewer than three cells, and cells with fewer than 200 distinct transcripts were removed). Data was normalized and scaled, followed by the detection of highly variable genes. Datasets were integrated with rPCR. scTCR data was added based on cell barcodes.
From the generated Seurat-Object, scale RNA data was exported as a comma separated table in an unique CSV files (processed_data_integrated.csv)
Assembly: GRCh38
Supplementary files format and content: Comma separated values files and matrix files for the scRNA; comma separated values files for the scTCR

value: kidney

value: CD4 CD8 TRM cells

value: sorted


title: Kidney transplant nephrectomy, G22, scRNA


title: Kidney transplant nephrectomy, G1, scTCR


title: Kidney transplant nephrectomy, G9, scRNA


title: Kidney transplant nephrectomy, G9, scTCR


title: Kidney transplant nephrectomy, G10, scRNA


title: MP41 Resistant 8


title: ID8.3 [BV-15]

data_processing:
Pseudoalignment and transcript quantification for each sample was performed using Kallisto (v0.45.0) with the GRCm38 build of the mouse genome. The R package tximport (v1.24.0) was used to load transcript quantifications, converting to gene-level transcript estimates.
Assembly: GRCm38
Supplementary files format and content: mouse_sample_annotation.csv - Annotation table providing metadata for each sample
Supplementary files format and content: txi_mouse.rds - R object containing raw counts and tpm matrices for each sample following import with tximport
Supplementary files format and content: tpm_matrix._mouse.csv - Transcripts per million (TPM) count matrix for all genes and samples

source_name: cell line


title: ID8.2 [BV-14]


title: CLL-Rat-input


title: KD_3

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequence reads were trimmed for adaptor sequence/low-quality sequence/containing poly-N sequence using CLC genomic benchwork (parameter- Quality limit: 0.05).
Trimmed sequence reads were mapped to the reference UCSC genome (RGSC6.0/rn6) using Hisat2 v2.0.5.
Read count extraction and normalization were performed using FeatureCounts v1.5.0-p3.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1). Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: rn6
Supplementary files format and content: all compare.txt: Tab-delimited text file includes counts and FPKM values for each Sample.

extract_protocol:
RNA was harvested using TRIzol (15596-018-056, Thermo Fisher, Cleveland, OH, USA) followed by purification using RNeasy Mini Kit (Qiagen, Valencia, CA, USA). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (New England Biolabs, Ipswich, MA, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: SCs were seeded at a density of 3 × 10^6 cells/ml in 24-well plates and cultured for 24 h, after which they were transfected with Stat1-siRNAs and non-targeting negative control (Scramble). 48 hours after transfection, the cells were cultured in differentiation medium containing DMEM/F12 (11320-033, Gibco) plus 1% FBS, 1 mM dibutyryl cyclic AMP (db-cAMP; D0627, Sigma) and 20 ng/ml Nrg1 for 3 d to acquire a differentiated phenotype.

value: Stat1 siRNA


title: MP41 Resistant 7


title: bulk RNA-seq of rat gastric antral organoids

value: Wild type

value: Untreated


title: CWR22Rv1 cells 72h RBMX knockdown 3

city: Newcastle upon Tyne

first: Beth

last: Adamson

address: Paul O'Gorman Building, Framlington Place

department: Translational and Clinical Research Institute

institute: Newcastle University

description:
RBMX_3
Rv1_RBMX_featureCounts.tsv
Rv1_RBMX_DESeq2_normalised_counts.csv

data_processing:
Quality control using fastqC
Cutadapt to trim adapter sequences from reads (CWR22Rv1 experiment only)
sequence reads were aligned to the human geneome (GRCh38) using STAR
Gene count matrix was generated using FeatureCounts
Differential gene expression using DESeq2
Assembly: GENCODE GRCh38 primary assembly and associated GTF annotation (release v36 (CWR22Rv1-AR-EK) release v43 (CWR22Rv1).
Supplementary files format and content: tab-seperated featurecounts.tsv file contains raw count data
Supplementary files format and content: DESeq2 comma seperated csv file contains normalised counts

source_name: Prostate

growth_protocol: CWR22Rv1-AR-EK and CWR22Rv1 cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and penicillin-streptomycin antibiotics in humidified atmosphere with 5% CO2 at 37 °C

extract_protocol:
Phenol/chloroform extraction using TRIzol
Illumina-compatible library samples (performed by GeneWiz)

treatment_protocol: CWR22Rv1-AR-EK cells were transfected with 25 nm siRNA for 48 hours then treated with either DMSO or 1 µM NU7441, NU5455 or AZD7648 for a further 24 hours, CWR22Rv1 cells were reverse transfected with 25 nm siRNA for 72 hours

value: Prostate

value: prostate epithelial cells

value: siRBMX


title: MP41 Resistant 6


title: CWR22Rv1 cells 72h RBMX knockdown 2

description:
RBMX_2
Rv1_RBMX_featureCounts.tsv
Rv1_RBMX_DESeq2_normalised_counts.csv


title: MOE_PTEN_KRAS.3 [BV-12]

extract_protocol:
Total RNA was extracted according to the manufacturer’s instructions with the RNeasy Plus Mini Kit (Qiagen) for the majority of samples. IP tumours collected from mice injected with ID8-Trp53-/-, ID8-Trp53-/-; Brca1-/-, ID8-Trp53-/-; Brca2-/-, ID8-Trp53-/-; Nf1-/-, and ID8-Trp53-/-; Pten-/- cells were isolated at endpoint using the total RNA Purification Kit (Norgen Biotek Corporation, ON, Canada) as per the manufacturer’s instructions.
RNA-Seq libraries were generated from 250 ng of total RNA as following: mRNA enrichment was performed using the NEBNext Poly(A) Magnetic Isolation Module (New England BioLabs). cDNA synthesis was achieved with the NEBNext RNA First Strand Synthesis and NEBNext Ultra Directional RNA Second Strand Synthesis Modules (New England BioLabs). The remaining steps of library preparation were done using and the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs). Adapters and PCR primers were purchased from New England BioLabs.
The pool was loaded at 200pM on a Illumina NovaSeq S4 lane using Xp protocol as per the manufacturer’s recommendations. The run was performed for 2x100 cycles (paired-end mode). A phiX library was used as a control and mixed with libraries at 1% level. Base calling was performed with RTA v3. Program bcl2fastq2 v2.20 was then used to demultiplex samples and generate fastq reads

value: cell line


title: MOE_PTEN_KRAS.2 [BV-11]


title: CWR22Rv1 cells 72h RBMX knockdown 1

description:
RBMX_1
Rv1_RBMX_featureCounts.tsv
Rv1_RBMX_DESeq2_normalised_counts.csv


title: MP41 Resistant 5


title: MP41 Resistant 4


title: KD_2


title: KD_1


title: CWR22Rv1 cells 72h Scrambled siRNA 3

description:
Control_3
Rv1_RBMX_featureCounts.tsv
Rv1_RBMX_DESeq2_normalised_counts.csv

value: siScr


title: NC_3

value: Negative control siRNA


title: MP41 Resistant 3

value: uveal melanoma


title: NC_1

value: Sciatic nerve

value: Primary cultured Schwann cells


title: NC_2

value: differentiation

value: WT


title: CWR22Rv1 cells 72h Scrambled siRNA 2

description:
Control_2
Rv1_RBMX_featureCounts.tsv
Rv1_RBMX_DESeq2_normalised_counts.csv


title: MOE_PTEN_p53.3 [BV-9]


title: MP41 Resistant 1


title: MOE_PTEN_p53.2 [BV-8]


title: CWR22Rv1 cells 72h Scrambled siRNA 1

description:
Control_1
Rv1_RBMX_featureCounts.tsv
Rv1_RBMX_DESeq2_normalised_counts.csv


title: MP41 Resistant 2


title: MOE_PTEN_p53.1 [BV-7]


title: ID8.1 [BV-13]


title: DM-P

city: Chengdu

first: Bo

last: Zhang

state: Sichuan

address: No. 14, 3rd Section, South Renmin Road, Chengdu, Sichuan, PR China

institute: Sichuan University

data_processing:
The Cell Ranger software pipeline (version 5.0.0) provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells. We processed the unique molecular identifier (UMI) count matrix using the R package Seurat (version 3.1.1).
Genome_build: mm10
Supplementary_files_format_and_content: gene files; gene-barcode counts; cell barcode files

source_name: gingiva from diabetic periodontitis

extract_protocol:
Buccal and lingual gingiva tissue around the maxillary left second molars were removed minced on ice to less than 1 mm cubic pieces. They were digested by collagenase I (2mg/mL, GIBCO), collagenase II (2 mg/mL, GIBCO) and trypsin-EDTA (0.25%, GIBCO) at 37℃ for 60 min. Cell suspension was then filtered through a 40-μm strainer (ThermoFisher Scientific), and the supernatant was removed after centrifugation.
RNA libraries were prepared with Chromium Single Cell 3’ Reagent v3 Kits according to to the manufacture's protocol.

value: gingiva

value: streptozotocin-induced diabetic rats with ligature-induced periodontitis

tag: strain background

value: Sprague-Dawley (SD)


title: MP41 wt


title: CWR22Rv1-AR-EK cells 72h DNA-PKcs knockdown/24h DMSO n3

description:
KD_3
AREK_DNAPK_featureCounts.tsv
AREK_DNAPK_DESeq2_normalised_counts.csv

value: CRISPR edited CWR22Rv1 derivative, prostate epithelial cells

value: siDNA-PKcs/DMSO


title: DM-NP

source_name: gingiva from diabetic individuals without periodontitis

value: streptozotocin-induced diabetes


title: MOE_PTEN.3 [BV-6]


title: hiPSC-derived islet cells - BHLHE41 siRNA

city: Leuven

first: Vincent

last: Pasque

address: Herestraat 49 bus 804

department: Development and Regeneration

country: Belgium

institute: KU Leuven

data_processing:
Raw data was processed using the 10x Genomics CellRanger software (v4.0.0) and mapped to the pre-built human reference genome GRCh38-2020-A. Contamination by background RNA from disrupted cells was estimated and corrected for using SoupX (Young and Behjati 2020) with Seurat identified clusters, and known cell type specific marker genes (GCG, TTR; INS, IAPP; SST; PPY; GHRL; CPA1, CLPS, CPA2, REG1A, CELA3A, CTRB1, CTRB2, PRSS2; KRT19, VTCN1). Cells with less than 200 expressed genes and more than 25% mitochondrial reads were excluded from future analyses. DoubletFinder (v2.0.3)(McGinnis, Murrow, and Gartner 2019) was used with default settings to identify and remove potential doublets. The resulting counts were normalized, scaled and analyzed for principal component analysis (PCA) and uniform manifold approximation and projection (UMAP) on the first 20 principle components (PCs) using 2000 variable genes using Seurat (v3.1.1).
Assembly: GRCh38-2020-A
Supplementary files format and content: Single cell read count matrix (matrix.mtx), Cell barcode (barcodes.tsv), Gene names (features.tsv), raw count matrix (countData.csv), metadata (metadata.csv)

source_name: iPSC-derived islets

growth_protocol: Control iPSC lines 1023A (Lytrivi et al. 2021) was differentiated into beta cells using a previously published 7-step protocol (Fantuzzi et al. 2022; De Franco et al. 2020). At the end of the stage 4, cells were seeded into 24-well Aggrewell 400 microwell plates (Stem Cell Technologies) at a density of 0.9 ·10^6 cells per well  after which differentiation was carried out as described previously (Cosentino et al. 2018).

extract_protocol:
hiPSC islets were washed with Versene (Thermo Fisher Scientific, 15040066) and incubated with Accutase (Sigma-Aldrich, A6964-100ML) for 10 min at 37°C. Dissociation was stopped by the addition of PBS supplemented with 1% Bovine Serum Albumin (BSA). Dissociated cells were washed twice in PBS (1%BSA) buffer, centrifuged at 300 rcf for 5 min, filtered using Flowmi 40µm tip strainer (Bel-Art, H13680-0040), counted and adjusted to 1  × 10^6 cells ml–1 cells in PBS (1%BSA) for encapsulation. Cell count and viability were measured using the Luna-Fl automated Fluorescence Cell Counter (Logos Biosystems).
For each siRNA treatment, 6000 cells were loaded onto the 10X Chromium Single Cell Platform (10X Genomics) using the Next GEM Single Cell 3’ library and Gel Bead Kit (v3.1 chemistry) according to manufacturer’s instructions (10x User Guide CG000204, Revision D). RNA quality was assessed using Tapestation (Agilent). Libraries were quantified using Tapestation (Agilent), the Qubit 2.0 (ThermoFisher Scientific) and KAPA Library Quantification Kit for Illumina Platform (KAPA Biosystems) before pooling. Libraries were pooled in equimolar amounts for paired-end sequencing on an Illumina NextSeq 2000 instrument to yield ∼168 million (range 147–195 million) 100-bp-long reads on average per sample.
10X Genomics scRNAseq

treatment_protocol: Stage 7 differentiated beta cells were washed twice with PBS containing 0.5 mM EDTA and incubated in Accumax (SIGMA #A7089) for 8 min at 37 °C after which 50% volume of KnockOut Serum Replacement (ThermoFisher #10828028) was added to stop the reaction. After centrifugation at 400 g for 5 min at room temperature, cells were resuspended in 1 mL HAM’s F-10 medium, supplemented as indicated before (Demine et al., 2020). 75,000 cells in 500 μL medium were seeded per square of a Nunc Lab-Tek II ICC chamber (ThermoFisher). Dispersed human islets and hiPSC-derived islets were transfected with siRNAs for human JUND, (Dharmacon, LQ-003900-00-0002) or human BHLHE41 (Dharmacon, LQ-010043-00-0002). siRNA with no homology to any known mammalian gene was used as negative control (AllStars Negative Control siRNA, Qiagen). siRNA-Lipofectamine RNAiMAX (Invitrogen, Life Technologies) complexes were formed in Opti-MEM and diluted four times in Ham’s F-10 medium without BSA or penicillin-streptomycin. Transfection was done using 30 nM siRNA and Lipofectamine at a final dilution of 1/250. Medium was refreshed after 16 hours and cells were studied after another 48 h.

value: iPSC-derived islets

tag: developmental stage

value: BHLHE41 siRNA


title: hiPSC-derived islet cells - JUND siRNA

value: JUND siRNA


title: CWR22Rv1-AR-EK cells 72h Scrambled siRNA/24h 1 µM AZD7648 n3

description:
AZD7648_3
AREK_DNAPK_featureCounts.tsv
AREK_DNAPK_DESeq2_normalised_counts.csv

value: Prostate


title: CTRL-NP

source_name: gingiva from normoglycemic individuals without periodontitis

value: no treatment


title: MOE_PTEN.2 [BV-5]

value: cell line


title: MOE_PTEN.1 [BV-4]


title: MOE_PTEN_KRAS.1 [BV-10]


title: CTRL-P

source_name: gingiva from normoglycemic periodontitis

value: ligature-induced periodontitis


title: HSAEC, pSARS2-1

city: Rockville

first: Peter

last: Sun

state: MD

address: 5625 Fishers Lane

department: National Institute of Allergy and Infectious Diseases (NIAID)

institute: National Institutes of Health (NIH)

data_processing:
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using CLC genomic bench work (parameter - Quality limit: 0.05).
The trimmed reads were mapped to the reference genome available on ENSEMBL using the STAR aligner v.2.5.2b (parameter - mismatch cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8). BAM files were generated as a result of this step. Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the groups of samples was performed. The Wald test was used to generate p‐values and Log2 fold changes. Genes with adjusted p‐values < 0.05 and absolute log2 fold changes > 1 were called as differentially expressed genes for each comparison. A gene ontology analysis was performed on the statistically significant set of genes by implementing the software GeneSCF. The mgi GO list was used to cluster the set of genes based on their biological process and determine their statistical significance.
Assembly: ENSEMBL
Supplementary files format and content: comma-separated values file includes raw counts for each sample.

source_name: human small airway epithelial cells

growth_protocol: The NHBE and HSAEC cell were maintained in Airway Epithelial Cell Basal Medium (ATCC cat no. PCS-300-030) supplemented with Bronchial Epithelial Cell Growth Kit (ATCC cat no. PCS-300-040) in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted from approximately 1 million of NHBE or HSAEC cells using Trizol (Invitrogen, Carlsbad, CA, USA) according to manufacturer’s instructions. Ten μg of purified RNA from each sample was sent to Genewiz commercial sequencing facility (South Plainfield, NJ) for Bioanalyzer quality control analysis (Agilent, Santa Clara, CA) and Illumina Next Generation Sequencing. All the submitted total RNA samples had an RNA integrity number (RIN) of 10.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer’s protocols.

treatment_protocol: NHBE and HSAEC cells at around 80% confluency were mock infected or infected with pSARS2 (40 viral RNA copies/cell) for 24 hrs prior to harvesting total RNA from the cell lysate. For infection with replication-competent SARS-CoV-2 delta variant, the NHBE cells at 80% confluency were mock infected or infected (MOI = 3) for 24 hrs before collecting total RNA from the cell lysate.

value: human small airway epithelial cells

value: SARS-CoV-2 spike pseudotyped lentiviruses


title: STOSE.3 [BV-3]

city: Ottawa

first: David

last: Cook

address: 501 Smyth Rd

institute: Ottawa Hospital Research Institute

value: STOSE


title: CWR22Rv1-AR-EK cells 72h Scrambled siRNA/24h 1 µM AZD7648 n2

description:
AZD7648_2
AREK_DNAPK_featureCounts.tsv
AREK_DNAPK_DESeq2_normalised_counts.csv

value: WT


title: hiPSC-derived islet cells - Control siRNA

value: Control siRNA


title: STOSE.1 [BV-1]


title: HSAEC, pSARS2-2


title: CWR22Rv1-AR-EK cells 72h Scrambled siRNA/24h 1 µM NU5455 n3

description:
NU5455_3
AREK_DNAPK_featureCounts.tsv
AREK_DNAPK_DESeq2_normalised_counts.csv


title: Microvascular endothelium, 16 Gy, 7d, rep3

city: Houston

first: Queeny

last: Dasgupta

state: Texas

address: 2450 holcombe blvd

institute: Systemic Bio

data_processing:
These sequence reads were trimmed using Trimmomatic v.0.36 to eliminate adapter sequences and nucleotides with poor quality.
These trimmed reads were mapped onto the Homo sapiens GRCh38 reference genome using STAR aligner v.2.5.2b.
Unique gene hit counts were computed using Counts from the Subread package v.1.5.2.
Differential expression analysis was performed
Supplementary files format and content: tab-delimited text files includes raw counts for each sample

source_name: Lung

growth_protocol: Human Alveolus chips were seeded with lung epithelial cells on the apical side of the membrane and endothelial cells on the basal side of the membrane. The apical and basal channels were perfused with Alveolar epithelial growth medium and endothelial growth medium , respectively at a flow rate of 45 uL/h. On day 5, the apical medium is supplemented with 1 uM dexamethasone to enhance barrier formation. Following this, on day 7, medium is removed from the apical channel to establish an air-liquid interface. Chips continued to be perfused with EGM2-MV in the basal channel.  On day 9, the perfusing medium was changed to EGM2-MV with 0.5% FBS. On day 11,  5% mechanical strain was applied, at 0.25 Hz frequency to mimic breathing. The mechanical strain is applied for 4 days before the chips are exposed to radiation on day 15.

extract_protocol:
RNA isolation is performed using the RNeasy Plus Micro Kit (Qiagen 74034),
RNA-seq package including polyA selection and sequencing using an Illumina HiSeq for 150 bp pair-ended reads.

treatment_protocol: PBMCs were perfused into the bottom endothelial channel. Following PBMC perfusion, alveolus chips were exposed to gamma radiation using a Cesium source (Cs-137). The chips were exposed to 16 Gy radiation. The control samples were left in the biosafety cabinet to mimic sham irradiation and were not exposed to radiation.

value: Lung

value: Human lung microvascular endothelial cells

value: Lung endothelium

value: 16 Gy radiation


title: HSAEC, UI-5

value: mock infection


title: CWR22Rv1-AR-EK cells 72h Scrambled siRNA/24h 1 µM AZD7648 n1

description:
AZD7648_1
AREK_DNAPK_featureCounts.tsv
AREK_DNAPK_DESeq2_normalised_counts.csv

value: CRISPR edited CWR22Rv1 derivative, prostate epithelial cells


title: Microvascular endothelium, 16 Gy, 7d, rep2


title: Microvascular endothelium, 16 Gy, 7d, rep1


title: CWR22Rv1-AR-EK cells 72h Scrambled siRNA/24h 1 µM NU5455 n2

description:
NU5455_2
AREK_DNAPK_featureCounts.tsv
AREK_DNAPK_DESeq2_normalised_counts.csv


title: CWR22Rv1-AR-EK cells 72h DNA-PKcs knockdown/24h DMSO n1

description:
KD_1
AREK_DNAPK_featureCounts.tsv
AREK_DNAPK_DESeq2_normalised_counts.csv

value: siDNA-PKcs/DMSO


title: CWR22Rv1-AR-EK cells 72h DNA-PKcs knockdown/24h DMSO n2

description:
KD_2
AREK_DNAPK_featureCounts.tsv
AREK_DNAPK_DESeq2_normalised_counts.csv


title: NHBE, Delta-1

source_name: normal human bronchial/tracheal epithelial

value: SARS-CoV-2 Delta variant


title: HSAEC, UI-6


title: MEF PME-1 KO3

city: yamaguchi

first: Shunta

last: Ikeda

state: yamaguchi

department: Joint faculty of veterinary medicine

institute: Yamaguchi University

data_processing:
The obtained next-generation sequencing data were subjected to reads cleaning with TrimGalore (version 0.6.6)
Trimmed sequence reads were mapped to the reference genome (hg38) with HISAT2 (version 2.2.1)
Read count extraction and normalization with the TMM method using TCC-GUI
Assembly: hg38
Supplementary files format and content: Comma-separated csv file including raw counts for each sample

source_name: Embryo

growth_protocol: Immortalized mouse embryonic fibroblasts (MEFs) were maintained in DMEM high glucose supplemented with 10% fetal bovine serum (FBS) and 1×antibiotic/antimycotic (AA) solution (Life Technologies).

extract_protocol:
RNAs were isolated using RNeasy mini kit (QIAGEN). 0.5 μg of RNA was reverse transcribed using QuantiTect Reverse Transcription Kit (QIAGEN).
RNA libraries were prepared according to the manual using the MGIEasy RNA Directional Library Prep Set (MGI Tech Co Ltd)

value: Embryo

value: Immortalized MEFs

value: Fibroblast

value: PME-3 knockout


title: MEF PME-1 KO2

value: PME-2 knockout


title: NHBE, Delta-2

value: normal human bronchial/tracheal epithelial


title: Microvascular endothelium, Ctrl 0 Gy, 7d, rep1

value: Human primary alveolar epithelial cells

value: Control 0 Gy


title: CWR22Rv1-AR-EK cells 72h Scrambled siRNA/24h 1 µM NU7441 n2

description:
NU7441_2
AREK_DNAPK_featureCounts.tsv
AREK_DNAPK_DESeq2_normalised_counts.csv

value: Prostate

value: WT


title: CWR22Rv1-AR-EK cells 72h Scrambled siRNA/24h 1 µM NU7441 n3

description:
NU7441_3
AREK_DNAPK_featureCounts.tsv
AREK_DNAPK_DESeq2_normalised_counts.csv


title: Microvascular endothelium, Ctrl 0 Gy, 7d, rep2

value: Lung

value: Human lung microvascular endothelial cells


title: NHBE, pSARS2-1

value: SARS-CoV-2 spike pseudotyped lentiviruses


title: MEF PME-1 KO1

value: PME-1 knockout


title: MEF PME-1 WT3


title: CWR22Rv1-AR-EK cells 72h Scrambled siRNA/24h 1 µM NU7441 n1

description:
NU7441_1
AREK_DNAPK_featureCounts.tsv
AREK_DNAPK_DESeq2_normalised_counts.csv

value: CRISPR edited CWR22Rv1 derivative, prostate epithelial cells


title: Alveolar epithelium, 16 Gy, 7d, rep3

value: Lung epithelium

value: 16 Gy radiation


title: NHBE, pSARS2-2


title: MEF PME-1 WT2

value: Embryo


title: STOSE.2 [BV-2]

description:
mouse_sample_annotation.csv
txi_mouse.rds
tpm_matrix._mouse.csv

value: cell line

value: STOSE


title: CWR22Rv1-AR-EK cells 72h Scrambled siRNA/24h DMSO n3

description:
Control_3
AREK_DNAPK_featureCounts.tsv
AREK_DNAPK_DESeq2_normalised_counts.csv

value: siScr/DMSO


title: MEF PME-1 WT1

value: Immortalized MEFs

value: Fibroblast


title: Alveolar epithelium, 16 Gy, 7d, rep2

value: Human primary alveolar epithelial cells


title: Microvascular endothelium, Ctrl 0 Gy, 7d, rep3

value: Lung endothelium

value: Control 0 Gy


title: CWR22Rv1-AR-EK cells 72h Scrambled siRNA/24h DMSO n2

description:
Control_2
AREK_DNAPK_featureCounts.tsv
AREK_DNAPK_DESeq2_normalised_counts.csv

value: Prostate

value: WT


title: CWR22Rv1-AR-EK cells 72h Scrambled siRNA/24h 1 µM NU5455 n1

description:
NU5455_1
AREK_DNAPK_featureCounts.tsv
AREK_DNAPK_DESeq2_normalised_counts.csv


title: Alveolar epithelium, Ctrl 0 Gy, 7d, rep3

value: Lung


title: NHBE, UI-2

value: normal human bronchial/tracheal epithelial

value: mock infection


title: NHBE, UI-3


title: CWR22Rv1-AR-EK cells 72h Scrambled siRNA/24h DMSO n1

description:
Control_1
AREK_DNAPK_featureCounts.tsv
AREK_DNAPK_DESeq2_normalised_counts.csv

value: CRISPR edited CWR22Rv1 derivative, prostate epithelial cells


title: NHBE, UI-1


title: pKrts_DKO_IFNB_3

city: Chapel Hill

first: Drake

last: Philip

address: 104 Airport Drive

institute: University of North Carolina-Chapel Hill

data_processing:
CLC Genomics Workbench v 23
Sequences were  aligned to mm10 (Ensembl GRCm39.110) according to default settings
Assembly: mm10
Supplementary files format and content: RPKM and TPM saved in excel file PrimaryKrtRawCounts

source_name: Tail skin

growth_protocol: Cells isolated from mouse tail skin and grown in Keratinocyte Growth Media (Lifeline) and growth in 12-well Tc treated plates for 3-4 days, with media changes every other day. 37C 5% CO2

extract_protocol:
RNEasy Mini Kit (Qiagen)
Kapa mRNA Stranded Library Preparation performed by UNC Highthoughput Sequence Facility

treatment_protocol: Cells once confluent after isolation in 12 well TC plates (3-4 days) were treated with 5ng of IFN-λ, 5ng of IFN-β, or Media only for 24 hours

value: Tail skin

tag: Sex

value: Male

value: primary keratinocytes

value: IFNAR1/IFNLR1KO (C57BL/6)

value: IFN-β


title: NHBE, UI-4


title: pKrts_DKO_IFNB_2

tag: tissue


title: Alveolar epithelium, Ctrl 0 Gy, 7d, rep2

value: Lung epithelium


title: pKrts_DKO_IFNB_1

tag: genotype


title: Microvascular endothelium, 16 Gy, 6h, rep2

value: Human lung microvascular endothelial cells

value: 16 Gy radiation


title: Microvascular endothelium, 16 Gy, 6h, rep3


title: Alveolar epithelium, Ctrl 0 Gy, 7d, rep1

value: Human primary alveolar epithelial cells


title: A549_IFNARKO_IFNL_3

data_processing:
CLC Genomics Workbench v 23
Sequences were  algined to hg38 (Ensembl GRCh38. 110)  according to default settings
Assembly: hg38
Supplementary files format and content: RPKM and TPM saved in excel file A549RawCounts

source_name: Lung adenocarcinoma

growth_protocol: A549 cells were transduced with indicated vector constructs and selected using 2.5 ug/ml puromycin for two weeks. Surviving cells were then single cell sorted into 96 well plates using a FACS ARIA II flow cytometer. Single clones of knockout monoclonal cultures were confirmed via Sanger sequencing and used for subsequent experiments. Cells were maintained in DMEM supplemented with 5% FBS, 1% Glutamax in a incubator at 37C 5% C02.

treatment_protocol: Cells were treated with 50ng of IFN-λ, 5ng of IFN-β, or Media only for 8 hours

value: Lung adenocarcinoma

value: epithelial

value: IFN-λ


title: A549_IFNARKO_IFNL_1


title: A549_IFNARKO_Media_3

value: Media


title: pKrts_DKO_IFNL_3


title: A549_IFNARKO_IFNL_2


title: pKrts_DKO_IFNL_2


title: Alveolar epithelium, 16 Gy, 7d, rep1

value: Lung


title: pKrts_DKO_IFNL_1


title: A549_IFNARKO_Media_2


title: pKrts_DKO_Media_3


title: A549_IFNARKO_Media_1


title: Microvascular endothelium, Ctrl 0 Gy, 6h, rep2

value: Lung endothelium

value: Control 0 Gy


title: Microvascular endothelium, Ctrl 0 Gy, 6h, rep3


title: A549_IFNLRKO_IFNB_3

value: IFNLR1 KO


title: MOLM-13, decitabine, 72 hours, replicate 1

city: Palo Alto

first: Abolfazl

last: Arab

address: 3160 Porter Dr

institute: Arc Institute

description:
molm13_t_1
DAC_RNA_seq_exp_counts_deseq2_norm.txt

data_processing:
The Salmon-tximport-DESeq2 pipeline was used for differential gene expression analysis. Salmon (version 1.2.1) was first used to quantify transcript abundance. A Salmon index was generated using the GENCODE (version 34) genome annotation, and subsequently the `salmon quant` tool was used with the `--validateMappings` option to calculate transcript abundances. Then, the R package tximport was used to import Salmon results into R and perform data preparation. The `summarizeToGene` function was used to collapse transcript abundances to the gene level. From here, the R package DESeq2 was used for differential gene expression analysis. We first extracted normalized counts for each RNA-seq experiment using DESeq2 by running the `estimateSizeFactors` function and then the `counts` function with option `normalized=TRUE`. For each individual experiment, the DESeq2 statistical model was modified based on the experimental design.
The STAR-featureCounts-REMBRANDTS-limma pipeline for differential RNA stability analysis. RNA-seq sequencing reads were first aligned to the hg38 reference genome using STAR5 (version 2.7.3a). Then, featureCounts was used to quantify intron and exon level counts. Finally, REMBRANDTS was used to calculate mRNA stability as previously described (PMID: 29030541; https://github.com/csglab/REMBRANDTS). Briefly, the package estimates a gene-specific bias function that is subtracted from Δexon–Δintron calculations to provide unbiased mRNA stability measurements. To assess differential RNA stability changes, we used limma, which was designed for microarray experiments and serves a similar function to DESeq2, though it supports negative values (relevant for RNA stability analysis). The model designs used here are analogous to the designs for differential expression analysis and based on the experiment design.
iPAGE run and downstream analysis pipeline for Gene Ontology analysis (see https://github.com/abearab/pager).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include DESeq2 normalized count values for each Sample

extract_protocol:
At 72 hours, RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
RNA-seq libraries were prepared using the SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian kit (Takara) due to retirement of the ScriptSeq v2 kit. Total RNA was depleted using the RiboGone module included with the SMARTer kit. All RNA-seq libraries were assessed on a BioAnalyzer 2100 (Agilent) for library quantification and quality control and sequenced on an Illumina HiSeq 4000 using single-end, 50–base pair sequencing.

treatment_protocol: Cells were seeded into 6-well plates at 100,000 cells/mL in duplicate or triplicate and were treated with decitabine (100 nM on days 0, 1 and 2) or DMSO.

value: cancer cell line

value: WT

value: decitabine

value: 72 hours


title: MOLM-13, DMSO, 72 hours, replicate 1

description:
molm13_u_1
DAC_RNA_seq_exp_counts_deseq2_norm.txt

value: DMSO


title: MOLM-13, DMSO, 72 hours, replicate 3

description:
molm13_u_3
DAC_RNA_seq_exp_counts_deseq2_norm.txt


title: MOLM-13, decitabine, 72 hours, replicate 2

description:
molm13_t_2
DAC_RNA_seq_exp_counts_deseq2_norm.txt


title: MOLM-13, DMSO, 72 hours, replicate 2

description:
molm13_u_2
DAC_RNA_seq_exp_counts_deseq2_norm.txt


title: pKrts_DKO_Media_1

value: Tail skin

value: Male

value: primary keratinocytes

value: IFNAR1/IFNLR1KO (C57BL/6)


title: MOLM-13, decitabine, 72 hours, replicate 3

description:
molm13_t_3
DAC_RNA_seq_exp_counts_deseq2_norm.txt


title: Microvascular endothelium, Ctrl 0 Gy, 6h, rep1

value: Human primary alveolar epithelial cells


title: SKM-1, DMSO, 72 hours, replicate 3

description:
skm1_u_3
DAC_RNA_seq_exp_counts_deseq2_norm.txt


title: A549_IFNLRKO_IFNB_2

value: Lung adenocarcinoma

value: epithelial

value: IFN-β


title: Alveolar epithelium, 16 Gy, 6h, rep3

value: Lung

value: Lung epithelium

value: 16 Gy radiation


title: pKrts_IFNARKO_IFNB_3

value: IFNAR1KO (C57BL/6)


title: A549_IFNLRKO_IFNB_1

value: IFNLR1 KO


title: A549_IFNLRKO_Media_3

value: Media


title: Microvascular endothelium, 16 Gy, 6h, rep1

value: Human lung microvascular endothelial cells

value: Lung endothelium


title: SKM-1, DMSO, 72 hours, replicate 1

description:
skm1_u_1
DAC_RNA_seq_exp_counts_deseq2_norm.txt

value: cancer cell line

value: WT

value: DMSO

value: 72 hours


title: pKrts_IFNARKO_IFNB_2

value: Tail skin

value: Male

value: primary keratinocytes


title: Alveolar epithelium, 16 Gy, 6h, rep1

value: Human primary alveolar epithelial cells


title: SKM-1, DMSO, 72 hours, replicate 2

description:
skm1_u_2
DAC_RNA_seq_exp_counts_deseq2_norm.txt


title: pKrts_IFNARKO_IFNB_1

value: IFN-β


title: Alveolar epithelium, 16 Gy, 6h, rep2

value: Lung


title: A549_IFNLRKO_Media_2

value: Lung adenocarcinoma

value: epithelial


title: SKM-1, decitabine, 72 hours, replicate 3

description:
skm1_t_3
DAC_RNA_seq_exp_counts_deseq2_norm.txt

value: decitabine


title: Alveolar epithelium, Ctrl 0 Gy, 6h, rep3

value: Lung epithelium

value: Control 0 Gy


title: A549_IFNLRKO_Media_1

value: IFNLR1 KO

value: Media


title: SKM-1, decitabine, 72 hours, replicate 2

description:
skm1_t_2
DAC_RNA_seq_exp_counts_deseq2_norm.txt

value: cancer cell line


title: pKrts_DKO_Media_2

value: IFNAR1/IFNLR1KO (C57BL/6)


title: Alveolar epithelium, Ctrl 0 Gy, 6h, rep2


title: A549_RenLuc_IFNB_3

value: RenLuc (WT)


title: Alveolar epithelium, Ctrl 0 Gy, 6h, rep1


title: MP46,FHT1015,1h,PRO-seq,Rep2

description: nascent RNA

data_processing:
Normalized directional bigwig coverage tracks were used with dREG for the identification of regions of bidirectional transcription
Differential enrichment of identified bidirectional transcription regions was performed using R limma package using as input normalized coverage data from consolidated dREG calls extended 200bp in each direction
Motif analysis was performed using HOMER findMotifsGenome function using the fragment size option “given”.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)
Library strategy: PRO-seq

extract_protocol:
MP46 uveal melanoma cells were treated with DMSO or 100 nM FHT-1015. Cells were chilled on ice, washed twice with ice-cold PBS and nuclei were isolated.
Nuclear run-on reactions were performed in isolated nuclei by Arpeggio Biosciences. Following RNA extraction with Trizol, libraries were prepared using NEB Next Multiple Small RNA Library kit.  Libraries were sequenced on the Illumina NextSeq 550.

value: uveal melanoma

value: 1 h


title: A549_RenLuc_IFNB_1


title: pKrts_IFNARKO_IFNL_1

value: Tail skin

value: Male

value: IFNAR1KO (C57BL/6)

value: IFN-λ


title: A549_RenLuc_IFNB_2

value: IFN-β


title: pKrts_IFNARKO_Media_2

value: primary keratinocytes


title: AMG510 Resistant NSCLC patient sample

city: New York

first: Ziyan

last: Lin

state: NY

department: Applied Bioinformatics Laboratories

institute: NYU Grossman School of Medicine

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing and gene counting were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Tumor samples dissociated into single cell suspensions. Epcam+ tumor cells were sorted out, total RNA were extracted. Magnetic bead based live cell enrichment was performed on the single cell suspension. Cell suspensions from different mice within each treatment code were hashtagged and pooled.
Libraries were prepared using the Chromium Next GEM Single Cell V(D)J Reagent Kits v1.1

value: Lung

value: lung tumor cell

value: AMG510 Resistant


title: MRTX849+TNO155 Resistant NSCLC patient sample

description: 10x Genomics

value: MRTX849+TNO155 Resistant


title: MP46,FHT1015,1h,PRO-seq,Rep1

city: Cambridge

first: Salih

last: Topal

institute: Foghorn Therapeutics

description: nascent RNA


title: pKrts_IFNARKO_Media_1


title: pKrts_IFNLRKO_IFNB_3

value: IFNLR1 KO (C57BL/6)


title: A549_RenLuc_IFNL_2

value: Lung adenocarcinoma

value: epithelial


title: A549_RenLuc_IFNL_3


title: pKrts_IFNARKO_IFNL_3


title: A549_RenLuc_IFNL_1


title: MP46,FHT1015,15min,PRO-seq,Rep2

description: nascent RNA

value: 15 min


title: AML_blood_healthy_HD8

city: San Diego

last: Croucher

address: 11055 Flintkote Avenue

institute: Cardiff Oncology Inc

data_processing:
Raw fastq files were pseudo-mapped to GRCh38 (Gencode v36) using Salmon v0.14
Salmon transcript counts were converted to genes using tximport (v1.18)
Genes were library size factor normalized and variance-stabilizing transformed (VST) using DESeq2.
The gene counts (VST) data were subject to principal components analysis (PCA). PCs were weighted by their degree of association with the percentage of peripheral leukemic blasts in the samples. The most strongly associated PCs were removed and the data backtransformed, controling for the influence of varying leukemic blast percentages on the data.
Subsequent differential gene expression analyses were based on moderated T-tests as implemented in Limma. For machine learning regression analyses data were Blom (inverse normal transformed).
Assembly: hg38
Supplementary files format and content: comma delimited text file (.csv) containing size-factor normalized gene counts for each sample
Supplementary files format and content: comma delimited text file (.csv) variance-stabilizing transformed and percent peripheral blast corrected gene counts for each sample
Supplementary files format and content: comma delimited text file (.csv) containing Blom (inverse normal) transformed  and percent peripheral blast gene counts for each sample

source_name: Blood

extract_protocol:
Blood samples were collected on day 1 of the trial prior to treatment with onvansertib and decitabine. RNA samples were collected in Paxgene tubes and total RNA extracted using the PAXgene blood RNA kit (Qiagen).
Samples were pre-treated with ezDNase (ThermoFisher). cDNA synthesis used the SMART-Seq v.4 Ultra-Low Input RNA Kit (Takara Bio). NGS libraries were generated using the Nextera XT DNA Library Preparation kit (Illumina) and sequenced (paired-end 100bp) on a HiSeq4000 (Illumina).

value: Blood

value: WBC

tag: disease

tag: percent peripheral_blasts

tag: response group


title: AML_blood_healthy_HD7

tag: cell type


title: pKrts_IFNARKO_IFNL_2


title: pKrts_IFNLRKO_IFNB_2


title: A549_RenLuc_Media_3

tag: cell line

value: RenLuc (WT)

value: Media


title: pKrts_IFNARKO_Media_3

value: Tail skin

value: Male

tag: treatment


title: SKM-1, decitabine, 72 hours, replicate 1

description:
skm1_t_1
DAC_RNA_seq_exp_counts_deseq2_norm.txt

value: cancer cell line

value: WT

value: decitabine

value: 72 hours


title: MP46,DMSO,1h,PRO-seq,Rep2

description: nascent RNA

value: uveal melanoma

value: DMSO

value: 1 h


title: MP46,DMSO,1h,PRO-seq,Rep1

description: nascent RNA


title: AML_blood_healthy_HD6


title: pKrts_IFNLRKO_IFNB_1

value: primary keratinocytes

value: IFNLR1 KO (C57BL/6)

value: IFN-β


title: AML_blood_time0_12_207

value: leukemic blasts and WBC

value: AML


title: pKrts_IFNLRKO_IFNL_3

value: IFN-λ


title: MP46,DMSO,15min,PRO-seq,Rep2

description: nascent RNA

value: 15 min


title: A549_RenLuc_Media_1

value: Lung adenocarcinoma

value: epithelial

value: RenLuc (WT)

value: Media


title: pKrts_IFNLRKO_IFNL_2

value: Tail skin

value: Male


title: Non KRAS G12C - treatment naïve NSCLC  patient sample

description: 10x Genomics

value: Lung

value: lung tumor cell

tag: group

value: Non KRAS G12C - treatment naive


title: 92-1,DMSO,4h,ChIP-seq,input

data_processing:
Reads were aligned using BWA mem with the default parameters
Alignments with a quality lower than 10 were discarded using samtools and duplicated alignments were removed with picard MarkDuplicates tool
Peaks were called with Macs2 callpeak function and fold enrichment coverage tracks were created using the bdgcmp function of the same package
For enhancer/superenhancer calling, broad peaks were called for H3K27Ac alignments using Macs2 callpeak function with –broad parameter and p-value threshold of 1e-9
ROSE was used to identify the enhancers/superenhancers in hg38 version of the human genome using the t parameter set to 2500. Gene mapping of called enhancers/superenhancers was performed using the geneMapper function of the same package
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak

extract_protocol:
Treated 92-1 cells were fixed with 1/10 volume freshly prepared Formaldehyde solution (37% Formaldehyde [Sigma], 5M NaCl [Sigma], 0.5 M EDTA pH 8.0 [Sigma], 1M HEPES pH 7.9 [Teknova]), and neutralized with 1/20 volumes of 2.5 M glycine (Sigma).  Cells were harvested and washed twice with ice-cold PBS (ThermoFisher) containing 0.5% Igepal (Sigma).  During the final wash, 1 mM PMSF was included. Cells were pelleted and following nuclei extraction, chromatin was sonicated. After centrifugating the sonicated chromatin for 10 min at 10,000 rpm, soluble fractions were incubated with the following antibodies: SMARCA4 (Abcam cat# ab110641), SOX10 (Abcam cat# ab155279), MITF (Active Motif cat# 39789), TFAP2A (Santa Cruz cat# sc-12726), H3K27ac (Active Motif cat# 39133).
Illumina libraries were prepared by Active Motif using standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation according to the standard Illumina ChIP-seq library.

value: uveal melanoma

tag: chip antibody

value: none (input)


title: MP46,FHT1015,15min,PRO-seq,Rep1

description: nascent RNA

tag: time


title: AML_blood_time0_09_227

value: Blood


title: pKrts_IFNLRKO_Media_3

value: primary keratinocytes

value: IFNLR1 KO (C57BL/6)


title: 92-1,FHT-1015,4h,ChIP-seq,SOX10

value: SOX10 (Abcam cat# ab155279)


title: pKrts_IFNLRKO_IFNL_1

value: IFN-λ


title: m6AeCLIP-Seq-DD-eIF3d-IP-Tg-1

city: Boston

first: Amy

middle: Si-Ying

last: Lee

state: MA

address: 450 Brookline Ave SM520

department: Cancer Immunology and Virology

institute: DFCI

data_processing:
For RNA-Seq and Subunit-Seq, reads were trimmed with Cutadapt and mapped to GRCh38 using STAR. Differential enrichment was performed using DESeq2
For m6A-eCLIP, UMIs were extracted using UMItools, reads were trimmed with Cutadapt and mapped to GRCh38 using bwa. m6A site identification was performed using CTK and CIMS/CITS analysis.
Assembly: GRCh38
Supplementary files format and content: For RNA-Seq and Subunit-Seq: RPKM; for m6A-eCLIP: m6A sites

growth_protocol: All cell lines were grown in DMEM with 10% FBS and 500 U mL-1 penicillin-streptomycin.

extract_protocol:
Cells were lysed in 50 mM HEPES-KOH pH 7.4, 150 mM KCl, 5 mM Mg(OAc)2, 1 % v/v NP-40, 0.25 mM DTT.
For RNA-Seq, polyadenylated RNA was purified and libraries were made using NEBNext Ultra II RNA Library Prep Kit for Illumina. For m6A-eCLIP, libraries were constructed using the m6A-eCLIP kit from Eclipse Bio. For Subunit-Seq, eIF3d was immunoprecipitated using anti-HA beads, the cap-binding domain was isolated by TEV protease digestion, contaminating RNAs were removed by enzymatic treatment and libraries were made using the NEBNext Ultra II Directional RNA Library Prep Kit

treatment_protocol: Cells were seeded to be at ~80 % confluency at time of treatment and then treated with 600 nM thapsigargin or equal volume of DMSO vehicle for 16 h.

value: Human embryonic kidney


title: AML_blood_time0_09_034

value: leukemic blasts and WBC

value: AML


title: AML_blood_time0_09_064


title: m6AeCLIP-Seq-DD-eIF3d-IP-DMSO-2

value: DMSO


title: pKrts_IFNLRKO_Media_2

value: Media


title: AML_blood_time0_09_026


title: 92-1,FHT-1015,4h,ChIP-seq,AP-2

address: 500 Technology Square Suite 700

value: TFAP2A (Santa Cruz cat# sc-12726)


title: A549_RenLuc_Media_2

value: Lung adenocarcinoma

value: epithelial

value: RenLuc (WT)


title: pKrts_IFNLRKO_Media_1

value: Tail skin

value: Male


title: AML_blood_time0_08_217


title: m6AeCLIP-Seq-DD-eIF3d-IP-DMSO-1


title: 92-1,DMSO,4h,ChIP-seq,AP-2

value: uveal melanoma


title: m6AeCLIP-Seq-WT-eIF3d-IP-Tg-2

value: WT


title: 92-1,FHT-1015,4h,ChIP-seq,MITF

value: MITF (Active Motif cat# 39789)


title: pKrts_WT_IFNB_3

value: Female

value: primary keratinocytes

value: IFN-β


title: pKrts_WT_IFNB_2


title: AML_blood_time0_12_048

value: Blood


title: m6AeCLIP-Seq-WT-eIF3d-IP-Tg-1

value: Human embryonic kidney


title: MP46,DMSO,15min,PRO-seq,Rep1

description: nascent RNA

value: 15 min


title: 92-1,DMSO,4h,ChIP-seq,MITF


title: AML_blood_time0_08_061

value: leukemic blasts and WBC

value: AML


title: m6AeCLIP-Seq-DD-eIF3d-IP-Tg-2


title: pKrts_WT_IFNB_1


title: m6AeCLIP-Seq-WT-eIF3d-IP-DMSO-2

value: DMSO


title: 92-1,DMSO,4h,ChIP-seq,SOX10

value: SOX10 (Abcam cat# ab155279)


title: AML_blood_time0_08_058


title: 92-1,FHT-1015,4h,ChIP-seq,SMARCA4

value: SMARCA4 (Abcam cat# ab110641)


title: 92-1,DMSO,4h,ChIP-seq,SMARCA4


title: m6AeCLIP-Seq-DD-eIF3d-Input-Tg-2


title: 92-1,FHT-1015,4h,ChIP-seq,H3K27ac

value: H3K27ac (Active Motif cat# 39133)


title: pKrts_WT_IFNL_2

value: Tail skin

value: IFN-λ


title: m6AeCLIP-Seq-DD-eIF3d-Input-Tg-1


title: AML_blood_time0_07_221


title: AML_blood_time0_08_205


title: AML_blood_time0_07_214


title: pKrts_WT_Media_3

value: Media


title: pKrts_WT_IFNL_1


title: m6AeCLIP-Seq-DD-eIF3d-Input-DMSO-2


title: AML_blood_time0_07_062


title: m6AeCLIP-Seq-DD-eIF3d-Input-DMSO-1


title: Hboit-3 Dox-

city: Copenhagen

first: William

last: Agace

address: Blegdamsvej 3B

institute: Copenhagen University

data_processing:
Abundances of transcripts from the bulk RNA sequencing reads were quantified using kallisto v0.46.0
Differential gene expression analysis was performed using DESeq2 v1.22.2
Assembly: gencode.v37.transcripts
Supplementary files format and content: Normalized counts (TPMs)

source_name: Jurkat

extract_protocol:
Qiagen Rneasy
NEBNext single-cell/low input library Prep Kit

value: Jurkat

value: Dox-


title: 92-1,DMSO,4h,ChIP-seq,H3K27ac

value: uveal melanoma


title: Hobit-1 Dox-


title: m6AeCLIP-Seq-WT-eIF3d-IP-DMSO-1

value: WT


title: pKrts_WT_Media_1

value: Female

value: primary keratinocytes


title: AML_blood_time0_07_036

value: Blood


title: Hobit-2 Dox+

value: Dox+


title: m6AeCLIP-Seq-WT-eIF3d-Input-Tg-2

value: Human embryonic kidney


title: pKrts_WT_Media_2


title: m6AeCLIP-Seq-WT-eIF3d-Input-Tg-1


title: AML_blood_time0_07_035

value: leukemic blasts and WBC

value: AML


title: pKrts_WT_IFNL_3


title: Hobit-2 Dox-


title: AML_blood_time0_08_050


title: AML_blood_time0_07_033


title: m6AeCLIP-Seq-WT-eIF3d-Input-DMSO-2

value: DMSO


title: KCL GEMM tumor nodule resistant to MRTX 849  replica 3

data_processing:
NovaSeq 6000 System
bcl2Fastq v2.20
Trimming, alignment and generating count matrix were all done by using the sns/rna-star pipeline (https://igordot.github.io/sns/routes/rna-star.html)
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: lung nodule

extract_protocol:
Tumor nodules were harvested from the treated mice, and dissociated into single cell suspensions. Libraries were prepared using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit and sequenced on an Illumina NovaSeq 6000 machine using 150bp paired end reads.
RNA library was prepared using SMARTER mRNA seq library prep kit following manufacturer's kit

treatment_protocol: Tumor-bearing mice were treated MRTX849 100mpk and or SHP099 75 mpk daily

value: lung nodule

value: lung tumor cell

value: KRAS G12C STK11 null


title: KCL GEMM tumor nodule resistant to MRTX 849  replica 2


title: AML_blood_time0_07_018


title: Hobit-1 Dox+

treatment_protocol: grown with or without 1 ug/uL of doxycycline


title: Hobit-3 Dox+


title: m6AeCLIP-Seq-WT-eIF3d-Input-DMSO-1


title: KCL GEMM tumor nodule control vehicle for MRTX 849 Resistance replica 3

value: vehicle for MRTX 849 Resistance


title: AML_blood_time0_07_013


title: KCL GEMM tumor nodule resistant to MRTX 849  replica 1


title: Subunit-Seq-IP-Tg-2


title: AML_blood_time0_07_011

value: unknown


title: Subunit-Seq-IP-Tg-1


title: AML_blood_time0_07_009


title: Subunit-Seq-Input-Tg-2


title: KCL GEMM tumor nodule control vehicle for MRTX 849 Resistance replica 2


title: H2122 treated MRTX-849 for 48 hrs Replica 1

data_processing:
NovaSeq 6000 System
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
Trimming, alignment and generating count matrix were all done by using the sns/rna-star pipeline (https://igordot.github.io/sns/routes/rna-star.html)
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: RPMI 10% FBS

extract_protocol:
RNA extraction
Libraries were prepared using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit and sequenced on an Illumina NovaSeq 6000 machine using 150bp paired end reads.

treatment_protocol: MRTX-849 IC50 treatment 48 hrs

value: Lung

value: KRAS G12C mut STK11 mut KEAP1 mut

value: MRTX-849 treated 48 hrs


title: KCL GEMM tumor nodule control vehicle for MRTX 849 Resistance replica 1


title: H2122 treated MRTX-849 for 48 hrs Replica 3


title: H2122 treated MRTX-849 for 48 hrs Replica 2


title: KCL GEMM tumor nodule resistant to MRTX849+SHP099 Replica 4

value: MRTX 849 + SHP099


title: Subunit-Seq-IP-DMSO-2


title: AML_blood_time0_05_239


title: KCL GEMM tumor nodule resistant to MRTX849+SHP099 Replica 3


title: AML_blood_time0_05_212


title: H2122 treated DMSO for 48 hrs Replica 3

value: DMSO treated 48 hrs


title: KCL GEMM tumor nodule resistant to MRTX849+SHP099 Replica 2


title: H2122 treated DMSO for 48 hrs Replica 2


title: AML_blood_time0_05_030


title: Subunit-Seq-Input-DMSO-2


title: KCL GEMM tumor nodule control vehicle for combo replica 4

value: vehicle for combo replica


title: H2030 treated MRTX-849 for 48 hrs Replica 3


title: H2030 treated MRTX-849 for 48 hrs Replica 2


title: Subunit-Seq-Input-DMSO-1


title: KCL GEMM tumor nodule resistant to MRTX849+SHP099 Replica 1


title: AML_blood_time0_03_238

value: Blood


title: RNA-Seq-DD-eIF3d-Tg-2


title: AML_blood_time0_03_222


title: H2030 treated MRTX-849 for 48 hrs Replica 1


title: KCL GEMM tumor nodule control vehicle for combo replica 3


title: RNA-Seq-DD-eIF3d-Tg-1


title: AML_blood_time0_07_008


title: Subunit-Seq-IP-DMSO-1


title: Subunit-Seq-Input-Tg-1


title: AML_blood_time0_03_219


title: AML_blood_time0_03_051


title: RNA-Seq-DD-eIF3d-DMSO-1


title: H2030 treated DMSO 48 hrs Replica 3


title: H2030 treated DMSO 48 hrs Replica 1


title: H2030 treated DMSO 48 hrs Replica 2


title: KCL GEMM tumor nodule control vehicle for combo replica 1


title: RNA-Seq-DD-eIF3d-DMSO-2


title: RNA-Seq-WT-eIF3d-Tg-2

value: WT


title: AML_blood_time0_03_060


title: HCC44 treated with DMSO at day 0, Replica 1

data_processing:
sgRNA count table and important genes identificantion were all done by using MAGeCK (https://sourceforge.net/p/mageck/wiki/Home/)
Assembly: hg38
Supplementary files format and content: Matrix table with raw single-guide RNA counts for every sample
Library strategy: CRISPR Screen

source_name: lung

growth_protocol: RPMI 10%FBS

extract_protocol:
Cells were lysed with Tris/SDS buffer supplemented with protease inhibitor, and DNA was precipitated with 40% isopropanol
Region contatining sgRNA sequence was amplified with two sequenctial PCR and final product was gel purified--genomic library is recovered

treatment_protocol: MRTX849 (2X IC50) and TNO155  (IC50) value

value: DMSO at day 0

value: lung


title: RNA-Seq-WT-eIF3d-Tg-1

value: Human embryonic kidney