title: WT + ConA_rep2 [O2]

source_name: WT + ConA_rep2


title: WT + DMSO_rep3 [M3]

status: Public on Jun 19 2023

type: SRA

city: Lausanne

first: Terytty Yang

last: Li

address: EPFL SV IBI-SV LISP AI 1145

country: Switzerland

institute: EPFL

library_source: transcriptomic

data_processing:
After sequencing on the BGIseq-500 platform, the raw reads were filtered. Data filtering includes removing adaptor sequences, contamination and low-quality (phred quality < 20) reads from raw reads.
Sequenced reads were mapped to the GRCm38.p6 assembly of the mouse genome using ensembl release 95 gene annotation with STAR aligner version 2.6.0a
Reads were counted using htseq-count version 0.10.0 using these flags: -f bam -r pos -s no -m union -t exon -i gene_id
Genome_build: Mus_musculus.GRCm38.95
Supplementary_files_format_and_content: xlsx file with counts per gene per sample

molecule: total RNA

organism: Mus musculus

source_name: WT + DMSO_rep3

growth_protocol: Mouse embryonic fibroblasts (MEFs) were maintained in DMEM medium containing 4.5 g glucose per liter and 10% FBS.

extract_protocol:
On the day of the extraction, 1 ml of TriPure Isolation Reagent (Cat. 11667165001, Roche) was added to each tube. RNA was then extracted by using a column-based kit from Macherey-Nagel (Cat. 740955.250).
RNA libraries were prepared for sequencing using standard BGISeq500 protocols with polyA enrichment

treatment_protocol: mouse embryonic fibroblasts (MEFs) pretreated with DMSO control or v-ATPase inhibitor Concanamycin A (ConA) (200 nM) for 1 h, and then co-treated with or without Dox (30 μg/ml) for 24 h

tag: cell type

value: MEFs

tag: genotype

value: WT

tag: treatment

value: DMSO


title: WT + ConA_rep1 [O1]

source_name: WT + ConA_rep1

value: ConA


title: WT + DMSO_rep1 [M1]

source_name: WT + DMSO_rep1


title: WT + ConA + FCCP_rep3

data_processing:
After sequencing on the BGIseq-500 platform, the raw reads were filtered. Data filtering includes removing adaptor sequences, contamination and low-quality (phred quality < 20) reads from raw reads.
Sequenced reads were mapped to the GRCm38.p6 assembly of the mouse genome using ensembl release 95 gene annotation with STAR aligner version 2.6.0a
Reads were counted using htseq-count version 0.10.0 using these flags: -f bam -r pos -s no -m union -t exon -i gene_id
Assembly: Mus_musculus.GRCm38.95
Supplementary files format and content: xlsx file with counts per gene per sample

source_name: MEFs

treatment_protocol: mouse embryonic fibroblasts (MEFs) pretreated with DMSO control or v-ATPase inhibitor Concanamycin A (ConA) (200 nM) for 1 h, and then co-treated with or without Dox (30 μg/ml), AntiA (2 μM) or FCCP (2 μM) for 24 h

value: ConA and FCCP


title: 3V_aged_NMR_epidermis

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

data_processing:
Alignment: CellRanger v3.0.2
Unique molecular identifiers (UMI) quantification: CellRanger v3.0.2
Gene annotations: Ensembl HetGla
After merging all samples on a single expression matrix containing UMI counts, it was filtered to retain only genes with UMI ≥ 1 in at least one cell.
Genome_build: HetGla_1.0
Supplementary_files_format_and_content: raw_data.csv: UMI counts per cell for each gene

organism: Heterocephalus glaber

source_name: skin

extract_protocol:
Epidermal cells from 3 young and 3 aged NMR were collected with punch biopsy devices on the backs of the animals. To preserve cell viability, skin pieces were immediately placed in PBS/BSA 3% medium on ice until dissection. Using a scalpel, the subcutaneous fat was removed from the dermis. The cleaned tissues were placed dermis side down in a sterile petri dish in a trypsin 0.25%/EDTA 1mM solution at 37°C for 1h. The enzymatic digestion was stopped by addition of PBS/FBS 10%. Epidermis was then mechanically dissociated and minced in small pieces with razor blades in PBS and then triturated. 3 rounds of washes were performed starting with 100µm filtration, 70µm and 40µm and interspersed with centrifugation cycles at 150g at 4°C for 5 minutes. Finally, the cell pellet was resuspended in PBS/BSA 3%.
Single cells were captured in droplet emulsion using the Chromium Controller (10× Genomics, Pleasanton, CA), and scRNA-seq libraries were constructed according to the 10× Genomics protocol using the Chromium Single-Cell 3′ Gel Bead and Library V2 Kit (10× Genomics, Pleasanton, CA). All reactions were performed in a C1000 Touch Thermal Cycler (Bio-Rad Laboratories, Hercules, CA) with a 96 Deep Well Reaction Module. Twelve cycles were used for cDNA amplification and sample index PCR. Amplified cDNA and final libraries were evaluated using a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA) with a high sensitivity chip. Samples were sequenced on an HiSeq 4000 instrument (Illumina, San Diego, CA).
ScRNA-seq

tag: mean age

value: 11.3 years

tag: tissue

value: epidermis

value: keratinocytes / immune cells


title: 4V_aged_NMR_epidermis


title: 5J_young_NMR_epidermis

value: 1.1 years


title: 1J_young_NMR_epidermis


title: WT + Dox_rep3 [P3]

source_name: WT + Dox_rep3

value: Dox


title: 2V_aged_NMR_epidermis


title: WT + DMSO_rep2 [M2]

source_name: WT + DMSO_rep2


title: mannitol and GlcN, 24h, whole genome

city: Ledien

first: Gilles

middle: P.

last: van Wezel

address: Sylviusweg 72

department: Institute of Biology Leiden

country: Netherlands

institute: Leiden University

library_source: genomic

data_processing:
Raw reads were cleaned by the sequencing contractor by removing adapter and low-quality sequences, leading to so-called clean reads.
These clean reads were aligned to the S. coelicolor M145 genome with GenBank accession number GCF_000203835.1 using Bowtie2 version 2.4.3
Resulting SAM files were sorted using SAMtools v1.9
MACS2 v2.2.7.1 was then used for binding peak prediction and peak modeling by comparing the chromatin- immunoprecipitated DNA sample with the corresponding whole-genome sample.
Assembly: GCF_000203835.1
Supplementary files format and content: *peaks.xls a tabular file which contains information about called peaks. Additional information includes pileup and fold enrichment
Supplementary files format and content: *.bdg bedGraph format showing coverage data

molecule: genomic DNA

organism: Streptomyces coelicolor A3(2)

source_name: mycelia

extract_protocol:
The mycelium was collected, washed in PBS, and resuspended in 0.5 mL lysis buffer (10 mM Tris-HCl [pH 8.0], 50 mM NaCl, 15 mg  mL21 lysozyme, 1 protease inhibitor; Roche, Germany) and incubated at 37°C for 20 min. After incubation, 0.5 mL IP buffer (100 mM Tris-HCl [pH 8.0], 250 mM NaCl, 0.8% [vol/vol] Triton X-100) was added to the sample, and chro- mosomal DNA was sheared to 100 to 500 bp using the Bioruptor Plus water bath sonication system (Diagenode, Liège, Belgium). After centrifugation to remove cell debris, lysates were incubated with 40 mL anti-FLAG M2 affinity gel (catalog no. A2220; Sigma-Aldrich, St. Louis, MO) suspension according to the manufacturer’s instructions and incubated at 4°C overnight. After centrifugation and washing, the pellets and 50 mL of untreated total extracts (controls) were incubated in 100 mL IP elution buffer (50 mM Tris-HCl [pH 7.5], 10 mM EDTA, 1% [w/v] SDS) at 65°C overnight to reverse cross-links. Beads were then removed by centrifugation before DNA extraction with phenol-chloroform. The DNA sample was then extracted with chloroform, and the water layer was further purified using a DNA Clean & Concentrator kit (catalog no. D4029; Zymo Research, CA).
The construction of the libraries is through the processes of end repairing, adding A to tails, purification, PCR amplification and so on.

tag: strain

value: mycelia

value: mannitol and GlcN, 24h


title: mannitol, 48h, whole genome

value: mannitol, 48h


title: mannitol and GlcN, 48h, whole genome

value: mannitol and GlcN, 48h


title: mannitol, 48h, ChIP sample


title: mannitol and GlcN, 24h, ChIP sample


title: mannitol, 24h, ChIP sample

value: mannitol, 24h


title: mannitol, 24h, whole genome


title: mannitol and GlcN, 48h, ChIP sample


title: wild type, mannitol and GlcN, 24h, sample3

data_processing:
Reads were cleaned using trimmomatic version 0.36
Reads were mapped to M145 genome (accession number GCF_000203835.1) using Bowtie2 version 2.4.3
Aligned reads were converted to sorted bam files using samtools version 1.11
Feature counts were generated using featureCounts version 2.0.1
All steps are with default parameters
Assembly: GCF_000203835.1
Supplementary files format and content: Tab dilimited files of raw counts

extract_protocol:
RNA was extracted using modified Kirby mix (Kieser et al. 2000), and purified using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra TM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: mannitol and GlcN


title: rokL6 mutant, mannitol and GlcN, 48h, sample1

value: rokL6 deletion mutant


title: rokL6 mutant, mannitol and GlcN, 24h, sample1


title: rokL6 mutant, mannitol and GlcN, 24h, sample3


title: wild type, mannitol and GlcN, 48h, sample2


title: rokL6 mutant, mannitol and GlcN, 48h, sample3


title: wild type, mannitol and GlcN, 24h, sample1


title: wild type, mannitol and GlcN, 48h, sample1


title: rokL6 mutant, mannitol and GlcN, 48h, sample2


title: rokL6 mutant, mannitol and GlcN, 24h, sample2


title: 6J_young_NMR_epidermis


title: Rat_Vehicle_06h_5

status: Public on Jun 20 2023

type: RNA

city: Liverpool

first: Ian

last: Copple

address: Ashton Street

department: Department of Pharmacology and Therapeutics

country: United Kingdom

institute: University of Liverpool

description: Gene expression data from liver of rats treated with vehicle at 6h after administration

hyb_protocol: Following fragmentation, 30 µg of cRNA were hybridized for 16h at 45°C on Affymetrix GeneChip™ Mouse Genome 430 2.0 Array or GeneChip™ Rat Genome 230 2.0 Array. GeneChips were washed and stained in an Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Quality control and low level analysis of raw fluorescence intensities was performed using the affy package (v1.64.0) in R v3.6.1. Raw data were processed using RMA normalization and a custom chip-definition file (CDF version 24 for mouse and version 19 for rat) from the BrainArray (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp) resource was used to map genes based on updated genome mappings and excludes inaccurate or wrongly annotated microarray probes to 18,180 and 13,877 genes for mouse and rat, respectively. Differential expression analyses were carried out using the limma package (v3.42.2) in R.

label: biotin

organism: Rattus norvegicus

source_name: Liver

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 µg total RNA.

extract_protocol: Frozen liver samples were homogenised in Qiazol Lysis Reagent (Qiagen), and total RNA was purified following the manufacturer’s instructions.

value: liver

value: Sprague-Dawley

tag: Sex

value: male

value: Vehicle (1% [w/v] hydroxyethylcellulose, o.g.)

tag: hours after treatment


title: Bulk 35, UC, sigmoid, male, 31

city: Barcelona

first: Azucena

last: Salas

address: Rosselló, 149-153

department: Gastroenterology

country: Spain

institute: IDIBAPS

data_processing:
Quality filtering and adapter trimming was performed using Skewer version 2.2.8
Reads were mapped against the human reference genome using the STAR aligner version 2.5.2a.
Read counts per gene were obtained using RSEM version 1.2.31 and the Ensembl GTF annotation file (EMBL-EBI, Hinxton, UK).
Assembly: The genome used was GRCh38.p10, and gene annotation was based on Gencode version 27 (EMBL-EBI, Hinxton, UK)
Supplementary files format and content: tab delimited RSEM.genes.results, include the following columns:
Supplementary files format and content: gene_id: gene id
Supplementary files format and content: transcript_id(s): transcript id
Supplementary files format and content: length: gene length
Supplementary files format and content: effective_length: the abundance-weighted mean effective length of its isoforms
Supplementary files format and content: expected_count
Supplementary files format and content: TPM: transcripts per million
Supplementary files format and content: FPKM: fragments per kilobase of transcript per million fragments mapped

organism: Homo sapiens

source_name: colon biopsy

extract_protocol:
RNA was isolated using an RNeasy Kit (QIAGEN, Hilden, Germany) according to the manufacturer’s instructions and sequenced for bulk RNA-seq.
Barcoded RNAseq libraries were prepared from total RNA using a TruSeq stranded mRNA kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. Libraries were subjected to single-end sequencing (100 bp) on a HighSeq-3000 platform (Illumina, CA, USA) at the Translational Medicine and Genomics group (Boehringer-Ingelheim GmbH & Co, Biberach, Germany).

treatment_protocol: Biopsies were placed in RNAlater RNA Stabilization Reagent (QIAGEN, Hilden, Germany) and stored at –80ºC until RNA isolation.

value: colon biopsy

tag: disease

value: UC

tag: tissue collection

value: sigmoid

tag: disease type

value: Pancolitis

tag: age

tag: publication id

value: Bulk 35

tag: batch

value: batch 2


title: rokL6 mutant, mannitol, 48h, sample3

value: mycelia

value: mannitol


title: wild type, mannitol and GlcN, 48h, sample3

value: WT


title: wild type, mannitol, 48h, sample3


title: wild type, mannitol, 48h, sample2


title: rokL6 mutant, mannitol, 48h, sample1


title: rokL6 mutant, mannitol, 48h, sample2


title: Rat_Vehicle_03h_5

description: Gene expression data from liver of rats treated with vehicle at 3h after administration


title: NL72

city: Tokyo

first: Y-H.

last: Taguchi

state: Non-US/Canada

address: 1-13-27 Kasuga,Bukyo-ku

department: Physics

country: Japan

institute: Chuo University

data_processing:
raw data was converted to fasta file at http://weizhong-lab.ucsd.edu/metagenomic-analysis/server/fastq2fasta/. Obtained fasta file was processed with miRDeep* v3.1  with using h19 genome and miRBase v19
Genome_build: h19
Supplementary_files_format_and_content: miRDeep* result file

extract_protocol:
Total RNA from 200 ul of serum was prepared using miRNeasy mini kit (Qiagen, Hilden Germany) according to the manufacturer’s instruction. Exosome rich fractionated RNA was prepared using Exoquick (System Biosciences, CA, USA). Briefly, 900 ul of serum was mixed with 250 ul of Exoquick and incubated for 12 hr at 4℃. The tubes were centrifuged at 1500 g for 30 min at room temperature and then supernatant was discarded. The pellet was dissolved with 200 ul of PBS with vigorous vortex. RNA was extracted using miRNeasy mini kit (Qiagen).
1) Filter Small RNA Separate RNA segment of different size by PAGE gel,　select 18-30nt stripe and recycle. 2) Adaptor ligation Prepare connection system，blend and centrifuge，connect warmly for a period of time. 3) RT-PCR Prepare reverse transcription system，connect warmly for a period on PCR instrument，then PCR amplification. 4) Purify PCR products: Recover the Purified PCR construct by PAGE gel, dissolve the recycled products in EB solution. Finally, label to finish the library construction. 5) Purify PCR products: Use Agilent 2100 Bio-analyzer and the ABI StepOnePlus Real-Time PCR System to test quality and production of the prepared library.

treatment_protocol: Peripheral blood was collected from all subjects directly into serum tubes before anti-viral treatment. The tubes were centrifuged at 1,500 g for 10 min at 4℃, sera were aliquoted and additionally centrifuged at 2,000 g to completely remove any remaining cells. Sera were stored at -80℃ until use.

tag: disease state

value: normal

value: peripheral blood

tag: gender

value: female

tag: date

tag: height

tag: weight

tag: bmi

tag: hbsag

tag: anti-hcv

tag: afp

value: NT

tag: dcp

tag: cea

tag: ast

tag: alt

tag: wbc

tag: plt

tag: t-bil

tag: alp

tag: cgtp

tag: hb

tag: alb

tag: bs

tag: tg

tag: t-chol

tag: hbalc


title: rokL6 mutant, mannitol, 24h, sample1

tag: strain

tag: cell type

tag: genotype

value: rokL6 deletion mutant

tag: treatment


title: wild type, mannitol and GlcN, 24h, sample2

value: mannitol and GlcN


title: rokL6 mutant, mannitol, 24h, sample3


title: wild type, mannitol, 48h, sample1


title: rokL6 mutant, mannitol, 24h, sample2


title: wild type, mannitol, 24h, sample1


title: wild type, mannitol, 24h, sample3


title: Arabidopsis cold mRNA-seq rep3

city: Fuzhou

first: mao

last: fei

state: Fujian

address: Shangxiadianlu NO.15

department: National Engineering Research Center of JUNCAO

country: China

institute: Fujian Agriculture and Forestry University

data_processing:
The reads of raw data were trimmed according to adapt sequence using cutadapt (v1.1) . then the clean data were mapped to Arabidopsis genome (TAIR10) using bowtie, the parameter of maximum insert size was reset to 1000. Only unique reads were used to detect 6mA enrichment region by SCIER (v1.1) (using parameters redundancy threshold = 1 window size (bp) = 200 fragment size = 100 effective genome fraction = 0.74 gap size (bp) = 200 FDR = 0.01). Overlapping peaks (at least 1 bp overlap) between 2 biological replicates of a sample were retained for next analyses. DESeq2 (1.24.0) [41] was used to compare all 6mA region from normal and cold stress with the consideration of sample variation. Differential regions with p value < 0.05 (false discovery rate<0.05) were considered significant (DMRs)
The sequencing data were mapped to the Arabidopsis genome with matching annotation by tophat (v2.1.1)]using default parameters. The expression value (FPKM) of each gene were calculated with cufflinks (v2.1.1). And cuffdiff (v2.1.1) was used to calculate the fold change of gene expression and FDR. Differential expression genes (DEGs) with false discovery rate < 0.05 were considered significant.
Assembly: Arabidopsis genome (TAIR10)  Rice (Tigr7)
Supplementary files format and content: Processed data were stored in bigWig files and xlsx files.

organism: Arabidopsis

source_name: leaves

growth_protocol: Arabidopsis thaliana Col-0 was grown in a growth chamber at 22℃ under long day conditions (16 h light/8 h dark) with a light intensity of 100 µmol m-2 sec-1.Rice was grown in a growth chamber at 28°C under long-day conditions (16 h light/8 h dark) with a light intensity of 200 µmol m-2 sec-1 for 2 weeks.

extract_protocol:
gDNA of Arabidopsis and rice were extracted by using a DNAsecure Plant Kit (TIANGEN, Cat. DP320-03) according to its procedures. Isolated gDNA was sonicated into 200-400 bp with Biorupter UCD-600, followed by end repair, 3′-adenylation, and adaptor ligation according to NEB Next Ultra Ⅱ DNA Library Prep Kit for Illumina (E764S, NEB). The ligated DNA was denatured at 95°C for 10 min and chilled on ice for 10 min. 10 µl of denatured DNA was saved as input. 1µg DNA was incubated with 3 µg of anti-m6A antibody (202-003, Synaptic Systems) at 4°C for 6 h in 1×IP buffer (10 mM Tris-HCl PH 7.4, 150 mM NaCl, 0.1% IGEPAL CA-630). Dynabeads Protein A (10001D, Invitrogen) was washed twice with 1×IP buffer and pre-blocked in 0.5 ml 1×IP buffer with 20 µg/µl BSA for 2 h at 4°C. After pre-blocked beads were washed twice with 1×IP buffer, the DNA-antibody mixture was added to beads, rotating overnight at 4°C. The beads were washed 4 times with 1×IP buffer. Methylated DNA was eluted twice by 100 ml elution buffer containing N6-methyladenosine 5’-monophosphatesodium salt (M2780, Sigma) at 4°C for 1 h. Eluted DNA was combined, then added to 20ml of 3 M NaOAc (PH 5.3), 500 ml ethanol, and 0.5 ml glycogen. The mixture was frozen at -80°C overnight, and centrifuged. The precipitated DNA was dissolved in 20 ml ddH2O, followed by 8-10 cycles PCR amplification. The PCR product was purified by VAHTS DNA clean beads (N411-01, Vazyme). Sequencing was conducted by the Illumina NovaSeq6000 platform with 150-bp paired-end reads at Jiangbei New Area Biopharmaceutical Public Service Platform Co., Ltd. (Nanjing, China).
RNA-seq and 6mA-IP-seq

treatment_protocol: In arabidopsis, 3-week-old plants were transfer to 4℃ for 24 h. In rice, 2-week-old seedlings were transferred to 4°C for 6 days.

tag: tissue

value: leaves


title: Arabidopsis cold mRNA-seq rep2


title: Arabidopsis normal mRNA-seq rep2

value: CK


title: Arabidopsis cold mRNA-seq rep1


title: Arabidopsis normal mRNA-seq rep3


title: male healthy control, recovery, replicate 14

city: Fort Lauderdale

first: Lubov

last: Nathanson

state: Florida

address: 3321 College Ave.

department: INIM

country: USA

institute: Nova Southeastern University

data_processing:
Raw reads were mapped to the reference human genome (GRCh38, release 86) using GSNAP, HISAT2, and STAR software.
For the analysis of differentially expressed known genes, reads for each gene aligned by GSNAP and HISAT2 were counted using HTSeq software. Alignment by STAR was run with the option “quantMode TranscriptomeSAM” that allowed for the counting of reads aligned to each gene.
Raw counts from HTSeq and STAR were imported into Bioconductor/R package DESeq2, normalized, and tested for differential gene expression. We used the Bioconductor/R package DEXSeq to count individual exons and compare expression of exons. This analysis was done separately for the files produced by each aligner.
Only genes with raw counts equal or more than 50 in all samples in at least one group were used for the differential gene expression analysis
For further analysis, we selected genes and exons that were differentially expressed based on one of the following two criteria: (a) either a fold change (FC) > |1.5| and false discovery rate (FDR) < 0.10 in one out of the three aligners and FC > |1.4| and FDR < 0.15 in the remaining two aligners, OR (b) a FC > |1.5| and FDR < 0.10 in two out of three aligners.
Assembly: GRCh38, release 86
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample, where only genes that had raw counts equal or more than 50 in all samples in at least one group

source_name: peripheral blood mononuclear cells

extract_protocol:
Total RNA was extracted using RNAzol (Molecular Research Center) according to the manufacturer’s instructions. RNA quality was assessed using Agilent TapeStation 4200 (Agilent Technologies). All RNA samples had an RNA Integrity number (RIN) above seven.
The libraries were generated using Illumina TruSeq Stranded Total RNA Library Prep Kit

value: peripheral blood mononuclear cells

tag: disease state

value: healthy control

tag: time point in exercise

value: T2 (recovery)

tag: Sex

value: male


title: male healthy control, recovery, replicate 9


title: male healthy control, recovery, replicate 8


title: male healthy control, recovery, replicate 12


title: male healthy control, recovery, replicate 13


title: Arabidopsis normal mRNA-seq rep1


title: male healthy control, recovery, replicate 10


title: male healthy control, recovery, replicate 11


title: male healthy control, maximal exertion, replicate 14

value: T1 (maximal exertion)


title: male healthy control, recovery, replicate 7


title: male healthy control, recovery, replicate 6


title: male healthy control, maximal exertion, replicate 12


title: male healthy control, maximal exertion, replicate 10


title: male healthy control, maximal exertion, replicate 11


title: male healthy control, maximal exertion, replicate 13


title: wild type, mannitol, 24h, sample2


title: male healthy control, maximal exertion, replicate 9


title: male healthy control, maximal exertion, replicate 8


title: male healthy control, maximal exertion, replicate 7


title: male healthy control, baseline, replicate 8

value: T0 (baseline)


title: male healthy control, baseline, replicate 7


title: male healthy control, baseline, replicate 10


title: male healthy control, maximal exertion, replicate 6


title: male healthy control, baseline, replicate 9


title: male healthy control, baseline, replicate 6


title: male healthy control, baseline, replicate 3


title: male healthy control, baseline, replicate 4


title: male healthy control, baseline, replicate 2


title: female ME/CFS patient, recovery, replicate 12

value: ME/CFS patient


title: female ME/CFS patient, recovery, replicate 14


title: female ME/CFS patient, recovery, replicate 15


title: female ME/CFS patient, recovery, replicate 17


title: female ME/CFS patient, recovery, replicate 16


title: female ME/CFS patient, recovery, replicate 18


title: female ME/CFS patient, recovery, replicate 8


title: female ME/CFS patient, recovery, replicate 9


title: female ME/CFS patient, recovery, replicate 10


title: female ME/CFS patient, recovery, replicate 6


title: female ME/CFS patient, recovery, replicate 5


title: female ME/CFS patient, recovery, replicate 4


title: female ME/CFS patient, recovery, replicate 13


title: female ME/CFS patient, recovery, replicate 1


title: female ME/CFS patient, recovery, replicate 2


title: female ME/CFS patient, maximal exertion, replicate 18


title: female ME/CFS patient, maximal exertion, replicate 17


title: male healthy control, baseline, replicate 5


title: female ME/CFS patient, maximal exertion, replicate 15


title: female ME/CFS patient, maximal exertion, replicate 13


title: female ME/CFS patient, maximal exertion, replicate 14


title: female ME/CFS patient, maximal exertion, replicate 16


title: female ME/CFS patient, maximal exertion, replicate 19


title: female ME/CFS patient, maximal exertion, replicate 12


title: female ME/CFS patient, recovery, replicate 7


title: female ME/CFS patient, maximal exertion, replicate 11


title: female ME/CFS patient, recovery, replicate 11


title: female ME/CFS patient, maximal exertion, replicate 10


title: female ME/CFS patient, maximal exertion, replicate 8


title: female ME/CFS patient, maximal exertion, replicate 9


title: female ME/CFS patient, maximal exertion, replicate 6


title: female ME/CFS patient, maximal exertion, replicate 7


title: female ME/CFS patient, maximal exertion, replicate 5


title: female ME/CFS patient, maximal exertion, replicate 4


title: female ME/CFS patient, maximal exertion, replicate 2


title: female ME/CFS patient, maximal exertion, replicate 20


title: female ME/CFS patient, recovery, replicate 3


title: female ME/CFS patient, baseline, replicate 19


title: female ME/CFS patient, baseline, replicate 17


title: female ME/CFS patient, baseline, replicate 16


title: female ME/CFS patient, maximal exertion, replicate 1


title: female ME/CFS patient, maximal exertion, replicate 3


title: female ME/CFS patient, baseline, replicate 14


title: female ME/CFS patient, baseline, replicate 15


title: female ME/CFS patient, baseline, replicate 11


title: female ME/CFS patient, baseline, replicate 12


title: female ME/CFS patient, baseline, replicate 13


title: female ME/CFS patient, baseline, replicate 9


title: female ME/CFS patient, baseline, replicate 7


title: female ME/CFS patient, baseline, replicate 8


title: female ME/CFS patient, baseline, replicate 18


title: female ME/CFS patient, baseline, replicate 6


title: female ME/CFS patient, baseline, replicate 2


title: female ME/CFS patient, baseline, replicate 4


title: female ME/CFS patient, baseline, replicate 3


title: female healthy control, recovery, replicate 19


title: female ME/CFS patient, baseline, replicate 1


title: female healthy control, recovery, replicate 18


title: female ME/CFS patient, baseline, replicate 10


title: female healthy control, recovery, replicate 17


title: female healthy control, recovery, replicate 16


title: female healthy control, recovery, replicate 12


title: female ME/CFS patient, baseline, replicate 5


title: female healthy control, recovery, replicate 15


title: female healthy control, recovery, replicate 14


title: female healthy control, recovery, replicate 13


title: female healthy control, recovery, replicate 11


title: female healthy control, recovery, replicate 10


title: N_PA20

type: genomic

city: Sao Paulo

first: Fabio

middle: Albuquerque

last: Marchi

address: Av Dr Arnaldo

department: CTO

country: Brazil

institute: ICESP

description:
Surrounding non-malignant tissue
Surrounding non-malignant tissue

hyb_protocol: This step of the methodology follow manufacturer's instructions

scan_protocol: The array images were acquired using the Scan Control (version 8.1) software program (Agilent Technologies, CA, USA).  Images were quantified using Agilent Feature Extraction Software version v.10.1.1.1 (Agilent Technologies, CA, USA)

data_processing: Agilent Feature Extraction Software (v. 10.1.1.1) was used for background subtraction and LOWESS normalization.

source_name: Surrounding non-malignant tissue

extract_protocol: DNA from frozen penile tissue was isolated using the DNeasy Blood & Tissue Kit (Qiagen, Valencia, CA, USA)

tag: hpv

value: no

value: Surrounding non-malignant tissue

source_name: pool of five normal glans obtained from necropsies

tag: sample type

value: reference


title: N_PE15

label_protocol: This step of the methodology follow manufacturer's instructions


title: N_PE4


title: female healthy control, recovery, replicate 8


title: N_PE18


title: N_PE2


title: N_PA6


title: female healthy control, recovery, replicate 7


title: N_PA29


title: female healthy control, recovery, replicate 6


title: T_PA13

description:
Penile tumor tissue
Penile tumor tissue

source_name: Penile tumor tissue

value: squamous cell carcinoma


title: T_PA5

description:
Penile tumor tissue
Penile tumor tissue

value: yes


title: N_PA13


title: T_PA12

description:
Penile tumor tissue
Penile tumor tissue


title: N_PA17


title: female healthy control, recovery, replicate 4

value: female


title: female healthy control, recovery, replicate 3


title: female healthy control, recovery, replicate 5


title: T_PA6

description:
Penile tumor tissue
Penile tumor tissue


title: T_PE1

description:
Penile tumor tissue
Penile tumor tissue


title: T_PA10

description:
Penile tumor tissue
Penile tumor tissue


title: T_PE4

description:
Penile tumor tissue
Penile tumor tissue


title: N_PA10


title: female healthy control, recovery, replicate 1


title: T_PA17

description:
Penile tumor tissue
Penile tumor tissue


title: female healthy control, recovery, replicate 9


title: T_PE9

description:
Penile tumor tissue
Penile tumor tissue


title: T_PA19

description:
Penile tumor tissue
Penile tumor tissue


title: female healthy control, recovery, replicate 2


title: T_PA7

description:
Penile tumor tissue
Penile tumor tissue


title: female healthy control, maximal exertion, replicate 20


title: female healthy control, maximal exertion, replicate 18


title: T_PA20

description:
Penile tumor tissue
Penile tumor tissue


title: female healthy control, maximal exertion, replicate 17


title: T_PE10

description:
Penile tumor tissue
Penile tumor tissue


title: female healthy control, maximal exertion, replicate 16


title: female healthy control, maximal exertion, replicate 15


title: T_PE2

description:
Penile tumor tissue
Penile tumor tissue


title: female healthy control, maximal exertion, replicate 14


title: T_PE15

description:
Penile tumor tissue
Penile tumor tissue


title: T_PE12

description:
Penile tumor tissue
Penile tumor tissue


title: female healthy control, maximal exertion, replicate 13


title: female healthy control, maximal exertion, replicate 12


title: TFAP2C control_1

city: Kansas City

first: Boryana

last: Koseva

state: MO

address: 2420 Pershing Road

department: CMRI

institute: Children's Mercy Hospital

data_processing:
Raw FASTQ files were trimmed using default parameters (-r 0.1 -d 0.03) in Skewer (Version 0.2.2), and reads shorter than 18 bp were discarded.
Transcripts were quantified using Kallisto (Version 0.46.2).
Differentially expressed genes at FDR of 0.05 were discovered using the Bioconductor package DESeq2 in R (Version 1.32.0)

growth_protocol: Human TS cells (Okae et al. 2018) were cultured in 100 mm tissue culture dishes coated with 5 μg/mL collagen IV (CB40233, Thermo-Fisher, Waltham, MA). Human TS cells were maintained in Complete human TS cell medium [DMEM/F12 (11320033, Thermo-Fisher), 100 μm 2-mercaptoethanol, 0.2% (vol/vol) fetal bovine serum (FBS), 50 μM penicillin, 50 U/mL streptomycin, 0.3% bovine serum albumin (BP9704100, Thermo-Fisher), 1% Insulin-Transferrin-Selenium-Ethanolamine solution (vol/vol, Thermo-Fisher)], 1.5 μg/mL L-ascorbic acid (A8960, Sigma-Aldrich, St. Louis, MO), 50 ng/mL epidermal growth factor (EGF, E9644, Sigma-Aldrich), 2 μM CHIR99021 (04-0004, Reprocell, Beltsville, MD), 0.5 μM A83-01 (04-0014, Reprocell), 1 μM SB431542 (04-0010, Reprocell), 0.8 mM valproic acid (P4543, Sigma-Aldrich), and 5 μM Y27632 (04-0012-02, Reprocell). EVT cell differentiation was induced by plating human TS cells onto 6-well plates pre-coated with 1 μg/mL collagen IV at a density of 80,000 cells per well. Cells were cultured in EVT Differentiation Medium [DMEM/F12 (11320033, Thermo-Fisher), 100 μm 2-mercaptoethanol, 0.2% (vol/vol) FBS, 50 μM penicillin, 50 U/mL streptomycin, 0.3% bovine serum albumin (BP9704100, Thermo-Fisher), 1% Insulin-Transferrin-Selenium-Ethanolamine solution (vol/vol, Thermo-Fisher)], 100 ng/mL of neuregulin 1 (NRG1, 5218SC, Cell Signaling, Danvers, MA), 7.5 μM A83-01 (04-0014, Reprocell, Beltsville, MD), 2.5 μM Y27632 (04-0012, Reprocell), 4% KnockOut Serum Replacement (KSR, 10828028, Thermo-Fisher), and 2% Matrigel® (CB-40234, Thermo-Fisher). On day 3 of EVT cell differentiation, the medium was replaced with EVT Differentiation Medium excluding NRG1 and with a reduced Matrigel® concentration of 0.5%. On culture day 6 of EVT cell differentiation, the medium was replaced with EVT Differentiation Medium excluding NRG1 and KSR, and with a Matrigel concentration of 0.5%. Cells were analyzed on day 8 of EVT cell differentiation.

extract_protocol:
Total RNA was isolated from cells and tissues using TRIzolreagent (cat no. 15596018, Thermo Fisher, Waltham, MA).
The Stranded mRNA-Seq was performed using the Illumina NovaSeq 6000 Sequencing Systemat the University of Kansas Medical Center –Genomics Core (Kansas City, KS). Quality control on RNA submissions was completed using the Agilent TapeStation 4200 using the RNA ScreenTape Assay kit (Agilent Technologies 5067-5576). Total RNA (1ug) was used toinitiatethe library preparation protocol.The total RNA fraction was processed by oligo dT bead capture of mRNA, fragmentation, reverse transcriptioninto cDNA, end repair of cDNA, ligation withthe appropriate Unique Dual Index (UDI) adaptors, strand selection and library amplification by PCR using the Universal Plus mRNA-seq with NuQuant library preparation kit (Tecan Genomics 0520-A01).Library validation was performed using the D1000 ScreenTape Assay kit (Agilent Technologies 5067-5582) on theAgilent TapeStation 4200. Concentration of each library was determined with the NuQuant module of the library prep kit using a Qubit 4 Fluorometer (ThermoFisher/Invitrogen),Libraries were pooled based on equal molar amounts and the multiplexed pool was quantitated, in triplicate, using the Roche Lightcycler96 withFastStart Essential DNA Green Master (Roche 06402712001) and KAPA Library Quant (Illumina) DNA Standards 1-6 (KAPA Biosystems KK4903). Using the qPCR results, theRNA-Seq library pool was adjusted to 2.125nM for multiplexed sequencing.Pooled libraries were denatured with 0.2N NaOH (0.04N final concentration) and neutralized with 400mM Tris-HCl pH 8.0. A dilution of the pooled libraries to 425 pM is performed in the sample tube, on instrument, followed by onboard clonal clustering of the patterned flow cell using the NovaSeq 6000 S1 Reagent Kit (200 cycle) (Illumina 20012864). A 2x101 cycle sequencing profile with dual index reads is completed using the following sequence profile: Read 1 – 101 cycles x Index Read 1 – 8 cycles x Index Read 2 – 8 cycles x Read 2 – 101 cycles. Following collection, sequence data is converted from .bcl file format to fastq file format using bcl2fastq software and de-multiplexed into individual sequences for data distribution using a secure FTP site or Illumina BaseSpace for further downstream analysis.

treatment_protocol: Lentivirus-mediated shRNA delivery was used as a tool to test the biological roles for TFAP2C, EPAS1, SNAI1, DLX5, and DLX6 in human TS cells. Several shRNAs designed for each target were subcloned into pLKO.1 and their efficacy tested by RT-qPCR and western blotting. An shRNA which does not recognize any known mammalian gene, pLKO.1-shSCR (Plasmid 1864) was used as a control (Addgene, Cambridge, MA). Construct design, lentivirus production, and lentiviral transduction were performed as previously described (Varberg et al. 2021).

tag: source

value: human trophoblast stem cells

tag: cell line

value: stem state trophoblast cell

value: Control shRNA lentiviral transduction and puromycin selection


title: TFAP2C control_2


title: female healthy control, maximal exertion, replicate 11


title: TFAP2C control_3


title: TFAP2C knockdown_3

value: TFAP2C-specific shRNA lentiviral transduction and puromycin selection


title: TFAP2C knockdown_2


title: TFAP2C knockdown_1


title: female healthy control, maximal exertion, replicate 10

value: peripheral blood mononuclear cells


title: T_PE16

description:
Penile tumor tissue
Penile tumor tissue


title: T_PE11

description:
Penile tumor tissue
Penile tumor tissue


title: female healthy control, maximal exertion, replicate 8

value: healthy control


title: T_PE18

description:
Penile tumor tissue
Penile tumor tissue


title: T_PE19

description:
Penile tumor tissue
Penile tumor tissue


title: female healthy control, maximal exertion, replicate 9


title: T_PE23

description:
Penile tumor tissue
Penile tumor tissue


title: female healthy control, maximal exertion, replicate 6


title: female healthy control, maximal exertion, replicate 7


title: SNAI1_knockdown_1

value: extravillous trophoblast cell

value: SNAI1-specific shRNA lentiviral transduction and puromycin selection


title: SNAI1_knockdown_3


title: SNAI1_knockdown_2


title: SNAI1_control_3


title: female healthy control, maximal exertion, replicate 5

value: T1 (maximal exertion)


title: SNAI1_control_2


title: SNAI1_control_1


title: female healthy control, maximal exertion, replicate 3


title: T_PE21

description:
Penile tumor tissue
Penile tumor tissue


title: female healthy control, maximal exertion, replicate 4


title: T_PL1

description:
Penile tumor tissue
Penile tumor tissue


title: female healthy control, maximal exertion, replicate 2


title: T_PL2

description:
Penile tumor tissue
Penile tumor tissue


title: EPAS1 control_2


title: EPAS1 control_3


title: EPAS1 control_1


title: female healthy control, baseline, replicate 19

value: T0 (baseline)


title: EPAS1 knockdown_2

value: EPAS1-specific shRNA lentiviral transduction and puromycin selection


title: EPAS1 knockdown_1


title: female healthy control, baseline, replicate 17


title: female healthy control, baseline, replicate 18


title: female healthy control, baseline, replicate 16


title: female healthy control, baseline, replicate 15


title: LM07T scRNA-seq

city: Guangzhou

first: Guopei

last: Zhang

address: 58 Zhongshan Road 2

institute: Sun Yat-sen University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Cell Ranger (v5.0, 10x Genomics) was used to align reads to the human reference genome (hg38).
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Liver cancer

extract_protocol:
After surgical resection, fresh tissues were collected rapidly, washed by cold PBS, transferred immediately to pre-chilled MACS Tissue Storage Solution (Miltenyi Biotec) and transported rapidly to the lab on ice prior to processing. Samples (no fat, fibrous or necrotic areas) were transferred to a 6-cm dish, minced into small pieces (~1mm3) using a scalpel and washed by cold PBS three times. Then tissues allocated for dissociation were transferred into gentleMACS C tubes (Miltenyi Biotec), each containing 4.7 mL RPMI-1640 medium supplemented with 200 µL of Enzyme H, 100 µL of Enzyme R and 25 µL of Enzyme A (Miltenyi Biotec, Human Tumor Dissociation kit). Then tissue pieces in the C tubes were digested using the gentleMACS Dissociator (Miltenyi Biotec) following the default gentleMACS program according to tumor type (HCC-P: 37C_Multi_B; HCC-T: 37h_h_TDK_3; CRLM: 37h_h_TDK_1).
Single-cell 5’ cDNA libraries and BCR VDJ libraries were constructed using 10x Genomics Chromium Single Cell 5’ V(D)J Reagnet Kit (V2 chemistry, 10x Genomics) following the 10x Genomics supplied protocol. Single cell RNA and BCR V(D)J libraries were sequenced on Illumina Novaseq platform.

value: Liver cancer

value: Immune cells


title: T_PL3

description:
Penile tumor tissue
Penile tumor tissue

value: reference


title: female healthy control, maximal exertion, replicate 19


title: LM06T scRNA-seq

description: 10x Genomics


title: LM05T scRNA-seq

description: 10x Genomics


title: EPAS1 knockdown_3


title: female healthy control, baseline, replicate 13


title: LM04T scRNA-seq

description: 10x Genomics


title: female healthy control, baseline, replicate 14


title: LM03T2 scRNA-seq

description: 10x Genomics


title: female healthy control, baseline, replicate 12


title: female healthy control, baseline, replicate 11


title: female healthy control, baseline, replicate 10


title: LM02T2 scRNA-seq

description: 10x Genomics


title: female healthy control, baseline, replicate 9


title: LM01T scRNA-seq

description: 10x Genomics


title: LM02T1 scRNA-seq

description:
10x Genomics
LM02T1_matrix.mtx


title: female healthy control, baseline, replicate 8


title: HCC10T scRNA-seq

description: 10x Genomics


title: female healthy control, baseline, replicate 6


title: female healthy control, baseline, replicate 7


title: HCC09T scRNA-seq

description: 10x Genomics


title: HCC09P scRNA-seq

description: 10x Genomics

value: Liver


title: female healthy control, baseline, replicate 3


title: Rice cold 6mA IP rep1

organism: Oryza sativa

value: leaves

value: 4C 6d


title: Rice cold 6mA IP rep2


title: female healthy control, baseline, replicate 4

value: female


title: HCC08T scRNA-seq

description: 10x Genomics


title: Rice normal 6mA IP rep1

value: CK


title: Rice normal Input


title: Rice normal 6mA IP rep2


title: LM03T1 scRNA-seq

description: 10x Genomics


title: female healthy control, baseline, replicate 2


title: HCC08P scRNA-seq

description: 10x Genomics


title: rli2 RNAi seedlings #12, rep2

city: Shanghai

first: Shi-Xia

last: Yu

address: Dongchuan Road, Shanghai Minhang District No. 800

institute: Shanghai Jiaotong University

data_processing:
The quality-filtered reads were mapped to the Arabidopsis Information Resource (TAIR10) version of the Arabidopsis genome by Hisat2 open-source software
StringTie calculates the FPKM value of each gene/transcript in the sample based on the comparison result of the Hisat2 software, and uses this value as the expression level of the gene/transcript in the sample
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files include RPKM values for all Sample

organism: Arabidopsis thaliana

source_name: Seedling

growth_protocol: For growth on plates, surface-sterilized Arabidopsis seeds were placed on half-strength Murashige and Skoog (MS) basal medium. Plates were kept at 4 °C for 3 days, then transferred to a growth chamber (Percival, Boone, IA, USA) with a 16-h-light/8-h-dark photoperiod at 22 °C for 7 days.

extract_protocol:
RNA was harvested using Plant RNA Purification Reagent (Invitrogen). 1.5 ug of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were prepared with the TruSeqTM RNA Sample Preparation Kit (Illumina)

value: Seedling

value: RLI2 knockdown #12


title: rli2 RNAi seedlings #12, rep1


title: female healthy control, baseline, replicate 1

value: peripheral blood mononuclear cells


title: rli2 RNAi seedlings #5, rep2

value: RLI2 knockdown #5


title: rli2 RNAi seedlings #12, rep3


title: HCC07T scRNA-seq

description: 10x Genomics


title: female healthy control, baseline, replicate 5

value: healthy control


title: FLAG-RBM39 rescue rep 3

city: London

first: Marc-David

last: Ruepp

address: 5 Cutcombe Road

department: Dementia Research Institute

institute: King's College

data_processing:
Mapping to human genome GRCh38 using STAR aligner version 2.5.2a
Gene level counts were computed with the featureCounts program of he Subread package (version 1.4.6)
Differential gene expression analysis using DESeq2 with default options
Alternative exon usage was analysed using DEXseq. Ensembl isoforms were filtered for main transcripts as classified in APRIS database.
Intron retention was quantified with custom python scripts based on PySam package.
Assembly: GRCh38
Supplementary files format and content: Xlsx files with log2-fold changes and adjusted p-values from DESEq2, DEX-Seq and Intron retention analyses.

molecule: polyA RNA

source_name: Cervix cancer

growth_protocol: HeLa cells were grown in DMEM/F-12 supplemented with 10% FBS, penicillin (100 IU/ml) and streptomycin (100 μg/ml)  at 37°C and 5% CO2.

extract_protocol:
Cells were dissolved in TriReagent and RNA was isolated by acidic phenol chloroform extraction.
Libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit

treatment_protocol: HeLa cells were seeded in 6-well plates and transfected on day 2 and 4 with 120 pmoles siRNA using lipofectamine2000. 300 ng FLAG-RBM39 expression plasmid was included in the rescue condition. Cells were harvested on day 5.

value: HeLa

value: RBM39 siRNA + FLAG-RBM39 overexpression


title: col-0 seedlings, rep3

value: WT


title: rli2 RNAi seedlings #5, rep1


title: col-0 seedlings, rep2


title: HCC06T scRNA-seq

description: 10x Genomics


title: FLAG-RBM39 rescue rep 2


title: HCC10P scRNA-seq

description: 10x Genomics


title: col-0 seedlings, rep1


title: FLAG-RBM39 rescue rep 1


title: HCC05T scRNA-seq

description: 10x Genomics


title: RBM39 KD rep 2

value: RBM39 siRNA


title: HCC05P scRNA-seq

description: 10x Genomics


title: RBM39 KD rep 1


title: HCC06P scRNA-seq

description: 10x Genomics


title: Enzalutamide 20uM 8hr rep3

city: Ann Arbor

first: Arul

middle: M.

last: Chinnaiyan

state: MICHIGAN

address: 1500 E. Medical Center Dr

institute: University of Michigan

data_processing:
Transcripts were quantified by kallisto with human reference genome (hg38) and then summarized to obtain gene level counts and TPM.
Assembly: hg38

source_name: Prostate

extract_protocol:
RNA was extracted from LNCaP cells treated with DMSO, 20 µM proxalutamide, or enzalutamide for 8 hours using Qiagen RNA extraction kit. RNA quality was determined using a Bioanalyzer RNA Nano Chip
Poly-A selection was performed with Sera-Mag Oligo(dT)-Coated Magnetic Particles (38152103010150; GE Healthcare Life Sciences), and libraries were generated using a KAPA RNA HyperPrep kit (KK8541; Roche Sequencing Solutions).

value: Prostate

value: LNCaP

value: Prostate luminal cell

value: Enzalutamide


title: Proxalutamide 20uM 8hr rep1

value: Proxalutamide


title: Enzalutamide 20uM 8hr rep1


title: Proxalutamide 20uM 8hr rep3


title: HCC04T scRNA-seq

description: 10x Genomics

value: Liver cancer

value: Immune cells


title: Enzalutamide 20uM 8hr rep2


title: Control rep1

value: Control


title: Proxalutamide 20uM 8hr rep2


title: Control rep3


title: Ctrl KD rep 3

value: Ctrl siRNA


title: HCC07P scRNA-seq

description: 10x Genomics

value: Liver


title: embryo, day-2, SSM, rep14

city: DIJON

first: Bastien

last: Ducreux

address: Batiment B3, 15 boulevard Maréchal de Lattre de Tassigny

institute: Inserm U1231

data_processing:
We computed sequencing quality checks with FastQC v0.11.9 and trimming of adapters and low-quality sequences using TrimGalore! v0.6.6. Paired-end reads alignment was performed onto Human reference genome (hg38) with STAR v2.7.9a 86 reporting randomly one position, allowing 6% of mismatches. As recommended in Teissandier et al. 87 repeat annotation was downloaded from RepeatMasker and joined with basic gene annotation from Gencode v19. The merged file was used as input for quantification with featureCounts v2.0.1. Genes with a minimum of count per million (cpm) > 1 in at least 4 samples were retained for further analysis. Principal component analyses were implemented with PCAtools v2.8.0 on log2(cpm+1) of all genes for single datasets and common genes for multiple datasets, excepting the lowest 10% genes based on variance. Differential expression analysis was performed using edgeR’s normalization (v3.38.1) combined with voom transformation from limma package v3.52.1.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: embryo

extract_protocol:
Free-zona pellucida embryo (after using acidic Tyrode’s solution) was individually placed in a lysis buffer containing MgCl2 (4379878, Applied Biosystems), DTT, Nonidet P-40 (11332473001, Roche), SUPERase-In (AM2694, Ambion) and RNase-inhibitor (AM2682, Ambion). Then, we performed a reverse transcription reaction (SuperScript III reverse transcriptase - 18080-044, Invitrogen) and a poly(A) tailing to the 3’ end of the first-strand cDNA (by using terminal deoxynucleotidyl transferase - 10533-073, Invitrogen). After the second-strand cDNA synthesis, 20 and 18 cycles (at day-2 and day-5, respectively) of PCR were performed to amplify the embryo cDNA using the TaKaRa ExTaq HS (TAKRR006B, Takara) and IS PCR primer (IDT). Following purification with Zymoclean Gel DNA Recovery Kit (ZD4008, Takara), product size distribution and quantity were assessed on a Bioanalyzer using an Agilent 2100 high-sensitivity DNA assay kit (5067-4626, Agilent Technologies).
The library preparation (KAPA Hyper Plus Library prep kit) and the sequencing of the scRNA-seq was performed by the ICGex - NGS platform (Curie Institute) on HiSeq 2500 Illumina sequencer for day-2 embryos and NovaSeq 6000 for day-5 embryos, for 100-bp paired-end sequencing

treatment_protocol:
All embryos used in the current study were cryopreserved individually 2 days post fertilization and had been in vitro cultured in different culture media (Global medium, LifeGlobal with or without 200µM methionine; FertiCult IVF medium, FertiPro; SSM, Irvine Scientific).
Embryos were thawed according to the strict protocol routinely used in human IVF-clinic to maintain as much as possible their integrity (Bechoua et al. 2009)
Immediately after thawing, embryos were transferred into preequilibrated Embryoslides (Unisense Fertilitech, Vitrolife) with 25 μl of culture medium and covered with 1.2 mL of oil (Nidoil, Nidacon). They were cultured up to the blastocyst stage at 37°C and a tri-gaz atmosphere (6%CO2, 5%O2, 89% N2)
Only blastocysts with at least B2 blastocoel cavity without lysis were analyzed.

value: embryo

tag: day

tag: culture media_day-2

value: SSM

tag: culture media_day-5

tag: couple


title: HCC04P scRNA-seq

description: 10x Genomics


title: RBM39 KD rep 3


title: embryo, day-2, SSM, rep13


title: HCC03P scRNA-seq

description: 10x Genomics


title: HCC03T scRNA-seq

description: 10x Genomics


title: Ctrl KD rep 2


title: embryo, day-2, SSM, rep10


title: embryo, day-2, SSM, rep9


title: embryo, day-2, SSM, rep8


title: embryo, day-2, SSM, rep7


title: Control rep2


title: HCC01P scRNA-seq

description: 10x Genomics


title: embryo, day-2, SSM, rep5


title: mES, dTAG_METTL14, HA_chromo_phd, HA, rep1

first: Hongjie

last: Shen

state: Shanghai

address: No.130, Dong'an Road, Xuhui District

department: Institutes of Biomedical Sciences

institute: Fudan University

data_processing:
Raw reads were aligned to the mm10 genome using Bowtie2 (v 2.2.5).
PCR duplicates were removed using samtools (v1.7) rmdup.
Genome coverage bigwig files were generated by deeptools (v 3.0.2) bamCoverage with the parameter “--normalizeUsing RPKM --binSize 5”.
Assembly: Genome_build: mm10
Supplementary files format and content: Genome coverage bigwig files

growth_protocol: E14Tg2a murine embryonic stem cells (mES) were cultured in Dulbecco’ s Modified Eagle’ s Medium (DMEM) supplemented with 10% fetal bovine serum (FBSGibco #16000-044), 1% MEM non-essential amino acid (Gibco #11140), 55 mM β-Mercaptoethanol (Gibco#21985-023), 100 U/mL Penicillin/Streptomycin (Hyclone #SV30010), 1000 units/mL LIF (Millipore #ESG1107,) and MEK inhibitor PD0325901 (1μM) and GSK3β inhibitor CH99021 (3μM) at 37℃ with 5% CO2.

extract_protocol:
Chromatin samples were incubated with specific antibodies in the ChIP Lysis buffer (20 mM Tris-HCl pH8.1, 150 mM NaCl, 2 mM EDTA, 1% TritonX-100 and 0.05% SDS) overnight at 4℃. The protein-DNA complexes were immobilized on pre-washed protein A/G beads (20μl per reaction). The bound fractions were washed 3 times with the Lysis buffer, and twice with the Low Salt Wash buffer (10 mM Tris-HCl, 250 mM LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% Na-deoxylcholate), and once with 10 mM Tris-HCl pH8.0. Elution and reverse crosslinking were carried out in the Elution buffer (50 mM Tris-HCl pH8.0, and 1% SDS) at 65℃ for 5 hours. After 1 hour of RNase A (1unit/μl) at 37℃ and Proteinase K (1unit/μl) digestion at 55℃, DNA samples were then purified using PCR extraction kit (QIAGEN #28006).
The precipitated DNA samples were prepared for DNA deep sequencing according to manufacturer’s guidelines (SWIFT, #21096).

value: Embryonic stem cells

tag: chip antibody


title: mES, dTAG_METTL14, EZH2i_7D, 24H, dTAG, H3K27me3, rep1


title: Ctrl KD rep 1

value: HeLa


title: mES, dTAG_METTL14, HA_chromo_phd, HA, rep2


title: embryo, day-2, SSM, rep11


title: embryo, day-2, SSM, rep3


title: mES, dTAG_METTL14, EZH2i_7D, 24H, dTAG, H3K27me3, rep2


title: embryo, day-2, SSM, rep12


title: HCC01T scRNA-seq

description: 10x Genomics


title: embryo, day-2, ferticult, rep6

value: Ferticult


title: mES, dTAG_METTL14, EZH2i_7D, 24H, DMSO, H3K27me3, rep2


title: mES, dTAG_METTL14, EZH2i_7D, 24H, DMSO, H3K27me3, rep1


title: embryo, day-2, ferticult, rep5


title: mES, dTAG_METTL14, EZH2i_7D, 0h, dTAG, H3K27me3, rep2


title: embryo, day-2, ferticult, rep4


title: embryo, day-2, ferticult, rep3


title: embryo, day-2, global, rep10

value: Global


title: embryo, day-2, SSM, rep4


title: embryo, day-2, SSM, rep6


title: embryo, day-2, global, rep11


title: embryo, day-2, global, rep8


title: HCC02T scRNA-seq

description: 10x Genomics


title: mES, dTAG_METTL14, EZH2i_7D, 0h, dTAG, H3K27me3, rep1


title: HCC02P scRNA-seq

description: 10x Genomics


title: embryo, day-2, global, rep6


title: mES, dTAG_METTL14, EZH2i_7D, 0h, DMSO, H3K27me3, rep2


title: embryo, day-2, global, rep5


title: embryo, day-2, global, rep9


title: embryo, day-2, global, rep3


title: embryo, day-2, global, rep4


title: embryo, day-2, SSM, rep2


title: embryo, day-2, global, rep2


title: embryo, day-2, SSM, rep1


title: mES, METTL14KO, dTAG_KDM5B, DMSO, FLAG, rep2

value: DYKDDDDK (Flag) (Smart-lifesciences, #SLAB01)


title: mES, dTAG_METTL14, EZH2i_7D, 0h, DMSO, H3K27me3, rep1


title: mES, METTL14KO, dTAG_KDM5B, DMSO, FLAG, rep1


title: mES, dTAG_KDM5B, DMSO, FLAG, rep1


title: embryo, day-2, global, rep1


title: embryo, day-2, ferticult, rep1


title: mES, METTL3KO, H3K27me3, rep1

value: METTL3 KO


title: *KD-TIP60 siTIP60 R1

city: Singapore

first: Shreshtha

middle: Sailesh

last: Bhatia

address: 14 Medical Drive

department: Cancer Science Institute of Singapore

country: Singapore

institute: National University of Singapore

data_processing:
RNA-seq fastq files of TIP60 knockdown in MSCV, MSCV-*WT and MSCV-*KD MCF10A cells of two biological replicates were mapped to hg38 reference genome using STAR.
MISO analysis was performed as described previously to call for skipped exon, retained intron, alternative 3’ splice site, alternative 5’ splice site and mutually exclusive exons for each dataset.
Differential analysis was performed using MISO, to compare MSCV siTIP60 to siControl, MSCV-*WT siTIP60 to MSCV-*WT siControl, MSCV-*KD siTIP60 to MSCV-*KD siControl and MSCV-*WT siTIP60 to MSCV-*KD siTIP60.
Events were filtered based on the recommended criteria (Bayes Factor > 6).
Genome_build: hg38
Supplementary_files_format_and_content: Text file containing skipped exon events and counts

source_name: epithelial cells

growth_protocol: Dulbecco’s modified eagle’s media (DMEM)/F12 (1:1) media (Gibco, Cat. No. 11330-032) with 5% horse serum (Gibco, Cat. No. 16050-122), 1% penicillin-streptomycin (Gibco Cat. No. 15140163), 20 ng/mL epithelial growth factor (Peprotech, Cat. No.AF-100-15), 0.5 mg/mL hydrocortisone (Sigma-Aldrich, Cat. No. H-0888), 100 ng/mL cholera toxin (Sigma-Aldrich, Cat. No. C-8052) and 10 μg/mL insulin (Sigma-Aldrich, Cat. No. I-1882). Cell cultures were incubated at 37˚C with 5% CO2.

extract_protocol:
Total RNA was isolated using TRIzol reagent (Thermo Fisher, Cat. No. 15596026) following the manufacturer’s instructions.
TruSeq Stranded mRNA LT Sample Prep Kit was used.

treatment_protocol: One million MCF10A cells were seeded and transfected with TIP60 or control siRNAs using Lipofectamine RNAiMAX following the manufacturer’s protocol. Transfected cells were harvested 72 h after transfection.

value: Breast

tag: stable expression

value: siRNA-resistant catalytically dead TIP60

value: TIP60 siRNA


title: *KD-TIP60 siTIP60 R2


title: *KD-TIP60 siControl R1

value: Control siRNA


title: *KD-TIP60 siControl R2


title: mES, WT, H3K27me3, rep4

tag: cell type

value: WT


title: mES, METTL3KO, H3K27me3, rep2

tag: genotype


title: embryo, day-2, global, rep7


title: *WT-TIP60 siTIP60 R2

value: siRNA-resistant wild-type TIP60

tag: treatment


title: *WT-TIP60 siTIP60 R1

tag: tissue


title: mES, WT, H3K27me3, rep3


title: patient sample with treatment

city: Bergen

first: Kristina Xiao

last: Liang

state: Hordaland

address: Jonas Lies vei 87, P. O. Box 7804

country: Norway

institute: University of Bergen

data_processing:
The library concentration was calculated using the Qubit 4.0 fluorometer and the libraries were pooled in an equimolar fashion. The single cell libraries were sequenced on an Illumina NovaSeq 6000 using a 2x150-bp approach to a final depth of 90 GB per library. The reads were demultiplexed according to the multiplexing index sequencing on Illumina’s BaseCloud platform.
Sample integration, dimensionality reduction and cell clustering:  The downstream bioinformatic analysis was performed by combining three samples using the concatenate function from the anndata package in Python. Data were log-normalized such that the total count for each cell was 10,000.  Highly variable genes (HVGs) were identified using dispersion-based methods with mean between 0.1 and 8 and dispersion of 0.5 and above using the function highly_variable_genes from scanpy. Principal component analysis (PCA) was performed on expressions from HVGs. The top 17 principal components were retrained from 50 by checking explained variance ratio of PCA instances. We used neighbors function in scanpy to calculate the neighborhood graph with 20 neighbors and 17 PC. The Uniform Manifold Approximation and Projection (UMAP) algorithm  was used to calculate the reduced dimensions from neighborhood graph with minimum distance of 0.5, spread scale of 1 and 200 maximum iterations. The cell clusters were identified using the unsupervised network-based leiden algorithm provided in the scanpy package with a resolution of 0.5 on the top 17 principal components.
Cell type annotation: To identify distinct cell populations based on shared and unique patterns of gene expression, we performed dimensionality reduction and unsupervised cell clustering using single cell multi-resolution marker-based annotation scMRMA32 (https://github.com/JiaLiVUMC/scMRMA) with cutoff of significant p value smaller than 0.05 for the fisher test for the significant cell type enrichment from 20 nearest neighbors. Cell type marker genes were obtained from the PanglaoDB   database (https://panglaodb.se/).
Differential gene expression analysis: The marker genes of the individual clusters were found by using the differential gene expression analysis algorithm scanpy.tl.rank_genes_groups in Python with the following parameters sc.tl.rank_genes_groups (adata, groupby=’leiden’, method='wilcoxon', corr_method='bonferroni', use_raw=False). A p-value of 0.05 was used to keep the DEGs that were significant. The top 9 DEGs were shown for each cluster in the figures.
Gene enrichment analysis Gene enrichment analysis was performed with the package gseapy in Python with the databases “GO_Biological_Process_2021”, “GO_Molecular_Function_2021”, “GO_Cellular_Component_2021”, “Reactome_2016”, “KEGG_2016” and “KEA_2015”.
Assembly: human reference GRCh38
Supplementary files format and content: Matrix table with raw read counts for every gene and every sample

source_name: human iPSCs

growth_protocol: To differentiate into cortical organoids, feeder-free iPSCs were fed daily with E8 medium for at least 7 days before differentiation. Colonies were dissociated using Accutase  in PBS (1:1) for 10 min at 37 °C and centrifuged for 3 min at 100 × g. The single cells were diluted in neural induction media and a total of 9,000 live cells were then seeded to 96-well ultra-low attachment tissue culture plates in 150 μl neural induction media and kept in suspension under rotation (95 rpm) in the presence of 50 μM ROCK inhibitor  and kept in suspension under rotation (85 rpm) for 24 h to form embryoid body (EB). To minimize un-directed differentiation, dual SMAD inhibition and canonical WNT inhibition are adopted during this period. On day 2, half of the media was replaced by human neural induction media in the presence of 50 μM ROCK inhibitor to each well. On day 4, 6, and 8, 100 μl medium was placed with 150 μl neural induction without ROCK inhibitor. After 10 days, the organoids were transferred into a 6-well ultra-low attachment tissue culture plates in neural differentiation mediaminus vitamin A for next 8 days using an orbital shaker to induce cortical organoids. On day 18, the organoids were subsequently matured in neural differentiation media with vitamin A  with media changes every 3-4 days. BDNF and ascorbic acid were supplemented to facilitate long term neural maturation.

extract_protocol:
Organoids were collected from their culture medium, washed with 1x PBS and dissociated with ophthalmic scissors to finely cut pieces of 1-2 mm. The pieces were digested in 2 ml CellLive™ Tissue Dissociation Solution at 37°C for 15 minutes in a 15-ml centrifuge tube with continuous agitation on a thermal shaker. The state of dissociation was checked at regular intervals under a light microscope. Following digestion, the suspension was filtered using a 40-µm sterile strainer. The cells were centrifuged at 350xg for 5 minutes at 4°C and the cell pellets were resuspended in 1 ml PBS. Cells were stained with a 0.4% w/v solution of Trypan Blue  and the cell number and viability were calculated in a hemacytometer under a light microscope.
The single cell RNA-seq libraries were constructed using (GEXSCOPE™ Single Cell RNAseq Library Kit, Singleron Biotechnologies, cat no. 4161031) according to manufacturer´s instructions. Briefly, for each library, the concentration of the single-cell suspension was adjusted to 3x105 cells/ml with PBS and the suspension was loaded onto an SD microfluidic chip to capture 6000 cells. Paramagnetic beads conjugated to oligodT probes that carry a unique molecular identifier (UMI) and a barcode unique to each bead (from the same kit) were loaded, after which the cells were lysed. The beads bound to polyadenylated mRNA were extracted from the chip and reverse transcribed into cDNA at 42°C for 1.5 hours, and the cDNA amplified by PCR. The cDNA was then fragmented and ligated to indexed Illumina adapters. The fragment size distribution of the final amplified library was obtained on an Agilent Fragment Analyzer.

treatment_protocol: For phenotype rescue experiments, organoids were treated with 250 μM metformin from day 6 of differentiation. The medium was changed every two days and the organoids were grown for 3 months. An equivalent amount of vehicle of Dimethylsulfoxide (DMSO) was added to grow untreated organoids.

value: iPSC derived cortical organoids

value: POLG mutation


title: embryo, day-2, ferticult, rep2


title: mES, dTAG_KDM5B, DMSO, FLAG, rep2


title: *WT-TIP60 siControl R2


title: mES, METTL3KO, H3K4me3, rep2


title: patient sample


title: *WT-TIP60 siControl R1


title: sWAT EC Control, biological rep3

city: Heidelberg

first: Andreas

last: Fischer

address: Im Neuenheimer Feld 280

country: Germany

institute: DKFZ

description: Gene expression data from murine adipose tissue endothelial cells

hyb_protocol: cDNA was hybridized onto Clariom S Assay according to manufacturer's instructions.

scan_protocol: Gene Expression Microarrays were scanned using the Affymetrix GeneChip® Scanner 3000 according to GeneChip® Expression Wash, Stain and Scan Manual for Cartridge Arrays

data_processing: All intensity data were quantile normalized.

source_name: Control sWAT EC3

label_protocol: Biotin

growth_protocol: Mice were housed under specific pathogen-free conditions until 8-9 weeks of age. Mice were injected with KPC pancreatic adenocarcinoma cells and compared to non-tumor bearing controls.

extract_protocol: RNA was isolated using Qiagen Rneasy mini kit.

treatment_protocol: Endothelial cells were isolated from white adipose tissue by collagenase-dispase digestion followed by CD45+ Dynabead negative selection and CD31+ Dynabead positive selection.

tag: condition

value: pre-cachexia

value: white adipose tissue

value: endothelial


title: control sample

value: wild type


title: MSCV siTIP60 R2

value: empty vector


title: sWAT EC Control, biological rep4

source_name: Control sWAT EC4


title: mES, METTL3KO, H3K4me3, rep1

value: Embryonic stem cells


title: mES, WT, H3K4me3, rep4


title: MSCV siControl R2


title: MSCV siControl R1


title: mES, WT, H3K4me3, rep3


title: Rice cold mRNA-seq rep2

value: leaves

value: 4C 6d


title: MSCV siTIP60 R1


title: Rice cold mRNA-seq rep1


title: Rice cold mRNA-seq rep3


title: mES, dTAG_METTL14, dTAG, H3K27me3, rep2


title: mES, dTAG_METTL14, dTAG, H3K27me3, rep1


title: mES, dTAG_METTL14, DMSO, H3K27me3, rep2


title: Rice normal mRNA-seq rep3

value: CK


title: mES, dTAG_METTL14, DMSO, H3K27me3, rep1


title: sWAT EC KPC, biological rep3

source_name: KPC sWAT EC3


title: Rice normal mRNA-seq rep2


title: Rice normal mRNA-seq rep1


title: mES, dTAG_METTL14, dTAG, H3K4me3, rep2


title: mES, dTAG_METTL14, dTAG, H3K4me3, rep1


title: sWAT EC Control, biological rep2

source_name: Control sWAT EC2


title: mES, dTAG_METTL14, DMSO, H3K4me3, rep2


title: TT-seq siRRP40 rep 2 [re-used]

city: Aarhus C

first: Søren

last: Lykke-Andersen

address: C.F.Møllers Allé 3

department: Molecular Biology and Genetics

country: Denmark

institute: Aarhus University

description:
purified 4sU-labeled RNA
GSM4593593
batch 2

data_processing:
Illumina software used for basecalling (Casava) and demultiplexing
the fastq files were mapped to the reference genome (GRCh38 + RNA spike-ins) using STAR aligner to generate the BAM alignment files
the BAM files were filtered to contain only uniquely mapped reads with Samtools
Size-factors for sequencing depth normalization were obtained using the DESeq2 algorithm from counts on reduced GenCode v21 annotation generated with HTSeq. The reads mapping to spike-ins were used to estimate antisense and contamination bias (contaminating unlabeled RNA in 4sU-labeled RNA).  TT- and RNA-seq data were corrected accordingly. The experiments were done in duplicates in two batches and the data were batch corrected using the limma package.
Assembly: GRCh38
Supplementary files format and content: bigWig format; normalized and antisense-bias corrected coverage of uniquely mapping read pairs
Supplementary files format and content: the coverage (without junction fragments) was corrected for antisense bias, contamination of unlabeled RNA and library-size corrected
Library strategy: TT-seq

source_name: cervix

growth_protocol: HeLa cells were cultured in standard DMEM medium supplemented with 10% FBS and penicillin-streptomycin mix.

extract_protocol:
TT-seq/RNA-seq: Six in vitro transcribed spike-in RNAs were added to the lysates (TRIzol, Thermo) followed by extraction of RNA according to the manufacturer’s protocol. The RNA was then sonicated and used as input for RNA-seq or for further purification of 4sU-labeled RNA. 4sU-labeled RNA was first biotinylated with EZ-Link HPDP-Biotin (Pierce) and isolated with µMACS Streptavidin Kit (Miltenyi). 4sU-labeld RNA was eluted by cleaving off the biotin with DTT. Both total RNA and 4sU-labeled RNA was purified prior to libary preparation using the miRNeasy Micro Kit (Qiagen) including DNse I treatment to remove genomic DNA.
TT-seq/RNA-seq: RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq Stranded Total RNA Sample Prep kit).

treatment_protocol: Two rounds of transfections were performed. The first transfections were performed using SilentFect (final dilution 1:1000) in RPMI 1640 medium. Two days after the first transfection, the media was changed, and the transfection was repeated using Lipofectamine 2000 (final dilution 1:1000) in RPMI 1640 medium. siRNAs were used at a final concentration of 15 nM of each siRNA. 24 hours after the second round of transfections, cells were labeled for 5 min with 500 µM 4-thiouridine minutes for TT-seq and harvested.

value: cervix

value: HeLa

value: epithelial

value: RRP40 knockdown


title: sWAT EC KPC, biological rep1

source_name: KPC sWAT EC1


title: TT-seq siINTS11 rep 1 [re-used]

description:
purified 4sU-labeled RNA
GSM4593588
batch 1

value: INTS11 knockdown


title: mES, dTAG_METTL14, dTAG, FLAG, rep1

value: DYKDDDDK (Flag) (Smart-lifesciences, #SLAB01)


title: TT-seq siINTS11 rep 2 [re-used]

description:
purified 4sU-labeled RNA
GSM4593589
batch 2


title: mES, dTAG_METTL14, dTAG, FLAG, rep2


title: MCF-7_input

first: Man-Li

last: Luo

address: No.107 Yanjiang West Road, Yuexiu District, Guangzhou

institute: Sun Yat-sen Memorial Hospital

data_processing:
Sequencing were performed using Illumina HiSeqTM 4000.
RIP-seq reads were aligned to the Ensembl_release100 genome using Bowtie version 2.2.8. Only uniquely mapping reads with at most two mismatches were retained.
The reconstruction of transcripts was carried out with software StringTie3, which allows to identify splice variants.
Peaks were called using RIPSeeker with the significance cut-off eFDR < 0.05
Processed data files were based on the fold enrichment (the odds ratio between IP fpkm and Input fpkm in a experiment) of different experiments. The odds ratio of fold   enrichment between two experiment > 2 was used to selected different genes.
Assembly: Ensembl_release100
Supplementary files format and content: tab-delimited text files include fold change values for each RNA precipitation Sample normalised to input respectively.
Supplementary files format and content: Peak related genes were used to analyse differences between two samples, different genes analysis was based on the fold enrichment (the odds ratio between IP fpkm and Input fpkm in a experiment) of different experiments. The odds ratio of fold enrichment between two experiment> 2 was used to selected different genes. Using the same method, different genes associated with peaks were identified, and also do GO and KEGG enrichment analysis.

growth_protocol: Breast cancer cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and penicillin-streptomycin in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Trizol reagent. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using illumina Ribo-Zero Gold（Human/Mouse/Rat）kit following manufacturer's protocols

treatment_protocol: We produced FLAG tagged-MDM2 protein in MDA-MB-231 and MCF-7 cells by transfection of FLAG tagged plasmids into cells. Cells were lysed by RIP lysis buffer, and incubated at 4 °C with antibody-conjugated Protein A/G Dynabeads overnight. Specific anti-FLAG antibody (Sigma) and normal mouse IgG (Santa Cruz) were used for the retrieval of RNA. RNA was extracted for subsequent sequencing analysis.

value: Flag-tagged MDM2 protein was expressed

value: Flag antibody immunoprecipitation


title: sWAT EC KPC, biological rep2

source_name: KPC sWAT EC2

value: pre-cachexia


title: mES, dTAG_METTL14, DMSO, FLAG, rep2


title: TT-seq siCPSF73 rep 1 [re-used]

description:
purified 4sU-labeled RNA
GSM4593590
batch 1

value: CPSF3 knockdown


title: MCF-7  Flag-tagged MDM2


title: LNCaP OC2 UTR_1_3

city: Los Angeles

first: Minhyung

last: Kim

state: CA

address: 8700 Beverly Blvd

department: Urology

institute: Cedars-Sinai Medical Center

description: Gene expression after  transfection of ONECUT2 3' UTR producing vector

hyb_protocol: 600ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25ul of 2x Hi-RPM hybridization buffer was added to the fragmentation mixture and hybridized to the Agilent SurePrint G3 Human Gene Expression v3 8x60K Microarray (catalog number G4851C) for 17 hours at 65 C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with pre-warmed at 37 °C overnight Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner G2505C using one color scan setting for G3 Microarray formats :Scan region  61x21.6 mm, Scan resolution 3um,Tiff file dynamic range 20 bit, Green PMT gain 100%.

data_processing: The scanned images were analyzed with Feature Extraction Software v11.5.1.1 (Agilent).

source_name: LNCaP Prostate Cancer cell line

label_protocol: 0.2 ug RNA was labeled with cyanine 3-dUTP by using One-Color Microarray -Based Gene Expression Analysis Low Input Quick Amp Labeling (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: RPMI 1640 10% FBS

extract_protocol: Qiagen Rneasy mini extraction with DNAse treatment

treatment_protocol: Cells were transfected stably and FAC sorted to ensure positivity

value: Prostate cancer

value: LNCaP

tag: treated

value: Treated


title: LNCaP OC2 UTR_2_2

value: transfection of ONECUT2 3' UTR producing vector


title: LNCaP OC2 UTR_1_1


title: LNCaP OC2 UTR_1_2


title: sWAT EC Control, biological rep1

source_name: Control sWAT EC1

value: white adipose tissue

value: endothelial


title: LNCaP_OC2_cDNA_1_1

description: Gene expression after stable transfection of ONECUT2 cDNA producing vector


title: LNCaP_OC2_cDNA_1_2

value: stable transfection of ONECUT2 cDNA producing vector


title: mES, dTAG_METTL14, DMSO, FLAG, rep1

value: Embryonic stem cells


title: LNCaP OC2 UTR_2_3


title: LNCaP_OC2_cDNA_1_3


title: mES, dTAG_METTL14, DMSO, H3K4me3, rep1


title: MCF-7 normal mouse igG

value: IgG antibody immunoprecipitation


title: TT-seq siRRP40 rep 1 [re-used]

description:
purified 4sU-labeled RNA
GSM4593592
batch 2

value: cervix

value: HeLa

value: epithelial


title: TT-seq siARS2 rep 2

description:
purified 4sU-labeled RNA
batch 2

value: ARS2 knockdown


title: LNCaP_OC2_cDNA_2_3


title: mES, METTL14KO+METTL14D312A, H3K4me3, rep2

value: METTL14 D312A


title: TT-seq siCPSF73 rep 2 [re-used]

description:
purified 4sU-labeled RNA
GSM4593591
batch 2


title: mES, METTL14KO+METTL14WT, H3K4me3, rep2

value: METTL14 WT


title: TT-seq siARS2 rep 1

description:
purified 4sU-labeled RNA
batch 1


title: mES, METTL14KO+METTL14R298A, H3K4me3, rep2

value: METTL14 R298A


title: MDA-MB-231_input

value: Flag-tagged MDM2 protein was expressed

value: Flag antibody immunoprecipitation


title: TT-seq siEGFP rep 1 [re-used]

description:
purified 4sU-labeled RNA
GSM4593586
batch 1

value: CTRL knockdown

value: si-EGFP


title: mES, METTL14KO, H3K4me3, rep2

value: METTL14 KO


title: Hair4

city: Nagoya

first: So

last: TAKEUCHI

address: 65 Tsurumai-cho, Showa-ku

department: Dermatology

institute: Nagoya University Graduate School of Medicine

data_processing:
Next-generation sequencing was performed using an Illumina Novaseq 6000 platform to obtain 101-bp paired-end reads.
We aligned the sequence reads to the GENCODE human reference transcriptome (version 39) and calculated transcript-expression levels using Kallisto (version 0.46.0). We then employed the R package DESeq2 to identify differentially expressed genes between hair follicle and skin samples.
Assembly: GENCODE human reference transcriptome (version 39)
Supplementary files format and content: DESeq2_all_result.xlsx: Excel file includes counts and normalized counts.

source_name: Hair follicle

extract_protocol:
RNA was harvested using RNeasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit following manufacturer's protocols.

value: Hair follicle


title: mES, H3K4me3, rep2

value: WT


title: Hair5


title: MDA-MB-231 Flag-tagged MDM2


title: LNCaP_mir-9_2

description: Gene expression after stable transfection of miR-9 producing vector

value: Prostate cancer

value: LNCaP

value: Treated


title: LNCaP OC2 UTR_2_1

value: transfection of ONECUT2 3' UTR producing vector


title: RNA-seq siRRP40 rep 1 [re-used]

description:
GSM4593600
batch 2

data_processing:
Illumina software used for basecalling (Casava) and demultiplexing
the fastq files were mapped to the reference genome (GRCh38 + RNA spike-ins) using STAR aligner to generate the BAM alignment files
the BAM files were filtered to contain only uniquely mapped reads with Samtools
Size-factors for sequencing depth normalization were obtained using the DESeq2 algorithm from counts on reduced GenCode v21 annotation generated with HTSeq. The reads mapping to spike-ins were used to estimate antisense and contamination bias (contaminating unlabeled RNA in 4sU-labeled RNA).  TT- and RNA-seq data were corrected accordingly. The experiments were done in duplicates in two batches and the data were batch corrected using the limma package.
Assembly: GRCh38
Supplementary files format and content: bigWig format; normalized and antisense-bias corrected coverage of uniquely mapping read pairs
Supplementary files format and content: the coverage was corrected for antisense bias and library-size corrected

value: cervix

value: HeLa

value: RRP40 knockdown


title: RNA-seq siRRP40 rep 2 [re-used]

description:
GSM4593601
batch 2

value: epithelial


title: Hair3


title: LNCaP_mir-9_3

value: stable transfection of miR-9 producing vector


title: LNCaP_OC2_cDNA_2_1

value: stable transfection of ONECUT2 cDNA producing vector


title: LNCaP_OC2_cDNA_2_2


title: Hair2


title: mES, METTL14KO, rep1

data_processing:
Raw reads were aligned to the mm10 genome using TopHat (v2.1.1) with parameter “--max-multihits 1”.
PCR duplicates were removed using samtools (v1.7) rmdup.
Strand specific reads were separated by samtools (v1.7) view with specific flags 99, 147, 83, 163.
Genome coverage bigwig files were generated by deeptools (v 3.0.2) bamCoverage with the parameter “--normalizeUsing RPKM --binSize 5”.
Assembly: Genome_build: mm10
Supplementary files format and content: Supplementary_files_format_and_content: Genome coverage bigwig files

extract_protocol:
Total RNAs were isolated using TRIzol reagent (Invitrogen) according to the manufacturer’s instruction. Strand specific total RNA library preparation was performed using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (E7420S).
The precipitated DNA samples were prepared for DNA deep sequencing according to manufacturer’s guidelines (SWIFT, #21096).

value: Embryonic stem cells


title: TT-seq siEGFP rep 2 [re-used]

description:
purified 4sU-labeled RNA
GSM4593587
batch 2


title: Hair1


title: mES, METTL14KO, rep2


title: mES, rep2


title: LNCaP_Empty_Vector_3

description: Gene expression after stable transfection of empty vector

value: Parent

value: stable transfection of empty vector


title: Skin6

source_name: Skin

value: Skin


title: mES, rep1


title: LNCaP_mir-9_1


title: SWAT-NICD3

description:
Technical replicate
AS-415608-LR-47716

data_processing:
low quality bases were removed with Fastq_quality_filter from the FASTX Toolkit 0.0.13
Homertools 4.7 was used for PolyA trimming
Genomic mapping was performed with STAR 2.3 with human genome 38
Count data were generated by FeatureCounts v1.4.5-p1 with the parameters “--minReadOverlap 10 -s 0 -T 4 -O -M -a” using gencode.v32.annotation.gtf
Assembly: hg38
Supplementary files format and content: Raw-count table and RPKM table for all samples, tab delimited (tsv) text file.

source_name: White adipose tissue

growth_protocol: Adipose tissue endothelial cells were isolated from subcutaneous or visceral abdominal adipose tissue biopsies from patients undergoing bariatric surgery using CD31 Dynabeads (Thermo Fisher). Cells were cultured in EGM-2 medium.

extract_protocol:
RNA was extracted using the RNAeasy mini kit (Qiagen).
Illumina TruSeq Stranded RNA

treatment_protocol: Cells were cultured to confluence and treated at P0 with adenoviruses overexpressing Notch1 ICD (NICD) or GFP. Medium was changed after 24 hours to fresh EGM-2. RNA was extracted after a further 24 hours.

value: subcutaneous white adipose tissue

value: endothelial cells

value: NICD


title: SWAT-NICD2

description:
Technical replicate
AS-415607-LR-47716


title: Skin5


title: SWAT-GFP3

description:
Technical replicate
AS-415605-LR-47716

value: GFP


title: Skin4


title: SWAT-GFP2

description:
Technical replicate
AS-415604-LR-47716


title: mES, METTL14KO, SUZ12, rep1

value: METTL14 KO


title: mES, METTL14KO, SUZ12, rep2


title: Skin3


title: SWAT-GFP1

description:
Technical replicate
AS-415603-LR-47716


title: Skin2


title: VWAT-NICD3

description:
Technical replicate
AS-415602-LR-47715

value: visceral white adipose tissue


title: mES, SUZ12, rep2

value: WT


title: LNCaP_Empty_Vector_2

value: Prostate cancer

value: LNCaP


title: SWAT-NICD1

description:
Technical replicate
AS-415606-LR-47716


title: Skin1


title: mES, SUZ12, rep1


title: mES, METTL14KO, EED, rep2

value: EED (Proteintec, #16818-1-AP)


title: VWAT-NICD2

description:
Technical replicate
AS-415601-LR-47715


title: mES, METTL14KO, EED, rep1


title: IMR32-ChIPseq-WDR5-rep1

city: Nashville

first: Jing

last: Wang

state: TN

address: 2220 Pierce Avenue

institute: Vanderbilt University Medical Center

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2.
Peaks were called by MACS2 with a q-value of 0.05.
Differential binding peaks were identified using DiffBind.
Assembly: hg19
Supplementary files format and content: peaks for each sample

growth_protocol: CHP-134 and IMR-32 cell lines were maintained in RPMI 1640 with l-glutamine (Corning) with 10% fetal bovine serum (FBS) and 1% Penicillin/Streptomycin

extract_protocol:
For ChIP-seq, chromatin from 10 million IMR-32 cells or CHP-134 cells treated with 0.005% dimethyl sulfoxide were crosslinked in 1% formaldehyde for 10 min, followed by quenching in 0.125 M glycine. Nuclei were extracted and chromatin was generated from nuclei through lysis in FALB buffer (50 mM HEPES, pH 7.5, 1% Triton, 1 mM EDTA, 140 mM NaCl) containing 1% SDS, PMSF, and protease inhibitor cocktail (Roche) using a Diagenode Bioruptor Plus instrument.
Three ChIPs from identical samples were pooled together and purified using a Qiagen PCR purification kit. Eluted DNA was used to generate libraries  using the Ultra II DNA library Prep protocol (New England Biolabs).
Ultra II DNA library Prep protocol (New England Biolabs) with dual index primers.

treatment_protocol: IMR-32 cells were untreated prior to chromatin collection. CHP-134 cells were treated with either 0.0005% DMSO or C91 (419) for 4 hrs prior to chromatin collection.

value: 5 microliter of anti-WDR5 (Cell Signaling, 13105)


title: IMR32-ChIPseq-WDR5-rep3


title: 22Rv1_OC2_UTR_1_3

source_name: 22Rv1 Prostate Cancer cell line

value: Treated

value: transfection of ONECUT2 3' UTR producing vector


title: 22Rv1_OC2_UTR_1_1


title: VWAT-GFP3

description:
Technical replicate
AS-415599-LR-47715


title: 22Rv1_OC2_UTR_1_2


title: IMR32-ChIPseq-MYC-rep2

value: 5 microliter of custom serum to target N-MYC


title: mES, EED, rep2

value: Embryonic stem cells


title: 22Rv1_OC2_UTR_2_3


title: 22Rv1_OC2_UTR_2_2


title: LNCaP_Empty_Vector_1

value: Parent

value: stable transfection of empty vector


title: VWAT-GFP1

description:
Technical replicate
AS-415597-LR-47715


title: VWAT-GFP2

description:
Technical replicate
AS-415598-LR-47715


title: 22Rv1_OC2_UTR_2_1


title: IMR32-ChIPseq-MYC-rep1


title: mES, METTL14KO, EZH2, rep2


title: mES, EED, rep1


title: VWAT-NICD1

description:
Technical replicate
AS-415600-LR-47715


title: 22Rv1_OC2_cDNA_3

value: stable transfection of ONECUT2 cDNA producing vector


title: mES, METTL14KO, EZH2, rep1


title: IMR32-ChIPseq-IgG-rep2

value: 800 ng IgG (Cell Signaling, 2729S)


title: RNA-seq siINTS11 rep 2 [re-used]

data_processing:
Illumina software used for basecalling (Casava) and demultiplexing
the fastq files were mapped to the reference genome (GRCh38 + RNA spike-ins) using STAR aligner to generate the BAM alignment files
the BAM files were filtered to contain only uniquely mapped reads with Samtools
Size-factors for sequencing depth normalization were obtained using the DESeq2 algorithm from counts on reduced GenCode v21 annotation generated with HTSeq. The reads mapping to spike-ins were used to estimate antisense bias and RNA-seq data were corrected accordingly. The experiments were done in duplicates in two batches and the data were batch corrected using the limma package.
Assembly: GRCh38
Supplementary files format and content: bigWig format; normalized and antisense-bias corrected coverage of uniquely mapping read pairs

source_name: tissue culture cells

extract_protocol:
Six in vitro transcribed spike-in RNAs were added to the lysates (TRIzol, Thermo) followed by extraction of RNA according to the manufacturer’s protocol. The RNA was then sonicated and used as input for RNA-seq or for further purification of 4sU-labeled RNA (the latter data not included here). Total RNA was purified prior to libary preparation using the miRNeasy Micro Kit (Qiagen) including DNase I treatment to remove genomic DNA.
RNA-seq libraries were prepared for sequencing using standard Illumina protocols (TruSeq Stranded Total RNA Sample Prep kit).

treatment_protocol: Two rounds of transfections were performed. The first transfections were performed using SilentFect (final dilution 1:1000) in RPMI 1640 medium. Two days after the first transfection, the media was changed, and the transfection was repeated using Lipofectamine 2000 (final dilution 1:1000) in RPMI 1640 medium. siRNAs were used at a final concentration of 15 nM of each siRNA. 24 hours after the second round of transfections, cells were labeled for 5 min with 500 µM 4-thiouridine minutes for TT-seq and harvested. The TT-seq data is not part of this submission (see GSE151919).

value: HeLa Kyoto

value: cervix

value: epithelial

tag: sirna

tag: batch

value: batch 2


title: 22Rv1_OC2_cDNA_2


title: 22Rv1_OC2_cDNA_1


title: RNA-seq siINTS11 rep 1 [re-used]

value: batch 1


title: IMR32-ChIPseq-IgG-rep1


title: mES, EZH2, rep2

value: WT


title: RNA-seq siCPSF73 rep 2 [re-used]


title: IMR32-ChIPseq-IgG-rep3


title: RNA-seq siCPSF73 rep 1 [re-used]


title: 22Rv1_mir-9_2_2

value: Prostate cancer

value: stable transfection of miR-9 producing vector


title: mES, EZH2, rep1


title: mES, METTL14KO+METTL14D312A, H3K4me3, rep1

value: METTL14 D312A


title: RNA-seq siARS2 rep 2


title: mES, METTL14KO+METTL14R298A, H3K4me3, rep1

value: METTL14 R298A


title: 22Rv1_mir-9_1_3

value: Treated


title: mES, METTL14KO+METTL14WT, H3K4me3, rep1

value: METTL14 WT


title: 22Rv1_mir-9_2_1


title: RNA-seq siARS2 rep 1


title: RNA-seq siEGFP rep 2 [re-used]

value: EGFP


title: Donor 3 - 72 hours treatment

city: Leiden

first: Françoise

last: Carlotti

state: FN

address: Albinusdreef 2

department: Internal Medicine

institute: Leiden University Medical Center

data_processing:
BCL files resulting from sequencing were transformed to FASTQ files with 10x Genomics Cell Ranger mkfastq.
FASTQ files were mapped with Cell Ranger count. During sequencing, 28 bp read 1 were used for identification of the Illumina library barcode, cell barcode and UMI. Read 2 was used to map to the reference transcriptome. Filtering of empty barcodes was done in Cell Ranger. HTO quantification was done using Cellranger by supplying the HTO barcodes.
The data from all samples were loaded in R (R version 3.6.2) and processed using the Seurat package (version 3.2.0).
Assembly: Human: Hg38
Supplementary files format and content: filtered_counts_data.mtx.gz; final dataset containing the expression counts for all genes across filtered cells
Supplementary files format and content: filtered_counts_barcodes.tsv.gz; cell-associated barcodes corresponding to the column indices of filtered_counts_data.mtx
Supplementary files format and content: filtered_counts_genes.tsv.gz; feature names corresponding to the row indices of filtered_counts_data.mtx
Supplementary files format and content: metadata_percell.csv; file containing metadata per single cell
Supplementary files format and content: matrix.mtx.gz; barcodes.tsv.gz, features.tsv.gz; cell ranger output for each 10X library including quantified HTO for D2 and D3.
Supplementary files format and content: barcodes.tsv.gz; cellranger output reporting the quantified HTO for D1
Supplementary files format and content: HTO_barcodes.xlsx; HTO barcode conversion table

source_name: Pancreatic islets

growth_protocol: Islets with a purity of at least 90% were cultured upon receipt in regular CMRL 1066 medium (5.5 mmol/L glucose) containing 10% fetal calf serum,  Islets were treated with the mentioned stressors for 24 and 72 hours.

extract_protocol:
After treatment islets were dispersed into single cells by dynamic incubation with 0.025% trypsin (Gibco) supplemented with 10 mg/mL DNase (Pulmozyme, Genentech) for 6–7 min and filtered through a 40 μm cell-strainer to remove undigested material. Islets exposed to the different treatments were multiplexed per timepoint and donor using cell hashing. Briefly, each treated islet cell suspension was incubated with a pool of barcoded antibodies directed against B2M and CD298 (TotalSeq-A BioLegend).
Labeled cell suspensions were pooled per donor and time point and processed for single-cell mRNA sequencing. Prior to loading the 10x Chromium controller, the pooled cell suspensions were counted to assess cell integrity and concentration. Cell suspensions were loaded, and the sequencing libraries were prepared following the standard 10x Genomics 3' V3 chemistry protocol.

treatment_protocol: glucose (22 mM) and/or palmitate (0.5 mM), thapsigargin (0.1 μM), IL-1β (1 ng/ml) and/or IFNγ (1000 U/ml), IFNα (2000 U/ml), hydrogen peroxide (H2O2, 50 μM), FGF2 (100 ng/ml) or hypoxia for 24h and 72h

tag: disease state

value: Healthy - non diabetic

tag: gender

value: M

tag: age

tag: time


title: Donor 2 - 72 hours treatment


title: Donor 3 - 24 hours treatment


title: Donor 2 - 24 hours treatment


title: mES, METTL14KO, H3K4me3, rep1

tag: cell line

value: Embryonic stem cells

value: METTL14 KO


title: mES, H3K4me3, rep1


title: Sup. Fig. 6, HeLa-R634Q ICS screen, lower, lib 5

first: Julia

last: Kornienko

state: Baden-Württemberg

address: Meyerhofstraße 1

institute: EMBL

description:
ICS R634Q screen lower 5
R634Q_screen_gene_stats.txt

library_source: other

data_processing:
library strategy: HeLa ICS screen Amplicon seq
RNAseq: Reads were aligned to GRCh38.101 using STAR (v2.7.5c), and bam files were sorted by coordinate using samtools (v.1.9). Read count files were generated with featureCounts52 v1.6.4 for each exon. For differential gene expression analysis, DeSeq253 (v. 1.36.0) was used, and pairwise comparisons between genotypes were performed (expression ~ genotype).
ICS screen: Abundance of gRNA was quantified from the sequencing reads using MAGeCK (v 0.5.9) tool with default parameters. To account for differences in sequencing depth, raw gRNA counts were normalized to the median count of the targeting control gRNAs in the corresponding sample. Scaling of the normalized counts was done by multiplication with the median count of targeting controls across all samples. The MAUDE package for R was used for hit calling, using targeting controls as a reference for MAUDE analysis.
Assembly: GRCh38.101
Supplementary files format and content: For RNAseq: tab-delimited text files containing read counts for all samples for all genes;  For ICS screen: csv file containing gene stats from MAUDE.

molecule: other

source_name: HeLa (Feldman at al., 2019)

growth_protocol: HeLa were maintained in DMEM, high glucose supplemented with 10% FBS, 1% Sodium Pyruvate, and 1% Penicillin-Streptomycin; in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA from HeLa: Direct-Zol (Zymo) kit was used according to manufacturer's instructions. DNA from HeLa: cells were palleted and genomic DNA was extracted using NEB Monarch genomic DNA purification kit, including the RNase treatment and elution in 50 µl elution buffer; 100-500 ng of DNA was used for library preparation.
HeLa RNAseq: Library preparation for HeLa cells was done based on RNA extracts from live cells. Barcoded stranded mRNA-seq libraries were prepared from 150ng of high quality total RNA samples using the NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs (NEB), Ipswich, MA, USA) implemented on the liquid handling robot Beckman i7. Obtained libraries that passed the QC step were pooled in equimolar amounts; 2.1 pM solution of this pool was loaded on the Illumina NextSeq 500and sequenced bi-directionally, generating ~500 million paired-end reads, each 75 bases long.HeLa ICS screen: see detailed methods in Schraivogel et al., 2022.

value: HeLa (Feldman at al., 2019)

value: human adenocarcinoma

value: TetO:Cas9; RBM20-R634Q

value: lower


title: 22Rv1_mir-9_1_1


title: Donor 1 - 24 hours treatment


title: embryo, day-5, ferticult, rep7

source_name: embryo

value: embryo

tag: day

tag: culture media_day-2

value: Ferticult

tag: culture media_day-5

value: Global


title: RNA-seq siEGFP rep 1 [re-used]

value: HeLa Kyoto

value: cervix

value: epithelial

value: batch 1


title: mES, METTL14KO+METTL14AGG, H3K27me3

value: METTL14 AGG

tag: chip antibody


title: Sup. Fig. 6, HeLa-R634Q ICS screen, lower, lib 4

description:
ICS R634Q screen lower 4
R634Q_screen_gene_stats.txt

tag: cell type


title: embryo, day-5, global_methionine, rep10

tag: couple


title: 22Rv1_Empty_Vector_3

value: Prostate cancer

value: Parent

tag: treatment

value: stable transfection of empty vector


title: 22Rv1_Empty_Vector_2


title: Sup. Fig. 6, HeLa-R634Q ICS screen, lower, lib 3

description:
ICS R634Q screen lower 3
R634Q_screen_gene_stats.txt

tag: genotype


title: embryo, day-5, global_methionine, rep7

tag: tissue


title: Sup. Fig. 6, HeLa-R634Q ICS screen, lower, lib 2

description:
ICS R634Q screen lower 2
R634Q_screen_gene_stats.txt


title: embryo, day-5, global, rep10


title: mES, METTL14KO+METTL14D312A, H3K27me3, rep1

value: Embryonic stem cells

value: METTL14 D312A


title: mES, METTL14KO+METTL14R298A, H3K27me3, rep2

value: METTL14 R298A


title: 22Rv1_Empty_Vector_1

tag: treated