title: skin wound tissue, control, day 4, biol rep 3

description:
Sample 3
control 3

value: WT

value: control, day 4


title: B_5_1

status: Public on Feb 22 2023

type: SRA

city: Sacramento

first: Guiyan

last: Yang

state: CA

address: 4645 2nd Ave

department: Department of Medical Pathology and Laboratory Medicine

country: USA

institute: University of California at Davis

library_source: transcriptomic

data_processing:
The NovaSeq 6000 uses RTA3 for its base calling. The version running on our machines is v3.4.4.
RNA-Seq data was analyzed using a Salmon-tximport-DESeq2 pipeline. The pair-ended reads (FASTQ format) were mapped to the reference mouse genome assembly (GRCm39, GENCODE release 27) and quantified with Salmon.
Gene-level counts were imported with tximport and differential expression analysis was performed with DESeq2 (version 1.18) with the corrected p value < 0.05 and fold change > 2.
Assembly: mm39
Supplementary files format and content: tab-delimited text files include normalized read count values for each sample

molecule: total RNA

organism: Mus musculus

source_name: Liver

extract_protocol:
Total RNA was extracted using TRIzol Reagent. 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using using NEBNext Ultra II non-directional RNA Library Prep kit (New England Biolabs, Inc., Ipswich, MA, USA). Library quality and concentration were assessed with Labchip and qPCR.

tag: tissue

value: Liver

tag: Sex

value: Male

tag: cell type

value: Bulk liver

tag: genotype

value: Wild-type

tag: treatment

value: Western diet

tag: timepoint


title: MPP2_Gata1pos_1_S1

city: Oxford

first: Claus

last: Nerlov

address: John Radcliffe Hospital, University of Oxford

department: MRC Molecular Haematology Unit

country: United Kingdom

institute: Weatheral Institute of Molecular Medicine

library_source: genomic

data_processing:
ATAC-seq: Raw reads were trimmed using TrimGalore! software and inspected using FastQC
ATAC-seq: Trimmed reads were aligned to the mouse genome (NCBI37 assembly (mm9)) using Bowtie2 software, the resulting SAM files were converted to BAM files using SAMtools
ATAC-seq: Duplicate reads were removed using Picard tools
ATAC-seq: Mitochondrial reads removal and read shift were performed using ATACseqQC R package.
ATAC-seq: Peak calling was perfoemd using MACS2 software and peaks within blacklist regions were filtered out before making the final bed file
Genome_build: NCBI37 (mm9)
Supplementary_files_format_and_content: Count matrix of reads mapped in MPP2 open chromatin regoins. Row names indicate the genomic coordinates of open chromatins.

molecule: genomic DNA

source_name: Bone marrow

extract_protocol:
Bone marrow cells were sorted by FACS and cDNA was generated according to Omni-ATAC-seq protocol
Illumina sequencing libraries were constructed using the Nextera DNA Sample Preparation kit according to manufacturer's protocol.

tag: strain

tag: phenotype

value: Vwf-Gata1+ MPP2


title: CG2

city: Wuxi

first: Jun

last: Qiang

state: Jiangsu

address: 9 Shanshi East road

country: China

institute: Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences

description: The culture conditions of the control group were the same as acclimation condition,

data_processing:
Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.
Subsequently, unique sequences with length in 18~26 nucleotide were mapped to specific species precursors in miRBase 21.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3pderived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 21.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations. The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the specific genomes, and the hairpin RNA structures containing sequences were predicated from the flank 80 nt sequences using RNAfold software
Differential expression of miRNAs based on normalized deep-sequencing counts was analyzed by selectively using Fisher exact test, Chi-squared 2X2 test, Chi-squared nXn test, Student t test, or ANOVA based on the experiments design. The significance threshold was set to be 0.01 and 0.05 in each test.
Genome_build: http://asia.ensembl.org/Oreochromis_niloticus/Info/Index
Supplementary_files_format_and_content: excel,expression profiles

organism: Oreochromis niloticus

source_name: Gill tissue

growth_protocol: A total of 90 experimental fish were used for the main acute hypoxic stress experiment. Ninety experimental fish were randomly placed in six tanks (15 fish per tank), three treatment tanks and three 5mg/L control tanks.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Small RNA enrichment was done by excision of the 15 to 50 nt fraction from a polyacrylamide gel. Approximately 1 ug of enriched RNA were used to prepare small RNA library according to protocol of TruSeq Small RNA Sample Prep Kits(Illumina, San Diego, USA).
And then we performed the single-end sequencing (36bp or 50bp ) on an Illumina Hiseq 2500 at the LC Sciences  following the vendor's recommended protocol.

treatment_protocol: The DO of the three treatment tanks was rapidly reduced to 96h-LH50 by pumping nitrogen into water from a nitrogen gas cylinder. Real-time reading with a DO meter were used to control the DO in water by adjusting oxygen intake. The sampling time was 96h.

tag: group

value: the control group

value: Gill tissue

tag: tag


title: skin wound tissue, control, day 4, biol rep 2

city: Whenzhou

first: Ruyi

last: Fan

address: Yongzhong

institute: Wenzhou Institute, University of Chinese Academy of Sciences

description:
Sample 2
control 2

data_processing:
CLC Genomics Workbenchv 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to NCBI_GRCm39 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: NCBI_GRCm39
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Mus

source_name: skin

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer's protocol. 1 ug of total RNA was used for the construction of sequencing libraries.
Then the libraries were constructed using TruSeq Stranded mRNALTSample Prep Kit(Ilumina,San Diego, CA, USA) . 1 ug of total RNA was used for the construction of sequencing libraries.

treatment_protocol: A skin biopsy punch was used to make a circular full-thickness skin wound with a diameter of 8mm on both sides of the dorsal skin. The wounds were treated with different hydrogel scaffolds for 4 days.

value: skin

value: Wounding


title: PLT-1

data_processing:
ATAC-seq: Raw reads were trimmed using TrimGalore! software and inspected using FastQC
ATAC-seq: Trimmed reads were aligned to the mouse genome (NCBI37 assembly (mm9)) using Bowtie2 software, the resulting SAM files were converted to BAM files using SAMtools
ATAC-seq: Duplicate reads were removed using Picard tools
ATAC-seq: Mitochondrial reads removal and read shift were performed using ATACseqQC R package.
ATAC-seq: Peak calling was perfoemd using MACS2 software and peaks within blacklist regions were filtered out before making the final bed file
Genome_build: NCBI37 (mm9)
Supplementary_files_format_and_content: Count matrix of reads mapped in HSC open chromatin regoins. Row names indicate the genomic coordinates of open chromatins.

value: PLT-HSC


title: skin wound tissue, control, day 4, biol rep 1

description:
Sample 1
control 1


title: A_5_3

value: Control diet


title: BG_BMDM_7

city: Chicago

first: Sarah

middle: J

last: Sun

state: Illinois

address: 900 E 57th Street

institute: University of Chicago

data_processing:
mm10
remove adapter sequences; trimmomatic-0.36; ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
read alignment; STAR; --sjdbOverhang 100
generate count matrix; featureCounts
processed_data: text file, raw counts matrix of reads overlapping each gene for each sample

source_name: BMDM

extract_protocol:
RNA extracted with Qiagen RNeasy kit
Illumina TruSeq

tag: cell line

value: BMDM

value: macrophage

tag: primary treatment

value: beta glucan

tag: secondary treatment


title: Meis1-overexpressing_EC_rep1

city: Vancouver

first: Aly

last: Karsan

state: British Columbia

country: Canada

institute: Canada's Michael Smith Genome Sciences Centre

data_processing:
Illumina RTA 2.7.7 software used for basecalling.
RNA-Seq reads were aligned to the mm10 genome assembly using star version 2.5.2b
Genome_build: mm10
Supplementary_files_format_and_content: meis1_oe_gene_counts.txt contains a matrix where each row represents a gene, columns represent the different samples, and values are count

source_name: primary aortic endothelial cells

growth_protocol: 100,000 primary endothelial cells were plated per well of a 6-well plate precoated with Gelatin-Based Coating Solution (Cell Biologics) 24h prior transduction with Meis1-OE vector or YFP-CTRL. Transduction was stopped after 48h by complete media change and cells were FACS at 72h to select for incorporation of the vector. Transduced endothelial cells (YFP+CD31+VEC+) were re-plated in a 6-well plate, expanded to confluency, and harvested for RNA.

extract_protocol: Total RNA was extracted from 300,000 cells using TRIzol reagent (Invitrogen) and between 300-400 ng of RNA was sent for RNA-seq

tag: age

value: Adult

value: WT

tag: transduction

value: overexpressed Meis1


title: C_BMDM_7


title: CG1


title: A_5_2

value: Liver

value: Male


title: PEM-5

value: PEM-HSC


title: PEM-6


title: PEM-4


title: a/alpha cell  [22-3_S61]

city: SAN FRANCISCO

first: Francesca

middle: Silvia

last: Del Frate

address: 329 Church St

department: Department of Biochemistry and Biophysics

institute: University of California, San Francisco

data_processing:
Quality of sequencing reads was determined using FastQC25. Filtering based on quality and trimming of reads was done using FastP26. The assembled genome for Lachancea kluyveri  NRRL Y-12651 was downloaded from the y1000+ genome database database17,27; Trimmed reads were aligned to this reference genome using STAR28. A table with counts assigned to genes was generated from the alignments using Rsubread29. This count table was then used to determine differentially expressed genes using DESeq230. DESeq2 was run with default parameters, resulting in a list of genes that were differentially expressed in yLB76(a cell)  when compared to FDy22(a/alpha cell). The same was done for LB77(alpha cell) compared to FDy22(a/alpha cell).
Assembly: NRRL Y-12651
Supplementary files format and content: csv, normalized abundance measurments, ouput from DESeq

molecule: polyA RNA

organism: Lachancea kluyveri

source_name: yeast-whole organism

growth_protocol: Grow up single yeast colony overnight in YPED at 30C. Dilute to OD=0.1 in 10 mls YPED, and grow to

extract_protocol:
RNA was extracted using the RiboPure RNA purification kit (ThermoFisher AM1924) according to manufacturer’s instructions.
Total RNA quality was verified on the Agilent Tapestation. Total RNA was poly-a selected with the NEBNext Poly(A) mRNA Magnetic Isolation Module(Neb E7490S). cDNA synthesis and library preparation was done with the NEBNext Ultra II Directional RNA Library Prep kit for Illumina (Neb E7760L). Quality and concentration of libraries were determined with the Agilent Tapestation. Libraries were pooled in equimolar amounts and sequenced using single end 65 base pair reads on an Illumina HiSeq 4000 in the UCSF Center for Advanced Technologies

value: yeast-whole organism

value: a/alpha cell

value: WT/prototroph


title: A_5_4

value: Bulk liver

value: Wild-type


title: MEF, Low Heteroplasmy, Biol Rep 5

city: Cambridge

first: Malwina

last: Prater

address: Hills Rd

department: MRC MBU

institute: University of Cambridge

description:
G10_109H
Clone_109

data_processing:
Sequence reads were mapped to GrCM38/mm10 using STAR (v2.7.8a) (parameters- default)
Mapped reads were quantified to gene counts with STAR.
Differential expression analysis was performed using DESeq2 (v.1.36.0) in R (version 4.2.1).
Assembly: mm10
Supplementary files format and content: comma-delimited text files include raw and normalised count values for each Sample

source_name: Embryo

growth_protocol: Cells cultured in High Glucose (4.5g/dL) DMEM supplemented with 10% FBS and 50µg/ml uridine, at 37ºC, 5%CO2 in a humidified incubator

extract_protocol:
Total RNA extracted using QIAGEN Rneasy Plus Mini Kit according to manufacturer's instructions, including gDNA elimination
Libraries constructed using NEBNext Poly(A) mRNA Kit & NEBNext Ultra II Directional RNA Library Prep Kit according to manufacturer's instructions

value: Embryo

value: Immortalized Embryonic Fibroblast

value: MEF


title: A_5_1

value: Control diet


title: a/alpha cell  [22-2_S60]


title: PEM-2


title: a/alpha cell  [22-1_S59]


title: PEM-1


title: MEF, High Heteroplasmy, Biol Rep 5

description:
A10_83H
Clone_83


title: alpha cell  [9-3_S53]

value: alpha cell


title: MEF, Low Heteroplasmy, Biol Rep 4

description:
D10_101H
Clone_101


title: alpha cell  [9-2_S52]


title: MEF, High Heteroplasmy, Biol Rep 4

description:
F9_62H
Clone_62


title: MUL-3

value: MUL-HSC


title: MUL-2


title: MEF, High Heteroplasmy, Biol Rep 3

description:
C9_59H
Clone_59


title: MUL-4


title: a cell  [10-3_S56]

value: a cell


title: MEF, Low Heteroplasmy, Biol Rep 3

description:
H8_48H
Clone_48


title: MEF, High Heteroplasmy, Biol Rep 2

description:
E8_44H
Clone_44


title: MEF, Low Heteroplasmy, Biol Rep 2

description:
B8_33H
Clone_33


title: MUL-1


title: Mouse cortex, EtOH 4

city: Hong Kong

first: Hei-Man Kim

last: Chow

address: Room 604, Mong Man Wai Building, CUHK

department: School of Life Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

description: EtOH 4M

data_processing:
The FASTQ files were first assessed using FastQC (V. 0.11.9) provided by Babraham Bioinformatics, which serves as a quality control tool for high throughput sequence data.
Once the data is evaluated and the quality is ensured, the genome indexes were generated using the STAR software.
The indexes were generated using the mouse annotation and mouse genome assembly provided by Gencode, Release 28 (GRCm39), which was released in May 2021.
The subsequent clean data was then aligned using the STAR alignment software using the genome indexes.
featureCounts was then used to quantify the sequencing data. Data extraction, matrix construction and differential gene expression analysis was then performed using DESeq2.
Assembly: mm39
Supplementary files format and content: tab-delimited text files include raw values from featureCounts for each sample.

source_name: Mouse brain cortex

extract_protocol:
RNA was harvested and used for the construction of sequencing libraries by the sequencing service from BGI.
RNA libraries for RNA-seq were prepared by the service purchased from the BGI

value: Mouse brain cortex

value: EtOH


title: PEM-3


title: a cell  [10-2_S55]


title: Mouse cortex, EtOH 3

description: EtOH 3M


title: MEF, High Heteroplasmy, Biol Rep 1

description:
G7_26H
Clone_26


title: MK_53_S12

city: Wauwatosa

first: Matthew

last: Kudek

state: WI

address: 8701 W Watertown Plank Rd

institute: Medical College of Wisconsin

data_processing:
Bulk RNA-seq data were aligned to the Mus musculus mm10 genome
Genome_build: mm10

source_name: enriched CD8 T cells

extract_protocol:
complementary DNA was generated from RNA using smart-seq2 protocol (Nat Protoc. 2014;9(1):171-181)
DNA library was prepared using the Nextera XT DNA Library Preparation Kit (Illumina).

treatment_protocol: LCMV Clone 13 infection

tag: background strain

value: DGKa-/-

tag: disease state

value: LCMV clone 13

value: CD8+ T cells


title: Mouse cortex, EtOH 2

description: EtOH 2M

tag: tissue


title: a cell [10-1_S54]

value: yeast-whole organism


title: MEF, Low Heteroplasmy, Biol Rep 1

description:
A7_12H
Clone_12


title: alpha cell  [9-1_S51]


title: Mouse cortex, EtOH 1

description: EtOH 1M


title: MK_51_S11


title: alpha cell_untagged_IP_biol_rep2

data_processing:
Quality of sequencing reads was determined using FastQC. Filtering based on quality and trimming of reads was done using FastP. The assembled genome for Lachancea kluyveri  NRRL Y-12651 was downloaded from the y1000+ genome database database; Trimmed reads were aligned to this reference genome using STAR, alignments output in bam format.
Bam files were indexed with Sam tools with the index command and converted to bigwig format with the Deep tools bamCoverage command.
Assembly: Lachancea kluyveri  NRRL Y-12651 (assembly ASM14922v2) accessed by downloading from y1000+ Project online database https://y1000plus.wei.wisc.edu/
Supplementary files format and content: bigwig

growth_protocol: Grew 200 ml of planktonic cells to OD= 0.4 in YPED at 30C

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 minutes. Cells were quenched with addition of 0.13M glycine, and lysed in a beadrupter (brand)  After quencing and cell lysis, chromatin was sheared by sonication in a Bioruptor Pico (Diagenode) to around 200bp fragments. Sheared chromatin was either saved as input, or immunoprecipitated with antibody, see ChIP antibody for  for antibody information.
Libraries were prepared with NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB E7645L). Library quality and concentration was assayed by Tapestation (Agilent), and pooled in equimolar concentrations.

tag: strain name

value: alpha

value: WT

tag: chip antibody


title: MK_50_S10

tag: genotype

tag: cell type


title: alpha cell_tagged_INPUT_biol_rep2

value: Anti-c-Myc 9E10.3 (ThermoFisher AHO0062)


title: Mouse cortex, EtOH 5

description: EtOH 5M

tag: treatment


title: MK_13_S9


title: Embryonic coronary endothelial cells, Wt1KOΔEC, mGFP+ sorted cells, biol rep 3

city: Barcelona

first: Ofelia

middle: M.

last: Martínez Estrada

state: Barcelona

address: Avinguda Diagonal, 643, Edifici Prevosti, Planta 1, Laboratori 2

department: Cell Biology, Physiology and Immunology

country: Spain

institute: University of Barcelona

data_processing:
Reads were mapped to the Mus musculus reference genome (GRCm38) using STAR/2.7.8a with ENCODE parameters.
Gene quantification was performed with RSEM/1.3.0 using the gencode.vM27 version with default parameters.
Differential expression analysis was done with the DESeq2 v1.18 R package with default parameters.
Genes with log2FC>|0.58| and FDR<%5 were considered differentially expressed.
Assembly: m38
Supplementary files format and content: tab-delimited text file includes normalized DESeq2 count values for each Sample

source_name: heart

growth_protocol: Mating between Pdgfb-CreERT2/+; Wt1-LoxP/+ males with Wt1-LoxP/+; R26-mTmG/mTmG females allowed us to obtain Pdgfb-CreERT2/+; Wt1-LoxP/LoxP; R26-mTmG/+ (Wt1KOΔEC) and Pdgfb-CreERT2/+; Wt1-+/+; R26-mTmG/+ (ControlΔEC) embryos from the same litter. Ethical committee authorization reference for the maintenance of these transgenic mouse models is #11152 (FUE-2020-01713465, ID: PH3BYSQCC) according to the animal committee commission from the Generalitat de Catalunya. Embryos were generated through timed matings, whereby females that had mated during the night were checked for plugs early the following morning. The morning on which a plug was found was considered E0.5.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA sequencing libraries were prepared following the SMARTseq2 protocol. RNA was quantified using the Qubit RNA HS Assay Kit (Thermo Fisher Scientific). Reverse transcription with the input material of 2ng was performed using SuperScrpit II (Invitrogen) in the presence of oligo-dT30VN, template-switching oligonucleotides and betaine. The cDNA was amplified using the KAPA Hifi Hotstart ReadyMix (Roche), 100 nM ISPCR primer and 12 cycles of amplification. Following purification with Agencourt Ampure XP beads (1:1 ratio; Beckmann Coulter), product size distribution and quantity were assessed on a Bioanalyzer High Sensitvity DNA Kit (Agilent). The amplified cDNA (200 ng) was fragmented for 10 min at 55 ºC using Nextera XT (Illumina) and amplified for 12 cycles with indexed Nextera PCR primers. The library was purified twice with Agencourt Ampure XP beads (0.8:1 ratio) and quantified on a Bioanalyzer using a High Sensitvity DNA Kit. The libraries were sequenced on NovaSeq 6000 (Illumina) in paired-end with a read length of 2x51bp according to the manufacturer’s protocol for dual indexing. Image analysis, base calling and quality scoring of the run are processed using the manufacturer’s software Real Time Analysis (RTA 3.4.4) and followed by generation of FASTQ sequence files.

treatment_protocol: To induce Cre recombination, tamoxifen (Sigma-Aldrich) was dissolved in corn oil (Sigma-Aldrich) and administered at a 75 mg tamoxifen/kg mouse weight through oral gavage, during embryonic stages E11.5-13.5.  At E15.5, pregnant females were sacrificed, and embryonic hearts were dissected.  To isolate coronary endothelial cells, heart ventricles were digested into digestion solution (1 mg/mL type 1 collagenase, Worthington, in HBSS Ca2+ Mg2+) for 20 min on a thermoblock with constant agitation (37ºC, 1.000rpm).  Collagenase activity was stopped by washing the cells in DMEM containing 5% of inactivated FBS. Cells were pelleted by centrifugation and resuspended in cold FACS buffer (5% FBS in HBSS Ca2+ Mg2+ containing) and incubated for at least 30 min at 4ºC with gentle rotation. Finally, cells were pelleted by centrifugation and re-suspended in HBSS Ca2+ Mg2+. FACS analysis were carried out were on a FACS Aria III (BD Bioscience), and data was analysed using FACSDivaTM software (BD Bioscience).

value: heart

tag: tissue region

value: Coronary plexus

value: Endothelial cell


title: alpha cell_tagged_IP_biol_rep2


title: Mouse cortex, Control  6

description: Control 6M

tag: strain

value: Vehicle


title: Embryonic coronary endothelial cells, Wt1KOΔEC, mGFP+ sorted cells, biol rep 1


title: alpha cell_untagged_INPUT_biol_rep1


title: MK_12_S8


title: Embryonic coronary endothelial cells, Wt1KOΔEC, mGFP+ sorted cells, biol rep 2


title: MK_54_S13


title: Embryonic coronary endothelial cells, ControlΔEC , mGFP+ sorted cells, biol rep 3


title: MK_11_S7


title: Mouse cortex, Control  4

description: Control 4M


title: alpha cell_untagged_IP_biol_rep1


title: Mouse cortex, Control  5

description: Control 5M


title: Embryonic coronary endothelial cells, ControlΔEC , mGFP+ sorted cells, biol rep 2


title: alpha cell_untagged_INPUT_biol_rep2


title: alpha cell_tagged_IP_biol_rep1


title: Luciferase RNAi induced_2

city: Vienna

first: Alwin

last: Koehler

address: Dr.-Bohr-Gasse 3/9

country: Austria

institute: Max F. Perutz Laboratories

data_processing:
Base calling was done following the HiSeq2500 instrument manufacturer's base calling software.
Reads were aligned against the Trypanosoma brucei reference genome (TriTrypDB 8.1 release) using TopHat version 2.0.9
After alignment reads were associated with known genes based on annotations derived from TriTrypDB and number of reads aligned with each gene was counted using Htseq tool version 0.5.4p3.
Data were normalized using TMM normalisation method of the edgeR R/Bioconductor package (R version 3.0.1, Bioconductor version 2.12)
For statistical testing data were log transformed using voom approach in the limma package.
For visualization and result files the TMM normalised counts are represented as RPKM values.
Genome_build: TriTrypDB 8.1
Supplementary_files_format_and_content: tab delimited text file including RPKM values for each sample

organism: Trypanosoma brucei brucei

source_name: Luciferase RNAi induced

growth_protocol: Medium used: SDM-79 medium supplemented with 15% Tet-System approved fetal calf serum, 7.5 μg/mL haemin, 15 μg/mL G418 and 50 μg/mL hygromycin, 1 µg/ml puromycin and 5  µg/ml phleomycine. A culture was seeded with a cell density of 1 mil/ml, grown for two days, reseeded and grown for 1.5 days before harvesting the cells for the RNA isolation.

extract_protocol:
RNeasy mini kit (Qiagen) using manufacturer's instruction including an additional step of DNase I (Promega) digestion.
rRNA was removed with Ribozero Kit (Epicentre) following manufacturers instructions. Libraray was generated following the instructions of the NEB RNA ultra Kit for library preparation
RNAseq with HiSeq2500. Single-end sequencing with 50bp read length.

treatment_protocol: see above

tag: strain genotype

value: 3xHA-SAC3 PAC RDNA::FLuc_RNAiTi BLE TETR T7RNAP NEO HYG

value: doxycycline 10ug/ml


title: Mouse cortex, Control  3

description: Control 3M


title: Embryonic coronary endothelial cells, ControlΔEC , mGFP+ sorted cells, biol rep 1


title: Luciferase RNAi induced _1


title: alpha cell_tagged_INPUT_biol_rep1


title: Mouse cortex, Control  2

description: Control 2M


title: Mouse cortex, Control  7

description: Control 7M


title: TbSAC3 RNAi uninduced_2

source_name: TbSAC3 RNAi uninduced

value: 3xHA-TbSAC3 PAC RDNA::TbSAC3_RNAiTi BLE TETR T7RNAP NEO HYG


title: a-alpha cell_untagged_INPUT_biol_rep2

value: a / alpha


title: PBS +CNV

city: Montreal

first: Mike

last: Sapieha

state: Quebec

address: 5415 Boul. L'Assomption

institute: Hôpital Maisonneuve-Rosemont

description: snATAC-seq

data_processing:
Raw scRNA-seq data were processed with the Cell Ranger software (version 1.2).
The ‘cellranger-atac count’ function was used to process fastq files, align reads to the mm10 mouse reference genome (Cellranger-atac reference v1.2.0, mm10) and produce the peak-barcode count matrix for each library.
The ‘cellranger-atac aggr' function was then used to aggregate all 3 samples while normalizing libraries for sequencing depth.
The resulting aggregted peak-barcode matrix was then used for downstream analysis in R with Signac package (version 1.1.1). Cells were filtered to keep only ones with the following criteria : 1) nucleosome signal < 4; 2) transcription start site enrichment > 2; 3) alignment to blacklisted regions < 5%; 4) number of reads in peaks < 40 000; 5) read fractions in peaks >20%.
Normalization and dimensionality reduction were performed using latent semantic indexing (LSI). Only LSI dimensions 2 to 10 were kept. Clusters were identified using the Leiden algorithm with a resolution of 0.4 and UMAP was applied for visualization.
Genome_build: mm10
Supplementary_files_format_and_content: Filtered peak-barcode matrix and fragments file output from CellRanger-ATAC and filtered cell annotation with cluster IDs

source_name: Retinal CX3CR1+ myeloid cells

extract_protocol:
Sorted CX3CR1+ cells were used for scATAC-seq and nuclei isolation was performed according to the protocol of 10x Genomics. Briefly, isolated cells were centrifuged at 300xg for 5 min at 4°C and then resuspended in ice-cold PBS+0.04% BSA. The cell lysis was performed for 4 minutes on ice by adding 45μl lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% Nonidet P-40, 0.01% Digitonin, and 1% BSA). After lysis, 50μl ice-cold wash buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, and 1% BSA) were added and then centrifuged at 500 × g for 5 min at 4 °C. After one more wash, the washed nuclei were counted and used for the transposase reaction.  After removing the supernatant, the pellet was resuspended in 7 ml 1x Nuclei Buffer (10x Genomics) and 2 ml of the nuclei suspension was taken for evaluation (nuclei quality control and determining nuclei concentration).
The library was constructed according to the Chromium Single Cell ATAC Reagent Kits protocol (10x Genomics).

value: CX3CR1 GFP/+

value: retina


title: Naives

description: snATAC-seq


title: a-alpha cell_untagged_IP_biol_rep2


title: a-alpha cell_tagged_INPUT_biol_rep2


title: gef_comb_d21

city: Okayama

first: Shuta

last: Tomida

address: 2-5-1 Shikata-cho, Kita-ku

department: Center for Comprehensive Genomic Medicine

country: Japan

institute: Okayama University Hospital

data_processing:
RNA sequencing was performed on a DNBSEQ-G400RS with DNBSEQ G400RS High throughput Sequencing Set via FCL PE150 setting.
Sequencing data were mapped and analyzed to calculate TPM (Transcripts Per Kilobase Million) values using the CLC Genomics Workbench (CLC bio, Aarhus, Denmark).
Genome_build: Mus_musculus_ensembl_v80_Sequence (mus_musculus_refseq_GRCm38.p6)
Supplementary_files_format_and_content: tab-delimited text files includeTPM values for each sample

source_name: Lung tumor

extract_protocol:
RNA was extracted from frozen tissues using an RNeasy Mini Kit (Qiagen) according to manufacturer protocol. rRNA was depleted using NEBNext rRNA Depletion Kit v2 (Human/Mouse/Rat) (E7405) (New England Biolabs).
cDNA libraries were prepared using the MGIEasy RNA Directional Library Prep Set.

value: Lung tumor

value: treatment with combination of DC101 and 4H2 for 7 days after treatment with gefitinib for 14 days


title: gef_4h2_d21

value: treatment with 4H2 for 7 days after treatment with gefitinib for 14 days


title: N-4-Y

city: Jinan

first: jinxiu

last: Hu

address: jingwuweiqi

institute: Shandong Provincial Hospital

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. The remaining reads were filtered against the rRNA database to remove possible ribosomal RNA contamination,  and then mapped to the hg19 whole genome using Hisat2 v2.1.0 with default parameters.
HTSeq v0.11.2 was subsequently employed to convert aligned short reads into read counts for each gene model.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include RPKM for each Sample

organism: Homo sapiens

source_name: renal cortex

extract_protocol:
Tatol RNA was extracted by Magzol Reagent (Magen, China)
Briefly, RNAs were ligated with 3' RNA adapter, and followed by 5' adapter ligation. Subsequently, the adapter-ligated RNAs were subjected to RT-PCR and amplified with a low-cycle. Then the PCR products were size selected by PAGE gel according to instructions of NEBNext® Ultra™ RNA Library Prep Kit for Illumina (Illumina, USA)

tag: source

value: non-diabetic renal cancer patients undergoing surgical resection


title: TbSAC3 RNAi  induced_1

source_name: TbSAC3 RNAi  induced


title: gef_dc101_d21

value: treatment with DC101 for 7 days after treatment with gefitinib for 14 days


title: jmj28-2_rep2_B

city: shanghai

first: li

last: peng

institute: PSC

data_processing:
RNA purification, reverse transcription, library construction and sequencing were performed according to the manufacturer’s instructions
Then clean reads were separately aligned to reference genome with orientation mode using TopHat
The expression level of each transcript was calculated according to the fragments per kilobase of exon per million mapped reads (FPKM) method
RSEM was used to quantify gene abundances. R statistical package software EdgeR was utilized for differential expression analysis.
Genome_build: TAIR10
Supplementary_files_format_and_content: excel table with FPKM value

organism: Arabidopsis

source_name: plant tissues

growth_protocol: All the plant seeds were sown and grown on 1/2 MS medium containing 1% sucrose. The seedlings were grown under a long- (16 h light/8 h dark)  photoperiod at 23 °C.

extract_protocol: Total RNAs were extracted from 12-day-old seedlings grown during long days using a RNeasy Plant Mini kit (Qiagen)

value: 12-day-old seedlings

tag: ecotype


title: N-2-G


title: a-alpha cell_tagged_IP_biol_rep2

value: yeast-whole organism

value: WT


title: a-alpha cell_untagged_INPUT_biol_rep1

value: Anti-c-Myc 9E10.3 (ThermoFisher AHO0062)


title: N-1-H


title: jmj28-2_rep1_B


title: gef_vehicle_d21

value: no treatment for 7 days after treatment with gefitinib for 14 days


title: 4xLPS +CNV

description: snATAC-seq


title: Col-0_rep2_B

value: wildtype


title: FN-2-L

value: diabetic kidney disease


title: a-alpha cell_tagged_IP_biol_rep1


title: a-alpha cell_untagged_IP_biol_rep1


title: Col-0_rep1_B


title: Mouse cortex, Control  1

description: Control 1M

value: Mouse brain cortex

value: Vehicle


title: vehicle_d3

value: no treatment


title: TbSAC3 RNAi induced_2

source_name: TbSAC3 RNAi induced

value: 3xHA-TbSAC3 PAC RDNA::TbSAC3_RNAiTi BLE TETR T7RNAP NEO HYG

value: doxycycline 10ug/ml


title: TbSAC3 RNAi uninduced_1


title: FN-1-Y


title: PFC, female, ethanol, input 5

status: Public on Feb 21 2023

city: Richmond

first: JENNIFER

last: WOLSTENHOLME

state: VA

address: 1217 E Marshall Street, KMSB Rm 536

institute: Virginia Commonwealth University

data_processing:
Quality of FastQ samples were assessed with FastQC. Adapter sequences and reads with quality scores <20 were removed using CutAdapt
FastQ files were aligned to the GRCm38/mm10 genome using Bowtie2 (v2.4.1)
Reads aligning to blacklisted regions, defined by ENCODE, were discarded using bamtools.
Peaks were identified using SICER, using the corresponding input sample for normalization  (v1.1, H3K36me3 settings = W200, G600, H3K9me3 settings = W200, G400)
Assembly: GRCm38/mm10
Supplementary files format and content: fastq files contain raw sequencing reads for ChIP-seq data. For each biological sample, H3K36me3-ChIP, H3K9me3-ChIP, and input samples exist; islands-summary files contain peak calls determined by SICER

source_name: Brain

extract_protocol:
H3K36me3 (active motif #61101) and H3K9me3 (abcam #ab8898) ChIP was performed on prefrontal cortex tissue using the MAGNA ChIP Hi-Sens kit (Millipore, Burlington, MA), following the manufacturer’s instructions. DNA was extracted using phenol:chloroform:isoamyl alcohol (Thermo Fisher, Waltham, MA) and purified with ethanol precipitation. Pellets were resuspended in 20uLTE buffer and stored at -20C. To obtain sufficient DNA for sequencing, 8 technical replicates from each sonicated sample were subjected to immunoprecipitation for each antibody. DNA from all 8 technical replicates were combined and concentrated using a speed-vacuum prior to library preparation.
Preparation of libraries were conducted following standard protocols using the Accel-NGS 2S PLUS DNA Library kit (Swift).

treatment_protocol: Adolescent male and female DBA/2J mice were dosed with 4 g/kg ethanol (25% w/v in water by gavage) or water intermittently (2 days on/2 days off) on PND 29, 30, 33, 34, 37, 38, 41, and 42. Prefrontal cortex tissue from three mice of the same sex and treatment were pooled, homogenized, and divided in half 24 hours after the last dose. Half of each pooled sample was subjected to RNA-Seq, and the other half was subjected to ChIP-Seq (n = 22).

value: Brain

tag: Sex

value: female

value: ethanol


title: PFC, female, ethanol, H3K9me3, 6


title: PFC, female, ethanol, input 4


title: PFC, female, ethanol, H3K36me3, 5


title: PFC, female, ethanol, H3K36me3, 6


title: PFC, female, ethanol, H3K9me3, 4


title: PFC, female, ethanol, H3K36me3, 4


title: PFC, female, ethanol, H3K9me3, 3


title: gef_d14

value: Lung tumor

value: treatment with gefitinib for 14 days


title: gef_d3

value: treatment with gefitinib for 3 days


title: PFC, female, ethanol, H3K9me3, 2


title: PFC, female, ethanol, H3K36me3, 2


title: PFC, female, ethanol, input 3


title: PFC, female, ethanol, H3K36me3, 3


title: FN-3-C


title: PFC, female, etahnol, H3K9me3, 1


title: PFC, female, ethanol, input 2


title: PFC, female, ethanol, input 1


title: PFC, female, water, input 5

value: water


title: PFC, female, water, H3K9me3, 5


title: PFC, female, water, input 4


title: PFC, female, water, H3K36me3, 5


title: PFC, female, water, H3K9me3, 4


title: PFC, female, water, H3K36me3, 4


title: PFC, female, ethanol, input 6


title: PFC, female, water, H3K9me3, 3


title: PFC, female, water, input 3


title: PFC, female, ethanol, H3K9me3, 5


title: PFC, female, water, H3K36me3, 3


title: PFC, female, water, input 2


title: a-alpha cell_tagged_INPUT_biol_rep1

value: yeast-whole organism

value: a / alpha


title: PFC, female, water, H3K36me3, 2


title: PFC, female, water, H3K9me3, 2


title: PFC, female, water, input 1


title: PFC, female, water, H3K36me3, 1


title: PFC, male, ethanol, input 6

value: male


title: PFC, male, ethanol, H3K36me3, 6


title: PFC, male, ethanol, H3K9me3, 5


title: PFC, male, ethanol, H3K9me3, 6


title: PFC, male, ethanol, input 5


title: PFC, male, ethanol, H3K36me3, 5


title: PFC, male, ethanol, input 4


title: PFC, male, ethanol, H3K9me3, 3


title: PFC, male, ethanol, H3K36me3, 4


title: PFC, male, ethanol, input 3


title: PFC, male, ethanol, H3K36me3, 3


title: PFC, male, ethanol, H3K9me3, 4


title: PFC, male, ethanol, input 2


title: PFC, male, ethanol, H3K9me3, 2


title: PFC, female, ethanol, H3K36me3, 1


title: PFC, male, ethanol, input 1


title: PFC, male, water, input 5


title: PFC, male, etahnol, H3K9me3, 1


title: PFC, male, water, H3K9me3, 5


title: PFC, male, water, H3K36me3, 5


title: PFC, male, ethanol, H3K36me3, 1


title: PFC, female, water, H3K9me3, 1


title: PFC, male, water, H3K9me3, 4


title: PFC, male, water, H3K36me3, 4


title: PFC, male, water, H3K9me3, 3


title: PFC, male, water, H3K36me3, 3


title: PFC, male, water, input 2


title: PFC, male, water, H3K9me3, 1


title: PFC, male, water, H3K36me3, 2


title: SH-SY5Y R495X DIFF 3

city: Poznan

first: Kishor

last: Gawade

address: Uniwersytetu Poznańskiego 10

department: Faculty of Biology

country: Poland

institute: Adam Mickiewicz University

description:
PsiScore.Sample_DRA21
HPS_PsiScore_SH_SY5Y_DIFF_FUS_WT_R495X

data_processing:
Trimming of adapter sequence by Trimmomatic
Bowtie2 alignment of trimmed reads to the reference sequence in E-to-E mode
Extraction of uniquely mapped reads
Counting of reads' 5'-extremities
Data processing of HydraPsiSeq, calculation of HydraPsiSeq scores
Assembly: NR_046235
Supplementary files format and content: .csv file containing PsiScores for known pseudouridylated positions on ribosomal RNA
Library strategy: HydraPsiSeq

source_name: cell line

growth_protocol: SH-SY5Y and HEK293T cells were grown in Dulbecco’s modified Eagle’s medium containing L-glutamine and 4.5 g/L glucose (DMEM; Lonza) and supplemented with 10% fetal calf serum (Gibco) and antibiotics (100 U/ml penicillin, 100 µg/ml streptomycin (Sigma-Aldrich)) at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was isolated using the Quick-RNA MiniPrep Kit (Zymo Research, R1055) according to the manufacturer's protocol.
250 ng of RNA from each replicate was used for hydrazine treatment for 30-60 min on ice. To stop the reaction, ethanol precipitation with 0.3 M NaOAc, pH 5.2 and Glycoblue was performed, and incubated at −80°C for 30 min, followed by centrifugation. The collected pellet was washed with 80% ethanol and resuspended in 1 M aniline, pH 4.5, followed by incubation in the dark for 15 min at 60°C and then ethanol precipitation. Dephosphorylation of RNA at the 3’ end was performed. Library preparation was carried out using the NEBNext Small RNA Library kit (NEB, UK), following the manufacturer’s protocol.
ncRNA-Seq: HydraPsiSeq, a quantitative ψ mapping technique relying on specific protection from hydrazine/aniline cleavage.

treatment_protocol: SH-SY5Y wild-type, FUS KO, and FUS R495X cells were subjected to retinoic acid (RA) treatment for 10 days. All-trans RA (USP, Tretinoin, 1674004) at a final concentration of 75 µM was added to DMEM with 10% FBS. The media, along with the RA, were replaced every 3 days.

tag: cell line

value: thrice-cloned sub-line of bone marrow biopsy-derived line SK-N-SH

value: FUS R495X

value: Differentiation using Retinoic Acid for 10 days


title: PFC, male, water, H3K36me3, 1


title: SH-SY5Y R495X DIFF 1

description:
PsiScore.Sample_DRA19
HPS_PsiScore_SH_SY5Y_DIFF_FUS_WT_R495X


title: SH-SY5Y FUSKO DIFF 2

description:
PsiScore.Sample_DRA17
HPS_PsiScore_SH_SY5Y_Diff_FUS_WT_FUSKO

value: FUS knock-out


title: SH-SY5Y R495X DIFF 2

description:
PsiScore.Sample_DRA20
HPS_PsiScore_SH_SY5Y_DIFF_FUS_WT_R495X


title: SH-SY5Y WT DIFF 1

description:
PsiScore.Sample_DRA13
HPS_PsiScore_SH_SY5Y_Diff_FUS_WT_FUSKO
HPS_PsiScore_SH_SY5Y_DIFF_FUS_WT_R495X

value: wild-type


title: SH-SY5Y WT DIFF 3

description:
PsiScore.Sample_DRA15
HPS_PsiScore_SH_SY5Y_Diff_FUS_WT_FUSKO
HPS_PsiScore_SH_SY5Y_DIFF_FUS_WT_R495X


title: SH-SY5Y FUSKO DIFF 3

description:
PsiScore.Sample_DRA18
HPS_PsiScore_SH_SY5Y_Diff_FUS_WT_FUSKO


title: SH-SY5Y FUSKO PROLI 2

description:
PsiScore.Sample_DRA11
HPS_PsiScore_SH_SY5Y_Proli_FUSWT_FUSKO


title: PFC, male, ethanol, H3K36me3, 2


title: PFC, male, water, input 4


title: SH-SY5Y WT PROLI 1

description:
PsiScore.Sample_DRA07
HPS_PsiScore_SH_SY5Y_Proli_FUSWT_FUSKO


title: SH-SY5Y FUSKO PROLI 1

description:
PsiScore.Sample_DRA10
HPS_PsiScore_SH_SY5Y_Proli_FUSWT_FUSKO


title: SH-SY5Y WT PROLI 3

description:
PsiScore.Sample_DRA09
HPS_PsiScore_SH_SY5Y_Proli_FUSWT_FUSKO


title: SH-SY5Y FUSKO PROLI 3

description:
PsiScore.Sample_DRA12
HPS_PsiScore_SH_SY5Y_Proli_FUSWT_FUSKO


title: PFC, male, water, input 3


title: HEK293T FUSKO 2

description:
PsiScore.Sample_DRA05
HPS_PsiScore_HEK_cells

value: immortalized human embryonic kidney cells


title: HEK293T FUSKO 1

description:
PsiScore.Sample_DRA04
HPS_PsiScore_HEK_cells


title: HEK293T FUSKO 3

description:
PsiScore.Sample_DRA06
HPS_PsiScore_HEK_cells


title: PFC, male, water, input 1


title: PFC, male, water, H3K9me3, 2


title: HEK293T WT 3

description:
PsiScore.Sample_DRA03
HPS_PsiScore_HEK_cells


title: SH-SY5Y WT DIFF 2

description:
PsiScore.Sample_DRA14
HPS_PsiScore_SH_SY5Y_Diff_FUS_WT_FUSKO
HPS_PsiScore_SH_SY5Y_DIFF_FUS_WT_R495X


title: HEK293T WT 2

description:
PsiScore.Sample_DRA02
HPS_PsiScore_HEK_cells


title: SH-SY5Y FUSKO DIFF 1

description:
PsiScore.Sample_DRA16
HPS_PsiScore_SH_SY5Y_Diff_FUS_WT_FUSKO


title: Bromocriptine treatment , AT10

city: Münster

first: Eberhard

last: Korsching

state: NRW

address: Niels-Stensen-Str. 14

department: Inst. of Bioinformatics

country: Germany

institute: University of Muenster

data_processing:
Data pruning also according to Hagemann-Jensen M, et al. doi: 10.1038/s41596-018-0049-y
Alignment with STAR aligner version 2.7.1a up to 2.7.10a using default values but transcriptome coordinates (for Salmon) according to protocol Dobin, A. and Gingeras, T.R. 2015 - section 7. Mapping RNA-seq reads with STAR. Curr. Protoc. Bioinform.51:11.14.1-11.14.19. doi: 10.1002/0471250953.bi1114s51.
Quantification with Salmon version 1.6-1.7 according to the manual and program defaults.
Further data handling, differential expression analysis [DESeq2], permutation controls, result visualization etc. with mathematical platform R version 3.6.1 to 4.0.5.
Assembly: Current builds of the Human genome reference GRCh38 / hg38 from EBI in England, mirBase release 22.1, GtRNA database version 18.1.
Supplementary files format and content: Tab separated table format, columns: samples/result parameters/annotation, rows expression features (microRNAs, genes, tRNAs, etc.)

source_name: Endometrium

extract_protocol:
RNeasy total RNA Kit (Qiagen, Hilden, Germany)
Hagemann-Jensen et al. Small-seq for single-cell small-RNA sequencing. Nature Protocols.2018;13(10):2407-24.
Small RNA sequencing, single end reads

value: Endometrium

tag: age

tag: bmi

tag: menstrual phase

value: Proliferative phase

value: 5mg of Bromocriptine daily


title: Bromocriptine treatment , AT09


title: Bromocriptine treatment , AT07

value: missing


title: Bromocriptine treatment , AT04


title: HEK293T WT 1

description:
PsiScore.Sample_DRA01
HPS_PsiScore_HEK_cells


title: Bromocriptine treatment , AT02


title: Baseline (before treatment) , AB09

value: No treatment


title: Baseline (before treatment) , AB10


title: Bromocriptine treatment , AT01


title: Baseline (before treatment) , AB04


title: Baseline (before treatment) , AB02


title: Baseline (before treatment) , AB07


title: NPM-1C

type: RNA

city: Tokyo

first: Masayuki

last: Komatsu

address: 5-1-1, Tsukiji, Chuo-ku

institute: National Cancer Center Research Institute

description: Parental line

hyb_protocol: Following fragmentation, 10µg of cRNA were hybridized for 16 hr at 45ﾟC on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 7G.

data_processing: The data were analyzed with GeneSpring version 14.9 using affymetrix expression analysis settings (Summarization algorithm: MAS5).

label: biotin

source_name: Mesothelioma cell line

label_protocol: Biotinylated cRNA were prepared from 100 ng total RNA by GeneChip 3' IVT Express Kit. The procedure was according to the standard Affymetrix protocol.

growth_protocol: Cells were maintained in 10% FBS-containing Ham's F12 medium under an atmosphere of 5% CO2 and 95% air at 37˚C.

extract_protocol: Cultured cells were washed by D-PBS and lysed by ISOGEN solution. Extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: No specific treatment.


title: NGBC-1C

description: Parental line

source_name: Gallbladder cancer cell line


title: HSC-2

description: Parental line

source_name: Head and neck cancer cell line


title: NBC-1C

description: Parental line

source_name: Breast cancer cell line


title: NKC-1C

description: Parental line

source_name: Kindey cancer cell line


title: SiHa

description: Parental line

source_name: Cervical cancer cell line

value: SiHa


title: SKG-II

description: Parental line

value: SKG-II


title: Baseline (before treatment) , AB01


title: SKG-I

description: Parental line

value: SKG-I


title: HCS-2

description: Parental line


title: BOKU

description: Parental line

value: BOKU


title: ST3C

city: New York

first: Osama

last: Al Dalahmah

state: NY

address: 622 West 168th Street

department: Pathology & Cell Biology

institute: Columbia University Irving Medical Center

description:
Spatial Transcriptomic
10X Genomics

data_processing:
library strategy: Spatial Transcriptomics (ST)
ST samples was processed with 10X genomics software Cell Ranger and Space Ranger
.Raw tiff images of the tissue were labeled with Cell Ranger which generated a json file for Space Ranger to use during alignment. Labeled spots from Cell Ranger were inputted into the loupe-alignment argument in Space Ranger along with its respective tiff image file, FASTQ reads, and slide numbers.
The reference genome used for alignment was built using the Space Ranger function spaceranger mkgtf with GRCh38 as the assembly and Ensemble 91 for the transcript annotations.
All other parameters to generating the counts data for ST were set to its default setting. After the alignment was complete, counts data were pre-processed using Seurat's SCTransform (version 4.06) function to account for technical variates while retaining biological variance in the tissues.
Assembly: GRCh38 Ensemble 91
Supplementary files format and content: .txt files of count matrix

source_name: GBM Tissue

extract_protocol:
Used 10X Visium Spatial Gene Expression Slide & Reagent kit and the CG000239_RevD protocol for extraction
Spatial Transcriptomics (ST) library was prepared using the protocols described in Visium Spatial Tissue Optimization Slide & Reagent Kit along with manufacturer's protocol CG000238_RevD

treatment_protocol: 10 micron-thick tissue were prepared and mounted on ST slides which were stained with antigens like DAPI (for nucleus identification) to image the samples according to 10X genomics CG000312-RevB protocol

value: GBM Tissue

tag: disease state

value: Primary


title: Ca Ski

description: Parental line

value: Ca Ski


title: A431

description: Parental line


title: SKG-IIIa

description: Parental line

value: SKG-IIIa


title: NLS-1C

description: Parental line

source_name: Sarcoma cell line


title: SKN-3

description: Parental line


title: ST2C

description:
Spatial Transcriptomic
10X Genomics

tag: tissue

value: female

value: Recurrent


title: SW576

description: Parental line


title: ST1D

description:
Spatial Transcriptomic
10X Genomics


title: ST2A

description:
Spatial Transcriptomic
10X Genomics


title: ST3B

description:
Spatial Transcriptomic
10X Genomics


title: ST3D

description:
Spatial Transcriptomic
10X Genomics

value: male


title: TOV-241G

description: Parental line

source_name: Ovarian cancer cell line


title: ST1C

description:
Spatial Transcriptomic
10X Genomics


title: ST1B

description:
Spatial Transcriptomic
10X Genomics


title: RMG-I

description: Parental line

value: RMG-I


title: RMUG-S

description: Parental line

value: RMUG-S


title: OVISE

description: Parental line

value: OVISE


title: NOVC-6C

description: Parental line


title: NOVC-8C

description: Parental line


title: Ngn3, scRNA

city: Boston

first: Judith

last: Kaye

state: Massachusetts

address: 240 Longwood Ave, LHRRB 6th floor

department: Cell Biology

institute: Harvard University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Sequence reads were aligned to the mm39 mouse transcriptome reference, and feature barcode matrices were generated using 10x Genomics CellRanger.
Assembly: mm39
Supplementary files format and content: HDF5 Feature-Barcode Matrix from CellRanger

source_name: gut

extract_protocol:
Intestinal tissue was obtained from Neurog3-Cre; lsl-tdTomato mice (1 adult male), or Neurod1-Cre; lsl-tdTomato (3 adult females), cut longitudinally, washed (cold phosphate-buffered saline or PBS), cut into small ~5 mm pieces, and incubated (gentle agitation, 20 minutes, 4C) in EDTA solution (20 mM EDTA-PBS, Ca/Mg-free) in LoBind Protein tubes (Eppendorf 0030122216). The specimen was shaken, the tissue allowed to settle, and the supernatants collected. The residual tissue was again incubated similarly with EDTA solution, and supernatants were combined, and centrifuged (300 g, 5 minutes, 4C) Pellets were washed (2x, PBS (Ca/Mg-free) supplemented with 5% Fetal Bovine Serum (FBS), 4C) and incubated (37C, 2 minutes) in protease solution (TrypLE express, Thermo Fisher 12604013) supplemented with DNase (100 U/ml, Worthington Biochemical LK003172). The suspension containing dissociated cells was centrifuged (300 g, 5 minutes), washed (2x, PBS (Ca/Mg-free) containing 5% FBS, 4C) The resulting pellet was resuspended in FACS buffer (5% FBS in DMEM/F12, HEPES, no phenol red) containing DNase (100 U/ml), TO-PRO-3 (Thermo Fisher T3605, 1:10,000) to label dead cells, and Calcein Violet (Thermo Fisher 65-0854-39, 1:10,000) to label living cells. Cells were filtered (1 x 70-um, 1 x 40-um) and tdTomato+, Calcein Violet+, TO-PRO-3- cells were collected by fluorescence activated cell sorting using a FACS Aria (BD Biosciences).
Collected cells were loaded into the 10x Genomics Chromium Controller, and cDNA prepared and amplified according to manufacturer’s protocol (10x Genomics, Chromium single cell 3’ reagent kit v3, 12 cycles per amplification step).

value: gut


title: NeuroD1, scRNA

description: 10x Genomics


title: C57BL/6J, postive_2, Day7

city: Shenzhen

first: Dong

last: Zhang

state: GuangDong

address: No. 1, Fuhua Road, Futian street, Futian District, Shenzhen

department: Digestive Department

institute: The Fourth Clinical Medical College of Guangzhou University of Traditional Chinese Medicine

data_processing:
The transcriptome sequencing and analysis were conducted by OE biotech Co., Ltd.(Shanghai, China).
Raw data (raw reads) were processed using Trimmomatic.
The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference genome using hisat2.
Assembly: hisat2
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: colonic mucosa

growth_protocol: The mice were raised in SPF environment, eating and drinking freely, with temperature of 20~25 ℃, relative humidity of 40%~60%, 12h light/12h darkness.

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego,CA, USA) according to the manufacturer’ s instructions.

treatment_protocol: The control group and model group were treated with normal saline enema, the treatment group with Kuiyangling 10 g/kg enema, and the mesalazine group with 50 mg/kg enema. The volume of enema in each group was 0.2ml.

value: colonic mucosa

value: WT

value: mesalazine enema


title: OVSAHO

description: Parental line

value: OVSAHO


title: C57BL/6J, treat_1, Day7

value: Kuiyangling enema


title: C57BL/6J, treat_2, Day7


title: C57BL/6J, postive_1, Day7


title: C57BL/6J, modell_2, Day7

value: normal saline enema


title: C57BL/6J, model_1, Day7


title: NOVC-3C

description: Parental line


title: NOVC-7C

description: Parental line


title: NOVC-5C

description: Parental line


title: NOVC-1C

description: Parental line


title: JHOM-1

description: Parental line


title: NOVC-4C

description: Parental line


title: MCAS

description: Parental line

value: MCAS


title: C57BL/6J, con_2, Day7


title: ST1A

description:
Spatial Transcriptomic
10X Genomics

value: GBM Tissue

value: Primary


title: ES-2

description: Parental line


title: C57BL/6J, con_1, Day7

source_name: colonic mucosa  colonic mucosa

value: colonic mucosa  colonic mucosa


title: JHOS2

description: Parental line


title: NOVC-2C

description: Parental line


title: CnT K36M iPSC K27me3 replicate 2

first: Michael

last: Hoetker

address: Simches Building, Mail code CPZN 4200

department: Department of Molecular Biology

institute: Massachusetts General Hospital

data_processing:
Sequencing reads were mapped to mm9 reference genome using bwa aligner. Peak calling was performed using Homer94. Heatmaps and average profiles of CUT&Tag read densities were generated using deepTools95. Bedtools was used to calculate read densities over given regions. Gene ontology analysis was performed with ClusterProfiler after annotation using ChipSeeker.
Assembly: mm9
Supplementary files format and content: read coverage (bigwig)
Library strategy: CUT&Tag

source_name: iPSC

growth_protocol: Samples underwent reprogramming for four days in AGi conditions. DMOG samples were also treated with DMOG for these four days. iPSC samples are from passaged iPSCs (S/L on feeders, off dox).

extract_protocol:
CUT&Tag was performed as previously described (Kaya-Okur, Janssens, Henikoff, Ahmad, & Henikoff, 2020). In brief, 100,000 bead-bound cells per sample were permeabilized and incubated with primary antibodies targeting the desired epitopes (anti-H3K4me3 (active motif 39060), anti-H3K27ac (Millipore Sigma MABE647), H3K27me3 (Cell Signaling 9733), anti-H3.3K36M (Revmab 31-1085-00-S), Sox2 (Cell Signaling 23064)). After incubation with secondary antibody (Guinea Pig anti-Rabbit IgG, antibodies online ABIN101961) to amplify local abundance of immunoglobulins, protein A/G-tethered transposase (pAG-Tn5, Epicypher) was added and bound in situ at target loci. E. coli DNA spike-in was added for normalization purposes.
After tagmentation and DNA clean-up, libraries were prepared by PCR amplification with barcoded Illumina-compatible primers. Tapestation 2200 analysis using High Sensitivity D1000 ScreenTape (Agilent) was performed to confirm successful library preparation before sequencing.

value: iPSC

value: anti-H3K27me3 (Cell Signaling 9733)


title: CnT K36M iPSC K4me3 replicate 2

value: anti-H3K4me3 (active motif 39060)


title: CnT K36M iPSC K4me3 replicate 1


title: A2780

description: Parental line


title: CnT K36M iPSC K27me3 replicate 1


title: CnT K36M iPSC K36me3 replicate 2

value: anti-K36me3 (Thermo Fisher MA5-24687)


title: CnT K36M iPSC K36me2 replicate 2

value: anti-K36me2 (Active motif 39256)


title: CnT K36M iPSC K36me2 replicate 1


title: CnT WT iPSC K4me3 replicate 2


title: Panc-1

description: Parental line

source_name: Pancreatic cancer cell line


title: PSN-1

description: Parental line


title: CnT WT iPSC K4me3 replicate 1


title: CnT WT iPSC K27me3 replicate 2


title: PK-9

description: Parental line


title: CnT WT iPSC K27me3 replicate 1


title: PK-45P

description: Parental line


title: NPC-8C

description: Parental line


title: NPC-42C

description: Parental line


title: CnT WT iPSC K36me2 replicate 2


title: NPC-7C

description: Parental line


title: 2008

description: Parental line


title: PK-59

description: Parental line


title: NPC-5C

description: Parental line


title: PK-1

description: Parental line


title: NPC-4C

description: Parental line


title: NPC-6C

description: Parental line


title: CnT WT iPSC K36me2 replicate 1


title: CnT WT iPSC K36me3 replicate 2


title: CnT WT iPSC K36me3 replicate 1


title: CnT K36M iPSC K36me3 replicate 1


title: CnT K36M+DMOG Sox2 run 2 replicate 2

source_name: reprogramming intermediate

value: reprogramming intermediate

value: anti-Sox2 (Cell Signaling 23064)


title: CnT K36M+DMOG Sox2 run 2 replicate 1


title: CnT K36M Sox2 run 2 replicate 2


title: CnT K36M Sox2 run 2 replicate 1


title: CnT WT Sox2 run 2 replicate 2


title: NPC-41C

description: Parental line


title: CnT WT Sox2 run 2 replicate 1


title: NPC-39C

description: Parental line


title: NPC-3C

description: Parental line


title: NPC-35C

description: Parental line


title: NPC-9C

description: Parental line


title: NPC-34C

description: Parental line


title: NPC-36C-w

description: Parental line


title: NPC-38C

description: Parental line


title: SingleMicroglialCells, NCvsHFD, rep13

city: Grand Rapids

first: Luca

last: Fagnocchi

state: MI

address: 333 Bostwick AVE NE

institute: VAI

description:
CEL-Seq2
total_cells_metadata.csv
total_filtered_raw_counts.csv

data_processing:
The scRNA-seq libraries were analyzed using snakePipes
Quality of the reads was evaluated with FastQC
Mapping to the mm10 mouse genome was performed by the STAR aligner
Read counts on features were quantified by featureCounts
Mapped and counted read were next analyzed with RaceID3, with default parameters [46]. Batch correction by plate, and preprocessing of data were completed within the RaceID3 pipeline.
Assembly: mm10
Supplementary files format and content: total_cells_metadata.csv; tab-delimited file with information on cell IDs, barcoding, mouse replicate and diet treatment, for each single cell profiled
Supplementary files format and content: total_filtered_raw_counts.csv; tab-delimited file with raw count of only the single cells used in the final figures of the paper, after subsetting data on 3-days HFD treatment and a cut-off of transcript count per cell >1000
Supplementary files format and content: plate_n_raw_counts.csv; 13 tab-delimited files matrices of raw count for each plate submitted, with cell IDs and genes identifiers

source_name: brain

growth_protocol: All mice were housed in a temperature-controlled environment (23°C) with a 12-h light and 12-h dark (07.00–19.00) photoperiod. Animals were provided standard chow diet (Research Diets #5021; 23,6% calories from fat; Mouse Breeder Diet #6539) or HFD (60% fat; Research diet, Rodent Chow #D12492) and water ad libitum unless otherwise stated.

extract_protocol:
Mice were anesthetized and blood was collected by ventricular puncture. Mice were then perfused with phosphate-buffered saline (PBS). For microglia isolation, the hypothalamus, cerebellum, hippocampus, and cortex were dissected from the brain and manually dissociated in HBSS buffer. A cell suspension was prepared with a continuous 37% Percoll gradient at 2300 rpm for 30 min without brake, then cells were washed with 1x PBS and resuspended in FACS buffer and non-specific binding to Fc receptors was blocked by incubation with anti-CD16/32 antibody (BD Pharmingen, Cat# 553141) and the FACS antibodies BV711 conjugated anti-CD11b and Pacific blue conjugated anti-CD45 antibodies (Cat# 101241, Cat# 103126, BioLegend).
The CEL-Seq2 method was used for single cell sequencing
pair-end multiplexing run, with 50-75 bp read length

treatment_protocol: Animal were fed HFD (60% fat; Research diet, Rodent Chow #D12492) for 3 days

value: brain

value: microglial cells from brain tissue

value: NCvsHFD


title: SingleMicroglialCells, NCvsHFD, rep12


title: NPC-37C

description: Parental line


title: NPC-40C-w

description: Parental line


title: SingleMicroglialCells, NCvsHFD, rep11


title: SingleMicroglialCells, NCvsHFD, rep10


title: NPC-31C

description: Parental line


title: NPC-32C

description: Parental line


title: SingleMicroglialCells, NCvsHFD, rep9


title: NPC-23C

description: Parental line


title: NPC-30C

description: Parental line


title: NPC-33C

description: Parental line


title: NPC-2C-1

description: Parental line


title: NPC-27C

description: Parental line


title: NPC-29C

description: Parental line


title: NPC-26C

description: Parental line


title: NPC-22C

description: Parental line


title: SingleMicroglialCells, NCvsHFD, rep8


title: NPC-24C

description: Parental line


title: NPC-25C

description: Parental line


title: NPC-28C

description: Parental line


title: NPC-20C

description: Parental line


title: NPC-21C

description: Parental line


title: NPC-1C

description: Parental line


title: SingleMicroglialCells, NCvsHFD, rep7


title: SingleMicroglialCells, NCvsHFD, rep6


title: SingleMicroglialCells, NCvsHFD, rep5


title: SingleMicroglialCells, NCvsHFD, rep4


title: SingleMicroglialCells, NCvsHFD, rep2


title: IgG_rep2

city: Beijing

first: Hailian

last: Zhao

state: Beijing

address: 15 Datun Road

institute: Institute of Biophysics, Chinese Academy of Sciences

description: replicates were merged for processing

data_processing:
Illumina bcl2fastq-1.8.4 conversion software used for basecalling.
After sequencing of LACE-seq libraries, the adapter sequences at the 3' end were removed using Cutadapt v1.15 with the parameter: -a ATCTCGTATGCCGTCTTCTGCTT
After filtering, the LACE-seq reads were aligned to mouse pre-rRNA by bowtie with default parameters.
The unmapped reads to mouse pre-rRNA were then aligned to the mm9 reference genome.
Assembly: mm9
Supplementary files format and content: LACE-seq reads coverage in bigwig format

source_name: oocyte

extract_protocol:
Cells were lysed on ice using 50 μl wash buffer for 10 min.
The preparation of protein A/G beads observed the instructions of the manufacturer, and their coupling with either anti-eIF4E or -eIF4E1B antibody took place. The lysate of oocytes was pre-treated with RQ1 DNase and incubated with antibody-coated beads. After extensive wash steps, the immunoprecipitated RNAs were fragmented, and experienced 3’-dephosphorylation and linker ligation, followed by reverse transcription on-beads. Then, first-strand cDNAs were derived from protein A/G beads and further captured by streptavidin C1 beads for pre-PCR and poly(A)-tailing to produce dsDNA as the template for IVT. IVT products were purified by the removal of DNA template using Turbo DNase and further purified by Agencourt RNA Clean beads based on the instructions of the manufacturer. Then, linear amplified RNA was transformed into cDNA and amplified by PCR with P7 and barcoded P5 index primers. Final PCR products with a size of 130-300 bp were excised from a 2% agarose gel and purified by use of Qiagen gel purification kit as per the instructions of the manufacturer. Illumina HiSeq 2500 at BerryGenomics was used for the single-end sequencing of all LACE-seq libraries.

treatment_protocol: 0.1% PFA was used for the 10-min crosslink of 100 mouse oocytes at room temperature for 10 min, followed by their quenching via 150 mM glycine

value: oocyte

tag: developmental stage

value: GV

tag: antibody

value: anti-IgG(Abclonal, AC005)

tag: protocol

value: LACE-seq


title: SingleMicroglialCells, NCvsHFD, rep1

tag: cell type


title: NPC-19C

description: Parental line


title: IgG_rep1

description: replicates were merged for processing


title: NPC-15C

description: Parental line


title: NPC-16C

description: Parental line


title: NPC-18C-1

description: Parental line


title: SingleMicroglialCells, NCvsHFD, rep3

tag: treatment


title: eIF4E_rep1

description: replicates were merged for processing

value: anti-eIF4E(Medical & Biological Laboratories, RN001P)


title: eIF4E1B_rep2

description: replicates were merged for processing

value: anti-eIF4E1B(Shanghai Youke Biotechnology, custom antibody specific to 1-244aa of eIF4E1B)


title: Dermal Fibroblasts - ATAC

city: Rochester

first: Alexandre

last: Gaspar-Maia

state: MN

address: 200 First street SW

institute: Mayo Clinic

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using TrimGalore v0.6.4 (Cutadapt v3.1)
Reads were then aligned to hg19 (mm9 for DF) whole genome using bowtie2 v2.3.3.1, alignment files were sorted and indexed using samtools v1.9, duplicate removal done using Picard v2.9.0
deepTools bamCoverage v3.5.0 was used to convert bam to bigWig
macs2 v2.2.7.1 was used to call peaks (to convert bam to bed)
Genome_build: hg19 (mm9 for DF)
Supplementary_files_format_and_content: bigWig (as produced by deepTools bamCoverage)
Supplementary_files_format_and_content: bed (as produced by macs2)

source_name: Dermal Fibroblasts

growth_protocol: Normal Human Melanocytes (NHM) were cultures in Dermal Cell Basal Medium (ATCC) with the addition of 5 µg/mL Insulin, 50 µg/mL Ascorbic Acid, 6 mM L-Glutamine, 1.0 µM Epinephrine, 1.5 mM Calcium Chloride, Peptide Growth Factor and M8 Supplement. MCF-7, DFs and MDA-MB-231L cells were grown in DMEM (Gibco) with 4.5 g/L D-glucose, 110 mg/L sodium pyruvate, 10% FBS and 1% Penicillin/Streptomycin (Hyclone). HMEC cells were grown in complete Mammary Epithelial Cell Growth Media.

extract_protocol:
DNA for ATAC-seq  was prepared from 20,000 cells following the OMNI-ATAC procedures from Corces et al. (Nature Methods 2017) and Buenrostro et al. (Curr Protoc Mol Biol 2016), with modifications, using the Nextera kit (Illumina).  The cells were lysed for 3 minutes on ice and transposed for 30 minutes at 37C.  DNA was cleaned-up using procedures of a DNA extraction column.
The DNA libraries were prepared with 5-9 cycles of PCR amplification with the NEB High Fidelity Master Mix (New England Biolabs).  Clean up was done using the Zymo DNA Clean and Concentrator kit (Zymo Research) and followed with AMPure XP (Beckman Coulter) bead cleanup to remove primer dimers and under-digested chromatin.

treatment_protocol: MCF7 cells were treated with estradiol (E2) treatment MCF-7 cells were grown for 5 days in modified DMEM without phenol-red (Hyclone) with 4.5 g/L D-glucose, 4.0 L-glutamine, 10% charcoal-dextran–stripped FBS, 1% Penicillin/Streptomycin and 1nM of 17-β-estradiol or EtOH.

value: Dermal Fibroblasts


title: NPC-17C

description: Parental line


title: NPC-14C

description: Parental line


title: eIF4E_rep2

description: replicates were merged for processing


title: 204958100087_R04C01

type: genomic

city: Berlin

first: David

last: Kaul

address: Augustenburger Platz 1

department: Department of Radiation Oncology

institute: Charité - Universitätsmedizin Berlin

hyb_protocol: After bisulfite conversion using the Zymo EZ Methylation Kit (Zymo Research Irvine, USA), the Infinium HD FFPE DNA Restore Kit was used for DNA restoration. DNA was amplified, fragmented and hybridised to Illumina Infinium Methylation450k BeadChip and Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina iScan system with default settings

data_processing:
The calculations were carried out in R, version 4.2.0 "Virgorous Calesthenics"
Average beta-Values after normalization using detection p values

label: cy3, cy5

source_name: Tumor

label_protocol: Standard Illumina protocol

extract_protocol: DNA was extracted form FFPE tumor samples using the Maxwell RSC FFPE Plus DNA Purification Kit (Promega, USA) , according to the manufacturer’s instructions

value: Female

tag: incoming diagnosis

value: Anaplastic ependymoma (WHO grade III)

tag: tumor location

value: infratentorial

tag: progression-free survival (months)

tag: progression (0=no, 1=yes)

tag: overall survival (months)

tag: death (0=no, 1=yes)

tag: material type

value: FFPE


title: 205537620156_R06C01

tag: Sex

tag: age

value: supratentorial


title: 204958100081_R03C01

value: Ependymoma (WHO grade II)


title: NPC-13C

description: Parental line

tag: cell line


title: MIAPaca-2

description: Parental line


title: NPC-10C-1

description: Parental line


title: CnT K36M Sox2 replicate 1

growth_protocol: Samples underwent reprogramming for four days in AGi conditions.

value: reprogramming intermediate

tag: genotype


title: KP4

description: Parental line


title: eIF4E1B_rep1

description: replicates were merged for processing


title: CnT K36M K4me3 replicate 2


title: KLM-1

description: Parental line


title: 204958100081_R07C01

value: Male


title: HPAF-II

description: Parental line

value: HPAF-II


title: 204958100081_R04C01


title: HPAC

description: Parental line

value: HPAC


title: CnT K36M K4me3 replicate 1


title: H5766T

description: Parental line


title: Capan2

description: Parental line


title: 205537620156_R08C01


title: CnT K36M K36me3 replicate 2


title: 204958100081_R06C01


title: CnT K36M K36me3 replicate 1


title: CnT K36M K36me2 replicate 2


title: CnT K36M Sox2 replicate 2


title: BxPC-3

description: Parental line


title: CnT K36M K36me2 replicate 1


title: CnT K36M K27ac replicate 2


title: CnT K36M K27ac replicate 1


title: TE9

description: Parental line

source_name: Esophageal cancer cell line


title: TE8

description: Parental line


title: CnT WT Sox2 replicate 1

value: WT


title: AsPC-1

description: Parental line


title: CnT WT Sox2 replicate 2


title: 205049770023_R01C01


title: CnT WT K4me3 replicate 1


title: CnT K36M K27me3 replicate 1


title: CnT WT K36me3 replicate 2


title: CnT WT K36me3 replicate 1


title: TE6

description: Parental line


title: CnT WT K36me2 replicate 2


title: TE15

description: Parental line


title: CnT K36M K27me3 replicate 2


title: TE14

description: Parental line


title: TE3

description: Parental line


title: TE10

description: Parental line


title: CnT WT K27me3 replicate 2


title: CnT WT K27me3 replicate 1


title: CnT WT K36me2 replicate 1


title: OE-21

description: Parental line


title: KYSE-960

description: Parental line


title: CnT WT K4me3 replicate 2


title: KYSE-850

description: Parental line


title: NEC-1C-1

description: Parental line


title: KYSE-790

description: Parental line


title: TE5

description: Parental line


title: T.T

description: Parental line


title: ATAC K36M iPSC replicate 2

data_processing:
Sequencing reads were mapped to mm9 reference genome using bwa aligner. Peak calling was performed using Homer. Heatmaps and average profiles of CUT&Tag read densities were generated using deepTools. Bedtools was used to calculate read densities over given regions. Gene ontology analysis was performed with ClusterProfiler after annotation using ChipSeeker R package.
Assembly: mm9
Supplementary files format and content: read coverage (bigwig)

growth_protocol: MEFs were cultured in DMEM 10%FBS, reprogramming was performed in AGi medium, iPSCs were passaged in S/L.

extract_protocol:
ATAC was performed as previously described (Buenrostro, Giresi, Zaba, Chang, & Greenleaf, 2013). In short, nuclei of 60,000 cells per sample were extracted and centrifuged before resuspension in transposition buffer with Tn5 transposase. DNA was isolated using a MinElute kit (Qiagen).
Libraries were amplified by PCR for 13 cycles using barcoded, Illumina-compatible primers. After amplification, DNA was size-selected for fragments between 100bp and 1000bp using AMPure XP beads (Beckman Coulter Life Sciences). Before sequencing, libraries for RNA- and ATAC-seq underwent analysis on Tapestation 2200 with High Sensitivity D1000 ScreenTape (Agilent).

value: iPSC


title: ATAC K36M iPSC replicate 1


title: T.Tn

description: Parental line


title: ATAC K36M d4 replicate 2


title: ATAC K36M d0 replicate 2

source_name: MEF

value: MEF


title: 204339300091_R02C01


title: CnT WT K27ac replicate 2


title: KYSE-70

description: Parental line


title: CnT WT K27ac replicate 1


title: ATAC WT iPSC replicate 2


title: ATAC WT d4 replicate 2


title: KYSE-590

description: Parental line


title: ATAC WT iPSC replicate 1


title: KYSE-410

description: Parental line


title: KYSE-510

description: Parental line


title: KYSE-520

description: Parental line


title: ATAC K36M d0 replicate 1


title: KYSE-770

description: Parental line


title: KYSE-50

description: Parental line


title: KYSE-3940

description: Parental line


title: KYSE-450

description: Parental line


title: Xyn6h_ii Stationaryl growth

city: Amsterdam

first: Biwen

last: Wang

address: Work, Science Park 904,1098 XH,Amsterdam,The Netherlands

department: Swammerdam Institute for Life Science

country: Netherlands

institute: University of Amsterdam

description: mRNA-enriched

data_processing:
Raw data were analyzed on the web-based platform Galaxy
Trimmomatic was applied to remove adaptors and filter bad reads
Bowtie2 was used to aligned trimed reads to reference genome fasta (NC_000964.3)
featureCounts was used to count reads for the gene features base on annotation GFF3 file (NC_000964.3) and using "locus_tag" as the GFF gene identifier
DEseq2 was used to normalized the count reads and compare the differences in the transcriptome between XynA overproducing (Xyn) and non-producing (Emp) samples
Assembly: NC_000964.3
Supplementary files format and content: featureCounts tabular files include raw counts for each gene/RNA features for each sample
Supplementary files format and content: Normalized_counts tabular file includes normalized counts for each gene/RNA features for all samples
Supplementary files format and content: DESeq2 tabular files include matrix table with Gene Identifiers, Gene name, mean normalised counts, the logarithm (to basis 2) of fold change, standard error estimate for the log2 fold change estimate, Wald statistic, p value for the statistical significance of this change and p value adjusted for multiple testing with the Benjamini-Hochberg procedure which controls false discovery rate (FDR) for each gene/RNA features between samples.

organism: Bacillus subtilis

source_name: Bacteria

growth_protocol: Cells were cultured at 37 °C in 10 ml LB medium with 50 μg/ml kanamycin in 125 ml flasks and sampled at 3 h (OD600~0.8) and 6 h growth (OD600 ~4).

extract_protocol:
Cell disruption was achieved by bead beating (Precellys 24). After centrifugation, the rough RNA in the upper aqueous phase was ethanol-precipitated, washed twice with 70% ethanol, dried and dissolved in water. DNA was removed by DNAseI (NEB) treatment; the pure total RNA was then extracted by a second-round of P/C/I extraction, following by ethonal-precipitation and 70% ethanol washing, and finally dissolved in water. The total RNA was subjected to MICROBExpress™ Bacterial mRNA Enrichment Kit (Thermo Fisher) to remove >95% of the 16S and 23S rRNA from total RNA.
Libraries were constructed using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs) and NEBNext® Multiplex Oligos for Illumina® (New England Biolabs), according to the manufacturer's protocol.

treatment_protocol: 2 mL cells were collected by centrifugation at 4°C, 20,000xrcf for 1 min. Cell pellets were resuspended in 0.4 ml ice-cold growth medium and added to a screw cap tube containing 1.5g glass beads(0.1 mm), 0.4 ml Phenol/ Chloroform / isoamyl alcohol mixture [P/C/I, 25:24:1, ROTH] and 50 ul 10% SDS, votex to mix, flash freeze in liquid nitrogen.

tag: growth phase

value: Stationaryl growth

tag: strain


title: ATAC K36M d4 replicate 1


title: ATAC WT d4 replicate 1


title: ATAC WT d0 replicate 2


title: Xyn6h_i Stationaryl growth

description: mRNA-enriched


title: ATAC WT d0 replicate 1


title: Emp6h_i Stationaryl growth

description: mRNA-enriched


title: 204086170045_R01C01


title: Xyn3h_ii Exponential growth

description: mRNA-enriched

value: Exponential growth


title: Emp3h_ii Exponential growth

description: mRNA-enriched


title: Emp3h_i Exponential growth

description: mRNA-enriched


title: Xyn3h_i Exponential growth

description: mRNA-enriched


title: KYSE-2880

description: Parental line


title: KYSE-350

description: Parental line


title: KYSE-2400

description: Parental line


title: KYSE-3410

description: Parental line


title: RNA K36M d8 replicate 2

data_processing:
RNA-seq reads were mapped by STAR v.2.5.0 aligner to mm9 reference genome using ENSEMBL annotation. Read counts for individual genes were produced using the unstranded count feature in HTSeq version 0.11.2. Differential expression analysis was performed using the edgeR package after normalizing read counts and including only those genes with count per million reads (CPM) > 1 for one or more samples. Differentially expressed genes were defined based on the criteria of >2-fold change in expression value.
Assembly: mm9
Supplementary files format and content: htseq raw count

growth_protocol: MEFs were cultured in DMEM 10%FBS, reprogramming was performed in AGi medium, iPSCs were passaged in S/L. For Repsox/TGFb samples, Repsox (Sigma) was added at a concentration of 250 nM, recombinant TGFb-1 (Peprotech) at 2.5 ng/ml.

extract_protocol:
RNA for RNA-seq was extracted using a Qiagen miRNeasy kit.
RNA-seq libraries were constructed using polyA selection followed by NEBNext UltraDirectional kit protocol (New England Biolabs) and sequenced on the Illumina HiSeq2500 instrument, resulting in approximately 30 million reads per sample on average. ATAC-seq libraries were constructed as previously described (Buenrostro 2013) and sequenced in paired-end 50 bp mode on the Illumina HiSeq2500 instrument, resulting in approximately 40 million reads per sample on average. CUT&Tag was performed as previously described (Kaya-Okur 2020), libraries were sequenced in paired-end 50 bp mode on the Illumina HiSeq2500 instrument, resulting in approximately 15 million reads per sample on average


title: RNA K36M iPSC replicate 1


title: RNA K36M d8 replicate 1


title: Emp6h_ii Stationaryl growth

description: mRNA-enriched


title: RNA K36M noOKSM replicate 2


title: RNA K36M noOKSM replicate 1


title: PND90-4

city: Ithaca

first: Jennifer

middle: K

last: Grenier

address: 526 Campus Rd

department: Biomedical Sciences

institute: Cornell University

description: PND90 Liter mates

data_processing:
Illumina pipeline software v1.8 was used for base calling.
cutadapt v1.8 (-m 50 -q 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTC --match-read-wildcards) was used to trim and filter reads.
tophat v2.1 (--library-type=fr-firststrand -G GCF_000247695.1_HetGla_female_1.0_genomic.gff) was used to map reads to the HetGla_female_1.0 reference.
Mapped reads were analyzed for transcript expression using cufflinks v2.2 (ref 3). A common transcriptome annotation file was generated with cuffmerge and used to generate FPKM values and statistical analysis of differential gene expression with cuffdiff.
Genome_build: HetGla_female_1.0 (GCF_000247695.1)
Supplementary_files_format_and_content: Tab delimited text files are standard cuffdiff2 output files for gene-level analysis, including counts, FPKM values, and q-values for differential expression testing (corrected for multiple hypothesis testing). The 'gene_exp.diff' file contains average FPKM values for each pair of replicates as well as results for statistical testing for differential expression. The 'genes.read_group_tracking' file contains raw mapped read counts and FPKM values for individual samples. Transcript annotation is in gtf format (merged.gtf).

organism: Heterocephalus glaber

source_name: ovary

growth_protocol: lab colony

extract_protocol:
Total RNA was isolated with Trizol, with an extra chloroform extraction to remove residual phenol and addition of glyco-blue as a carrier to promote RNA precipitation. RNA concentration was determined on a Nanodrop.
Ribosomal RNA was subtracted by hybridization from total RNA samples using the RiboZero Magnetic Gold H/M/R Kit (Illumina) using 100ng total RNA and a modified protocol scaled for lower input (90ul magnetic bead stock, and 2 ul removal solution in a 20ul reaction). The rRNA-depleted RNA samples were cleaned up by ethanol precipitation. TruSeq-barcoded RNAseq libraries were generated with the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs).

value: Postnatal day 90

value: wild type


title: PND90-3

description: PND90 Liter mates


title: KYSE-30

description: Parental line


title: KYSE-3210

description: Parental line


title: KYSE-3650

description: Parental line


title: 204086170050_R07C01


title: KYSE-2780

description: Parental line


title: PND90-2

description: PND90 Liter mates


title: KYSE-2710

description: Parental line


title: KYSE-270

description: Parental line


title: RNA K36M iPSC replicate 2


title: KYSE-2300

description: Parental line


title: RNA K36M d6 replicate 1


title: KYSE-220

description: Parental line


title: KYSE-2270

description: Parental line


title: PND28-17

description: PND28 Litter mates

value: Postnatal day 28


title: RNA K36M d6 replicate 2


title: KYSE-1860

description: Parental line


title: RNA K36M d4 replicate 1


title: PND28-12

description: PND28 Litter mates


title: PND8-10

description: PND8 Litter mates

value: Postnatal day 8


title: PND8-9

description: PND8 Litter mates


title: RNA K36M d4 replicate 2


title: RNA K36M d2 replicate 1


title: PND8-7

description: PND8 Litter mates


title: RNA K36M d2 replicate 2


title: RNA K36M d0 replicate 2


title: PND1-3

description: PND1 Litter mates

value: Postnatal day 1


title: RNA K36M d0 replicate 1


title: KYSE-190

description: Parental line


title: RNA WT noOKSM replicate 2


title: PND1-1

description: PND1 Litter mates


title: E56-3

description: E56 Litter mates

value: Embryonic day 56


title: E56-9

description: E56 Litter mates


title: RNA WT iPSC replicate 1


title: RNA WT noOKSM replicate 1


title: RNA WT d8 replicate 2


title: RNA WT d8 replicate 1


title: KYSE-140

description: Parental line


title: KYSE-170

description: Parental line


title: RNA WT d6 replicate 2


title: KYSE-1250

description: Parental line


title: KYSE-1440

description: Parental line


title: KYSE-150

description: Parental line


title: KYSE-1260

description: Parental line


title: B16/F10-shCtrl

city: Singapore

first: Ying

last: Li

state: --- Select a state ---

address: 14 Medical Dr, Singapore

country: Singapore

institute: Cancer Science Institute of Singapore

data_processing:
Reads were mapped to Mus musculus genome by STAR(2.4.0i) with default parameters for paired-end
Gene expression were called by featureCounts(v1.5.0-p1)
Assembly: GRCm38.p6
Supplementary files format and content: gene expression in matrix table

source_name: murine melanoma cell line

growth_protocol: The cells were grown in DMEM medium supplemented with 10% FBS and 1% penicillin-streptomycin.

extract_protocol:
standard protocol for BGISEQ-500 by BGI
Total RNAs were extracted using Rneasy Mini kit (Qiagen).

value: Control shRNA (Ctrl) was transfected into B16/F10 cells via lentivirus. Two weeks (at least) after viral transfection, total RNA was extracted for NGS seq.

tag: expression manipulation technique

value: shRNA


title: TA+/-, CD8+ T

city: Guangzhou

first: Jie

last: Long

address: No.106 Zhongshan 2nd Road

institute: Guangdong Provincial People's Hospital

description:
TA+/-CD8
liver_cd8_rpkm.txt

data_processing:
STAR-2.5.2b software was used to map reads to the reference genome.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for bulk RNA-seq Samples

source_name: murine liver tissue

extract_protocol:
Total RNA was extracted utilizing RNA iso Plus (TaKaRa, 9109) from liver tissues or 5×10^5 CD8+ T cells that were isolated using a FACS Aria II cell sorter
RNA libraries were prepared for sequencing using standard Illumina protocols or BGI protocols.

tag: tissue

value: murine liver tissue

value: 2-4 weeks

value: TG Aire+/-

value: CD8+ T cells

value: no treatment


title: TA-/-, CD8+ T

description:
TA-/-CD8
liver_cd8_rpkm.txt

value: TG Aire-/-

tag: cell type


title: A-/-, CD8+ T

description:
A-/-CD8
liver_cd8_rpkm.txt

value: Aire-/-

tag: treatment


title: KYSE-1230

description: Parental line


title: KYSE-1190

description: Parental line


title: KYSE-1240

description: Parental line


title: KYSE-180

description: Parental line


title: B16/F10-shXrn1

value: shXrn1#2 was transfected into B16/F10 cells via lentivirus. Two weeks (at least) after viral transfection, total RNA was extracted for NGS seq.


title: RNA WT d6 replicate 1

value: reprogramming intermediate

value: WT


title: RNA WT iPSC replicate 2

value: iPSC


title: EC-GI-10

description: Parental line

source_name: Gastroesophageal junction cell line


title: KYSE-1140

description: Parental line


title: RNA WT d4 replicate 1


title: RNA WT d4 replicate 2


title: sample27

city: Shenyang

first: Hongyan

last: Qi

state: Liaoning

address: No.120 Dongling Road, Shenhe District

department: College of Horticulture

institute: Shenyang Agricultural University

description: Hybridized to OncoScan® CNV FFPE Arrays

hyb_protocol: After amplification, the fragments are subjected to HaeⅢ endonuclease digestion and hybridized to OncoScan® CNV FFPE Arrays on Affymetrix Genechip® Hybridization Oven 645 (Thermo Fisher Scientific, Waltham, MA, USA) set at 49℃, 60rpm for 16-18h (overnight), then stained (Affymetrix Genechip® Fluidics Station 450Dx, Thermo Fisher Scientific, Waltham, MA, USA).

scan_protocol: scanned (Affymetrix Genechip® Scanner 3000 7G, Thermo Fisher Scientific, Waltham, MA, USA) following the manufacturer’s instructions

data_processing: Scanning results from both arrays (AT/GC) are combined and subjected to further analysis in Chromosome Analysis Suite (Thermo Fisher Scientific, Waltham, MA, USA).

label: Biotin

source_name: tissue sample

label_protocol: The DNA was incubated using a PCR amplifier (ABI GeneAmp® PCR system 9700, Thermo Fisher Scientific, Waltham, MA, USA) with biotin-labeled Molecular Inversion Probes (MIP) for 16h at 58℃.

growth_protocol: All samples were collected from Henan Cancer Hospital from Jan. 1st, 2014, to Jan. 30th, 2022.

extract_protocol: Tissue slices were then continually performed with QIAamp DNA FFPE Tissue Kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions, and DNA concentration and purity were quantified by a Qubit fluorescence analyzer (Thermo Fisher Scientific, Waltham, MA, USA), with a minimum concentration of 12 ng/μl.

value: ovarian cancer


title: NEGJC-1C

description: Parental line


title: sample26

description: Hybridized to OncoScan® CNV FFPE Arrays


title: RNA WT d2 replicate 2


title: NSCE-5

description: Parental line

source_name: Gastric cancer cell line


title: sample24

description: Hybridized to OncoScan® CNV FFPE Arrays


title: RNA WT d2 replicate 1


title: RNA WT d0 replicate 2

value: MEF


title: KYSE-1170

description: Parental line


title: RNA K36M d8 TGFb replicate 2

extract_protocol: RNA-seq libraries were prepared using rRNA depletion and sequenced on the Illumina HiSeq2500 instrument, resulting in approximately 30 million reads per sample on average. ATAC-seq libraries were constructed as previously described (Buenrostro 2013) and sequenced in paired-end 50 bp mode on the Illumina HiSeq2500 instrument, resulting in approximately 40 million reads per sample on average. CUT&Tag was performed as previously described (Kaya-Okur 2020), libraries were sequenced in paired-end 50 bp mode on the Illumina HiSeq2500 instrument, resulting in approximately 15 million reads per sample on average

treatment_protocol: RNA for RNA-seq was extracted using a Qiagen miRNeasy kit.

value: TGFb-1 2.5 ng/ml


title: sample22

description: Hybridized to OncoScan® CNV FFPE Arrays


title: NSCE-41

description: Parental line

extract_protocol: Cultured cells were washed by D-PBS and lysed by ISOGEN solution. Extraction of total RNA was performed according to the manufacturer's instructions.


title: 203866300017_R01C01

value: Male

tag: incoming diagnosis

value: Anaplastic ependymoma (WHO grade III)

value: supratentorial

value: FFPE


title: sample23

description: Hybridized to OncoScan® CNV FFPE Arrays


title: 203866300119_R08C01

value: Ependymoma (WHO grade II)

tag: tumor location


title: sample25

description: Hybridized to OncoScan® CNV FFPE Arrays


title: sample20

description: Hybridized to OncoScan® CNV FFPE Arrays


title: RNA K36M d8 TGFb replicate 1


title: RNA K36M d8 Repsox replicate 2

value: Repsox 250 nM


title: sample19

description: Hybridized to OncoScan® CNV FFPE Arrays


title: NSCE-18

description: Parental line


title: N87

description: Parental line


title: MKN74

description: Parental line


title: sample21

description: Hybridized to OncoScan® CNV FFPE Arrays


title: NSCE-33

description: Parental line


title: MKN28

description: Parental line


title: 203774250049_R03C01

value: Female

value: infratentorial

tag: progression-free survival (months)


title: MKN7

description: Parental line


title: RNA WT d0 replicate 1


title: RNA K36M d8 Repsox replicate 1


title: sample18

description: Hybridized to OncoScan® CNV FFPE Arrays


title: 203774250049_R02C01

tag: progression (0=no, 1=yes)


title: PND28-19

description: PND28 Litter mates

value: Postnatal day 28

value: wild type


title: RNA WT d8 TGFb replicate 1


title: IM95

description: Parental line


title: 203810690149_R04C01

tag: overall survival (months)


title: HSC-57

description: Parental line


title: RNA WT d8 Repsox replicate 2


title: sample15

description: Hybridized to OncoScan® CNV FFPE Arrays


title: sample17

description: Hybridized to OncoScan® CNV FFPE Arrays


title: HSC-42

description: Parental line


title: sample14

description: Hybridized to OncoScan® CNV FFPE Arrays


title: RNA WT d8 Repsox replicate 1


title: sample16

description: Hybridized to OncoScan® CNV FFPE Arrays


title: HSC-41

description: Parental line


title: sample13

description: Hybridized to OncoScan® CNV FFPE Arrays


title: sample11

description: Hybridized to OncoScan® CNV FFPE Arrays


title: RNA WT d8 TGFb replicate 2


title: sample12

description: Hybridized to OncoScan® CNV FFPE Arrays


title: SNU16

description: Parental line


title: sample10

description: Hybridized to OncoScan® CNV FFPE Arrays


title: 203821710038_R06C01

tag: death (0=no, 1=yes)


title: KGN, biol rep 1

first: Merrick

middle: Pierson

last: Smela

state: MA

address: 3 Blackfan Circle

data_processing:
kallisto v0.46.2 was used to determine transcript abundances based on the Ensembl GRCh38 v96 reference transcriptome
Assembly: GrCh38
Supplementary files format and content: Abundance tables (abundance.tsv) are output from kallisto and contain TPM abundances for transcripts.

source_name: KGN

growth_protocol: KGN cells were cultured in DMEM + 10% FBS + 1X GlutaMax (Gibco).

extract_protocol:
Monarch Total RNA Miniprep kit (NEB).
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (with PolyA Enrichment Beads)

value: KGN

value: granulosa cell tumor

value: wild-type

value: No TFs


title: KGN, biol rep 2


title: OCUM-1

description: Parental line

data_processing: The data were analyzed with GeneSpring version 14.9 using affymetrix expression analysis settings (Summarization algorithm: MAS5).


title: TE1

description: Parental line


title: NSC-70C

description: Parental line


title: NSC-71C

description: Parental line


title: sample8

description: Hybridized to OncoScan® CNV FFPE Arrays

value: ovarian cancer


title: OKAJIMA

description: Parental line

value: OKAJIMA


title: Human iPSCs, mesoderm differentiation day 2, GATA4 overexpression, biol rep 2

description:
Column GATA4
TF_gene_expression.csv

data_processing:
For the first six samples (sorted FOXL2+, COV434, iPSCs), kallisto v0.46.2 was used to determine transcript abundances based on the Ensembl GRCh38 v96 reference transcriptome, with additional TF transgenes added.
For the mesoderm differentiation samples (with and without TF expression), reads were aligned to the GrCh38 genome assembly using STAR v2.7.9a, and differential expression analysis was performed using DESeq2 1.28.1 with the iPSC samples as a reference.
Assembly: GrCh38
Supplementary files format and content: Abundance tables (abundance.tsv) are output from kallisto and contain TPM abundances for transcripts.
Supplementary files format and content: TF_gene_expression.csv is output from DESeq2 and contains: the basal gene expression (in iPSCs), the log2 fold change from iPSCs to the other samples, and the adjusted p-values for changes in gene expression.

growth_protocol: iPSCs containing integrated transcription factor expression transposons were dissociated with TRYPLE, and plated in DK10 medium (DMEM-F12, 15 mM HEPES, 1X GlutaMax, 10% KSR) with Y-27632 (10 µM), CHIR99021 (3 µM), and doxycycline (1 µg/mL) at a cell density of 12,500/cm2 on Matrigel-coated polystyrene plates. The medium volume per well of 6-well plate was 2 mL. RNA was extracted 48 hours after plating.

value: induced pluripotent stem cell, mesoderm differentiation


title: Human iPSCs, mesoderm differentiation day 2, GATA4 overexpression, biol rep 1

description:
Column GATA4
TF_gene_expression.csv

value: GATA4 overexpression


title: sample9

description: Hybridized to OncoScan® CNV FFPE Arrays


title: 203774250149_R07C01

tag: material type


title: sample6

description: Hybridized to OncoScan® CNV FFPE Arrays


title: Human iPSCs, mesoderm differentiation day 2, biol rep 1

description:
Column No_TFs
TF_gene_expression.csv

growth_protocol: iPSCs were dissociated with TRYPLE, and plated in DK10 medium (DMEM-F12, 15 mM HEPES, 1X GlutaMax, 10% KSR) with Y-27632 (10 µM), CHIR99021 (3 µM), and doxycycline (1 µg/mL) at a cell density of 12,500/cm2 on Matrigel-coated polystyrene plates. The medium volume per well of 6-well plate was 2 mL. RNA was extracted 48 hours after plating.


title: Human iPSCs, mesoderm differentiation day 2, FOXL2 overexpression, biol rep 1

description:
Column FOXL2
TF_gene_expression.csv

value: FOXL2 overexpression


title: 203866300034_R07C01

tag: Sex

value: supratentorial


title: Human iPSCs, mesoderm differentiation day 2, RUNX1 overexpression, biol rep 2

description:
Column RUNX1
TF_gene_expression.csv


title: sample5

description: Hybridized to OncoScan® CNV FFPE Arrays


title: Human iPSCs, mesoderm differentiation day 2, RUNX1 overexpression, biol rep 1

description:
Column RUNX1
TF_gene_expression.csv

value: RUNX1 overexpression


title: Human iPSCs, mesoderm differentiation day 2, FOXL2 overexpression, biol rep 2

description:
Column FOXL2
TF_gene_expression.csv


title: sample4

description: Hybridized to OncoScan® CNV FFPE Arrays


title: Human iPSCs, mesoderm differentiation day 2, biol rep 2

description:
Column No_TFs
TF_gene_expression.csv


title: sample7

description: Hybridized to OncoScan® CNV FFPE Arrays


title: 203821710038_R01C01

value: Male

tag: age

value: Ependymoma (WHO grade II)

tag: tert mutation status

tag: chromosome 6 status

value: loss

value: FFPE


title: Human iPSCs, mesoderm differentiation day 2, NR5A1 overexpression, biol rep 2

description:
Column NR5A1
TF_gene_expression.csv

tag: cell line

tag: genotype


title: NSC-69C

description: Parental line


title: NUGC-4

description: Parental line


title: NSC-66C

description: Parental line


title: NSC-65C

description: Parental line


title: NSC-68C

description: Parental line


title: NSC-67C

description: Parental line


title: sample3

description: Hybridized to OncoScan® CNV FFPE Arrays


title: NSC-63C

description: Parental line


title: sample2

description: Hybridized to OncoScan® CNV FFPE Arrays


title: 203740910036_R07C01

value: Female

value: infratentorial


title: sample1

description: Hybridized to OncoScan® CNV FFPE Arrays


title: Human iPSCs, mesoderm differentiation day 2, WT1 overexpression, biol rep 2

description:
Column WT1
TF_gene_expression.csv

value: FOXL2-T2A-tdTomato, WT1 overexpression


title: Human iPSCs, mesoderm differentiation day 2, NR5A1 overexpression, biol rep 1

description:
Column NR5A1
TF_gene_expression.csv

value: NR5A1 overexpression


title: Human iPSCs, mesoderm differentiation day 2, WT1 overexpression, biol rep 1

description:
Column WT1
TF_gene_expression.csv

value: WT1 overexpression