title: scRNAseq_tumor_Ahr_cKO_rep1

city: Braunschweig

first: Andreas

last: Kloetgen

state: NI

address: Inhoffenstr 7

department: Department for Computational Biology of Infection Research

institute: Helmholtz Centre for Infection Research

description:
Sample 2
scRNA
scRNAseq_UMAP_embedding.tsv
scRNAseq_scaled_data.tsv

data_processing:
Preprocessing: alignment and counting was done with cellranger version 3.0.0, using the 'count' command with default parameters and specifying the mm10 transcriptome database.
Postprocessing: Further processing was done with the R package Seurat version 3.1.4. Cells were filtered if they had < 200 genes expressed. Both samples were aligned (functions FindIntegrationAnchors and IntegrateData), normalization was done with the ScaleData command and a single UMAP for both samples was created with the RunUMAP command.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: tsv - UMAP embeddings and scaled data.

source_name: Whole tumor

growth_protocol: Tumors were implanted orthotopically in the pancreas with 10x10^3 cells of the KPC primary pancreatic adenocarcinoma organoid cell line MT4. 14 days after tumor implantation, tumors were dissociated using Collagenase and DNase 1 and live cells were used for scRNA experiment.

extract_protocol:
Tumors from three Ahrfl/fl or three LysM-CRE cKO mice were digested, pooled, and stained with DAPI. Live cells were FACS-sorted into buffer (PBS + 2% FBS).
Cells were washed 2 times with PBS + 0.04% BSA, and then only 10x10^3 cells mixed with 10X Genomics Chromium single-cell RNA master mix, followed by loading onto a 10X Chromium chip according to the manufacturer’s protocol to obtain single-cell cDNA.

value: C57/BL6 Ahr fl/fl Lys M

value: tumor


title: Cortex_nucleus_mTLE non-HS7 [Cx_nuc_E07-24]

status: Public on Mar 31 2022

type: SRA

city: Utrecht

first: Ronald

middle: Jeroen

last: Pasterkamp

state: Utrecht

address: Universiteitsweg 100

department: Translational Neuroscience

country: Netherlands

institute: UMC Utrecht

description: mTLE non-HS

library_source: transcriptomic

data_processing:
mRNAs:
For analyzing mRNAs, following trimming of low-quality bases and adapter sequences with FASTQ-MCF (version 0.0.13), processed reads were mapped to the hg19/GCh37 reference human genome (iGenomes) with TopHat2 (version 2.0.13) (Kim et al., 2013. Genome Biology). For the alignments of the total RNA-seq data, the ‘fr-secondstrand’ option was chosen. Mapped counts for each gene were summarised using the python script htseq-count (Anders et al., 2015. Bioinformatics).
For differential expression analysis, genes and transcripts count data was analysed for differential expression in R using the Bioconductor package EdgeR version 3.12.1 (Robinson et al., 2010. Bioinformatics) with the trimmed mean of M-values (TMM) normalisation method (Robinson and Oshlack., 2010. Genome Biology). Gene expression levels were corrected for batch and gender effects by including the series of sequencing rounds, sexes of controls and patients to a generalised linear model. Using the Benjamini-Hochberg false discovery rate (FDR) adjusted P-values for multiple testing were calculated and only genes with an FDR < 0.05 were considered significantly differentially expressed (DE). Visualisation of data was performed in R using the ggplot2 library (version 2.1.0).
circRNAs:
For analyzing circularRNAs (circRNA), sequencing data were preprocessed by removing adapter sequences and trimming away low quality bases (Phred score 20) with Trim Galore which uses the Cutadapt algorithm (Martin, 2011. EMBnet.journal). CircRNA detection was performed by mapping filtered reads to the human genome (hg19) with Bowtie (Langmead et al., 2009. Genome Biology), using find_circ (Memczak et al., 2013. Nature) to detect back-splice junction (BSJ) spanning reads from the reads that do not map linearly to the human genome. Only circRNAs with two or more supporting BSJ reads within single samples were kept. A second circRNA detection algorithm, CIRCexplorer (Zhang et al., 2014. Cell), was used to verify the detected circRNAs. CIRCexplorer was guided by Ensembl Release 71 gene annotations on human genome (hg19).
Differential expression analysis was done using DESeq2 (Love et al., 2014. Genome Biology) in R. Raw counts of BSJ read numbers detected by find_circ were used as input for DESeq2. Statistical metrics produced by DESeq2 including probability value (p-value, p) and Benjamini-Hochberg adjusted p-values are reported with the normalized BSJ expression values generated by DESeq2.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: guide_*txt: ordered IDs; Abundance measurements or Significant genes

molecule: total RNA

organism: Homo sapiens

source_name: Cortex

extract_protocol:
Complete details can be found on manuscripts methods section. Briefly, subcellular fractionation was performed isolating pure cytosolic and nuclei cell compartments. Isolated cytoplasmic and nuclei samples were stored in Qiazol (Qiagen) at -80oC until RNA extraction was performed. Total RNA was extracted using miRNeasy kit (Qiagen), according to manufacturer’s protocol.
A total of 2 ug of RNA per sample in a 5 ul volume was rRNA-depleted using the Ribo-Zero Magnetic Kit (human/mouse/rat; Illumina) before library preparation. Stranded, paired-end sequencing libraries were prepared using the ScriptSeq v2 (Epicentre), after which samples were subjected to quality control on the 2100 Bioanalyzer (Agilent). Sequencing was performed as paired end 100 bp reads on an Illumina HiSeq 4000 sequencer at the Beijing Genomics Institute (BGI) (Hongkong, China).

tag: fraction

value: Nucleus

tag: sample type

value: mTLE non-HS

tag: tissue

value: Cortex


title: plate_056s_J8_S253_L004

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

country: Sweden

institute: Uppsala University

description: Brain single cell 50

data_processing:
The sequencing reads were first aligned to the mouse reference genome Gencode M26 genome with STAR software.
Genome_build: Gencode M26
Supplementary_files_format_and_content: tab-delimited text files include raw counts values for each sample

organism: Mus musculus

source_name: Brain

extract_protocol:
We used transgenic mouse reporter line (SM22-Cre;Rosa26-stop-tdTomato). We chosed to focus our efforts to adult mice brain cells and we chose a methodology based on fluorescence-activated cell sorting (FACS) into 384-well plates followed by the SmartSeq2 methodology for the generation and sequencing of full length polyadenylated cDNAs
Libraries for RNA-seq were prepared by using SMART-seq2 methodology

tag: strain

value: brain

tag: age

value: adult mice

tag: notch3 genotype

value: Het

tag: celltype

value: Macrophages


title: scRNAseq_tumor_fl_fl_rep1

country: Germany

description:
Sample 1
scRNA
scRNAseq_UMAP_embedding.tsv
scRNAseq_scaled_data.tsv

tag: genotype

value: C57/BL6 Ahr fl/fl


title: plate_056s_J6_S237_L004

description: Brain single cell 49


title: plate_059s_A8_S57_L005

description: Brain single cell 56

value: WT

value: Microglia


title: Cortex_nucleus_mTLE non-HS6 [Cx_nuc_E07-21]

description: mTLE non-HS


title: Typ2-US-1

city: Chicago

first: Harrison

middle: Shea

last: Greenbaum

state: Illinois

address: GCIS W325, 929 E. 57th Street

country: USA

institute: Ben May Department for Cancer Research

description: BaF3 cell line with plasmid overexpression

data_processing:
The libraries were sequenced by a Novaseq 6000 in two runs to generate paired-end 100bp reads. For each sample, the raw FASTQ files from two flow cells were combined before downstream processing.
RNA-seq data were analyzed using a local Galaxy  20.05 instance. Quality and adapter trimming were performed on the raw sequencing reads using Trim Galore! 0.6.3.
The reads were mapped to the mouse genome (GRCm38.p4 with GENCODE annotation) using RNA STAR  2.7.5b.
The resulting mapped reads from each sample were counted by featureCounts  1.6.4 for per gene read counts.
The raw counts were analyzed for differential expression between experimental conditions using DESeq2  1.22.1 .
Genome_build: Mouse (GRCm38.p4)
Supplementary_files_format_and_content: Comma delimited text file containing a matrix table with raw gene counts for every gene and every sample

source_name: CALR type 2 mutation unstarved rep 1

growth_protocol: BaF3 cells were maintained in 10% FBS RPMI media in 5% CO2.

extract_protocol:
Total RNA extraction by the Rneasy Mini Kit (Qiagen, 74104).
RNA libraries were prepared for sequencing by the University of Chicago Genomics Facility following standard protocols.

treatment_protocol: Cells were washed three times with PBS followed by media replacement using growth media with or without IL3 addition. In unstarved conditions, cells were supplied with the cytokine IL3 at a 1:10,000 dilution for a final concentration of 2 ng/mL; in starved conditions, cells were depleted of the IL3 cytokine addition for twenty-four hours.

tag: cell line

tag: overexpression

value: Thrombopoietin receptor and Type 2 mutant CALR

tag: treatment

value: IL3 (2 ng/mL)


title: E13-5_BPTF_cKO4

city: Ottawa

first: Dave

last: Picketts

state: Ontario

address: 501 Smyth Road

department: Regenerative Medicine

country: Canada

institute: OHRI

data_processing:
Pseudoalignment to mm10 transcriptome with Salmon (v1.4.0)
Differencial expression analysis by DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: raw files - .fastq       Pseudoaligned and quantified - .sf

source_name: Cortical whole tissue

growth_protocol: Murine cortical tissue dissected at E13.5

extract_protocol:
RNA was extracted in Trizol and purified by PureLink RNA cleanup kit (Thermo Fisher, cat 12183020) with in-column DNaseI treatment
NEB mRNA stranded library preparation was carried out following Bioanalyser analysis of RNA

tag: genotype/variation

value: Cre +/-


title: Cortex_nucleus_mTLE non-HS3 [Cx_nuc_E05-33]

description: mTLE non-HS


title: Cortex_nucleus_mTLE non-HS1 [Cx_nuc_E06-13]

description: mTLE non-HS


title: E13-5_BPTF_cKO3


title: plate_056s_J10_S269_L004

description: Brain single cell 46


title: plate_056s_J4_S221_L004

description: Brain single cell 48


title: plate_056s_J2_S205_L004

description: Brain single cell 47


title: plate_056s_I5_S37_L004

description: Brain single cell 45


title: E13-5_BPTF_cKO1


title: Cortex_nucleus_mTLE non-HS2 [Cx_nuc_E05-35]

description: mTLE non-HS


title: Cortex_nucleus_control7 [Cx_nuc_S11-028]

description: Control

value: Postmortem controls


title: Cortex_nucleus_control5 [Cx_nuc_S12-002]

description: Control


title: E13-5_BPTF_cKO2


title: E13-5_BPTF_WT04

value: Cre -/-


title: Cortex_nucleus_control6 [Cx_nuc_S10-109]

description: Control


title: plate_056s_I4_S29_L004

description: Brain single cell 44


title: E13-5_BPTF_WT02


title: E13-5_BPTF_WT03


title: Cortex_nucleus_control4 [Cx_nuc_S02-071]

description: Control


title: Cortex_nucleus_control3 [Cx_nuc_C05-93]

description: Control


title: plate_056s_I12_S93_L004

description: Brain single cell 42


title: plate_056s_I1_S5_L004

description: Brain single cell 41


title: E13-5_BPTF_WT01


title: Cortex_nucleus_control1 [Cx_nuc_C02-05]

description: Control


title: plate_056s_H4_S220_L004

description: Brain single cell 40


title: Cortex_cytoplasm_mTLE non-HS17_pre [Cx_cyt_015-02-Pre]

description: mTLE non-HS

value: Cytoplasm


title: plate_056s_H3_S212_L004

description: Brain single cell 39


title: Cortex_cytoplasm_mTLE non-HS17_post [Cx_cyt_015-02-Post]

description: mTLE non-HS


title: plate_056s_H2_S204_L004

description: Brain single cell 38


title: Cortex_cytoplasm_mTLE non-HS16_post [Cx_cyt_E15-07-Post]

description: mTLE non-HS


title: plate_056s_H12_S284_L004

description: Brain single cell 37


title: Cortex_cytoplasm_mTLE non-HS16_pre [Cx_cyt_E15-07-Pre]

description: mTLE non-HS


title: plate_056s_H10_S268_L004

description: Brain single cell 36


title: plate_056s_H1_S196_L004

description: Brain single cell 35


title: Cortex_cytoplasm_mTLE non-HS15_post [Cx_cyt_E15-06-Post]

description: mTLE non-HS


title: plate_056s_I3_S21_L004

description: Brain single cell 43


title: plate_056s_G9_S68_L004

description: Brain single cell 34


title: Cortex_cytoplasm_mTLE non-HS15_pre [Cx_cyt_E15-06-Pre]

description: mTLE non-HS


title: Cortex_cytoplasm_mTLE+HS14 [Cx_cyt_E11-17]

description: mTLE+HS

value: mTLE+HS


title: plate_056s_G6_S44_L004

description: Brain single cell 32


title: Cortex_cytoplasm_mTLE+HS13 [Cx_cyt_E07-28]

description: mTLE+HS


title: plate_056s_G7_S52_L004

description: Brain single cell 33


title: plate_056s_G5_S36_L004

description: Brain single cell 31


title: Surgical resection GBM-OM03244

type: genomic

city: Lausanne

first: Pierre

last: Bady

address: Quartier UNIL-Sorge

department: Swiss Institute of Bioinformatics

country: Switzerland

institute: CHUV / BCF / SIB

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03244

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

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

data_processing:
BeadStudio software v3.2 was used for primary data acqusition. Raw data was imported into R and further processed using R/Bioconductor package “minfi”. The raw pre-processing (Illumina method) was used for data normalization.
normalized (Illumina pre-processing) Average Beta

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Surgical resection GBM-OM03244

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was isolated using Qiagen AllPrep DNA/RNA Kit (Qiagen, 80204).

tag: patient

tag: batch

tag: gender

value: Male

tag: disease state

value: glioblastoma (GBM)

value: RT

tag: os month

tag: OS status

tag: tissue type

value: glioma tumor sample, FFPE

tag: grade

value: grade IV


title: Cortex_cytoplasm_mTLE+HS12 [Cx_cyt_E06-19]

description: mTLE+HS

tag: fraction

tag: sample type

tag: tissue

value: Cortex


title: D. melanogaster_head_experimental 2-4

type: RNA

city: Kanazawa

first: Takumi

last: Nishiuchi

address: 13-1 Takaramachi

country: Japan

institute: Kanazawa University

description: gene expresion in head with induced neural activity

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Microarray 4x44K (G4131F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried by raise it slowly from buffer 2.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green. Scan mode is eXtended Dynamic range Scan mode and PMT is set to 10% and 100%).

data_processing: The images were analyzed using Feature Extraction Software (Ver. 9.1.3.1; Agilent Technologies). These data were analyzed further with GeneSpring GX12.1 software (Agilent Technologies).  Normalization was performed as follows: 1, intensity-dependent Lowess normalization; 2, data transformation, with measurements less than 0.01 set to 0.01; 3, per-chip normalization, in which the 75th percentile method was used to normalize each array

organism: Drosophila melanogaster

source_name: D. melanogaster head, elav>dTrpA1, 31C

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.4 ug RNA using the Low RNA Input Fluorescent Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Standard methods

extract_protocol: Control group (Sample 1-1 to 1-4) were kept at 23C. Experimental group (Sample 2-1 to 2-4) received heat treatment (31C 1h). Heads were dissected immediately after the treatment, and RNA was extracted from heads (20 heads/sample) using TRIzol following the standard protocol.

treatment_protocol: w, elav-GAL4/+; UAS-dTrpA1/+ animals were reared at 23˚C until adulthood on standard fly food.

value: head

value: w, elav-GAL4/+; UAS-dTrpA1/+

value: 31C (neural activity induced)

value: pooled male and female


title: plate_056s_G3_S20_L004

description: Brain single cell 30

tag: strain

value: brain

tag: age

value: adult mice

tag: notch3 genotype

value: Het

tag: celltype

value: Macrophages


title: D. melanogaster_head_control 1-4

description: gene expresion in head without induced neural activity

source_name: D. melanogaster head, elav>dTrpA1, 23C

tag: genotype

tag: treatment

value: 23C (control)


title: Surgical resection GBM-OM03125

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03125

source_name: Surgical resection GBM-OM03125

tag: patient


title: Surgical resection GBM-MD1000

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-MD1000

source_name: Surgical resection GBM-MD1000

tag: batch

value: Female


title: Cortex_cytoplasm_mTLE+HS11 [Cx_cyt_E08-17]

description: mTLE+HS

value: Cytoplasm

value: mTLE+HS


title: D. melanogaster_head_experimental 2-2

tag: gender


title: D. melanogaster_head_control 1-1


title: D. melanogaster_head_experimental 2-3


title: Surgical resection GBM-OM03200

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03200

source_name: Surgical resection GBM-OM03200

value: Male

tag: disease state

value: glioblastoma (GBM)


title: Surgical resection GBM-OM03165

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03165

source_name: Surgical resection GBM-OM03165

value: RT

tag: os month

value: glioma tumor sample, FFPE


title: Cortex_cytoplasm_mTLE+HS10 [Cx_cyt_E06-21]

description: mTLE+HS

value: Cortex


title: plate_056s_G2_S12_L004

description: Brain single cell 29


title: D. melanogaster_head_experimental 2-1

value: head


title: plate_056s_G10_S76_L004

description: Brain single cell 27

value: Microglia


title: Surgical resection GBM-MD1015

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-MD1015

source_name: Surgical resection GBM-MD1015

value: TMZ

tag: OS status

value: grade IV


title: plate_056s_G12_S92_L004

description: Brain single cell 28

value: brain


title: Cortex_cytoplasm_mTLE+HS9 [Cx_cyt_E05-03]

description: mTLE+HS


title: Surgical resection GBM-OM03188

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03188

source_name: Surgical resection GBM-OM03188

tag: tissue type


title: D. melanogaster_head_control 1-3

value: w, elav-GAL4/+; UAS-dTrpA1/+

value: pooled male and female


title: plate_056s_F9_S259_L004

description: Brain single cell 26

value: adult mice

value: Het

value: Macrophages


title: Surgical resection GBM-OM03166

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03166

source_name: Surgical resection GBM-OM03166

tag: grade


title: Surgical resection GBM-MD1042

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-MD1042

source_name: Surgical resection GBM-MD1042


title: D. melanogaster_head_control 1-2

value: 23C (control)


title: Cortex_cytoplasm_mTLE non-HS6 [Cx_cyt_E07-21]

description: mTLE non-HS

tag: fraction

value: Cytoplasm

value: mTLE non-HS


title: Cortex_cytoplasm_mTLE non-HS3 [Cx_cyt_E05-33]

description: mTLE non-HS

tag: sample type


title: plate_056s_F8_S251_L004

description: Brain single cell 25

tag: tissue


title: plate_056s_F7_S243_L004

description: Brain single cell 24

tag: strain


title: Surgical resection GBM-OM03070

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03070

source_name: Surgical resection GBM-OM03070

value: Female

value: glioblastoma (GBM)

tag: age


title: Cortex_cytoplasm_mTLE non-HS2 [Cx_cyt_E05-35]

description: mTLE non-HS


title: plate_056s_F5_S227_L004

description: Brain single cell 22

tag: notch3 genotype


title: plate_056s_F6_S235_L004

description: Brain single cell 23

tag: celltype


title: Cortex_cytoplasm_mTLE non-HS1 [Cx_cyt_E06-13]

description: mTLE non-HS


title: Cortex_cytoplasm_control7 [Cx_cyt_S11-028]

description: Control

value: Postmortem controls


title: Cortex_cytoplasm_mTLE non-HS8 [Cx_cyt_E11-18]

description: mTLE non-HS

value: Cortex


title: Surgical resection GBM-OM03164

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03164

source_name: Surgical resection GBM-OM03164

value: Male

value: RT

value: glioma tumor sample, FFPE


title: plate_056s_F2_S203_L004

description: Brain single cell 21


title: Surgical resection GBM-OM03066

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03066

source_name: Surgical resection GBM-OM03066

value: TMZ

value: grade IV


title: plate_056s_F12_S283_L004

description: Brain single cell 20

source_name: Brain

value: brain


title: Surgical resection GBM-MD1040

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-MD1040

source_name: Surgical resection GBM-MD1040


title: Cortex_cytoplasm_control6 [Cx_cyt_S10-109]

description: Control

source_name: Cortex


title: Surgical resection GBM-OM03103

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03103

source_name: Surgical resection GBM-OM03103


title: plate_056s_F1_S195_L004

description: Brain single cell 19


title: Cortex_cytoplasm_control5 [Cx_cyt_S12-002]

description: Control


title: Cortex_cytoplasm_control4 [Cx_cyt_S02-071]

description: Control


title: Cortex_cytoplasm_control3 [Cx_cyt_C05-93]

description: Control


title: plate_056s_E12_S91_L004

description: Brain single cell 17


title: Cortex_cytoplasm_control1 [Cx_cyt_C02-05]

description: Control


title: plate_056s_E10_S75_L004

description: Brain single cell 16

value: Microglia


title: Surgical resection GBM-MD1036

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-MD1036

source_name: Surgical resection GBM-MD1036


title: Surgical resection GBM-OM03069

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03069

source_name: Surgical resection GBM-OM03069


title: plate_056s_C6_S42_L004

description: Brain single cell 15

value: adult mice


title: ES CD34+ cell-derived ortho rep2 [ATAC-seq]

city: New York

first: Xiuli

last: An

address: 310 E 67th St

institute: New York Blood Center

library_source: genomic

data_processing:
Raw Bulk-RNA-seq data of ES-ortho was filtered by fastp to remove low quality reads. Reads were mapped to UCSC hg19 by STAR and quantified by FeatureCounts.
Raw reads were filtered by fastp and then mapped to the hg19 genome using Bowtie2. Reads mapping to ENCODE blacklist regions and the mitochondrial genome were removed. Peaks were called using MACS2with parameters --nomodel --shift -100 --extsize 200.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample; peak text files

source_name: ES CD34+ cell-derived_orthochromatic erythroblasts

growth_protocol: Human ES cell line H1 cells were seeded onto irradiated OP9 cells and cultured in hESCs maintenance medium. Three days later, medium was replaced by hematopoiesis-inducing medium. H1 cells were co-cultured with OP9 cells for 15 days. On day 15, the cells were stained with PE-conjugated CD34 and APC-conjugated CD71 at 4℃ in the dark. The CD34+CD71- hematopoietic stem cells were sorted using BD FACSAria fusion Cell Sorter.

extract_protocol:
RNA was extracted using QIAGEN RNA isolation kit (QIAGEN#74104). The transposition reaction was performed with Tn5 transposase and the transposed DNA was purified and amplified using a Zymo DNA clean and concentrator-5 kit (Zymo#D4014) to generate sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: Orthochromatic erythroblasts

tag: cell subtype

value: ES CD34+ cell-derived


title: ES CD34+ cell-derived ortho rep1 [ATAC-seq]


title: ES CD34+ cell-derived ortho rep3 [ATAC-seq]


title: Surgical resection GBM-OM03080

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03080

source_name: Surgical resection GBM-OM03080

tag: patient

tag: treatment


title: plate_056s_C11_S82_L004

description: Brain single cell 13

value: Het


title: Surgical resection GBM-MD1037

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-MD1037

source_name: Surgical resection GBM-MD1037

tag: batch

tag: gender


title: Surgical resection GBM-MD1034

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-MD1034

source_name: Surgical resection GBM-MD1034

tag: disease state

tag: os month


title: Surgical resection GBM-OM03067

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03067

source_name: Surgical resection GBM-OM03067

tag: OS status

tag: tissue type


title: CB CD34+ cell-derived ortho rep3 [ATAC-seq]

source_name: CB CD34+ cell-derived_orthochromatic erythroblasts

value: CB CD34+ cell-derived


title: plate_056s_C1_S2_L004

description: Brain single cell 12


title: plate_056s_B9_S257_L004

description: Brain single cell 11

value: Macrophages


title: plate_056s_C5_S34_L004

description: Brain single cell 14


title: plate_056s_B4_S217_L004

description: Brain single cell 10


title: CB CD34+ cell-derived ortho rep2 [ATAC-seq]


title: Surgical resection GBM-MD1033

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-MD1033

source_name: Surgical resection GBM-MD1033

value: Female

tag: grade


title: Surgical resection GBM-OM03094

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03094

source_name: Surgical resection GBM-OM03094

value: glioblastoma (GBM)


title: Surgical resection GBM-OM03078

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03078

source_name: Surgical resection GBM-OM03078


title: plate_056s_B3_S209_L004

description: Brain single cell 9


title: CB CD34+ cell-derived ortho rep1 [ATAC-seq]


title: Surgical resection GBM-OM03072

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03072

source_name: Surgical resection GBM-OM03072


title: ES CD34+ cell-derived ortho rep3 [RNA-seq]


title: plate_056s_B2_S201_L004

description: Brain single cell 8


title: ES CD34+ cell-derived ortho rep2 [RNA-seq]


title: Surgical resection GBM-MD1056

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-MD1056

source_name: Surgical resection GBM-MD1056


title: ES CD34+ cell-derived ortho rep1 [RNA-seq]


title: Surgical resection GBM-MD1031

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-MD1031

source_name: Surgical resection GBM-MD1031


title: plate_056s_B12_S281_L004

description: Brain single cell 7

source_name: Brain


title: Surgical resection GBM-OM03071

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03071

source_name: Surgical resection GBM-OM03071


title: Cortex_cytoplasm_mTLE non-HS7 [Cx_cyt_E07-24]

description: mTLE non-HS

source_name: Cortex

tag: fraction

value: Cytoplasm

tag: sample type

value: mTLE non-HS


title: Surgical resection GBM-MD1054

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-MD1054

source_name: Surgical resection GBM-MD1054


title: Surgical resection GBM-MD1028

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-MD1028

source_name: Surgical resection GBM-MD1028

value: Male


title: IL-25 , 3DHD5E

city: Geneva

first: Barbara

last: Russo

address: Rue Michel Servet 1

department: DEPARTEMENT DE MEDECINE (DEMED)

institute: Centre Medical Universitaire

data_processing:
The reads were mapped with STAR aligner v.2.5.3a to the UCSC human hg38 reference. The transcriptome metrics were evaluated with the Picard tools v.1.141. The table of counts with the number of reads mapping to each gene feature of the UCSC human hg38 reference was prepared with HTSeq v0.9.1. Data were normalized with EdgeR.
Genome_build: hg38
Supplementary_files_format_and_content: 3D_treatedvsuntreated.xlsx (Analysis2_normalized_counts_cpm)

source_name: Healthy donor epidermal equivalent

growth_protocol: EE were generated according to (Borowczyk et al., 2020).

extract_protocol:
qiagen miniprep
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The medium containing or not IL-25 (100 ng/ml) was changed every other day for 11 days from air exposure

value: primary adult kerationcytes


title: plate_056s_B1_S193_L004

description: Brain single cell 4

tag: strain

tag: tissue


title: Control , 3DHD5


title: Control , 3DHD4


title: plate_056s_B10_S265_L004

description: Brain single cell 5

tag: age

tag: notch3 genotype


title: plate_056s_A8_S57_L004

description: Brain single cell 3

tag: celltype


title: IL-25 , 3DHD3E

tag: cell type


title: plate_056s_A6_S41_L004

description: Brain single cell 2


title: Surgical resection GBM-MD1024

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-MD1024

source_name: Surgical resection GBM-MD1024

tag: patient

value: glioma tumor sample, FFPE


title: Surgical resection GBM-OM03068

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03068

source_name: Surgical resection GBM-OM03068

tag: treatment

value: RT


title: plate_056s_A11_S81_L004

description: Brain single cell 1


title: Control , 3DHD3


title: Surgical resection GBM-MD1049

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-MD1049

source_name: Surgical resection GBM-MD1049

tag: batch

value: grade IV


title: Surgical resection GBM-MD1050

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-MD1050

source_name: Surgical resection GBM-MD1050

tag: gender


title: Surgical resection GBM-OM03064

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03064

source_name: Surgical resection GBM-OM03064

tag: disease state


title: Surgical resection GBM-MD1021

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-MD1021

source_name: Surgical resection GBM-MD1021

value: TMZ

tag: os month


title: Surgical resection GBM-OM03169

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03169

source_name: Surgical resection GBM-OM03169

tag: OS status


title: Surgical resection GBM-MD1047

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-MD1047

source_name: Surgical resection GBM-MD1047

tag: tissue type


title: KO-1

city: Suita

first: Takahiro

last: Kodama

state: Osaka

address: 2-2 Yamadaoka

department: Department of Gastroenterology and Hepatology

institute: Osaka university, Graduate School of Medicine

data_processing:
Sequencing was performed on an Illumina HiSeq 3000 platform in a 75-base single-end mode.
Sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat v2.1.1.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cufflinks version 2.2.1.
Genome_build: mm10
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

extract_protocol:
mRNA was extracted from frozen tissues with the RNeasy Plus Mini kit (Qiagen). Concentrations and quality were assessed using the Agilent Pico 6000 kit on the Bioanalyzer 2100.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Liver

tag: genotype

value: Alb-CreERT2(+) Pten fl/fl Traf3 fl/fl


title: KO-2


title: KO-3


title: WT-3

value: Wild type


title: WT-2


title: IL-25 , 3DHD4E


title: plate_056s_B11_S273_L004

description: Brain single cell 6

value: brain

value: adult mice


title: Surgical resection GBM-MD1016

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-MD1016

source_name: Surgical resection GBM-MD1016

tag: grade


title: WT-1


title: Surgical resection GBM-OM03167

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03167

source_name: Surgical resection GBM-OM03167


title: plate_056s_E6_S43_L004

description: Brain single cell 18

value: Het

value: Microglia


title: Surgical resection GBM-MD1043

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-MD1043

source_name: Surgical resection GBM-MD1043


title: Ctrl-2-IN

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

description:
Ribosome profiling
Total mRNA from BEAS-2B cells transiently expressing empty vector rep2

data_processing:
Library strategy: Ribo-Seq
Raw sequencing reads were trimmed for adapter sequences using cutadapt (v1.14). Trimmed reads were mapped against RepBase (v18.05) to remove reads mapping to repetitive sequences. Remaining reads were mapped to the appropriate genome build using STAR aligner (v2.5.2b). Raw read counts were generated from all mapped reads using featureCounts (v1.5.3) package.
Normalized counts were derived from DESeq output.
Assembly: hg19 (GRCh37)
Supplementary files format and content: counts_for_pub.txt contains featureCounts output in comma-delimited format.
Supplementary files format and content: diffexp.tsv files contain DESeq2 output in tab-separated format.

source_name: BEAS-2B cells

growth_protocol: Standard cell culture in PneumaCult+supplements media on matrigel coated plates for BEAS-2B cells.

extract_protocol:
Cells were treated with CHX at 100 µg/ml before fractionation. Total and polysome derived RNA were extracted using Trizol reagent.
Illumina polyA Total RNA kit.

treatment_protocol: BEAS-2B cells were nucleofected with the Lonza T1 kit using pcDNA3.4 plasmids expressing ORF9c-3xFLAG, and the empty pcDNA3.4 vector.

tag: cell line

tag: transient expression

value: Control


title: Ctrl-1-IN

description:
Ribosome profiling
Total mRNA from BEAS-2B cells transiently expressing empty vector rep1


title: Ctrl-2-poly

description:
Ribosome profiling
mRNA from polysome fraction from BEAS-2B cells transiently expressing empty vector rep2

molecule: polyA RNA


title: Surgical resection GBM-MD1014

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-MD1014

source_name: Surgical resection GBM-MD1014

value: Female

value: glioblastoma (GBM)


title: Surgical resection GBM-OM03102

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03102

source_name: Surgical resection GBM-OM03102


title: Surgical resection GBM-OM03159

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03159

source_name: Surgical resection GBM-OM03159


title: Surgical resection GBM-OM03085

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03085

source_name: Surgical resection GBM-OM03085


title: ORF9c-1-IN

description:
Ribosome profiling
Total mRNA from BEAS-2B cells transiently expressing ORF9c_3XFLAG rep1


title: ORF9c-2-poly

description:
Ribosome profiling
mRNA from polysome fraction from BEAS-2B cells transiently expressing ORF9c_3XFLAG rep2


title: Ctrl-1-poly

description:
Ribosome profiling
mRNA from polysome fraction from BEAS-2B cells transiently expressing empty vector rep1


title: ORF9c-1-poly

description:
Ribosome profiling
mRNA from polysome fraction from BEAS-2B cells transiently expressing ORF9c_3XFLAG rep1


title: Surgical resection GBM-OM03227

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03227

source_name: Surgical resection GBM-OM03227


title: UCD4 E2+R5020 24h replicate 1 [22_S100_L003]

city: Aurora

first: Jessica

last: Finlay-Schultz

state: CO

department: Pathology

institute: University of Colorado Denver Anschutz Medical Campus

data_processing:
adaptrer trimming was done for raw fastq files cutadapt
Alignment to the reference genome was done using STAR
the aligned bam files were indexed and sorted using samtools
sorted bam files were used for gene expression quantification using Gsubread and DESeq2
Genome_build: GRCh38

source_name: UCD4 cell line

growth_protocol: UCD4 cells were maintained in DMEM/F12 media supplemented with 10% fetal bovine serum, 100 ng/mL choleratoxin, and 10^-9 M insulin.

extract_protocol:
Extraction of total RNA was performed using the Qiagen miRNeasy Mini Kit with DNase treatment according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols at the University of Colorado Denver Genomics and Microarray Core facility.

treatment_protocol: Cells were treated for 24 hours with indicated hormones or ethanol vehicle

value: hormone receptor positive breast cancer


title: Surgical resection GBM-OM03240

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03240

source_name: Surgical resection GBM-OM03240

value: Male


title: UCD4 E2+R5020 24h replicate 2 [23_S101_L003]


title: Surgical resection GBM-OM03145

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03145

source_name: Surgical resection GBM-OM03145


title: UCD4 E2+R5020 24h replicate 3 [24_S102_L003]


title: Surgical resection GBM-OM03189

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03189

source_name: Surgical resection GBM-OM03189


title: Surgical resection GBM-OM03115

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03115

source_name: Surgical resection GBM-OM03115


title: Surgical resection GBM-OM03083

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03083

source_name: Surgical resection GBM-OM03083


title: Surgical resection GBM-OM03099

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03099

source_name: Surgical resection GBM-OM03099


title: UCD4 R5020 24h replicate 3 [21_S99_L003]


title: UCD4 R5020 24h replicate 2 [20_S98_L003]


title: Surgical resection GBM-OM03114

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03114

source_name: Surgical resection GBM-OM03114


title: Surgical resection GBM-OM03190

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03190

source_name: Surgical resection GBM-OM03190


title: ORF9c-2-IN

description:
Ribosome profiling
Total mRNA from BEAS-2B cells transiently expressing ORF9c_3XFLAG rep2


title: UCD4 E2 24h replicate 3 [18_S96_L003]

value: estrogen


title: UCD4 E2 24h replicate 2 [17_S95_L003]


title: Surgical resection GBM-OM03129

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03129

source_name: Surgical resection GBM-OM03129

value: glioma tumor sample, FFPE


title: Surgical resection GBM-OM03141

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03141

source_name: Surgical resection GBM-OM03141

value: RT


title: UCD4 E2 24h replicate 1 [16_S94_L003]


title: UCD4 OH 24h replicate 3 [15_S93_L003]

value: ethanol vehicle


title: UCD4 OH 24h replicate 2 [14_S92_L003]


title: Surgical resection GBM-OM03180

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03180

source_name: Surgical resection GBM-OM03180

value: TMZ

value: grade IV


title: Surgical resection GBM-MD1004

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-MD1004

source_name: Surgical resection GBM-MD1004


title: Surgical resection GBM-OM03252

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03252

source_name: Surgical resection GBM-OM03252


title: Surgical resection GBM-OM03076

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03076

source_name: Surgical resection GBM-OM03076


title: UCD4 OH 24h replicate 1 [13_S91_L003]


title: Surgical resection GBM-OM03270

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03270

source_name: Surgical resection GBM-OM03270


title: DMSO

city: Beijing

first: Miaoqing

last: Zhang

state: Please Select

address: No. 1, TianTan XiLi, Dong-cheng district

country: China

institute: Institute of Medicinal Biotechnology

data_processing:
FastQC software used for basecalling.
Sequences were aligned by using Hisat2/Topha software
Data were filtered using the fastp software,In short, filter the original data, delete the reads that do not meet the analysis criteria, and obtain clean reads that can be used for alignment, statistics and analysis.
Genome_build: Danio_rerio.GRCz11.dna.toplevel.REF.fa
Supplementary_files_format_and_content: tab-delimited text files include gene enrichment analysis for each Sample

organism: Danio rerio

source_name: liver

extract_protocol:
Total RNA were extracted from dissected liver of larvae by using TRIzol reagent, RNA was quantified by using Agilent 2100 BioAnalyzer
Libraries were prepared according to Illumina's instructions accompanying the NEBNext Ultra RNA Library Prep Kit (NEB #E7530S/L)

treatment_protocol: Wild-type AB strain zebrafish (Danio reio) were reared in a standard laboratory environment with a 14 h light/10 h dark cycle at 28±1°C,3 days postfertilization (3 dpf) zebrafish larvae were exposed to azithromycin and its different structural impurities solutions at the same concentration (2 mmol/L) for 72 hours.

tag: tissue

value: liver

value: larvae

tag: strain

value: Wild-type AB

value: DMSO


title: Surgical resection GBM-OM03248

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03248

source_name: Surgical resection GBM-OM03248

tag: age


title: UCD4 R5020 24h replicate 1 [19_S97_L003]

source_name: UCD4 cell line


title: Surgical resection GBM-OM03138

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03138

source_name: Surgical resection GBM-OM03138


title: T47D E2+R5020 24h replicate 2 [11_S89_L003]

source_name: T47D cell line

growth_protocol: T47D cells were maintained in MEM/EBSS supplemented with 5% fetal bovine serum, 1x NEAA, 1 mM sodium pyruvate, and 10^-9 M insulin.

treatment_protocol: Cells were treated for 24 hours with indicated hormones or ethanol vehicle.


title: Surgical resection GBM-OM03128

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03128

source_name: Surgical resection GBM-OM03128


title: T47D R5020 24h replicate 2 [8_S86_L003]


title: T47D E2+R5020 24h replicate 1 [10_S88_L003]


title: T47D R5020 24h replicate 3 [9_S87_L003]


title: Surgical resection GBM-MD1003

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-MD1003

source_name: Surgical resection GBM-MD1003


title: Surgical resection GBM-OM03152

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03152

source_name: Surgical resection GBM-OM03152


title: T47D R5020 24h replicate 1 [7_S85_L003]


title: Surgical resection GBM-OM03269

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03269

source_name: Surgical resection GBM-OM03269


title: T47D E2 24h replicate 3 [6_S84_L003]


title: C2C12 siSatb2 rep 3

first: Lynn

last: Megeney

department: Regenerative Medicine Program

institute: Ottawa Hospital Research Institute

data_processing:
Reads were mapped to GRCm38 (mm10) using tophat2 v2.1.1;
Mapped reads were assigned to transcripts (GENCODE M23) using FeatureCounts v1.5.2;
DEseq2 v1.12.0 was used for differential expression between siControl and siSatb2 replicates;
Fold changes were shrunk using apeglm method (DEseq v1.12.0);
List of differentially expressed genes were filtered using adjusted p value <= 0.05.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: 1. Transcript counts from FeatureCounts; 2. DEseq2 output: Differentially expressed genes (unfiltered)

source_name: 24 h differentiated C2C12 cells

growth_protocol: Cells of the immortalized mouse cell line, C2C12, were grown on non-collagen coated cell culture plates in Dulbecco’s Modified Eagle’s medium (DMEM) with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin (growth medium).

extract_protocol:
Total RNA was isolated using a RNeasy Kit (QIAGEN) using an on-column DNase digestion (RNase-Free DNase Set, QIAGEN) to avoid genomic DNA contamination.
Library preparation and 126-bp paired-end RNA-seq was performed by the Next-Generation Sequencing Facility at The Centre for Applied Genomics in The Hospital for Sick Children. RNA integrity was assessed using the Bioanalyzer platform (Agilent Technologies, Inc.). Sequencing was performed using standard procedures for the Illumina HiSeq 2500 platform.

treatment_protocol: siRNA duplexes were used to suppress Satb2 gene expression in C2C12 cells. C2C12 cells were transfected at 25% confluence with 10 nM siRNA (siSatb2 or siControl) and the Lipofectamine RNAiMAX reagent, as directed by the manufacturer’s protocol (Invitrogen). After an overnight incubation, fresh media was added onto the cells and the cells were re-transfected. This continued until the cells reached 100% confluence, after which differentiation media was added to the cells. Media change and re-transfection occurred every 24 h throughout the indicated time course.

value: differentiated


title: Surgical resection GBM-OM03137

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03137

source_name: Surgical resection GBM-OM03137


title: T47D E2 24h replicate 2 [5_S83_L003]


title: C2C12 siSatb2 rep 2


title: Surgical resection GBM-OM03127

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03127

source_name: Surgical resection GBM-OM03127


title: T47D E2 24h replicate 1 [4_S82_L003]


title: T47D OH 24h replicate 3 [3_S81_L003]


title: Surgical resection GBM-OM03146

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03146

source_name: Surgical resection GBM-OM03146


title: Surgical resection GBM-MD1001

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-MD1001

source_name: Surgical resection GBM-MD1001


title: C2C12 siControl rep 2

value: siControl


title: C2C12 siControl rep 3


title: T47D OH 24h replicate 2 [2_S80_L003]


title: T47D E2+R5020 24h replicate 3 [12_S90_L003]


title: Surgical resection GBM-OM03212

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03212

source_name: Surgical resection GBM-OM03212


title: Surgical resection GBM-OM03268

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03268

source_name: Surgical resection GBM-OM03268


title: T47D OH 24h replicate 1 [1_S79_L003]


title: Surgical resection GBM-OM03110

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03110

source_name: Surgical resection GBM-OM03110


title: C2C12 siControl rep 1


title: Surgical resection GBM-OM03124

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03124

source_name: Surgical resection GBM-OM03124


title: Foxp3Spleen-3

city: Charlestown

first: Jason

last: Griffith

state: MA

address: 149 13th Street

department: Medicine

institute: Massachusetts General Hospital

description: Total Foxp3+ Treg cells sorted from spleen

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 instrument, resulting in approximately 30 million single-end 50 bp reads per sample on average.
Sequencing reads were mapped in a splice-aware fashion to the mouse reference transcriptome (mm10 assembly) using STAR (Dobin et al., 2013).
Read counts over transcripts were calculated using HTSeq (Anders et al., 2015) based on the Ensembl annotation for GRCm38/mm10 assembly.
For differential expression analysis we used the EdgeR method (Robinson et al., 2010) and classified genes as differentially expressed based on the cutoffs of 2-fold change in expression value and false discovery rates (FDR) below 0.05.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Samples_JAa1_complete_CPM_table.txt: Matrix table for CPM of every gene and every sample.
Supplementary_files_format_and_content: Samples_JAa1_complete_RPKM_table.txt: Matrix table for RPKM of every gene and every sample.

source_name: Sorted CD3+CD4+Foxp3YFP+ Treg cells from spleen 3

extract_protocol:
ST2+, CXCR3+ and ST2-CXCR3- Treg cells (viable, CD3+, CD4+, YFP+) were sorted from the lungs of day 7 H1N1 (PR8) influenza infected Foxp3YFPCre mice. Total Treg cells (Viable, CD3+, CD4+, YFP+) were sorted from the spleens of naïve Foxp3YFPCre mice. Cells were sorted on a FACSaria Fusion (BD Biosciences) into RLT buffer (Qiagen) supplemented with beta-mercaptoethanol (Sigma-Alrich). RNA was then isolated on a RNeasy micro plus spin column (Qiagen) and validated by bioanalzyer.
The libraries were prepared by the MGH NextGen Sequencing Core using the Clontech SMARTer Ultra Low Input RNA Kit V4 (Clontech Laboratories).

value: No infection, naive

value: Spleen

tag: cell population

value: Total Foxp3+ Treg cells


title: 5-CSF-1R+

city: 南通

first: xingchao

last: wang

state: Jiangsu

address: Xinchengqiao

institute: Affiliated Hospital of Nantong University

data_processing:
Qualitycontrol using Fastqc
Alignment using Hisat2 2.1.0
Using Stringtie 2.1.3 to calculate gene counts
Genome_build: hg38
Supplementary_files_format_and_content: Gene level counts

source_name: Colon adenocarcinoma

extract_protocol:
Tissue was dissociated and single cells sorted into the lysate.The Smart-seq2 technique was used as  full-length transcriptome amplification and library construction of the mRNA.
150bp Paired end

value: colon adenocarcinoma


title: 5-CSF-1R-

value: CSF-1R- TAMs


title: Foxp3Spleen-1

source_name: Sorted CD3+CD4+Foxp3YFP+ Treg cells from spleen 1


title: 4-CSF-1R+


title: Foxp3Spleen-2

source_name: Sorted CD3+CD4+Foxp3YFP+ Treg cells from spleen 2


title: Surgical resection GBM-OM03267

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03267

source_name: Surgical resection GBM-OM03267

value: Male

value: glioblastoma (GBM)


title: Surgical resection GBM-OM03204

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03204

source_name: Surgical resection GBM-OM03204

value: RT

value: glioma tumor sample, FFPE


title: C2C12 siSatb2 rep 1

tag: cell type


title: Surgical resection GBM-OM03105

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03105

source_name: Surgical resection GBM-OM03105

tag: patient


title: ST2-3

description: ST2+ Treg cells sorted from lung

source_name: Sorted CD3+CD4+Foxp3YFP+ST2+CXCR3- Treg cells from lung 3

value: PR8 influenza infection day 7

value: Lung

value: ST2+ Treg cells


title: 4-CSF-1R-


title: ST2-2

description: ST2+ Treg cells sorted from lung

source_name: Sorted CD3+CD4+Foxp3YFP+ST2+CXCR3- Treg cells from lung 2


title: Surgical resection GBM-OM03123

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03123

source_name: Surgical resection GBM-OM03123

value: Female

tag: treatment

value: grade IV


title: 3-CSF-1R+


title: 3-CSF-1R-


title: CXCD3-3

description: CXCR3+ Treg cells sorted from lung

source_name: Sorted CD3+CD4+Foxp3YFP+ST2-CXCR3+ Treg cells from lung 3

value: CXCR3+ Treg cells


title: C2C12 Gr_SATB2

data_processing:
Reads aligned to GRCm38 (UCSC mm10, Dec/2011) with bowtie2 v2.2.6 using default parameters;
Peaks called with MACS2 v2.1.0 with default parameters and IgG as control.
Genome_build: mm10
Supplementary_files_format_and_content: peak files

source_name: C2C12 cells

growth_protocol: Cells of the immortalized mouse cell line, C2C12, were grown on non-collagen coated cell culture plates in Dulbecco’s Modified Eagle’s medium (DMEM) with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin (growth medium). When confluent, cells were differentiated in DMEM supplemented with 2% horse serum and 1% penicillin/streptomycin (differentiation medium).

extract_protocol:
C2C12 cells were grown on 15 cm plates and allowed to reach 100% confluence before twenty million proliferating cells were collected (n = 1). Cells were fixed for 10 min using 1% formaldehyde in DMEM. Cell fixation was quenched by removing the fixation solution, rinsing the plates with PBS, and then pouring a solution of 0.125 M glycine in PBS onto the cells and incubating for 5 min. Subsequently, plates were washed 2× with PBS and then cells were scraped from the plates, pelleted, and stored at -80 °C until used. Given that SATB2 is a nuclear matrix attachment protein, it required an alternative protocol for chromatin shearing than standard preparations. First, a commercial hypotonic solution (Active Motif) was used to lyse cellular membranes but retain intact nuclear membranes. We subsequently performed additional lysis using a handheld glass Dounce homogenizer. After centrifugation, the supernatant was discarded and the pelleted nuclei were treated with Active Motif’s Pro-enzymatic Digestion Nuclear Extraction Solution. After incubation at 37 °C for 5 min, we supplemented the reaction with 1 U micrococcal nuclease (New England Biolabs) and allowed it to incubate for 10 min. We then supplemented the reaction with SDS to a final volume 2% SDS-chromatin solution. We proceeded to the second stage of shearing using sonication via a Covaris M220 Focused-Ultrasonicator instrument, setting the parameters to produce sheared DNA of 200 bp. After sonication, we performed a final centrifugation at 16 000 × g at 4 °C for 20 min and collected the supernatant containing the sheared chromatin. We performed immunoprecipitations with 5 μg 1°Ab (Target: SATB2, Abcam, positive control: RNA pol II, Active Motif, negative control: mouse IgG, Santa Cruz) using magnetic beads (Active Motif) diluted in commercial ChIP-buffer (Active Motif) overnight at 4 °C. Captured chromatin was isolated using magnetic stands to pulldown the beads. Bound DNA was subsequently eluted with commercial elution, reverse cross-linking, protein digestion, and RNA digestion solutions (Active Motif). The resulting samples of DNA were further purified using phenol:chloroform extraction procedures. Final DNA was quantified using a NanoDrop spectrophotometer, with a 25 μL final volume having concentrations of 75–100 ng/μL.
For genome-wide analysis, immunoprecipitated DNA was amplified and 75 bp single read sequencing was performed on an Illumina HiSeq 2500 at the Next-Generation Sequencing Facility at The Centre for Applied Genomics in The Hospital for Sick Children (Toronto, Ontario, Canada). The data were summarized and basic comparisons performed using the Excel spreadsheet program (Microsoft). Reads were aligned to the GRCm38 (UCSC mm10, Dec/2011) mouse genome from the UCSC genome browser with bowtie2 (v2.2.6) using the default parameters, and peaks were called using MACS version 2.1.0, again with default parameters, and using IgG ChIP-seq data as a control.

value: Proliferating

tag: chip antibody


title: ST2-1

description: ST2+ Treg cells sorted from lung

source_name: Sorted CD3+CD4+Foxp3YFP+ST2+CXCR3- Treg cells from lung 1


title: 2-CSF-1R+


title: CXCD3-2

description: CXCR3+ Treg cells sorted from lung

source_name: Sorted CD3+CD4+Foxp3YFP+ST2-CXCR3+ Treg cells from lung 2


title: Surgical resection GBM-OM03266

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03266

source_name: Surgical resection GBM-OM03266

tag: batch

tag: gender

value: TMZ


title: Surgical resection GBM-OM03253

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03253

source_name: Surgical resection GBM-OM03253

tag: disease state

tag: os month


title: C2C12 Gr_IgG

value: IgG


title: Surgical resection GBM-OM03263

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03263

source_name: Surgical resection GBM-OM03263

tag: OS status

tag: tissue type


title: Surgical resection GBM-OM03228

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03228

source_name: Surgical resection GBM-OM03228

tag: grade


title: 2-CSF-1R-

source_name: Colon adenocarcinoma

tag: cell line


title: Surgical resection GBM-OM03203

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03203

source_name: Surgical resection GBM-OM03203


title: 1-CSF-1R+


title: CXCD3-1

description: CXCR3+ Treg cells sorted from lung

source_name: Sorted CD3+CD4+Foxp3YFP+ST2-CXCR3+ Treg cells from lung 1


title: DN-3

description: ST2-CXCR3- Tregs sorted from lung

source_name: Sorted CD3+CD4+Foxp3YFP+ST2-CXCR3- Treg cells from lung 3

value: ST2-CXCR3- Treg cells


title: Surgical resection GBM-OM03122

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03122

source_name: Surgical resection GBM-OM03122


title: Surgical resection GBM-OM03101

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03101

source_name: Surgical resection GBM-OM03101


title: miR-31 KO-3

city: Tianjin

first: Peitao

address: Qixiangtai Road 22

institute: Tianjin Medical University

description: knock out miR-31 with sgRNA

data_processing:
We use  Bowtie2  to map clean reads to reference gene and use  HISAT to reference genome.Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using   Bowtie2  parameters for SE reads: -q --phred64 --sensitive --dpad 0 --gbar,HISTA parameters for SE reads: -p 8 --phred64 --sensitive -I 1 -X 1000
The FPKM is calculated by RSEM, which is the quantification tool that computed Maximum likelihood abundance estimates using the Expectation Maximization (EM) algorithm for its statistical model, including the modeling of paired-end (PE) and variable-length reads, fragment length distributions, and quality scores, to determine which transcripts are isoforms of the same gene.
Genome_build: hg38 for Homo sapiens
Supplementary_files_format_and_content: FPKM

growth_protocol: K1 cells were cultured in DMEM with 10% FBS

extract_protocol:
RNA was harvested using Trizol reagent. First Strand cDNA Synthesis Kit (04 896 866 001, Roche) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: K1 cells were transfected with control and sgRNA targeting miR-31

value: papillary thyroid carcinoma cells

value: knock out miR-31 with sgRNA


title: 1-CSF-1R-

value: CSF-1R- TAMs

value: colon adenocarcinoma


title: S43414

city: Dallas

first: Sara

middle: K

last: Hildebrand

state: TX

address: 5323 Harry Hines blvd

department: Center for the Genetics of Host Defense

institute: UT Southwestern Medical Center

description:
Rnps1 ub/ub
Dataset S1 gene_exp_diff_F181I/F181I_WT (primary CD8+ T cells)
Dataset S2 Dataset isoform_switches_with_consequence_primary_CD8_T_cells
Dataset S4 Dataset_splicing F181I/F181I_WT (primary CD8+ T cells)

data_processing:
Adapters were trimmed from fastq.gz files using cutadapt v1.9.dev4
Trimmed fastq.gz were aligned to the mm10 reference genome using tophat-2.0.10
BAM files resulting from alignments were run through cuffdiff (cufflinks v2.1.1) for differential expression
BAM files were also run through ASpli v1.8.1 (R v3.5.3) for splicing analysis
Genome_build: mm10
Supplementary_files_format_and_content: excel file include FPKM values for each Sample (Cd8+ T cells)
Supplementary_files_format_and_content: excel files including PIR and PSI metrics for splicing (all samples)

source_name: Cd8+ T-cells

extract_protocol:
Total RNAs from the splenic CD8+ T or HECs cells were extracted using the RNeasy Plus kit with genomic DNA elimination (Qiagen), according to the manufacturer’s instructions.
Libraries were prepared using the KAPA Stranded RNA-Seq kit with RiboErase (HMR) (Kapa Biosystems), according to the manufacturer’s instructions.

value: Cd8+ T-cells

tag: genotype

value: Rnps1 ub/ub

value: no treatment


title: miR-31 KO-2

description: knock out miR-31 with sgRNA


title: Surgical resection GBM-OM03143

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03143

source_name: Surgical resection GBM-OM03143

value: glioblastoma (GBM)

value: RT

value: glioma tumor sample, FFPE


title: DN-2

description: ST2-CXCR3- Tregs sorted from lung

source_name: Sorted CD3+CD4+Foxp3YFP+ST2-CXCR3- Treg cells from lung 2

value: PR8 influenza infection day 7

tag: tissue

value: Lung


title: Surgical resection GBM-OM03265

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03265

source_name: Surgical resection GBM-OM03265

value: Female

value: grade IV


title: Surgical resection GBM-OM03251

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03251

source_name: Surgical resection GBM-OM03251

value: Male


title: Control-3

description: control

value: control


title: Surgical resection GBM-OM03198

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03198

source_name: Surgical resection GBM-OM03198


title: S43412

description:
wild-type
Dataset S1 gene_exp_diff_F181I/F181I_WT (primary CD8+ T cells)
Dataset S2 Dataset isoform_switches_with_consequence_primary_CD8_T_cells
Dataset S4 Dataset_splicing F181I/F181I_WT (primary CD8+ T cells)

value: wild-type


title: Surgical resection GBM-OM03139

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03139

source_name: Surgical resection GBM-OM03139


title: Control-1

description: control

value: papillary thyroid carcinoma cells


title: Control-2

description: control


title: Surgical resection GBM-OM03220

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03220

source_name: Surgical resection GBM-OM03220


title: Surgical resection GBM-MD1013

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-MD1013

source_name: Surgical resection GBM-MD1013


title: Sample 9_Endothelial cells from Eltd1-/- mice brain

data_processing:
Library strategy: TRAP
The sequence reads were aligned to the Ensembl mouse gene assembly (GRCm38) using Tophat2 software (version 2.1.1).
FPKM summary was performed using the Cufflinks tool (version 2.2.1)
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files with RPKM values for each sample

extract_protocol:
GL261 tumors were dissected under a stereological microscope. GFP tagged polysomes was isolated using anti-GFP bound Dynabeads (Qiagen). After extensive washing, mRNA of endothelial cells from healthy brain tissue and GL261 tumor tissue were obtained by Trizol and further purified by RNeasyMicro kit (Qiagen).
Ribosome-RNA was removed from the sample using RiboGone kit (Clontech Laboratories). The RNA concentration and quality was measured by Agilent 2100 bioanalyzer. Samples with RIN value >7 were selected for further cDNA synthesis and purification. Three mouse samples from each group (healthy wild type mice, healthy Eltd1-/- mice, GL261 tumor wild type mice and GL261 tumor Eltd1-/- mice) were selected for library preparation using SMARTer® Stranded RNA-Seq Kit (Clontech Laboratories), and were submitted for sequencing on HiSeq2500.

tag: strain

value: Brain

value: endothelial

value: adult


title: Surgical resection GBM-OM03249

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03249

source_name: Surgical resection GBM-OM03249

tag: age


title: Sample 8_Endothelial cells from wild type mice brain


title: Surgical resection GBM-OM03195

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03195

source_name: Surgical resection GBM-OM03195

value: TMZ


title: Sample 11_Endothelial cells from Eltd1-/- mice brain


title: Sample 10_Endothelial cells from Eltd1-/- mice brain


title: DN-1

description: ST2-CXCR3- Tregs sorted from lung

source_name: Sorted CD3+CD4+Foxp3YFP+ST2-CXCR3- Treg cells from lung 1

tag: cell population

value: ST2-CXCR3- Treg cells


title: Surgical resection GBM-OM03264

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03264

source_name: Surgical resection GBM-OM03264


title: S43107

tag: cell type

value: Cd8+ T-cells

value: Rnps1 ub/ub

value: no treatment


title: miR-31 KO-1

description: knock out miR-31 with sgRNA

value: knock out miR-31 with sgRNA


title: Sample 5_Endothelial cells from tumor grown on wild type mice

value: Tumors


title: Sample 6_Endothelial cells from wild type mice brain


title: Sample 4_Endothelial cells from tumor grown on wild type mice


title: A2780 si-MEX3A#3

city: Jinan

first: Chen

last: Zhao

state: China

address: 107 Wenhua Xi Road

department: Department of Obstetrics and Gynecology

institute: Qilu Hospital, Shandong University

data_processing:
Sequenced reads were generated by base calling using the Illumina standard pipeline
Raw reads were first filtered to obtain clean reads using FASTX-Toolkit
High-quality reads were mapped to the human reference genome hg19 using HISAT2 software with default parameters
Alignment was independently performed for reads from each sample, and reads mapping to more than three genomic sites were discarded
Based on the value of reads per kilobase per million mapped reads, gene expression levels were determined using Cufflinks software

extract_protocol:
Total RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ovarian cancer cell line

tag: transfection


title: Surgical resection GBM-OM03098

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03098

source_name: Surgical resection GBM-OM03098

tag: patient

value: glioblastoma (GBM)

tag: treatment

value: glioma tumor sample, FFPE


title: Surgical resection GBM-OM03097

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03097

source_name: Surgical resection GBM-OM03097

tag: batch

value: Male

value: grade IV


title: S43103

value: wild-type


title: A2780 si-MEX3A#2


title: A2780 si-MEX3A#1


title: Sample 3_Endothelial cells from tumor grown on wild type mice

first: L.

institute: Uppsala University


title: Sample 2_Endothelial cells from tumor grown on Eltd1-/- mice


title: Surgical resection GBM-OM03261

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03261

source_name: Surgical resection GBM-OM03261

tag: gender

value: RT


title: A2780 si-NC#3

value: si-NC


title: A2780 si-NC#2


title: Sample 1_Endothelial cells from tumor grown on Eltd1-/- mice

value: endothelial


title: Surgical resection GBM-OM03089

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03089

source_name: Surgical resection GBM-OM03089

value: Female

tag: disease state


title: Surgical resection GBM-OM03087

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03087

source_name: Surgical resection GBM-OM03087

value: TMZ

tag: os month


title: Surgical resection GBM-OM03118

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03118

source_name: Surgical resection GBM-OM03118

tag: OS status


title: Surgical resection GBM-OM03091

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03091

source_name: Surgical resection GBM-OM03091

tag: tissue type


title: carnosol_3

first: Yue

last: Ren

address: Beijing University of Chinese Medicine

institute: Beijing University of Chinese Medicine

data_processing:
Illumina software used for basecalling.
The genes expression level was calculated by the fragments per kilobase million (FPKM) methods.
Genome_build: 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.

source_name: Retina

growth_protocol: HRMECs were maintained in DMEM containing 10% FBS and 1% PS.

extract_protocol:
Total RNA of HRMECs was isolated by TRIzol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HRMECs were treated with 10 μM carnosol for 24 h, followed by 300 μM t-BHP for 4 h.

value: Human retinal microvascular endothelial cells

value: 10 μM carnosol


title: Surgical resection GBM-MD1009

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-MD1009

data_processing:
BeadStudio software v3.2 was used for primary data acqusition. Raw data was imported into R and further processed using R/Bioconductor package “minfi”. The raw pre-processing (Illumina method) was used for data normalization.
normalized (Illumina pre-processing) Average Beta

source_name: Surgical resection GBM-MD1009

extract_protocol: Genomic DNA was isolated using Qiagen AllPrep DNA/RNA Kit (Qiagen, 80204).

tag: grade


title: carnosol_1


title: carnosol_2


title: Surgical resection GBM-OM03086

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03086

source_name: Surgical resection GBM-OM03086


title: Surgical resection GBM-OM03119

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03119

source_name: Surgical resection GBM-OM03119


title: model 3

value: 300 μM t-BHP


title: Surgical resection GBM-OM03134

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03134

source_name: Surgical resection GBM-OM03134


title: Surgical resection GBM-OM03117

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03117

source_name: Surgical resection GBM-OM03117


title: Control RNASeq rep3

first: Ping

last: Wang

address: No22.Qixiangtai Rd.,Heping Dist

data_processing:
Adapters and low-quality bases in reads were trimmed by trim_galore.
We employed Kallisto (v0.46.0) to determine the read count for each transcript and quantified transcript abundance as transcripts per kilobase per million reads mapped, using gene annotation in the GENCODE database (v33).
Then we summed the read counts and TPM of all alternative splicing transcripts of a gene to obtain gene expression levels.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include gene counts for every gene and every sample

source_name: breast cancer cell lines

growth_protocol: MDA-MB-453 cells were cultured in DMEM growth medium supplemented with 10% FBS, 1% 100x penicillin-streptomycin-amphotericin B, and 1% 100x nonessential amino acid solution in a humidified incubator at 37°C with 5% carbon dioxide.

extract_protocol:
Total RNA (approximately 10 µg) was extracted from triplicate MDA-MB-453 cells, transfected with si-N6AMT1 or Control, using an RNeasy Plus Mini kit (QIAGEN).
Total RNA with an RNA integrity number of ≥ 8.0 was used for library construction by a TruSeq stranded mRNA sample preparation kit (Illumina).

treatment_protocol: siRNA (10 nM) targeting human N6AMT1 and scramble siRNA (Control)  were transfected into MDA-MB-453 cells using Lipofectamine RNAiMAX Transfection Reagent (Invitrogen) for 48 hours.

tag: cell line

tag: transfected

value: control


title: Surgical resection GBM-OM03104

first: Pierre

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03104

source_name: Surgical resection GBM-OM03104


title: model 2


title: model 1


title: Control RNASeq rep2


title: Surgical resection GBM-OM03088

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03088

source_name: Surgical resection GBM-OM03088


title: normal 3

value: untreated


title: A2780 si-NC#1

tag: tissue


title: Surgical resection GBM-OM03111

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03111

source_name: Surgical resection GBM-OM03111


title: Surgical resection GBM-OM03153

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03153

source_name: Surgical resection GBM-OM03153


title: Control RNASeq rep1


title: Surgical resection GBM-OM03260

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03260

source_name: Surgical resection GBM-OM03260


title: Surgical resection GBM-OM03255

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03255

source_name: Surgical resection GBM-OM03255


title: Surgical resection GBM-MD1005

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-MD1005

source_name: Surgical resection GBM-MD1005


title: si-N6AMT1 RNASeq rep2


title: normal 2


title: si-N6AMT1 RNASeq rep1


title: Surgical resection GBM-OM03116

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03116

source_name: Surgical resection GBM-OM03116


title: Surgical resection GBM-OM03246

description:
grade IV glioma tumor sample from Nordic study
genomic DNA from Surgical resection GBM-OM03246

source_name: Surgical resection GBM-OM03246


title: genomic_DNA_from_Surgical_resection_GBM-28

description: grade IV glioma tumor sample from EORTC26981 study

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

source_name: Surgical resection GBM-28

value: GBM

value: TMZ+RT

value: FFPE


title: genomic_DNA_from_Surgical_resection_GBM-P-243

description: grade IV glioma tumor sample from Pilot study

source_name: Surgical resection GBM-P-243

value: Pilot


title: genomic_DNA_from_Surgical_resection_GBM-286

source_name: Surgical resection GBM-286

value: Male


title: genomic_DNA_from_Surgical_resection_GBM-46

source_name: Surgical resection GBM-46


title: 5hmC_Seal_E90

first: Wei

state: IL

address: 680 N Lake Shore Drive, Suite 1400

department: Preventive Medicine

institute: Northwestern University

data_processing:
Library strategy: 5hmC-Seal
raw sequencing reads were trimmed for adaptor sequences using Trimmomatic
Low quality bases were also trimmed , followed by alignment to the current human genome reference (hg19) using Bowtie2 with the end-to-end alignment mode,Read pairs were concordantly aligned with fragment length ≤ 500 bp and with average ≤ 1 ambiguous base and up to four mismatched bases per 100 bp length.
Alignments with Mapping Quality Score ≥ 10 were counted for gene bodies, according to the gene start and gene end annotations by the GENCODE Project(release 19), using featureCounts without strand information.
Genome_build: hg19
Supplementary_files_format_and_content: counts

source_name: Plasma

extract_protocol:
CfDNA samples from T2D patients were prepared from peripheral blood with EDTA anticoagulation. Briefly, 5 mL of peripheral blood was collected from each subject, and plasma was separated within 4 h by centrifuging twice, one at 1 350× g for 12 min, and another at 13 500× g for 5 min. The processed plasma samples were stored at –80 °C immediately. CfDNA was extracted using the Circulating Nucleic Acid Kit (Qiagen, Germany) according to the manufacturer’s instructions. On average, 1-2 ng of cfDNA was obtained from each cfDNA sample. The quality of cfDNA was checked using the standard molecular biology approach
Each cfDNA sample was first repaired and ligated with adaptors. Next, the T4 bacteriophage enzyme β-glucosyltransferase (β-GT) was used to transfer an engineered glucose moiety containing an azide-group to 5hmC in duplex DNA. A biotin tag was then installed onto the azide group using Huisgen cycloaddition (click) chemistry, followed by capturing of 5hmC-containing DNA fragments using avidin beads. The 5hmC-Seal library for each cfDNA sample was then constructed through PCR amplification, followed by paired-end sequencing (PE38) at Shanghai Epican Genetech, Co. Ltd. (Shanghai, China), using the Illumina NextSeq500 platform according to Illumina’s protocol. We randomized cfDNA samples when constructing the 5hmC-Seal libraries and sequencing.

tag: population

value: Chinese

tag: diagnosis

value: plasma

tag: molecule subtype

value: cfDNA


title: HDpS6hi2

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

description: pS6 high iTreg cells in response to high dose TCR

data_processing:
Library strategy: CRISPR screen
Adapter sequences were removed by mageck 0.5.9.4 software
and aligned them to the sgRNA sequence of Brie CRISPR library
Supplementary files format and content: sgRNA counts for all samples which includes sgRNA sequence  and raw counts

source_name: pS6 high iTreg cells in response to 4ug/ml-aCD3-3hr

growth_protocol: Naïve CD4 T cells transduced with indicated sgRNA library were cultured with 2ng/ml TGFb and 10ng/ml IL-2

extract_protocol:
Genomic DNA was extracted with the 'DNeasy Blood & Tissue Kits' from Qiagen
The barcoding reaction was run using the NEBNext HiFi kit on the basis of the manufacturer’s instructions and amplified for five cycles

treatment_protocol: iTreg cells were restimulated with  0.25 or 4 ug/ml aCD3 for 3 hrs

tag: cell type

value: sgRNA-transduced iTreg cells

tag: strain


title: input1

description: Input iTreg cells before restimulation

source_name: Input iTreg cells before aCD3 stimulation


title: 5hmC_Seal_E84


title: HDpS6lo2

description: pS6 low iTreg cells in response to high dose TCR

source_name: pS6 low iTreg cells in response to 4ug/ml-aCD3-3hr


title: genomic_DNA_from_Surgical_resection_GBM-49

institute: CHUV / BCF / SIB

source_name: Surgical resection GBM-49

tag: patient

tag: age

value: RT


title: LDpS6hi2

description: pS6 high iTreg cells in response to low dose TCR

source_name: pS6 high iTreg cells in response to 0.25ug/ml-aCD3-3hr


title: input2

description: Input iTreg cells before restimulation


title: 5hmC_Seal_E81


title: HDpS6lo1


title: si-N6AMT1 RNASeq rep3

source_name: breast cancer cell lines


title: LDpS6lo2

description: pS6 low iTreg cells in response to low dose TCR

source_name: pS6 low iTreg cells in response to 0.25ug/ml-aCD3-3hr


title: genomic_DNA_from_Surgical_resection_GBM-P-233

source_name: Surgical resection GBM-P-233

tag: batch

tag: treatment


title: normal 1

source_name: Retina


title: genomic_DNA_from_Surgical_resection_GBM-P-229

source_name: Surgical resection GBM-P-229

tag: gender

value: Female

tag: disease state


title: 5hmC_Seal_E76


title: LDpS6lo1


title: HDpS6hi1


title: genomic_DNA_from_Surgical_resection_GBM-P-106

source_name: Surgical resection GBM-P-106


title: genomic_DNA_from_Surgical_resection_GBM-P-103

source_name: Surgical resection GBM-P-103


title: 66_MSEC_HARD_12h_3

city: Rochester

first: Aditya

last: Bhagwate

state: MN

address: 200 1st Street SW

institute: Mayo Clinic

description:
GeneCount_mouse.tsv
MSEC_SOFT_12h_vs_MSEC_HARD_12h.diff.xls

data_processing:
Reads aligned using Tophat v2.1.0
FeatureCounts used for calculating gene counts
edgeR used for differential expression
Assembly: GRCh38 (hg38) for human; mm10 for mouse
Supplementary files format and content: tsv format containing gene counts

source_name: Primary Isolated cells

growth_protocol: Company derived human hepatic sinusoidal endothelial cells grown in Endothelial Cell Growth Media

extract_protocol:
RNA was extracted according to manufacturer's instruction
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were plated on gels of stiffness 0.2kPa and 32 kPa

value: Mouse Sinusoidal Endothelial Cells

value: Plated on Hard gel


title: 5hmC_Seal_E72

city: Chicago


title: genomic_DNA_from_Surgical_resection_GBM-423

last: Bady

address: Quartier UNIL-Sorge

source_name: Surgical resection GBM-423


title: 65_MSEC_HARD_12h_2


title: 5hmC_Seal_E70


title: genomic_DNA_from_Surgical_resection_GBM-412

source_name: Surgical resection GBM-412


title: 64_MSEC_HARD_12h_1


title: ODcells_input2  (equal mixture of duplicates of si-IKBZ-treated OD cells)

city: Okayama

first: Shigeki

last: Suzuki

state: Okayama

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

department: Department of Operative Dentistry

institute: Okayama University

data_processing:
Adapter trimming and quality check were conducted with Trim galore and then aligned to a reference genome (hg38) using Bowtie2 with `-seed` parameters to efficiently use multimap reads with assuring reproducibility. Tag directories were generated using `makeTagDirectory` command in HOMER and ChIP-seq peaks were identified using the `getDiffrentialPeaksReplicates.pl` command in HOMER, specifying `-style histone` to generate a high confidence set of peaks across duplicates. This HOMER command internally calls DESeq2 to calculate enrichment value for each peak using the individual raw counts and return only those peaks that pass 2-fold enrichment and a FDR-adjusted p-value of < 0.05. Input chromatin DNA was used as controls.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files were generated by bamCoverage commond.

source_name: odontoblasts like cells differentiated from dental pulp cells

growth_protocol: OD cells were maintained in low glucose DMEM with ascorbic acid (100 g/ml) and -glecerophosphate (10 mM), LPS (0.1 mg/mll), and Dexamethasone (10-8 M))

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Cells used for ChIP-seq analysis were fixed with formaldehyde and ChIP was performed using the SimpleChIP plus enzymatic chromatin IP kit and magnetic beads (Cell Signaling Technologies) following the manufacturer’s protocol. Equal amounts of chromatin (estimated as chromatin obtained from 4 x 106 cells) were used for precipitation of protein-DNA complex with ChIP-validated anti-H3K27ac antibody (ab4729: Abcam). After reverse-crosslinking with proteinase K treatment, chromatin was eluted using ChIP DNA clean and concentrator (Zymo Research). Libraries were sequenced using 150-bp paired-end reads on an NovaSeq instrument to a depth of >10 million mapped reads.

treatment_protocol: OD cells were forward-transfected with control siRNA (Negative Control DsiRNA: IDT) and siRNAs for human IκBζ (hs.Ri.NFKBIZ.13.2: IDT) at a final concentration of 10 nM using Lipofectamine RNAiMAX (Thermo Fisher Scientific) reagent and incubated for 24 h.

value: dental pulp

tag: antibody

value: input

tag: differentiated cell type

value: odontoblasts like cells

tag: sirna

value: si-IKBz

value: inputDNA


title: genomic_DNA_from_Surgical_resection_GBM-410

city: Lausanne

source_name: Surgical resection GBM-410

value: GBM

value: TMZ+RT


title: 62_MSEC_SOFT_12h_2

value: Plated on Soft get


title: 5hmC_Seal_E62

source_name: Plasma


title: 5hmC_Seal_E55


title: genomic_DNA_from_Surgical_resection_GBM-403

source_name: Surgical resection GBM-403

value: Male

value: FFPE


title: 5hmC_Seal_E67

value: Chinese

value: plasma


title: ODcells_input2  (equal mixture of duplicates of control siRNA-treated OD cells)

value: si-control


title: H3K4me3_ODcells_si-IKBz_duplicate2

value: anti-H3K4me3 antibody (ab213224)

value: ChIP-DNA


title: genomic_DNA_from_Surgical_resection_GBM-386

source_name: Surgical resection GBM-386

value: RT


title: genomic_DNA_from_Surgical_resection_GBM-406

source_name: Surgical resection GBM-406


title: LDpS6hi1

source_name: pS6 high iTreg cells in response to 0.25ug/ml-aCD3-3hr

value: sgRNA-transduced iTreg cells


title: 5hmC_Seal_E54

value: cfDNA


title: H3K4me3_ODcells_si-control_duplicate1

value: dental pulp


title: 5hmC_Seal_E73


title: H3K4me3_ODcells_si-control_duplicate2

value: odontoblasts like cells


title: 5hmC_Seal_E134


title: H3K4me3_ODcells_si-IKBz_duplicate1

value: si-IKBz


title: 5hmC_Seal_E135


title: 61_MSEC_SOFT_12h_1

value: Mouse Sinusoidal Endothelial Cells


title: genomic_DNA_from_Surgical_resection_GBM-385

source_name: Surgical resection GBM-385

value: GBM


title: genomic_DNA_from_Surgical_resection_GBM-384

source_name: Surgical resection GBM-384


title: 5hmC_Seal_E115


title: H3K27me3_ODcells_si-IKBz_duplicate2

value: anti-H3K27me3 antibody (ab192985)


title: genomic_DNA_from_Surgical_resection_GBM-383

source_name: Surgical resection GBM-383

value: Female

value: TMZ+RT


title: 63_MSEC_SOFT_12h_3

value: Plated on Soft get


title: H3K27me3_ODcells_si-IKBz_duplicate1


title: 5hmC_Seal_E113

value: Chinese


title: genomic_DNA_from_Surgical_resection_GBM-382

source_name: Surgical resection GBM-382

value: Male

value: FFPE


title: genomic_DNA_from_Surgical_resection_GBM-381

source_name: Surgical resection GBM-381


title: 5hmC_Seal_E112

value: plasma


title: H3K27me3_ODcells_si-control_duplicate2

value: si-control

value: ChIP-DNA


title: genomic_DNA_from_Surgical_resection_GBM-378

source_name: Surgical resection GBM-378

value: RT


title: 5hmC_Seal_E110

value: cfDNA


title: H3K27me3_ODcells_si-control_duplicate1

value: dental pulp


title: 5hmC_Seal_E103


title: genomic_DNA_from_Surgical_resection_GBM-379

source_name: Surgical resection GBM-379


title: 5hmC_Seal_E50


title: genomic_DNA_from_Surgical_resection_GBM-360

source_name: Surgical resection GBM-360


title: 5hmC_Seal_E254


title: 5hmC_Seal_E52


title: 5hmC_Seal_E183


title: 5hmC_Seal_E136


title: GIRK_KO_244

first: Samantha

last: Weaver

department: Orthopedic Surgery

data_processing:
Illumina BCL2FASTQ v2.19.0 was used for basecalling
Sample data was aligned with STAR-2.5.2b against MM10
STAR alignment parameters used were as follows:    --outSAMtype BAM   Unsorted      --outSAMstrandField intronMotif   --outSAMunmapped Within   KeepPairs      --outSAMheaderCommentFile /tmp/5495998.1.ngs-pri/tmp.3KqV9fnoSN   --alignIntronMax 200000   --alignMatesGapMax 200000   --alignSJDBoverhangMin 10   --chimSegmentMin 12   --chimJunctionOverhangMin 12   --twopass1readsN 18446744073709551615   --twopassMode Basic
Reads Per Kilobase of exon per Megabase of library size (RPKM) were generated
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts and rpkm for each gene and sample

source_name: Chondrocyte

extract_protocol:
Primary epiphyseal chondrocytes were harvested from five-day-old male wildtype (n=3) and Girk3-/- (n=3) mice. Chondrocytes were digested for one hour in 0.5mg/mL collagenase II in DMEM culture medium, then digested overnight in 3mg/mL collagenase II in DMEM culture media. Cells were isolated the next day, washed in ice-cold PBS three times, then resuspended in Trizol for RNA extraction. Total RNA was extracted using phenol-chloroform.
TruSeq RNA method was used for analysis of polyadenylated mRNAs that were selected using oligo dT magnetic beads. TruSeq Kits were used for indexing to permit multiplex sample loading on the flow cells of an Illumina HiSeq 2000 sequencer. Gene expression was normalized to one million reads and corrected for gene length (reads per kilobasepair per million mapped reads, RPKM).

value: Immature epiphyseal chondrocyte

tag: Sex

tag: genotype

value: Girk3 KO


title: GIRK_KO_140

tag: tissue


title: GIRK_KO_242


title: genomic_DNA_from_Surgical_resection_GBM-353

source_name: Surgical resection GBM-353


title: 5hmC_Seal_E87

tag: population


title: genomic_DNA_from_Surgical_resection_GBM-342

source_name: Surgical resection GBM-342


title: genomic_DNA_from_Surgical_resection_GBM-356

source_name: Surgical resection GBM-356


title: genomic_DNA_from_Surgical_resection_GBM-359

source_name: Surgical resection GBM-359


title: genomic_DNA_from_Surgical_resection_GBM-354

source_name: Surgical resection GBM-354


title: 5hmC_Seal_E86

source_name: Plasma

tag: diagnosis


title: genomic_DNA_from_Surgical_resection_GBM-341

source_name: Surgical resection GBM-341


title: GIRK_WT_243

value: WT


title: genomic_DNA_from_Surgical_resection_GBM-369

source_name: Surgical resection GBM-369

value: GBM


title: GIRK_WT_156


title: 5hmC_Seal_E69

tag: molecule subtype


title: genomic_DNA_from_Surgical_resection_GBM-340

source_name: Surgical resection GBM-340


title: 5hmC_Seal_E83


title: genomic_DNA_from_Surgical_resection_GBM-337

source_name: Surgical resection GBM-337


title: MafB GFP/GFP (KO) Male E16.5

city: Wakayama

first: Gen

last: Yamada

address: 811–1 Kimiidera

department: Institute of Advanced Medicine

institute: Wakayama Medical University

data_processing:
s
Genome_build: s
Supplementary_files_format_and_content: s

source_name: embryonic external genitalia

growth_protocol: Pregnant ICR mice were housed in breeding cages following the Wakayama Medical University guidelines. Noon of the day when the vaginal plug was detected was designated as E0.5.

extract_protocol:
Urethral bilateral region from eEXG were collected and extracted RNA by ISOGEN2 (NIPPON GENE).
RNA libraries were prepared for sequencing by entrusting Novogene Advancing Genomics, Improving Life.

value: urethral bilateral region

tag: embryonic day

value: MafB GFP/GFP (KO)


title: MafB GFP/+ Male E16.5

tag: strain

value: MafB GFP/+


title: Female E16.5

value: CD1 (ICR)

value: wild type


title: 5hmC_Seal_E61

value: Chinese


title: 5hmC_Seal_E63


title: genomic_DNA_from_Surgical_resection_GBM-P-217

source_name: Surgical resection GBM-P-217

tag: patient

value: Male

value: Pilot

value: FFPE


title: genomic_DNA_from_Surgical_resection_GBM-P-223

source_name: Surgical resection GBM-P-223

tag: age


title: 5hmC_Seal_E60

value: plasma


title: Male E16.5


title: genomic_DNA_from_Surgical_resection_GBM-532

source_name: Surgical resection GBM-532

tag: batch

value: TMZ+RT


title: 5hmC_Seal_E58

value: cfDNA


title: Female E13.5


title: genomic_DNA_from_Surgical_resection_GBM-P-110

source_name: Surgical resection GBM-P-110

tag: treatment


title: si-N6AMT1 input

data_processing:
The high quality of reads was aligned to the human reference genome (hg19) by bowtie2 (v2.3.5) (PMID: 22388286).
Duplicated reads were removed by samtools (v1.9).
6mA methylated regions were identified with MACS2 with parameters -p 1e-5.
Genome_build: hg19
Supplementary_files_format_and_content: peak text files

source_name: breast cancer cell lines

extract_protocol:
Genomic DNA was extracted from cultured cells via a TIANamp Genomic DNA Kit (Tiangen Biotech, China). To exclude contaminating RNA, the genomic DNA was treated with 0.1 mg/ml RNase A.
Six libraries (two biological replicates each for immune-precipitated DNA and their input) were prepared using a NovaSeq 6000 S4 Reagent Kit (300 cycles) according to the manufacturer’s instructions

tag: cell line

tag: 6ma-ip-seq antibody


title: Male E13.5


title: BPTF KO12

city: Ottawa

first: Dave

last: Picketts

address: 501 Smyth Road

institute: OHRI

data_processing:
Pseudoalignment to GRCm38 (release 88) with kallisto (v0.44.0)
Differencial expression analysis by DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: Pseudoaligned and quantified - .h5

source_name: BPTF KO P0 forebrain

growth_protocol: Murine cortical tissue dissected at P0

extract_protocol:
RNA was extracted in Trizol and purified by PureLink RNA cleanup kit (Thermo Fisher, cat 12183020) with in-column DNaseI treatment
NEB mRNA stranded library preparation was carried out following Bioanalyser analysis of RNA

tag: strain background

tag: genotype/variation

value: Cre +/-

value: Cortical whole tissue


title: GIRK_WT_150

source_name: Chondrocyte

value: Immature epiphyseal chondrocyte


title: genomic_DNA_from_Surgical_resection_GBM-493

source_name: Surgical resection GBM-493

tag: gender

value: Female

tag: disease state


title: 5hmC_Seal_E49


title: BPTF KO11


title: genomic_DNA_from_Surgical_resection_GBM-367

source_name: Surgical resection GBM-367

value: GBM


title: Control input


title: 5hmC_Seal_E46


title: BPTF KO8


title: si-N6AMT1 6mA-IP-seq rep2

value: 6mA antibodies (Synaptic Systems)


title: genomic_DNA_from_Surgical_resection_GBM-322

source_name: Surgical resection GBM-322


title: BPTF KO7


title: si-N6AMT1 6mA-IP-seq rep1


title: 5hmC_Seal_E44


title: Control 6mA-IP-seq rep2


title: BPTF WT13

source_name: BPTF WT P0 forebrain

value: Cre -/-


title: 5hmC_Seal_E122

source_name: Plasma


title: genomic_DNA_from_Surgical_resection_GBM-574

source_name: Surgical resection GBM-574

value: RT


title: 5hmC_Seal_E43


title: genomic_DNA_from_Surgical_resection_GBM-270

source_name: Surgical resection GBM-270


title: Control 6mA-IP-seq rep1


title: BPTF WT5


title: BPTF WT4


title: genomic_DNA_from_Surgical_resection_GBM-P-244

source_name: Surgical resection GBM-P-244


title: 5hmC_Seal_E53


title: 5hmC_Seal_E107


title: genomic_DNA_from_Surgical_resection_GBM-13

source_name: Surgical resection GBM-13


title: 5hmC_Seal_E119


title: Group 2 COVID-19 [PR1798_31_a]

city: San Francisco

first: Tsukasa

last: Kadota

address: 513 Parnassus Ave.

institute: UCSF

data_processing:
Single-end sequenced reads were checked by FastQC. The QIAseq miRNA Library specific 3′ adapter sequence was trimmed from the 3’ ends of sequenced reads using cutadapt.
Reads with less than 16 bp insert sequences or with less than 10 bp Unique Molecular Index (UMI) were discarded.
Alignment of reads was performed using bowtie.
miRBase Release 22.1 was used for miRNAs.
The StrandNGS was applied to normalize the data using the transcript per million (TPM) method and to determine significant differentially expressed miRNAs between groups.
Genome_build: hg38
Supplementary_files_format_and_content: .xlsx file was generated by Qiagen online primary data analysing tool: (http://ngsdataanalysis.sabiosciences.com/QIAseqmiRNA).
Supplementary_files_format_and_content: TPM

source_name: circulating miRNAs

extract_protocol:
Total RNA was extracted using QIAzol and the miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to manufacturer’s protocols. RNA was Total RNA was extracted from aliquots (200 μL) of the serum samples using QIAzol and the miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's protocol.
The miRNA sequencing library was prepared using the QIAseq miRNA Library Kit (Qiagen, 331502)

tag: who category

value: mild→ severe

tag: Sex

value: M

tag: group

value: Group 2 COVID-19


title: Group 2 COVID-19 [PR1798_30_a]


title: genomic_DNA_from_Surgical_resection_GBM-333

source_name: Surgical resection GBM-333


title: 5hmC_Seal_E74

tag: population

value: Chinese

tag: diagnosis

tag: tissue


title: genomic_DNA_from_Surgical_resection_GBM-571

source_name: Surgical resection GBM-571


title: 5hmC_Seal_E71

tag: molecule subtype


title: genomic_DNA_from_Surgical_resection_GBM-103

source_name: Surgical resection GBM-103

tag: patient


title: 5hmC_Seal_E88


title: Group 2 COVID-19 [PR1798_07_a]

tag: age


title: 5hmC_Seal_E85


title: Group 2 COVID-19 [PR1798_06_a]


title: 5hmC_Seal_E77


title: genomic_DNA_from_Surgical_resection_GBM-564

source_name: Surgical resection GBM-564

tag: batch

value: Male


title: Group 2 COVID-19 [PR1798_05_a]


title: 5hmC_Seal_E68


title: 5hmC_Seal_E66


title: Group 2 COVID-19 [PR1798_04_a]


title: genomic_DNA_from_Surgical_resection_GBM-559

source_name: Surgical resection GBM-559

tag: treatment

value: FFPE


title: genomic_DNA_from_Surgical_resection_GBM-563

source_name: Surgical resection GBM-563


title: Group 2 COVID-19 [PR1798_03_a]


title: genomic_DNA_from_Surgical_resection_GBM-560

source_name: Surgical resection GBM-560


title: genomic_DNA_from_Surgical_resection_GBM-558

source_name: Surgical resection GBM-558


title: 5hmC_Seal_E216

value: plasma


title: BPTF WT3


title: 5hmC_Seal_E41


title: 5hmC_Seal_E148