title: DNA methylation profile for 202410000108_R03C01

value: adult


title: DAR05_post_AR

status: Public on Jun 27 2022

type: SRA

city: Amsterdam

first: Wilbert

last: Zwart

address: Plesmanlaan 121

department: Oncogenomics

country: Netherlands

institute: Netherlands Cancer Institute

library_source: genomic

data_processing:
Sequences were generated by the Illumina Hiseq 2500 genome analyser (using 65bp reads) and were processed by the Illumina pipeline.
Reads were aligned to the Human Reference Genome (hg19) using BWA. Reads were filtered based on mapping quality (MAPQ ≥ 20) and duplicate reads were removed.
Peak calling over paired input controls (per tissue sample and treatment) was performed using MACS2 and Dfilter. Peaks called by both peak callers were used for analysis.
Genome_build: hg19
Supplementary_files_format_and_content: peaks.narrowPeak.bed

molecule: genomic DNA

organism: Homo sapiens

source_name: primary prostate cancer

growth_protocol: fresh frozen material

extract_protocol:
Chromatin immunoprecipitations were performed as described previously with minor changes (Zwart et al., 2013). Samples were crosslinked in solution A (50 mM HEPES-KOH, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) with 2 mM DSG (CovaChem) for 25 minutes at room temperature. After 25 minutes, 1% formaldehyde (Merck) was added for 20 minutes and subsequently quenched with 2.5 M glycine. Samples were lysed as described (Schmidt et al., 2009) and sonicated for at least 10 cycles of 30 sec on, 30 sec off using a Diagenode Bioruptor Pico. For each ChIP, 5 µg of antibody was conjugated with 50 µL magnetic protein A or G beads (10008D or 10009D, Thermo Fisher Scientific). Antibodies used were AR (06-680, Merck Millipore), FOXA1 (ab5089, Abcam) and H3K27ac (39133, Active Motif).
Immunoprecipitated DNA was processed for library preparation using a KAPA library preparation kit (KK8234, Roche)

treatment_protocol: Neoadjuvant enzalutamide treatment (160 mg/day) followed by Robotic-Assisted Laparoscopic Prostatectomy (RALP).

tag: chip antibody

value: AR (Merck Millipore, 06-680)

tag: patient id

tag: enz treatment

value: post


title: DAR07_pre_AR

value: pre


title: SRM202772_MLL34DKO_H4K20Ac-AB2

city: Memphis

first: Wojciech

last: Rosikiewicz

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

country: USA

institute: St. Jude Childrens Research Hospital

data_processing:
Raw reads in fastq format were processed with Trim-Galore tool (v0.4.4)
Reads were mapped to mice reference genome (mm10) with bwa aln, followed by bwa samse or sampe (0.7.17-r1188), dependently on single, or pair-end design; with -K flag set to 10000000
Duplicated reads were marked with bamsormadup tool from biobambam2 (v2.0.87) and Cross-Correlation analysis was conducted with SPP (v1.11)
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

organism: Mus musculus

source_name: mES cells

growth_protocol: All mESCs were cultured under chemically defined naïve culture conditions (2iL) in 0.1% gelatin-coated flasks or plates.

extract_protocol:
After sequential lysis of the crosslinked cells in Lysis Buffer 1 and Lysis Buffer 2, the nuclear pellet was sonicated in Lysis Buffer 3 with a probe sonicator (Fisher Scientific Model 705 Sonic Dismembrator) at output level 55 (27–33 W) for 16 cycles with each cycle constituting of a 30 sec sonication on followed by a 60 sec off. For each ChIP, 100 ?L Protein G Dynabeads (Invitrogen, 10003D) slurry and 10 µg of antibody was used. Chromatin incubation with antibody was carried out at 4°C with end-to-end rotation for 4-6 hours.
DNA was quantified using the Quant-iT PicoGreen dsDNA Assay (Thermo Fisher Scientific, P11496). Libraries were prepared with the KAPA HyperPrep Library Kit (Roche, 07962363001) and analyzed for insert size distribution with the High Sensitivity DNA Kit (Agilent, 5067–4626) on a 2100 Bioanalyzer or the High Sensitivity D1000 ScreenTape Assay (Agilent, 5067–5584, 5067–5585, 5067–5587, 5067–5603) on a 4200 TapeStation. Libraries were quantified using the Quant-iT PicoGreen dsDNA Assay.

treatment_protocol: Dual crosslinking was performed at room temperature first for 30 min with 2 mM disuccinimidyl glutarate (DSG) in DPBS and then by addition of paraformaldehyde to a final concentration of 1% for another 15 minutes. Crosslinking was quenched with 150 mM glycine for 5 min at room temperature. Single crosslinking was performed solely with  paraformaldehyde for 20 min.

tag: cell full name

value: Mouse embryonic stem cells

tag: cell type

value: rabbit alpha-H4K20ac (RevMAb, 31-1084-00)


title: SRM202772_MLL34DKO_H3K4me1-AB4

value: Rabbit alpha-H3K4me1 (RevMAb, 31-1046-00)


title: SRM200254_Dnttip1KO1E6_H4K20Ac-AB2


title: Lck-cre-Tcf7KO1-DN3_BC_11

city: Beijing

first: Shuyang

last: Yu

address: 2 Yuanmingyuan West Road

department: College of Biological Sciences

country: China

institute: China Agricultural University

description:
PolyA RNA
processed data file: barcode_information.xlsx
processed data file: count_matrix.csv
processed data file: expression_matrix_log2(TPM:10+1).csv

library_source: transcriptomic

data_processing:
Unique molecular identifier (UMI) information were added into the corresponding read 1 which were then trimmed to remove template switch oligo (TSO) sequence and polyA tails.
Next, we removed reads with adapter contaminants and low-quality bases (N>10%).
The cleaned reads were aligned to the mm10 mouse transcriptome (Genocode) using Tophat (version 2.1.1).
Uniquely mapped reads were counted using htseq-count of the HTSeq package. For each gene, duplicated transcripts with the same UMI sequence were removed. For each cell, the transcript copy number of each gene were counted on the basis of the number of distinct UMIs of that gene.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: barcode_information.xlsx
Supplementary_files_format_and_content: count_matrix.csv
Supplementary_files_format_and_content: expression_matrix_log2(TPM:10+1).csv

molecule: total RNA

source_name: thymus DN2&DN3 cells (CD45+Lin-CD4-CD8-CD25+)

extract_protocol:
Single-cell cDNA amplification was carried out by using the STRT protocol with several modifications to allow for multiplexed single-cell RNA-seq. Libraries were prepared using KAPA Hyper Prep Kits (KK8505). The NEB U-shaped adapter was used for ligation. The libraries were sequenced on an Illumina Hiseq x ten platform to generate 150-bp paired-end reads (sequenced by BGI).
Libraries are constructed according to the standard protocol for Smart-seq2.

tag: strain/background

tag: genotype/variation

value: Lck-cre; Tcf7fl/fl

tag: tissue

value: thymus

value: DN2 & DN3

tag: age

value: 6~8 wks


title: DNA methylation profile for 202410160041_R01C01

type: genomic

city: Exeter

first: Eilis

last: Hannon

address: RILD building

country: United Kingdom

institute: University of Exeter

hyb_protocol: Samples were processed according to the Illumina Infinium HumanMethylationEPIC BeadChip (Illumina) protocol.

scan_protocol: Samples were assessed using the Illumina Infinium HumanMethylationEPIC BeadChip (Illumina) using a Illumina iScan System (Illumina).

data_processing:
Data was imported using the R package methylumi methylumIDAT function. Data was then pre-processed in the R package wateRmelon using the pfilter and dasen functions.
Dasen normalized betas (BDR_processed_signals.csv.gz)
Unmethylated and methylated signal intensities (BDR_raw_Signal.csv.gz)

label: Cy3, Cy5

label_protocol:
500 ng DNA from each sample was sodium bisulfite-treated using the EZ-96 DNA Methylation-Gol Kit (Zymo Research) according to the manufacturer’s standard protocol.
hapten-labeled dideoxynucleotides

extract_protocol: DNA was extracted using a phenol/chloroform method

tag: developmental stage

value: brain

tag: brain region

value: Occipital

tag: gender

value: female

tag: cell proportion double negative

tag: cell proportion neun+

tag: cell proportion sox10+


title: SRM200254_Dnttip1KO1E6_H3K4me1-AB4


title: SRM202772_MLL34DKO_H3K27Ac-AB6

value: rabbit alpha-H3K27ac (RevMAb, 31-1056-00)


title: Res_LNCaP-42D_ARNTL_siNT_2

data_processing:
Sequences were generated by the Illumina Hiseq 2500 genome analyser (using 65bp reads) and were processed by the Illumina pipeline.
Reads were aligned to the Human Reference Genome (hg19) using BWA. Reads were filtered based on mapping quality (MAPQ ≥ 20) and duplicate reads were removed.
Peak calling over mixed input controls (per cell line) was performed using MACS2.
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak

source_name: prostate cancer cell line

growth_protocol: LNCaP and LNCaP-42D cells were maintained in RPMI-1640 medium (Gibco, Thermo Fisher Scientific) supplemented with 10% FBS (Sigma-Aldrich) and 1% Pen-Strep (Gibco, Thermo Fisher Scientific). ENZ-resistant LNCaP-42D cells were further supplemented with 10 µM ENZ (MedChemExpress).

extract_protocol:
Chromatin immunoprecipitations were performed as described previously (Stelloo et al., 2018). Samples were crosslinked in 1% formaldehyde (Merck)  for 10 minutes and subsequently quenched with 2.5 M glycine. Samples were lysed as described (Schmidt et al., 2009) and sonicated for at least 10 cycles of 30 sec on, 30 sec off using a Diagenode Bioruptor Pico. For each ChIP, 5 µg of antibody was conjugated with 50 µL magnetic protein A or G beads (10008D or 10009D, Thermo Fisher Scientific). Antibodies used were FOXA1 (ab5089, Abcam) and ARNTL (ab93806, Abcam).
Immunoprecipitated DNA was processed for library preparation using a KAPA library preparation kit (KK8234, Roche)

treatment_protocol: For in vitro AR blockade, cells were treated with 10 µM ENZ (MedChemExpress) and harvested at the indicated time points. For ARNTL ChIP-seq upon FOXA1 knockdown, LNCaP and LNCaP-42D cells were reverse transfected with 50 nM siFOXA1 using Lipofectamine RNAiMAX (Invitrogen). ENZ (10 µM) was added after 24 h, and cells were fixed and harvested for ChIP-seq analysis 72 h post-transfection.

tag: cell line

value: LNCaP

value: ARNTL (Abcam, ab93806)

tag: replicate

tag: treatment

value: ENZ


title: Res_LNCaP-42D_ARNTL_siNT_1

tag: chip antibody


title: SRM200254_Dnttip1KO1E6_H3K27me3-AB4

value: rabbit alpha-H3K27me3 (Cell Signaling Technology, 9733S)


title: Vav-cre-Tcf7KO-DN3_BC_94

value: Vav-cre; Tcf7fl/fl


title: Vav-cre-Tcf7KO-DN3_BC_96


title: Vav-cre-Tcf7KO-DN3_BC_9


title: Res_LNCaP-42D_ARNTL_siFOXA1_1


title: Res_LNCaP-42D_ARNTL_siFOXA1_2


title: DNA methylation profile for 202410000108_R04C01

value: adult

value: Prefrontal


title: Vav-cre-Tcf7KO-DN3_BC_93


title: DNA methylation profile for 202410000208_R06C01

value: male


title: Post_LNCaP_ARNTL_siFOXA1_1

value: ENZ (48 h)


title: SRM200254_Bruce4_INPUT

value: Mouse embryonic stem cells


title: Vav-cre-Tcf7KO-DN3_BC_95

value: thymus


title: Post_LNCaP_ARNTL_siNT_2


title: SRM200254_Bruce4_H4K20Ac-AB2

value: rabbit alpha-H4K20ac (RevMAb, 31-1084-00)


title: DNA methylation profile for 202410000150_R07C01


title: DNA methylation profile for 202410000150_R08C01


title: DNA methylation profile for 202410000233_R02C01


title: SRM202772_MLL34DKO_DNTTIP1-AB1

value: rabbit alpha-DNTTIP1 (Bethyl Laboratories, A304-048A)


title: Post_LNCaP_ARNTL_siFOXA1_2


title: Res_LNCaP-42D_ARNTL_2


title: Vav-cre-Tcf7KO-DN3_BC_91

value: DN2 & DN3

value: 6~8 wks


title: DNA methylation profile for 202410000233_R01C01

value: brain

value: Occipital

value: female


title: SRM200254_Dnttip1KO1E6_H3K27Ac-AB6

value: rabbit alpha-H3K27ac (RevMAb, 31-1056-00)


title: SRM200254_Dnttip1KO1E6_INPUT


title: DNA methylation profile for 202410000205_R07C01


title: Vav-cre-Tcf7KO-DN3_BC_92


title: Post_LNCaP_ARNTL_1

value: LNCaP

value: ARNTL (Abcam, ab93806)


title: SRM167213_WT_rep2_H4K20Ac-AB2


title: Post_LNCaP_ARNTL_siNT_1


title: DNA methylation profile for 202410000208_R03C01


title: Pre_LNCaP_ARNTL_2

value: Untreated


title: SRM167213_WT_rep2_H3K4me2-AB4

value: mouse alpha-H3K4me2 (Active Motif, 39679)


title: Vav-cre-Tcf7KO-DN3_BC_86

value: Vav-cre; Tcf7fl/fl


title: SRM200254_Bruce4_H3K4me1-AB4

value: Rabbit alpha-H3K4me1 (RevMAb, 31-1046-00)


title: Vav-cre-Tcf7KO-DN3_BC_90


title: DNA methylation profile for 202410000208_R04C01

value: adult

value: Prefrontal

value: male


title: Res_LNCaP-42D_ARNTL_1

value: ENZ


title: SRM200254_Bruce4_H3K27me3-AB4

value: Mouse embryonic stem cells

value: rabbit alpha-H3K27me3 (Cell Signaling Technology, 9733S)


title: Vav-cre-Tcf7KO-DN3_BC_8

value: thymus

value: DN2 & DN3

value: 6~8 wks


title: DNA methylation profile for 202410000150_R04C01

value: brain

value: female


title: DNA methylation profile for 202410000210_R05C01

value: Occipital


title: DNA methylation profile for 202410000208_R05C01


title: SRM167213_WT_rep2_H3K27me3-AB4


title: Res_LNCaP-42D_FOXA1_2

value: LNCaP

value: FOXA1 (Abcam, ab5089)


title: Vav-cre-Tcf7KO-DN3_BC_85


title: SRM167213_WT_rep1_INPUT


title: Post_LNCaP_ARNTL_2

value: ARNTL (Abcam, ab93806)

value: ENZ (48 h)


title: DNA methylation profile for 202410000210_R06C01


title: SRM167213_WT_rep1_H4K20Ac-AB2

value: rabbit alpha-H4K20ac (RevMAb, 31-1084-00)


title: Vav-cre-Tcf7KO-DN3_BC_89

value: Vav-cre; Tcf7fl/fl


title: DNA methylation profile for 202410000217_R05C01

value: adult


title: DNA methylation profile for 202410000150_R03C01


title: DNA methylation profile for 202410000205_R08C01

value: Prefrontal


title: DNA methylation profile for 202410000217_R06C01

value: male


title: Post_LNCaP_FOXA1_1


title: Vav-cre-Tcf7KO-DN3_BC_82


title: Vav-cre-Tcf7KO-DN3_BC_87


title: SRM167213_WT_rep2_INPUT

value: Mouse embryonic stem cells


title: Vav-cre-Tcf7KO-DN3_BC_88


title: SRM167213_Kmt2cdDKO_rep2_INPUT


title: SRM200254_Bruce4_H3K27Ac-AB6

value: rabbit alpha-H3K27ac (RevMAb, 31-1056-00)


title: Vav-cre-Tcf7KO-DN3_BC_7

value: thymus


title: DNA methylation profile for 202410160029_R02C01


title: Pre_LNCaP_ARNTL_1

value: Untreated


title: Pre_LNCaP_FOXA1_1


title: SRM167213_Kmt2cdDKO_rep2_H4K20Ac-AB2


title: Res_LNCaP-42D_FOXA1_1

value: ENZ


title: LNCaP-42D_input

value: N/A (mixed input)


title: Vav-cre-Tcf7KO-DN3_BC_81

value: DN2 & DN3

value: 6~8 wks


title: Vav-cre-Tcf7KO-DN3_BC_79


title: LNCaP_input

value: LNCaP


title: SRM167213_WT_rep1_H3K4me2-AB4

value: mouse alpha-H3K4me2 (Active Motif, 39679)


title: DNA methylation profile for 202410160029_R01C01

value: brain

value: Occipital


title: Pre_LNCaP_FOXA1_2

value: FOXA1 (Abcam, ab5089)


title: Post_LNCaP_FOXA1_2

value: ENZ (48 h)


title: SRM167213_Kmt2cdDKO_rep2_H3K27me3-AB4

value: rabbit alpha-H3K27me3 (Cell Signaling Technology, 9733S)


title: DNA methylation profile for 202410000157_R06C01

value: adult

value: Prefrontal


title: Vav-cre-Tcf7KO-DN3_BC_84

value: Vav-cre; Tcf7fl/fl


title: Vav-cre-Tcf7KO-DN3_BC_80


title: SRM167213_Kmt2cdDKO_rep1_H4K20Ac-AB2

value: Mouse embryonic stem cells

value: rabbit alpha-H4K20ac (RevMAb, 31-1084-00)


title: Bewo_H2O2_1_EVs

city: Boston

first: Guoping

last: Li

state: MA

address: Cardiovascular Research Center, 185 Cambridge St, Simches 3.5000

department: CVRC

institute: Massachusetts General Hospital

description: small RNAs

data_processing:
Library strategy: ARM-seq
Adapters were removed and reads were merged with SeqPrep [John st. John unpub] using a minimum read length of 15 and adapters AGATCGGAAGAGCACACGTC and GATCGTCGGACTGTAGAACTC.  Reads that could not be merged were discarded before mapping.
Data were analyzed with tRAX (http://trna.ucsc.edu/tRAX/), tRAX maps reads using bowtie2 v2.3.5.1 with parameters --very-sensitive --ignore-quals --np 5 -k 100,  to a custom database containing mature tRNA transcripts and the genome sequence.
ENSEMBL (release 96) small ncRNA annotations were used to count the number of small RNA transcripts using only primary alignments to prevent double counting. Transcripts with 0 reads across all samples were removed.
tDRnamer (http://trna.ucsc.edu/tDRnamer/) was used to generate unique identifiers for each of the reads which mapped to a tRNA transcript based on the isodecoder(s) they mapped to and positions of any misincorporations.
DESeq2 v1.30.1 was used to generate normalized read counts for each of the transcripts across each sample.
Genome_build: Homo Sapiens GRCh38/hg38 and Rattus Norvegicus rn6
Supplementary_files_format_and_content: Processed data files are comma-separated files containing DESeq2 normalized read counts.

source_name: Bewo

growth_protocol: HEK293 cells and cardiac fibroblasts (CFs) were grown in DMEM medium containing 10% FBS and 1% Pen/Strep; Bewo cells were maintained in F12K medium containing 10% FBS and 1% Pen/Strep; cardiomyocytes (CMs) were cultured in DMEM meidum containing 10% horse serum, 5% FBS and 1% Pen/Strep.

extract_protocol:
Cellular total RNAs were isolated by using TRIzol™ and then small RNAs were extracted by using mirVana™ miRNA Isolation Kit; extracellular RNAs were extracted by using exoRNeasy Midi kit.
Small RNAs were sequentially treated with DNase I, T4 PNK, and His-AlkB and then subjected to NEBNext® Multiplex Small RNA Library Prep Set for Illumina®.

treatment_protocol: For glucose and serum deprivation (GSD) treatment, HEK and Bewo cells were cultured in glucose free DMEM basal medium for 24 hours; CF and CM cells were exposed to glucose free DEME basal medium for 5 hours. For hypoxia treatment, HEK and Bewo cells were fed with complete medium and maintained in hypoxia chamber with 0.2% oxygen for 24 hours; CF and CM cells were fed with glucose free DMEM basal medium and maintained in hypoxia chamber with 0.2% oxygen for 5 hours. For oxidative stress, HEK and Bewo cells were treated with 0.7mM H2O2 and 1.7 mM H2O2 in complete medium for 24 hours; CF and CM cells were exposed to hypoxia treatment for 5 hours and then fed with complete medium in normal incubator for additional 24 hours. FBS and horse serum used here were extracellular vesicle-depleted by 24 hours of ultracentrifugation.

value: Human Choriocarcinoma Cell line

tag: strain

value: H2O2 treatment for 24 hours

tag: sample type

value: Extracellular Vesicles


title: Vav-cre-Tcf7KO-DN3_BC_75

value: thymus

tag: cell type

value: DN2 & DN3


title: Vav-cre-Tcf7KO-DN3_BC_83

tag: strain/background

value: 6~8 wks


title: DNA methylation profile for 202410000205_R03C01

value: female


title: Vav-cre-Tcf7KO-DN3_BC_74

tag: genotype/variation


title: DNA methylation profile for 202410000150_R01C01

tag: tissue

value: brain


title: DNA methylation profile for 202410000157_R05C01

value: Occipital

value: male


title: Bewo_H2O2_3_EVs

description: small RNAs


title: DNA methylation profile for 202410000205_R04C01


title: SRM167213_WT_rep1_H3K27me3-AB4

tag: cell full name


title: Bewo_Hypoxia_1_EVs

description: small RNAs

value: Hypoxia for 24 hours


title: SRM167213_Kmt2cdDKO_rep1_H3K27me3-AB4

value: rabbit alpha-H3K27me3 (Cell Signaling Technology, 9733S)


title: SRM166780_Kmt2cdDKO_rep2_INPUT


title: Vav-cre-Tcf7KO-DN3_BC_76

tag: age


title: Vav-cre-Tcf7KO-DN3_BC_72


title: SRM167213_Kmt2cdDKO_rep1_INPUT


title: SRM167213_Kmt2cdDKO_rep2_H3K4me2-AB4

value: mouse alpha-H3K4me2 (Active Motif, 39679)


title: Vav-cre-Tcf7KO-DN3_BC_77


title: DNA methylation profile for 202410160041_R08C01

tag: developmental stage

value: adult

tag: brain region

value: Prefrontal


title: Bewo_Hypoxia_3_EVs

description: small RNAs


title: Vav-cre-Tcf7KO-DN3_BC_71

value: Vav-cre; Tcf7fl/fl


title: Bewo_H2O2_2_EVs

description: small RNAs


title: SRM166780_Kmt2cdDKO_rep2_DNTTIP1-AB1

value: Mouse embryonic stem cells

value: rabbit alpha-DNTTIP1 (Bethyl Laboratories, A304-048A)


title: DNA methylation profile for 202410000205_R02C01

tag: gender

tag: cell proportion double negative


title: DNA methylation profile for 202410160041_R07C01

tag: cell proportion neun+

tag: cell proportion sox10+


title: Bewo_GSD_2_EVs

description: small RNAs

value: Human Choriocarcinoma Cell line

value: Glucose and serum deprivation for 24 hours


title: Vav-cre-Tcf7KO-DN3_BC_78

value: thymus


title: Vav-cre-Tcf7KO-DN3_BC_73

value: DN2 & DN3


title: DNA methylation profile for 202410000150_R02C01


title: Bewo_Hypoxia_2_EVs

description: small RNAs

value: Extracellular Vesicles


title: SRM166780_Kmt2cdDKO_rep1_DNTTIP1-AB1


title: Vav-cre-Tcf7KO-DN3_BC_70

value: 6~8 wks


title: Bewo_GSD_1_EVs

description: small RNAs


title: Vav-cre-Tcf7KO-DN3_BC_6


title: Vav-cre-Tcf7KO-DN3_BC_69


title: DNA methylation profile for 202410000205_R01C01

value: brain


title: SRM166780_Kmt2cdDKO_rep1_INPUT


title: SRM167213_Kmt2cdDKO_rep1_H3K4me2-AB4


title: Bewo_CTRL_3_EVs

description: small RNAs

value: Untreated


title: SRM166780_Bruce4_rep2_DNTTIP1-AB1


title: Vav-cre-Tcf7KO-DN3_BC_67


title: DNA methylation profile for 202410000150_R06C01

value: male


title: HEK_H2O2_3_EVs

description: small RNAs

value: Human Embryonic Kidney Cell line

value: H2O2 treatment for 24 hours


title: Bewo_CTRL_1_EVs

description: small RNAs


title: Vav-cre-Tcf7KO-DN3_BC_68


title: Bewo_GSD_3_EVs

description: small RNAs


title: SRM166780_Bruce4_rep1_DNTTIP1-AB1


title: DNA methylation profile for 202410160041_R06C01

value: female


title: HEK_H2O2_2_EVs

description: small RNAs


title: Vav-cre-Tcf7KO-DN3_BC_66


title: Bewo_CTRL_2_EVs

description: small RNAs


title: DNA methylation profile for 202410160041_R05C01

value: adult

value: Occipital


title: DNA methylation profile for 202410160029_R04C01

value: Prefrontal


title: VsWAT_total_IN_LFD3

city: Munich

first: Raffaele

last: Teperino

address: Ingolstaedter Landstrasse 1

department: IEG

country: Germany

institute: Helmoltz Munich

data_processing:
trimming for adaptor and read quality. Aligned using STAR to mm10 genome built with  --sjdbOverhang 35 --outFilterIntronMotifs --outFilterMultimapNmax 100 --outFilterMismatchNoverLmax 0.16 . star output to htseq-count with --minaqual 10 and --nonunique none
Genome_build: mm10
Supplementary_files_format_and_content: count files from htseq-count

extract_protocol:
tissues were dissected and flash frozen. Plasma collected and filtered through a 22um spin-filter. RNA from plasma was extracted Tri reagent BD, RNA from tissues was extracted using NucleoZOL
CATS small RNA library kit from Diaganode cat #C05010048

value: VsWAT

tag: in/pd

value: Total

tag: diet

value: low fat


title: DNA methylation profile for 202410000234_R05C01


title: SRM166780_Bruce4_rep1_INPUT

value: Mouse embryonic stem cells

tag: chip antibody


title: VsWAT_total_IN_HFD3

tag: strain

value: high fat


title: DNA methylation profile for 202410000217_R04C01


title: DNA methylation profile for 202410000150_R05C01


title: Vav-cre-Tcf7KO-DN3_BC_65

value: Vav-cre; Tcf7fl/fl

value: thymus

value: DN2 & DN3


title: VsWAT_total_IN_HFD1


title: HEK_Hypoxia_1_EVs

description: small RNAs

tag: treatment

value: Hypoxia for 24 hours

tag: sample type

value: Extracellular Vesicles


title: DNA methylation profile for 202410000157_R07C01

value: brain

value: male


title: VsWAT_total_IN_LFD1


title: VsWAT_total_IN_LFD2


title: SRM166780_Bruce4_rep2_INPUT

tag: cell type


title: Vav-cre-Tcf7KO-DN3_BC_64

tag: strain/background

tag: genotype/variation

value: 6~8 wks


title: HEK_GSD_2_EVs

description: small RNAs

value: Human Embryonic Kidney Cell line

value: Glucose and serum deprivation for 24 hours


title: HEK_H2O2_1_EVs

description: small RNAs

value: H2O2 treatment for 24 hours


title: Vav-cre-Tcf7KO-DN3_BC_60

tag: tissue


title: HEK_GSD_3_EVs

description: small RNAs


title: DNA methylation profile for 202410000234_R06C01

value: adult

value: Prefrontal


title: HEK_Hypoxia_3_EVs

description: small RNAs


title: DNA methylation profile for 202410160029_R03C01

value: Occipital

value: female


title: Vav-cre-Tcf7KO-DN3_BC_63

tag: age


title: Vav-cre-Tcf7KO-DN3_BC_59


title: Plasma_sRNA_IP_HFD2

value: Plasma

value: Pull-down


title: Plasma_sRNA_IP_LFD2

value: low fat


title: HEK_Hypoxia_2_EVs

description: small RNAs


title: DNA methylation profile for 202410000234_R03C01

tag: developmental stage


title: HEK_GSD_1_EVs

description: small RNAs


title: HEK_CTRL_3_EVs

description: small RNAs

value: Untreated


title: Vav-cre-Tcf7KO-DN3_BC_58

value: Vav-cre; Tcf7fl/fl

value: thymus

value: DN2 & DN3


title: DNA methylation profile for 202410000157_R08C01

value: brain

tag: brain region


title: Plasma_sRNA_IP_LFD1


title: DNA methylation profile for 202410000217_R03C01

tag: gender


title: Vav-cre-Tcf7KO-DN3_BC_62


title: Vav-cre-Tcf7KO-DN3_BC_61


title: HEK_CTRL_2_EVs

description: small RNAs

value: Extracellular Vesicles


title: DNA methylation profile for 202410000233_R08C01

value: male

tag: cell proportion double negative


title: Vav-cre-Tcf7KO-DN3_BC_57

value: 6~8 wks


title: DNA methylation profile for 202410000210_R01C01

tag: cell proportion neun+


title: Vav-cre-Tcf7KO-DN3_BC_56


title: VsWAT_total_IN_HFD2

value: VsWAT

value: Total

value: high fat


title: Plasma_sRNA_IN_LFD1

value: Input


title: Vav-cre-Tcf7KO-DN3_BC_55


title: Vav-cre-Tcf7KO-DN3_BC_5


title: Plasma_sRNA_IN_HFD2


title: Bewo_H2O2_3

description: small RNAs

value: Human Choriocarcinoma Cell line

value: H2O2 treatment for 24 hours

value: Cells


title: Plasma_sRNA_IN_LFD2

value: Plasma


title: Plasma_sRNA_IP_HFD1

value: Pull-down


title: Bewo_H2O2_2

description: small RNAs


title: DNA methylation profile for 202410000205_R06C01

value: adult

value: Prefrontal

tag: cell proportion sox10+


title: DNA methylation profile for 202410000234_R04C01


title: HEK_CTRL_1_EVs

description: small RNAs

value: Human Embryonic Kidney Cell line

value: Untreated


title: VsWAT_sRNA_IP_LFD3

tag: in/pd

value: low fat


title: Bewo_H2O2_1

description: small RNAs


title: Vav-cre-Tcf7KO-DN3_BC_52

value: Vav-cre; Tcf7fl/fl

value: thymus

value: DN2 & DN3


title: Vav-cre-Tcf7KO-DN3_BC_53

value: 6~8 wks


title: DNA methylation profile for 202410000210_R02C01

value: brain

value: male


title: DNA methylation profile for 202410000205_R05C01

value: Occipital


title: DNA methylation profile for 202410000157_R01C01

value: female


title: Plasma_sRNA_IN_HFD1

value: Input

tag: diet

value: high fat


title: Vav-cre-Tcf7KO-DN3_BC_54


title: DNA methylation profile for 202410000233_R04C01


title: DNA methylation profile for 202410000157_R02C01


title: DNA methylation profile for 202410000233_R03C01


title: Bewo_GSD_3

description: small RNAs

value: Human Choriocarcinoma Cell line

value: Glucose and serum deprivation for 24 hours

value: Cells


title: Bewo_Hypoxia_3

description: small RNAs

value: Hypoxia for 24 hours


title: Vav-cre-Tcf7KO-DN3_BC_51


title: VsWAT_sRNA_IP_LFD2

value: VsWAT

value: Pull-down


title: Bewo_Hypoxia_2

description: small RNAs


title: Bewo_Hypoxia_1

description: small RNAs


title: DNA methylation profile for 202410000217_R02C01

value: adult

value: Prefrontal


title: Vav-cre-Tcf7KO-DN3_BC_50

value: Vav-cre; Tcf7fl/fl

value: thymus


title: VsWAT_sRNA_IN_LFD3

value: low fat


title: Vav-cre-Tcf7KO-DN3_BC_48

value: DN2 & DN3

value: 6~8 wks


title: Bewo_GSD_2

description: small RNAs


title: DNA methylation profile for 202410000217_R01C01

value: brain

value: Occipital


title: VsWAT_sRNA_IP_HFD2


title: DNA methylation profile for 202410000108_R05C01

value: female


title: VsWAT_sRNA_IP_HFD3

value: high fat


title: Vav-cre-Tcf7KO-DN3_BC_46


title: Vav-cre-Tcf7KO-DN3_BC_4


title: VsWAT_sRNA_IP_LFD1


title: VsWAT_sRNA_IP_HFD1


title: Vav-cre-Tcf7KO-DN3_BC_47


title: Vav-cre-Tcf7KO-DN3_BC_49


title: Bewo_Ctrl_2

description: small RNAs

value: Human Choriocarcinoma Cell line

value: Untreated


title: DNA methylation profile for 202410000108_R06C01


title: VsWAT_sRNA_IN_LFD1

value: Input


title: DNA methylation profile for 202410160041_R03C01

value: male


title: Bewo_Ctrl_3

description: small RNAs

value: Cells


title: VsWAT_sRNA_IN_LFD2

value: VsWAT


title: Bewo_GSD_1

description: small RNAs

value: Glucose and serum deprivation for 24 hours


title: DNA methylation profile for 202410160041_R04C01

value: adult

value: Prefrontal


title: Vav-cre-Tcf7KO-DN3_BC_44

value: Vav-cre; Tcf7fl/fl

value: thymus


title: Vav-cre-Tcf7KO-DN3_BC_45

value: DN2 & DN3


title: VsWAT_sRNA_IN_HFD3


title: HEK_H2O2_3

description: small RNAs

value: Human Embryonic Kidney Cell line

value: H2O2 treatment for 24 hours


title: VsWAT_sRNA_IN_HFD2


title: HEK_H2O2_2

description: small RNAs


title: DNA methylation profile for 202410000208_R01C01

value: brain

value: Occipital


title: VsWAT_sRNA_IN_HFD1

value: high fat


title: DNA methylation profile for 202410000208_R02C01


title: Vav-cre-Tcf7KO-DN3_BC_43

value: 6~8 wks


title: Liver_sRNA_IP_LFD3

value: Liver

value: Pull-down

value: low fat


title: DNA methylation profile for 202410000173_R07C01

value: male


title: Vav-cre-Tcf7KO-DN3_BC_40


title: HEK_H2O2_1

description: small RNAs

value: Cells


title: DNA methylation profile for 202410000233_R05C01

value: female


title: Bewo_Ctrl_1

description: small RNAs

value: Human Choriocarcinoma Cell line

value: Untreated


title: Vav-cre-Tcf7KO-DN3_BC_41

value: Vav-cre; Tcf7fl/fl


title: HEK_Hypoxia_2

description: small RNAs

value: Hypoxia for 24 hours


title: Vav-cre-Tcf7KO-DN3_BC_42

value: thymus

value: DN2 & DN3


title: DNA methylation profile for 202410000233_R06C01

value: adult

value: Prefrontal


title: HEK_GSD_3

description: small RNAs

value: Human Embryonic Kidney Cell line

value: Glucose and serum deprivation for 24 hours


title: HEK_Hypoxia_1

description: small RNAs


title: Vav-cre-Tcf7KO-DN3_BC_3

value: 6~8 wks


title: DNA methylation profile for 203205080093_R03C01

value: brain

value: Occipital


title: Vav-cre-Tcf7KO-DN3_BC_39


title: DNA methylation profile for 203205080093_R04C01


title: Liver_sRNA_IP_HFD2

value: Liver

value: Pull-down

value: high fat


title: Vav-cre-Tcf7KO-DN3_BC_38


title: HEK_Hypoxia_3

description: small RNAs

value: Cells


title: Liver_sRNA_IP_HFD1


title: DNA methylation profile for 203205080127_R01C01

value: male


title: Liver_sRNA_IP_LFD1

value: low fat


title: HEK_GSD_2

description: small RNAs


title: DNA methylation profile for 203205080127_R02C01


title: Liver_sRNA_IN_LFD2

value: Input


title: HEK_GSD_1

description: small RNAs


title: Liver_sRNA_IN_LFD3


title: Vav-cre-Tcf7KO-DN3_BC_37

value: Vav-cre; Tcf7fl/fl


title: DNA methylation profile for 203205080012_R08C01

value: female


title: Liver_sRNA_IN_LFD1


title: Liver_sRNA_IP_HFD3


title: HEK_Ctrl_3

description: small RNAs

value: Untreated


title: Vav-cre-Tcf7KO-DN3_BC_36

value: thymus

value: DN2 & DN3


title: DNA methylation profile for 203205080127_R05C01

value: adult


title: HEK_Ctrl_1

description: small RNAs

value: Human Embryonic Kidney Cell line


title: Liver_sRNA_IN_HFD3


title: Vav-cre-Tcf7KO-DN3_BC_34

value: 6~8 wks


title: Liver_sRNA_IN_HFD2


title: HEK_Ctrl_2

description: small RNAs


title: Vav-cre-Tcf7KO-DN3_BC_33


title: Vav-cre-Tcf7KO-DN3_BC_35


title: ZDF 48

city: Wien

first: Andreas

middle: B

last: Diendorfer

address: Leberstraße 20

country: Austria

institute: TAmiRNA GmbH

data_processing:
fastQ quality assessment
cutadapt adater trimming
bowtie1 genome alignment
miRDeep2 miRNA quantification
edgeR differential expression
Assembly: Rnor.6.0 (GCA_000001895.4)
Supplementary files format and content: CSV with miRNA quantifications (raw and rpm)

organism: Rattus norvegicus

source_name: ulna bone

extract_protocol:
RNA extraction was performed in 100 microL of serum samples and ulna bone homogenized samples with miRNeasy Mini Kits (Qiagen)
RealSeq-Biofluids Plasma/Serum miRNA Library kit for Illumina sequencing

value: ulna bone

value: PTH

tag: group

value: WT

tag: disease state

value: control

tag: time

value: samples collected 12 weeks after receiving treatment


title: Vav-cre-Tcf7KO-DN3_BC_32


title: DNA methylation profile for 203205080154_R01C01

value: brain

value: Occipital


title: ZDF 47

tag: treatment


title: DNA methylation profile for 203205080154_R02C01

value: Prefrontal


title: ZDF 46

value: Placebo

value: ZDF

value: model of type II diabetes


title: Vav-cre-Tcf7KO-DN3_BC_31

value: Vav-cre; Tcf7fl/fl

tag: cell type


title: DNA methylation profile for 203205080107_R05C01

value: male


title: Kidney_mRNA_IP_LFD1

tag: strain

value: Kidney

value: Pull-down

value: low fat


title: ZDF 45


title: DNA methylation profile for 203205080107_R06C01

value: adult


title: Kidney_mRNA_IP_HFD3

value: high fat


title: Vav-cre-Tcf7KO-DN3_BC_30

tag: strain/background

tag: genotype/variation

value: thymus

value: DN2 & DN3

value: 6~8 wks


title: Vav-cre-Tcf7KO-DN3_BC_2

tag: tissue

tag: age


title: DNA methylation profile for 203205080127_R06C01

tag: developmental stage

tag: brain region

value: female


title: Kidney_mRNA_IP_HFD2


title: ZDF 44

source_name: serum

value: serum

value: anti-sclerostin

value: samples collected 12 weeks after receiving treatment


title: DNA methylation profile for 202410000162_R01C01

value: brain

value: Occipital

tag: gender

tag: cell proportion double negative


title: Vav-cre-Tcf7KO-DN3_BC_28


title: ZDF 43

value: WT

value: control


title: DNA methylation profile for 203205080107_R07C01

value: male

tag: cell proportion neun+

tag: cell proportion sox10+


title: ZDF 42

value: Insulin

value: ZDF

value: model of type II diabetes


title: Vav-cre-Tcf7KO-DN3_BC_29

value: Vav-cre; Tcf7fl/fl


title: Liver_sRNA_IN_HFD1

value: Liver

tag: in/pd

value: Input

tag: diet

value: high fat


title: DNA methylation profile for 203205080107_R08C01

value: adult

value: Prefrontal


title: Kidney_mRNA_IN_LFD2

value: Kidney

value: low fat


title: Vav-cre-Tcf7KO-DN3_BC_27

value: thymus

value: DN2 & DN3

value: 6~8 wks


title: Kidney_mRNA_IP_LFD2

value: Pull-down


title: DNA methylation profile for 203205080012_R01C01

value: brain

value: Occipital


title: Kidney_mRNA_IN_LFD1


title: ZDF 41

value: serum

value: PTH

tag: group

value: WT

tag: disease state

value: control

value: samples collected 12 weeks after receiving treatment


title: Vav-cre-Tcf7KO-DN3_BC_26

value: Vav-cre; Tcf7fl/fl


title: Kidney_mRNA_IN_HFD3

value: Input

value: high fat


title: DNA methylation profile for 203205080012_R02C01

value: adult

value: Prefrontal

value: male


title: ZDF 40

tag: treatment

tag: time


title: Kidney_mRNA_IP_HFD1

tag: strain

value: Kidney


title: Vav-cre-Tcf7KO-DN3_BC_25

tag: strain/background

value: thymus

tag: cell type

value: DN2 & DN3


title: ZDF 39

tag: tissue

value: Placebo

value: ZDF

value: model of type II diabetes


title: Kidney_mRNA_IN_HFD2


title: Vav-cre-Tcf7KO-DN3_BC_23

tag: genotype/variation

tag: age

value: 6~8 wks


title: DNA methylation profile for 203205080093_R08C01

tag: developmental stage

value: brain

tag: brain region


title: Vav-cre-Tcf7KO-DN3_BC_24


title: Liver_mRNA_IP_LFD3

source_name: Liver mRNA

value: Liver

value: Pull-down

value: low fat


title: DNA methylation profile for 203205080093_R07C01

value: Occipital

tag: gender

tag: cell proportion double negative


title: DNA methylation profile for 203205080012_R05C01

value: female

tag: cell proportion neun+

tag: cell proportion sox10+


title: ZDF 35

value: ulna bone

value: samples collected 12 weeks after receiving treatment


title: Liver_mRNA_IP_LFD2

tag: in/pd

tag: diet


title: ZDF 38

value: serum

tag: group

value: WT

tag: disease state

value: control


title: Liver_mRNA_IP_LFD1


title: ZDF 37

tag: treatment

value: PTH

tag: time


title: ZDF 34


title: Liver_mRNA_IP_HFD3

tag: strain

value: high fat


title: Vav-cre-Tcf7KO-DN3_BC_22

tag: strain/background

value: Vav-cre; Tcf7fl/fl

value: thymus

tag: cell type

value: DN2 & DN3


title: DNA methylation profile for 203205080012_R06C01

value: adult

tag: tissue

value: Prefrontal


title: Liver_mRNA_IP_HFD2

value: Liver


title: Vav-cre-Tcf7KO-DN3_BC_21

tag: genotype/variation

tag: age

value: 6~8 wks


title: Vav-cre-Tcf7KO-DN3_BC_19


title: ZDF 33

value: Placebo


title: Vav-cre-Tcf7KO-DN3_BC_20


title: ZDF 31

value: anti-sclerostin


title: ZDF 32

value: ZDF

value: model of type II diabetes


title: Kidney_mRNA_IN_HFD1

value: Kidney

value: Input


title: DNA methylation profile for 203205080093_R05C01

tag: developmental stage

value: brain

tag: brain region

value: Occipital

value: female


title: Vav-cre-Tcf7KO-DN3_BC_18


title: Vav-cre-Tcf7KO-DN3_BC_1


title: DNA methylation profile for 202410160226_R07C01

tag: gender

value: male

tag: cell proportion double negative


title: DNA methylation profile for 203205080093_R01C01

tag: cell proportion neun+

tag: cell proportion sox10+


title: Vav-cre-Tcf7KO-DN3_BC_16

value: Vav-cre; Tcf7fl/fl


title: DNA methylation profile for 203205080093_R06C01


title: DNA methylation profile for 203205080153_R03C01


title: Vav-cre-Tcf7KO-DN3_BC_17

value: thymus


title: Liver_mRNA_IP_HFD1

tag: in/pd

value: Pull-down

tag: diet

value: high fat


title: Liver_mRNA_IN_LFD3

value: low fat


title: ZDF 30

value: serum

value: Insulin

tag: group

tag: disease state

value: samples collected 12 weeks after receiving treatment


title: Liver_mRNA_IN_HFD3

value: Liver


title: ZDF 29

tag: treatment

value: PTH

value: ZDF

tag: time


title: DNA methylation profile for 203205080153_R04C01

value: adult

value: Prefrontal


title: ZDF 27

value: Placebo

value: model of type II diabetes


title: Liver_mRNA_IN_LFD2

tag: strain

value: Input


title: Liver_mRNA_IN_LFD1


title: DNA methylation profile for 203205080093_R02C01

value: brain

value: male


title: Liver_mRNA_IN_HFD2


title: ZDF 28

value: WT

value: control


title: ZDF 36

value: ulna bone


title: DNA methylation profile for 203205080107_R04C01


title: Vav-cre-Tcf7KO-DN3_BC_15

tag: strain/background

value: Vav-cre; Tcf7fl/fl

value: thymus

tag: cell type

value: DN2 & DN3

value: 6~8 wks


title: ZDF 25

tag: tissue

value: serum

value: samples collected 12 weeks after receiving treatment


title: Vav-cre-Tcf7KO-DN3_BC_13

tag: genotype/variation

tag: age


title: Vav-cre-Tcf7KO-DN3_BC_12


title: Vav-cre-Tcf7KO-DN3_BC_14


title: ZDF 24

value: PTH

value: ZDF


title: U2OS_SLAMseq_No_alk_III

city: Copenhagen N

first: Mads

last: Lerdrup

address: Blegdamsvej 3C

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

data_processing:
All processing was done by Lexogen services (Vienna) using the SlamDunk pipeline (v.0.2.4, PMID: 28945705) (http://github.com/t-neumann/slamdunk).
Genome_build: hg38
Supplementary_files_format_and_content: TSV separated count tables from SLAMdunk

molecule: polyA RNA

source_name: U2OS osteosarcoma cell line

growth_protocol: U2OS (osteosarcoma; ATCC Cat. # HTB-96) cells were grown in Dulbecco’s modified Eagle’s medium (DMEM; Invitrogen, Cat. # 11960) supplemented with 10% fetal bovine serum (FBS; Invitrogen, Cat. # 10500) and 1% penicillin-streptomycin (Invitrogen, Cat. # 10378016) antibiotics under standard cell culture conditions (in a humidified atmosphere with 5% CO2) at 37°C.

extract_protocol:
Total RNA was isolated from the sorted cells using RNeasy Plus Mini RNA isolation kit (Cat# 74136, Qiagen) and treated with RNase-free DNase (Cat# EN0521, Thermo Fisher Scientific). Finally, the RNA was alkylated with SLAMseq Kinetics kit (Cat# 061.24, Lexogen) as described by the manufacturer. Till this point samples were kept in dark as much as possible.
500ng of RNA was subjected to library preparation using QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina (Cat# 015.24) following manufacturer's Instructions. All the reagents and seath fluid used for flow cytometry were treated with RNase inhibitor RNAsin Ribonuclease Inhibitor (Cat# N2615, Promega).

treatment_protocol: For nascent as well as steady state transcriptome analysis from different phases of the cell cycle (G1, Early S, Late S, G2/M) we performed SLAM-seq (PMID: 28945705) combined with flow sorting of different phases of the human cell cycle on the basis of replication level and DNA content. Briefly, we exposed asynchronously growing U2OS cells to 4-thiouridine (Cat# GN6085, Glentham Life Sciences,) and EdU (Cat# E10345, Thermo Fisher Scientific) for 45 minutes followed by fixation with glyoxal and methanol (to keep the RNA intact) as described previously (PMID: 33481798). After that, incorporated EdU was labelled using Click-iT™ Plus Alexa Fluor™ 647 Picolyl Azide Toolkit (Cat# C10643, Thermo Fisher Scientific) following manufacturer's instructions and the DNA content of the EdU labelled cells were detected by treating the cells with SYTOX™ Green Ready Flow™ Reagent (Cat# R37168, Thermo Fisher Scientific), as recommended by the manufacturer. Labelled cells were then sorted using BD FACS aria.

value: U2OS osteosarcoma cell line

tag: condition


title: DNA methylation profile for 202410160226_R08C01

tag: developmental stage

value: adult

tag: brain region

value: Prefrontal

tag: gender


title: DNA methylation profile for 202410160156_R04C01

value: female

tag: cell proportion double negative

tag: cell proportion neun+

tag: cell proportion sox10+


title: U2OS_SLAMseq_No_alk_II


title: DNA methylation profile for 202410160156_R03C01

value: brain

value: Occipital


title: ZDF 26

value: Placebo

tag: group

value: model of type II diabetes


title: ZDF 23

value: ulna bone

value: WT

tag: disease state

value: control


title: Vav-cre-Tcf7KO-DN3_BC_11

value: Vav-cre; Tcf7fl/fl

value: thymus

value: DN2 & DN3


title: DNA methylation profile for 203205080154_R07C01

value: male


title: Vav-cre-Tcf7KO-DN3_BC_10

value: 6~8 wks


title: U2OS_SLAMseq_No_alk_I


title: Vav-cre-Tcf7KO-DN1_BC_9

source_name: thymus DN1 cells (CD45+Lin-CD4-CD8-CD25-CD44+)


title: DNA methylation profile for 203205080107_R03C01


title: DNA methylation profile for 203205080154_R08C01


title: U2OS_SLAMseq_G2_III


title: Vav-cre-Tcf7KO-DN1_BC_96


title: U2OS_SLAMseq_Late_S_III


title: ZDF 21

tag: treatment

value: samples collected 12 weeks after receiving treatment


title: Vav-cre-Tcf7KO-DN1_BC_95


title: DNA methylation profile for 203205080154_R05C01


title: DNA methylation profile for 203205080154_R06C01


title: Liver_mRNA_IN_HFD1

value: Liver

tag: in/pd

value: Input

tag: diet

value: high fat


title: ZDF 20

tag: time


title: ZDF 19

value: serum

value: anti-sclerostin

value: ZDF


title: ZDF 22

value: Placebo


title: U2OS_SLAMseq_G1_III

tag: cell type

value: U2OS osteosarcoma cell line


title: U2OS_SLAMseq_Early_S_III


title: ZDF 18

tag: tissue


title: U2OS_SLAMseq_G2_II


title: DNA methylation profile for 203205080153_R01C01

value: adult

value: brain

value: Occipital

value: female


title: Vav-cre-Tcf7KO-DN1_BC_94

tag: strain/background

tag: genotype/variation

value: Vav-cre; Tcf7fl/fl

value: thymus


title: Vav-cre-Tcf7KO-DN1_BC_93

tag: age


title: DNA methylation profile for 203205080152_R07C01

tag: developmental stage

value: male


title: U2OS_SLAMseq_Late_S_II

tag: condition


title: DNA methylation profile for 203205080153_R02C01

tag: brain region

value: Prefrontal

tag: gender


title: ZDF 17

value: Insulin

value: model of type II diabetes

value: samples collected 12 weeks after receiving treatment


title: ZDF 16

value: PTH


title: U2OS_SLAMseq_Early_S_II


title: Vav-cre-Tcf7KO-DN1_BC_90

value: 6~8 wks


title: DNA methylation profile for 203205080152_R08C01

tag: cell proportion double negative

tag: cell proportion neun+


title: DNA methylation profile for 203205080152_R01C01

tag: cell proportion sox10+


title: U2OS_SLAMseq_G1_II


title: Vav-cre-Tcf7KO-DN1_BC_8


title: ZDF 14

value: serum

tag: group

tag: disease state


title: ZDF 13

tag: treatment

value: WT

value: control


title: U2OS_SLAMseq_G2_I

value: U2OS osteosarcoma cell line


title: DNA methylation profile for 203205080152_R02C01

value: adult


title: U2OS_SLAMseq_Late_S_I


title: Vav-cre-Tcf7KO-DN1_BC_89


title: Vav-cre-Tcf7KO-DN1_BC_92


title: Vav-cre-Tcf7KO-DN1_BC_88


title: Vav-cre-Tcf7KO-DN1_BC_91


title: ZDF 11

value: ulna bone

value: ZDF


title: ZDF 10


title: U2OS_SLAMseq_G1_I


title: Vav-cre-Tcf7KO-DN1_BC_87


title: PD1 and IL-2 combination treated GP33+ CD8 T cells from LCMV chronically infected mice

city: Atlanta

first: Haydn

last: Kissick

state: Georgia

address: 1462 Clifton Rd

institute: Emory University

library_source: transcriptomic single cell

data_processing:
Alignment, filtering, barcode counting, and unique molecular identifier counting were performed using Cell Ranger v3.1. Data were further analyzed using Seurat v.3.074. Briefly, cells with a percentage of mitochondrial genes below 0.05% were included. Cells with more than 4,000 or less than 1,000 detected genes were considered as outliers and excluded from the downstream analyses. Raw unique molecular identifier counts were normalized to unique molecular identifier count per million total counts and log-transformed. Variable genes were selected based on average expression and dispersion. PCA was performed using variable genes. Clusters were identified using the shared nearest neighbor algorithmin Seurat and t-SNE plots were generated based on selected principal component analysis dimensions. Marker genes were identified by the Seurat function FindAllMarkers. Log normalized data are shown in the form of feature plots with the scale in a range of0 (grey) to 2.5~5 (purple). Gene set scoring was performed using the VISION R package v.1.1.0. Briefly, expression of signature genes is weighted based on predicted dropout probability calculated from nearest neighbors, and the normalized expression summed for all genes in the gene set.
Assembly: mm10
Supplementary files format and content: Gene name and raw counts for sequenced cells for each sample

source_name: spleen

extract_protocol:
Cell sorting was performed byFACS Aria II (BD Biosciences).For scRNA-seq (10X Genomics), LCMV chronically infectedmice (> day 40 p.i.) were untreated or treated with various therapeutic modalities for 2 weeks, and DbGP33+CD8+T cells in spleens were sorted from pooled spleens. Naïve (CD44lo) CD8+T cells were sorted from pooled spleens from uninfected mice (n=2).
Single cell RNAseq libraries were generated using the Chromium Single Cell 5’1007Library & Gel Bead Kit (10x Genomics) according to the manufacturer’s protocol. Briefly, DbGP33+CD8+T cellsor naïve CD44loCD8+T cells were sorted and captured into the Gel Beads-in-emulsion (GEMs). After reverse transcription, the GEMs were disrupted and the barcoded cDNA was isolated, pooled, and amplified by PCR (13cycles). The amplified cDNA was fragmented, and subjected to end repair and A-tailing followed by a sample index PCR (16 cycles). The purified libraries were sequenced to a depth of 50,000 reads/cell on a 1013HiSeq3000 (Illumina) with 26 cycles for read 1, 8 cycles for index 1 (i7), and 91 cycles for read 2.

treatment_protocol: For PD-1 monotherapy, 200 μg of rat anti-mouse PD-L1 antibody (10F.9G2,prepared in house) or rat IgG2b isotype control (LTF-2, BioXCell) was administered i.p. into LCMV chronically infectedmice every 3 days for 2 weeks. For IL-2 therapy, 15,000 IU of recombinant human IL-2 (Amgen) diluted in PBS with 0.1% normal mouse serum was given i.p. twice daily for 2 weeks.For examining a requirement of PD-1 blockade for improving viral control during IL-2 therapy, 500 μg of anti-PD-L1 antibody was administered at day 10 and 12 after starting IL-2 treatment.

value: spleen

tag: strain

value: GP33+ CD8+T cells

value: >D40 p.i. LCMV Clone 13

value: PD1 and IL-2


title: Naive CD8 T cells (CD44 low) from uninfected mice

value: CD44 low CD8 T cells

value: uninfected

value: untreated


title: IL-2 treated GP33+ CD8 T cells from LCMV chronically infected mice


title: AGO2KO_Ctrl_EV_3

description: small RNAs

data_processing:
Library strategy: ARM-seq
Adapters were removed and reads were merged with SeqPrep [John st. John unpub] using a minimum read length of 15 and adapters AGATCGGAAGAGCACACGTC and GATCGTCGGACTGTAGAACTC.  Reads that could not be merged were discarded before mapping.
Data were analyzed with tRAX (http://trna.ucsc.edu/tRAX/), tRAX maps reads using bowtie2 v2.3.5.1 with parameters --very-sensitive --ignore-quals --np 5 -k 100,  to a custom database containing mature tRNA transcripts and the genome sequence.
ENSEMBL (release 96) small ncRNA annotations were used to count the number of small RNA transcripts using only primary alignments to prevent double counting. Transcripts with 0 reads across all samples were removed.
tDRnamer (http://trna.ucsc.edu/tDRnamer/) was used to generate unique identifiers for each of the reads which mapped to a tRNA transcript based on the isodecoder(s) they mapped to and positions of any misincorporations.
DESeq2 v1.30.1 was used to generate normalized read counts for each of the transcripts across each sample.
Genome_build: Homo Sapiens GRCh38/hg38
Supplementary_files_format_and_content: Processed data files are comma-separated files containing DESeq2 normalized read counts.

growth_protocol: HEK293 cells were grown in DMEM medium containing 10% FBS and 1% Pen/Strep.

extract_protocol:
Cellular total RNAs were isolated by using TRIzol™ and then small RNAs were extracted by using mirVana™ miRNA Isolation Kit; extracellular RNAs were extracted by using exoRNeasy Maxi kit.
Small RNAs were sequentially treated with DNase I, T4 PNK, and His-AlkB and then subjected to NEBNext® Multiplex Small RNA Library Prep Set for Illumina®.

treatment_protocol: For hypoxia treatment, HEK cells were fed with complete medium and maintained in hypoxia chamber with 0.2% oxygen for 24 hours; For oxidative stress, HEK cells were treated with 0.7mM H2O2 in complete medium for 24 hours;  FBS  used here were extracellular vesicle-depleted by 24 hours of ultracentrifugation.

value: Human Embryonic Kidney Cell line

tag: genotype

value: Untreated

tag: sample types

value: Extracellular Vesicles


title: Untreated GP33+ CD8 T cells from LCMV chronically infected mice 2

tag: tissue

tag: cell type


title: ZDF 15

value: serum

value: PTH

tag: time

value: samples collected 12 weeks after receiving treatment


title: ZDF 12

value: Placebo

value: WT

value: control


title: Vav-cre-Tcf7KO-DN1_BC_85

tag: strain/background

tag: genotype/variation

value: Vav-cre; Tcf7fl/fl

value: thymus

tag: age

value: 6~8 wks


title: AGO2KO_Ctrl_EV_1

description: small RNAs


title: Vav-cre-Tcf7KO-DN1_BC_84


title: PD1 treated GP33+ CD8 T cells from LCMV chronically infected mice

value: spleen

value: GP33+ CD8+T cells

value: >D40 p.i. LCMV Clone 13


title: ZDF 7

value: anti-sclerostin

value: ZDF

value: model of type II diabetes


title: U2OS_SLAMseq_Early_S_I

value: U2OS osteosarcoma cell line

tag: condition


title: RNASE1KO_H2O2_EV_3

description: small RNAs

value: Human Embryonic Kidney Cell line

value: H2O2 treatment for 24 hours

value: Extracellular Vesicles


title: Vav-cre-Tcf7KO-DN1_BC_83


title: Untreated GP33+ CD8 T cells from LCMV chronically infected mice 1

value: untreated


title: Vav-cre-Tcf7KO-DN1_BC_86


title: ZDF 6

value: serum

value: samples collected 12 weeks after receiving treatment


title: AGO2KO_Ctrl_EV_2

description: small RNAs

value: Untreated


title: Brunello_Input_S1_VSVG_Cre

city: Brookings

first: Adam

middle: D.

last: Hoppe

state: South Dakota

address: 1055 CAMPANILE AVE BOX 2202, Avera Health and Science

department: Chemistry and Biochemistry

institute: South Dakota State University

library_source: other

data_processing:
Sequencing reads were aligned to the Brunello library file and counted using MAGeCK 0.5.9.4.
Assembly: Brunello library
Supplementary files format and content: All the raw read count files from MAGeCK were combined into a single .txt file called “Count.files.txt”
Library strategy: CRISPR screen

molecule: other

organism: synthetic construct

source_name: Brunello plasmid DNA library

growth_protocol: HEK293T cells were cultured in DMEM suppelemented with 10% FBS and 1% Penicillin/Streptomycin at 37C in 5% CO2 incubator.

extract_protocol:
The genomic DNA was extracted from the sorted cells using Thermo scientific GeneJet Genomic DNA purification kit (Catalogue# K0721). Following extraction of genomic DNA, sgRNAs were amplified for seuqencing.
Equal molar amounts PCR gel-purified samples were pooled, denatured and diluted to 1.8pM, of which 1.3 ml was sequenced on a NextSeq 550 using a high output 75 cycle sequencing kit (Illumina)

treatment_protocol: The cells were transduced with human CRISPR Brunello lentiviral pooled libraries and selected with Puromycin at 1ug/mL. Following selection, they were treated with different pseudoviruses for 48h. Then the cells were sorted in high and low  GFP fluorescence in FACS.

value: Brunello plasmid DNA library

tag: cell line


title: ZDF 9

value: PTH


title: Vav-cre-Tcf7KO-DN1_BC_82

value: Vav-cre; Tcf7fl/fl

value: thymus

value: 6~8 wks


title: RNASE1KO_H2O2_EV_1

description: small RNAs


title: Vav-cre-Tcf7KO-DN1_BC_81


title: RNASE1KO_H2O2_EV_2

description: small RNAs


title: Brunello_Input_S8_Spike_VSVG


title: ZDF 4


title: Vav-cre-Tcf7KO-DN1_BC_80


title: ZDF 5

value: Insulin


title: Pod

type: RNA

city: Chongqing

first: Zhaoming

last: Cai

state: Fuling

address: Juxian Road NO. 16 Fuling

institute: Yangtze Normal University

description:
test
SAMPLE 23

data_processing: Bio-Rad CFX manager. The relative expression levels were calculated using the 2-ΔΔCT method. For the normalization it uses the housekeeping gene: BjuACTIN3 (accession number BjuA014894). Target gene signals normalized to housekeeping genes, using the 2-ΔΔCT method.

label: SYBR Green

organism: Brassica juncea var. tumida

source_name: seedlings Pod

label_protocol: SYBR Premix Ex TaqTM kits (TransStart® Tip Green qPCR SuperMix kit, Beijing, China)

growth_protocol: The seeds of Brassica juncea var tumida cultivar Yong’an was used as plant material, permissions were obtained from Yangtz Normal Universtiy. The seeds were cultivated in light culture room following the methods previously used. The detail was as follows: the seeds were sterilized and sowed in MS medium. The growth room was at 22°C and 6000 lx (long-day conditions; 16 h light/8 h dark).

extract_protocol: Total RNA of tuber mustard was extracted in seedlings under pathogen and abiotic stresses treatment. The extracted RNA was reverse transcripted to cDNA, and then used for qRT-PCR analysis.

treatment_protocol: To analyze the gene expression patterns of clade A BjuPP2Cs genes under biotic stress, 14-day-old seedlings were treated with P. brassicae liquid (OD600=0.07) for 0, 0.25, 0.5, 1, 3, 5, 7, and 9 days; to analyze the gene expression patterns of clade A BjuPP2Cs genes under abiotic stresses, 5-day-old seedlings were treated with 50 μM ABA, 100 mM NaCl and 4℃ treatment for 3 h. To analysis the gene expression level in different growth stages of stem swelling, the samples D1 (the stems of 1-month-old seedlings, six leaf stage), D2 (the stems of 2-month-old seedlings, primary stage of stem swelling), D3 (the stems of 3-month-old seedlings, early stage of stem swelling), D4 (the stems of 4.5-month-old seedlings, fast-growing stage of stem swelling) and D5 (the stems of 5-month-old seedlings, last stage of stem swelling) of B. juncea var. tumida which were grown in the field were collected.

value: Pod


title: ZDF 3

value: WT

value: control


title: Vav-cre-Tcf7KO-DN1_BC_7


title: RNASE1KO_Ctrl_EV_3

description: small RNAs


title: RNASE1KO_Ctrl_EV_2

description: small RNAs


title: Root

description:
test
SAMPLE 22

source_name: seedlings Root

value: Root


title: RNASE1KO_Ctrl_EV_1

description: small RNAs

value: Human Embryonic Kidney Cell line


title: Vav-cre-Tcf7KO-DN1_BC_78


title: Vav-cre-Tcf7KO-DN1_BC_79


title: ZDF 8

value: ZDF

value: model of type II diabetes


title: Stem

description:
test
SAMPLE 21

source_name: seedlings Stem

value: Stem


title: ANGKO_Hypoxia_EV_2

description: small RNAs

value: Hypoxia for 24 hours

value: Extracellular Vesicles


title: Vav-cre-Tcf7KO-DN1_BC_76


title: RNA-seq_bte1btl1_rep3

first: Yangyang

last: Fan

address: No.5 Yiheyuan Road Haidian District,

institute: Peking University

data_processing:
Illumina bcl-convert v3.7.5 software used for basecalling.
After removing reads with adapter sequences and low quality by fastp, the high-quality reads were mapped to the TAIR10 genome assembly of Arabidopsis thaliana using HISAT2 (version 2.1.0) with parameters “--dta --min-intronlen 50 --max-intronlen 6000”. Only unique mapping and MAPQ score > 20 reads were kept using SAMtools version 1.6 for subsequent analysis.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Arabidopsis thaliana

source_name: total seedlings

extract_protocol:
Total RNA from 9-d-old WT and mutant seedlings grown in continuous white light were isolated using RNeasy Plant Mini Kits (Sigma). Three biological replicates for each sample were subjected to RNA-seq.
Poly (A) RNA from 1 μg total RNA was used to generate the cDNA library according to the TruSeq RNA Sample Prep Kit protocol. The library was then sequenced using a HiSeq Xten system (Illumina).

value: total seedlings

tag: developmental stage

value: 9-day-old seedlings grown under continuous white light

value: bte1 btl1 double mutant


title: ZDF 2

value: serum

value: Placebo

value: samples collected 12 weeks after receiving treatment


title: ANGKO_Hypoxia_EV_3

description: small RNAs


title: RNA-seq_bte1btl1_rep1


title: Vav-cre-Tcf7KO-DN1_BC_77

value: Vav-cre; Tcf7fl/fl

value: thymus

value: 6~8 wks


title: RNA-seq_btl1_rep3

value: btl1 mutant


title: Flower

description:
test
SAMPLE 19

source_name: seedlings Flower

value: Flower


title: Vav-cre-Tcf7KO-DN1_BC_73


title: D4

description:
test
SAMPLE 16

source_name: seedlings stems

value: stem


title: D3

description:
test
SAMPLE 15


title: ANGKO_Ctrl_EV_3

description: small RNAs

value: Human Embryonic Kidney Cell line

value: Untreated


title: Vav-cre-Tcf7KO-DN1_BC_75


title: Swollen stem

description:
test
SAMPLE 18

source_name: seedlings Swollen stem

value: Swollen stem


title: ANGKO_Hypoxia_EV_1

description: small RNAs

value: Hypoxia for 24 hours


title: ANGKO_Ctrl_EV_2

description: small RNAs

value: Extracellular Vesicles


title: Leaf

description:
test
SAMPLE 20

source_name: seedlings Leaf

value: Leaf


title: ZDF 1

value: WT

value: control


title: Vav-cre-Tcf7KO-DN1_BC_74


title: HEKAGO2_Ctrl_EV_2

description: small RNAs

value: HEK wild type


title: D5

description:
test
SAMPLE 17


title: RNA-seq_btl1_rep1

value: total seedlings

value: 9-day-old seedlings grown under continuous white light


title: ANGKO_Ctrl_EV_1

description: small RNAs


title: RNA-seq_e2f_rep2

value: e2fa e2fb e2fc triple mutant


title: Vav-cre-Tcf7KO-DN1_BC_72

value: Vav-cre; Tcf7fl/fl

value: thymus


title: HEKAGO2_Ctrl_EV_1

description: small RNAs


title: RNA-seq_bte1btl1_rep2

value: bte1 btl1 double mutant


title: D2

description:
test
SAMPLE 14


title: HEKAGO2_Ctrl_EV_3

description: small RNAs


title: Vav-cre-Tcf7KO-DN1_BC_6

value: 6~8 wks


title: Pb 7d

description:
test
SAMPLE 11

source_name: seedlings roots

value: root

tag: stress

value: Pathogen Plasmodiophora brassicae


title: RNA-seq_e2f_rep3


title: RNA-seq_WT_rep2

value: Col-0 ecotype


title: Vav-cre-Tcf7KO-DN1_BC_71


title: RNA-seq_btl1_rep2

value: btl1 mutant


title: Pb 3d

description:
test
SAMPLE 9


title: RNASE1KO_H2O2_Cells_3

description: small RNAs

value: Human Embryonic Kidney Cell line

value: H2O2 treatment for 24 hours

value: Cells


title: RNA-seq_WT_rep1


title: RNA-seq_e2f_rep1


title: D1

description:
control  D1 is the control of Samples 14-17
SAMPLE 13

value: stem


title: Pb 24h

description:
test
SAMPLE 8


title: Vav-cre-Tcf7KO-DN1_BC_67


title: RNA-seq_WT_rep3


title: RNA-seq_475A2_rep2

description: phil1: mutation of proximal-promoter region of HIL1

value: hid1 phil1 double mutant


title: Vav-cre-Tcf7KO-DN1_BC_70


title: RNASE1KO_H2O2_Cells_2

description: small RNAs


title: Vav-cre-Tcf7KO-DN1_BC_65


title: Pb 9d

description:
test
SAMPLE 12


title: Pb 5d

description:
test
SAMPLE 10


title: Vav-cre-Tcf7KO-DN1_BC_69


title: Pb 6h

description:
test
SAMPLE 6


title: Vav-cre-Tcf7KO-DN1_BC_68


title: RNASE1KO_H2O2_Cells_1

description: small RNAs


title: RNASE1KO_Ctrl_Cells_3

description: small RNAs

value: Untreated


title: RNASE1KO_Ctrl_Cells_2

description: small RNAs


title: Vav-cre-Tcf7KO-DN1_BC_66


title: RNA-seq_475A2_rep3

value: total seedlings


title: ANGKO_Hypoxia_Cells_3

description: small RNAs

value: Hypoxia for 24 hours


title: RNA-seq_475A2_rep1

value: 9-day-old seedlings grown under continuous white light


title: Pb 12h

description:
test
SAMPLE 7


title: RNASE1KO_Ctrl_Cells_1

description: small RNAs


title: RNA-seq_bte1hid1_rep3

value: bte1 hid1 double mutant


title: Vav-cre-Tcf7KO-DN1_BC_64

value: Vav-cre; Tcf7fl/fl

value: thymus


title: ANGKO_Hypoxia_Cells_2

description: small RNAs


title: RNA-seq_bte1hid1_rep2


title: RNA-seq_bte1hid1_rep1


title: Vav-cre-Tcf7KO-DN1_BC_62

value: 6~8 wks


title: Vav-cre-Tcf7KO-DN1_BC_63


title: Pb 0h

description:
control  Pb 0h is the control of Samples 6-12
SAMPLE 5

value: root

value: control


title: Vav-cre-Tcf7KO-DN1_BC_61


title: ANGKO_Ctrl_Cells_3

description: small RNAs


title: ANGKO_Hypoxia_Cells_1

description: small RNAs


title: Vav-cre-Tcf7KO-DN1_BC_60


title: ANGKO_Ctrl_Cells_2

description: small RNAs


title: RNA-seq_bte1_rep3

value: bte1 mutant


title: CB-86-m

city: Huddinge

first: Ani

last: Azatyan

state: Stockholm

address: Hälsovägen 7C

department: Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

data_processing:
Basecalling and demultiplexing were performed using bcl2fastq (v2.20.0).
Quality and adapter trimming of reads were performed using TrimGalore (v0.6.4).
standard mRNA detection: reads from the poly(A) enriched fraction were aligned to the Gencode GRCh38 reference genome assembly using the Star (v2.5.2) aligner. Counts were assigned to genes using featureCounts (v1.5.1)
circRNA detection: reads from the circRNA enriched fraction were analysed with the CIRCexplorer2 characterization pipeline to identify circular back spliced junctions and aligned to Gencode GRCh38 using CIRCexplorer2/Star (PMID: 27365365) with the default parameters.
linear back spliced transcript detection: reads from poly(A) enriched fraction were analysed with the CIRCexplorer2 characterization pipeline to identify linear back spliced junctions and aligned to Gencode GRCh38 using CIRCexplorer2/Star (PMID: 27365365) with the default parameters.
Fusion detections: reads from the poly(A) enriched fraction and circRNA enriched fraction were aligned to Gencode GRCh38 using Star-Fusion (PMID: 31639029) with the default parameters.
Normalized counts were generated using DESeq2 (v1.32.0).
Assembly: GRCh38
Supplementary files format and content: tab delimited text file with raw mRNA counts for every sample generated by featureCounts
Supplementary files format and content: tab delimited text file with raw circRNA counts for every sample generated by CIRCexplorer2
Supplementary files format and content: tab delimited text file with raw fusion transcript counts for every sample generated by StarFusion

source_name: Cerebellum Normal

extract_protocol:
The medulloblastoma tumor RNA samples were provided by the Childhood Brain Tumor Tissue Consortium (www.cbttc.org), and 5 normal cerebellum RNA samples were purchased commercially from Takara (Japan), Amsbio (UK) or BioChain (USA).
mRNA / poly(A) enriched fraction: ≈ 100 ng of total RNA was used to generate stranded mRNA libraries with the TruSeq®Stranded mRNA Low Throughput Sample Preparation kit according to the manufacturer’s instructions (15031047, Illumina, USA). This protocol involves a poly(A) selection/enrichment and ribosomal RNA depletion step.
circRNA / (poly(A-) / RNaseR+)  fraction: 1 μg of total RNA was used. First, ribosomal RNA was depleted using the RiboMinusTM Eukaryote System V2 (Ambion) (A15026, ThermoFisher USA), followed by digestion with 5U RNase R for 1 hr to degrade linear RNAs and purification with the RNeasy MinElute Cleanup Kit (74204, Qiagen). The concentration and quality of the enriched circRNA RiboMinus/RNase R preparations were assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, USA). 1 ng of RiboMinus/RNase R treated RNA was used for cDNA library generation. Random hexamer primers and Superscript III reverse transcriptase (18080055, Invitrogen, USA) were used for 1st strand synthesis and stranded mRNA library was generated according to the TruSeq®Stranded mRNA Low Throughput Sample Preparation protocol (15031047, Illumina, USA). The concentration and quality of the cDNA libraries were assessed with Qubit (Life Technologies, USA) and TapeStation, respectively.

value: normal

tag: sample location

value: Amsbio/BioChain _Human normal Cerebellum RNA, Male 24 Y

tag: medulloblastoma subgroup

value: CB

tag: biospecimen id

tag: research subject id

tag: molecule subtype

value: mRNA / poly(A)


title: NaCl

description:
test
SAMPLE 2

source_name: seedlings

value: seedlings

value: NaCl


title: RNA-seq_bte1_rep2

tag: genotype


title: 4degC

description:
test
SAMPLE 3


title: ABA

description:
test
SAMPLE 4

value: ABA


title: CK

description:
control  CK is the control of Samples 2-4
SAMPLE 1


title: Vav-cre-Tcf7KO-DN1_BC_5


title: ANGKO_Ctrl_Cells_1

description: small RNAs

value: Human Embryonic Kidney Cell line

tag: treatment

value: Untreated

tag: sample types

value: Cells


title: RNA-seq_bte1_rep1

tag: tissue

value: total seedlings

value: 9-day-old seedlings grown under continuous white light


title: Vav-cre-Tcf7KO-DN1_BC_59

value: Vav-cre; Tcf7fl/fl

value: thymus

tag: cell type


title: CB-85-m

tag: disease state

value: Amsbio/BioChain _Human normal Cerebellum RNA, Male 29 Y


title: 786-O_H3K4me3_ChIP_input_Rep2

city: Chapel Hill

first: Austin

middle: J

last: Hepperla

state: NC

address: 7018B Mary Ellen Jones Building

department: Genetics

institute: University of North Carolina at Chapel Hill

description: Input for H3K4me3 ChIP Rep2

data_processing:
For RNA-seq: Reads were filtered for adapter contamination using cutadapt (v1.12) and filtered such that at least 90% of bases of each read had a quality score >20. Reads were aligned to the reference genome (hg19) using STAR (v2.5.2b) retaining only primary alignments. Reads overlapping blacklisted regions of the genome were then removed. Transcript abundance was then estimated using Salmon, and differential expression was detected using DESeq2.
For ChIP: Reads from the sequencer were demultiplexed using bcl2fastq (v2.20.0). Sequencing adapters on reads were trimmed using cutadapt (v1.12) using options -a GATCGGAAGAGC -A GATCGGAAGAGC and --minimum-length 36 in paired mode. After trimming, reads were filtered for quality using the fastq_quality_filter in FASTX-Toolkit (v0.0.12), with options -Q 33, -p 90, and -q 20. In-house scripts were used to limit potential PCR duplicates by limiting reads with the same sequence to a maximum of 5 copies and discarding the copies beyond that limit. Since the previous filtering steps may remove one end of a read pair but not the other, both read-pair fastq files were synced using in-house scripts to ensure proper order for alignment. Read alignment was done using STAR (v2.5.2b) and options --outFilterMismatchNmax 2, --chimSegmentMin 15, --chimJunctionOverhangMin 15, --outSAMtype BAM Unsorted, --outFilterType BySJout, --outFilterScoreMin 1, and --outFilterMultimapNmax 1. Post-alignment, Samtools (v1.31) and bedtools (2.26) were used to generate bigWig files for downstream analyses. MACS2 (v2.1.2) was used for peak calling on each individual sample with the designated inputs.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.sf: Salmon files are tab-delimited text files with the per-transcript expression.
Supplementary_files_format_and_content: *.bw: BigWig files show the per-base signal across the genome.
Supplementary_files_format_and_content: *.narrowpeak: narrowPeak files contain the peak calls from MACS2.

source_name: 786-O cell line

growth_protocol: 786-O cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin, incubated in a 5% CO2 humidified incubator at 37°C. 786-O cells were obtained from Sigma. All cells were used for experiments within 10-20 passages from thawing, and they were mycoplasma-free guaranteed by applying mycoplasma detection kit (Lonza, LT07–218) or mycoplasma elimination reagent-plasmocin (Invivogen, ant-mpt).

extract_protocol:
ChIP assay was performed on 786-O cells with anti-JMJD6 (Abcam, ab64575) and anti-H3K4me3 (Abcam, ab8580) antibody. Briefly, samples were cross-linked with 1% formaldehyde on a shaker for 10 min, followed by adding 125 mM glycine to quench unreacted formaldehyde. Samples were collected by centrifuging at 1500 × g, 4°C for 10 min (50 ml tube, 20 150 mm dishes per sample), followed by lysis and sonication (in 5 ml lysis buffer with 1 ml 0.5 mm glass beads; 30 s on 30 s off/cycle, 50 cycles in total). Meanwhile, incubate dynabeads with JMJD6 or H3K4me3 antibody at 4°C (100 ml beads using 10 mg antibody), rotating overnight. The sonicated samples were then incubated with antibody-bound dynabeads overnight at 4°C. Wash beads 8 times by applying magnetic stand, spin to collect samples, and elute 30 min at 65°C, further reverse crosslink at 65°C overnight. Digest RNA using RNase (Roche, 11119915001) at 37°C for 1 h, and digest protein using Proteinase K (Sigma-Aldrich, 3115828001) at 55°C for 2 h. Purify DNA using Qiagen PCR purification kit.
We prepared DNA library using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (New England Biolabs, E7645S) combined with NEBNext Multiplex Oligos for Illumina (New England Biolabs, E7335S) according to manufacturer’s instructions. The quality of prepared DNA library was checked by applying high sensitivity D1000 reagents and corresponding screen tape (Agilent Technologies, 5067-5585/5584), followed by sequencing at the CRI’s Sequencing Facility at UT Southwestern.

treatment_protocol:
Seed cells (786-O) in 6-well plates to be 60-70% confluent at transfection, followed by transfection using the Invitrogen™ lipofectamine™ RNAiMAX transfection reagent (Thermo Fisher Scientific, 13778150), change medium after 12 h transfection. Incubate cells for 48 h at 37°C. Then further use the cells to perform experiments (immunoblots, cell proliferation assay and soft agar colony formation assay). Non-targeting siRNA was used as control and obtained from Dharmacon (D0012100220). The sequence of main siRNAs used in this study is as below:
JMJD6 siRNA (1): GGAGAGCACUCGAGAUGAU
JMJD6 siRNA (4): GGAUAACGAUGGCUACUCA
Other 2-OG family siRNAs sequence is showed in Supplementary table.

value: JMJD6 WT

tag: chip target

tag: sequencing batch

value: Batch 2


title: CB-84-m

value: normal

value: Takara _Human normal Cerebellum RNA, Pool from 3 Asian Males 21-29 Y


title: RNA-seq_hid1_rep3

value: hid1 mutant


title: RNA-seq_hid1_rep2


title: Vav-cre-Tcf7KO-DN1_BC_57

tag: strain/background

tag: genotype/variation

tag: age

value: 6~8 wks


title: Vav-cre-Tcf7KO-DN1_BC_56


title: Vav-cre-Tcf7KO-DN1_BC_55


title: Group3-17-m

source_name: Medullobalstoma Group 19

value: Medulloblastoma

value: Cerebellum/Posterior Fossa

value: mRNA / poly(A)


title: RNA-seq_hid1_rep1

tag: developmental stage


title: Group3-16-m

source_name: Medullobalstoma Group 18

tag: sample location


title: External beam radiation therapy (EBRT) treated 2

city: New York

first: Benjamin

middle: S

last: Glicksberg

state: NY

address: 1 Gustave Levy Place

department: Genetics and Genomics

institute: Icahn School of Medicine at Mt Sinai

data_processing:
Quality control of raw samples in .fastq format using FASTQC
Alignment of paired-end reads to human reference genome using STAR
Conversion of aligned reads to readcounts using htseq-count
DEG analysis of readcounts using edgeR package in R
Assembly: GRCh38
Supplementary files format and content: Raw readcounts provided in matrix format as text file
Supplementary files format and content: Normalised readcounts via edgeR package provided in matrix format as text file

source_name: xenograft of LNCAP

growth_protocol: LNCAP cells were cultured according to ATCC instructions (RPMI+10% FBS)

extract_protocol:
Tumors were extracted and homogenized. RNA was purified with Rneasy Mini Kit columns (Qiagen).
Truseq library preparation (Illumina) following manufacturer's instructions.

treatment_protocol: External beam radiation therapy (5 fractions x 10Gy)

value: xenograft of LNCAP

tag: cell line

value: LNCAP

tag: disease

value: human prostate cancer

value: Case

value: EBRT treated


title: CB-82-m

value: Amsbio_Human nomral cerebellum, Total RNA , Male 26 Y

tag: medulloblastoma subgroup

value: CB

tag: biospecimen id

tag: research subject id


title: Vav-cre-Tcf7KO-DN1_BC_54

source_name: thymus DN1 cells (CD45+Lin-CD4-CD8-CD25-CD44+)

value: Vav-cre; Tcf7fl/fl

value: thymus


title: Group3-15-m

source_name: Medullobalstoma Group 17

tag: molecule subtype


title: 786-O_JMJD6_ChIP_input_Rep4

description: Input for JMJD6 ChIP Rep4

tag: genotype

value: JMJD6 WT

value: input

value: Batch 2


title: External beam radiation therapy (EBRT) treated 3

tag: tissue

tag: treatment


title: External beam radiation therapy (EBRT) treated 1


title: 786-O_JMJD6_ChIP_input_Rep2

description: Input for JMJD6 ChIP Rep2

value: Batch 1


title: 786-O_H3K4me3_ChIP_Rep1


title: 786-O_JMJD6_ChIP_input_Rep3

description: Input for JMJD6 ChIP Rep3


title: Non-treated 3

value: Control

value: Non-treated


title: Vav-cre-Tcf7KO-DN1_BC_52

tag: cell type

value: 6~8 wks


title: 786-O_H3K4me3_ChIP_input_Rep1

description: Input for H3K4me3 ChIP Rep1

tag: chip target


title: Group3-14-m

source_name: Medullobalstoma Group 16

tag: disease state

value: Medulloblastoma

value: Cerebellum/Posterior Fossa

value: mRNA / poly(A)


title: CB-83-m

value: normal

value: Amsbio_Human brain cerebellum (left), Total RNA, Male 24 Y


title: Vav-cre-Tcf7KO-DN1_BC_53

tag: strain/background


title: Vav-cre-Tcf7KO-DN1_BC_58

tag: genotype/variation


title: 786-O_H3K4me3_ChIP_Rep2

tag: sequencing batch


title: 786-O_JMJD6_ChIP_input_Rep1

description: Input for JMJD6 ChIP Rep1


title: Non-treated 2

value: xenograft of LNCAP

value: LNCAP

value: human prostate cancer


title: Group3-13-m

source_name: Medullobalstoma Group 15

value: Ventricles


title: Vav-cre-Tcf7KO-DN1_BC_51

value: Vav-cre; Tcf7fl/fl

value: thymus

tag: age


title: Group3-12-m

source_name: Medullobalstoma Group 14

tag: sample location


title: Non-treated 1

tag: cell line


title: 786-O_JMJD6_ChIP_Rep4

value: JMJD6 WT


title: Group3-11-m

source_name: Medullobalstoma Group 13

value: Cerebellum/Posterior Fossa,Spinal Cord- Cervical,Spinal Cord- Lumbar/Thecal Sac,Spinal Cord- Thoracic


title: 786-O_JMJD6_ChIP_Rep3

value: Batch 2


title: Vav-cre-Tcf7KO-DN1_BC_50


title: Vav-cre-Tcf7KO-DN1_BC_4


title: DIPGXIII-ko-c5p32-H3-1WT-p6-Rx_Input

city: Montréal

first: Claudia

middle: L

last: Kleinman

state: Québec

address: 3999 Côte Ste-Catherine Road

department: Human Genetics

country: Canada

institute: Lady Davis Institute for Medical Research

data_processing:
ChIP-seq datasets were processed using the ChIP-seq module of GenPipes (v3.1.0 for isogenic cell lines, v3.1.2 for parental cell lines). Raw reads were trimmed using Trimmomatic (v0.32) to remove adaptor and sequencing-primer associated reads then aligned to hg19 using bwa-mem (v0.7.12) with default parameters. PCR duplicate reads as defined by reads with identical mapping coordinates were then collapsed by Picard (v2.0.1) to produce uniquely aligned reads. Reads with a mapping quality of 5 or less were then filtered out. For single-end (SE) 50bp datasets, reads were extended by 250bp.
Wiggle tracks are generated using uniquely aligned reads using Homer (v4.9.1). ChIP-seq RPKM values over CGIs and genome-wide 100kb bins for scatterplots were calculated using VisRSeq (v0.9.40).
Rx- and RPKM-normalized BigWig tracks were produced using the “bamCoverage” functionality of deeptools (v3.5.1). Rx ratios were supplied via the ‘--scaleFactor’ option.  Reads flagged as duplicates, mapping to random, mitochondrial or sex chromosomes, as well as low-mappability regions according to ENCODE’s blacklist were discarded.
Assembly: hg19
Supplementary files format and content: bigwig files. Read coverage for each sample over the human genome

source_name: Pons

extract_protocol:
Reverse cross linking took place on a heat block at 65°C for 4 hr. ChIP samples were then treated with 2ul RNase Cocktail at 65°C for 30 min followed by 2ul Proteinase K at 65°C for 30 min. Samples were then purified with QIAGEN MiniElute PCR purification kit as per manufacturers’ protocol. In parallel, input samples (chromatin from about 50,000 cells) were reverse crosslinked and DNA was isolated following the same protocol.
Library preparation was carried out using Kapa HTP or HyperPrep Illumina library preparation reagents. Ffor HTP kit, 25ul of ChIP sample was incubated with 45ul end repair mix at 20°C for 30 min followed by Ampure XP bead purification. A tailing: bead bound sample was incubated with 50ul buffer enzyme mix for 30°C 30 min, followed by PEG/NaCl purification. Adapter ligation: bead bound sample was incubated with 45ul buffer enzyme mix and 5ul of different TruSeq DNA adapters (Illumina) for each sample, at 20°C for 15 min, followed by PEG/NaCl purification (twice). Library enrichment: 12 cycles of PCR amplification. For HyperPrep kit, end-repair and A tailing were performed in one reaction: 15ul of ChIP sample was incubated with 45ul end repair+A-tailing mix at 20°C for 30 min, then 65°C for 30 min. Directly proceeded to adapter ligation by adding 5ul of IDT for Illumina Unique Dual Indexes (IDT) adapters and 45ul ligation buffer enzyme mix, incubating at 20°C for 15 min, followed by Ampure XP bead purification. Library enrichment: 10 cycles of PCR amplification. Size selection was performed after PCR using a 0.6x/0.8x ratio of Ampure XP beads (double size selection) set to collect 250-450bp fragments.

tag: material

value: cell line

tag: histone mark/factor

value: Input

tag: perturbation

tag: clone or passage


title: DIPGXIII-ko-c5p32-H3-1WT-p6-Rx_H3K27me3-C


title: 786-O_JMJD6_ChIP_Rep1

value: Batch 1


title: Vav-cre-Tcf7KO-DN1_BC_48

value: 6~8 wks


title: DIPGXIII-ko-c5p32-H3-1K27M-p6-Rx_Input


title: Vav-cre-Tcf7KO-DN1_BC_49


title: Vav-cre-Tcf7KO-DN1_BC_47


title: Group3-10-m

source_name: Medullobalstoma Group 12

value: Medulloblastoma

value: Cerebellum/Posterior Fossa,Ventricles

tag: medulloblastoma subgroup

tag: biospecimen id

tag: research subject id

tag: molecule subtype


title: Rep1_4J_75min_VCPinh_RPB1ChIP

city: Freiburg

first: Barbara

last: Hummel

address: Stübeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

description: ChIP-seq

data_processing:
Reads were aligned to a hybrid genome (hg38 and mm10) using the DNAmapping and ChIPseq modules from snakePipes
Mouse spike-in reads were used to calculate size factors. Normalized bigwig files for human reads were generated using deeptools based on the calculated size factors
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files for ChIP-seq coverage

extract_protocol: Cells were fixed in 1% methanol-free formaldehyde (Thermo Scientific, 28906) in PBS at room temperature for 10 min, followed by 5 min blocking in 0.125 M glycine. Cells were washed twice with ice-cold PBS. The cell pellet was resuspended in Farnham buffer (5 mM PIPES, pH 8; 85 mM KCl; 0.5% Igepal). Cell suspensions were sonicated for 4 min in 1 ml Covaris tubes (Covaris, 520130) using Covaris S220 with the following settings: peak power = 75; duty factor = 2; cycles/burst = 200. Isolated nuclei were washed with Farnham buffer and suspended in shearing buffer (10 mM Tris-HCl, pH 8; 0.1% SDS; 1 mM EDTA). Chromatin was sheared by sonication for 12 min in 1-ml Covaris tubes using the following settings: peak power = 140; duty factor = 5; cycles/burst = 200. Debris was removed by centrifugation. A DNA fragment–size distribution of 200–600 bp was considered as ideal chromatin for ChIP. Chromatin was diluted 1:1 with IP buffer (10 mM Tris-HCl, pH 8; 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxicholate, 0.1% N-lauroylsarcosine) to achieve a final 0.05% SDS concentration. Good quality chromatin (200 μg) was used for immunoprecipitation as described {Montrose, 1985 #102}. Briefly, Protein A magnetic beads (Life Technologies, 10002D) were incubated (rotated) with 10 μg of f Rpb1 NTD (D8L4Y) Rabbit mAb (Cell Signaling #14958) for 6 h at 4 °C. This bead–antibody complex was then incubated overnight at 4 °C with chromatin.

tag: treatment

value: 4J irradiation for 75min in the presence of VCP inhibitor

tag: chip antibody

value: RPB1 NTD (D8L4Y), Cell signaling #14958


title: Group3-7-m

source_name: Medullobalstoma Group 9

tag: disease state

value: Cerebellum/Posterior Fossa,Spinal Cord- Lumbar/Thecal Sac,Spinal Cord- Thoracic

value: mRNA / poly(A)


title: Group3-6-m

source_name: Medullobalstoma Group 8

value: Cerebellum/Posterior Fossa


title: DIPGXIII-ko-c5p32-H3-1WT-p6-Rx_H3K27me2


title: Group3-5-m

source_name: Medullobalstoma Group 7


title: Rep1_4J_75min_RPB1ChIP

description: ChIP-seq

value: 4J irradiation for 75min


title: Vav-cre-Tcf7KO-DN1_BC_44

data_processing:
Unique molecular identifier (UMI) information were added into the corresponding read 1 which were then trimmed to remove template switch oligo (TSO) sequence and polyA tails.
Next, we removed reads with adapter contaminants and low-quality bases (N>10%).
The cleaned reads were aligned to the mm10 mouse transcriptome (Genocode) using Tophat (version 2.1.1).
Uniquely mapped reads were counted using htseq-count of the HTSeq package. For each gene, duplicated transcripts with the same UMI sequence were removed. For each cell, the transcript copy number of each gene were counted on the basis of the number of distinct UMIs of that gene.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: barcode_information.xlsx
Supplementary_files_format_and_content: count_matrix.csv
Supplementary_files_format_and_content: expression_matrix_log2(TPM:10+1).csv

extract_protocol:
Single-cell cDNA amplification was carried out by using the STRT protocol with several modifications to allow for multiplexed single-cell RNA-seq. Libraries were prepared using KAPA Hyper Prep Kits (KK8505). The NEB U-shaped adapter was used for ligation. The libraries were sequenced on an Illumina Hiseq x ten platform to generate 150-bp paired-end reads (sequenced by BGI).
Libraries are constructed according to the standard protocol for Smart-seq2.

tag: strain/background

value: Vav-cre; Tcf7fl/fl

tag: tissue

tag: cell type


title: Vav-cre-Tcf7KO-DN1_BC_46

tag: genotype/variation

value: thymus

tag: age


title: DIPGIV-nko-c3p5-Rx_Input

value: NKO


title: Vav-cre-Tcf7KO-DN1_BC_45


title: Rep1_0J_VCPinh_RPB1ChIP

description: ChIP-seq

value: No irradiation in the presence of VCP inhibitor


title: Rep1_0J_RPB1ChIP

description: ChIP-seq

value: No irradiation


title: Group3-4-m

source_name: Medullobalstoma Group 6

tag: sample location


title: DIPGXIII-ko-c5p32-H3-1K27M-p6-Rx_H3K27me2

tag: material

value: cell line


title: Group3-8-m

source_name: Medullobalstoma Group 10


title: MAC_3′seq_LPS 4h_rep2

city: Ithaca

first: Andrew

last: Grimson

state: New York

address: Biotechnology building, 526 campus road,  room 445

department: Molecular biology and genetics

institute: Cornell University

description:
processed data: peaks.txt
processed data: Readcounts_peak.txt

data_processing:
Library strategy: 3′-seq
RTA v2 software used for basecalling on NextSeq 500 and HiSeq 4000.
5′ RNA adaptor sequence was removed from the 3′ end of sequencing reads using Cutadapt with option -e 0.10, --overlap 2, --minimum-length=10, --nextseq-trim 20. After adaptor removal, reads with at least one quality score below 20 were filtered out. The first 30 nucleotides containing UMI barcode of 8 nucleotides were used to deduplicate the reads. After trimming 16 nucleotides (8-mer UMI barcode and 8-mer dTs) off of the 5′ end, the remaining reads with minimum 10 nucleotides were finally mapped to hg38 human genome using STAR.
The aligned reads were represented by their 5′ end mapping position on the opposite strand, and converted to a BedGraph format
The mapping position and the corresponding read counts of a 3′-seq peak were used to determine the cleavage and polyadenylation site and mRNA abundance of a transcript isoform.  We defined the 3'seq position with the totalled readcounts  across all samples more than 5 CPMs as the actually expressed PAS isoforms.
Genome_build: hg38
Supplementary_files_format_and_content: PROseq_rep1.txt: matrix_Normalized PROseq readcounts (RPKM)
Supplementary_files_format_and_content: PROseq_rep2.txt: matrix_Normalized PROseq readcounts (RPKM)
Supplementary_files_format_and_content: peaks.txt: matrix_Identification of 3′-seq peak positions  with more than 5 CPM.
Supplementary_files_format_and_content: Readcounts_peak.txt: matrix_Normalized abundance (CPM) per the identified 3′-seq peak positions.
Supplementary_files_format_and_content: PASisoforms_summary_rep1.txt: matrix_Mean poly(A) tail length for every de novo PAS isoforms.
Supplementary_files_format_and_content: PASisoforms_summary_rep2.txt: matrix_Mean poly(A) tail length for every de novo PAS isoforms.
Supplementary_files_format_and_content: ActD_PASisoforms_summary_rep1.txt: matrix_Mean poly(A) tail length for every de novo PAS isoforms.
Supplementary_files_format_and_content: ActD_PASisoforms_summary_rep2.txt: matrix_Mean poly(A) tail length for every de novo PAS isoforms.
Supplementary_files_format_and_content: Integrated_datasets.txt: matrix_Transcription in RPKM, mRNA level in CPM, and mean poly(A) tail length for every transcript isoform for the actinomycin D-untrreated conditions.

source_name: Monocyte-derived macrophage cells

growth_protocol: THP-1 cells were cultured in RPMI1640 supplemented with 10% FBS and 1% antibiotics.

extract_protocol:
After washing the cells with DPBS three times, total RNA was extracted by directly adding TRIzol  to the plate with the adherent cells on it. 5 million cells were used for the construction of PRO-seq libraries. For 3′-seq and TED-seq, 10 ug of total RNAs were used.
RNA libraries were prepared to be compatible with Illumina small RNA sequencing.
We prepared 3′-seq libraries as follows: total RNAs was extracted with TRIzol (Invitrogen). For each sample, poly(A) RNAs were isolated from 10 ug total RNAs, and proceeded with RNA fragmentation, 5′ RNA phosphorylation, and 5′ RNA ligation. After heat denaturation at 65C for 2 min, 5′ adapter-ligated poly(A)-containing RNA fragments were reverse transcribed by superscript II enzyme (Invitrogen) using RT primer ( CPS_RTP: 5′ - GTTCAGAGTTCTACAGTCCGACGATC NNNNNNNNT8VN-3′) at 50 C for 1hr. CPS_RTP was designed to anneal to the junction of 3′ cleaved site and poly(A) tail using its short oligo dT residues and two degenerate nucleotides, and also to contain UMI barcode and adaptor for PCR deduplication, and universal PCR amplification, respectively. The resulting cDNA molecules were amplified by PCR, followed by gel purification of 200 to 500 bp PCR products on 6% PAGE gel in TBE buffer. The eluted PCR products proceed with sequencing on Illumina Nextseq 500.

treatment_protocol: THP-1 cells were differentiated to macrophage-like cells by incubating them overnight in the 200 ng/ml PMA-containing (sigma Aldrich, P1585-1MG) complete media, followed by 3 days incubation in fresh media without PMA. The resulting differentiated cells were stimulated with 200 ng/mL LPS and collected at four consecutive time points 0 (no stimulation), 1, 2, and 4 hours.

tag: cell state

value: Differentiated into macrophage-like state

value: Monocyte

tag: cell line

value: THP-1 monocyte cells were differentiated into macrophage-like cells by PMA for 24 h, followed by treatment with LPS for 4 hour.


title: DIPGIV-nko-c3p5-Rx_H3K27me3-C

tag: histone mark/factor

tag: perturbation

tag: clone or passage


title: Group3-9-m_rec

source_name: Medullobalstoma Group 11

value: Medulloblastoma

value: Cerebellum/Posterior Fossa, reccurent tumor

tag: medulloblastoma subgroup

tag: biospecimen id

tag: research subject id


title: MAC_3′seq_LPS 4h_rep1

tag: treatment

value: THP-1 monocyte cells were differentiated into macrophage-like cells by PMA for 24 h, followed by treatment with LPS for 2 hour.


title: DIPGIV-nko-c3p5-Rx_H3K27me2


title: Group3-3-m

source_name: Medullobalstoma Group 5

tag: disease state

tag: molecule subtype


title: Group3-2-m_rec

source_name: Medullobalstoma Group 4


title: 786-O_JMJD6_ChIP_Rep2

source_name: 786-O cell line

tag: genotype

value: JMJD6 WT

tag: chip target

tag: sequencing batch

value: Batch 1


title: DIPGXIII-ko-c5p32-H3-1K27Mp6-Rx_H3K27me3-C


title: Vav-cre-Tcf7KO-DN1_BC_40

source_name: thymus DN1 cells (CD45+Lin-CD4-CD8-CD25-CD44+)

tag: strain/background

tag: genotype/variation

tag: tissue

tag: cell type

tag: age

value: 6~8 wks


title: Group4-35-m

tag: sample location

value: Cerebellum/Posterior Fossa,Ventricles

value: mRNA / poly(A)


title: Vav-cre-Tcf7KO-DN1_BC_42

value: Vav-cre; Tcf7fl/fl


title: MAC_3′seq_LPS 1h_rep1

tag: cell state

tag: cell line


title: MAC_3′seq_LPS 0h_rep2

value: THP-1 monocyte cells were differentiated into macrophage-like cells by PMA for 24 h, followed by treatment with LPS for 1 hour


title: BT245-ko-c2p25-H3-1WT-p6-Rx_H3K27me2

source_name: Thalamus

tag: material

tag: histone mark/factor

tag: perturbation

tag: clone or passage


title: Vav-cre-Tcf7KO-DN1_BC_43

value: thymus


title: BT245-ko-c2p25-H3-1K27M-p6-Rx_Input

value: Input


title: Vav-cre-Tcf7KO-DN1_BC_38


title: Vav-cre-Tcf7KO-DN1_BC_41


title: Group3-1-m

source_name: Medullobalstoma Group 3

tag: disease state

value: Cerebellum/Posterior Fossa

tag: medulloblastoma subgroup

tag: biospecimen id

tag: research subject id


title: MAC_3′seq_LPS 1h_rep2

tag: treatment


title: Group4-27-m

tag: molecule subtype


title: BT245-ko-c2p25-H3-1K27M-p6-Rx_H3K27me2

value: cell line


title: MAC_3′seq_LPS 0h_rep1

value: Differentiated into macrophage-like state

value: THP-1 monocyte cells were differentiated into macrophage-like cells by PMA for 24 h.


title: BT245-ko-c2p25-H3-1K27M-p6-Rx_H3K27me3-C


title: BT245-ko-c2p25-H3-1WT-p6-Rx_H3K27me3-C


title: U2OS_siRAD51_MiDAS-seq

data_processing:
The quality of sequenced reads was assessed using FastQC v. 0.10.1, www.bioinformatics.babraham.ac.uk/projects/fastqc/), fastqScreen v. 0.11.4 (PMID: 30254741), and MultiQC v. 1.7 (PMID: 27312411).
Reads were trimmed twice using cutadapt (v.1.16, DOI: https://doi.org/10.14806/ej.17.1.200) with the minimum length set to 20 bp and the adapter sequences defined as “GATCGGAAGAGCACACGTCTGAACTCCAGTCAC” and “AATGATACGGCGACCACCGAGATCTACAC”.
Filtered mapped reads were deduplicated and imported into EaSeq v. 1.2 (http://easeq.net - PMID: 26926434) for subsequent analysis and generation of wig-files.
Trimmed reads were aligned to hg38 using bowtie v. 1.1.2 (PMID: 19261174) and the settings -m 1 –S.
Sam output was converted to bam-files and filtered for alignment using Samtools v. 1.3.1 (PMID: 19505943).
Mapped reads were imported into EaSeq (Lerdrup et al., 2016), filtered for duplicate coordinates and exported as a wig-file.
Genome_build: hg38
Supplementary_files_format_and_content: Gzip compressed wig files generated using EaSeq. Scores represent fragments per kilobasepairs per million reads

source_name: U2OS osteosarcoma cell line

extract_protocol:
After fixation, the cells were permeabilized with 0.2% Triton-X in PBS, and EdU was attached to a cleavable biotin linker (Azide-PEG(3 + 3)-S-S-biotin) (Jena Biosciences, Cat. No. CLK-A2112-10) using the reagents of the Click-it Kit (Invitrogen, Cat. No. C-10424). The DNA was isolated by phenol-chloroform extraction and ethanol precipitation and then sonicated to a size of 100–500 bp. Dynabeads MyOne streptavidin C1 (Invitrogen, Cat. No. 65001) were used to isolate the EdU-labeled DNA fragments. The beads were washed three times with Binding and Washing Buffer 1× (5 mM Tris-HCl, pH 7.5, 0.5 mM EDTA, 1 M NaCl, 0.5% Tween-20) and then resuspended in twice their original volume with an equal volume of Binding and Washing Buffer 2× containing the sonicated DNA. The DNA-bead mixture was incubated 15 min at room temperature with rotation, prior to washing the beads three times with Binding and Washing Buffer 1× and once with TE buffer (10 mM Tris-HCl, pH 8.0, 10 mM EDTA). To elute the EdU-labeled DNA from the streptavidin beads, 2% β-mercaptoethanol (Sigma, Cat. No. M6250) was added for 1 h at room temperature. The eluted DNA was finally used for library preparation.
Sequencing libraries were made by the Genomics Platform of the University of Geneva using the TruSeq ChIP Sample Prep Kit (Illumina, Cat. No. IP-202-1012). Please note that previously published (PMID: 32561860) MiDAS-seq samples from U2OS cells treated with low and high doses of Aphidicolin were collected concurrently with the siRAD51 sample preparation and are accessible from the Sequence Read Archive as BioProject PRJNA588267.

treatment_protocol: Asynchronously growing U2OS cells transfected with RAD51 siRNA, at 70% confluency, were treated with 2 mM thymidine (Sigma-Aldrich, T1895) for 18 h to synchronize at the G1/S transition. G1/S synchronized cells were then washed four times with warm PBS and released into warm medium containing aphidicolin (0.4 µM) (Sigma-Aldrich, A0781) and RO3306 (9 µM) (APExBio, A8885) for 16 h to expose the cells to replication stress during S phase and arrest them into following G2 phase, respectively. Then the G2-arrested cells were washed three times with warm medium for 5 min and released for 1 h into warm medium containing 200 ng/mL nocodazole (Tocris, Cat. No. 1228) and 10 µM EdU (Thermo Fisher, A10044) to label DNA synthesis during early mitosis and subsequently arrest them in prometaphase. The nocodazole-arrested cells were then collected by mitotic shake-off and fixed with ice-cold 90% methanol overnight at −20 °C. All the treatments were performed within 48 hours of siRNA transfection. To suppress the EdU incorporation in the small proportion of cells that had not yet reached G2 phase at the time of the EdU treatment and might get detached to contaminate the shaken off mitotic cells, 2 mM hydroxyurea (Sigma-Aldrich, H8627) was also added to the cells for the last 1.5 h of the RO3306 treatment and for the entire time of the EdU and nocodazole treatment.

value: U2OS osteosarcoma cell line

value: siRAD51 knockdown


title: MAC_3′seq_LPS 2h_rep1

value: Monocyte


title: Group4-25-m

value: Medulloblastoma

value: Cerebellum/Posterior Fossa,Spinal Cord- Cervical,Spinal Cord- Lumbar/Thecal Sac,Spinal Cord- Thoracic


title: Vav-cre-Tcf7KO-DN1_BC_3

tag: strain/background

tag: genotype/variation


title: Vav-cre-Tcf7KO-DN1_BC_36

tag: tissue

tag: cell type


title: Group4-23-m

tag: sample location


title: Group4-26-m


title: MAC_TEDseq_LPS 4h_rep2

description: processed data: PASisoforms_summary_rep2.txt

data_processing:
Library strategy: TED-seq
RTA v2 software used for basecalling on NextSeq 500 and HiSeq 4000.
After poly-(A) tail trimming, the reads with the length shorter than 15 nucleotides and mean quality score below 20 were filtered out. After PCR duplicates were removed based on UMI barcode, the remaining sequences were mapped to hg38 whole genome using STAR (2.4.2a).  For spike-in genome mapping, BWA was used.
The mapped reads were represented by their 5' terminal  posistions on the same strand, and converted into BED format.
After identifying which transcript isoform a TED-seq read is derived from, we estimated poly(A) tail length by subtracting the distance between the 5' end of a TED-seq read and the cleavage and polyadenylation site of the corresponding transcript isoform from 300 nucleotides (insert size). For the transcript isoforms that have TED-seq reads more than 50 within 300 nucleotide window upstream of the cleavage and polyadenylation site, ,ean of  poly(A) tail lengths was used to represent poly(A) tail length distributions for transcripts derived from a transcript isoform.
Genome_build: hg38
Supplementary_files_format_and_content: PROseq_rep1.txt: matrix_Normalized PROseq readcounts (RPKM)
Supplementary_files_format_and_content: PROseq_rep2.txt: matrix_Normalized PROseq readcounts (RPKM)
Supplementary_files_format_and_content: peaks.txt: matrix_Identification of 3′-seq peak positions  with more than 5 CPM.
Supplementary_files_format_and_content: Readcounts_peak.txt: matrix_Normalized abundance (CPM) per the identified 3′-seq peak positions.
Supplementary_files_format_and_content: PASisoforms_summary_rep1.txt: matrix_Mean poly(A) tail length for every de novo PAS isoforms.
Supplementary_files_format_and_content: PASisoforms_summary_rep2.txt: matrix_Mean poly(A) tail length for every de novo PAS isoforms.
Supplementary_files_format_and_content: ActD_PASisoforms_summary_rep1.txt: matrix_Mean poly(A) tail length for every de novo PAS isoforms.
Supplementary_files_format_and_content: ActD_PASisoforms_summary_rep2.txt: matrix_Mean poly(A) tail length for every de novo PAS isoforms.
Supplementary_files_format_and_content: Integrated_datasets.txt: matrix_Transcription in RPKM, mRNA level in CPM, and mean poly(A) tail length for every transcript isoform for the actinomycin D-untrreated conditions.

extract_protocol:
After washing the cells with DPBS three times, total RNA was extracted by directly adding TRIzol  to the plate with the adherent cells on it. 5 million cells were used for the construction of PRO-seq libraries. For 3′-seq and TED-seq, 10 ug of total RNAs were used.
RNA libraries were prepared to be compatible with Illumina small RNA sequencing.
We prepared TED-seq libraries as described in Woo et. al. (2018) Cell Reports.

tag: cell state

value: THP-1 monocyte cells were differentiated into macrophage-like cells by PMA for 24 h, followed by treatment with LPS for 4 hour.


title: Vav-cre-Tcf7KO-DN1_BC_39

tag: age

value: 6~8 wks


title: BT245-ko-c2p25-H3-1WT-p6-Rx_Input

tag: material


title: Vav-cre-Tcf7KO-DN1_BC_37


title: Group4-24-m


title: Vav-cre-Tcf7KO-DN1_BC_34