title: ovary_w17_rep-3


title: DNA-methylation array data_203072530029_R05C01

status: Public on Feb 24 2025

type: genomic

city: Berlin

first: Philipp

last: Euskirchen

address: Charitéplatz 1

country: Germany

institute: Charité - Universitätsmedizin Berlin

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 850k or 935k Beadchip, respectively, using standard Illumina protocol.

scan_protocol: Arrays were scanned on the iscan instument acording to standarad protocol.

data_processing:
IDAT files were preprocessed using R/minfi.
*processed value definition: Average beta value

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: tumor

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from human tumor samples using Maxwell RSC FFPE Plus DNA Purification Kit (Promega, USA) according to standard instructions.

tag: tissue

value: tumor

tag: tumor type

value: Astrocytoma, IDH-mutant

tag: age

tag: Sex

value: Female

tag: beadchip name


title: DNA-methylation array data_203550290069_R06C01

value: Male


title: Mouse pancreatic acinar cell line, 9-cis retinoic acid, RNA-seq, rep 2

type: SRA

city: Knoxville

first: Conner

last: Hawkins

state: TN

address: 309 Ken and Blaire Mossman Bldg.

department: BCMB

country: USA

institute: University of Tennessee

description:
Library name: 9-cis_RA_2
NC2

library_source: transcriptomic

data_processing:
Raw read fastq files were downloaded from the JP Sulzberger Columbia Genome Center and subsequently checked for quality of reads and presence of adaptor sequences through the Fastqc (version v0.12.1) tool. This was followed by the same trimming protocol as mentioned above. These reads were then aligned using HISAT2 (version 2.2.1) as it is better optimized for shorter read alignments and intron sensitivity. The mm10 genome index was downloaded directly from HISAT Download and reads were aligned pair-ended. The resulting sam file output was then converted to bam format via the view function in samtools (version 1.18) prior to being sorted and indexed with the sort and index functions respectively. These sorted files were then subjected to quantification of transcript abundance relating to coding regions through the counting tool HTSeq.
Assembly: mm10
Supplementary files format and content: CSV file of all the raw counts for the samples

molecule: total RNA

organism: Mus musculus

growth_protocol: Grown in DMEM, 10% FBS, 1XPen/Strep, 37 Celsius, 5% CO2

extract_protocol:
Isolation and purification of RNA was performed following the Invitrogen TRIzol Reagent protocol for cells grown in a monolayer with 1 ml of TRIzol reagent utilized per sample with corresponding volumes of ensuing reagents
Library construction was done at the JP Sulzberger Columbia Genome Center

treatment_protocol: 24 hour incubtion in stripped DMEM media, 24 hour ligand incubation

tag: cell line

tag: cell type

value: Mouse pancreatic acinar cell line

tag: treatment

value: 9-cis retinoic acid


title: lung_d7_rep-2

type: RNA

city: Jingzhou

first: Tinghua

last: Huang

address: Jingmi Road #266

country: China

institute: Yangtze University

description: Gene expression data from Gallus Gallus lung 7 days

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Chicken Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Probeset-level intensity acquisition was performed by using Expression Console 1.1 (Affymetrix, Santa Clara, CA).

label: biotin

organism: Gallus gallus

source_name: lung 7 days

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

tag: gender

value: male


title: lung_d7_rep-3

value: female


title: DNA-methylation array data_203017150025_R03C01


title: lung_d28_rep-3

description: Gene expression data from Gallus Gallus lung 28 days

source_name: lung 28 days


title: DNA-methylation array data_205046550112_R04C01


title: DNA-methylation array data_205049770024_R06C01


title: Mouse pancreatic acinar cell line, 9-cis retinoic acid, RNA-seq, rep 1

description:
Library name: 9-cis_RA_1
NC1


title: lung_d21_rep-3

description: Gene expression data from Gallus Gallus lung 21 days

source_name: lung 21 days


title: lung_d28_rep-1


title: oocytes_w21_rep-1

description: Gene expression data from Gallus Gallus oocytes 21 weeks

source_name: oocytes 21 weeks


title: oocytes_w21_rep-2


title: Mouse pancreatic acinar cell line, DMSO, CUT&RUN, rep 3

description:
Library name: No_Ligand_3
NL_peaks.narrowPeak

library_source: genomic

data_processing:
The raw sequences were directly used as pair-ended FASTAQ file and quality of sequencing reads were checked with FastQC (version v0.12.1). Samples had a total average of 32,108,102 reads produced with an average of 80.7% of all reads being unique. Reads had all Phred scores above 32 and the subsequent identification of adapter sequences through FastQC were trimmed with Skewer (version 0.2.2) for better downstream processing in read alignments. Bowtie 2 (version 2.5.1) was used first to build a reference genome to align raw reads. We used the mm10 fasta file from the UCSC Genome Browser database and implemented the bowtie2-build function to create the mm10 index. This mm10 index was then implemented in bowtie2’s alignment function alongside the argument --very-sensitive-local to align pair-ended reads of each replicate to the genome. The output sam files were converted into bam files through samtools (version 1.18) view function. Next the bam files were sorted by genomic coordinates and indexed via samtools sort and index functions respectively. The sorted files then underwent filtering to exclude reads that had been multi-mapped to the genome with sambamba’s (version 1.0.0) function sambamba-view with corresponding filtering argument -F “mapping_quality >= 2”. Filtered files were finally subjected to peak calling by the MACS2 (version 2.2.7.1) program. The parameters used for peak calling were -f BAMPE in order for MACS2 to utilize its paired-end mode calling peaks by piling up the real fragments defined by both aligned ends rather than predicted fragment size and extending the reads, as well as a minimum FDR cutoff value of 0.05 -q 0.05. Of the peak file outputs from MACS2 we used the narrowPeak files for all further downstream applications. Once all individual samples had their peaks identified, replicates within conditions had their peaks integrated to better represent true binding peaks for RARα. To integrate all peaks from replicates into one file bedtools (version v2.31.0) intersect function was used with parameters -wa, to write the overlapping intervals in regard to the first file given, and -u, which qualifies an overlap if any feature from one interval coincides with another.
Assembly: mm10
Supplementary files format and content: narrowPeak (generated from all replicates and linked to the corresponding rep1 sample records)
Library strategy: CUT&RUN

extract_protocol:
EpiCypher CUTANA™ ChIC / CUT&RUN Kit Version 3 kit and protocol was used to isolate DNA via an antibody targeted to retinoic acid receptor alpha
Library preparation was performed utilizing the NEBNext Ultra II DNA Library Preparation Kit (Cat: E76455, Lot: 10169202) in which all samples were within the concentration range for 1:10 adaptor dilutions and 9 cycles of denaturation and annealing/extension to be implemented. NebNext Multiplex Oligos (Cat: E73356, Lot: 10136460) were used for downstream analysis of each sample. No size selection step was taken within the sample preparations as TapeStation characterization showed CUT&RUN samples had an overwhelming population of DNA fragments in the 200bp range. Samples were then characterized again on the Agilent 2200 TapeStation System prior to sequencing.

value: DMSO


title: DNA-methylation array data_203013220074_R08C01


title: Mouse pancreatic acinar cell line, 9-cis retinoic acid, RNA-seq, rep 3

description:
Library name: 9-cis_RA_3
NC3


title: lung_d21_rep-2


title: lung_d21_rep-1


title: Mouse pancreatic acinar cell line, DMSO, CUT&RUN, rep 2

description:
Library name: No_Ligand_2
NL_peaks.narrowPeak


title: DNA-methylation array data_204229180059_R03C01


title: lung_d28_rep-4


title: DNA-methylation array data_204229180151_R03C01


title: lung_d28_rep-2


title: lung_d21_rep-4


title: Mouse pancreatic acinar cell line, AM+CD, CUT&RUN, rep 3

description:
Library name: AM+CD_3
CD-AM_peaks.narrowPeak

value: AM+CD


title: Mouse pancreatic acinar cell line, AM+CD, CUT&RUN, rep 2

description:
Library name: AM+CD_2
CD-AM_peaks.narrowPeak


title: DNA-methylation array data_205107400096_R06C01


title: lung_d14_rep-4

description: Gene expression data from Gallus Gallus lung 14 days

source_name: lung 14 days


title: DNA-methylation array data_205589750027_R02C01


title: liver_d56_rep-2

description: Gene expression data from Gallus Gallus liver 8 weeks

source_name: liver 56 days


title: lung_d14_rep-1


title: DNA-methylation array data_203866300105_R01C01

value: Oligodendroglioma, IDH-mutant and 1p/19q-codeleted


title: Mouse pancreatic acinar cell line, AM+CD, CUT&RUN, rep 1

description:
Library name: AM+CD_1
CD-AM_peaks.narrowPeak


title: lung_d14_rep-3


title: liver_d56_rep-1


title: lung_d7_rep-1


title: lung_d14_rep-2


title: liver_d56_rep-3


title: liver_d49_rep-4

description: Gene expression data from Gallus Gallus liver 7 weeks

source_name: liver 49 days


title: liver_d9_rep-3

description: Gene expression data from Gallus Gallus liver 9 days

source_name: liver 9 days


title: liver_d9_rep-2


title: lung_d7_rep-4


title: liver_d49_rep-1


title: liver_d49_rep-2


title: liver_d7_rep-4

description: Gene expression data from Gallus Gallus liver 7 days

source_name: liver 7 days


title: Mouse pancreatic acinar cell line, CD3254, CUT&RUN, rep 2

description:
Library name: CD3254_2
CD_peaks.narrowPeak


title: liver_d49_rep-3


title: Mouse pancreatic acinar cell line, CD3254, CUT&RUN, rep 3

description:
Library name: CD3254_3
CD_peaks.narrowPeak


title: Mouse pancreatic acinar cell line, CD3254, CUT&RUN, rep 1

description:
Library name: CD3254_1
CD_peaks.narrowPeak


title: liver_d9_rep-4


title: DNA-methylation array data_206486300107_R07C01


title: DNA-methylation array data_205495890161_R02C01


title: liver_d7_rep-2


title: Mouse pancreatic acinar cell line, AM580, CUT&RUN, rep 2

description:
Library name: AM580_2
AM_peaks.narrowPeak


title: liver_d7_rep-3


title: DNA-methylation array data_205041760051_R06C01


title: liver_d7_rep-1


title: liver_d3_rep-3

description: Gene expression data from Gallus Gallus liver 3 days

source_name: liver 3 days


title: liver_d3_rep-2


title: DNA-methylation array data_205041760055_R01C01


title: DNA-methylation array data_204339300083_R01C01


title: liver_d3_rep-4


title: liver_d9_rep-1


title: Mouse pancreatic acinar cell line, 9-cis retinoic acid, CUT&RUN, rep 2

description:
Library name: 9-cis_RA_2
9C_peaks.narrowPeak


title: DNA-methylation array data_206486300068_R06C01


title: liver_d1_rep-1

description: Gene expression data from Gallus Gallus liver 1 days

source_name: liver 1 days


title: DNA-methylation array data_205689130023_R05C01


title: Mouse pancreatic acinar cell line, AM580, CUT&RUN, rep 1

description:
Library name: AM580_1
AM_peaks.narrowPeak


title: Mouse pancreatic acinar cell line, 9-cis retinoic acid, CUT&RUN, rep 1

description:
Library name: 9-cis_RA_1
9C_peaks.narrowPeak


title: liver_d0_rep-3

description: Gene expression data from Gallus Gallus liver 0 days

source_name: liver 0 days


title: liver_d0_rep-4


title: DNA-methylation array data_205800610172_R01C01


title: liver_d0_rep-1


title: liver_d1_rep-4


title: liver_d0_rep-2


title: RAW264.7,LPS+ Anti-CD36 antibodies, 12h, rep2

city: Beijing

first: Weixuan

last: Wang

address: No. 38 Xueyuan Road, Haidian District

institute: Peking University

description:
Library name: LPS+Anti-CD36 Abs 2
10x Genomics

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted with Trizol reagent (Invitrogen) and reverse transcribed into cDNA with GoScriptTM Reverse Transcription System (Promega). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using standard Illumina protocols.

tag: genotype

value: WT

value: RAW264.7,LPS+ Anti-CD36 antibodies, 12h


title: liver_d1_rep-2


title: DNA-methylation array data_207521860089_R02C01


title: Mouse pancreatic acinar cell line, 9-cis retinoic acid, CUT&RUN, rep 3

description:
Library name: 9-cis_RA_3
9C_peaks.narrowPeak


title: liver_d1_rep-3


title: liver_d3_rep-1


title: RAW264.7,LPS+ Anti-CD36 antibodies, 12h, rep1

description:
Library name: LPS+Anti-CD36 Abs 1
10x Genomics


title: tibiotarsus-growth-plate_d21_rep-3

description: Gene expression data from Gallus Gallus growth-plate 21 days

source_name: growth-plate 21 days


title: gastrocnemius-muscle_d7_rep-3

description: Gene expression data from Gallus Gallus leg-muscle 7 days

source_name: leg-muscle 7 days


title: gastrocnemius-muscle_d7_rep-4


title: DNA-methylation array data_207129460032_R03C01


title: RAW264.7, Anti-CD36 antibodies 1:100 dilution, 12h, rep2

description:
Library name: Anti-CD36 Abs 2
10x Genomics


title: gastrocnemius-muscle_d14_rep-3

description: Gene expression data from Gallus Gallus leg-muscle 14 days

source_name: leg-muscle 14 days


title: gastrocnemius-muscle_d7_rep-2


title: gastrocnemius-muscle_d14_rep-2


title: DNA-methylation array data_206486300125_R07C01


title: RAW264.7, Anti-CD36 antibodies 1:100 dilution, 12h, rep1

description:
Library name: Anti-CD36 Abs 1
10x Genomics


title: gastrocnemius-muscle_d14_rep-4


title: DNA-methylation array data_206359150189_R06C01


title: T23-190

description:
Library name: T23-190
low-pass WGS

data_processing:
Processing of WGBS data from 22 human diffuse glioma samples was erformed using the One Touch Pipeline (OTP) which uses bwa v0.6.1 for alignment and methylCtools v1.0.0 for methylation calling. Plus- and minus-strand methylated allele frequencies at CpG sites were merged using custom scripts. For nanopore sequencing data, raw sequencing data were basecalled using ONT's proprietary software (guppy or dorado) and aligned to hg19 using minimap2. Methylated allele frequencies were extracted using modkit.
Assembly: hg19
Supplementary files format and content: bedMethyl
The BED files adhere to the ENCODE bedMethyl standard outlined in 'Whole-Genome Bisulfite Sequencing Data Standards and Processing Pipeline – ENCODE' (encodeproject.org)
https://www.encodeproject.org/data-standards/wgbs/

extract_protocol:
Genomic DNA was extracted from tumor tissue using commercial extraction kits as part of neuropathological routine workup.
WGBS libraries were prepared using a NEBNext Methyl-seq Kit (NEB), and were then sequenced on an Illumina NovaSeq 6000 platform at the BIH Core Unit Genomics over two S4 flow cells in a paired-end setting of 2 x 150 bp. Nanopore libraries were prepared using Rapid Barcoding Kit (ONT) and sequenced on R9 or R10.4.1 flow cells on MinION/GridION or P2 Solo devices.

value: Glioblastoma, IDH-wildtype


title: DNA-methylation array data_207166150139_R01C01


title: DNA-methylation array data_205828600005_R07C01


title: RAW264.7, LPS 50ng/mL, 12h, rep1

description:
Library name: LPS 1
10x Genomics

value: LPS 50ng/mL, 12h


title: RAW264.7, untreat, rep2

description:
Library name: UT 2
10x Genomics

value: untreat


title: DNA-methylation array data_205689140178_R04C01


title: DNA-methylation array data_207129460039_R04C01


title: RAW264.7, untreat, rep1

description:
Library name: UT 1
10x Genomics


title: jejunum_d21_rep-2

description: Gene expression data from Gallus Gallus jejunum 21 days

source_name: jejunum 21 days


title: T23-134

description:
Library name: T23-134
low-pass WGS

source_name: tumor


title: jejunum_d21_rep-3


title: jejunum_d28_rep-1

description: Gene expression data from Gallus Gallus jejunum 4 weeks

source_name: jejunum 28 days


title: RAW264.7, LPS 50ng/mL, 12h, rep2

description:
Library name: LPS 2
10x Genomics


title: 4T1, IL13RA2 CRISPR knockout, IL13 treated, rep3

city: Nashville

first: Wendy

middle: E

last: Bindeman

address: Preston Research Building 738 2220 Pierce Ave

department: Cancer Biology

institute: Vanderbilt University

description:
Library name: 4T1_RA2_IL13_3
column name in 4T1IL13_gene_fpkm: RA2_IL13_3

data_processing:
Raw data reads were processed using in-house perl scripts by Novogene Corporation. Company documentation states that reads containing adaptor contamination, N>10%, and base quality <5 for >50% of reads were removed.
Clean reads were aligned to hg38/mm10 using Hisat2 v2.0.5 with default parameters. Performed by Novogene Corporation.
Mapped reads were quantified using FeatureCounts v1.5.0-p3 with default parameters and counts were normalized using FPKM. Performed by Novogene.
Assembly: hg38, mm10
Supplementary files format and content: .csv files containing FPKM values for each sample

source_name: Mammary gland

growth_protocol: 100,000 cells/well were plated in DMEM + 2% FBS for 48h.

extract_protocol:
RNA was extracted using the Direct-zol RNA Miniprep kit (Zymo Research) and submitted to Novogene Corporation Inc (Sacramento, CA). Subsequent processing was performed by Novogene. Sample quality was re-confirmed by Novogene using the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Performed by Novogene Corporation Inc

treatment_protocol: IL13-treated cells were treated with 20ng/mL murine IL13 for 48h in DMEM + 2% FBS

value: Mammary gland

value: epithelial cells

value: IL13RA2 KO

value: IL13 treated


title: DNA-methylation array data_207269880006_R04C01

value: tumor

value: Female


title: T23-092

description:
Library name: T23-092
low-pass WGS


title: 4T1, IL13RA2 CRISPR knockout, IL13 treated, rep2

description:
Library name: 4T1_RA2_IL13_2
column name in 4T1IL13_gene_fpkm: RA2_IL13_2


title: jejunum_d28_rep-2


title: jejunum_d28_rep-3


title: jejunum_d28_rep-4


title: 4T1, IL13RA2 CRISPR knockout, IL13 treated, rep1

description:
Library name: 4T1_RA2_IL13_1
column name in 4T1IL13_gene_fpkm: RA2_IL13_1


title: DNA-methylation array data_206100100005_R06C01


title: T23-046

description:
Library name: T23-046
low-pass WGS


title: T23-174

description:
Library name: T23-174
low-pass WGS


title: T23-051

description:
Library name: T23-051
low-pass WGS


title: DNA-methylation array data_205617080146_R05C01

value: Male


title: T23-052

description:
Library name: T23-052
low-pass WGS

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


title: DNA-methylation array data_206467010139_R02C01


title: 4T1, CRISPR control, IL13 treated, rep2

description:
Library name: 4T1_CTL_IL13_2
column name in 4T1IL13_gene_fpkm: CTL_IL13_2


title: gastrocnemius-muscle_d7_rep-1

value: male


title: gastrocnemius-muscle_d14_rep-1


title: jejunum_d21_rep-4

value: female


title: jejunum_d21_rep-1


title: jejunum_d14_rep-2

description: Gene expression data from Gallus Gallus jejunum 14 days

source_name: jejunum 14 days


title: T23-020

description:
Library name: T23-020
low-pass WGS


title: DNA-methylation array data_205828600101_R04C01


title: 4T1, CRISPR control, IL13 treated, rep1

description:
Library name: 4T1_CTL_IL13_1
column name in 4T1IL13_gene_fpkm: CTL_IL13_1


title: DNA-methylation array data_205460720133_R08C01


title: T22-174

description:
Library name: T22-174
low-pass WGS


title: T22-170

description:
Library name: T22-170
low-pass WGS

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


title: DNA-methylation array data_204237150113_R08C01

value: Oligodendroglioma, IDH-mutant and 1p/19q-codeleted


title: 4T1, IL13RA2 CRISPR knockout, no treatment, rep3

description:
Library name: 4T1_RA2_Unstim_3
column name in 4T1_gene_fpkm: R2_C

value: untreated


title: DNA-methylation array data_205041750127_R08C01


title: 4T1, CRISPR control, IL13 treated, rep3

description:
Library name: 4T1_CTL_IL13_3
column name in 4T1IL13_gene_fpkm: CTL_IL13_3

value: WT


title: 4T1, IL13RA2 CRISPR knockout, no treatment, rep2

description:
Library name: 4T1_RA2_Unstim_2
column name in 4T1_gene_fpkm: R2_B


title: 4T1, IL13RA2 CRISPR knockout, no treatment, rep1

description:
Library name: 4T1_RA2_Unstim_1
column name in 4T1_gene_fpkm: R2_A


title: jejunum_d14_rep-4


title: 4T1, IL13RA1 CRISPR knockout, no treatment, rep3

description:
Library name: 4T1_RA1_Unstim_3
column name in 4T1_gene_fpkm: R1_C

value: IL13RA1 KO


title: DNA-methylation array data_205041760067_R07C01


title: jejunum_d14_rep-3


title: whole-intestine_d7_rep-4

description: Gene expression data from Gallus Gallus intestine 7 days

source_name: intestine 7 days


title: whole-intestine_d7_rep-1


title: 4T1, IL13RA1 CRISPR knockout, no treatment, rep2

description:
Library name: 4T1_RA1_Unstim_2
column name in 4T1_gene_fpkm: R1_B


title: DNA-methylation array data_204237150093_R01C01


title: T22-050

description:
Library name: T22-050
low-pass WGS

value: Ganglioglioma


title: T22-164

description:
Library name: T22-164
low-pass WGS


title: whole-intestine_d7_rep-3


title: 4T1, IL13RA1 CRISPR knockout, no treatment, rep1

description:
Library name: 4T1_RA1_Unstim_1
column name in 4T1_gene_fpkm: R1_A


title: DNA-methylation array data_205495890138_R03C01


title: DNA-methylation array data_203740910031_R08C01


title: T22-144

description:
Library name: T22-144
low-pass WGS

value: Glioblastoma, IDH-wildtype


title: 4T1, CRISPR control, no treatment, rep3

description:
Library name: 4T1_CTL_Unstim_3
column name in 4T1_gene_fpkm: WT_C

value: Mammary gland


title: 4T1, CRISPR control, no treatment, rep2

description:
Library name: 4T1_CTL_Unstim_2
column name in 4T1_gene_fpkm: WT_B

value: epithelial cells


title: DNA-methylation array data_204774160071_R06C01


title: whole-intestine_d3_rep-4

description: Gene expression data from Gallus Gallus intestine 3 days

source_name: intestine 3 days


title: T22-046

description:
Library name: T22-046
low-pass WGS


title: T22-024

description:
Library name: T22-024
low-pass WGS

value: Supratentorial ependymoma, ZFTA fusion positive


title: T22-055

description:
Library name: T22-055
low-pass WGS


title: Mouse pancreatic acinar cell line, DMSO, CUT&RUN, rep 1

description:
Library name: No_Ligand_1
NL_peaks.narrowPeak

value: Mouse pancreatic acinar cell line

value: DMSO


title: 4T1, CRISPR control, no treatment, rep1

description:
Library name: 4T1_CTL_Unstim_1
column name in 4T1_gene_fpkm: WT_A


title: whole-intestine_d3_rep-2


title: DNA-methylation array data_204964480096_R05C01

value: tumor

value: Female


title: whole-intestine_d3_rep-1


title: jejunum_d14_rep-1


title: DNA-methylation array data_202760950025_R05C01

value: Male


title: whole-intestine_d7_rep-2

value: male


title: T, PP

city: Columbus

first: Hsin-Jung Joyce

last: Wu

state: Ohio

address: 480 Medical Center Drive

department: Department of Internal Medicine

institute: The Ohio State University

description:
Library name: T_PP
10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoding processing and gene counting were made by using Cell Ranger. The annotation, gene counts filtering and DESeq2 normalization were done by using PartekFlow (https://www.partek.com/partek-flow/).
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes raw counts.

source_name: Peyer's patch

extract_protocol:
CD4+ T cells were purified from KRN.IL17Cre/eGFP.Rosa. STOPfl/fl.TdTom mice and transferred into SFB+ TCRa−/−.BxN recipient mice. Two weeks after transfer, total PP CD4+ T cells (50,809 cells) were sorted and TdTom+ Tfh cells (2984 cells) were also sorted and combined with the PP CD4+ T cells before submitting for single cell analysis (10x Genomics). The addition of TdTom+ Tfh cells (containing both Tfh17 and exTh17-Tfh cells) was done to increase and visibility of Tfh17 cells, a rare T cell population, in the trajectory analysis and would roughly double the amount of TdTom+ Tfh cells in the sample.
10x Genomics library construction kit (Cat # 1000190)

value: Peyer's patch

value: CD4+T cells


title: whole-intestine_d1_rep-3

description: Gene expression data from Gallus Gallus intestine 1 days

source_name: intestine 1 days

value: female


title: DNA-methylation array data_205041760141_R05C01

value: Oligodendroglioma, IDH-mutant and 1p/19q-codeleted


title: T22-006

description:
Library name: T22-006
low-pass WGS

value: Pilocytic astrocytoma


title: T21-350

description:
Library name: T21-350
low-pass WGS


title: whole-intestine_d1_rep-4


title: T22-038

description:
Library name: T22-038
low-pass WGS

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


title: N2a cells,siOPA1/OPA1-V465F,Day3, 3

city: Changsha

first: Lin

last: Zhang

state: Hunan

address: No. 87, Xiangya Road, Kaifu District, Changsha City

institute: Xiangya Hospital, Central South University

description:
Library name: sample15
SiRNA1393-3-FPKM

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated. About 47.87M raw reads for each sample were generated. Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. Then about 42.00M clean reads for each sample were retained for subsequent analyses. The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count. PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples.
Assembly: GRCm39
Supplementary files format and content: Gene expression files containing FPKM and count  processed_data.xls

source_name: Neuroblastoma

growth_protocol: N2a cells (ATCC: CCL-131) was grown and maintained in Dulbecco’s modified Eagle’s medium (DMEM, Gibco, C11995500BT) ,supplemented with 10% FBS and 1% penicillin/streptomycin at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

treatment_protocol: siRNAs (50 nM) and plasmid were transfected into N2a cell using DharmaFECT Duo Transfection Reagent (Dharmacon, T-2010-02).

value: Neuroblastoma

value: Neuroblastoma cells

value: OPA1 knockdown/OPA1-V465F

value: Transfection


title: DNA-methylation array data_206503150006_R06C01


title: T21-318

description:
Library name: T21-318
low-pass WGS


title: DNA-methylation array data_204503540034_R03C01


title: T21-320

description:
Library name: T21-320
low-pass WGS


title: T21-302

description:
Library name: T21-302
low-pass WGS

value: Ganglioglioma


title: N2a cells,siOPA1/OPA1-V465F,Day3, 2

description:
Library name: sample14
SiRNA1393-2-FPKM


title: DNA-methylation array data_206503150006_R01C01


title: N2a cells,siOPA1/OPA1-V465F,Day3, 1

description:
Library name: sample13
SiRNA1393-1-FPKM


title: whole-intestine_d14_rep-4

description: Gene expression data from Gallus Gallus intestine 14 days

source_name: intestine 14 days


title: whole-intestine_d1_rep-2


title: whole-intestine_d1_rep-1


title: T21-301

description:
Library name: T21-301
low-pass WGS

value: Glioblastoma, IDH-wildtype


title: DNA-methylation array data_205800610172_R03C01


title: N2a cells,siOPA1/Control,Day3, 3

description:
Library name: sample12
SiRNA-GWl-myc-3-FPKM

value: OPA1 knockdown/WT


title: T21-289

description:
Library name: T21-289
low-pass WGS

value: tumor


title: whole-intestine_d14_rep-3


title: N2a cells,siOPA1/Control,Day3, 2

description:
Library name: sample11
SiRNA-GWl-myc-2-FPKM


title: DNA-methylation array data_205814880164_R05C01


title: DCs from mice that received CD8 Tcells from PLP stimulated mice

city: North Liberty

first: Kai

middle: Jordan

last: Rogers

state: IA

address: 2205 Oak Terrace Avenue

department: Pathology

institute: University of Iowa

description:
Library name: Sample 1
Sample 9 is the PLP group, Sample 10 is the OVA group

data_processing:
The resulting FASTQ files were further processed using the Parse Biosciences pipeline to identify the barcodes, align the reads, and create a gene-cell count matrix. Downstream data analysis and visualization were performed using the R package Seurat (Version 4).
Assembly: Mouse mm10
Supplementary files format and content: CSV files and matrix files

source_name: Spleen + Inguinal lymph nodes

extract_protocol:
Spleens were harvested from PLP178-191-immunized mice at day 10 and homogenized using 200 U/ml of collagenase (Worthington Type 3) and 10 mM EDTA (Invitrogen). The homogenates were incubated at 37℃  for 30 minutes and made into single-cell suspensions. Antigen-presenting cells were enriched using Nycodenz gradient centrifugation. Briefly, cells were washed with RPMI and resuspended in 5 ml of Nycodenz working solution and 5 ml of 1% HBSS was overlaid spun at 1800g for 15 minutes without deceleration. The isolate was collected, and dendritic cells (DC) were further enriched using magnetic bead sorting (CD11c MicroBeads UltraPure, Miltenyi Biotech, Auburn, CA) with > 90% purity.
Splenic DC were isolated from CD8 recipients, PLP-CD8-DC and OVA-CD8-DC, on day 12 post-EAE induction. DC were strained through a 40-µm filter, fixed using the Cell Fixation Kit and processed with the Evercode Whole Transcriptome Mini Kit from Parse Biosciences (Seattle, Washington, USA) according to the manufacturer’s guidelines. Sub-libraries were evaluated for adequacy (Agilent BioAnalyzer RNA integrity number >8) and sent for Next Generation Sequencing on the Illumina NovaSeq 6000 using 100bp paired-end reads (Iowa Institute of Human Genetics, University of Iowa).

value: Spleen + Inguinal lymph nodes

value: Dendritic cells

value: WT C57B/6


title: T21-277

description:
Library name: T21-277
low-pass WGS


title: N2a cells,siOPA1/Control,Day3, 1

description:
Library name: sample10
SiRNA-GWl-myc-1-FPKM


title: DNA-methylation array data_205814880119_R08C01

value: Female


title: T21-261

description:
Library name: T21-261
low-pass WGS


title: DNA-methylation array data_206702500010_R07C01


title: whole-intestine_d14_rep-2

value: male


title: N2a cells,siOPA1/OPA1,Day3, 3

description:
Library name: sample9
SiRNA-GWl-OPA-3-FPKM

value: OPA1 knockdown/OPA1


title: T21-216

description:
Library name: T21-216
low-pass WGS


title: DNA-methylation array data_206999330185_R07C01

value: Oligodendroglioma, IDH-mutant and 1p/19q-codeleted


title: T21-242

description:
Library name: T21-242
low-pass WGS


title: N2a cells,siOPA1/OPA1,Day3, 2

description:
Library name: sample8
SiRNA-GWl-OPA-2-FPKM


title: DNA-methylation array data_206648960111_R01C01

value: Male


title: whole-intestine_d0_rep-3

description: Gene expression data from Gallus Gallus intestine 0 days

source_name: intestine 0 days

value: female


title: T21-176

description:
Library name: T21-176
low-pass WGS


title: N2a cells,siOPA1/OPA1-V560F,Day3, 3

description:
Library name: sample6
SiRNA-1678-3-FPKM

value: Neuroblastoma

value: OPA1 knockdown/OPA1-V560F


title: N2a cells,siOPA1/OPA1,Day3, 1

description:
Library name: sample7
SiRNA-GWl-OPA-1-FPKM

value: Neuroblastoma cells


title: DNA-methylation array data_206600570019_R05C01


title: DNA-methylation array data_206600570024_R07C01


title: N2a cells,siOPA1/OPA1-V560F,Day3, 2

description:
Library name: sample5
SiRNA-1678-2-FPKM

value: Transfection


title: whole-intestine_d14_rep-1


title: T21-171

description:
Library name: T21-171
low-pass WGS


title: whole-intestine_d0_rep-2


title: DNA-methylation array data_206486310053_R07C01


title: DNA-methylation array data_206486300166_R02C01


title: whole-intestine_d3_rep-3


title: N2a cells,siControl/Control,Day3, 3

description:
Library name: sample3
NC-Gwl-myc-3-FPKM

value: WT/WT


title: ileum_d28_rep-4

description: Gene expression data from Gallus Gallus illium 4 weeks

source_name: ileum 28 days


title: DNA-methylation array data_206639830040_R06C01


title: ileum_d28_rep-3


title: T21-186

description:
Library name: T21-186
low-pass WGS

value: Glioblastoma, IDH-wildtype


title: T21-130

description:
Library name: T21-130
low-pass WGS


title: T21-124

description:
Library name: T21-124
low-pass WGS


title: ileum_d28_rep-2


title: DNA-methylation array data_205030230031_R05C01


title: N2a cells,siControl/Control,Day3, 2

description:
Library name: sample2
NC-Gwl-myc-2-FPKM


title: duodenum_d7_rep-4

description: Gene expression data from Gallus Gallus duodenum 7 days

source_name: duodenum 7 days


title: whole-intestine_d0_rep-4


title: N2a cells,siControl/Control,Day3, 1

description:
Library name: sample1
NC-Gwl-myc-1-FPKM


title: DNA-methylation array data_202995850067_R08C01


title: T21-120

description:
Library name: T21-120
low-pass WGS

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


title: ileum_d28_rep-1


title: whole-intestine_d0_rep-1


title: DNA-methylation array data_204964480108_R06C01

value: tumor


title: Input-ChIP-seq_NIH3T3_SVI_6h_2025

city: Athens

first: Marios

last: Agelopoulos

state: Attica

address: 4 Soranou Ephessiou Str

department: Center of Basic Research

country: Greece

institute: Biomedical Research Foundation Academy of Athens

description:
Library name: Input-ChIP-seq_NIH3T3_SVI_6h_2025
ATCC, CRL-1658™

data_processing:
Galaxy online platform (https://usegalaxy.org/)
Quality Control steps (QC) were employed on raw sequencing reads by the FastQC application (Galaxy Version 0.72+galaxy1).
Adaptors’ contaminants and low-quality reads, were trimmed, and thus excluded from the downstream analyses, by the application of Trim Galore (Galaxy Version 0.6.7+galaxy0). Trimmed sequencing reads were mapped to the reference human (hg19) or mouse (mm9) genome by the application of the Bowtie2 software (Galaxy Version 2.4.2+galaxy0), with “very sensitive end to end” parameters (Langmead and Salzberg, 2012). The input data were utilized as controls.
Duplicate reads were eliminated using the RmDup tool (Galaxy Version 2.0.1) of the SAMtools package (Li et al., 2009). Samples were normalized to the same sequencing depth using the Downsample SAM/BAM (Galaxy Version 2.18.2.1) tool from Picard.
Peaks were called by MACS2 callpeak algorithm (Galaxy Version 2.1.1.20160309.6) following the above outlined parameters: (a) band width=150 bp, (b) lower mfold=5, (c) upper mfold=50, and (d) q value=0.05 (Feng et al., 2012).
Peaks detected in unplaced contigs (chrUn, chrM) and in ENCODE hg19 and mm9 blacklisted regions were excluded from the downstream analyses (Amemiya HM, et al., Sci Rep. 2019). Reads that mapped within peaks were tallied using bedtools' MultiCovBed tool (Galaxy Version 2.30.0) (Quinlan and Hall, 2010).
Assembly: hg19 (Homo sapiens), mm9 (Mus musculus)
Supplementary files format and content: bigwig files including RPKM normalized signal and BED files of total peaks

growth_protocol: Human and mouse cells were cultured under optimum conditions according to the manufacturer’s instructions. A549 cells (ATCC, CCL-185™) and NIH/3T3 cells (ATCC, CRL-1658™) were grown in DMEM medium (Sigma-Aldrich). THP-1 cells (ATCC, TIB-202™) were grown in RPMI 1640 medium (Sigma-Aldrich). Culture media for A549 and NIH/3T3 cells were supplemented with 1% Pen-Strep (Gibco) and 10% (v/v) heat-inactivated Fetal Bovine Serum (FBS) (Gibco,  Biowest). For THP-1 cells the culture medium was supplemented with 1% Pen-Strep (Gibco), 20% v/v heat-inactivated Fetal Bovine Serum (FBS) (Gibco, Biowest), and 2-mercaptoethanol to a final concentration of 0.05 mM. All cell cultures were established in laboratory incubators under optimum conditions (37°C, 5% CO2).

extract_protocol:
ChIP-seq assays on human and mouse cells were carried out based on published protocols (Agelopoulos et al 2014; Agelopoulos et al 2012; Agelopoulos and Thanos 2006) with modifications. Cells were fixed in 1% formaldehyde (F8775, Sigma-Aldrich), for 30 minutes at room temperature, followed by quenching of the reaction by 0.125M Glycine. Cell pellets were diluted in 15 ml Buffer I [10 mM Tris-Cl pH 8.0, 10 mM EDTA, 0.25% Triton X-100] and incubated for 10 minutes on ice, followed by centrifugation at 3,500 rpm for 5 minutes at 4 °C and aspiration. Pellets were diluted in 15 ml Buffer II [10 mM Tris-Cl pH 8.0, 200 mM NaCl, 1 mM EDTA] and incubated for 10 minutes on ice, followed by centrifugation at 3,500 rpm for 5 minutes at 4 °C and aspiration. Pellets were diluted in sonication Buffer [10 mM Tris-Cl pH 8.0, 1 mM EDTA] and chromatin filaments were sheared to a range of 200-2,000 bp using a Covaris S220 Sonicator , followed by two sequential steps of 2,000 rpm and 12,000 rpm centrifugation, for 8 minutes at 4 °C, to avoid trapping of chromatin by the cell debris.
Multiplexed-DNA-libraries were prepared according to a published protocol (Ford et al., 2014) with modifications. The NEBNext Multiplex Oligos for illumina (Index Primers Set 1 and 2) (E7335S and E7500S, illumina) were used to produce compatible ends to the DNA fragments.

treatment_protocol: Cell cultures were grown at 85–95% confluence and subjected to mock-infection (control; 0h) or Sendai-Virus-infection (Cantell strain, Charles River lab., 2000 HA units/ml) for 3 or 6 hrs, prior to proceeding in downstream examinations. Sendai Virus was supplied directly in the culture medium at a ratio of 1/10 (v/v).

value: Fibroblasts

tag: chip antibody

value: Sendai Virus Cantell strain, Charles River lab

tag: time

value: 6 hrs


title: N2a cells,siOPA1/OPA1-V560F,Day3, 1

description:
Library name: sample4
SiRNA-1678-1-FPKM


title: T21-118

description:
Library name: T21-118
low-pass WGS

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


title: T21-107

description:
Library name: T21-107
low-pass WGS


title: Input-ChIP-seq_NIH3T3_SVI_0h_2025

description:
Library name: Input-ChIP-seq_NIH3T3_SVI_0h_2025
ATCC, CRL-1658™

value: 0 hrs (naïve)


title: DNA-methylation array data_206503150022_R08C01


title: T21-143

description:
Library name: T21-143
low-pass WGS

value: Pilocytic astrocytoma


title: H3K27ac-ChIP-seq_NIH3T3_SVI_6h_2025

description:
Library name: H3K27ac-ChIP-seq_NIH3T3_SVI_6h_2025
ATCC, CRL-1658™

value: H3K27ac (CST;Cell Signaling Technology,#8173)


title: DNA-methylation array data_202010290110_R08C01

value: Oligodendroglioma, IDH-mutant and 1p/19q-codeleted

value: Female


title: duodenum_d7_rep-2

value: male


title: duodenum_d7_rep-1


title: T21-058

description:
Library name: T21-058
low-pass WGS


title: DNA-methylation array data_204234660035_R04C01

value: Male


title: T21-036

description:
Library name: T21-036
low-pass WGS


title: DNA-methylation array data_205814880089_R03C01


title: duodenum_d7_rep-3

value: female


title: Lcn2-ko, CD45 positive cells, scRNA seq

city: Shanghai

first: zhu

last: Qingchen

address: 320 Yue Yang Rd, Xuhui District

institute: Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences

description:
Library name: sample2
BD Rhapsody

data_processing:
Cell Ranger software was used to process Chromium single cell data to align reads, generate feature-barcode matrices, make gene counting and aggregation.
Assembly: mm10
Supplementary files format and content: Compressed tab-separated values files and matrix files.

source_name: MB49 tumor tissue

extract_protocol:
We generated the chimeric mice by reconstitution of male WT or Lcn2-KO bone marrows into lethally irradiated female mice, which mimicked the mice with Lcn2-conditional knockout in myeloid cells. The MB49 tissue samples were processed as described below. Briefly, samples were first washed with phosphate-buffered saline (PBS), minced into small pieces (approximately 1mm3) on ice and enzymatically digested with 10 U/mL collagenase I (Worthington) and 400 U/mL collagenase Ⅳ (Worthington) and 30 U/mL DNase I (Worthington) and 1mg/mL Dispase Ⅱ (Worthington) for 45 min at 37°C, with agitation. After digestion, samples were sieved through a 70µm cell strainer, and centrifuged at 300 g for 5 min. After the supernatant was removed, the pelleted cells were suspended in red blood cell lysis buffer (Miltenyi Biotec) to lyse red blood cells. After washing with PBS containing 0.04% BSA, the cell pellets were stained with mouse CD45 antibody and underwent flow sorting to obtain live CD45+ cells. Dissociated single cells were then stained for viability assessment using Calcein-AM (Thermo Fisher Scientific) and Draq7 (BD Biosciences).
BD Rhapsody system was used to capture the transcriptomic information of the male and female mouse MB49 tumor derived CD45+ single cells.Single-cell capture was achieved by random distribution of a single-cell suspension across >200,000 microwells through a limited dilution approach. Beads with oligonucleotide barcodes were added to saturation so that a bead was paired with a cell in a microwell. The cells were lysed in the microwell to hybridize mRNA molecules to barcoded capture oligos on the beads. Beads were collected into a single tube for reverse transcription and ExoI digestion. Upon cDNA synthesis, each cDNA molecule was tagged on the 5′ end (that is, the 3′ end of a mRNA transcript) with a unique molecular identifier (UMI) and cell barcode indicating its cell of origin. Whole transcriptome libraries were prepared using the BD Rhapsody single-cell whole-transcriptome amplification (WTA) workflow including random priming and extension (RPE), RPE amplification PCR and WTA index PCR. The libraries were quantified using a High Sensitivity DNA chip (Agilent) on a Bioanalyzer 2200 and the Qubit High Sensitivity DNA assay (Thermo Fisher Scientific). Sequencing was performed by illumina sequencer (Illumina, San Diego, CA) on a 150 bp paired-end run.

value: MB49 tumor tissue

value: sorted CD45 positive cells


title: duodenum_d35_rep-3

description: Gene expression data from Gallus Gallus duodenum 35 days

source_name: duodenum 35 days


title: T21-034

description:
Library name: T21-034
low-pass WGS

value: Medulloblastoma, SHH-activated


title: wt,CD45 positive cells,scRNAseq

description:
Library name: sample1
BD Rhapsody

value: wt


title: DNA-methylation array data_205689110054_R03C01

value: tumor


title: H3K27ac-ChIP-seq_NIH3T3_SVI_0h_2025

description:
Library name: H3K27ac-ChIP-seq_NIH3T3_SVI_0h_2025
ATCC, CRL-1658™

value: Fibroblasts


title: T21-018

description:
Library name: T21-018
low-pass WGS

value: High-grade astrocytoma with piloid features


title: duodenum_d35_rep-4


title: DNA-methylation array data_203960260023_R04C01


title: T21-002

description:
Library name: T21-002
low-pass WGS

value: Diffuse midline glioma, H3 K27-altered


title: duodenum_d35_rep-2


title: duodenum_d35_rep-1


title: PBS infusion

city: guangzhou

first: Tenghui

last: Ye

address: 777 Xingye Avenue

department: School of Biomedical Science and Engineering

institute: South China University of Technology

description: Library name: PBS

data_processing:
Reads were processed using the Cell Ranger 7.1.0 pipeline with default and recommended parameters.
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

source_name: liver

extract_protocol:
Mouse liver were dissociated at 37 ℃ with a shaking speed of 50 r.p.m for about 40 min.We repeatedly collected the dissociated cells at interval of 20 min to increase cell yield and viability. Cell suspensions were filtered using a 40 um nylon cell strainer and red blood cells were removed by 1X Red Blood Cell Lysis Solution (Thermo Fisher, Cat. no. 00-4333-57) . Dissociated cells were washed with 1x DPBS containing 2% FBS. Cells were stained with 0.4% Trypan blue (Thermo Fisher, Cat. no. 14190144) to check the viability on Countess® II Automated Cell Counter (Thermo Fisher).
Beads with unique molecular identifier (UMI) and cell barcodes were loaded close to saturation, so that each cell was paired with a bead in a Gel Beads-in-emulsion(GEM). After exposure to cell lysis buffer, polyadenylated RNA molecules hybridized to the beads. Beads were retrieved into a single tube for reverse transcription. On cDNA synthesis, each cDNA molecule was tagged on the 5’end (that is, the 3’end of a messenger RNA transcript) with UMI and cell label indicating its cell of origin. Briefly, 10× beads that were then subject to second-strand cDNA synthesis, adaptor ligation, and universal amplification.Sequencing libraries were prepared using randomly interrupted whole-transcriptome amplification products to enrich the 3’ end of the transcripts linked with the cell barcode and UMI. All the remaining procedures including the library construction were performed according to the standard manufacturer’s protocol (Chromium Single Cell 3ʹ v3.1). Sequencing libraries were quantified using a High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2100 and the Qubit High Sensitivity DNA Assay (Thermo Fisher Scientific). The libraries were sequenced on NovaSeq6000 (Illumina), and 150 bp paired-end reads were generated. The sequencing and bioinformatics analysis were performed by Majorbio Co., Ltd (Shanghai, China).

value: liver

value: PBS infusion


title: T21-001

description:
Library name: T21-001
low-pass WGS

source_name: tumor

value: Atypical meningioma


title: duodenum_d28_rep-4

description: Gene expression data from Gallus Gallus duodenum 28 days

source_name: duodenum 28 days


title: Engineered mesenchymal stromal cells with bispecific polyvalent peptides

description: Library name: PPE


title: DNA-methylation array data_203068650138_R08C01


title: DNA-methylation array data_203249020036_R06C01


title: T20-171

description:
Library name: T20-171
low-pass WGS

value: Glioblastoma, IDH-wildtype


title: Native mesenchymal stromal cells

description: Library name: Native

value: Native mesenchymal stromal cells


title: duodenum_d28_rep-3


title: duodenum_d28_rep-2


title: DNA-methylation array data_203960260003_R01C01

value: Oligodendroglioma, IDH-mutant and 1p/19q-codeleted

value: Female


title: T20-168

description:
Library name: T20-168
low-pass WGS


title: M3, replicate 3, RNAseq

city: Yangzhou

first: Tianfeng

address: 98 Nantong West Road

institute: Northern Jiangsu People's Hospital

description: Coll IV

data_processing:
Reads were aligned to the human Ensemble genome GRCh38 (mouse Ensemble genome GRCm38) using Hisat2 aligner (v2.1.0) under parameters: “--rna-strandness RF”. The reads mapped the genome were calculated using featureCounts (v1.6.3).
Assembly: mm10
Supplementary files format and content: read counts table (All.count.txt) and fpkm table (All.fpkm.anno.txt)

source_name: thalamus

extract_protocol:
Total RNA was extracted using TRIzol™ Reagent (Invitrogen, 15596018).
EpiTM mini longRNA-seq kit (Epibiotek, E1802) was used for library preparation according to the instructions.

value: thalamus

value: tissue

value: neuron, glia

value: total RNA


title: duodenum_d28_rep-1

value: male


title: T20-076

description:
Library name: T20-076
low-pass WGS

value: Pilocytic astrocytoma (supratentorial)


title: M2, replicate 2, RNAseq

description: Coll IV


title: M1, replicate 1, RNAseq

description: Coll IV


title: DNA-methylation array data_202013790104_R05C01

value: tumor


title: DNA-methylation array data_204229190143_R08C01

value: Male


title: C3, replicate 3, RNAseq

description: saline


title: duodenum_d21_rep-4

description: Gene expression data from Gallus Gallus duodenum 21 days

source_name: duodenum 21 days

value: female


title: C2, replicate 2, RNAseq

description: saline


title: T22-062

description:
Library name: T22-062
low-pass WGS


title: C1, replicate 1, RNAseq

description: saline


title: duodenum_d21_rep-3


title: duodenum_d21_rep-2


title: duodenum_d21_rep-1


title: S12, Hippocampus, wild-type, 12m

city: Birmingham

first: Brittany

last: Lasseigne

state: AL

address: 1900 University Boulevard

department: Cell, Developmental and Integrative Biology

institute: University of Alabama at Birmingham

description: 10x Genomcis

data_processing:
We processed data using 10X Genomics Cell Ranger (version 6.1.1). We aligned sequencing reads to the mouse reference genome (mm10) to generate feature-barcode matrices. The average paired-end sequencing depth was 34,000 reads per nucleus, with approximately 15,500 nuclei per sample.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: left hippocampus

extract_protocol:
We adapted our single nuclei isolation for mouse hippocampus samples from the previously described protocol for rats in Phillips et al. Cell Reports 2022 and sorted nuclei at the University of Alabama at Birmingham's (UAB) Comprehensive Flow Cytometry Core (CFCC) using fluorescence-activated cell sorting (FACS) on an Atlas BD ARIA II.
Per the standard 10X protocol, the UAB CFCC used the 10X Chromium Controller to partition hippocampal nuclei into droplets with a barcoded gel bead where nuclei were lysed, and RNA was reverse transcribed, creating cDNA encapsulated in each droplet. After fragmenting and amplifying cDNA, they added Illumina adapters using the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (10X#: PN-1000121). The UAB Heflin Center for Genomic Sciences at the UAB Sequencing Core indexed and sequenced all samples on a NovaSeq 6000 (Illumina). For each sample, they loaded approximately 20,000 nuclei onto an S4 flow cell.

value: left hippocampus

value: 12 months

value: wild-type


title: S11, Hippocampus, wild-type, 6m

description: 10x Genomcis

value: 6 months


title: DNA-methylation array data_202915460087_R03C01


title: T21-008

description:
Library name: T21-008
low-pass WGS

value: Glioblastoma, IDH-wildtype


title: S10, Hippocampus, 3xTg-AD, 12m

description: 10x Genomcis


title: duodenum_d14_rep-2

description: Gene expression data from Gallus Gallus duodenum 14 days

source_name: duodenum 14 days


title: duodenum_d14_rep-4


title: duodenum_d14_rep-3


title: DNA-methylation array data_203927450079_R06C01


title: DNA-methylation array data_203017150041_R06C01


title: DNA-methylation array data_205049770014_R06C01


title: DNA-methylation array data_205537620156_R01C01


title: DNA-methylation array data_203866300058_R07C01


title: T21-146

description:
Library name: T21-146
low-pass WGS

value: Glioblastoma, IDH-wildtype, subtype gliosarcoma


title: duodenum_d14_rep-1


title: S8, Hippocampus, wild-type, 12m

description: 10x Genomcis


title: S7, Hippocampus, wild-type, 6m

description: 10x Genomcis


title: DNA-methylation array data_204964480101_R07C01

value: Oligodendroglioma, IDH-mutant and 1p/19q-codeleted


title: S6, Hippocampus, 3xTg-AD, 12m

description: 10x Genomcis


title: DNA-methylation array data_205041760152_R01C01


title: DNA-methylation array data_204963470149_R03C01

value: Female


title: Hep2_HRSV_20H_UV-1 (UV-inactivated RSV)

city: Singapore

first: Richard

middle: J

last: Sugrue

address: 60 Nanyang Drive

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

description: Gene expression data from HRSV infected Hep2 20 hpi rep 1 (UV)

hyb_protocol: Following fragmentation, 15 ug of aRNA were hybridized for 20 hr at 45˚C on Human U133 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with GeneChip Operating Software 5.0 (GCOS 5.0) using Affymetrix default analysis settings. Further analysis was done in GeneSpring 11.0. The normalization was done using internal and external control genes as assigned by Affymetrix. The target intensity of each array on a given time point was first filtered by the flagging of Present (P) in 3 replicates at one time-point, which then further calculated in fold change up- or downregulation with respect to the signal intensity in MOCK infected cells, after analyzed by ANOVA with p value ≤ 0.05.

source_name: HRSV infected Hep2 20 hpi rep 1 (UV)

label_protocol: Biotinylated mRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA (Expression Analysis Technical Manual, 2009, Affymetrix).

growth_protocol: The cells were grown in DMEM 10% Fetal Bovine Serum (FBS)100 units/ml of Penicillin/Sreptomycin (Gibco), at 37˚C, 5% CO2

extract_protocol: RNA extraction was performed using RNAeasy MiniKit (Qiagen) according to the manufacturer's instruction at 4˚C

treatment_protocol: The cells were infected with HRSV MOI=5 in DMEM + Glutamax (Gibco) with 2% Fetal Bovine Serum (FBS) and 100 units/ml of Penicillin/Sreptomycin (Gibco), at 33˚C, 5% CO2

value: Hep2 cells

value: HRSV infected (UV inativated)


title: duodenum_d0_rep-4

description: Gene expression data from Gallus Gallus duodenum 0 days

source_name: duodenum 0 days


title: Hep2_HRSV_20H_UV-2 (UV-inactivated RSV)

description: Gene expression data from HRSV infected Hep2 20 hpi rep 2 (UV)

source_name: HRSV infected Hep2 20 hpi rep 2 (UV)


title: DNA-methylation array data_204776820059_R07C01


title: DNA-methylation array data_205689130023_R03C01


title: Hep2_HRSV_20H-3

description: Gene expression data from HRSV infected Hep2 20 hpi rep 3

source_name: HRSV infected Hep2 20 hpi rep 3

value: HRSV infected


title: S5, Hippocampus, 3xTg-AD, 6m

description: 10x Genomcis


title: DNA-methylation array data_204229180070_R02C01


title: S9, Hippocampus, 3xTg-AD, 6m

description: 10x Genomcis


title: duodenum_d0_rep-3


title: duodenum_d0_rep-1


title: Hep2_HRSV_0H-3 (mock-infected)

description: Gene expression data from mock infected Hep2 rep 3

source_name: Mock infected Hep2 rep 3

value: Mock infected


title: Hep2_HRSV_20H-2

description: Gene expression data from HRSV infected Hep2 20 hpi rep 2

source_name: HRSV infected Hep2 20 hpi rep 2


title: Hep2_HRSV_20H_UV-3 (UV-inactivated RSV)

description: Gene expression data from HRSV infected Hep2 20 hpi rep 3 (UV)

source_name: HRSV infected Hep2 20 hpi rep 3 (UV)


title: duodenum_d0_rep-2

value: male


title: PC9, NCAPD2_Knockdown, rep2

city: Fuzhou

first: Yun

state: Fujian

address: 134 Dong Street, Gulou District

institute: Fujian Provincial Hospital

description:
Library name: sample5
KD2_fpkm

data_processing:
Reads were processed using the following workflow: raw reads were quality-checked using FastQC (version 0.11.9), and adapter sequences were trimmed using Trimmomatic (version 0.39). The clean reads were then aligned to the human reference genome (hg38) using STAR (version 2.7.9a). Gene expression quantification was performed using featureCounts (version 2.0.1).
Assembly: The human genome reference used for alignment was GRCh38 (hg38).
Supplementary files format and content: Processed data file is provided in the form of an Excel file (.xlsx) containing normalized gene expression counts for each sample.

extract_protocol:
Total RNA was extracted from PC9 cell lines using TRIzol reagent (Thermo Fisher Scientific), followed by purification with an RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA integrity was verified using an Agilent 2100 Bioanalyzer to ensure a RIN value greater than 7 for all samples before library preparation.
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB) following the manufacturer’s instructions. Poly(A)+ RNA was enriched from total RNA using oligo(dT) beads, fragmented, and reverse-transcribed into cDNA. The cDNA was end-repaired, ligated to sequencing adapters, and PCR amplified to create the final library. Libraries were quantified and assessed for quality using an Agilent 2100 Bioanalyzer before sequencing.

value: lung adenocarcinoma cell

value: NCAPD2 knockdown


title: PC9, NCAPD2_Knockdown, rep3

description:
Library name: sample6
KD3_fpkm


title: S3, Hippocampus, wild-type, 6m

description: 10x Genomcis


title: cerebral-cortex_d7_rep-4

description: Gene expression data from Gallus Gallus cerebral-cortex 7 days

source_name: cerebral-cortex 7 days


title: DNA-methylation array data_203821710016_R04C01

data_processing:
IDAT files were preprocessed using R/minfi.
*processed value definition: Average beta value

extract_protocol: Genomic DNA was extracted and purified from human tumor samples using Maxwell RSC FFPE Plus DNA Purification Kit (Promega, USA) according to standard instructions.

value: tumor

value: Male


title: S4, Hippocampus, wild-type, 12m

description: 10x Genomcis

value: left hippocampus

value: female


title: PC9, NCAPD2_Knockdown, rep1

description:
Library name: sample4
KD1_fpkm


title: DNA-methylation array data_205537620011_R01C01


title: Hep2_HRSV_20H-1

description: Gene expression data from HRSV infected Hep2 20 hpi rep 1

source_name: HRSV infected Hep2 20 hpi rep 1


title: S1, Hippocampus, 3xTg-AD, 6m

description: 10x Genomcis


title: Hep2_HRSV_0H-2 (mock-infected)

description: Gene expression data from mock infected Hep2 rep 2

source_name: Mock infected Hep2 rep 2


title: PC9, control, rep3

description:
Library name: sample3
NC3_fpkm

value: control


title: cerebral-cortex_d7_rep-3


title: Hep2_HRSV_0H-1 (mock-infected)

description: Gene expression data from mock infected Hep2 rep 1

source_name: Mock infected Hep2 rep 1


title: DNA-methylation array data_204229190148_R08C01

source_name: tumor


title: cerebral-cortex_d7_rep-1


title: Tfh_B, scRNAseq

description: 10x Genomics

source_name: spleen

extract_protocol:
To characterize the Tfh and B conjugates, CD4+ T cells were enriched from the spleen of K/BxN Th17 fate-mapping mice by positive selection using CD4 microbeads (Miltenyi Biotec). Enriched CD4+ T cells (containing single cell and T-B doublet) were then stained with Abs against CD4 (GK1.5), TCRβ, CD25, CXCR5, PD-1 and CD19, and then sorted for B cells conjugated with ZsGreen+ Tfh and ZsGreen−Tfh, defining as CD4+TCR+CD25−CXCR5+PD-1+ZsGreen+CD19+ and CD4+TCR+CD25−CXCR5+PD-1+ZsGreen−CD19+, respectively. For the ScRNA-seq, T- B conjugates were separated by incubating the conjugates in 10 mM EDTA for 5 mins at room temperature with vortex every 30 seconds. Cells were then washed with FACS buffer and suspended in DPBS. Single cells were separated into droplet emulsions according to manufacturer’s instructions (10x Genomics). scRNA-seq was performed according to manufacturer’s instructions (10x Genomics).
10x Genomics library construction kit (Cat # 1000190)

value: spleen

value: follicular helper T cells

tag: sorted cell_type


title: PC9, control, rep2

description:
Library name: sample2
NC2_fpkm


title: DNA-methylation array data_203810640111_R08C01


title: cecal-epithelia_d14_rep-3

description: Gene expression data from Gallus Gallus cecal-epithelia 14 days

source_name: cecal-epithelia 14 days

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


title: S2, Hippocampus, 3xTg-AD, 12m

description: 10x Genomcis

value: 12 months


title: cerebral-cortex_d7_rep-2


title: DNA-methylation array data_202259490002_R02C01

value: Oligodendroglioma, IDH-mutant and 1p/19q-codeleted


title: cecal-epithelia_d14_rep-4


title: PC9, control, rep1

description:
Library name: sample1
NC1_fpkm


title: DNA-methylation array data_203810640148_R06C01

value: Female


title: cecal-epithelia_d14_rep-2


title: DNA-methylation array data_205096370095_R02C01


title: spleen-derived WT Treg cells

city: Memphis

first: Hongbo

last: Chi

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

description: Library name: spleenWT1

data_processing:
The Cell Ranger 2.1.1 Single-Cell Software Suite (10x Genomics) was implemented to process the raw sequencing data from the Illumina HiSeq run.
This pipeline performed de-multiplexing, alignment (mm10), and barcode processing to generate gene-cell matrices used for downstream analysis.
Assembly: mm10
Supplementary files format and content: cell ranger count matrix for single cells in each sample

growth_protocol: 10-day-old perinatal control (Foxp3CrePik3c3+/fl) or Foxp3CrePik3c3fl/fl mice were used directly for experiments.

extract_protocol:
Splenic Treg cells were sorted from 10-day-old perinatal control (Foxp3CrePik3c3+/fl) and Foxp3CrePikc3cfl/fl mice and loaded onto the Chromium Controller according to their respective cell counts to target 9,000 single cell GEMs (gel beads in emulsion) per sample.
Libraries were prepared using the Chromium Single Cell 3’ v3 Library and Gel Bead Kit (10x Genomics)

value: Primary Treg cells

value: Wild-type

value: Sort-purified Foxp3-YFP+CD4+TCRb+ Treg cells


title: cecal-epithelia_d14_rep-1

data_processing: Probeset-level intensity acquisition was performed by using Expression Console 1.1 (Affymetrix, Santa Clara, CA).


title: DNA-methylation array data_202013790104_R03C01


title: TfhZG_B, scRNAseq

description: 10x Genomics

value: ZG


title: Vps34KO2 Treg cells, ATAC

description: Library name: KO2_ATAC

data_processing:
The Cell Ranger ARC 2.0.2 Single-Cell Software Suite (10x Genomics) was implemented to process the raw sequencing data from the Illumina HiSeq run.
This pipeline performed de-multiplexing, alignment (mm10), and barcode processing to generate gene-cell and peak-cell matrices used for downstream analysis.
Assembly: mm10
Supplementary files format and content: cell ranger arc count matrix for single cells in each sample
Library strategy: Single Cell Multiome ATAC+Gene Expression

growth_protocol: 12-day-old perinatal control (Foxp3CrePikc3c3+/fl) or Foxp3CrePik3c3fl/fl mice were used directly for experiments.

extract_protocol:
Splenic Treg cells were sorted from 12-day-old perinatal control (Foxp3CrePik3c3+/fl) and Foxp3CrePik3c3fl/fl mice and loaded onto the Chromium Controller according to their respective cell counts to target 9,000 single-cell GEMs (gel beads in emulsion) per sample.
Libraries were prepared using the Chromium Next GEM Single Cell Multiome ATAC+Gene Expression Library and Gel Bead Kit (10x Genomics)

value: Sort-purifed Foxp3-YFP+CD4+ Treg cells


title: DNA-methylation array data_201465970005_R01C01


title: DNA-methylation array data_205814880087_R08C01


title: Vps34KO1 Treg cells, ATAC

description: Library name: KO1_ATAC


title: pectoralis-muscle_d7_rep-3

description: Gene expression data from Gallus Gallus pectoralis-muscle 7 days

source_name: pectoralis-muscle 7 days


title: pectoralis-muscle_d7_rep-2

value: male


title: DNA-methylation array data_203927450079_R08C01


title: Vps34KO1 Treg cells, GEX

description: Library name: KO1_mRNA


title: DNA-methylation array data_205862290139_R05C01

value: Haemangioblastoma


title: WT1 Treg cells, ATAC

description: Library name: WT1_ATAC

value: Control


title: spleen-derived Vps34-deficient Treg cells

description: Library name: spleenKO1


title: pectoralis-muscle_d0_rep-4

description: Gene expression data from Gallus Gallus pectoralis-muscle 0 days

source_name: pectoralis-muscle 0 days


title: DNA-methylation array data_206238130124_R03C01

value: tumor


title: WT1 Treg cells, GEX

description: Library name: WT1_mRNA


title: KO3-IP

first: Chenbo

last: Ding

state: None Selected

address: 280 Chongqing South Rd

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Visualizations using volcano-plots and heatmaps were produced with R. Gene Ontology
Assembly: mm10
Supplementary files format and content: Table-delimited text file includes raw counts for each sample
Supplementary files format and content: Table-delimited text file includes RPKM vaules for each sample
Library strategy: Ribo-seq

source_name: Intestine

extract_protocol:
RiboTag lysis buffer (containing heparin, cycloheximide and RNase inhibitor SuperaseIN)
mRNA for RNA-seq analysis was purified using polyA+ selection
RNA samples were transferred to OE Biotech Co., Ltd. for cDNA library preparation using an NEBNext Ultra II Directional RNA Library Prep Kit according to the manufacturer’s instructions

value: Intestine

value: Primary cell

value: enteric neurons

value: KO-IP


title: pectoralis-muscle_d0_rep-3

value: female


title: KO3-input

value: KO-input


title: DNA-methylation array data_203991470086_R03C01

first: Philipp

address: Charitéplatz 1

institute: Charité - Universitätsmedizin Berlin

value: Male


title: pectoralis-muscle_d0_rep-2


title: lung derived Vps34 deficient Treg cells2

description: Library name: lungKO2

data_processing:
Adapter sequences were removed using cutadapt v.1.9
and aligned them to the mouse genome mm10 (GRCm38_68 from Sanger; ftp://ftp-mouse.sanger.ac.uk/ref/GRCm38_68.fa) using the Burrows–Wheeler algorithm32 (version 0.5.9-r26-dev, default parameter)
duplicated reads were then marked with Picard (version 1.65 (1160)) and only non-duplicated reads were kept, using samtools (parameter ‘-q 1 -F 1024’ version 0.1.18 (r982:295))
After adjustment using the Tn5 shift (by which reads were offset by +4 bp for the sense strand and −5 bp for the antisense strand), we separated reads into nucleosome-free, mononucleosome, dinucleosome and trinucleosome by fragment size
performed peak-calling for nucleosome-free reads using MACS2 (version 2.1.0.20150603, default parameters with ‘–extsize 200 –nomodel’, merged by bedtools if within 100 bp) for individual samples
Assembly: mm10
Supplementary files format and content: Consensus peaks and fragment counts for all samples

source_name: lung

growth_protocol: 10-day-old perinatal control (Foxp3CrePikc3c+/+ or Foxp3CrePikc3c+/fl) or Foxp3CrePik3c3fl/fl mice were used directly for experiments.

extract_protocol:
Cells were lysed in 50 μl ATAC-seq lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630 detergent) on ice for 10 min. Resulting nuclei were pelleted at 500g for 10 min at 4 °C. Supernatant was carefully removed with a pipette and discarded. The pellet was resuspended in 50 μl transposase reaction mix (25 μl 2 × TD buffer, 22.5 μl nuclease-free water, 2.5 μl transposase) and incubated for 30 min at 37 °C. After the reaction, the DNA was cleaned up using the Qiagen MinElute kit
The barcoding reaction was run using the NEBNext HiFi kit on the basis of the manufacturer’s instructions and amplified for five cycles

value: lung

value: Sort-purified CD4+Foxp3-YFP+TCRb+ Treg cells


title: DNA-methylation array data_205828610104_R02C01

value: Diffuse paediatric-type high-grade glioma, H3-wildtype and IDH-wildtype

value: Female


title: pectoralis-muscle_d7_rep-1


title: Vps34KO2 Treg cells, GEX

description: Library name: KO2_mRNA

value: spleen

value: Primary Treg cells


title: lung derived Vps34 deficient Treg cells1

description: Library name: lungKO1


title: pectoralis-muscle_d7_rep-4


title: KO2-IP


title: DNA-methylation array data_207355710034_R07C01


title: KO2-input


title: DNA-methylation array data_206644420175_R04C01

value: Glioblastoma, IDH-wildtype


title: pectoralis-muscle_d0_rep-1

value: male


title: lung derived WT Treg cells1

description: Library name: lungWT1

value: Control


title: KO1-IP


title: brain_d42_rep-3

description: Gene expression data from Gallus Gallus brain 42 weeks

source_name: brain 42 days


title: brain_d42_rep-4


title: DNA-methylation array data_206503150006_R05C01

value: tumor


title: brain_d42_rep-2


title: spleen derived Vps34 deficient Treg cells4

description: Library name: spleenKO4


title: lung derived WT Treg cells2

description: Library name: lungWT2


title: KO1-input

value: Intestine


title: DNA-methylation array data_206999330143_R07C01


title: DNA-methylation array data_202790040015_R08C01


title: WT3-IP

value: Primary cell

value: WT-IP


title: spleen derived Vps34 deficient Treg cells2

description: Library name: spleenKO2


title: WT3-input

value: enteric neurons

value: WT-input


title: brain_d35_rep-4

description: Gene expression data from Gallus Gallus brain 35 weeks

source_name: brain 35 days

value: female


title: brain_d35_rep-3


title: WT2-IP


title: DNA-methylation array data_204081560059_R01C01


title: spleen derived Vps34 deficient Treg cells1

description: Library name: spleenKO1


title: DNA-methylation array data_202995850016_R01C01


title: spleen derived WT Treg cells2

description: Library name: spleenWT2


title: spleen derived WT Treg cells1

description: Library name: spleenWT1


title: WT2-input


title: brain_d28_rep-4

description: Gene expression data from Gallus Gallus brain 28 weeks

source_name: brain 28 days


title: brain_d35_rep-2


title: DNA-methylation array data_207513910035_R05C01


title: brain_d28_rep-3


title: spleen derived Vps34 deficient Treg cells3

description: Library name: spleenKO3


title: brain_d42_rep-1


title: DNA-methylation array data_205567980118_R06C01

value: Male


title: WT1-IP


title: WT1-input


title: RNA-seq_NIH3T3_SVI_7h_exp2_2023

data_processing:
Galaxy online platform (https://usegalaxy.org/)
Quality Control (QC) steps were employed on raw sequencing reads by the FastQC application (Galaxy Version 0.74+galaxy0).
Processed sequencing reads were mapped to the reference human (hg19) or mouse (mm9) genome by the HISAT2 alignment tool (Galaxy Version 2.2.1+galaxy1) under “single-end”, “stranded” and “reverse” options.
RNA integrity was measured by the Transcript Integrity Number tool (Galaxy Version 5.0.1+galaxy2). The enrichment of RNA-sequencing reads within gene bodies was examined using Gene Body Coverage (ΒΑΜ) tool.
Calculation of sequencing reads that are mapped into genes was performed with the htseq-count tool (Galaxy Version 0.9.1+galaxy1), in “union” mode, with “stranded”, “reverse”, and “minimum alignment quality 1” and “–nonunique All" options.
Assembly: hg19 (Homo sapiens), mm9 (Mus musculus)
Supplementary files format and content: bigwig files including RPKM normalized signal

source_name: NIH/3T3 (ATCC, CRL-1658)

growth_protocol: Human and mouse cells were cultured under optimum conditions according to the manufacturer’s instructions. MRC-5 cells (ATCC, CCL-171™) and NIH/3T3 cells (ATCC, CRL-1658™) were grown in DMEM medium (Sigma-Aldrich). All culture media were supplemented with 1% Pen-Strep (Biowest) and 10% (v/v) heat-inactivated Fetal Bovine Serum (FBS) (Biowest). All cell cultures were established in laboratory incubators under optimum conditions (37°C, 5% CO2).

extract_protocol:
Total RNA was extracted from cells using the Monarch Total RNA Miniprep Kit (T2010S, NEB) that includes treatment with DNase I for 15 minutes at 37°C to remove any DNA remnants.
RNA quality was evaluated at the Bioanalyzer 2100 DNA Chip 7500 (Agilent Technologies). RNA-seq libraries were generated using the NEBNext Ultra II Directional RNA Library Prep Kit (E7760L) for Illumina following the manufacturer's instructions. Samples were subjected to beads-purification (NEBNext Sample Purification Beads, E7767L), and the quality of the isolated libraries was evaluated at the Bioanalyzer 2100 DNA Chip 7500 (Agilent Technologies).

treatment_protocol: Cell cultures were grown at 85–95% confluence and subjected to mock-infection (control; 0h) or Sendai-Virus-infection (Cantell strain, Charles River lab., 2000 HA units/ml) for 3, or 6 (MRC-5 cells) or 7 hrs (NIH/3T3 cells), prior to proceeding in downstream examinations. Sendai Virus was supplied directly in the culture medium at a ratio of 1/10 (v/v).

value: NIH/3T3 (ATCC, CRL-1658)

value: Fibroblasts

value: Sendai Virus Cantell strain, Charles River lab

value: 7 hrs


title: Atg14KO eTreg cells4

description:
Library name: eTregAtg14KO4
eTregAtg14KO4

source_name: Spleen

growth_protocol: Mixed bone marrow chimeras were generated by mixing CD45.2+ bone marrow from control (Foxp3CreAtg14+/fl) or Foxp3CreAtg14fl/fl mice at a 1:1 ratio with CD45.1+ WT spike bone marrow, followed by adoptive transfer into sublethally irradiated Rag1–/– mice. Bone marrow was allowed to reconstitute for 6–8 weeks before experiments.

value: Spleen

value: Sort-purified CD4+Foxp3-YFP+CD44+CD62L– eTreg cells


title: DNA-methylation array data_206687210001_R08C01

value: Glioblastoma, IDH-wildtype


title: Atg14KO eTreg cells2

description:
Library name: eTregAtg14KO2
eTregAtg14KO2

value: Primary Treg cells


title: RNA-seq_NIH3T3_SVI_0h_exp2_2023

value: 0 hrs (naive)


title: Atg14KO eTreg cells3

description:
Library name: eTregAtg14KO3
eTregAtg14KO3


title: DNA-methylation array data_203068650138_R05C01

value: tumor

value: Female


title: brain_d35_rep-1

value: male


title: brain_d28_rep-2


title: RNA-seq_NIH3T3_SVI_7h_exp1_2023


title: Control eTreg cells3

description:
Library name: eTregWT3
eTregWT3

value: Control


title: brain_d28_rep-1


title: brain_d9_rep-3

description: Gene expression data from Gallus Gallus brain 9 days

source_name: brain 9 days


title: brain_d9_rep-4


title: DNA-methylation array data_204237150093_R02C01


title: Control eTreg cells1

description:
Library name: eTregWT1
eTregWT1


title: Female, CD45 negative cells, scRNAseq

description: BD Rhapsody

data_processing:
Basecalls performed using CASAVA version 1.8
Umi-tools was utilized to calculate the raw counts and cell whitelist by default parameter
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:  MT% < 20%;   Cell Gene Number < Median Gene Number * 2;  Cell Gene Number > 200. PCA and tSNE analysis was used for the single cell to cell relation description. Graphcluster and K-mean was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Assembly: mm10
Supplementary files format and content: Compressed tab-separated values files and matrix files.

source_name: MB49 tumor tissue

extract_protocol:
The MB49 tissue samples were processed as described below. Briefly, samples were first washed with phosphate-buffered saline (PBS), minced into small pieces (approximately 1mm3) on ice and enzymatically digested with 10 U/mL collagenase I (Worthington) and 400 U/mL collagenase Ⅳ (Worthington) and 30 U/mL DNase I (Worthington) and 1mg/mL Dispase Ⅱ (Worthington) for 45 min at 37°C, with agitation. After digestion, samples were sieved through a 70µm cell strainer, and centrifuged at 300 g for 5 min. After the supernatant was removed, the pelleted cells were suspended in red blood cell lysis buffer (Miltenyi Biotec) to lyse red blood cells. After washing with PBS containing 0.04% BSA, the cell pellets were stained with mouse CD45 antibody and underwent flow sorting to obtain live CD45- and CD45+ cells. Dissociated single cells were then stained for viability assessment using Calcein-AM (Thermo Fisher Scientific) and Draq7 (BD Biosciences).
BD Rhapsody system was used to capture the transcriptomic information of the male and female mouse MB49 tumor derived CD45+ and CD45- single cells.Single-cell capture was achieved by random distribution of a single-cell suspension across >200,000 microwells through a limited dilution approach. Beads with oligonucleotide barcodes were added to saturation so that a bead was paired with a cell in a microwell. The cells were lysed in the microwell to hybridize mRNA molecules to barcoded capture oligos on the beads. Beads were collected into a single tube for reverse transcription and ExoI digestion. Upon cDNA synthesis, each cDNA molecule was tagged on the 5′ end (that is, the 3′ end of a mRNA transcript) with a unique molecular identifier (UMI) and cell barcode indicating its cell of origin. Whole transcriptome libraries were prepared using the BD Rhapsody single-cell whole-transcriptome amplification (WTA) workflow including random priming and extension (RPE), RPE amplification PCR and WTA index PCR. The libraries were quantified using a High Sensitivity DNA chip (Agilent) on a Bioanalyzer 2200 and the Qubit High Sensitivity DNA assay (Thermo Fisher Scientific). Sequencing was performed by illumina sequencer (Illumina, San Diego, CA) on a 150 bp paired-end run.

value: MB49 tumor tissue

value: sorted CD45 negative cells


title: brain_d9_rep-2


title: RNA-seq_NIH3T3_SVI_0h_exp1_2023


title: Atg14KO cTreg cells4

description:
Library name: cTregAtg14KO4
cTregAtg14KO4

value: Sort-purified CD4+Foxp3-YFP+CD44–CD62L+ cTreg cells


title: DNA-methylation array data_207385100013_R04C01

value: Male


title: Atg14KO eTreg cells1

description:
Library name: eTregAtg14KO1
eTregAtg14KO1


title: DNA-methylation array data_203867050007_R03C01


title: brain_d8_rep-4

description: Gene expression data from Gallus Gallus brain 8 days

source_name: brain 8 days

value: female


title: DNA-methylation array data_205041760141_R07C01


title: Male, CD45 negative cells, scRNAseq

description: BD Rhapsody


title: Male,CD45 positive cells,scRNAseq

description: BD Rhapsody

value: sorted CD45 positive cells


title: Female, CD45 positive cells, scRNA seq

description: BD Rhapsody


title: Atg14KO cTreg cells3

description:
Library name: cTregAtg14KO3
cTregAtg14KO3


title: DNA-methylation array data_205495890138_R06C01


title: Atg14KO cTreg cells2

description:
Library name: cTregAtg14KO2
cTregAtg14KO2


title: Control eTreg cells2

description:
Library name: eTregWT2
eTregWT2


title: Input-ChIP-seq_NIH3T3_SVI_6h_2023

data_processing:
Galaxy online platform (https://usegalaxy.org/)
Quality Control steps (QC) were employed on raw sequencing reads by the FastQC application (Galaxy Version 0.72+galaxy1).
Adaptors’ contaminants and low-quality reads, were trimmed, and thus excluded from the downstream analyses, by the application of Trim Galore (Galaxy Version 0.6.7+galaxy0). Trimmed sequencing reads were mapped to the reference human (hg19) or mouse (mm9) genome by the application of the Bowtie2 software (Galaxy Version 2.4.2+galaxy0), with “very sensitive end to end” parameters (Langmead and Salzberg, 2012). The input data were utilized as controls.
Duplicate reads were eliminated using the RmDup tool (Galaxy Version 2.0.1) of the SAMtools package (Li et al., 2009). Samples were normalized to the same sequencing depth using the Downsample SAM/BAM (Galaxy Version 2.18.2.1) tool from Picard.
Peaks were called by MACS2 callpeak algorithm (Galaxy Version 2.1.1.20160309.6) following the above outlined parameters: (a) band width=150 bp, (b) lower mfold=5, (c) upper mfold=50, and (d) q value=0.05 (Feng et al., 2012).
Peaks detected in chrY and unplaced contigs (chrUn, chrM) and in ENCODE hg19 and mm9 blacklisted regions were excluded from the downstream analyses (Amemiya HM, et al., Sci Rep. 2019). Reads that mapped within peaks were tallied using bedtools' MultiCovBed tool (Galaxy Version 2.30.0) (Quinlan and Hall, 2010).
Assembly: hg19 (Homo sapiens), mm9 (Mus musculus)
Supplementary files format and content: bigwig files including RPKM normalized signal and BED files of total peaks

growth_protocol: Human and mouse cells were cultured under optimum conditions according to the manufacturer’s instructions. HeLa cells (ATCC, CCL-2™) were grown in DMEM medium (Sigma-Aldrich), Namalwa cells (ATCC, CRL-1432™) in RPMI 1640 medium (Sigma-Aldrich), and NIH/3T3 cells (ATCC, CRL-1658™) in DMEM medium (Sigma-Aldrich).  All culture media were supplemented with 1% Pen-Strep (Gibco) and 10% (v/v) heat-inactivated Fetal Bovine Serum (FBS) (Gibco). All cell cultures were established in laboratory incubators under optimum conditions (37°C, 5% CO2).

value: Fibroblasts

value: Sendai Virus Cantell strain, Charles River lab

value: 6 hrs


title: DNA-methylation array data_204229180126_R06C01


title: DNA-methylation array data_205832310023_R08C01


title: DNA-methylation array data_205689110069_R04C01


title: Atg14KO cTreg cells1

description:
Library name: cTregAtg14KO1
cTregAtg14KO1

value: Spleen


title: brain_d8_rep-2


title: Input-ChIP-seq_NIH3T3_SVI_0h_2023

value: 0 hrs


title: brain_d7_rep-4

description: Gene expression data from Gallus Gallus brain 7 days

source_name: brain 7 days


title: brain_d9_rep-1


title: DNA-methylation array data_205567980118_R04C01

value: Glioblastoma, IDH-wildtype


title: IRF3-ChIP-seq_NIH3T3_SVI_6h_2023

value: IRF3 (CST;Cell Signaling Technology,#4302S)


title: Control cTreg cells3

description:
Library name: cTregWT3
cTregWT3

value: Primary Treg cells


title: DNA-methylation array data_204316970077_R08C01

value: tumor


title: brain_d8_rep-3


title: Control cTreg cells2

description:
Library name: cTregWT2
cTregWT2


title: IRF3-ChIP-seq_NIH3T3_SVI_0h_2023


title: Control cTreg cells1

description:
Library name: cTregWT1
cTregWT1


title: brain_d7_rep-3


title: DK3

data_processing:
Visualizations using volcano-plots and heatmaps were produced with R. Gene Ontology
Assembly: mm10
Supplementary files format and content: Table-delimited text file includes raw counts for each sample
Supplementary files format and content: Table-delimited text file includes RPKM vaules for each sample

extract_protocol:
TRIzol reagent
mRNA for RNA-seq analysis was purified using polyA+ selection
RNA-seq libraries were constructed by Yale Center for Genome Analysis (YCGA) using SMARTer® Stranded Total RNA-Seq Kit-Pico Input Mammalian (Clontech)

value: Intestine

value: Primary cell

value: Intestinal epithelial cells, immune cells, and enteric neurons

value: KO


title: ACHN-sgZCCHC8-rep2

first: Jianxiu

last: Yu

address: No. 280, Chongqing South Road

description: Library name: Sample 4

data_processing:
Paired-end reads were harvested from Illumina NovaSeq sequencer, and were quality controlled by by Q30, FastQC, and FastQ Screen.
3’ adaptor- and low quality reads were trimmed by cutadapt software (v1.9.3), the high quality trimmed reads (clean reads) were aligned to the reference genome using NextGenMap with default parameters.
The mismatch of T to C sites were extracted by VarScan2 software. Any called T to C SNPs from this dunk will be excluded in the subsequent analyses to reduce the false-positive number.
Assembly: hg19
Supplementary files format and content: Excel file includes mRNA expression profiling and newly mRNA Expression Profiling
Supplementary files format and content: Excel file includes lncRNA expression profiling and newly lncRNA Expression Profiling

source_name: ACHN

extract_protocol:
Total RNA was extracted with Trizol, and RNA were treated with iodoacetamide under optimal reaction conditions.
Ribosomal RNA (rRNA) was removed from the samples by the GenSeq® rRNA Removal Kit (GenSeq, Inc.) kit. The rRNA-depleted samples were subjected to library construction with GenSeq® Low Input RNA Library Prep Kit (GenSeq, Inc.) according to the manufacturer’s instructions.

value: ACHN

value: 4-thiouridine (S4U) label


title: ACHN-sgZCCHC8-rep1

description: Library name: Sample 3


title: DNA-methylation array data_205814880164_R08C01

source_name: tumor

value: Diffuse paediatric-type high-grade glioma, H3-wildtype and IDH-wildtype

value: Female


title: DK2


title: ACHN-Ctrl-rep2

description: Library name: Sample 2


title: DNA-methylation array data_206152230086_R04C01


title: DK1


title: ACHN-Ctrl-rep1

description: Library name: Sample 1


title: DNA-methylation array data_202013790105_R01C01

value: Male


title: DW3

value: WT


title: DNA-methylation array data_204964480107_R08C01


title: DNA-methylation array data_203175700077_R02C01


title: brain_d21_rep-5

first: Tinghua

address: Jingmi Road #266

description: Gene expression data from Gallus Gallus brain 21 days

source_name: brain 21 days

value: male


title: DW2


title: A1-35-8 avc1-del CO2 3

city: Iowa City

first: Damian

last: Krysan

address: 25 South Grand, 2040 ML

department: Division of Pediatrics & Infectious Disease

institute: University of Iowa Hospitals and Clinics

description:
Library name: A1-35-8 avc1-del CO2 3
A1-35-8 avc1-del CO2 3

data_processing:
Paired-end Illumina sequence read files were evaluated for quality and the absence of adaptor sequence using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Read files were mapped to C. neoformans reference genome H99 v48 (FungiDB).
Gene transcript expression was quantified using HISAT2 and Stringtie.
Differential expression fold change, Wald test p value and Benjamini-Hochberg adjustment for multiple comparisons were determined using DESeq2.
Assembly: FungiDB-48_CneoformansH99
Supplementary files format and content: Normalized_counts.xlsx - normalized gene counts
Supplementary files format and content: Raw_gene_counts.xlsx - non-normalized gene counts

organism: Cryptococcus neoformans

source_name: yeast

growth_protocol: Overnight cultures of indicated strains were washed and diluted to 7.5x10^5 cells/mL, 3 mL cultured per condition in a 6-well plate in RPMI 1640 medium with 165 mM MOPS, pH 7 for 24 hours at 37°C in ambient air or 5% CO2.

extract_protocol:
Cells were collected via centrifugation from growth medium, lyophilized overnight and RNA harvested according to manufacturer protocol for Invitrogen PureLink RNA Mini Kit.
Total RNA was submitted to Azenta Life Sciences for standard RNA-Seq next-generation sequencing. The RNA samples were quantified using Qubit 2.0 Fluorometer (ThermoFisher) and RNA integrity was checked using TapeStation (Agilent Technologies). The RNA sequencing libraries were prepared using the NEB Next Ultra II RNA Library Prep Kit for Illumina using manufacturer instructions (New England Biolabs). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 min at 94°C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3' ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies) and quantified by using Qubit 2.0 Fluorometer (ThermoFisher) as well as by quantitative PCR (KAPA Biosystems). The sequencing libraries were multiplexed and clustered onto a flowcell. After clustering, the flowcell was loaded onto the Illumina HiSeq instrument according to manufacturer instructions. The samples were sequenced using a 2x150 bp Paired End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.20 software. One mismatch was allowed for index sequence identification.

tag: strain

value: yeast


title: DNA-methylation array data_205617080094_R07C01

city: Berlin

last: Euskirchen


title: brain_d8_rep-1

institute: Yangtze University


title: DNA-methylation array data_205828600005_R04C01


title: brain_d7_rep-1


title: brain_d21_rep-2

value: female


title: A1-35-8 avc1-del CO2 2

description:
Library name: A1-35-8 avc1-del CO2 2
A1-35-8 avc1-del CO2 2


title: DNA-methylation array data_202915420104_R02C01

value: Glioblastoma, IDH-wildtype


title: brain_d21_rep-4


title: brain_d21_rep-3


title: root_doubleKO_rep4

city: Villenave d'Ornon

first: Pascal

middle: GP

last: Martin

address: 71 avenue Edouard Bourlaux

department: UMR1332 BFP

country: France

institute: INRAE

data_processing:
RNAseq data were analyzed with TuxNet (Spurney et al., Plant J., 2019, https://doi.org/10.1111/tpj.14558)
TuxNet uses ea-utils fastq-mcf for pre-processing; to remove the adapters (barcodes) and eliminate the short and low quality reads
Cleaned reads were aligned to the TAIR10 genome using HiSat2
Cufflinks was used to generate FPKMs and perform differential expression analysis
Assembly: TAIR10
Supplementary files format and content: FPKM_matrix.tsv is a tab-delimited text file containing the gene identifiers as the first column and FPKM (fragments per kilobase per million) values for each sample in the next columns

organism: Arabidopsis thaliana

source_name: root

growth_protocol: Seeds were sown on MS plates and stratified for 2 days at 4°C in the dark. Plates were transfered to a growth chamber at 21°C and grown for 5 days under long day conditions (16h light/8h dark).

extract_protocol:
The roots were ground into fine powder in liquid nitrogen. Total RNA was extracted using Trizol reagent following the manufacturer's instructions
Libraries were prepared from 1.5µg of total RNA using Illumina TruSeq Stranded mRNA Library Prep kit. Libraries were sequenced on an Illumina NovaSeq 6000 instrument at the Genome & Transcriptome facility of Genopole Toulouse (GeT-PlaGE, https://get.genotoul.fr/).

value: root

value: 5-day old seedlings

tag: ecotype

value: mctp3-2 / mctp4-1 double mutant


title: DW1

value: Intestine


title: A1-35-8 avc1-del CO2 1

description:
Library name: A1-35-8 avc1-del CO2 1
A1-35-8 avc1-del CO2 1


title: brain_d7_rep-2

city: Jingzhou

last: Huang


title: DNA-methylation array data_203068760184_R04C01

value: tumor

value: Unknown


title: root_doubleKO_rep3


title: brain_d21_rep-1


title: DNA-methylation array data_207335100018_R04C01


title: root_doubleKO_rep2


title: A1-35-8 CO2 2

description:
Library name: A1-35-8 CO2 2
A1-35-8 CO2 2

value: wild-type


title: A1-35-8 CO2 1

description:
Library name: A1-35-8 CO2 1
A1-35-8 CO2 1


title: brain_d0_rep-4

description: Gene expression data from Gallus Gallus brain 0 days

source_name: brain 0 days


title: brain_d21_rep-6


title: brain_d0_rep-3


title: DNA-methylation array data_205814880164_R01C01


title: root_doubleKO_rep1


title: H99 WT CO2 3

description:
Library name: H99 CO2 3
H99 CO2 3


title: DNA-methylation array data_205617080096_R04C01


title: root_mctp3-2_rep4

value: mctp3-2 single mutant (GABI_285E06)


title: H99 WT CO2 2

description:
Library name: H99 CO2 2
H99 CO2 2


title: A1-35-8 CO2 3

description:
Library name: A1-35-8 CO2 3
A1-35-8 CO2 3


title: brain_d0_rep-2


title: brain_d0_rep-1


title: DNA-methylation array data_205689140009_R06C01


title: root_mctp3-2_rep3


title: H99 WT CO2 1

description:
Library name: H99 CO2 1
H99 CO2 1


title: A1-35-8 avc1-del Amb 3

description:
Library name: A1-35-8 avc1-del Amb 3
A1-35-8 avc1-del Amb 3

value: Ambient Air


title: DNA-methylation array data_205617080145_R04C01


title: root_mctp3-2_rep2


title: A1-35-8 avc1-del Amb 2

description:
Library name: A1-35-8 avc1-del Amb 2
A1-35-8 avc1-del Amb 2


title: root_mctp3-2_rep1


title: abdominal-fat_d49_rep-4

description: Gene expression data from Gallus Gallus adipose 49 days

source_name: abdominal-fat 49 days


title: DNA-methylation array data_203890880016_R03C01


title: abdominal-fat_d49_rep-2


title: A1-35-8 avc1-del Amb 1

description:
Library name: A1-35-8 avc1-del Amb 1
A1-35-8 avc1-del Amb 1


title: root_mctp4-1_rep4

value: mctp4-1 single mutant (Salk_089046C)


title: DNA-methylation array data_203960260023_R03C01


title: abdominal-fat_d49_rep-1


title: root_mctp4-1_rep3


title: A1-35-8 Amb 3

description:
Library name: A1-35-8 Amb 3
A1-35-8 Amb 3


title: DNA-methylation array data_206144080070_R01C01


title: abdominal-fat_d21_rep-3

description: Gene expression data from Gallus Gallus adipose 21 days

source_name: abdominal-fat 21 days


title: A1-35-8 Amb 2

description:
Library name: A1-35-8 Amb 2
A1-35-8 Amb 2


title: root_mctp4-1_rep2


title: abdominal-fat_d49_rep-3


title: root_mctp4-1_rep1


title: A1-35-8 Amb 1

description:
Library name: A1-35-8 Amb 1
A1-35-8 Amb 1


title: abdominal-fat_d21_rep-4


title: DNA-methylation array data_203867050006_R03C01

value: Female


title: DNA-methylation array data_204776820059_R05C01


title: root_WT_rep4


title: H99 WT Amb 3

description:
Library name: H99 Amb 3
H99 Amb 3


title: abdominal-fat_d21_rep-2


title: abdominal-fat_d21_rep-1


title: DNA-methylation array data_205041760067_R03C01


title: root_WT_rep3


title: H99 WT Amb 2

description:
Library name: H99 Amb 2
H99 Amb 2


title: root_WT_rep2


title: H99 WT Amb 1

description:
Library name: H99 Amb 1
H99 Amb 1


title: abdominal-fat_d14_rep-3

description: Gene expression data from Gallus Gallus adipose 14 days

source_name: abdominal-fat 14 days


title: DNA-methylation array data_205291540188_R04C01

value: Male


title: abdominal-fat_d14_rep-2


title: abdominal-fat_d14_rep-4


title: DNA-methylation array data_203960260023_R05C01


title: HEK293, VIP, rep3

city: Minneapolis

first: Emily

last: Blythe

state: MN

address: 420 Washington Avenue SE

department: Genetics, Cell Biology and Development

institute: University of Minnesota

description:
Library name: VIP.3
column name in processed data files: EB18

data_processing:
Raw reads were preprocessed using HTStream, version 1.3.3.
Reads were aligned to GRCh38 using STAR, version 2.7.9a.
Differential expression analyses were conducted using limma-voom (limma version 3.50.0, edgeR version 3.36.0) in R version 4.1.0.
Assembly: GRCh38
Supplementary files format and content: text file of raw reads for all samples
Supplementary files format and content: text file of normalized reads for all samples

growth_protocol: HEK293 cells (ATCC CRL1573) were cultured in DMEM (Gibco 1196511) supplemented with 10% FBS (Hyclone SH30910.03 or R&D Systems S12495 via UCSF Tissue Culture Facility) and grown at 37 °C with 5% CO2.

extract_protocol:
Cell lysis and initial RNA extraction was carried out using the Qiagen RNeasy Mini kit, and then RNA was further purified using the Zymo RNA Clean & Concentrator kit.
Barcoded 3'Tag-Seq libraries were prepared using the QuantSeq FWD kit (Lexogen, Vienna, Austria) for multiplexed sequencing according to the recommendations of the manufacturer.

treatment_protocol: Cells were washed twice in DMEM before addition of control/agonist diluted in DMEM for 90 minutes.

value: Human embryonic kidney cell

value: WT

value: 500 nM VIP, 90 min


title: abdominal-fat_d10_rep-4

description: Gene expression data from Gallus Gallus abdominal-fat 10 days

source_name: abdominal-fat 10 days

value: female


title: DNA-methylation array data_204229190143_R01C01

value: Glioblastoma, IDH-wildtype


title: DNA-methylation array data_202790040013_R04C01


title: HEK293, VIP control, rep3

description:
Library name: VIP.C3
column name in processed data files: EB17

value: No treatment


title: DNA-methylation array data_204339300083_R03C01


title: abdominal-fat_d14_rep-1

value: male


title: DNA-methylation array data_207269880006_R03C01


title: DNA-methylation array data_203010900136_R05C01


title: root_WT_rep1

value: root

value: 5-day old seedlings


title: HEK293, NECA control, rep3

description:
Library name: NECA.C3
column name in processed data files: EB15


title: kidney biopsy [f65]

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

department: Medicine

country: Canada

institute: University of Alberta

hyb_protocol: (Affymetrix, Santa Clara, CA).  Amplified RNA (10ug) was hybridized for 16 hr at 45C on  GeneChip® PrimeView™ Human Gene Expression Array . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Gene Array Scanner 3000 7G (Affymetrix) and processed with GeneChip® Command Console® Software (AGCC)(Affymetrix).

data_processing: Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.

source_name: kidney biopsy

label_protocol: Total RNA (0.5µg) was labeled using GeneChip 3` IVT Express Labeling kit. Quality of labeled aRNA was assessed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) before hybridization to GeneChip® PrimeView™ Human Gene Expression Array

extract_protocol:
All human kidney biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNAlater.
Tissue was homogenization in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA) and total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 8µg/core, (RNA integrity number >7).

tag: center (berlin, vienna)

value: VIENNA

tag: patient

tag: datebx

tag: felzartamab (placebo, felzartamab)

value: Felzartamab

tag: group (index, fu1, fu2)

tag: followup (baseline, week24, week52)

tag: felzartamab_group (index_placebo, fu1_placebo, fu2_placebo, index_felzartamab, fu1_felzartamab, fu2_felzartamab)

tag: cortexprob

tag: abmrpm

tag: nkb

tag: dsast

tag: tcmrt

tag: tcb

tag: qcat

tag: qcmat

tag: bat

tag: igt

tag: mcat

tag: endat

tag: ficol

tag: abmract

tag: abmrifng

tag: abmrnk

tag: abmrendo

value: kidney biopsy


title: HEK293, NECA, rep3

description:
Library name: NECA.3
column name in processed data files: EB16

tag: cell line

tag: cell type

tag: genotype

tag: treatment

value: 20 μM NECA in 0.05% DMSO, 90 min


title: DNA-methylation array data_201465930022_R01C01

tag: tissue

value: tumor

tag: tumor type

tag: age

tag: Sex

tag: beadchip name


title: HEK293, Iso control, rep3

description:
Library name: Iso.C3
column name in processed data files: EB13

value: 1 μM acsorbic acid, 90 min