title: 3543_OF1A_1-4-I1-J7

value: Female


title: KO2_ISC

status: Public on Dec 13 2023

type: SRA

city: Guangzhou

first: Ye-Guang

last: Chen

address: 190 Kaiyuan Avenue, Guangzhou Science Park, Luogang District

country: China

institute: Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences

library_source: transcriptomic

data_processing:
Quality control was performed using FastQC v0.19.7.
For bulk RNA-seq, sequencing reads were aligned to mm10 mouse genome reference (GRCh38) using STAR with default parameter (Dobin et al., 2013).
For small RNA-seq, clean data was mapped to mm10 mouse genome reference (GRCh38) and miRbase with Bowtie2 and the counts were summarized and normalized by RDeseq2.
Assembly: Sequencing reads were aligned using GRCm38/mm10 assembly of the mouse genome.
Supplementary files format and content: gene_count_matrix.csv: Comma-delimited text file includes reads counts for each sample.

molecule: total RNA

organism: Mus musculus

source_name: Intestinal epithelial cells

growth_protocol: Villin-creERT; Lgr5-EGFP-IRES-creERT2; Dgcr8loxP/loxP intestinal organoids were stimulated with 4-OHT or ethanol for 24 hours and then cultured in ENR medium for an additional 3 days. Intestinal organoids and sorted Lgr5-GFPhigh ISCs were collected. Intestinal epithelial cells from WT and epithelial Dgcr8 knockout mice were also collected.

extract_protocol:
Total RNA was extracted and purified by using TRIZOL reagent (Thermo Fisher Scientific). 1.5ug of total RNA was used for the construction of sequencing libraries.
RNA integrity was measured using electrophoresis. Subsequently, First-strand cDNA was generated using random hexamer primers. Then, a second-strand cDNA was synthesized. A-Tailing Mix and RNA Index Adapters followed to subjected to the end of the cDNA. The cDNA fragments were amplified by PCR and the product was qualified by Qubit 2.0 Fluorometer (Life Technologies, Grand Island, NY) and the 2100 Bioanalyzer (Agilent). After it, the products were denatured and circularized to collect the final library.
Bulk RNA-seq and small RNA-seq

treatment_protocol: WT and epithelial Dgcr8 knockout mice (8-10 weeks old) were applied with 5-FU (HY-90006, MCE) administration for consecutive 2 days, and intestinal crypts were collected one day after 5-FU administration.

tag: tissue

value: Intestinal epithelial cells

tag: cell line

tag: cell type

value: Dgcr8 KO_2

tag: genotype

tag: treatment


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026425LR01-GA3-1-8-25]

city: Houston

first: yi

last: chai

address: pgpr

country: USA

institute: Biostate AI

description: Carbon tetrachloride, 1.5 ml/kg, Day 1, Repeat 1

data_processing:
Raw data from Illumina sequencer
illumina Adaptor Trim
HISAT2 Alignment
Assembly: NCBI GCF_015227675.2, Genome assembly mRatBN7.2
Supplementary files format and content: csv

molecule: polyA RNA

organism: Rattus norvegicus

source_name: Blood

growth_protocol: Animals were kept under a standard condition with room temperature at 21-23 ºC, 40-70% relative humidity, and a 12/12h light: dark cycle. Chow and water are available ad libitum.

extract_protocol:
Trizol based total RNA extraction method
RNA libraries for RNA-Seq were prepared by using mRNA capture based standard library preparation kit (Vazyme) following manufacturer's protocol.

tag: age

value: 8 wks

tag: Sex

value: male

value: whole blood


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026428LR01-GA4-1-8-25]

description: Carbon tetrachloride, 2 ml/kg, Day 1, Repeat 1


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026424LR01-GA2-3-8-25]

description: Carbon tetrachloride, 1 ml/kg, Day 1, Repeat 3


title: KH20-22437

city: Monrovia

first: Liangliang

last: Gao

state: CA

address: 1225 S Shamrock Ave

institute: ChromoLogic

data_processing:
Isis (Analysis Software): 2.5.52.11
Bowtie (Aligner): 0.12.8
SAMtools: 0.1.19-isis-1.0.2
miRDeep*: 3.2
DESeq2: 1.0.17
Assembly: GRCh38
Supplementary files format and content: csv counts for all samples
Supplementary files format and content: csv counts

molecule: cytoplasmic RNA

organism: Homo sapiens

source_name: Plasma

extract_protocol:
miRCL (ChromoLogic)
TruSeq

value: Plasma

tag: condition

value: Covid


title: KH20-23544


title: WT1_Org

value: Ethanol


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026427LR01-GA3-3-8-25]

description: Carbon tetrachloride, 1.5 ml/kg, Day 1, Repeat 3


title: 3543_OF1A_1-4-I1-I19

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimmed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted hg38 reference genome using Hisat-3n.
The raw BAM files were filtered using samtools to keep only uniquely mapped reads and use Picard to remove PCR duplicates.
From the filtered BAM file, DNA reads are selected by read-level mCH base coverage >= 3 and read-level mCH fraction < 0.5, selected reads will be processed by ALLCools package to produce ALLC files (allcools allc-to-bam function). The ALLC files are Tab-delimited files describing the quantity of unmethylated and methylated cytosine base calls.
Trimmed reads will also be mapped by Hisat2 to map to hg38 reference genome with GENCODE human v37 gene annotation. RNA reads are selected by read-level mCH base coverage >= 3 and read-level mCH fraction > 0.9, selected reads will be processed by featureCount to quantify gene level (exon + intron) RNA counts.
Assembly: hg38
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column.
Library strategy: snmCT-seq

molecule: genomic DNA

source_name: OF1A human BA46

extract_protocol: Library prepared following protocol discribed in Luo, Chongyuan, Hanqing Liu, Fangming Xie, Ethan J. Armand, Kimberly Siletti, Trygve E. Bakken, Rongxin Fang, et al. 2019. “Single Nucleus Multi-Omics Links Human Cortical Cell Regulatory Genome Diversity to Disease Risk Variants.” bioRxiv. https://doi.org/10.1101/2019.12.11.873398. https://www.protocols.io/view/snmcat-v1-bwubpesn

tag: brain region

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

tag: molecule subtype

value: nuclear RNA + genomic DNA


title: KH20-22432


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026422LR01-GA2-1-8-25]

description: Carbon tetrachloride, 1 ml/kg, Day 1, Repeat 1


title: KO2_Org


title: KO2_5FU_Crypts

source_name: Intestinal epithelium

value: Intestinal epithelium


title: pmmehp5

city: Austin

first: Xin

last: Fang

state: Texas

address: 107 W Dean Keeton St, Austin, TX 78712

institute: University of Texas at Austin

data_processing:
Illumina Novaseq 6000
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Fastqc, reads shorter than 50bp were discarded
Trimmed sequence reads were mapped to Rnor_6.0(from Ensembl)/mm10(from Gencode) using Bowtie2 tool
Read count extraction and normalization were performed using DESeq2 package
Gene Ontology enrichment analysis was performed using GO-MWU tool which is available https://github.com/z0on/GO_MWU
Assembly: Rnor_6.0     mm10
Supplementary files format and content: excel file including the differntial expression gene information and Gene ontology enrichment information
Supplementary files format and content: deseq_result_rat.xlsx and deseq_result_mouse.xlsx file are the result of DESeq2
Supplementary files format and content: deseq results contain gene_id, gene_name, base_mean, log2FoldChange, ifcSE, stat, pvalue, padj columns
Supplementary files format and content: gomwu_adult_rat.xlsx, gomwu_pubertal_rat.xlsx, and gomwu_mouse.xlsx are the result from gomwu analysis (GO analysis), which is developed from Matz lab at UT Austin, the enrichment analysis can be found here https://github.com/z0on/GO_MWU
Supplementary files format and content: gomwu results table contains GO ID, name, constituent, n, nsig, p, fdr columns

source_name: testis

extract_protocol:
RNA was harvested using AllPrep DNA/RNA/miRNA Universal Kit (QIANGEN, Germany). 2000 ng of total RNA per sample was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEXTSEQ 500/550 HIGH OUTPUT KIT V2.5 (75 CYCLES) following manufacturer's protocols.

treatment_protocol:
animals were exposed to 700 mg/kg MEHP or equivalent amount of Corn oil as control via oral gavage
700mg MEHP is mixed with 300mg Corn oil to make MEHP solution, it is mixed well everytime before treating animals

value: testis

value: MEHP

tag: time

value: day 2


title: 3543_OF1A_1-4-I1-H8


title: KH20-22460


title: KH20-17817


title: pmmehp4


title: 3543_OF1A_1-4-I1-G7


title: 3543_OF1A_1-4-I1-G20


title: 3543_OF1A_1-4-I1-H7


title: KH20-17790


title: KH20-22452-RR2


title: 3543_OF1A_1-4-I1-H19


title: 3543_OF1A_1-4-I1-H20


title: WT2_5FU_Crypts


title: pmmehp3


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026423LR01-GA2-2-8-25]

description: Carbon tetrachloride, 1 ml/kg, Day 1, Repeat 2


title: pmmehp6


title: 3543_OF1A_1-4-I1-G8


title: 3543_OF1A_1-4-I1-F8


title: KH20-22416


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026417LR01-1-2-8-25]

description: Sodium chloride, 0.9%, Day 1, Repeat 2

value: Sodium chloride, 0.9%, Day 1, Repeat 2


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026421LR01-GA1-3-8-25]

description: Carbon tetrachloride, 0.5 ml/kg, Day 1, Repeat 3


title: KH20-23532


title: KH20-17797


title: WT1_5FU_Crypts


title: KH20-17768-RR1


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026420LR01-GA1-2-8-25]

description: Carbon tetrachloride, 0.5 ml/kg, Day 1, Repeat 2


title: 3543_OF1A_1-4-I1-G19


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026419LR01-GA1-1-8-25]

description: Carbon tetrachloride, 0.5 ml/kg, Day 1, Repeat 1


title: RNA-Seq of rattus norvegicus: 8 wks female PBMC [Sample_R23025940LR02-6FP-PBMC]

description: No Drug Usage, Day 21, Repeat 3

value: female

value: PBMC

value: No Drug Usage, Day 21, Repeat 3


title: pmmehp2


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026418LR01-1-3-8-25]

description: Sodium chloride, 0.9%, Day 1, Repeat 3

value: Sodium chloride, 0.9%, Day 1, Repeat 3


title: pmco6

value: Corn oil


title: pmmehp1


title: RNA-Seq of rattus norvegicus: 8 wks female PBMC [Sample_R23025939LR02-5FP-PBMC]

description: No Drug Usage, Day 21, Repeat 2

value: 8 wks

value: No Drug Usage, Day 21, Repeat 2


title: KH20-17785

value: Plasma


title: pmco4


title: KH20-16663

value: Covid


title: RNA-Seq of rattus norvegicus: 8 wks female PBMC [Sample_R23025938LR02-4FP-PBMC]

description: No Drug Usage, Day 21, Repeat 1

value: No Drug Usage, Day 21, Repeat 1


title: 3543_OF1A_1-4-I1-E8

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female


title: KH20-16659-RR1


title: pmco3


title: RNA-Seq of rattus norvegicus: 8 wks male PBMC [Sample_R23025937LR02-3MP-PBMC]

description: No Drug Usage, Day 21, Repeat 3

value: male


title: pmco7

value: testis


title: 3543_OF1A_1-4-I1-F7

value: nuclear RNA + genomic DNA


title: KH20-17782


title: 3543_OF1A_1-4-I1-F20


title: KH20-16652


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026416LR01-1-1-8-25]

description: Sodium chloride, 0.9%, Day 1, Repeat 1

value: whole blood

value: Sodium chloride, 0.9%, Day 1, Repeat 1


title: 3543_OF1A_1-4-I1-E20


title: KH20-17751


title: 3543_OF1A_1-4-I1-F19


title: pmco5

value: day 2


title: 3543_OF1A_1-4-I1-E19


title: 3543_OF1A_1-4-I1-E7


title: RNA-Seq of rattus norvegicus: 8 wks male PBMC [Sample_R23025936LR02-2MP-PBMC]

description: No Drug Usage, Day 21, Repeat 2

value: PBMC


title: S_V_C_2

city: Beijing

first: Yanmeng

last: Tao

state: Beijing

address: #5 Yiheyuan Road

department: Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies

institute: Peking University

description:
S_V_C_2
RNAseq_2_gene_count.xls

data_processing:
After the library is qualified, the different libraries are pooling according to the effective concentration and the target amount of data off the machine, then being sequenced by the Illumina NovaSeq 6000. The end reading of 150bp pairing is generated. The basic principle of sequencing is to synthesize and sequence at the same time (Sequencing by Synthesis). Four fluorescent labeled dNTP, DNA polymerase and splice primers were added to the sequenced flowcell and amplified. When the sequence cluster extends the complementary chain, each dNTP labeled by fluorescence can release the corresponding fluorescence. The sequencer captures the fluorescence signal and converts the optical signal into the sequencing peak by computer software, so as to obtain the sequence information of the fragment to be tested.
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Assembly: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.

source_name: skin

growth_protocol: Cells were cultured in reprogramming medium (DMEM/M199 (4:1) supplemented with 10% FBS,10% KnockOut Serum Replacement, 1% MEM Non-Essential Amino Acids, 1% GlutaMAX, 1% penicillin-streptomycin, 2 µg/mL Doxycycline hyclate)

extract_protocol:
Performed according to RNeasy Plus Mini Kit (QIAGEN, Cat#74134)
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.  In order to ensure the quality of the library, the library needs to be tested. After the construction of the library, the library was initially quantified by Qubit2.0 Fluorometer, then diluted to 1.5ng/ul, and the insert size of the library is detected by Agilent 2100 bioanalyzer. After insert size meets the expectation, qRT-PCR is used to accurately quantify the effective concentration of the library (the effective concentration of the library is higher than that of 2nM) to ensure the quality of the library.

treatment_protocol: Cells were treated with Ctrl (DMSO) or 2C (SB431542 and Baricitinib)

value: skin

value: Adult mouse skin fibroblasts

value: Cardiac fibroblasts

value: WT

value: Vector+Ctrl for 2 weeks


title: pmco2

value: Corn oil


title: RNA-Seq of rattus norvegicus: 8 wks female red blood cell [Sample_R23025934LR02-6FR-RBC]

description: No Drug Usage, Day 21, Repeat 3

value: 8 wks

value: female

value: red blood cell

value: No Drug Usage, Day 21, Repeat 3


title: 3543_OF1A_1-4-I1-D20

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female


title: KH20-16403

value: Plasma

value: Covid


title: RNA-Seq of rattus norvegicus: 8 wks female red blood cell [Sample_R23025933LR02-5FR-RBC]

description: No Drug Usage, Day 21, Repeat 2

value: No Drug Usage, Day 21, Repeat 2


title: pmco1

value: testis

value: day 2


title: 3543_OF1A_1-4-I1-D19

value: nuclear RNA + genomic DNA


title: S_2_D_2

description:
S_2_D_2
RNAseq_2_gene_count.xls

value: skin

value: Adult mouse skin fibroblasts

value: MT+2C for 2 weeks


title: 3543_OF1A_1-4-I1-D8


title: KH20-16648


title: RNA-Seq of rattus norvegicus: 8 wks male PBMC [Sample_R23025935LR02-1MP-PBMC]

description: No Drug Usage, Day 21, Repeat 1

value: male

value: PBMC

value: No Drug Usage, Day 21, Repeat 1


title: RNA-Seq of rattus norvegicus: 8 wks female red blood cell [Sample_R23025932LR02-4FR-RBC]

description: No Drug Usage, Day 21, Repeat 1

value: 8 wks

value: female


title: 3543_OF1A_1-4-I1-C8


title: S_2_D_1

description:
S_2_D_1
RNAseq_2_gene_count.xls

value: Cardiac fibroblasts

value: WT


title: KH20-16388


title: KH20-16390


title: S_V_C_1

description:
S_V_C_1
RNAseq_2_gene_count.xls

value: Vector+Ctrl for 2 weeks


title: S_2_C_2

description:
S_2_C_2
RNAseq_2_gene_count.xls

value: MT+Ctrl for 2 weeks


title: KH20-16395

value: Plasma

value: Covid


title: KH20-16405


title: 3543_OF1A_1-4-I1-J19

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female


title: S_2_C_1

description:
S_2_C_1
RNAseq_2_gene_count.xls


title: RNA-Seq of rattus norvegicus: 8 wks male red blood cell [Sample_R23025931LR02-3MR-RBC]

description: No Drug Usage, Day 21, Repeat 3

value: red blood cell

value: No Drug Usage, Day 21, Repeat 3


title: 3543_OF1A_1-4-I1-D7

value: nuclear RNA + genomic DNA


title: KH20-16352-RR1


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23025928LR02-6F-8-27]

description: No Drug Usage, Day 21, Repeat 3

value: whole blood


title: KH20-16346


title: H_V_C_2

description:
H_V_C_2
RNAseq_2_gene_count.xls

source_name: heart

value: heart

value: Adult mouse cardiac fibroblasts


title: H_V_C_1

description:
H_V_C_1
RNAseq_2_gene_count.xls


title: RNA-Seq of rattus norvegicus: 8 wks male red blood cell [Sample_R23025929LR02-1MR-RBC]

description: No Drug Usage, Day 21, Repeat 1

value: male

value: No Drug Usage, Day 21, Repeat 1


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23025927LR02-5F-8-27]

description: No Drug Usage, Day 21, Repeat 2

value: 8 wks

value: female

value: No Drug Usage, Day 21, Repeat 2


title: 3543_OF1A_1-4-I1-C19


title: KH20-16341-RR1


title: H_2_D_2

description:
H_2_D_2
RNAseq_2_gene_count.xls

value: Cardiac fibroblasts

value: WT

value: MT+2C for 2 weeks


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23025926LR02-4F-8-27]

description: No Drug Usage, Day 21, Repeat 1


title: KH20-16330

value: Plasma

value: Covid


title: 3543_OF1A_1-4-I1-B20

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23025925LR02-3M-8-27]

description: No Drug Usage, Day 21, Repeat 3

value: No Drug Usage, Day 21, Repeat 3


title: RNA-Seq of rattus norvegicus: 8 wks male red blood cell [Sample_R23025930LR02-2MR-RBC]

description: No Drug Usage, Day 21, Repeat 2

value: red blood cell


title: KH20-16333


title: 3543_OF1A_1-4-I1-B8

value: nuclear RNA + genomic DNA


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23025924LR02-2M-8-27]

description: No Drug Usage, Day 21, Repeat 2

value: whole blood


title: H_2_D_1

description:
H_2_D_1
RNAseq_2_gene_count.xls

value: heart

value: Adult mouse cardiac fibroblasts


title: 3543_OF1A_1-4-I1-B19


title: H_2_C_2

description:
H_2_C_2
RNAseq_2_gene_count.xls

value: MT+Ctrl for 2 weeks


title: KH20-16323


title: 3543_OF1A_1-4-I1-B7


title: 3543_OF1A_1-4-I1-C7


title: H_2_C_1

description:
H_2_C_1
RNAseq_2_gene_count.xls


title: KH20-16344-RR1


title: 3543_OF1A_1-4-I1-C20


title: nCM_3

description:
nCM_3
RNAseq_1_gene_count.xls

value: Neonatal mouse cardiomyocytes

value: Cardiomyocytes

value: No treatment


title: KH20-16305


title: 3543_OF1A_1-4-I1-A20


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23025920LR02-4F-8-26]

description: No Drug Usage, Day 20, Repeat 1

value: 8 wks

value: female

value: No Drug Usage, Day 20, Repeat 1


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23025922LR02-6F-8-26]

description: No Drug Usage, Day 20, Repeat 3

value: No Drug Usage, Day 20, Repeat 3


title: nCM_2

description:
nCM_2
RNAseq_1_gene_count.xls

value: WT


title: 3543_OF1A_1-4-I1-A7

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: 3543_OF1A_1-4-I1-A8

value: Female


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23025917LR02-1M-8-26]

description: No Drug Usage, Day 20, Repeat 1

value: male


title: 3543_OF1A_1-3-I1-P6


title: 3543_OF1A_1-4-I1-A19


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23025919LR02-3M-8-26]

description: No Drug Usage, Day 20, Repeat 3


title: 3543_OF1A_1-3-I1-P18


title: MTCtd2_2

description:
MTCtd2_2
RNAseq_1_gene_count.xls

value: Neonatal mouse cardiac fibroblasts

value: Cardiac fibroblasts

value: MT+Ctrl for 2 days


title: KH20-16271

value: Plasma

value: Covid


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23025918LR02-2M-8-26]

description: No Drug Usage, Day 20, Repeat 2

value: whole blood

value: No Drug Usage, Day 20, Repeat 2


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23025921LR02-5F-8-26]

description: No Drug Usage, Day 20, Repeat 2


title: KH20-16270


title: KH20-16297


title: KH20-16269


title: MTCld10_2

description:
MTCld10_2
RNAseq_1_gene_count.xls

value: heart

value: MT+Ctrl for 10 days


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23025916LR02-6F-8-25]

description: No Drug Usage, Day 19, Repeat 3

value: 8 wks

value: No Drug Usage, Day 19, Repeat 3


title: 3543_OF1A_1-3-I1-P17

value: nuclear RNA + genomic DNA


title: nCM_1

description:
nCM_1
RNAseq_1_gene_count.xls

value: Neonatal mouse cardiomyocytes

value: Cardiomyocytes

value: No treatment


title: KH20-16294


title: MTCtd2_3

description:
MTCtd2_3
RNAseq_1_gene_count.xls

value: WT


title: MTCld10_1

description:
MTCld10_1
RNAseq_1_gene_count.xls


title: MTCtd2_1

description:
MTCtd2_1
RNAseq_1_gene_count.xls


title: KH20-16311


title: 3543_OF1A_1-3-I1-P5

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23025923LR02-1M-8-27]

description: No Drug Usage, Day 21, Repeat 1

value: male

value: No Drug Usage, Day 21, Repeat 1


title: KH20-15901

value: Plasma


title: KH20-15907

value: Covid


title: 3543_OF1A_1-3-I1-O6


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23025915LR02-5F-8-25]

description: No Drug Usage, Day 19, Repeat 2

value: female

value: whole blood

value: No Drug Usage, Day 19, Repeat 2


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23025912LR02-2M-8-25]

description: No Drug Usage, Day 19, Repeat 2


title: KH20-15530


title: KH20-15434


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23025914LR02-4F-8-25]

description: No Drug Usage, Day 19, Repeat 1

value: No Drug Usage, Day 19, Repeat 1


title: MTCl_5

description:
MTCl_5
RNAseq_1_gene_count.xls

value: heart

value: Neonatal mouse cardiac fibroblasts

value: Cardiac fibroblasts

value: MT+Ctrl for 5 weeks


title: MTCld6_3

description:
MTCld6_3
RNAseq_1_gene_count.xls

value: MT+Ctrl for 6 days


title: 3543_OF1A_1-3-I1-O5

value: nuclear RNA + genomic DNA


title: MTCld6_2

description:
MTCld6_2
RNAseq_1_gene_count.xls

value: WT


title: KH20-15895


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23025910LR02-6F-8-24]

description: No Drug Usage, Day 18, Repeat 3

value: 8 wks

value: No Drug Usage, Day 18, Repeat 3


title: MTCl_4

description:
MTCl_4
RNAseq_1_gene_count.xls


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23025913LR02-3M-8-25]

description: No Drug Usage, Day 19, Repeat 3

value: male

value: No Drug Usage, Day 19, Repeat 3


title: MTCl_3

description:
MTCl_3
RNAseq_1_gene_count.xls


title: 3543_OF1A_1-3-I1-N18

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female


title: MTCl_2

description:
MTCl_2
RNAseq_1_gene_count.xls


title: MTCld6_1

description:
MTCld6_1
RNAseq_1_gene_count.xls


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23025908LR02-4F-8-24]

description: No Drug Usage, Day 18, Repeat 1

value: female

value: No Drug Usage, Day 18, Repeat 1


title: 3543_OF1A_1-3-I1-O17


title: 3543_OF1A_1-3-I1-O18


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23025911LR02-1M-8-25]

description: No Drug Usage, Day 19, Repeat 1

value: whole blood


title: KH20-15414

value: Plasma

value: Covid


title: KH20-06865


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23025907LR02-3M-8-24]

description: No Drug Usage, Day 18, Repeat 3


title: 3543_OF1A_1-3-I1-M6


title: KH20-06860


title: 3543_OF1A_1-3-I1-N6


title: 3543_OF1A_1-3-I1-N5


title: MT2Cd10_2

description:
MT2Cd10_2
RNAseq_1_gene_count.xls

value: heart

value: Neonatal mouse cardiac fibroblasts

value: MT+2C for 10 days


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23025906LR02-2M-8-24]

description: No Drug Usage, Day 18, Repeat 2

value: No Drug Usage, Day 18, Repeat 2


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23025909LR02-5F-8-24]

description: No Drug Usage, Day 18, Repeat 2


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23025904LR02-6F-8-23]

description: No Drug Usage, Day 17, Repeat 3

value: No Drug Usage, Day 17, Repeat 3


title: KH20-06867-RR1


title: 1573426-F-61-

value: Normal


title: MTCl_1

description:
MTCl_1
RNAseq_1_gene_count.xls

value: Cardiac fibroblasts

value: WT

value: MT+Ctrl for 5 weeks


title: 3543_OF1A_1-3-I1-N17

value: nuclear RNA + genomic DNA


title: KH20-10140


title: BRH1577342-Norm


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23025905LR02-1M-8-24]

description: No Drug Usage, Day 18, Repeat 1

value: 8 wks

value: male


title: MT2Cd10_3

description:
MT2Cd10_3
RNAseq_1_gene_count.xls


title: 3543_OF1A_1-3-I1-M18

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female


title: BRH1577323-Norm


title: 3543_OF1A_1-3-I1-M17


title: MT2Cd6_3

description:
MT2Cd6_3
RNAseq_1_gene_count.xls

value: MT+2C for 6 days


title: MT2Cd6_2

description:
MT2Cd6_2
RNAseq_1_gene_count.xls


title: MT2Cd10_1

description:
MT2Cd10_1
RNAseq_1_gene_count.xls


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23025903LR02-5F-8-23]

description: No Drug Usage, Day 17, Repeat 2

value: female

value: whole blood

value: No Drug Usage, Day 17, Repeat 2


title: 1570459-F-28-

value: Plasma


title: 3543_OF1A_1-3-I1-L6


title: 1570458-F-24-


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23025902LR02-4F-8-23]

description: No Drug Usage, Day 17, Repeat 1

value: No Drug Usage, Day 17, Repeat 1


title: MT2Cd6_1

description:
MT2Cd6_1
RNAseq_1_gene_count.xls

value: heart

value: Neonatal mouse cardiac fibroblasts


title: 3543_OF1A_1-3-I1-M5


title: 3543_OF1A_1-3-I1-L5


title: MT2Cd2_3

description:
MT2Cd2_3
RNAseq_1_gene_count.xls

value: MT+2C for 2 days


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23025901LR02-3M-8-23]

description: No Drug Usage, Day 17, Repeat 3

value: No Drug Usage, Day 17, Repeat 3


title: 3543_OF1A_1-3-I1-L17


title: 3543_OF1A_1-3-I1-L18


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23025900LR02-2M-8-23]

description: No Drug Usage, Day 17, Repeat 2


title: 1551319-M-61-NA

value: Normal


title: MT2Cd2_2

description:
MT2Cd2_2
RNAseq_1_gene_count.xls

value: Cardiac fibroblasts

value: WT


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23025899LR02-1M-8-23]

description: No Drug Usage, Day 17, Repeat 1

value: 8 wks


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23025898LR02-6F-8-22]

description: No Drug Usage, Day 16, Repeat 3

value: No Drug Usage, Day 16, Repeat 3


title: 3543_OF1A_1-3-I1-K5

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: nuclear RNA + genomic DNA


title: 1548575-M-68-NA


title: MT2C_3

description:
MT2C_3
RNAseq_1_gene_count.xls

value: MT+2C for 5 weeks


title: MT2Cd2_1

description:
MT2Cd2_1
RNAseq_1_gene_count.xls


title: 3543_OF1A_1-3-I1-K18

value: Female


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23025897LR02-5F-8-22]

description: No Drug Usage, Day 16, Repeat 2

value: female

value: whole blood

value: No Drug Usage, Day 16, Repeat 2


title: 1548571-M-45-NA

value: Plasma


title: MT2C_2

description:
MT2C_2
RNAseq_1_gene_count.xls

value: heart


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23025896LR02-4F-8-22]

description: No Drug Usage, Day 16, Repeat 1

value: No Drug Usage, Day 16, Repeat 1


title: 1568633-F-69-


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23025895LR02-3M-8-22]

description: No Drug Usage, Day 16, Repeat 3

value: male


title: 3543_OF1A_1-3-I1-J5


title: 3543_OF1A_1-3-I1-K17


title: MT2C_1

description:
MT2C_1
RNAseq_1_gene_count.xls

value: Neonatal mouse cardiac fibroblasts


title: GMTSX_5

description:
GMTSX_5
RNAseq_1_gene_count.xls

value: GMT+SB431542+XAV939 for 5 weeks


title: 1548031-M-40-NA

value: Normal


title: GMTSX_4

description:
GMTSX_4
RNAseq_1_gene_count.xls

value: Cardiac fibroblasts

value: WT


title: 3543_OF1A_1-3-I1-J18


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23025894LR02-2M-8-22]

description: No Drug Usage, Day 16, Repeat 2

value: 8 wks


title: 3543_OF1A_1-3-I1-J17

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23025893LR02-1M-8-22]

description: No Drug Usage, Day 16, Repeat 1


title: 3543_OF1A_1-3-I1-K6

value: nuclear RNA + genomic DNA


title: 1544802-M-53-NA


title: 1549008-M-76-NA


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23025891LR02-5F-8-21]

description: No Drug Usage, Day 15, Repeat 2

value: No Drug Usage, Day 15, Repeat 2


title: 3543_OF1A_1-3-I1-I6

value: Female


title: 3543_OF1A_1-3-I1-I5


title: 1548570-M-73-NA


title: GMTCl_4

description:
GMTCl_4
RNAseq_1_gene_count.xls

value: GMT+Ctrl for 5 weeks


title: 3543_OF1A_1-3-I1-I18


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23025889LR02-3M-8-21]

description: No Drug Usage, Day 15, Repeat 3

value: whole blood

value: No Drug Usage, Day 15, Repeat 3


title: 1533537-M-65-NA

value: Plasma


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23025890LR02-4F-8-21]

description: No Drug Usage, Day 15, Repeat 1

value: female

value: No Drug Usage, Day 15, Repeat 1


title: 1545304-M-63-NA


title: 3543_OF1A_1-3-I1-I17


title: 1541122-F-69-NA


title: GMTCl_5

description:
GMTCl_5
RNAseq_1_gene_count.xls

value: heart


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23025888LR02-2M-8-21]

description: No Drug Usage, Day 15, Repeat 2

value: male


title: GMTCl_3

description:
GMTCl_3
RNAseq_1_gene_count.xls

value: Neonatal mouse cardiac fibroblasts


title: GMTCl_2

description:
GMTCl_2
RNAseq_1_gene_count.xls


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23025887LR02-1M-8-21]

description: No Drug Usage, Day 15, Repeat 1


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23025886LR02-6F-8-20]

description: No Drug Usage, Day 14, Repeat 3

value: No Drug Usage, Day 14, Repeat 3


title: GMT2C_3

description:
GMT2C_3
RNAseq_1_gene_count.xls

value: Cardiac fibroblasts

value: GMT+2C for 5 weeks


title: GMTSX_2

description:
GMTSX_2
RNAseq_1_gene_count.xls

value: WT

value: GMT+SB431542+XAV939 for 5 weeks


title: 3543_OF1A_1-3-I1-H5

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: nuclear RNA + genomic DNA


title: U2OS_TERRA_pulldown

city: Gothenburg

first: Tanmoy

last: Mondal

state: Västra Götaland

address: Bruna Stråket 16

department: Department of Clinical Chemistry and Transfusion Medicine

country: Sweden

institute: University of Gothenburg

description: TERRA-enriched RNA

data_processing:
Raw Illumina short-reads data obtained from SMARTER-Stranded Total RNA-Seq Kit v2 sequencing was processed using Trim Galore v0.6.6 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with a minimal length threshold of 20bp. Quality control of Illumina short-reads was performed using FastQC v0.11.9 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) with default parameters (-q 20). Trimmed reads were mapped with HISAT2 v2.2.1 (Kim et al. 2019) using the Telomere-to-Telomere (T2T) human reference genome assembly (T2T-CHM13 v1.1) (Nurk et al. 2022). Duplicate reads were labeled using MarkDuplicates from Picard v2.23.4 (http://broadinstitute.github.io/picard/). Mapping files were processed after duplicate removal using Sambamba v0.7.1.
Assembly: T2T CHM13 v1.1
Supplementary files format and content: bigwig files for coverage on TERRA and Luciferase RIP-seq

extract_protocol:
Specific RNA capture from total RNA was performed. In brief, ~300 μg of DNase I treated RNA isolated from U2O-S cells was mixed with 400 pmoles of biotinylated DNA probe against TERRA or Luciferase probe (negative control) in 5x SSC buffer and denatured at 90°C for 3 min. This mixture was immediately cooled down on the ice and again heated at 65°C for 10 min after which the samples were left to cool down at RT to allow hybridization of the probe. To pulldown the RNA hybridized with biotinylated DNA probes, MyOne Streptavidin C1 magnetic Dynabeads (Thermo Fisher Scientific) were added and incubated for 30 min at room temperature. The magnetic beads were washed once with 1x SSC buffer and thrice with 0.1x SSC buffer. To elute the captured RNA, the magnetic beads were resuspended in nuclease- free water, and heated at 75°C for 3 min. The eluted RNA was treated with RNase-free DNase I for 30 min at 37°C. Finally, the RNA was precipitated with 3 volumes of 100% ethanol, 0.5 M ammonium acetate, and GlycoBlue (Thermo Fisher Scientific) at -80°C for 2 h. The precipitated RNA was washed with 80% ethanol and resuspended in nuclease-free water. The RNA captured using TERRA or Luciferase probe (Luciferase) was first checked for specificity by a slot blot assay using TERRA probe. Further, the captured TERRA RNA along with synthetic RNA oligo were digested with RNase T1 and analyzed on a mass spectrometer (MS).
Sequencing libraries were prepared using SMARTer Stranded Total RNA-Seq Kit V2 (Pico Input Mammalian) from Takara and single end sequenced (1X 75 bp) on illumina NextSeq 550 platform.

tag: probe

value: TERRA probe


title: 3543_OF1A_1-3-I1-H18

value: Female


title: U2OS_Luciferase_pulldown

description: Luciferase-enriched RNA

value: Luciferase probe


title: 1541110-M-64-NA

value: Normal


title: GMT2C_1

description:
GMT2C_1
RNAseq_1_gene_count.xls


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23025885LR02-5F-8-20]

description: No Drug Usage, Day 14, Repeat 2

value: 8 wks

value: whole blood

value: No Drug Usage, Day 14, Repeat 2


title: MOLM-13, PR-957, H3K4me3 rep 2

city: Hannover

first: Tina

middle: M.

last: Schnoeder

address: Carl-Neuberg-Str. 1

country: Germany

institute: Hannover Medical School

data_processing:
CUT&TAG reads were trimmed using Trimmomatic v0.39 with following parameters ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:20
Aligment was performed using bowtie2 v2.2.5 against the human reference genome hg38
Duplicated reads were removed using picard v2.27.1, BAM files were sorted and indexed using samtools v1.7
Peaks were called using SEACR v1.3
bigWig files were generated using bamCoverage v3.5.1
Supplementary files format and content: bigWig, tab-delimited matrix table (.txt)
Library strategy: CUT&TAG

growth_protocol: MOLM-13 cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were washed in Wash Buffer (20 mmol/L HEPES pH 7.5, 150 mmol/L NaCl, 0.5 mmol/L Spermidine, protease inhibitor cocktail) and bound to Concanavalin A beads.  Cells were resuspended  in  50μL  Digitonin Wash  Buffer (20 mmol/L HEPES pH 7.5, 150 mmol/L NaCl, 0.5 mmol/L Spermidine, protease inhibitor cocktail, 2 mmol/L EDTA, 0.05% Digitonin) and incubated with anti-H3K4me3, -H3K4me1, -H3K27ac, -and H3K27me3 antibody at a 1:100 dilution overnight at 4°C. Beads were resuspended  in  100μL  Digitonin Wash  Buffer  with  a  secondary  antibody  diluted  1:100  and  incubated  for 30min at  room  temperature.  Cells were washed three times in Digitonin Wash Buffer and resuspended in Digitonin-300 Buffer (0.05% Digitonin, 20 mmol/L HEPES, pH 7.5, 300 mmol/L NaCl, 0.5 mmol/L Spermidine, protease inhibitor cocktail) containing 1:250 pA-Tn5 transposase and incubated at room temperature for 1 hour. Subsequently, cells were washed three times in Digitonin-300 Buffer and resuspended in 100 μL Tagmentation Buffer (10 mmol/L MgCl2 in Digitonin-300 Buffer) and incubated at 37°C for 1 hour. Tagmentation was stopped by adding 10μL of 0.5 M EDTA, 3 μL of 10% SDS, and 2.5 μL of 20 mg/mL Proteinase K, and samples were incubated 37°C overnight.  Tagmented DNA was purified using AMPureXP-beads from Beckman Coulter.
Cut&Tag libraries were amplified from tagmented DNA isolates using 14 cycles on the thermocycler. Post amplification libraries were size selected using  AMPureXP-beads. Library fragment lenght was checked by HSD5000 Tape and DNA concentration by Qubit.

treatment_protocol: MOLM-13 cells were treated for 72hours with 100nM of the immunoproteasome inhibitor PR-957 (ONX-0914) or DMSO as a diluent control

value: acute myeloid leukemia

tag: antibody


title: MOLM-13, PR-957, H3K4me3 rep 1


title: MOLM-13, DMSO, H3K4me3 rep 2

value: DMSO


title: 1533536-M-56-NA

value: Plasma


title: 3543_OF1A_1-3-I1-H17


title: GMTCl_1

description:
GMTCl_1
RNAseq_1_gene_count.xls

value: heart

value: Neonatal mouse cardiac fibroblasts

value: GMT+Ctrl for 5 weeks


title: 3543_OF1A_1-3-I1-H6


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23025883LR02-3M-8-20]

description: No Drug Usage, Day 14, Repeat 3

value: male

value: No Drug Usage, Day 14, Repeat 3


title: MOLM-13, DMSO, H3K4me3 rep 1


title: CF_3

description:
CF_3
RNAseq_1_gene_count.xls

value: Cardiac fibroblasts

value: WT

value: No treatment


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23025884LR02-4F-8-20]

description: No Drug Usage, Day 14, Repeat 1

value: female

value: No Drug Usage, Day 14, Repeat 1


title: MOLM-13, PR-957, H3K4me1 rep 2


title: CF_2

description:
CF_2
RNAseq_1_gene_count.xls


title: 3543_OF1A_1-3-I1-G6

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female

value: nuclear RNA + genomic DNA


title: aCM_3

description:
aCM_3
RNAseq_1_gene_count.xls

value: Adult mouse cardiomyocytes

value: Cardiomyocytes


title: 3543_OF1A_1-3-I1-G5


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23025882LR02-2M-8-20]

description: No Drug Usage, Day 14, Repeat 2

value: 8 wks

value: whole blood

value: No Drug Usage, Day 14, Repeat 2


title: 3543_OF1A_1-3-I1-G18


title: CF_1

description:
CF_1
RNAseq_1_gene_count.xls

value: heart

value: Neonatal mouse cardiac fibroblasts


title: aCM_2

description:
aCM_2
RNAseq_1_gene_count.xls


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23025881LR02-1M-8-20]

description: No Drug Usage, Day 14, Repeat 1

value: male


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23025880LR02-6F-8-19]

description: No Drug Usage, Day 13, Repeat 3

value: No Drug Usage, Day 13, Repeat 3


title: 3543_OF1A_1-3-I1-F6


title: MOLM-13, PR-957, H3K4me1 rep 1

value: acute myeloid leukemia


title: MOLM-13, DMSO, H3K4me1 rep 2

value: DMSO


title: aCM_1

description:
aCM_1
RNAseq_1_gene_count.xls

value: WT

value: No treatment


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23025879LR02-5F-8-19]

description: No Drug Usage, Day 13, Repeat 2

value: female

value: No Drug Usage, Day 13, Repeat 2


title: 3543_OF1A_1-3-I1-F5

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female


title: MOLM-13, DMSO, H3K4me1 rep 1


title: MOLM-13, PR-957, H3K27me3 rep 2


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23025877LR02-3M-8-19]

description: No Drug Usage, Day 13, Repeat 3


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23025878LR02-4F-8-19]

description: No Drug Usage, Day 13, Repeat 1

value: No Drug Usage, Day 13, Repeat 1


title: 3543_OF1A_1-3-I1-F17

value: nuclear RNA + genomic DNA


title: 3543_OF1A_1-3-I1-F18


title: C2C12,WT, PrPc, Rip

city: Wuhan

first: Jing

state: Hubei Province

address: 299 Bayi Road, Wuchang District

institute: wuhan university

data_processing:
The FASTQ file is encoded with Illumina version 1.8+, and the Q value of the base is obtained by subtracting the offset value of 33 from the ASCII value of all characters.
The script independently developed by personal company was used to remove the adapter, and the quality of the sequence was cut according to the quality of the sequence. The original sequence was searched with a window of 5 bases in length. When the average sequencing quality of the bases in the window was lower than 20. Finally, the part starting from the front of the window will be truncated and discarded.
Genome alignment analysis was performed using miRDeep2 software, in which the mapper.pl program called Bowtie to align Unique Reads with the reference genome sequence
The precursor and mature miRNA sequences of this species were downloaded from miRBase, and then the deduplicated sequences were aligned with them respectively to annotate the detected miRNAs.
Assembly: m39
Supplementary files format and content: tab-delimited text files include CPM values for each Sample

growth_protocol: DMEM, 20% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.  When cells were differentiated, DMEM, 2% horse serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 0.1% formaldehyde for 10 min at room temperature. Cells added 1.25M glycine solution for 5min.
RIP-seq libraries were prepared using VAHTS Small RNA Library Prep Kit for Illumina. 1 μg of total RNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 300-400bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

tag: rip antibody

value: cells stably transfected with PrP (WT PrP)

tag: fraction

value: miRNA


title: C2C12, WT, PrPc, Input


title: C2C12, Control, Rip

value: control


title: 3543_OF1A_1-3-I1-E6


title: C2C12, Control, Input


title: MOLM-13, PR-957, H3K27me3 rep 1


title: MOLM-13, DMSO, H3K27me3 rep 2


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23025875LR02-1M-8-19]

description: No Drug Usage, Day 13, Repeat 1

value: 8 wks

value: whole blood


title: 3543_OF1A_1-3-I1-E5


title: RNA-seq_pEF-2

first: Jianyong

last: Han

address: 2rd, Yuanmingyuan West Road

department: State Key Laboratory of Agrobiotechnology

institute: China Agricultural University

data_processing:
High quality reads were mapped to the pig reference genome (Sscrofa 11.1, GCA_000003025.6) using STAR alignment tool (version 2.6.0c) with parameters --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --chimSegmentMin 10
Expression level of protein coding genes (gene annotation file [GTF] from Ensembl Sscrofa 11.1 release 92) were quantified as transcripts per million (TPM) using Kallisto(version 0.44.0).
Genome_build: Suscrofa.11.1
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each sample.

organism: Sus scrofa

source_name: Porcine embryonic fibroblast

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Cat.N: 74106)
We used an rRNA depletion protocol (Globin-Zero Gold rRNA Removal Kit, Illumina, Cat.N: GZG1224) coupled with the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, Cat.N: E7420S) to construct the strand-specific RNA-seq library for each sample. All libraries were quantified using the Qubit dsDNA High Sensitivity Assay Kit (Invitrogen, Life Technologies, Cat.N: Q32851) and sequenced on HiSeq 4000 platform (Illumina) to produce an average of ~127.83 million 150-bp paired-end raw reads and ~126.01 million high-quality reads for each library.

tag: developmental stage

value: E30 fetal

value: Embryonic fibroblast


title: MOLM-13, DMSO, H3K27me3 rep 1

value: acute myeloid leukemia


title: 3543_OF1A_1-3-I1-G17


title: RNA-seq_pEF-1


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23025873LR02-5F-8-18]

description: No Drug Usage, Day 12, Repeat 2

value: No Drug Usage, Day 12, Repeat 2


title: 3543_OF1A_1-3-I1-E17


title: 3543_OF1A_1-3-I1-E18


title: MOLM-13, PR-957, H3K27ac rep 2


title: RNA-seq_pgEpiSC-4

source_name: Pig pre-gastrulation epiblast stem cells (pig pgEpiSCs)

value: E10 embryonic epiblast

value: Embryonic epiblast


title: MOLM-13, PR-957, H3K27ac rep 1


title: 3543_OF1A_1-3-I1-D6


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23025871LR02-3M-8-18]

description: No Drug Usage, Day 12, Repeat 3

value: male

value: No Drug Usage, Day 12, Repeat 3


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23025876LR02-2M-8-19]

description: No Drug Usage, Day 13, Repeat 2

value: No Drug Usage, Day 13, Repeat 2


title: MOLM-13, DMSO, H3K27ac rep 2

value: DMSO


title: MOLM-13, DMSO, H3K27ac rep 1


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23025870LR02-2M-8-18]

description: No Drug Usage, Day 12, Repeat 2


title: 3543_OF1A_1-3-I1-D18

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female


title: RNA-seq_pgEpiSC-2


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23025872LR02-4F-8-18]

description: No Drug Usage, Day 12, Repeat 1

value: female

value: No Drug Usage, Day 12, Repeat 1


title: MOLM-13, PR-957, IgG

value: IgG


title: RNA-seq_pgEpiSC-1


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23025874LR02-6F-8-18]

description: No Drug Usage, Day 12, Repeat 3

value: 8 wks


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23025869LR02-1M-8-18]

description: No Drug Usage, Day 12, Repeat 1

value: whole blood


title: MOLM-13, DMSO, IgG


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23025868LR02-6F-8-17]

description: No Drug Usage, Day 11, Repeat 3

value: No Drug Usage, Day 11, Repeat 3


title: 3543_OF1A_1-3-I1-D17

value: nuclear RNA + genomic DNA


title: 3543_OF1A_1-3-I1-C6


title: 3543_OF1A_1-3-I1-C5


title: RKO Cardiac Fibroblast differentiated from Patient 1 iPSCs, replicate 2, clonal pair #2

first: Adam

middle: Jeffrey

last: Engler

address: 9500 Gilman Drive, MC 0412

department: Bioengineering

institute: UC San Diego

description:
Tn5 ATAC Seq
WB46_Biol_Replicate_2

data_processing:
All data processing was performed by UCSD Center for Epigenomics using the following pipeline: https://github.com/epigen-UCSD/atac_seq_pipeline
Additional details can be found: https://biomystery.gitbooks.io/ataq_seq/content/pipeline/overall_steps.html
Bams and provided peaks.xls files were read into Diffbind in R for differential accessibility testing
Peaks were annotated using HOMER's annotatePeaks.pl script
Assembly: hg38
Supplementary files format and content: MACS2 Peak-Calling Results

source_name: Cardiac

growth_protocol: Differentiations performed as written in Whitehead Protocol (PMID: 34826415)

extract_protocol:
Extraction was perfomed by the UCSD Center for Epigenomics using the following protocl: https://medschool.ucsd.edu/som/cmm/research/epigenomics/Partnerships/Documents/EPIGEN_ATACseq_cells%20protocol_05102019.pdf
Libraries were constructed using a protocol adapted from Buenrostro et. al (doi: 10.1002/0471142727.mb2129s109) by the UCSD Center for Epigenomics (https://medschool.ucsd.edu/som/cmm/research/epigenomics/Partnerships/Documents/EPIGEN_ATACseq_cells%20protocol_05102019.pdf)
Tn5 ATAC-seq

value: Cardiac

value: Cardiac Fibroblast

value: RKO

tag: donor


title: 7.5 years old baboon heart

city: Winston-Salem

first: Jeannie

last: Chan

state: NC

address: Medical Center Boulevard

department: Internal Medicine

institute: Wake Forest School of Medicine

data_processing:
Raw sequencing data were de-multiplexed using Illumina bcl2fastq.
Prealignment QC was performed, and bases with Phred scores below 30 were removed prior to alignment.
Trimmed reads were aligned against the olive baboon reference genome (Panu_3.0) using HISAT2.
Aligned reads were quantified using an expectation-maximization algorithm in Partek Flow with Panu_3.0 annotation (NCBI release 103) for transcripts.
Read counts were normalized by the Trimmed mean of M-values method.
Assembly: Panu_3.0, GCF_000264685.3
Supplementary files format and content: Matrix table of transcript counts before normalization for 35 samples.
Supplementary files format and content: Matrix table of transcript counts after normalization for 35 samples.

organism: Papio sp.

source_name: heart_left ventricle

extract_protocol:
Total RNA was extracted from frozen liver tissues using the Direct-zol RNA MiniPrep Plus kits (Zymo).
RNA quality was assessed using the TapeStation high-sensitivity RNA Screen Tape (Agilent).
Stranded RNA-Seq libraries were constructed from total RNA using the KAPA RNA HyperPrep Kit with RiboErase according to the manufacturer's protocol.
RNA-Seq (2x150 bp)

treatment_protocol: Baboons were fed normal monkey chow diet ad libitum and had free access to water. They were provided with veterinary care throughout their lives.

tag: tissue

value: heart_left ventricle

tag: age (years)

tag: animal id


title: 8.6 years old baboon heart


title: 12.2 years old baboon heart


title: RNA-seq_pgEpiSC-3

value: E10 embryonic epiblast

value: Embryonic epiblast


title: 3543_OF1A_1-3-I1-D5


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23025866LR02-4F-8-17]

description: No Drug Usage, Day 11, Repeat 1

value: No Drug Usage, Day 11, Repeat 1


title: 3543_OF1A_1-3-I1-C18


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23025865LR02-3M-8-17]

description: No Drug Usage, Day 11, Repeat 3

value: male


title: 3543_OF1A_1-3-I1-C17

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: RKO Cardiac Fibroblast differentiated from Patient 1 iPSCs, replicate 1, clonal pair #2

description:
Tn5 ATAC Seq
WB46_Biol_Replicate_1

tag: cell line

tag: cell type

tag: genotype


title: 17.8 years old baboon heart

tag: Sex


title: 3543_OF1A_1-3-I1-B6

tag: age

value: Female


title: R/R Cardiac Fibroblast differentiated from Patient 1 iPSCs, replicate 3, clonal pair #2

description:
Tn5 ATAC Seq
TAL2-3_Biol_Replicate_3

value: RR


title: 8.7 years old baboon heart

value: female


title: RKO Cardiac Fibroblast differentiated from Patient 1 iPSCs, replicate 3, clonal pair #2

description:
Tn5 ATAC Seq
WB46_Biol_Replicate_3


title: R/R Cardiac Fibroblast differentiated from Patient 1 iPSCs, replicate 2, clonal pair #2

description:
Tn5 ATAC Seq
TAL2-3_Biol_Replicate_2


title: 8.9 years old baboon heart


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23025864LR02-2M-8-17]

description: No Drug Usage, Day 11, Repeat 2

tag: treatment

value: No Drug Usage, Day 11, Repeat 2


title: 3543_OF1A_1-3-I1-B5

tag: brain region

tag: molecule subtype


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23025863LR02-1M-8-17]

description: No Drug Usage, Day 11, Repeat 1

value: 8 wks


title: R/R Cardiac Fibroblast differentiated from Patient 1 iPSCs, replicate 1, clonal pair #2

description:
Tn5 ATAC Seq
TAL2-3_Biol_Replicate_1


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23025862LR02-6F-8-16]

description: No Drug Usage, Day 10, Repeat 3

value: whole blood

value: No Drug Usage, Day 10, Repeat 3


title: 10.9 years old baboon heart


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23025867LR02-5F-8-17]

description: No Drug Usage, Day 11, Repeat 2


title: 3543_OF1A_1-3-I1-B18

value: nuclear RNA + genomic DNA


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23025861LR02-5F-8-16]

description: No Drug Usage, Day 10, Repeat 2

value: No Drug Usage, Day 10, Repeat 2


title: RKO Cardiac Fibroblast differentiated from Patient 1 iPSCs, replicate 3, clonal pair #1

description:
Tn5 ATAC Seq
TAL1-9_Biol_Replicate_3

value: Cardiac

value: Cardiac Fibroblast


title: 3543_OF1A_1-3-I1-B17


title: RKO Cardiac Fibroblast differentiated from Patient 1 iPSCs, replicate 2, clonal pair #1

description:
Tn5 ATAC Seq
TAL1-9_Biol_Replicate_2

value: RKO


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23025860LR02-4F-8-16]

description: No Drug Usage, Day 10, Repeat 1

value: No Drug Usage, Day 10, Repeat 1


title: 3543_OF1A_1-3-I1-A6


title: RKO Cardiac Fibroblast differentiated from Patient 1 iPSCs, replicate 1, clonal pair #1

description:
Tn5 ATAC Seq
TAL1-9_Biol_Replicate_1


title: R/R Cardiac Fibroblast differentiated from Patient 1 iPSCs, replicate 3, clonal pair #1

description:
Tn5 ATAC Seq
TAL1-5_Biol_Replicate_3


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23025859LR02-3M-8-16]

description: No Drug Usage, Day 10, Repeat 3


title: 3543_OF1A_1-3-I1-A5


title: 11 years old baboon heart

value: heart_left ventricle


title: 10.4 years old baboon heart


title: R/R Cardiac Fibroblast differentiated from Patient 1 iPSCs, replicate 2, clonal pair #1

description:
Tn5 ATAC Seq
TAL1-5_Biol_Replicate_2


title: 3543_OF1A_1-3-I1-A18


title: 9.4 years old baboon heart


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23025858LR02-2M-8-16]

description: No Drug Usage, Day 10, Repeat 2


title: 13.7 years old baboon heart


title: 10.2 years old baboon heart


title: R/R Cardiac Fibroblast differentiated from Patient 1 iPSCs, replicate 1, clonal pair #1

description:
Tn5 ATAC Seq
TAL1-5_Biol_Replicate_1


title: 11.1 years old baboon heart


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23025857LR02-1M-8-16]

description: No Drug Usage, Day 10, Repeat 1


title: 3543_OF1A_1-3-I1-A17


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23023724LR02-F6-8-15]

description: No Drug Usage, Day 9, Repeat 3

value: No Drug Usage, Day 9, Repeat 3


title: 3543_OF1A_1-2-I1-P4


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23023723LR02-5F-8-15]

description: No Drug Usage, Day 9, Repeat 2

value: No Drug Usage, Day 9, Repeat 2


title: R/R Cardiac Fibroblast differentiated from Patient 2 iPSCs, replicate 3, clonal pair #3

description:
Tn5 ATAC Seq
ED2_70_Biol_Replicate_3


title: 3543_OF1A_1-2-I1-P3

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: R/R Cardiac Fibroblast differentiated from Patient 2 iPSCs, replicate 2, clonal pair #3

description:
Tn5 ATAC Seq
ED2_70_Biol_Replicate_2


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23023722LR02-4F-8-15]

description: No Drug Usage, Day 9, Repeat 1

value: No Drug Usage, Day 9, Repeat 1


title: 12 years old baboon heart


title: 3543_OF1A_1-2-I1-P16

value: Female


title: R/R Cardiac Fibroblast differentiated from Patient 2 iPSCs, replicate 1, clonal pair #3

description:
Tn5 ATAC Seq
ED2_70_Biol_Replicate_1

value: RR


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23023721LR02-3M-8-15]

description: No Drug Usage, Day 9, Repeat 3

value: male


title: 12.9 years old baboon heart

value: female


title: RKO Cardiac Fibroblast differentiated from Patient 2 iPSCs, replicate 3, clonal pair #3

description:
Tn5 ATAC Seq
ED2_65_Biol_Replicate_3


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23023720LR02-2M-8-15]

description: No Drug Usage, Day 9, Repeat 2

value: 8 wks

value: whole blood


title: 13.2 years old baboon heart


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23023719LR02-1M-8-15]

description: No Drug Usage, Day 9, Repeat 1


title: 3543_OF1A_1-2-I1-O3

value: nuclear RNA + genomic DNA


title: 13.8 years old baboon heart


title: 3543_OF1A_1-2-I1-P15


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23023718LR02-F6-8-14]

description: No Drug Usage, Day 8, Repeat 3

value: No Drug Usage, Day 8, Repeat 3


title: 11.9 years old baboon heart


title: RKO Cardiac Fibroblast differentiated from Patient 2 iPSCs, replicate 2, clonal pair #3

description:
Tn5 ATAC Seq
ED2_65_Biol_Replicate_2

value: Cardiac


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23023717LR02-5F-8-14]

description: No Drug Usage, Day 8, Repeat 2

value: No Drug Usage, Day 8, Repeat 2


title: RKO Cardiac Fibroblast differentiated from Patient 2 iPSCs, replicate 1, clonal pair #3

description:
Tn5 ATAC Seq
ED2_65_Biol_Replicate_1

value: Cardiac Fibroblast

value: RKO


title: 21.3 years old baboon heart

value: heart_left ventricle


title: 3543_OF1A_1-2-I1-O4


title: 13.6 years old baboon heart


title: 19.8 years old baboon heart


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23023716LR02-4F-8-14]

description: No Drug Usage, Day 8, Repeat 1

value: No Drug Usage, Day 8, Repeat 1


title: NB1_m6ARIP

description: m6A-modified RNA immunoprecipitation

data_processing:
Raw Illumina short-reads data obtained from SMARTER-Stranded Total RNA-Seq Kit v2 sequencing was processed using Trim Galore v0.6.6 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with a minimal length threshold of 20bp. Quality control of Illumina short-reads was performed using FastQC v0.11.9 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) with default parameters (-q 20). Trimmed reads were mapped with HISAT2 v2.2.1 (Kim et al. 2019) preserving strand information (-U –rna-strandness R) using the Telomere-to-Telomere (T2T) human reference genome assembly (T2T-CHM13 v1.1) (Nurk et al. 2022) . The Escherichia coli K12 genome was concatenated to the T2T reference assembly for further spike-in normalization. To control the systematic variation across m6A-RIP experiments, the amount of spiked-in bacterial RNA was estimated by counting the total number of reads uniquely mapping to the E. coli K-12 reference genome using Sambamba v0.7.1 (Tarasov et al. 2015). The E. coli spike-in Bacterial counts were further used to calculate scaling factors for each batch of m6A-RIP-seq samples. Duplicate reads were labeled using MarkDuplicates from Picard v2.23.4 (http://broadinstitute.github.io/picard/). Alignments were downsampled according to calculated spike-in scaling factors using DownsampleSam from Picard (--strategy HighAccuracy). Mapping files were separated by strand after duplicate removal using Sambamba v0.7.1.
Assembly: T2T CHM13 v1.1 (Homo sapiens)
Assembly: U00096.2 (Escherichia coli K-12, substr. MG1655)
Supplementary files format and content: bigwig files for coverage on input RNA and m6A-RIP

source_name: Neuroblastoma

extract_protocol:
Tumor RNA was extracted from frozen tumor samples using AllPrep DNA/RNA/Protein Mini Kit (Qiagen) according to the manufacturer’s instructions. Tumor samples were analyzed with Applied biosystems CytoScan HD array (Thermo Fisher Scientific, Waltham, MA, USA) according to the experimental procedure previously described (Caren, Kryh et al. 2010, Fransson, Ostensson et al. 2016). The arrays detect both copy number alterations and allele-specific information at high resolution. For primary data analysis, GDAS software (Thermo Fisher Scientific) was used. Chromosome Analysis Suite (ChAS v.3.3; Thermo Fisher Scientific) was used for the generation of genomic profiles and determination of chromosomal aberration, MYCN amplification and ATRX status.
Sequencing libraries were prepared using SMARTer Stranded Total RNA-Seq Kit V2 (Pico Input Mammalian) from Takara and single end sequenced (1X 75 bp) on illumina NextSeq 550 platform.

value: Neuroblastoma

value: m6A (Synaptic Systems, Cat# 202003)

tag: spike-in organism

value: Escherichia coli K-12

tag: rna fraction

value: m6A-modified RNA


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23025892LR02-6F-8-21]

description: No Drug Usage, Day 15, Repeat 3

value: No Drug Usage, Day 15, Repeat 3


title: NB2_m6ARIP

description: m6A-modified RNA immunoprecipitation

tag: antibody


title: 3543_OF1A_1-2-I1-N3

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female


title: 22.1 years old baboon heart

value: female


title: 3543_OF1A_1-2-I1-N4


title: NB1_inputRNA

description:
Total RNA used as reference input for m6A detection compared to m6A-RNA immunoprecipitated sample
featureCounts_matrix_NB.tsv

value: Total RNA


title: 15.1 years old baboon heart


title: 3543_OF1A_1-2-I1-N16

value: nuclear RNA + genomic DNA


title: 17.9 years old baboon heart


title: 3543_OF1A_1-2-I1-O15


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23023713LR02-1M-8-14]

description: No Drug Usage, Day 8, Repeat 1

value: 8 wks

value: male

value: whole blood


title: SK-N-F1_m6ARIP

description: m6A-modified RNA immunoprecipitation

data_processing:
Raw Illumina short-reads data obtained from SMARTER-Stranded Total RNA-Seq Kit v2 sequencing was processed using Trim Galore v0.6.6 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with a minimal length threshold of 20bp. Quality control of Illumina short-reads was performed using FastQC v0.11.9 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) with default parameters (-q 20). Trimmed reads were mapped with HISAT2 v2.2.1 (Kim et al. 2019) preserving strand information (-U –rna-strandness R) using the Telomere-to-Telomere (T2T) human reference genome assembly (T2T-CHM13 v1.1) (Nurk et al. 2022) . The Escherichia coli K12 genome was concatenated to the T2T reference assembly for further spike-in normalization. To control the systematic variation across m6A-RIP experiments, the amount of spiked-in bacterial RNA was estimated by counting the total number of reads uniquely mapping to the E. coli K-12 reference genome using Sambamba v0.7.1 (Tarasov et al. 2015). The E. coli spike-in Bacterial counts were further used to calculate scaling factors for each batch of m6A-RIP-seq samples. Duplicate reads were labeled using MarkDuplicates from Picard v2.23.4 (http://broadinstitute.github.io/picard/). Alignments were downsampled according to calculated spike-in scaling factors using DownsampleSam from Picard (--strategy HighAccuracy). Mapping files were separated by strand after duplicate removal using Sambamba v0.7.1.
Direct RNA Oxford Nanopore Technology (ONT) sequencing data was base-called using Guppy v5.0.16 (flowcell FLO-MIN106, kit SQK-RNA002). Quality control was performed with PycoQC (https://github.com/a-slide/pycoQC) and NanoPlot (https://github.com/wdecoster/NanoPlot) on base-called data. ONT reads were mapped to the T2T-CHM13 v1.1 reference genome using Minimap v2.24 (-map-ont -uf -k14)
Assembly: T2T CHM13 v1.1 (Homo sapiens)
Assembly: U00096.2 (Escherichia coli K-12, substr. MG1655)
Supplementary files format and content: bigwig files for coverage on input RNA and m6A-RIP

growth_protocol: U2OS cells were procured from Sigma and cultured in DMEM media. Two Mettl3 KD and one control U2OS stable cell line were generated using lentivirus expressing shRNA against METTL3 or non-targeted genomic region. Here known as Control-sh and METTL3sh-1, METTLsh-2. CHLA-90 (CCOG) and SK-N-F1 (Sigma Aldrich) cells were cultured in DMEM media supplemented with 20% and 10% FBS respectively.

extract_protocol:
Nuclear fractionation of Control-sh and METTL3sh-2 cells was carried out by washing the trypsinized cells in ice-cold PBS and resuspending them in ice-cold RLN1 buffer (50 mM Tris pH 8.0, NaCl 500 mM, MgCl2 1.5 mM and 0.5% NP-40) and after 5 min incubation for on ice, the samples were spun at 300g for 2 min at 4°C. The supernatant containing cytoplasmic fraction was discarded and RNA from the nuclear pellet was isolated using TRIzol reagent (Invitrogen).  RNA fragmentation followed by m6A RIP was performed with 15 µg of RNA spiked in with 9 ng of Bacterial RNA as previously described by Zeng et al 2018.
Sequencing libraries were prepared using SMARTer Stranded Total RNA-Seq Kit V2 (Pico Input Mammalian) from Takara and single end sequenced (1X 75 bp) on illumina NextSeq 550 platform.  Total RNA isolated from Control-sh and METTL3 KD cells, 20-25 ug was directly sequenced on the Oxford nanopore platform. In brief Total RNA quantification and quality control was performed on Fragment Analyzer 5300 system and showed RNA integrity number (RIN) of 10 for both samples. Poly(A) RNA Selection Kit V1.5 (Lexogen) was used to enrich for polyadenylated transcripts with minor changes to the protocol. All the processing volumes were doubled, and 4ug of Control-sh or METTL3-KD RNA was used as an input in a single reaction. Each sample was batch-processed in 5 separate reactions that were combined at the final elution step. Control-sh and METTL3-KD poly(A)-enriched RNA was analyzed on Fragment Analyzer showing remaining rRNA contamination to be 11% and 21% of mass for each sample respectively. Enriched poly(A)-RNA was then purified using 1x of RNAClean XP (Beckman Coulter) beads to concentrate the sample and remove very short RNA fragments and eluted into 11ul of water. Qubit™ RNA High Sensitivity kit (Invitrogen) was used to quantify the RNA before direct RNA sequencing. SQK-RNA002 (ONT) kit was used for library preparation and followed according to the manufacturer’s protocol. Briefly, 400ng of poly(A)-enriched RNA was used as an input, and recommended reverse-transcription step was performed. Control-sh and METTL3-KD libraries were loaded on individual FLO-MIN106 (ONT) flowcells and sequenced on GridION Mk1 device (ONT) for 72 hours yielding 1.65 and 1.35 million long-reads respectively.
direct-RNA Nanopore sequencing

value: Human Neuroblastoma Cells

value: WT


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23023714LR02-2M-8-14]

description: No Drug Usage, Day 8, Repeat 2

value: No Drug Usage, Day 8, Repeat 2


title: 3543_OF1A_1-2-I1-O16


title: 20.8 years old baboon heart

value: heart_left ventricle


title: 3543_OF1A_1-2-I1-N15


title: NB2_inputRNA

value: Neuroblastoma


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23023712LR02-F6-8-13]

description: No Drug Usage, Day 7, Repeat 3

value: No Drug Usage, Day 7, Repeat 3


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23023711LR02-5F-8-13]

description: No Drug Usage, Day 7, Repeat 2

value: No Drug Usage, Day 7, Repeat 2


title: SK-N-F1_inputRNA

description:
Nuclear RNA used as reference input for m6A detection compared to m6A-RNA immunoprecipitated sample
featureCounts_matrix.tsv

value: Escherichia coli K-12

value: total RNA


title: 3543_OF1A_1-2-I1-M3

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: 3543_OF1A_1-2-I1-M4

value: Female


title: 14.8 years old baboon heart

value: female


title: IgG_U2OS_RIP

description: IgG purified RNA

value: Human Bone Osteosarcoma Epithelial Cells

value: Normal rabbit IgG (sc-2027)

value: IgG purified RNA


title: 3543_OF1A_1-2-I1-M16

value: nuclear RNA + genomic DNA


title: METTL3KD_U2OS_m6ARIP

description: m6A-modified RNA immunoprecipitation

value: METTL3 knockdown

value: m6A (Synaptic Systems, Cat# 202003)

value: m6A-modified RNA


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23023715LR02-3M-8-14]

description: No Drug Usage, Day 8, Repeat 3

value: 8 wks

value: male

value: whole blood

value: No Drug Usage, Day 8, Repeat 3


title: 18.3 years old baboon heart

value: heart_left ventricle


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23023710LR02-4F-8-13]

description: No Drug Usage, Day 7, Repeat 1

value: No Drug Usage, Day 7, Repeat 1


title: 18.6 years old baboon heart


title: 18.63 years old baboon heart


title: Controlsh_U2OS_m6ARIP

description: m6A-modified RNA immunoprecipitation

value: WT

value: Escherichia coli K-12


title: 3543_OF1A_1-2-I1-M15

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female


title: 3543_OF1A_1-2-I1-L4


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23023708LR02-2M-8-13]

description: No Drug Usage, Day 7, Repeat 2

value: No Drug Usage, Day 7, Repeat 2


title: Controlsh_U2OS_inputRNA

value: Human Bone Osteosarcoma Epithelial Cells

value: Nuclear RNA


title: 18.9 years old baboon heart

value: female


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23023707LR02-1M-8-13]

description: No Drug Usage, Day 7, Repeat 1


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23023706LR02-F6-8-12]

description: No Drug Usage, Day 6, Repeat 3

value: No Drug Usage, Day 6, Repeat 3


title: 3543_OF1A_1-2-I1-L16

value: nuclear RNA + genomic DNA


title: 18.5 years old baboon heart


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23023705LR02-5F-8-12]

description: No Drug Usage, Day 6, Repeat 2

value: No Drug Usage, Day 6, Repeat 2


title: 18.4 years old baboon heart


title: 3543_OF1A_1-2-I1-L15


title: 15.7 years old baboon heart


title: 3543_OF1A_1-2-I1-L3


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23023703LR02-3M-8-12]

description: No Drug Usage, Day 6, Repeat 3

value: 8 wks


title: 3543_OF1A_1-2-I1-K4


title: 19.2 years old baboon heart


title: METTL3KD_U2OS_inputRNA

value: METTL3 knockdown


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23023702LR02-2M-8-12]

description: No Drug Usage, Day 6, Repeat 2

value: male

value: whole blood


title: 20.9 years old baboon heart

value: heart_left ventricle


title: 3543_OF1A_1-2-I1-K16


title: 3543_OF1A_1-2-I1-K3


title: 3543_OF1A_1-2-I1-K15


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23023701LR02-1M-8-12]

description: No Drug Usage, Day 6, Repeat 1

value: No Drug Usage, Day 6, Repeat 1


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23023709LR02-3M-8-13]

description: No Drug Usage, Day 7, Repeat 3

value: No Drug Usage, Day 7, Repeat 3


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23023699LR02-5F-8-11]

description: No Drug Usage, Day 5, Repeat 2

value: No Drug Usage, Day 5, Repeat 2


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23023700LR02-F6-8-11]

description: No Drug Usage, Day 5, Repeat 3

value: No Drug Usage, Day 5, Repeat 3


title: 3543_OF1A_1-2-I1-J4

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23023698LR02-4F-8-11]

description: No Drug Usage, Day 5, Repeat 1

value: No Drug Usage, Day 5, Repeat 1


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23023704LR02-4F-8-12]

description: No Drug Usage, Day 6, Repeat 1


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23023696LR02-2M-8-11]

description: No Drug Usage, Day 5, Repeat 2


title: 3543_OF1A_1-2-I1-I4


title: 3543_OF1A_1-2-I1-I3


title: 3543_OF1A_1-2-I1-J16


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23023697LR02-3M-8-11]

description: No Drug Usage, Day 5, Repeat 3


title: 3543_OF1A_1-2-I1-J15


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23023695LR02-1M-8-11]

description: No Drug Usage, Day 5, Repeat 1


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23023694LR02-F6-8-10]

description: No Drug Usage, Day 4, Repeat 3

value: No Drug Usage, Day 4, Repeat 3


title: muscle_day1 of differentiation_control_rep3

type: RNA

city: Paris

first: sebastien

last: jacques

address: 24 rue du faubourg saint jacques

department: Genomic

country: France

institute: Institut Cochin

hyb_protocol: After control of fragmentation using Bioanalyzer 2100, cDNA is then hybridized to GeneChip® ClariomS Mouse (LifeTechnologies) at 45°C for 17 hours.

scan_protocol: After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G

data_processing: The scanned images are then analyzed with Expression Console software (Affymetrix) to obtain raw data (cel files) and metrics for Quality Controls. The observations of some of these metrics and the study of the distribution of raw data show no outlier experiment.  RMA normalization is performed using R with Version 23 of Entrezgene CDF brain array.

label: Biotin

source_name: skeletal muscle_primary myoblast isolated by FACS_day1 of differentiation_control

label_protocol: 100 ng of total RNA is reverse transcribed following the GeneChip® WT Plus Reagent Kit (Affymetrix) .  Briefly, the resulting double strand cDNA is used for in vitro transcription with T7 RNA polymerase (all these steps are included in the WT cDNA synthesis and amplification kit of Affymetrix). After purification according to Affymetrix protocol, 5.5 ug of Sens Target DNA are fragmented and biotin labelled.

extract_protocol: The cells were collected and centrifuged. After centrifuge the pellet was lysed in RLT buffer with β-mercapto comes from the micro kit RNAeasy by Quiagen, used to extract RNA. The samples were all treated with DNAsi.

value: adult muscle stem cells


title: muscle_day0 of differentiation (proliferation state)_control_rep3

source_name: skeletal muscle_primary myoblast isolated by FACS_proliferation_control


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23023693LR02-5F-8-10]

description: No Drug Usage, Day 4, Repeat 2

value: female

value: No Drug Usage, Day 4, Repeat 2


title: 3543_OF1A_1-2-I1-I16

value: nuclear RNA + genomic DNA


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23023692LR02-4F-8-10]

description: No Drug Usage, Day 4, Repeat 1

value: 8 wks

value: No Drug Usage, Day 4, Repeat 1


title: muscle_day3 of differentiation_RhoA-deleted_rep3

source_name: skeletal muscle_primary myoblast isolated by FACS_day3 of differentiation_RhoA-deleted


title: 3543_OF1A_1-2-I1-H4


title: muscle_day3 of differentiation_control_rep3

source_name: skeletal muscle_primary myoblast isolated by FACS_day3 of differentiation_control


title: 3543_OF1A_1-2-I1-J3


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23023691LR02-3M-8-10]

description: No Drug Usage, Day 4, Repeat 3

value: male


title: 3543_OF1A_1-2-I1-I15


title: muscle_day1 of differentiation_RhoA-deleted_rep3

source_name: skeletal muscle_primary myoblast isolated by FACS_day1 of differentiation_RhoA-deleted


title: 3543_OF1A_1-2-I1-H3


title: muscle_day3 of differentiation_control_rep2


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23023690LR02-2M-8-10]

description: No Drug Usage, Day 4, Repeat 2

source_name: Blood

value: whole blood


title: muscle_day1 of differentiation_control_rep2


title: 3543_OF1A_1-2-I1-H16


title: muscle_day0 of differentiation (proliferation state)_RhoA-deleted_rep3

source_name: skeletal muscle_primary myoblast isolated by FACS_proliferation_RhoA-deleted


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23023688LR02-F6-8-9]

description: No Drug Usage, Day 3, Repeat 3

value: No Drug Usage, Day 3, Repeat 3


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23023689LR02-1M-8-10]

description: No Drug Usage, Day 4, Repeat 1


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23023687LR02-5F-8-9]

description: No Drug Usage, Day 3, Repeat 2

value: No Drug Usage, Day 3, Repeat 2


title: 3543_OF1A_1-2-I1-H15

source_name: OF1A human BA46


title: muscle_day3 of differentiation_RhoA-deleted_rep1


title: 3543_OF1A_1-2-I1-G4


title: muscle_day0 of differentiation (proliferation state)_control_rep2


title: muscle_day3 of differentiation_RhoA-deleted_rep2


title: muscle_day1 of differentiation_RhoA-deleted_rep2


title: muscle_day1 of differentiation_RhoA-deleted_rep1


title: 3543_OF1A_1-2-I1-G3


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23023686LR02-4F-8-9]

description: No Drug Usage, Day 3, Repeat 1

value: No Drug Usage, Day 3, Repeat 1


title: 3543_OF1A_1-2-I1-G15


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23023685LR02-3M-8-9]

description: No Drug Usage, Day 3, Repeat 3


title: 3543_OF1A_1-2-I1-G16


title: muscle_day3 of differentiation_control_rep1


title: muscle_day0 of differentiation (proliferation state)_RhoA-deleted_rep1


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23023684LR02-2M-8-9]

description: No Drug Usage, Day 3, Repeat 2


title: 3543_OF1A_1-2-I1-F4


title: muscle_day0 of differentiation (proliferation state)_RhoA-deleted_rep2


title: glioma_Primary [TCGA-DU-6407-TP-13M-450-2G6KI4]

type: genomic

city: Detroit

first: Laila

middle: M

last: Poisson

state: MI

address: 2799 W Grand Blvd

institute: Henry Ford Health

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Beadchip using standard Illumina protocol

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

data_processing:
The raw DNA methylation intensity data files (IDAT) were processed with the minfi package. We performed noob (Normal-exponential convolution using out-of-band probes) background correction and dye bias correction using the minfi package (v 1.36.0). The DNA methylation value for each locus is presented as a beta (β) value (β = (M/(M+U)) in which M and U indicate the mean methylated and unmethylated signal intensities for each locus, respectively. β-values range from zero to one, with scores of zero indicating no DNA methylation and scores of one indicating complete DNA methylation. A detection p-value also accompanies each data point and compares the signal intensity difference between the analytical probes and a set of negative control probes on the array. Any data point with a corresponding p-value greater than 1E-4 is deemed not to be statistically significantly different from background and was thus masked as “NA”.
matrix processed value definition: Average Beta

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified at each institution following standard protocols that ensure high quality DNA.

tag: gender

value: Astrocytoma, IDH-mutant (WHO grade 2)

value: Primary

value: IDHmut

value: noncodel

value: G-CIMP-high

value: astrocytoma


title: 3543_OF1A_1-2-I1-F16

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female


title: glioma_Recurrence 2 [TCGA-DU-6407-R2-11M-450-DU6R11]

value: female

value: Astrocytoma, IDH-mutant (WHO grade 4)

value: Recurrence

value: G-CIMP-low

value: high grade astrocytoma


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23023682LR02-F6-8-8]

description: No Drug Usage, Day 2, Repeat 3

value: 8 wks

value: whole blood

value: No Drug Usage, Day 2, Repeat 3


title: 3543_OF1A_1-2-I1-F3

value: nuclear RNA + genomic DNA


title: 3543_OF1A_1-2-I1-F15


title: 3543_OF1A_1-2-I1-E15


title: 3543_OF1A_1-2-I1-E3


title: muscle_day0 of differentiation (proliferation state)_control_rep1

value: adult muscle stem cells


title: glioma_Primary [TCGA-TQ-A8XE-TP-11M-450-OD11JS]

value: Astrocytoma, IDH-mutant (WHO grade 2)

value: Primary


title: muscle_day1 of differentiation_control_rep1


title: 3543_OF1A_1-2-I1-D16


title: glioma_Recurrence 1 [TCGA-DU-6407-R1-12M-450-V1ZOL5]

value: IDHmut

value: noncodel


title: glioma_Primary [TCGA-TQ-A7RR-TP-01M-450-6C850C]

value: male

value: G-CIMP-high

value: astrocytoma


title: glioma_Recurrence 1 [TCGA-TQ-A8XE-R1-11M-450-WLFHXP]

value: female

value: Astrocytoma, IDH-mutant (WHO grade 3)


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23023681LR02-5F-8-8]

description: No Drug Usage, Day 2, Repeat 2

value: No Drug Usage, Day 2, Repeat 2


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23023683LR02-1M-8-9]

description: No Drug Usage, Day 3, Repeat 1

value: No Drug Usage, Day 3, Repeat 1


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23023679LR02-3M-8-8]

description: No Drug Usage, Day 2, Repeat 3


title: glioma_Primary [TCGA-TQ-A7RW-TP-01M-450-0F3063]

value: Unknown


title: glioma_Recurrence 1 [TCGA-TQ-A7RR-R1-01M-450-01F584]

value: Recurrence


title: 3543_OF1A_1-2-I1-D4

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23023678LR02-2M-8-8]

description: No Drug Usage, Day 2, Repeat 2

value: 8 wks

value: whole blood


title: glioma_Recurrence 1 [TCGA-TQ-A7RW-R1-01M-450-66E0A6]

value: high grade astrocytoma


title: 3543_OF1A_1-2-I1-C4

value: nuclear RNA + genomic DNA


title: glioma_Primary [TCGA-TQ-A7RV-TP-21M-450-TV0QJ2]

value: Astrocytoma, IDH-mutant (WHO grade 2)

value: Primary

value: IDHmut


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23023677LR02-1M-8-8]

description: No Drug Usage, Day 2, Repeat 1

value: male

value: No Drug Usage, Day 2, Repeat 1


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23022883LR01-2M]

description: No Drug Usage, Day 1, Repeat 2

value: No Drug Usage, Day 1, Repeat 2


title: 3543_OF1A_1-2-I1-E4


title: glioma_Recurrence 2 [TCGA-TQ-A7RK-R2-11M-450-8ZHO2D]

value: noncodel

value: G-CIMP-high

value: astrocytoma


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23022887LR01-F6]

description: No Drug Usage, Day 1, Repeat 3

value: female

value: No Drug Usage, Day 1, Repeat 3


title: glioma_Recurrence 1 [TCGA-TQ-A7RV-R1-11M-450-3ETTB6]

value: Recurrence


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23022886LR01-5F]

description: No Drug Usage, Day 1, Repeat 2


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23023680LR02-4F-8-8]

description: No Drug Usage, Day 2, Repeat 1


title: RNA-Seq of rattus norvegicus: 8 wks female whole blood [Sample_R23022885LR01-4F]

description: No Drug Usage, Day 1, Repeat 1

value: No Drug Usage, Day 1, Repeat 1


title: 3543_OF1A_1-2-I1-D3

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23022882LR01-1M]

description: No Drug Usage, Day 1, Repeat 1

value: 8 wks

value: whole blood


title: glioma_Primary [TCGA-TQ-A7RK-TP-11M-450-61T2CA]

value: Astrocytoma, IDH-mutant (WHO grade 2)


title: 3543_OF1A_1-2-I1-C3

value: nuclear RNA + genomic DNA


title: glioma_Recurrence 1 [TCGA-TQ-A7RK-R1-11M-450-0L00IF]

value: IDHmut


title: 3543_OF1A_1-2-I1-C16


title: 3543_OF1A_1-2-I1-C15


title: pMEHP7

value: testis

value: MEHP

tag: time

value: day 2


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23022884LR01-3M]

description: No Drug Usage, Day 1, Repeat 3

value: male


title: 3543_OF1A_1-2-I1-D15


title: pMEHP6


title: 3543_OF1A_1-2-I1-B4


title: glioma_Primary [TCGA-TM-A7CF-TP-11M-450-A7B9ED]

value: Primary

value: noncodel

value: G-CIMP-high


title: 3543_OF1A_1-2-I1-B16


title: 3543_OF1A_1-2-I1-B3


title: pMEHP4


title: glioma_Recurrence 1 [TCGA-FG-A4MT-R1-11M-450-P2ILGT]

value: female

value: Astrocytoma, IDH-mutant (WHO grade 3)

value: astrocytoma


title: glioma_Primary [TCGA-FG-6691-TP-01M-450-CA46A7]


title: pMEHP3


title: pMEHP2


title: 3543_OF1A_1-2-I1-B15

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: 3543_OF1A_1-2-I1-A4

value: Female


title: glioma_Primary [TCGA-FG-5965-TP-11M-450-4K77U2]


title: 3543_OF1A_1-2-I1-A3


title: pCO7

value: Corn oil


title: glioma_Recurrence 2 [TCGA-FG-5965-R2-11M-450-YDZD5D]

value: Astrocytoma, IDH-mutant (WHO grade 4)

value: Recurrence

value: control


title: glioma_Recurrence 1 [TCGA-FG-6691-R1-01M-450-211EB3]

value: Astrocytoma, IDH-mutant (WHO grade 2)

value: IDHmut


title: pCO6

value: testis


title: 3543_OF1A_1-2-I1-A15

value: nuclear RNA + genomic DNA


title: glioma_Recurrence 1 [TCGA-FG-5965-R1-11M-450-T3VSRV]

value: high grade astrocytoma


title: pMEHP5

value: MEHP

value: day 2


title: pCO4


title: glioma_Primary [TCGA-FG-A4MT-TP-11M-450-6RSSPS]

value: Primary

value: noncodel

value: G-CIMP-high


title: glioma_Recurrence 1 [TCGA-FG-5963-R1-12M-450-KICV7S]

value: male

value: Glioblastoma, IDH-wildtype (WHO grade 4)

value: IDHwt

value: midline


title: pCO5

value: Corn oil


title: glioma_Primary [TCGA-FG-5963-TP-11M-450-67KBIY]

value: no class


title: pCO3


title: 3543_OF1A_1-1-I1-P2

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female


title: 3543_OF1A_1-1-I1-P1


title: 3543_OF1A_1-1-I1-P14


title: pCO2


title: 3543_OF1A_1-1-I1-P13


title: glioma_Recurrence 1 [TCGA-DU-7304-R1-12M-450-ZDRTKO]

value: Astrocytoma, IDH-mutant (WHO grade 3)

value: Recurrence

value: IDHmut


title: glioma_Primary [TCGA-DU-7304-TP-12M-450-VQITWQ]

value: Astrocytoma, IDH-mutant (WHO grade 2)

value: astrocytoma


title: MS_27_3

first: SUN

last: WAN

address: o. 2 Yuanmingyuan West Road, Haidian District

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Triticum aestivum

source_name: wheat spikelet

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: wheat spikelet

value: 27 days after terminal spikelet

tag: position

value: central spikelet

value: untreated


title: pMEHP1

source_name: testis

tag: tissue

value: testis

value: MEHP

value: day 2


title: MS_27_2


title: 3543_OF1A_1-2-I1-A16

value: nuclear RNA + genomic DNA


title: pCO1

value: Corn oil


title: glioma_Recurrence 1 [TCGA-TM-A7CF-R1-11M-450-IVILY5]

value: female

value: noncodel

value: G-CIMP-high


title: 3543_OF1A_1-1-I1-O2

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female


title: glioma_Primary [TCGA-DU-6404-TP-11M-450-1WUO60]

value: Glioblastoma, IDH-wildtype (WHO grade 4)

value: Primary

value: IDHwt

value: no class


title: MS_27_1

value: wheat spikelet

value: 27 days after terminal spikelet


title: armehp4


title: 3543_OF1A_1-1-I1-O1


title: armehp5


title: BS_27_3

value: basal spikelet

value: untreated


title: glioma_Recurrence 2 [TCGA-DU-6404-R2-11M-450-8SL9O5]

value: Unknown

value: Recurrence


title: 3543_OF1A_1-1-I1-O13

value: nuclear RNA + genomic DNA


title: glioma_Recurrence 1 [TCGA-DU-6404-R1-21M-450-OEKA4K]


title: BS_27_1


title: glioma_Primary [TCGA-DU-6397-TP-11M-450-5LIWE1]

value: male

value: Oligodendroglioma, IDH-mutant and 1p/19q-codeleted (WHO grade 3)

value: IDHmut

value: codel

value: Codel

value: 1p/19q codeleted oligodendroglioma


title: MS_21_2

value: 21 days after terminal spikelet

value: central spikelet


title: armehp2

value: testis

value: MEHP

value: day 2


title: armehp3


title: glioma_Recurrence 1 [TCGA-DU-6397-R1-12M-450-U8QZUQ]


title: 3543_OF1A_1-1-I1-N1

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female


title: 3543_OF1A_1-1-I1-N2


title: armehp1


title: 3543_OF1A_1-1-I1-N14


title: MS_21_1

value: wheat spikelet

value: untreated


title: glioma_Recurrence 1 [TCGA-DU-5872-R1-21M-450-LXD7NY]

value: female

value: Astrocytoma, IDH-mutant (WHO grade 2)

value: Recurrence

value: noncodel

value: control


title: arCO7

value: Corn oil


title: 3543_OF1A_1-1-I1-N13

value: nuclear RNA + genomic DNA


title: BS_21_3

value: basal spikelet


title: arCO6


title: 3543_OF1A_1-1-I1-M1


title: glioma_Primary [TCGA-DU-5870-TP-11M-450-FOTKBT]

value: Oligodendroglioma, IDH-mutant and 1p/19q-codeleted (WHO grade 2)

value: Primary

value: IDHmut

value: codel

value: Codel

value: 1p/19q codeleted oligodendroglioma


title: BS_21_1

value: 21 days after terminal spikelet


title: BS_21_2

value: wheat spikelet


title: 3543_OF1A_1-1-I1-M14

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female


title: 3543_OF1A_1-1-I1-M13


title: arCO4

value: testis

value: day 2


title: arCO5


title: BS_27_2

value: 27 days after terminal spikelet

value: untreated


title: MS_15_3

value: 15 days after terminal spikelet

value: central spikelet


title: arCO3

value: Corn oil


title: MS_15_2


title: glioma_Primary [TCGA-DU-5872-TP-11M-450-EGJX4P]

value: female

value: Astrocytoma, IDH-mutant (WHO grade 2)

value: noncodel

value: G-CIMP-high

value: astrocytoma


title: 3543_OF1A_1-1-I1-L2

value: nuclear RNA + genomic DNA


title: arCO2


title: 3543_OF1A_1-1-I1-L1


title: MS_15_1


title: glioma_Primary [TCGA-19-4065-TP-01M-450-7DXWB2]

value: male

value: Glioblastoma, IDH-wildtype (WHO grade 4)

value: Primary

value: IDHwt

value: Mesenchymal-like

value: control


title: arCO1

value: testis

value: day 2


title: glioma_Recurrence 1 [TCGA-DH-A669-R1-11M-450-W7XM5M]

value: Oligodendroglioma, IDH-mutant and 1p/19q-codeleted (WHO grade 3)

value: Recurrence

value: IDHmut

value: codel

value: Codel

value: 1p/19q codeleted oligodendroglioma


title: glioma_Primary [TCGA-19-1389-TP-01M-450-CSRJQZ]

value: noncodel

value: mesenchymal


title: LICs from Eu-RET pups treated with PAU, 7 days post treatment 5

city: Vancouver

first: Tanmaya

last: Atre

address: 938 W 28th Ave

country: Canada

institute: BC Children's Hospital Research Institute

data_processing:
Sequence reads de-multiplexed and trimmed using BCL Convert application
rRNA filtered out and remaining reads aligned to mm10 reference sequence using DRAGEN RNA pipeline | Version: 4.0.4
Transcript-level counts imported and gene-level summarization performed using TxImport package | Version 1.24.0
Gene-level estimated counts normalized using EdgeR package | Version 3.38.4
Assembly: mm10
Supplementary files format and content: 10 tab-delimited *.quant.sf files, containing transcript-level abundance data for each sample
Supplementary files format and content: tab-delimited *.tsv file, containing normalized gene-level counts for each sample

source_name: Spleen

growth_protocol: LICs were FACS sorted from PBS or Poly (A:U) treated mice into RNA later.

extract_protocol: RNA was isolated from sorted LICs using AllPrep DNA/RNA Mini kit

treatment_protocol: Eu-RET pups were treated with 50ul PBS or 20ug of Poly (A:U).

value: Spleen

value: 7 days post treatment

value: Leukemia initiating cells (LIC)

value: RFP/RET transgene

value: 13 days

value: Poly (A:U)


title: LICs from Eu-RET pups treated with PAU, 7 days post treatment 3


title: glioma_Primary [TCGA-19-0957-TP-01M-450-58TSX9]

value: female

value: Glioblastoma, IDH-wildtype (WHO grade 4)

value: Primary

value: IDHwt

value: Classic-like

value: RTK I


title: BS_15_1

value: wheat spikelet

value: 15 days after terminal spikelet

value: basal spikelet

value: untreated


title: LICs from Eu-RET pups treated with PAU, 7 days post treatment 2


title: glioma_Recurrence 1 [TCGA-19-1389-R1-21M-450-9WZ33C]

value: male

value: Recurrence

value: noncodel

value: Mesenchymal-like

value: mesenchymal


title: BS_15_2


title: LICs from Eu-RET pups treated with PAU, 7 days post treatment 4

value: Spleen

value: 7 days post treatment

value: Leukemia initiating cells (LIC)

value: RFP/RET transgene

value: 13 days


title: glioma_Recurrence 1 [TCGA-19-0957-R1-11M-450-IWFIBJ]

value: female

value: Glioblastoma, IDH-wildtype (WHO grade 4)

value: IDHwt


title: 3543_OF1A_1-1-I1-K2

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female

value: nuclear RNA + genomic DNA


title: glioma_Primary [TCGA-DH-A669-TP-12M-450-QDG6WF]

value: Oligodendroglioma, IDH-mutant and 1p/19q-codeleted (WHO grade 3)

value: Primary

value: IDHmut

value: codel

value: Codel

value: 1p/19q codeleted oligodendroglioma


title: MS_12_3

value: wheat spikelet

value: 12 days after terminal spikelet

value: central spikelet

value: untreated


title: 3543_OF1A_1-1-I1-K1


title: glioma_Recurrence 1 [TCGA-DU-5870-R1-12M-450-T5T4I6]

value: Recurrence


title: MS_12_2


title: 3543_OF1A_1-1-I1-K14


title: MS_12_1


title: BS_12_3

value: basal spikelet


title: 3543_OF1A_1-1-I1-K13


title: 3543_OF1A_1-1-I1-L14


title: glioma_Primary [TCGA-14-1402-TP-01M-450-Z1WJEV]

value: female

value: Glioblastoma, IDH-wildtype (WHO grade 4)

value: noncodel

value: Classic-like

value: mesenchymal


title: LICs from Eu-RET pups treated with PBS, 7 days post treatment 5

value: Spleen

value: 7 days post treatment

value: Leukemia initiating cells (LIC)

value: RFP/RET transgene

value: 13 days

value: PBS


title: LICs from Eu-RET pups treated with PAU, 7 days post treatment 1

value: Poly (A:U)


title: glioma_Recurrence 1 [TCGA-19-4065-R1-11M-450-T2ZZWK]

value: male

value: IDHwt

value: Mesenchymal-like


title: 3543_OF1A_1-1-I1-L13

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female

value: nuclear RNA + genomic DNA


title: glioma_Recurrence 1 [TCGA-14-1402-R1-01M-450-MKAY9C]

value: female

value: Glioblastoma, IDH-wildtype (WHO grade 4)

value: Recurrence

value: RTK II


title: BS_12_2

value: wheat spikelet

value: 12 days after terminal spikelet

value: basal spikelet

value: untreated


title: 3543_OF1A_1-1-I1-J1


title: LICs from Eu-RET pups treated with PBS, 7 days post treatment 4

value: Spleen

value: 7 days post treatment

value: Leukemia initiating cells (LIC)

value: RFP/RET transgene

value: 13 days


title: 3543_OF1A_1-1-I1-J2


title: BS_12_1


title: glioma_Primary [TCGA-14-0736-TP-01M-450-1VSUVF]

value: male

value: Primary

value: IDHwt

value: noncodel

value: Mesenchymal-like


title: glioma_Recurrence 1 [TCGA-14-0736-R1-01M-450-KIHOXS]

value: Glioblastoma, IDH-wildtype (WHO grade 4)

value: mesenchymal


title: 3543_OF1A_1-1-I1-J14

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female

value: nuclear RNA + genomic DNA


title: 3543_OF1A_1-1-I1-J13


title: LICs from Eu-RET pups treated with PBS, 7 days post treatment 2

value: PBS


title: glioma_Recurrence 1 [TCGA-06-0221-R1-11M-450-BV33CH]

value: Astrocytoma, IDH-mutant (WHO grade 4)

value: Recurrence

value: IDHmut

value: G-CIMP-low

value: high grade astrocytoma


title: glioma_Primary [TCGA-06-0221-TP-01M-450-Z6T93Z]

value: G-CIMP-high


title: 3543_OF1A_1-1-I1-I2


title: MS_9_2

value: wheat spikelet

value: 9 days after terminal spikelet

value: central spikelet

value: untreated


title: MS_9_1


title: 3543_OF1A_1-1-I1-I1


title: LICs from Eu-RET pups treated with PBS, 7 days post treatment 3

value: Spleen

value: 7 days post treatment

value: Leukemia initiating cells (LIC)

value: RFP/RET transgene

value: 13 days


title: LICs from Eu-RET pups treated with PBS, 7 days post treatment 1


title: BS_9_3

value: basal spikelet


title: glioma_Primary [TCGA-06-0211-TP-01M-450-7QXLC9]

value: male

value: Glioblastoma, IDH-wildtype (WHO grade 4)

value: Primary

value: IDHwt

value: noncodel

value: Classic-like

value: mesenchymal