title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 70

value: KRAS, CDKN2A


title: Liver, Sedentary 3(S3)

status: Public on Aug 08 2024

type: SRA

city: Wuhan

first: Yan

last: Wang

state: China

address: Luojiashan, wuchang, wuhan

country: China

institute: College of Life Sciences, Wuhan University

library_source: transcriptomic

data_processing:
ThesequencingdatawasfilteredwithSOAPnuke( v 1.6.5)by(1)Removingreadscontainingsequencingadapter;(2)Removingreadswhoselow-qualitybaseratio(basequalitylessthanorequalto15)ismorethan20%;(3)Removingreadswhoseunknownbase('N'base)ratioismorethan5%,afterwardscleanreadswereobtainedandstoredinFASTQformat.
ThecleandataweremappedtothereferencegenomebyHISAT(v2.1.0)
The clean data were mapped to the assembled unique gene by Bowtie2 (v2.3.4.3). The expression level of genes was calculated by RSEM (v1.3.1).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes FPKM for each Sample

molecule: total RNA

organism: Mus musculus

source_name: Liver

extract_protocol:
Total RNA was extracted from tissues or cells with TRI Reagent (Sigma-Aldrich).1ug of total RNA was used for construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using BGI Optimal Dual-mode mRNA-Seq Library Prep Kit following manufactuer's protocols.

tag: tissue

value: Liver

tag: genotype

value: WT

tag: treatment

value: Sedentary


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 69

city: Utrecht

first: Joost

last: Koedijk

address: Heidelberglaan 25

country: Netherlands

institute: Princess Máxima Center for Pediatric Oncology

data_processing:
After pre-processing, reads were aligned to GRCh38 and gencode version 31. Pre-processing of RNA-seq data was done with the institute's standardized pipelines implementing GATK 4.0 best practices for variant calling using a wdl and cromwell-based workflow (PMID: 25431634 by Van der Auwera et al. & van Belzen et al. PMID 37400763).
Assembly: GRCh38
Supplementary files format and content: Raw counts

organism: Homo sapiens

source_name: bone marrow

extract_protocol:
Total RNA was isolated from tumor samples using the AllPrep DNA/RNA/Protein Mini Kit (QIAGEN) according to standard protocol on the QiaCube (Qiagen).
RNA-sequencing libraries were generated from 300 ng RNA using the KAPA RNA HyperPrep Kit with RiboErase (Roche). Sequencing was performed using the NovaSeq 6000 (2 x 150 bp) (Illumina).

value: bone marrow

tag: cytogenetics

value: No relevant fusions

tag: relevant mutations

value: treatment-naïve


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 72

value: NRAS, CREBBP


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 80


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 68

value: NRAS


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 67

value: TP53, NUP93


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 66

value: KRAS


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 75

value: ETV6-RUNX1 + PAX5-NAP1L4


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 64


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 62


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 60


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 59

value: MGA


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 58

value: ETV6-RUNX1 + PAX5-ZCCHC7


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 57

value: KRAS, FLT3


title: ∆6 trastuzumab rep3

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

country: USA

institute: Koch Institute

description:
∆TOS1,∆CRH1,∆EXG1,∆5326,∆LSC2,∆TFS1
220706Lov_D22-208054

data_processing:
Illumina NextSeq 500 using v3 chemistry. NextSeq Software: Control v4.0.0.19, RTA 2.11.3. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
Paired-end RNA-seq data was used to quantify transcripts from the WT.fa Komagataella phaffii and exogenous transgenes (see phaffi_plus_083022_transgenes.fa.gz supplemental file) using Salmon version 1.6.0. Gene level summaries were prepared using tximport version 1.24.0 running under R version 4.2.1
Assembly: WT.fa Komagataella phaffii genome
Supplementary files format and content: 220706Lov_dalvie_IntCt.txt.gz is a tab delimited text file of integer count data
Supplementary files format and content: 220706Lov_dalvie_l2tpm.txt.gz is a tab delimited text file of log 2 TPM data with a +1 offset
Supplementary files format and content: PhaffiWT_annotation.xlsx is an excel file that associates geneIDs with gene symbols
Supplementary files format and content: transcript2gene.xlsx is an excel file that associates transcript IDs with gene IDs
Supplementary files format and content: WT.fa.gz is a fasta formatted file of the Komagataella genome assembly used in processing
Supplementary files format and content: phaffi_plus_083022_transgenes.fa.gz is a fasta formatted file of Komagataella transcripts and transgenes

organism: Komagataella phaffii

source_name: Trastuzumab expression

growth_protocol: Cells were outgrown by cultivation in glycerol medium at 3 mL plate scale for 24 h

extract_protocol:
RNA was extracted and purified according to the Qiagen RNeasy kit (cat #74104) and RNA quality was analyzed to ensure RNA Quality Number >6.5.
Sequencing libraries were prepared using the Nextera XT kit according to the manufacturer's instructions.

treatment_protocol: Cells were exchanged into methanol medium and cultivated for 18 h at 3 mL plate scale

tag: strain

tag: cell line

value: Trastuzumab expression

tag: cell type

value: Yeast

value: Methanol induction for 18h


title: Day3 PFI set1260 Rep2

type: RNA

city: Durham

first: James

middle: M

last: Ward

state: NC

address: 111 TW Alexander Dr

department: Integrative Bioinformatics

institute: NIEHS

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Data were processed in R oligo, using RMA signal extraction and normalization, and processing each experimental batch independently. Statistical comparisons were performed using limma moderated t-tests, analyzing each experimental batch independently.

label: biotin

source_name: human dermal fibroblasts

label_protocol: standard Affymetrix protocol

growth_protocol: Human dermal fibroblasts were reprogrammed into induced pluripotent stem cells (iPSCs) via lentiviral transduction using six transcription factors contained in three plasmids (ADDGENE/PSIN4-EF2-N2L, ADDGENE/PSIN4-EF2-O2S and ADDGENE/PSIN4-CMV-K2M).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: PFI-3 (10 uM working concentration) was added from Day 1 to 7 of iPSCs generation, during a 21-day protocol.

tag: time

value: PFI

tag: experiment batch


title: Day5 Control set1260 Rep1

value: Control


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 63


title: Day5 Control set1260 Rep3


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 56


title: Day3 PFI set1260 Rep1


title: Day5 PFI set1260 Rep1


title: ∆6 trastuzumab rep1

description:
∆TOS1,∆CRH1,∆EXG1,∆5326,∆LSC2,∆TFS1
220706Lov_D22-208052


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 61


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 55


title: ∆6 HSA rep3

description:
∆TOS1,∆CRH1,∆EXG1,∆5326,∆LSC2,∆TFS1
220706Lov_D22-208051

source_name: HSA expression

value: HSA expression


title: Day5 PFI set1260 Rep2


title: Day3 Control set1260 Rep1


title: Day0 Control set1260 Rep2


title: Day3 Control set1260 Rep3


title: Day21 PFI set1123 Rep3


title: Day5 Control set1260 Rep2


title: Day21 PFI set1123 Rep2


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 54

value: bone marrow


title: Base trastuzumab rep3

value: Base strain


title: Day3 Control set1260 Rep2


title: Day5 PFI set1260 Rep3


title: Day3 PFI set1260 Rep3


title: Day0 Control set1260 Rep3


title: Day21 PFI set1123 Rep1


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 53

value: No relevant fusions

value: treatment-naïve


title: Day0 Control set1260 Rep1


title: Base trastuzumab rep1


title: Day14 PFI set1123 Rep3


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 65


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 52


title: ∆6 trastuzumab rep2

description:
∆TOS1,∆CRH1,∆EXG1,∆5326,∆LSC2,∆TFS1
220706Lov_D22-208053


title: Base HSA rep1


title: Base HSA rep2


title: ∆6 HSA rep1

description:
∆TOS1,∆CRH1,∆EXG1,∆5326,∆LSC2,∆TFS1
220706Lov_D22-208049


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 51

value: ETV6-RUNX1 + PAX5-EEF1A1 + PAX5-TP53BP1


title: Base trastuzumab rep2


title: Base HSA rep3


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 50


title: Day14 PFI set1123 Rep2


title: P2 CFM_Day8 C3

city: Bielefeld

first: Ingo

last: Todt

address: Morgenbreede 1

department: Ear, nose and throat medicine

country: Germany

institute: University of Bielefeld

data_processing:
The single-end reads were mapped to the human transcriptome (RefSeq Transcripts GRCh38; downloaded from NCBI) and quantified using Kallisto v0.44.0.
Estimated counts were statistically analyzed usingedgeRv3.28. The fold-change gene expression values were calculated in pairwise comparisons between the undifferentiated cancer cells as the control and differentiated cancer cells as treated. Genes were considered differentially expressed if their p-value was <0.05.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file

source_name: Tongue base

extract_protocol:
Cells were cultured for eight days. Total RNA was isolated from cell culture (n=3) usinginnuPREPDNA/RNA Mini Kit (AnalytikJena, Jena, Germany) as recommended by the manufacturer's protocol. RNA quality was determined with aBioDropDuo+ spectral photometer (Biochrom, Holliston, USA).
PolyA-selected libraries were prepared from 200 ng of total RNA usingQuantSeq3′mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen), according to the manufacturer's instructions. Size distribution and quality of the libraries were assessedby fragment analyzer (Agilent) and final libraries were sequenced in 75 bp single-end mode on a NextSeq2000 with P3 chemistry.

value: Tongue base

value: epithelial cancer cells

value: differentiated


title: P2 CFM_Day8 C1


title: P2 CFM_Day8 C2


title: P2_PNEU_Day8 K3

value: undifferentiated


title: P2_PNEU_Day8 K2


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 48

value: KRAS


title: P2_PNEU_Day8 K1


title: P1 CFM_Day8 C3

source_name: Oropharynx / Tonsil

value: Oropharynx / Tonsil


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 47

value: TCF3-PBX1 + PAX5-CDC42


title: P1_PNEU_Day8 K1


title: P1_PNEU_Day8 K3


title: P1_PNEU_Day8 K2


title: P1 CFM_Day8 C2


title: P1 CFM_Day8 C1


title: HL60_shCTRL_IgG

city: Vienna

first: Thomas

last: Eder

address: Veterinaerplatz 1

department: Department for Biological Sciences and Pathobiology

country: Austria

institute: University of Veterinary Medicine, Vienna

library_source: genomic

data_processing:
Raw files were preprocessed with prinseq-lite, aligned against the human reference genome (hg38)  with BWA (version 0.7.17-r1188), post-processed and sorted with samtools (version 1.13). The function bamCoverage from Deeptools (version 3.5.1) was then used to create BigWig files with a binSize of 10 and using CPM for normalization. Also tornado -and profile-plots were created with Deeptools (computeMatrix and then plotHeatmap or plotProfile). Peaks were called with macs2 (version 2.1.0) and the --broad option. The R package DiffBind was then used to get differential ChIP-seq regions applying DESeq2. Read counts per genes were obtained with featureCounts from the subread package and all scatter-plots were created with ggplot2 in R.
Assembly: hg38
Supplementary files format and content: bigwig files and peak files (except for IgG controls)
Library strategy: CUT&Tag

molecule: genomic DNA

growth_protocol: Cells were maintained in RPMI supplemented 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol: iDeal CUT&tag kit for histones compatible with histones and some non-histones proteins (Diagenode, Belgium)

treatment_protocol: Cells were treated with doxycycline (1 µg/ml) for 5 days to induce shRNA expression prior to CUT&Tag

tag: antibody

value: IgG

value: shCTRL


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 45

value: NRAS, FLT3


title: Day7 PFI set1123 Rep2

value: PFI


title: Day7 PFI set1123 Rep3


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 49


title: HL60_shCTRL_H3K9me3_2


title: Day0 PFI set1123 Rep3


title: HL60_shCTRL_H3K4me3_2


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 44


title: Day7 PFI set1123 Rep1


title: HL60_shCTRL_H3K4me3_1


title: HL60_shCTRL_H3K9me3_1


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 46


title: Day0 PFI set1123 Rep1


title: Day21 Control set1123 Rep3

value: Control


title: Day21 Control set1123 Rep2


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 42

value: bone marrow


title: HL60_shCTRL_H3K27me3_2


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 41

value: NRAS


title: Day0 PFI set1123 Rep2


title: HL60_shCTRL_H3K27ac_1


title: HL60_shCTRL_H3K27ac_2


title: Day14 PFI set1123 Rep1


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 43

value: No relevant fusions


title: HL60_shDDX6_IgG


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 40

value: treatment-naïve


title: Day21 Control set1123 Rep1


title: HL60_shDDX6_H3K9me3_2


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 39


title: HL60_shCTRL_H3K27me3_1


title: HL60_shDDX6_H3K9me3_1


title: HL60_shDDX6_H3K4me3_2


title: HL60_shDDX6_H3K4me3_1


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 38


title: HL60_shDDX6_H3K27me3_2


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 37


title: HL60_shDDX6_H3K27me3_1


title: HL60_shDDX6_H3K27ac_2


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 36


title: Day14 Control set1123 Rep3


title: Day14 Control set1123 Rep1


title: Day7 Control set1123 Rep2


title: Day14 Control set1123 Rep2


title: Day7 Control set1123 Rep3


title: ∆6 HSA rep2

description:
∆TOS1,∆CRH1,∆EXG1,∆5326,∆LSC2,∆TFS1
220706Lov_D22-208050

value: HSA expression

value: Yeast

value: Methanol induction for 18h


title: 7.0 μM SR-18292

city: Boston

first: Single Cell

last: Sequencing Core

address: 72 E. Concord St

institute: BU Single Cell Sequencing Core

library_source: transcriptomic single cell

data_processing:
BaseCalls performed using Illumina
Demultiplexing performed using Cell Ranger v6.1.2 with default settings
Reads aligned to GRCh38-2020-A reference genome using Cell Ranger v6.1.2 with --expect-cells=6000
Assembly: GRCh38
Supplementary files format and content: Tab separated and matrix files

source_name: human CD34+ cells

growth_protocol: Three-phase cell culture system

extract_protocol:
Cell concentration and viability of mouse samples were measured using a hemocytomter and ranged from 910,000 - 1,180,000 cells/mL with ~90% viability. Cell samples were input into 10x Genomics Single Cell 3′ v3.1D workflow and processed according to the manufacturer’s instructions for a targeted recovery of 6000 cells (10X Genomics, USA). The resulting gene expression libraries were sequenced on an Illumina NextSeq 2000 instrument with 850pM input and 2% PhiX control library spike-in (Illumina, USA).
scRNA-seq libraries were generated in BU DOM Single Cell sequencing core facility and sequenced by BU Microarray and Sequencing Resource Core Facility according to 10x Genomics protocol

treatment_protocol: human CD34+ cells were treated with DMSO and 5.0 μM and 7.5 μM SR-18292

value: human CD34+ cells


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 35


title: HL60_shDDX6_H3K27ac_1


title: 5.0 μM SR-18292


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 34


title: Vehicle control

value: DMSO


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 33


title: Day 42 iPSC-derived chondrocytes + TGFb, scRNAseq

city: Bethesda

first: Pamela

middle: Gehron

last: Robey

state: MD

address: 30 Convent Dr

department: NIDCR

institute: NIH

description: 10x Genomics

data_processing:
Reads were mapped using GRCh38-2020-A reference transcriptome
Libraries were processed using Cell Ranger version 7.0.
Secondary analysis was performed using Seurat's R package
Assembly: Reads were mapped using GRCh38-2020-A reference transcriptome
Supplementary files format and content: Cellranger filtered feature barcode matrix in HDF5 format
Supplementary files format and content: Cellranger raw feature barcode matrix in HDF5 format

source_name: Organoid

extract_protocol:
Tissues were digested in high-glucose DMEM containing 0.2% collagenase II and 0.1% dispase with gentle pipetting every 20-30 minutes.  Enzymatic digestion was observed in 6 well-plates, and digestion was terminated when aggregates were completely dissolved, for up to 2 hours.  Enzyme was inhibited with 20% FBS, and cells were filtered through 70 µm strainers and re-suspended in PBS supplemented with 0.04% high-quality bovine serum albumin at 1000 cells/µL for single-cell capture.
Single-cell RNA sequencing was performed using 10X Genomics Chromium instruments.

treatment_protocol: hiPSC-derived sclerotome was differentiated in chondrogenic medium with TGFb alone (controls) or supplemented with BMP2 and GDF5 (experimental).  At day 42 of differentiation of suspension cultures, tissues were digested in collagenase II and filtered for single cell RNA sequencing.

value: Organoid

value: NL5 hiPSC line

tag: differentiation

value: chondrogenic medium

value: control (TGFb only)

value: iPSC-derived chondrocytes

value: Day 42


title: Δ855-879 AtrR, phleoR, YG+vori, replicate 3

city: Iowa City

first: Scott

last: Moye-Rowley

state: Iowa

address: 6-530 Bowen Science Bldg./Dept. of Mol Physio

department: Molecular Physiology & Biophysics

institute: University of Iowa

data_processing:
Paired end reads were mapped to the Af293 A. fumigatus genome using HISAT2.  Transcript assembly, quantification of expression levels and analysis of differential expression were done using Stringtie and the DESeq2 R package. Bigwig files were generated using the GenomicAlignments and rtracklayer R packages
Assembly: Aspergillus fumigatus FungiDB-57
Supplementary files format and content: BigWig files for RNA-seq reads; Excel file with DEseq listing of all genes significantly (padj<0.05) altered by log 2=>1

organism: Aspergillus fumigatus

growth_protocol: Cell lysates were prepared from mycelial biofilm cultures formed upon inoculating 1X10^6 spores in a petri dish containing 20 ml of YG (0.5% yeast extract, 2% glucose) broth and grown for 24 hours at 37°C under non-shaking conditions.

extract_protocol:
Mycelia that formed as a biofilm on the top were collected (∼100 mg) and ground into a fine powder in liquid nitrogen using a mortar and pestle. Total RNA was then isolated from the ground mycelium using the Trizol reagent (Ambion) according to the manufacturer's instructions. Traces of contaminating genomic DNA were eliminated by treating the RNA with turbo DNase followed by a DNase inactivation reagent (both reagents from Ambion).
Libraries were constructed by Omega Bioservices (omegabioservcies.com).

treatment_protocol: Voriconazole was added to 0.06 mg/ml for 8 hours following growth in YG for 16 hours.

value: akuA::loxP {delta}855-879 atrR-phleoR

value: 16h YG + 8h Vori (0.06 mg/ml)


title: Δ855-879 AtrR, phleoR, YG, replicate 3

value: 24h YG


title: Transplanted hBMSC/SSCs with HyA-FMBs, donor 1, scRNAseq

description: 10x Genomics

source_name: Bone marrow (right hip)

extract_protocol:
Control and HyA-FMB organoids from days 1-10 and ectopic HyA-FMB transplant were digested in high-glucose DMEM containing 0.2% collagenase II, 0.1% hyaluronidase, and 0.1% dispase with gentle pipetting every 20-30 minutes.  Enzymatic digestion was observed in 6 well-plates, and digestion was terminated when aggregates were completely dissolved, for up to 2 hours.  Enzyme was inhibited with 20% FBS, and cells were filtered through 70 µm strainers and re-suspended in PBS supplemented with 0.04% high-quality bovine serum albumin at 1000 cells/µL for single-cell capture.  Naïve hBMSC/SSC controls (from donor 3) required a 10-minute incubation with collagenase II on monolayer cultures prior to cell detachment and cell capture.
Single-cell RNA sequencing was performed using 10X Genomics Chromium instruments.

value: Bone marrow (right hip)

tag: age

value: 14 year old

tag: Sex

value: female

value: hBMSC/SSC

value: HyA-FMB scaffold


title: Day 42 iPSC-derived chondrocytes + TGFb + BMP2 + GDF5, scRNAseq

description: 10x Genomics

value: TGFb + BMP2 + GDF5


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 32

value: bone marrow

value: No relevant fusions

value: treatment-naïve


title: Day7 Control set1123 Rep1

value: Control


title: Naïve hBMSC/SSC, donor 3/replicate 2, scRNAseq

description: 10x Genomics

source_name: Bone marrow (femur)

value: Bone marrow (femur)

value: 8 year old

value: male

value: control (no scaffold)


title: Day0 Control set1123 Rep3


title: Naïve hBMSC/SSC, donor 3/replicate 1, scRNAseq

description: 10x Genomics


title: Day 10 HyA-FMB organoid, donor 2, scRNAseq

description: 10x Genomics

value: 18 year old


title: Day0 Control set1123 Rep2


title: Wild-type, phleoR, YG, replicate 3

value: akuA::loxP atrR-phleoR


title: Day0 Control set1123 Rep1


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 31


title: Day 10 control organoid, donor 2, scRNAseq

description: 10x Genomics


title: Day 5 HyA-FMB organoid, donor 2, scRNAseq

description: 10x Genomics


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 30


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 28

value: NRAS


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 29


title: AIS2

city: Nanjing

first: Qiang

last: Peng

address: No. 68 Changle Road

department: Neurology

institute: Nanjing First Hospital, Nanjing Medical University

data_processing:
Reads obtained from the sequencing machines included dirty reads containing adapters or low quality bases which would affect the following assembly and analysis. Thus, to get clean tags,raw reads were further filtered according to the following rules:
1) Removing low quality reads containing more than one low quality (Q-value≤20) base or
containing unknown nucleotides(N);
2) Removing reads without 3’adapters;
3) Removing reads containing 5’adapters;
4) Removing reads containing 3’ and 5’ adapters but no small RNA fragment between them;
5) Removing reads containing ployA in small RNA fragment;
6) Removing reads shorter than 18nt (not include adapters).
Subsequent RNA-seq reads were mapped to GenBank, Rfam, Genome and miRBase databases.
miRNAs differential expression analysis was performed by edgeR software between two different groups or samples.We identified miRNAs with a fold change ≥2 and P value <0.05 in a comparison as significant DE miRNAs
Assembly: hg38
Supplementary files format and content: Microsoft xlsx files containing count, TPM, fold change, and p-value

source_name: peripheral blood

extract_protocol:
Total RNA was extracted from the plasma of AIS patients and healthy controls using miRNeasy Mini Kit, and the RNA molecules in a size range of 18-30 nt were enriched by polyacrylamide gel electrophoresis.
The 3’ adapters were added and the 36-44 nt RNAs were enriched. The 5’ adapters were subsequently ligated to the RNAs as well. The ligation products were reverse transcribed by PCR amplification and the 140-160bp size PCR products were enriched to generate a cDNA library.Then RNAs were sequenced using Illumina HiSeqTM 2500 by Gene Denovo Biotechnology Co. (Guangzhou, China).

value: peripheral blood

tag: disease state

value: acute ischemic stroke


title: Day 5 control organoid, donor 2, scRNAseq

description: 10x Genomics


title: AIS1


title: HC2

value: healthy control


title: Day 3 HyA-FMB organoid, donor 2, scRNAseq

description: 10x Genomics

value: hBMSC/SSC


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 27


title: HC1


title: Δ855-879 AtrR, phleoR, YG, replicate 2

value: akuA::loxP {delta}855-879 atrR-phleoR

value: 24h YG


title: Wild-type, phleoR, YG+vori, replicate 2

value: 16h YG + 8h Vori (0.06 mg/ml)


title: Day 3 control organoid, donor 2, scRNAseq

description: 10x Genomics


title: Wild-type, phleoR, YG+vori, replicate 3


title: Day 1 control organoid, donor 2, scRNAseq

description: 10x Genomics


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 25

value: bone marrow


title: Wild-type, phleoR, YG, replicate 2


title: Day 42 chondrospheroid, replicate 3, RNAseq

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sequenced reads were mapped to GRCh38.v32 humangenome using STAR v2.7.2a in single-pass mode
Gene counts were generated with STAR v2.7.2a built-in counting option --quantMode GeneCounts against a custom GRCh38.v32 genome annotation GTF which included ERCCs.
A expression matrix was assembled using R. Genes with less than 5 reads in at least one of the samples were filtered out before differential gene expression analysis.
Differential expression was performed using the EdgeR R package.
Assembly: GRCh38.v32
Supplementary files format and content: Raw gene counts in tab-delimited txt format.
Supplementary files format and content: Filtered raw gene counts in tab-delimited txt format, after removal of genes with less that 5 reads in at least 1 sample.
Supplementary files format and content: TMM-normalized annotated gene expression matrix in counts per million reads units, tab-delimited txt format.

source_name: Differentiated cell aggregates

extract_protocol:
RNA from hiPSCs, sclerotome cells, and chondrospheroids (days 14, 28, and 42) was isolated using Qiagen’s RNeasy Mini Kit with DNAse treatment.
mRNA libraries were prepared using the polyA TruSeq method (Illumina) and sequenced on an Illumina NextSeq500 configured for 100 paired-end reads.

value: Differentiated cell aggregates

value: Day 42

value: NCRM NL5 hiPSC line derived from CD34+ cord blood cells

value: not applicable


title: Day 1 HyA-FMB organoid, donor 2, scRNAseq

description: 10x Genomics

value: Bone marrow (femur)

value: male

value: HyA-FMB scaffold


title: atrRΔ, YG+vori, replicate 3

value: akuA::loxP atrR{delta}


title: atrRΔ, YG+vori, replicate 2


title: Wild-type, YG+vori, replicate 3


title: RH-36 cells-BAY 11-7082-treated, replicate 2

city: Birmimgham

first: Romi

last: Gupta

state: Alabama

address: 720, 20th street south

institute: University of Alabama at Birmingham

data_processing:
The reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw count values for each Sample

growth_protocol: Cells were grown in DMEM medium or RPMI medium with 10% Fetal bovine serum and Penicilline and Streptomycin at  37 C under 5% CO2 condition.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) as per the instruction from the manufacture and then purified using RNAeasy mini columns (Qiagen) as per the manufactures instructions.
mRNA is purified from approximately 500ng of total RNA with oligo-dT beads and sheared by incubation at 94C.  Following first-strand synthesis with random primers, second strand synthesis is performed with dUMP for generating strand-specific sequencing libraries.  The cDNA library is then end-repaired, and A-tailed, adapters are ligated and second-strand digestion is performed by Uricil-DNA-Glycosylase. Indexed libraries that meet appropriate cut-offs for both are quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution determined with the LabChip GX or Agilent Bioanalyzer. Samples with a yield of ≥0.5 ng/ul are used for sequencing.


title: Δ855-879 AtrR, phleoR, YG+vori, replicate 2


title: Day 42 chondrospheroid, replicate 2, RNAseq


title: atrRΔ, YG, replicate 2


title: Day 42 chondrospheroid, replicate 1, RNAseq


title: RH-36 cells-BAY 11-7082-treated, replicate 1


title: RH-36 cells-DMSO treated, replicate 3

value: DMSO


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 24

value: treatment-naïve


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 22

value: No relevant fusions


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 23


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 26

value: TCF3-PBX1 + TCF3-TPM4


title: Wild-type, YG, replicate 2


title: Day 28 chondrospheroid, replicate 3, RNAseq

value: Day 28


title: Δ855-879 AtrR, phleoR, YG+vori, replicate 1

value: akuA::loxP {delta}855-879 atrR-phleoR


title: RH-36 cells-DMSO treated, replicate 2


title: RH-36 cells-BAY 11-7082-treated, replicate 3


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 21


title: Day 28 chondrospheroid, replicate 2, RNAseq


title: Δ855-879 AtrR, phleoR, YG, replicate 1

value: 24h YG


title: Day 14 chondrospheroid, replicate 3, RNAseq

value: Day 14


title: AsPC1 cells-BAY 11-7082-treated, replicate 3


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 20

value: bone marrow


title: Day 28 chondrospheroid, replicate 1, RNAseq

value: Differentiated cell aggregates


title: RH-36 cells-DMSO treated, replicate 1


title: Wild-type, phleoR, YG+vori, replicate 1

value: akuA::loxP atrR-phleoR

value: 16h YG + 8h Vori (0.06 mg/ml)


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 19


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 18

value: NRAS


title: Wild-type, phleoR, YG, replicate 1


title: AsPC1 cells-BAY 11-7082-treated, replicate 2


title: Day 14 chondrospheroid, replicate 2, RNAseq

value: NCRM NL5 hiPSC line derived from CD34+ cord blood cells

value: not applicable


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 17


title: atrRΔ, YG+vori, replicate 1


title: Day 14 chondrospheroid, replicate 1, RNAseq


title: AsPC1 cells-DMSO treated, replicate 3


title: atrRΔ, YG, replicate 1


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 15


title: AsPC1 cells-DMSO treated, replicate 1


title: Day 6 sclerotome, replicate 1, RNAseq

source_name: Differentiated monolayer cells

value: Differentiated monolayer cells

value: Day 6


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 14

value: NRAS, KRAS, PTPN11, NUP93


title: Wild-type, YG, replicate 1


title: AsPC1 cells-DMSO treated, replicate 2

value: DMSO


title: Wild-type, YG+vori, replicate 1


title: Day 6 sclerotome, replicate 3, RNAseq


title: SKMEL-103 cells-BAY 11-7082-treated, replicate 3


title: Day 6 sclerotome, replicate 2, RNAseq


title: SKMEL-103 cells-BAY 11-7082-treated, replicate 2


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 13

value: treatment-naïve


title: Day 0 hiPSC, replicate 3, RNAseq

source_name: Undifferentiated monolayer cells

value: Undifferentiated monolayer cells

value: Day 0


title: Day 0 hiPSC, replicate 2, RNAseq


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 12


title: Epididymal white adipose tissue,  IGF2-RNAi lentivirus knockdown,  IGF2-RNAi-2

city: Hangzhou

first: Xihua

last: Lin

state: Zhejiang

address: 3 East Qingchun Road

department: Department of Endocrinology and Metabolism

institute: Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University

data_processing:
The bioinformatics analysis was conducted utilizing the OmicStudio tools available at the following website: https://www.omicstudio.cn/tool. The differential expression cut-off threshold was determined relied on |log2fold change (log2FC) | > 1 and p-value < 0.05.
Assembly: RNA was extracted, sequenced, and analyzed by a custom service provided by Novogene using an Illumina NovaSeq 6000. The bioinformatics analysis was conducted utilizing the OmicStudio tools available at the following website: https://www.omicstudio.cn/tool.
Supplementary files format and content: tab-delimited text fle includes raw counts for each Sample
Supplementary files format and content: tab-delimited text fles include baseMean values for each Sample

source_name: Epididymal white adipose tissue

growth_protocol: The animal care techniques and procedures adhered to the instructions set forth by the Animal Care Committee of Zhejiang University. The animals were kept in a controlled environment that was free from any known pathogens. Male C57BL/6 mice have been obtained from Slack Experimental Animal Center of the Chinese Academy of Sciences (Shanghai, China). A group of 15 mice were kept in cages and kept under a 12-h light-dark cycle. Following a period of 1 week during which mice were habituated and maintained on a regular chow diet, they underwent a process of being weighed and were afterwards sorted into two separate groups: 5 mice were assigned to a normal-chow diet group (NCD group; carbohydrate, 63.92%; protein, 26.18%; fat, 9.9%) and 10 into a high-fat diet group (HFD group, 35% carbohydrate, 20% protein and 45% fat; Research Diets, NJ) for a duration of 8 weeks. The mice were granted unrestricted access to water and were exposed to either a NCD or a HFD in a controlled environment with regulated light and temperature settings. Following a duration of 8 weeks during which maintenance was conducted on either a NCD or an HFD, an intraperitoneal glucose tolerance test (GTT) was conducted subsequent to an overnight fasting period of the animals. Following a duration of 10 weeks, an intraperitoneal insulin tolerance test (ITT) was conducted subsequent to a period of fasting lasting 4h.

extract_protocol:
The Trizol reagent (Invitrogen) was used to isolate total RNA from the treated cells, followed by reverse transcription utilizing a reverse transcription reagents kit (TaKaRa) to produce a cDNA template.
RNA was extracted, sequenced, and analyzed by a custom service provided by Novogene using an Illumina NovaSeq 6000. The bioinformatics analysis was conducted utilizing the OmicStudio tools available at the following website: https://www.omicstudio.cn/tool.

treatment_protocol: The Ad-green fluorescent protein (Ad-GFP) and adenoviruses expressing IGF2 (Ad-IGF2) were constructed by Shanghai Genechem Company using pGV314 (CMV-MCS-3FLAG-SV40-EGFP) vector. The stock solutions of Ad-IGF2 or Ad-GFP were prepared using a concentration of 1×1011 plaque formation unit (PFU)/mL. To overexpress IGF2 in DIO mice, 2×1010 purified adenovirus particles Ad-IGF2 and its control adenovirus Ad-GFP were multi-point administrated into eWAT on the two sides (injected two times per week, for a duration of 4 weeks of injection, n=6 in each group). For recombinant lentivirus IGF2-RNAi construction, oligonucleotides containing the IGF2 targeting sequences were utilized to facilitate the cloning of short hairpin RNA (shRNA)-encoding sequences into pGV248 (hU6-MCS-Ubiquitin-EGFP-IRES- puromycin) vector, as well as their lentiviral vector construction (obtained from Genchem Co. Ltd, Shanghai, China). The stock solutions of IGF2-RNAi or NC-RNAi have been prepared with 1×1011 plaque formation unit (PFU)/mL. The target sequences of IGF2 were shown in Supplementary Table 4. For IGF2 knockdown, 3-4-week-old male mice we injected into the tail vein wieh IGF2 shRNA knockdown lentivirus (IGF2-RNAi) and its control lentivirus (NC-RNAi), 1×1010pfu/mouse, n=6 in each group.

value: Epididymal white adipose tissue

value: IGF2-RNAi lentivirus knockdown


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 16

value: KRAS


title: AsPC1 cells-BAY 11-7082-treated, replicate 1


title: Epididymal white adipose tissue,  NC-RNAi lentivirus knockdown, NC-RNAi-3

value: NC-RNAi

value: NC-RNAi lentivirus knockdown


title: SKMEL-103 cells-DMSO treated, replicate 3


title: Epididymal white adipose tissue,  NC-RNAi lentivirus knockdown, NC-RNAi-2


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 11

value: bone marrow


title: SKMEL-103 cells-BAY 11-7082-treated, replicate 1


title: Epididymal white adipose tissue,  IGF2-RNAi lentivirus knockdown,  IGF2-RNAi-1


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 10

value: No relevant fusions


title: Day 0 hiPSC, replicate 1, RNAseq


title: mVICs, Tert-/-, OST

city: Pittsburgh

first: Rolando

last: Cuevas

state: PA

address: 200 LOTHROP ST

institute: University of Pittsburgh

data_processing:
Calls were obtained with CLC Genomic Workbench, version 24.0.1, from Qiagen.
CUT&Tag reads were aligned to the UCSC mm10 genome using CLC Genomic Workbench, version 24.0.1, from Qiagen.
Assembly: mm10
Supplementary files format and content: Comma delimited CSV file containing chromosome coorddinates, lengths, scores, p-values, and annotations.
Library strategy: CUT&Tag

source_name: Aortic valve

growth_protocol: Mice VICs were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1x P/S in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Chromatin fragments were isolated using CUT&Tag-IT Assay Kit  from Active Motif following the manufacturer’s instructions.
Tagmentated DNA was purified and indexed with 14 PCR cycles with Q5 Polymerase from Active Motif. Libraries were generated with unique combinations of i7/i5 primers from Active Motif.

treatment_protocol: MEM alpha with nucleosides, 10% FBS, 1X P/S, 10 mM glycerol phosphate, 50 μM ascorbic acid 2-phosphate, and 100 nM dexamethasone.

value: Aortic valve

value: Mouse valve valve interstitial cell, primary line

value: VIC

value: Tert-/-

value: Osteogenic differentiation media

value: STAT5 antibody


title: SKMEL-103 cells-DMSO treated, replicate 2

value: DMSO


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 9

value: treatment-naïve


title: Epididymal white adipose tissue,  NC-RNAi lentivirus knockdown, NC-RNAi-1


title: SKMEL-103 cells-DMSO treated, replicate 1


title: Epididymal white adipose tissue,  Ad-IGF2 adenovirus overexpression, Ad-IGF2-2

value: Ad-IGF2 adenovirus overexpression


title: HUVECs,HPHG_3

city: hangzhou

first: Ming

last: Zhang

state: zhejiang

address: Zijingang Campus of Zhejiang University,Yuhangtang Road No.388

institute: School of Biosystems Engineering and Food Science

data_processing:
ACGT101-miR (LC Sciences, Houston, Texas, USA)，
clean reads were obtained after quality control of the original data. clean reads removed the 3 'joint and performed length screening to retain the sequence with base length of 18-26nt.
the remaining sequences were compared with the sequences of various RNA databases (excluding miRNA), such as mRNA database, RFam database (including rRNA, tRNA, snRNA, snoRNA, etc.) and Repbase database (repeat sequence database), and filtered. The final data obtained is the valid data, which can be used for subsequent small RNA data analysis.
Assembly: hg38
Supplementary files format and content: tab-delimited text files includes raw counts for each Sample

source_name: HUVECs

growth_protocol: Human umbilical vein endothelial cells (HUVECs) were cultured in high glucose Dulbecco's Modified Eagle Medium (DMEM; Hyclone, Waltham, MA, USA) supplemented with 10% fetal bovine serum (FBS; Gibco, Carlsbad, CA, USA), 100 U/ml penicillin, and 100 μg/ml streptomycin. Culturing was done at 37°C in a humidified incubator with 95% air and 5% CO2.

extract_protocol:
Total RNA was extracted from HUVECs, both with and without HFHG stimulation, utilizing Trizol (Invitrogen, Carlsbad, CA, USA) following the manufacturer's instructions.
The Small RNA sequencing library was prepared using the TruSeq Small RNA Sample Prep Kits(Illumina, San Diego, USA)

treatment_protocol: HUVECs were cultured in high fat/high glucose (PAHG) medium. The medium contained 25 mM glucose and 250 μM saturated free fatty acid (FFA) palmitate (16:C; Sigma, USA) and was incubated for 24 h.

value: HUVECs

value: Primary Human Umbilical Vein Endothelial Cells

value: WT

value: 25 mM glucose and 250 uM  palmitate,24h


title: Epididymal white adipose tissue,  Ad-IGF2 adenovirus overexpression, Ad-IGF2-1

value: Epididymal white adipose tissue


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 8

source_name: bone marrow


title: mVICs, Tert+/+, OST

value: Tert+/+


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 7

value: bone marrow


title: HUVECs,HPHG_2


title: Epididymal white adipose tissue,  Ad-GFP adenovirus overexpression, Ad-GFP-3

value: Ad-GFP

value: Ad-GFP adenovirus overexpression


title: Epididymal white adipose tissue,  Ad-GFP adenovirus overexpression, Ad-GFP-2


title: HUVECs,HPHG_1


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 6

value: ETV6-RUNX1 + PAX5-PRKCH


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 4

value: No relevant fusions


title: Normox_Ctrl_2

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

institute: University Heidelberg

description: Nfat5fl/fl, normoxia

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 15, from SAS. Gene expression profiling was performed using MoGene-2_0-st arrays from Thermo Fischer Scientific. A Custom CDF Version 22 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

label: Biotin

source_name: mouse lung

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol: Lungs were perfused by 4°C Ringer solution to remove the blood. RNA was extracted by lysing lung tissue in RLT buffer (Cat. no. 79216, Qiagen).

treatment_protocol: Genetic ablation of NFAT5 was induced  in adult male and female mice (age 10-12 weeks) by application of 1 mg tamoxifen per day i.p. on 5 consecutive days (Nfat5(EC)-/-) or miglyol as solvent control (Nfat5fl/fl). Mice were used in experiments after a recovery period of 2-3 weeks.

value: whole lung tissue

tag: oxygen status

value: normoxia


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 3


title: HUVECs,control-3


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 5


title: HUVECs,control-1


title: HUVECs,control-2


title: WT_uninfected_2wpi

city: Montreal

first: Jo

middle: Anne

last: Stratton

state: Quebec

address: 3801 University street

department: Neurology and Neurosurgery

country: Canada

institute: McGill University

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.1
Seurat standard pipeline for the downstream analysis
Assembly: mm10
Supplementary files format and content: Rds file of the integrated seurat object

source_name: Colon

extract_protocol:
Our group has developed GI-targeted pathogen-induced PD mouse modeling systems (in PINK1 KO mice with gram negative bacterial infections) and isolated the cells using scRNAseq technique
Library preparation was performed according to the manufacturer's instructions (10X Single Cell 3' GEM Kit v3.1)

value: Colon

value: Colonic lamina propria cells

value: uninfected at 2weeks


title: WT_uninfected_1wpi

value: uninfected at 1week


title: Normox_Ctrl_4

description: Nfat5fl/fl, normoxia


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 1

extract_protocol:
Total RNA was isolated from tumor samples using the AllPrep DNA/RNA/Protein Mini Kit (QIAGEN) according to standard protocol on the QiaCube (Qiagen).
RNA-sequencing libraries were generated from 300 ng RNA using the KAPA RNA HyperPrep Kit with RiboErase (Roche). Sequencing was performed using the NovaSeq 6000 (2 x 150 bp) (Illumina).

value: treatment-naïve


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 2


title: hiPSC, 317-12, with mESCs, day 5, biol rep1

city: Cincinnati

first: Kentaro

last: Iwasawa

state: OH

address: 3333 BURNET AVENUE

department: Division of Gastroenterology, Hepatology and Nutrition

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Samples were sequenced with single-end sequencing by DNA Sequencing and Genotyping Core (RRID SCR_022630).
The function bbsplit from the bbtools suite was used to bin each read from the RNA-seq fastq into a separate fastq files based on whether the read was specific to the human (hg19) or mouse (mm10) genome. To create the most stringent conditions, perfect mode was set to true and all ambiguous reads were discarded.
Reads that were specific to mouse within the human cells were then aligned to the mm10 genome using STAR (v2.5.1b). The resulting aligned sam file was sorted and converted to a bam file using the samtools sort function.
Reads for each gene were counted using the R function summarizeOverlaps from the GenomicAlignments library using the counting mode of Union.
Assembly: GRCm38/mm10, GRCh37/hg19
Supplementary files format and content: raw_reads_counts.txt: Tab-delimited text file includes gene count values for each sample.

extract_protocol:
RNA was harvested using RNeasy mini plus kit (Qiagen). Over 1ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Human Pluripotent Stem Cells

tag: condition

value: With mESCs

tag: time point

value: Day 5


title: hiPSC, 317-12, with mESCs, day 5, biol rep2


title: WT_infected_1wpi

tag: tissue

tag: genotype

value: WT

value: infected at 1week


title: WT_infected_2wpi

tag: treatment

value: infected at 2weeks


title: Bulk RNA-seq of BMMCs from pediatric AML patient 40 (t(8;21) group)

data_processing:
After pre-processing, reads were aligned to GRCh38 and gencode version 31. Pre-processing of RNA-seq data was done with the institute's standardized pipelines implementing GATK 4.0 best practices for variant calling using a wdl and cromwell-based workflow (PMID: 25431634 by Van der Auwera et al. & van Belzen et al. PMID 37400763).
Assembly: GRCh38
Supplementary files format and content: Raw counts

value: bone marrow

tag: cytogenetics

tag: relevant mutations

value: NO


title: Normox_KO_1

description: Nfat5(EC)-/-, normoxia


title: Normox_KO_2

description: Nfat5(EC)-/-, normoxia


title: Bulk RNA-seq of BMMCs from pediatric AML patient 39 (other genotype group)


title: Normox_Ctrl_1

description: Nfat5fl/fl, normoxia


title: Normox_KO_4

description: Nfat5(EC)-/-, normoxia


title: hiPSC, 317D6, with mESCs, day 5, biol rep2

tag: cell line


title: Epididymal white adipose tissue,  Ad-GFP adenovirus overexpression, Ad-GFP-1

value: Epididymal white adipose tissue

value: Ad-GFP

value: Ad-GFP adenovirus overexpression


title: Hypox_21d_Ctrl_4

description: Nfat5fl/fl, hypoxia 21d

value: whole lung tissue

value: hypoxia


title: hiPSC, 317D6, with mESCs, day 5, biol rep1

tag: cell type


title: PiKO_uninfected_1wpi

value: Colon

value: Colonic lamina propria cells

value: PINK1 KO


title: Hypox_21d_Ctrl_2

description: Nfat5fl/fl, hypoxia 21d


title: Bulk RNA-seq of BMMCs from pediatric AML patient 38 (other genotype group)

value: NRAS

value: treatment-naïve


title: Bulk RNA-seq of BMMCs from pediatric AML patient 37 (other genotype group)


title: Hypox_21d_KO_4

description: Nfat5(EC)-/-, hypoxia 21d


title: PiKO_infected_2wpi


title: Hypox_21d_Ctrl_1

description: Nfat5fl/fl, hypoxia 21d


title: hiPSC, 317-12, without mESCs, day 5, biol rep2

value: Human Pluripotent Stem Cells

value: Without mESCs


title: PiKO_infected_1wpi


title: hiPSC, 317-12, without mESCs, day 5, biol rep1

value: Day 5


title: NBProstate

city: shanghai

first: Jian

last: Wang

address: yueyang road 320

institute: Shanghai Institutes for Biological Sciences CAS

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0
Assembly: mm10
Supplementary files format and content: h5 file

molecule: polyA RNA

source_name: urogenital sinus

extract_protocol:
Neonatal mice were euthanized, the urogenital tract was removed and placed into cold PBS. After removal of the bladder and vas deferens and as much of the seminal vesicle and urethra as possible, the urogenital tissues with prostate buds were sectioned under a stereomicroscope, followed by enzymatic dissociation with 0.5 mL of 1% Trypsin for 30 min at 4°C. The dissociated tissues were washed with DMEM twice, and further dissociated by 0.1% collagenase B, with 1% DNase for 15 min at 37°C. After quenched by DMEM with 10% FBS, the urogenital tract cells were passed through a 45 μm filter.
Library was performed according to the manufacter's instructions (Single cell 3' v3.1 protocol, 10x Genomics)

value: urogenital sinus

value: postnatal day 0

value: wild-type


title: Bulk RNA-seq of BMMCs from pediatric AML patient 35 (other genotype group)

city: Utrecht

first: Joost

last: Koedijk

institute: Princess Máxima Center for Pediatric Oncology

value: bone marrow


title: Hypox_21d_KO_3

description: Nfat5(EC)-/-, hypoxia 21d


title: hiPSC, 317D6, without mESCs, day 5, biol rep1


title: PiKO_uninfected_2wpi

value: uninfected at 2weeks


title: hiPSC, 317D6, without mESCs, day 5, biol rep2


title: Bulk RNA-seq of BMMCs from pediatric AML patient 34 (other genotype group)


title: VJ001_S012_large_mg1_r3

city: London

first: Anton

last: Patrikeev

state: London

address: Chester Beatty Laboratories, 237 Fulham Rd.

department: Targeted Therapy

country: United Kingdom

institute: The Institute of Cancer Research

description: large tumor

data_processing:
Low quality bases and adaptor sequences were removed using Trimmomatic.
Reads were mapped to the M. musculus GRCm38 reference genome using HISAT2 and StringTie was used for gene count matrix generation.
Assembly: M. musculus GRCm38
Supplementary files format and content: comma-delimited text file includes raw counts for each sample

source_name: tumour

growth_protocol: Five- to six-week-old female C57Bl/6 mice (Charles River, UK) or Nr4a3 Tocky mice (C57Bl/6 background) were used for tumour implantation. These were conducted at the ICR Biological Services Unit and were approved by the ICR local Ethical Review Committee and standards of care were based upon the UKCCCR Guidelines for the welfare and use of animals in cancer research. 4434 murine melanoma tumours were established by 100 µL subcutaneous injection of 4x106 cells respectively into the right flank of each mouse. Tumour measurements were taken twice weekly in three dimensions using Venier callipers and the tumour volume estimated using the formula: length x width x height (mm) x 0.5236.

extract_protocol:
Small or Large 4434 tumours were explanted from animals 48 hrs following treatment and stored in RNALater (AM7020, Thermo Fisher) at -20°C prior to RNA extraction.
Samples were homogenised as described previous and RNA extraction performed using RNEasy kit (74104, Qiagen, Germantown, USA) as per manufacturer protocol.

treatment_protocol: A single intra-tumoural dose of PBS or MG-FLUC (1x107PFU) was given when tumours reached the desired volume. Tumour measurements were recorded twice weekly.

value: tumour

value: WT


title: Bulk RNA-seq of BMMCs from pediatric AML patient 33 (other genotype group)

address: Heidelberglaan 25


title: VKO_2mon

city: Oklahoma City

first: Xiang

last: Ma

state: OK

address: 825 NE 13th St

department: Cardiovascular biology

institute: Oklahoma Medical Research Foundation

description: 10x Genomics

data_processing:
Raw sequencing data were generated in .fastq files and converted to a single-cell expression matrix in the Cell Ranger pipeline (version 3.0, 10x Genomics, USA). Data analysis and visualization were performed using the Seurat package (version 4.0; https://satijalab.org/seurat/index.html) in R studio (version 4.2.1; https://cran.r-project.org/bin/windows/base/). Cells with detected genes between 100 and 10,000 and with less than 25% mitochondrial genes were kept. Genes that were expressed by more than 3 cells were kept. After the filter step, 7,943 cells (WT: 4,236 cells and Vldlr-/-: 3,707 cells) were used for downstream analysis. To eliminate batch variability, “FindIntegrationAnchors” function was used to integrate 4 datasets from WT and Vldlr-/- mice at ages of 1 month and 2 months.
Unsupervised clustering analysis was conducted using the Seurat R package. After normalizing data using the “LogNormalize” method, principal component analysis (PCA) was performed to reduce dimensionality with the top 30 principal component (PC) calculated. Based on p values from “JackStrawPlot”, FindClusters function with a resolution of 1.0 was used to identify 27 different clusters. Clusters were virtualized in Uniform Manifold Approximation and Projection (UMAP). Differentially expressed genes among clusters were listed using “FindAllMarkers” function and matched with known cell markers. Markers across all clusters were shown in stacked violin plots and UMAP plots.
Gene Ontology (GO) enrichment analysis and Gene Set Enrichment Analysis (GSEA) were performed using the ClusterProfiler package (version 4.0). Significantly up- and down-regulated genes of Vldlr-/- mice compared to WT mice were used for analyses. Biological pathways with the largest changes were virtualized using the dotplot function of ggplot2 package. Differential gene expression between clusters from different genotypes was analyzed using the “Findmarker” function in the Seurat package. The fold change of gene expression and adjusted p values were calculated with a Bonferroni correction.
N/A
Assembly: mm9
Supplementary files format and content: matrix
Supplementary files format and content: features
Supplementary files format and content: barcode

source_name: posterior of eye

extract_protocol:
RPE-choroid tissues were harvested from WT and Vldlr-/- mice at the ages of 1 month and 2 months. The isolation of viable single cells from RPE-choroid tissue was performed according to a published protocol . Briefly, the eyeballs were enucleated and kept in pre-chilled PBS. Extraocular muscles were cleaned from the eyeballs, and a circumferential incision around the limbus was performed to remove the anterior segments. The neural retina was then gently separated from the RPE. RPE-choroid tissues were gently scraped from the sclera and sequentially digested with collagenase A (6.25 mg/ml) and Dispase II (6.25 mg/ml) at 37°C for 15 min and then with Trypsin (0.25%) at 37°C for 5 min. After neutralization in a buffer containing 10% FBS, the tissue suspension was filtered through a 40-μm strainer to generate a single cell suspension. Dead Cell Removal Kit (Miltenyi Biotec, San Jose, CA) was used to eliminate dead cells. A low-speed (200 g, 10 min) and large-volume (40 ml in 50 ml tube) wash was performed to remove the cellular debris. Finally, the dissociated RPE/choroid cells with viability higher than 90%, as measured by a trypan blue assay, were used for cDNA library construction.
Cell suspensions in PBS containing 0.5% BSA with a density of approximate 200 cells/μl were used on the 10x Genomics Chromium platform to generate barcoded single-cell gel bead-in-emulsion (GEMs), targeting ~ 5,000 cells per library. Barcoded libraries were sequenced on an Illumina HiSeq4000 (Illumina, USA) at Wake Forest University Cancer Genomics Shared Resource (CGSR).

value: posterior of eye

value: NO

value: Vldlr-/-


title: Hypox_21d_KO_2

description: Nfat5(EC)-/-, hypoxia 21d

value: whole lung tissue

value: hypoxia


title: VJ001_S011_large_mg1_r2

description: large tumor


title: VJ001_S010_large_mg1_r1

description: large tumor


title: WT_2mon

description: 10x Genomics


title: Hypox_7d_KO_1

description: Nfat5(EC)-/-, hypoxia 7d


title: Bulk RNA-seq of BMMCs from pediatric AML patient 32 (other genotype group)

value: No relevant fusions


title: VJ001_S009_large_pbs_r3

description: large tumor

value: PBS


title: Hypox_7d_KO_3

description: Nfat5(EC)-/-, hypoxia 7d


title: Bulk RNA-seq of BMMCs from pediatric AML patient 36 (other genotype group)

value: treatment-naïve


title: Hypox_7d_KO_4

description: Nfat5(EC)-/-, hypoxia 7d


title: VJ001_S008_large_pbs_r2

description: large tumor


title: WT_1mon

description: 10x Genomics


title: Hypox_7d_Ctrl_3

description: Nfat5fl/fl, hypoxia 7d


title: NitrogenPlus, RNA-seq, Replicate 2

city: Freiburg

first: Rick

last: Gelhausen

state: Baden Württemberg

address: Georges-Köhler-Allee 106

department: Department of Computer Science

institute: Albert-Ludwigs-University Freiburg

description: Total RNA extracted from WT strain biological replicate 2 under nitrogen Plus condition, DNaseI digested, rRNA depleted, fragmented and subjected to cDNA library preparation

data_processing:
Base calling with Illumina NextSeq RTA v2.4.11
FASTQ conversion with bcl2fastq v2.20.0.422
FASTQ quality and adapter trimming using Cutadapt (Martin, 2011) version 2.1 (cutadapt parameters: -q 20 --trim-n -m 10 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) (HRIBO 1.7.0)
Mapping with segemehl 0.3.4 (HRIBO 1.7.0)
rRNA filtering was done using samtools 1.9 (HRIBO 1.7.0)
Coverage files were created using HRIBO 1.7.0
Assembly: ASM706v1
Supplementary files format and content: bigwig format files containing normalized read coverage for each sample

organism: Methanosarcina mazei Go1

source_name: archaeal cell

growth_protocol: M. mazei Gö1 was cultivated either under nitrogen sufficient (+N) or nitrogen limited conditions (-N) as described (Ehlers et al. 2002). Cells corresponding to 60 OD600 equivalent units were harvested rapidly by fast-chilling in an ice bath to halt cell growth and translation, without the use of antibiotics

extract_protocol:
RNA was extracted from fractions or cell pellets for total RNA using hot phenol-chloroform-isoamyl alcohol (25:24:1, Roth) or hot phenol (Roth), respectively, as described previously (Sharma et al. 2007).
Total RNA was first rRNA-depleted, fragmented then subjected to cDNA library preparation. Size selcted RNA for Riboseq samples were directly subjected to cDNA library preparation. The obtained small RNA samples were first treated with Antarctic Phosphatase and re-phosphorylated with T4 Polynucleotide Kinase (PNK). Then,  oligonucleotide adapters were ligated to the 5' and 3' ends of the RNA samples. First-strand cDNA  synthesis was performed using M-MLV reverse transcriptase and the 3’ adapter as primer. The  resulting cDNA was amplified with PCR using a high fidelity DNA polymerase.

treatment_protocol: No treatment applied during growth.

value: archaeal cell

tag: growth condition

value: NitrogenPlus

tag: fraction

value: rRNA-depleted, fragmented total RNA


title: Bulk RNA-seq of BMMCs from pediatric AML patient 30 (other genotype group)

value: WT1, FLT3-ITD


title: Bulk RNA-seq of BMMCs from pediatric AML patient 29 (other genotype group)


title: NitrogenPlus, RNA-seq, Replicate 1

description: Total RNA extracted from WT strain biological replicate 1 under nitrogen Plus condition, DNaseI digested, rRNA depleted, fragmented and subjected to cDNA library preparation


title: VJ001_S007_large_pbs_r1

description: large tumor


title: GWS_CNC

city: Vienna

first: Thomas

last: Eder

address: Veterinaerplatz 1

institute: University of Veterinary Medicine, Vienna

description:
genomic DNA
GWS_norm_CNC_dropout.tsv

data_processing:
Genome wide screen:
Nextflow pipeline available at: https://github.com/ZuberLab/crispr-process-nf
Trimming with: fastx_trimmer from the fastx-toolkit, demultiplexing with fastx_barcode_splitter, alignment with Bowtie2 and quantification with featureCounts
Nextlow pipeline: https://github.com/ZuberLab/crispr-mageck-nf applying MAGeCK
Normalization with inhouse R script (see methods)
RNA-seq:
Quality check with FastQC, alignment against the human reference genome (GRCh38) with STAR. Alignments were post-processed with SAMtools and counts per gene were obtained with featureCounts.
Normalization of counts and the differential gene expression analysis (input shRenilla versus input shDDX6) where  done with DESeq2
Polysome-seq:
Quality check with FastQC and alignement against the human reference genome (GRCh38) with STAR. We processed the alignments with SAMtools and obtained counts per gene with featureCounts. Differential translation analysis with Xtail with parameters bins=10000 and minMeanCount=20
Assembly: hg38
Supplementary files format and content: POLYSOME tsv from polysome-seq: xtail results
Supplementary files format and content: GWS tsv from genome wide screen: logfold-change and normalized lfc
Supplementary files format and content: RIP and RNA tsv´s from RIP- and RNA-seq: DESeq2 results

source_name: CNC

extract_protocol:
For genome wide screen, genomic DNA was extracted using phenol/chloroform
For RNA- and polysome-seq, total and polysomes RNAs were extracted using TRIzol
DNA library for Genome wide screen was performed as previously described by Michlits et al, 2020 Nature Methods (DOI:  10.1038/s41592-020-0850-8)
RNA libraries for RIP-seq were constructed using NEBNext Ultra II Directional RNA library prep and Unique Dual Index Primer Pairs
RNA libraries for total and polysomes RNA-seq were constructed at Beijing Genomics Institute (BGI Group)

value: CNC

value: Cebpa N-mut/C-mutant


title: GWS_Plasmid_Pool

description:
DNA
GWS_norm_CNC_dropout.tsv

source_name: sgRNA library

value: sgRNA library


title: NitrogenPlus, Ribo-seq, Replicate 2

description: RNA purified from WT ribosome footpints replicate 2 under nitrogen Plus condition, size selected and subjected to cDNA library preparation

data_processing:
Base calling with Illumina NextSeq RTA v2.4.11
FASTQ conversion with bcl2fastq v2.20.0.422
FASTQ quality and adapter trimming using Cutadapt (Martin, 2011) version 2.1 (cutadapt parameters: -q 20 --trim-n -m 10 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) (HRIBO 1.7.0)
Mapping with segemehl 0.3.4 (HRIBO 1.7.0)
rRNA filtering was done using samtools 1.9 (HRIBO 1.7.0)
Coverage files were created using HRIBO 1.7.0
Assembly: ASM706v1
Supplementary files format and content: bigwig format files containing normalized read coverage for each sample
Library strategy: Ribo-seq

value: ribosome footprint generated by MNase


title: VJ001_S006_small_mg1_r3

description: small tumor

value: tumour

value: WT


title: Hypox_7d_Ctrl_4

description: Nfat5fl/fl, hypoxia 7d


title: VJ001_S005_small_mg1_r2

description: small tumor


title: NitrogenPlus, Ribo-seq, Replicate 1

description: RNA purified from WT ribosome footpints replicate 1 under nitrogen Plus condition, size selected and subjected to cDNA library preparation


title: DOCA, After Treatment, rep 2

city: Athens

first: Dimitris

last: Valakos

address: Soranou Ephessiou 4

department: Center of Basic Research

country: Greece

institute: Biomedical Reasearch Foundation Academy of Athens

description:
DOCA_After_rep2
DOCA_Before_vs_After.xlsx

data_processing:
For RNAseq samples, Quality Control (QC) was performed at the FASTQ raw data file for each sample using the FASTQC software. FASTQ files were aligned to rn6 rat genome using HISAT2 . Counts were defined using HTSeq htseq-count command with the “-m intersection-nonempty” and “-s reverse" option after removing the hemoglobin gene annotations from the rn6 gtf file. The count files were used as input for DESeq2.
Assembly: rn6
Supplementary files format and content: Counts.txt contains all the counts per gene for all the samples; AngII_Before_vs_After.xlsx and DOCA_Before_vs_After.xlsx contain the results from DESeq2 analysis.

organism: Rattus norvegicus

source_name: Whole Blood

extract_protocol:
Cardiac Puncture and collection in Heparin 1000IU/mL
Libraries were constructed using the NEBNext Ultra II RNA Library Prep Kit for Illumina (E7775) according to the manufacturer’s guidelines

treatment_protocol: Mastic 220mg/kg

value: Whole Blood

tag: strain

value: Wistar

value: wild type

value: DOCA (100 mg/kg) 0.9% NaCl + 1% KCl + mastic 220mg/kg


title: Bulk RNA-seq of BMMCs from pediatric AML patient 27 (other genotype group)

value: bone marrow


title: Bulk RNA-seq of BMMCs from pediatric AML patient 26 (other genotype group)


title: DOCA, After Treatment, rep 1

description:
DOCA_After_rep1
DOCA_Before_vs_After.xlsx


title: Bulk RNA-seq of BMMCs from pediatric AML patient 31 (other genotype group)


title: NitrogenMinus, RNA-seq, Replicate 2

description: Total RNA extracted from WT strain biological replicate 2 under nitrogen minus condition, DNaseI digested, rRNA depleted, fragmented and subjected to cDNA library preparation

value: NitrogenMinus


title: VJ001_S004_small_mg1_r1

description: small tumor


title: VJ001_S003_small_pbs_r3

description: small tumor

value: PBS


title: Bulk RNA-seq of BMMCs from pediatric AML patient 25 (other genotype group)

value: treatment-naïve


title: DOCA, Before Treatment, rep 1

description:
DOCA_Before_rep1
DOCA_Before_vs_After.xlsx

value: DOCA (100 mg/kg) 0.9% NaCl + 1% KCl


title: Hypox_7d_Ctrl_1

description: Nfat5fl/fl, hypoxia 7d

value: whole lung tissue

value: hypoxia


title: NitrogenMinus, RNA-seq, Replicate 1

description: Total RNA extracted from WT strain biological replicate 1 under nitrogen minus condition, DNaseI digested, rRNA depleted, fragmented and subjected to cDNA library preparation

value: archaeal cell

value: rRNA-depleted, fragmented total RNA


title: VJ001_S002_small_pbs_r2

description: small tumor


title: NitrogenMinus, Ribo-seq, Replicate 2

description: RNA purified from WT ribosome footpints replicate 2 under nitrogen minus condition, size selected and subjected to cDNA library preparation


title: Bulk RNA-seq of BMMCs from pediatric AML patient 24 (t(8;21) group)

value: YES


title: AngII, After Treatment, rep 2

description:
AngII_After_rep2
AngII_Before_vs_After.xlsx

value: Angiotensin II (0.4mg/kg/day), Mastic 220mg/kg


title: Bulk RNA-seq of BMMCs from pediatric AML patient 23 (t(8;21) group)


title: Bulk RNA-seq of BMMCs from pediatric AML patient 22 (other genotype group)

value: No relevant fusions


title: Bulk RNA-seq of BMMCs from pediatric AML patient 28 (other genotype group)


title: AngII, After Treatment, rep 1

description:
AngII_After_rep1
AngII_Before_vs_After.xlsx


title: NitrogenMinus, Ribo-seq, Replicate 1

description: RNA purified from WT ribosome footpints replicate 1 under nitrogen minus condition, size selected and subjected to cDNA library preparation

value: ribosome footprint generated by MNase


title: AngII, Before Treatment, rep 2

description:
AngII_Before_rep2
AngII_Before_vs_After.xlsx

value: Whole Blood

value: Angiotensin II (0.4mg/kg/day)


title: VKO_1mon

description: 10x Genomics

value: posterior of eye

value: NO

value: Vldlr-/-


title: wt_input_2

first: Rahul

last: Rajala

state: Oklahoma

address: 825 NE 13th Street

department: Cardiovascular Biology

data_processing:
Fastq generation was performed using Illumina’s CASAVA-1.8.2 software
Alignment of raw sequences using HISAT2
Differential gene expression performed by Deseq2 and edgeR
Assembly: HISAT2 (Mus_musculus.GRCm39.dna.primary_assembly) /SALMON (Mus_musculus.GRCm39.107.transcripts.fa.salmon)
Supplementary files format and content: Collated HISAT2 data given as (FinalCountsSheet.csv)

source_name: Retina

extract_protocol:
RNA (before/after TRAP) was isolated using the Trizol/Pure Link RNA Kit (Ambion). 100 ng RNA was used for cDNA conversion. Takara SMART-Seq V4 kit was used for cDNA conversion
libraries were prepared by MedGenome Inc. | Foster City, CA

treatment_protocol: Tissues were flash-frozen in liquid nitrogen following a cycloheximide perfusion and mechanically dissociated

value: Retina


title: wt_input_3


title: DOCA, Before Treatment, rep 2

description:
DOCA_Before_rep2
DOCA_Before_vs_After.xlsx

value: Wistar

value: wild type


title: wt_input_1


title: Bulk RNA-seq of BMMCs from pediatric AML patient 20 (other genotype group)

value: bone marrow

value: treatment-naïve


title: wildtype myoblasts, differentiating (D2), lamin B1 ChIP, rep 1

first: Roland

last: Foisner

address: Dr.-Bohr-Gasse 9

department: Center for Medical Biochemistry

institute: Max Perutz Labs, Medical University of Vienna

description: linked to Input 1

data_processing:
Raw sequencing reads in bam format were converted into fastq using bamtofastq from bedtools
Qualities of the reads were evaluated using FastQC
Reads were mapped to the reference genome using NextGenMap with default settings
EDD was used to generate the log2ratio files for Lamin B1 Lamin AC and LAP2alpha samples
bamCoverage from deepTools was used to generate the histone mark coverage files with the RPKM normalization method
Assembly: Mus musculusgenome assembly GRCm38 (mm10)
Supplementary files format and content: Lamin B1 (LB1), Lamin AC (LAC_3A6 and LAC_E1), and LAP2alpha (LAP2a) processed files contain log2ratios calculated by normalizing CHIP signals to INPUT signals
Supplementary files format and content: Processed files of all input (Input1,2,3) and histone mark samples (H3K27ac and H3K4me3) contain RPKM normalized coverage signals

source_name: immortalized myoblasts

growth_protocol: Ham's F10 nutrient mix with 20% fetal calf serum, 100 U/ml penicillin and 100 μg/ml streptomycin; cells were cultured at 37°C and 5%CO2

extract_protocol:
Cells were fixed in 1% formaldehyde, followed by formaldehyde quenching, washing and cell lysis. Lysed cells were sonicated using the Bioruptor PICO sonicator (Diagenode).
Libraries were prepared by the Next Generation Sequencing facility at the Vienna Biocenter Core Facilities, Vienna, Austria, using the NEBNext® UltraTM II DNA Library Prep Kit for Illumina and unique NEB adaptors. Libraries were validated using the Agilent High Sensitivity DNA Kit.

treatment_protocol: To induce differentiation, cells were grown to confluence and switched to 5% fetal calf serum for 48 hours (day 2 of differentiation)

value: immortalized myoblasts

value: LAP2alpha wildtype; p53 knockout

value: Day 2 of differentiation

tag: chip antibody

value: lamin B1 antibody (PMID:26798136)


title: Placebo [620260389622]

city: Oxford

first: Timothy

last: Hinks

state: United Kingdom

address: John Radcliffe Hospital, Headley Way, Oxford

department: NDM Experimental Medicine - New College

institute: University of  Oxford

data_processing:
Sequences in fastq files (in single and pair ends) were aligned using STAR aligner (version 2.7.1a)
; R package (17)Rsubread was employed for quantification of reads assigned to genes
Assembly: GRCh38
Supplementary files format and content: Raw_counts_B_BR_Pl.txt
Supplementary files format and content: Normalized_counts_B_BR_Pl.txt

source_name: BRUSHING

extract_protocol:
Total RNA was extracted from subjects biopsies and brushing using RNeasy mini kits (Qiagen).
TruSeq library preparation kits were used for RNA samples. Starting with total RNA, the messenger RNA was first purified using polyA.

treatment_protocol: Randomised open-label bronchoscopy study of high dose ICS therapy in 30 healthy adult volunteers randomised 2:1 to i) fluticasone propionate 500 mcg bd or ii) no treatment, for 4 weeks. Laboratory staff were blinded to allocation. Biopsies and brushings were analysed by bulk RNA sequencing.

value: BRUSHING


title: LAP2alpha knockout myoblasts, proliferating, lamin B1 ChIP, rep 1

description: linked to Input 1

value: LAP2alpha knockout; p53 knockout

value: proliferating


title: AngII, Before Treatment, rep 1

description:
AngII_Before_rep1
AngII_Before_vs_After.xlsx

value: Whole Blood


title: Placebo [620260389422]


title: wildtype myoblasts, proliferating, lamin B1 ChIP, rep 1

description: linked to Input 1


title: Bulk RNA-seq of BMMCs from pediatric AML patient 19 (other genotype group)


title: ko_input_3


title: Bulk RNA-seq of BMMCs from pediatric AML patient 18 (other genotype group)

value: No relevant fusions


title: ko_input_1


title: Bulk RNA-seq of BMMCs from pediatric AML patient 17 (other genotype group)

value: NRAS, KRAS, PTPN11


title: CD19+ Splenocytes, MN, 4hEtop, rep3

city: Philadelphia

first: Craig

last: Bassing

address: 3501 Civic Center Blvd

institute: Children's Hospital of Philadelphia

data_processing:
The RNA-seq fastq files were analyzed using the snakemake pipeline:https://github.com/khayer/rna_seq_standard_pipeline. In brief, raw RNA-seq reads were trimmed using bbduk as part of bbmap (version 38.92:https://sourceforge.net/projects/bbmap/).The trimmed reads were then aligned to mm10 using STAR (version 2.7.9a) (37). Next, bamCoverage from the deeptools package (version 3.5.1) was employed to generate bigWig coverage files, applying flags to differentiate coverage tracks by strand and to normalize using counts per million (cpm) (38). The normalized bigWig coverage files were thenuploaded to the UCSC genome browser (39).
Gene expression levels were quantified using TPMcalculator (version 0.0.3) with the GENCODE annotation for the mm10 genome (version M23_GRCm38.p6) (40). For normalization and identification of significantly differentially expressed genes, the raw read counts were analyzed with the limma-voom package from Bioconductor (version 3.54.2) (41). From this data, we defined three subsets of genes. The first subset was etoposide-dependent genes, which had a log2(Fold-Change Etoposide/DMSO) > 1 or < -1 and ap-value< 0.05 when comparing etoposide and DMSO treated CD19+splenocytes fromWTmice. Within the etoposide-dependent genes that were expressed above the 20thquantile in average expression, we defined the Nemo-dependent ones as genes with a log2(Fold-Change Etoposide/DMSO) < 1 or > -1 inNemo-CD19+splenocytes and ap-value< 0.05 when comparing the log2(Fold-Change Etoposide/DMSO) betweenWTandNemo-splenocytes. We intorduced the qualification that the genes be expressed above the 20th quantile of average expression in this group to ensure observed changes in fold-change values were not an artifact of low expression. Finally, within the etoposide and Nemo-dependent genes, we defined a subset of genes as Nemo3SAΔT-dependent, meaning when the log2(Fold-Change Etoposide/DMSO) betweenWTandNemo3SAΔTsamples were compares, thep-value< 0.05. To visually depict expression patterns of these subsets of genes inWTCD19+splenocytes relative to eitherNemo-orNemo3SAΔTCD19+splenocytes, scatterplots of the log2(Fold-Change Etoposide/DMSO) values were plotted using the R package ggplot2 (42).
37. Dobin, A., C. A. Davis, F. Schlesinger, J. Drenkow, C. Zaleski, S. Jha, P. Batut, M. Chaisson, and T. R. Gingeras. 2013. STAR: Ultrafast universal RNA-seq aligner. Bioinformatics 29: 15–21. 38. Ramírez, F., D. P. Ryan, B. Grüning, V. Bhardwaj, F. Kilpert, A. S. Richter, S. Heyne, F. Dündar, and T. Manke. 2016. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res. 44: W160–W165.  39. Kent, W. J., C. W. Sugnet, T. S. Furey, K. M. Roskin, T. H. Pringle, A. M. Zahler, and  and D. Haussler. 2002. The Human Genome Browser at UCSC. Genome Res. 12: 996–1006.  40. Vera Alvarez, R., L. S. Pongor, L. Mariño-Ramírez, and D. Landsman. 2019. TPMCalculator: one-step software to quantify mRNA abundance of genomic features. Bioinformatics 35: 1960–1962.  41. Law, C. W., Y. Chen, W. Shi, and G. K. Smyth. 2014. Voom: Precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biol. 15: 1–17.  42. Wickham, H. 2016. ggplot2: Elegant Graphics for Data Analysis,. Springer-Verlag New York.
Assembly: mm10
Supplementary files format and content: Raw read counts as produced by TPMCalculator

source_name: CD19+ Splenocyte

extract_protocol:
CD19+ splenocytes were isolated from single-cell suspensions of spleens using the EasySep™ Mouse CD19 Positive Selection Kit II (STEMCELL Cat. No. 18954)
Strand-specific RNA sequencing libraries was prepared by using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, the enriched RNAs were fragmented for 8 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. The second strand of cDNA was marked by incorporating dUTP during the synthesis. cDNA fragments were adenylated at 3’ends, and indexed adapter was ligated to cDNA fragments. Limited cycle PCR was used for library enrichment. The incorporated dUTP in second strand cDNA quenched the amplification of second strand, which helped to preserve the strand specificity. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

treatment_protocol: CD19+ splenocytes were resuspended to ~2million cells per milliliter in IL7- media and ~2million cells were treated with DMSO or 10 μg/mL etoposide (Sigma-Aldrich, E2600000). The cells were collected after four hours of treatment in 250 μL of Trizol (Life Technologies, 15596018) for RNAseq analysis.

value: CD19+ Splenocyte

value: 4h DMSO


title: CD19+ Splenocytes, MN, 4hDMSO, rep3

value: 4h Etoposide


title: LAP2alpha knockout myoblasts, differentiating (D2), lamin B1 ChIP, rep 1

description: linked to Input 1


title: VJ001_S001_small_pbs_r1

description: small tumor

value: tumour

value: WT

value: PBS


title: Placebo [620091230111]


title: Placebo [620260389322]


title: CD19+ Splenocytes, MN, 4hEtop, rep2


title: Bulk RNA-seq of BMMCs from pediatric AML patient 21 (other genotype group)

value: bone marrow

value: NRAS

value: treatment-naïve


title: Placebo [620091229911]


title: wt_bead_1

source_name: Rod PR

value: Rod PR


title: Bulk RNA-seq of BMMCs from pediatric AML patient 16 (other genotype group)

value: FLT3, KIT


title: Bulk RNA-seq of BMMCs from pediatric AML patient 14 (other genotype group)


title: CD19+ Splenocytes, MN, 4hDMSO, rep2


title: Bulk RNA-seq of BMMCs from pediatric AML patient 13 (other genotype group)


title: wt_bead_2


title: Bulk RNA-seq of BMMCs from pediatric AML patient 15 (other genotype group)

value: KRAS, FLT3


title: ko_bead_3


title: Placebo [S18110500041]

value: BRUSHING


title: Placebo [S18110500043]


title: Placebo [S18110500035]


title: Placebo [S18110500032]


title: ko_input_2

value: Retina


title: CD19+ Splenocytes, MN, 4hEtop, rep1


title: wt_bead_3


title: CD19+ Splenocytes, MN, 4hDMSO, rep1


title: Placebo [620091230311]


title: Bulk RNA-seq of BMMCs from pediatric AML patient 12 (t(8;21) group)

value: NO


title: CD19+ Splenocytes, Nemo3SAΔT, 4hEtop, rep3


title: CD19+ Splenocytes, Nemo3SAΔT, 4hEtop, rep2


title: CD19+ Splenocytes, Nemo3SAΔT, 4hDMSO, rep3


title: RAW264.7, 10-7M melatonin+LPS, rep2

city: Shanghai

first: Yuying

last: Cai

state: Please Select

address: 450 Tengyue Road, Shanghai 200090, China

institute: Yangpu Hospital, Tongji University

data_processing:
Raw reads were trimmed the adaptors by using cutadapt. The sequenced reads were single-end mapped to mouse reference genome sequences by using NextGenMap. We use featureCounts to perform quantification on the mapped sequences.
Assembly: mm10
Supplementary files format and content: raw read counts table and fpkm table

source_name: cell line

extract_protocol:
Total RNA was extracted by using Trizol reagent.
Population RNA-seq libraries were constructed according to manufacturer’s instruction (Illumina Truseq library construction).

value: cell line

value: RAW 264.7 cell

value: Macrophage

value: LPS+10-7M melatonin


title: ko_bead_1


title: Bulk RNA-seq of BMMCs from pediatric AML patient 11 (t(8;21) group)


title: RAW264.7, 10-7M melatonin+LPS, rep3


title: ko_bead_2


title: CD19+ Splenocytes, Nemo3SAΔT, 4hEtop, rep1

value: CD19+ Splenocyte

value: 4h Etoposide


title: CD19+ Splenocytes, Nemo3SAΔT, 4hDMSO, rep2

value: 4h DMSO


title: Bulk RNA-seq of BMMCs from pediatric AML patient 8 (t(8;21) group)

value: YES


title: RAW264.7, 10-6M melatonin+LPS, rep3

value: WT

value: LPS+10-6M melatonin


title: Bulk RNA-seq of BMMCs from pediatric AML patient 7 (t(8;21) group)

value: bone marrow

value: treatment-naïve


title: CD19+ Splenocytes, WT, 4hEtop, rep3


title: RAW264.7, 10-6M melatonin+LPS, rep2


title: CD19+ Splenocytes, Nemo3SAΔT, 4hDMSO, rep1


title: Placebo [S18110500027]


title: Bulk RNA-seq of BMMCs from pediatric AML patient 6 (other genotype group)

value: No relevant fusions

value: FLT3-ITD, NPM1


title: Placebo [S18110500031]

value: BRUSHING


title: RAW264.7, 10-6M melatonin+LPS, rep1


title: Bulk RNA-seq of BMMCs from pediatric AML patient 5 (t(8;21) group)


title: Placebo [S18110500009]


title: CD19+ Splenocytes, WT, 4hDMSO, rep3


title: Bulk RNA-seq of BMMCs from pediatric AML patient 10 (t(8;21) group)

value: NRAS, KIT


title: CD19+ Splenocytes, WT, 4hEtop, rep2


title: Placebo [S18110500025]


title: Bulk RNA-seq of BMMCs from pediatric AML patient 9 (other genotype group)

value: NPM1, WT1


title: RAW264.7, 10-5M melatonin+LPS, rep3

value: cell line

value: LPS+10-5M melatonin


title: RAW264.7, 10-5M melatonin+LPS, rep2

value: RAW 264.7 cell

value: Macrophage


title: Placebo [S18110500004]


title: Bulk RNA-seq of BMMCs from pediatric AML patient 4 (t(8;21) group)


title: CD19+ Splenocytes, WT, 4hDMSO, rep2

value: CD19+ Splenocyte


title: Placebo [S18110500003]


title: Bulk RNA-seq of BMMCs from pediatric AML patient 3 (other genotype group)


title: RAW264.7, 10-7M melatonin+LPS, rep1

value: LPS+10-7M melatonin


title: Placebo [S18110500002]


title: Bulk RNA-seq of BMMCs from pediatric AML patient 2 (other genotype group)

value: WT1, CEBPA


title: Placebo [S18110500028]


title: RAW264.7, 10-5M melatonin+LPS, rep1


title: CD19+ Splenocytes, WT, 4hDMSO, rep1

value: 4h DMSO


title: Placebo [S18110500001]


title: LAP2alpha knockout myoblasts, differentiation D2, rep 3

data_processing:
50bp single-end read sequencing libraries were converted to fastq format with bam2fastq v1.1.0 from BEDtools
Reads were trimmed with cutadapt for both truseq adapters and low quality bases below Q20 at the end of the reads
Reads were mapped with NextGenMap 0.5.2
Transcript abundance quantification was done using RSEM (rsem-calculate-expression) with a minimum fragment length of 5
Transcript-level estimates were imported and summarized to gene-level estimates using the R package tximportand counts were TMM normalized using the calcNormFactors function from edgeR
Assembly: Mus musculus GRCm38.86 transcriptome (prepared for mapping using RSEM rsem-prepare-reference) (mm10)
Supplementary files format and content: TMM normalizedcounts for each mouse gene (shown with ENSEMBL ID's) with expected counts of more than 5 in all 3 replicates

extract_protocol:
Total RNA was extracted with the RNAeasy® mini kit from Qiagen
Libraries were prepared by the Next Generation Sequencing facility at the Vienna Biocenter Core Facilities, Vienna, Austria, starting with polyA enrichment using the NEBNext® Poly(A) mRNA Magnetic Isolation Module, followed by the NEBNext® UltraTM II Directional RNA Library Prep Kit for Illumina®.

treatment_protocol: To induce differentiation, cells were grown to confluence (D0: start of differentiation) and switched to 5% fetal calf serum for 48 hours (D2: day 2 of differentiation)

value: immortalized myoblasts

value: LAP2alpha knockout; p53 knockout

value: Day 2 of differentiation


title: RAW264.7, 10-4M melatonin+LPS, rep2

value: WT

value: LPS+10-4M melatonin


title: RAW264.7, 10-4M melatonin+LPS, rep3


title: RAW264.7, 10-4M melatonin+LPS, rep1


title: ICS [620356901422]


title: ICS [620356899811]


title: Placebo [S18110500030]


title: LAP2alpha knockout myoblasts, differentiation D2, rep 2


title: ICS [620260389522]


title: RAW264.7, 10-3M melatonin+LPS, rep3

value: LPS+10-3M melatonin


title: DON_2

city: Qingdao

first: Guofeng

address: Jiangsu Road

institute: Affiliated Hospital of Qingdao University

description: DON_2 FPKM

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastpsoftware. In this step, clean data (clean reads) were obtained by removingreads containing adapter, reads containing ploy-N and low quality reads fromraw data. At the same time, Q20, Q30 and GC content the clean data werecalculated. All the downstream analyses were based on the clean data withhigh quality.
Reference genome and gene model annotation files were downloadedfrom genome website directly. Index of the reference genome was built usingHisat2 v2.0.5 and paired-end clean reads were aligned to the referencegenome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene modelannotation file and thus a better mapping result than other non-splice mappingtools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped toeach gene. And then FPKM of each gene was calculated based on the lengthof the gene and reads count mapped to this gene. FPKM, expected number ofFragments Per Kilobase of transcript sequence per Millions base pairssequenced, considers the effect of sequencing depth and gene length for thereads count at the same time, and is currently the most commonly used methodfor estimating gene expression levels.
Assembly: Index of the reference genome was built usingHisat2 v2.0.5 and paired-end clean reads were aligned to the referencegenome using Hisat2 v2.0.5.
Supplementary files format and content: Excel file includes FPKM values for each sample
Supplementary files format and content: Excel file includes Read Count for each sample

growth_protocol: T24 cells were cultured in DMEM medium supplemented with 10% FBS and antibiotics (100 U/mL streptomycin and 100 U/mL penicillin) at 37℃ in a 5% CO2 cell incubator.

extract_protocol:
Total RNA was harvested using TRIzol reagent (Takara). 2 ug of total RNA was used for the construction of sequencing libraries
cDNA library was constructed following the manufacturer's instructions on the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina ® (NR604-01/02), and the constructed cDNA library was sequenced using the Illumina Novaseq6000 (Illumina, USA)

treatment_protocol: The bladder cancer cell line T24 was treated with DON or cultured under normal conditions for 48 h

value: Bladder Cancer Cell Lines

value: DON treatment


title: ICS [620260389122]

value: BRUSHING


title: RAW264.7, 10-3M melatonin+LPS, rep2

value: cell line


title: RAW264.7, 10-3M melatonin+LPS, rep1


title: wildtype myoblasts, differentiation D2 rep 2

value: LAP2alpha wildtype; p53 knockout


title: wildtype myoblasts, differentiation D2, rep 3


title: DON_1

description: DON_1 FPKM


title: LAP2alpha knockout myoblasts, differentiation D2, rep 1


title: ICS [620260389022]


title: Control_3

description: Control_3 FPKM

value: control treatment


title: CD19+ Splenocytes, WT, 4hEtop, rep1

value: 4h Etoposide


title: wildtype myoblasts, differentiation D2, rep 1


title: Control_2

description: Control_2 FPKM


title: Bulk RNA-seq of BMMCs from pediatric AML patient 1 (other genotype group)

value: bone marrow

value: FLT3, IDH

value: treatment-naïve


title: ICS [620091230710]


title: RAW264.7, 10-7M melatonin, rep3

value: RAW 264.7 cell

value: Macrophage

value: 10-7M melatonin


title: Control_1

description: Control_1 FPKM


title: RAW264.7, 10-7M melatonin, rep2


title: ICS [620091230611]


title: RAW264.7, 10-7M melatonin, rep1


title: LAP2alpha knockout myoblasts, differentiation D0, rep 3

value: immortalized myoblasts

value: LAP2alpha knockout; p53 knockout

value: Day 0 of differentiation


title: DON_3

description: DON_3 FPKM

value: WT


title: LAP2alpha knockout myoblasts, differentiation D0, rep 2


title: SUDHL4_GNASKO3_RGFP5_2

city: Toronto

first: Robert

last: Kridel

state: ON

address: 101 College St

institute: Princess Margaret Cancer Centre – University Health Network

data_processing:
Sequencing data were first processed by trimming the low-quality reads and adapters using fastp (v0.23.2). The clean reads were then mapped to a reference genome (GRCh38, GENCODE Ensembl 104 annotation) using the STAR aligner (v2.7.9a). Aligned BAM files were subsequently collected as input to the counting tool HTSeq-count (v0.11.0) to obtain the read count per gene per sample, then merged into a count matrix for differential analysis. Differential gene expression analysis was performed using edgeR (v3.32.1).
Assembly: GRCh38, GENCODE Ensembl 104 annotation
Supplementary files format and content: tab-delimited text files include raw counts for each sample

growth_protocol: Human diffuse large B-cell lymphoma cell line SU-DHL-4 was incubated in RPMI 1640 medium supplemented with 20% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37 ºC.

extract_protocol:
Total RNA was isolated RNeasy Mini Kit (QIAGEN) according to the manufacturer’s instructions. Samples were quantified by Qubit RNA Kit (Life Technologies) and quality was assessed by Agilent Bioanalyzer. All samples had RIN ≥ 9.4.
Libraries were prepared with 100 ng of total RNA using Stranded Total RNA prep with Ribo-Zero Plus kit (Illumina) with 13 cycles of amplification used. Final cDNA libraries were size validated using Agilent Bioanalyzer or Tapestation and concentration validated by qPCR (Kapa Biosystems/Roche). All libraries were normalized and pooled together, denatured with 0.2 N NaOH, and diluted to a final concentration of 250 pM.

treatment_protocol: Cells were treated with 5 µM RGFP966 (Selleckchem) or DMSO for five days.

value: diffuse large B-cell lymphoma cells

value: GNAS knockout

value: RGFP966 (5 µM)


title: ICS [S18110500044]

value: BRUSHING


title: SUDHL4_GNASKO3_RGFP0_2

value: DMSO


title: SUDHL4_GNASKO3_RGFP5_1


title: RAW264.7, 10-6M melatonin, rep2

value: cell line

value: 10-6M melatonin


title: ICS [620091230011]


title: wildtype myoblasts, differentiation D0, rep 3

value: LAP2alpha wildtype; p53 knockout


title: ICS [S18110500042]


title: RAW264.7, 10-6M melatonin, rep1


title: RAW264.7, 10-6M melatonin, rep3


title: SUDHL4_GNASKO2_RGFP5_2


title: wildtype myoblasts, differentiation D0, rep 2


title: SUDHL4_GNASKO3_RGFP0_1


title: ICS [S18110500039]


title: SUDHL4_GNASKO2_RGFP5_1


title: RAW264.7, 10-5M melatonin, rep2

value: 10-5M melatonin


title: LAP2alpha knockout myoblasts, proliferating, rep 3

value: proliferating


title: RAW264.7, 10-5M melatonin, rep3

value: RAW 264.7 cell


title: ICS [S18110500036]


title: SUDHL4_GNASKO2_RGFP0_2


title: LAP2alpha knockout myoblasts, proliferating, rep 2


title: ICS [S18110500034]


title: RAW264.7, 10-4M melatonin, rep3

value: Macrophage

value: 10-4M melatonin


title: ICS [S18110500033]


title: LAP2alpha knockout myoblasts, proliferating, rep 1

value: immortalized myoblasts


title: RAW264.7, 10-5M melatonin, rep1


title: RAW264.7, 10-4M melatonin, rep2


title: wildtype myoblasts, proliferating, rep 3


title: ICS [S18110500029]


title: ICS [S18110500040]


title: SUDHL4_LacZ_RGFP5_1


title: LAP2alpha knockout myoblasts, differentiation D0, rep 1

value: LAP2alpha knockout; p53 knockout


title: RAW264.7, 10-4M melatonin, rep1


title: ICS [S18110500026]


title: wildtype myoblasts, proliferating, rep 2


title: RAW264.7, 10-3M melatonin, rep3

value: 10-3M melatonin


title: SUDHL4_LacZ_RGFP0_2

value: WT


title: ICS [S18110500024]


title: SUDHL4_LacZ_RGFP0_1

value: diffuse large B-cell lymphoma cells


title: ICS [S18110500023]


title: wildtype myoblasts, proliferating, rep 1


title: RAW264.7, 10-3M melatonin, rep2


title: Sarcoidosis (Progressive) 9 [miRNA-seq]

city: Aurora

first: Ivana

last: Yang

state: CO

institute: University of Colorado - Anschutz Medical Campus

data_processing:
forward read of FASTQ files were aligned to sequences from miRBase v22.1 using miR-MaGiC
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for all samples

source_name: bronchoalveolar lavage cells

growth_protocol: Cells were stored in RLT buffer at –80°C

extract_protocol:
DNA and RNA were extracted using the Qiagen AllPrep DNA/RNA extraction mini kit.
miRNA libraries were constructed using Lexogen Small RNA-Seq library preparation kits

value: bronchoalveolar lavage cells

tag: diagnosis

value: sarcoidosis (progressive)

tag: age

value: female

tag: race

value: white

tag: ethnicity

value: not Hispanic or Latino

tag: smoking status

value: never

tag: scadding stage

tag: acute disease

value: n

tag: multiorgan involvement

tag: fvc (%_predicted)

tag: fev1 (%_predicted)

tag: dlco (%_predicted)

tag: ever treated_for_sarcoidosis

tag: pc1 (mirna)

tag: pc2 (mirna)

tag: pc3 (mirna)

tag: pc4 (mirna)

tag: pc5 (mirna)


title: wildtype myoblasts, differentiating (D2), lamin AC E1 ChIP

description: linked to Input 1

data_processing:
Raw sequencing reads in bam format were converted into fastq using bamtofastq from bedtools
Qualities of the reads were evaluated using FastQC
Reads were mapped to the reference genome using NextGenMap with default settings
EDD was used to generate the log2ratio files for Lamin AC and LAP2alpha samples
bamCoverage from deepTools was used to generate the histone mark coverage files with the RPKM normalization method
Assembly: Mus musculusgenome assembly GRCm38 (mm10)
Supplementary files format and content: Lamin AC (LAC_3A6 and LAC_E1) and LAP2alpha (LAP2a) processed files contain log2ratios calculated by normalizing CHIP signals to INPUT signals
Supplementary files format and content: Processed files of all input (Input1,2,3) and histone mark samples (H3K27ac and H3K4me3) contain RPKM normalized coverage signals

tag: cell type

tag: genotype

value: LAP2alpha wildtype; p53 knockout

tag: treatment

value: Day 2 of differentiation

tag: chip antibody

value: lamin A/C antibody E1 (Santa Cruz, # sc-376248)


title: RAW264.7, 10-3M melatonin, rep1

tag: tissue

value: cell line

tag: cell line

value: RAW 264.7 cell

value: Macrophage


title: SUDHL4_GNASKO2_RGFP0_1

value: GNAS knockout

value: DMSO


title: Sarcoidosis (Progressive) 8 [miRNA-seq]

tag: diagnosis

tag: age

tag: Sex

tag: race

tag: ethnicity

tag: smoking status

tag: scadding stage

tag: acute disease

value: y


title: SUDHL4_LacZ_RGFP5_2

value: diffuse large B-cell lymphoma cells

value: WT

value: RGFP966 (5 µM)


title: wildtype myoblasts, proliferating, lamin AC E1 ChIP

description: linked to Input 1

value: immortalized myoblasts

value: proliferating


title: wildtype myoblasts, differentiation D0, rep 1

value: Day 0 of differentiation


title: ICS [S18110500022]

value: BRUSHING


title: RAW264.7, LPS, rep3

value: LPS


title: Sarcoidosis (Progressive) 7 [miRNA-seq]

value: bronchoalveolar lavage cells

value: sarcoidosis (progressive)

value: male

value: white

value: not Hispanic or Latino

value: never

tag: multiorgan involvement

tag: fvc (%_predicted)

tag: fev1 (%_predicted)

tag: dlco (%_predicted)

tag: ever treated_for_sarcoidosis

tag: pc1 (mirna)

tag: pc2 (mirna)

tag: pc3 (mirna)


title: ICS [S18110500021]

tag: tissue

tag: treatment


title: RAW264.7, LPS, rep2

value: cell line

tag: cell line

value: RAW 264.7 cell

tag: cell type

value: Macrophage

tag: genotype


title: LAP2alpha knockout myoblasts, proliferating, lamin AC 3A6 ChIP, rep 1

description: linked to Input 1

value: LAP2alpha knockout; p53 knockout

tag: chip antibody

value: lamin A/C antibody 3A6 (PMID:26798136)


title: RAW264.7, LPS, rep1

value: WT


title: Sarcoidosis (Progressive) 4 [miRNA-seq]

tag: diagnosis

tag: age

tag: Sex

tag: race

tag: ethnicity

tag: smoking status

value: former

value: n

value: y

tag: pc4 (mirna)

tag: pc5 (mirna)


title: wildtype myoblasts, differentiating (D2), lamin AC 3A6 ChIP, rep 1

description: linked to Input 1

value: immortalized myoblasts

value: LAP2alpha wildtype; p53 knockout

value: Day 2 of differentiation


title: ICS [S18110500020]

value: BRUSHING


title: Sarcoidosis (Progressive) 26 [miRNA-seq]

value: bronchoalveolar lavage cells

value: sarcoidosis (progressive)

value: male

value: black

tag: scadding stage

tag: acute disease

tag: multiorgan involvement

tag: fvc (%_predicted)

tag: fev1 (%_predicted)

tag: dlco (%_predicted)

tag: ever treated_for_sarcoidosis

tag: pc1 (mirna)


title: wildtype myoblasts, proliferating, lamin AC 3A6 ChIP, rep 1

description: linked to Input 1

tag: cell type

tag: genotype

tag: treatment

value: proliferating

tag: chip antibody


title: ICS [S18110500018]

tag: tissue


title: RAW264.7, solvent, rep3

value: cell line

tag: cell line

value: RAW 264.7 cell

value: Solvent


title: Sarcoidosis (Progressive) 23 [miRNA-seq]

tag: diagnosis

tag: age

tag: Sex

tag: race

value: white

tag: ethnicity

value: not Hispanic or Latino

tag: smoking status

value: never

tag: pc2 (mirna)

tag: pc3 (mirna)


title: RAW264.7, solvent, rep1

value: Macrophage

value: WT


title: Sarcoidosis (Progressive) 22 [miRNA-seq]

tag: scadding stage

tag: acute disease

value: n

tag: multiorgan involvement

tag: fvc (%_predicted)

tag: fev1 (%_predicted)

tag: dlco (%_predicted)

value: y

tag: pc4 (mirna)

tag: pc5 (mirna)


title: ICS [S18110500015]

tag: tissue

tag: treatment


title: ICS [S18110500016]


title: wildtype myoblasts, proliferating, LAP2alpha ChIP, rep 1

description: linked to Input 1

tag: cell type

value: immortalized myoblasts

tag: genotype

value: LAP2alpha wildtype; p53 knockout

tag: chip antibody

value: LAP2alpha antibody 1H11 (PMID:26798136)


title: ICS [S18110500014]

value: BRUSHING


title: Sarcoidosis (Progressive) 25 [miRNA-seq]

value: bronchoalveolar lavage cells

tag: diagnosis

value: sarcoidosis (progressive)

tag: age

tag: Sex

value: male

tag: race

tag: ethnicity

value: former

tag: ever treated_for_sarcoidosis

tag: pc1 (mirna)


title: wildtype myoblasts, differentiating (D2), LAP2alpha ChIP, rep 1

description: linked to Input 1

value: Day 2 of differentiation


title: RAW264.7, solvent, rep2

value: cell line

tag: cell line

value: RAW 264.7 cell

value: Solvent


title: LAP2alpha knockout myoblasts, differentiating (D2), Input 1

value: LAP2alpha knockout; p53 knockout

value: no antibody - Input