title: NCM460 cells,input,linear pcDNA3.1-neo,rep3 (ChIP-seq)

data_processing:
ChIP-seq data were aligned to the reference genome hg19 using Bowtie2 (2.5.1).
After removing duplicates using the MarkDuplicates command of Picard (3.1.1), peaks were called from the bam files by MACS2 (2.2.9.1).
BigWig files were obtained using the bamCoverage command with –normalizeUsing RPKM option from deeptools (3.5.1).
Assembly: hg19
Supplementary files format and content: bigWig

growth_protocol: plasmid of pcDNA3.1-neo or linear pcDNA3.1-neo  were transfected into HeLa and NCM460 cells grown on the 6-well plates, and incubated for 24h

extract_protocol:
1% Formaldehyde (Sigma, F8775) was added into each well to crosslink the cells for 10 min with a slight shaking at room temperature.chromtin was sonicated using Covaris M220 sonicator.
DNA was isolated by performing a phenol/chloroform/isoamyl alcohol extraction to prepare the ChIP-seq library using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (NEB, E7645).

value: human normal adult colon mucosal epithelial cell

tag: chip antibody

value: transfected with linear pcDNA3.1-neo plasmid


title: 5LRV_CD8_Empty_TGCAGCTA_TACTCCTT

status: Public on May 21 2025

type: SRA

city: Boston

first: Zhaorong

last: Li

address: 60 Fenwood Road

country: USA

institute: Dana Farber Cancer Institute

library_source: transcriptomic

data_processing:
The raw sequences are aligned to the GRCm38 reference genome and quantified using kallisto.
Assembly: GRCm38
Supplementary files format and content: tar gzipped kallisto quantification output.

molecule: total RNA

organism: Mus musculus

growth_protocol: Mice. C57BL/6J mice (The Jackson Laboratory, 000664) were used as a genetic background for all in vivo experiments. Mice were housed in a conventional, pathogen-free facility at the Hale Building for Transformative Medicine under a standard 12h light/dark cycle at 20–23°C and 50% humidity with access to water and food ad libitum, in accordance with guidelines for care and experimentation defined by the Institutional Animal Care and Use Committee (IACUC). Transgenic mouse genotypes were confirmed by PCR (Transnetyx). When Aldh1l1Cre-ERT2/TdTomato astrocyte reporter mice (The Jackson Laboratory, #031008 and #007909) were used, 200mg/kg Tamoxifen (Sigma-Aldrich, T5648) diluted in corn oil (Sigma-Aldrich, C8267) was administered intraperitoneally 2-4 weeks before starting the experiment and TdTomato induction was confirmed by flow cytometry at the time of measurement.

extract_protocol:
Cells were lysed in 350µL RLT buffer and stored at -80°C until extraction following manufacturer’s instructions. RNA was transcribed to cDNA using the High-Capacity cDNA Reverse Transcription Kit (Life Technologies, 4368813)
Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described (Trombetta et al 2014).

tag: strain

tag: Sex

value: Female

tag: age

value: 8 week

tag: tissue

value: Brain

tag: cell type

value: CD8 T Cells

tag: treatment

value: TRAIL Knockdown by sgRNA


title: 5LRV_CD8_Empty_TCGACGTC_TACTCCTT


title: UPF2_iKO, NPC, Rep1

city: La Jolla

first: Kun

last: Tan

state: CA

address: 9500 Gilman Drive # 0695

department: Dept. of Obstetrics, Gynecology & Reproductive Science

institute: UCSD

data_processing:
Reads were filtered for quality and aligned with STAR (2.5.2b) against the GRCh38 (Ensembl version 106).
To detect genes expression, reads were filtered for quality and aligned with STAR (2.5.2b) against the GRCh38 (Ensembl version 106). The exon counts were aggregated for each gene to build a read count table using SubRead function featureCounts. Differentially expressed genes (DEGs) were defined using the DESeq2 program with the following thresholds: |Log2FC|>1 and q-val<0.01.
To measure transcript (or isoforms) expression levels, we used the RSEM package. Differential expressed transcripts (DETs) were defined using the EBSeq program with the following thresholds: PPEE<0.01 and PostFC>2 or <0.5.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited txt file including raw counts for each sample

organism: Homo sapiens

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen), following the manufacturer’s protocol. Ribosomal RNAs were removed using NEBNext® rRNA Depletion Kit v2 (New England Biolabs).
The enriched mRNA was then used to make the library using the SMART-Seq® v4 PLUS Kit (Takara Bio), as per manufacturer's instructions. Libraries were sequenced (pair-end reads) with an Illumina NovaSeq 6000 platform for 100 cycles at the UCSD institute for Genomic Medicine (IGM) core.

treatment_protocol: hESCs were harvested and seeded as single cells at 6x104 cells per cm2. Once 80% confluent, the hESCs were cultured in DMEM/F12 (Gibco) supplemented with N2 (1:100; Gemini), 5 μM Rock inhibitor, 1 μM Dorsomorphin and 10 μM SB431542 (STEMCELL Technologies) for 2 days. Colonies were then cut into a big chess pattern, and cultured in DMEM/F12 (Gibco) supplemented with N2 (1:100; Gibco), 1 μM Dorsomorphin and 10 μM SB431542 for 5 days under rotation (95 rpm) inside a 37°C incubator. Embryoid bodies were then replated on plates coated with hESC-qualified Matrigel (Corning) in DMEM/F12 media supplemented with N2 (1:200; Gemini), and Gem21 (1:100; Gemini) for 7 days. Neural rosettes were picked and dissociated with Accutase (Gibco) and plated on plates coated with poly-ornithine/Laminin in DMEM/F12 media supplemented with N2 (1:200; Gemini), Gem21 (1:100; Gemini), and 20 ng/mL bFGF (Sigma). Homogeneous populations of NPCs were achieved after 2-3 passages with accutase in the same condition.

tag: cell line

value: human embryonic stem cells

tag: genotype

value: Induced to form NPCs


title: LD45

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

description: Library name: LD45

data_processing:
Data were analysed using the Lexogen's proprietary sequence analysis platform. Trimming using Bbduk and quality control with FASTQC.
Assembly: Assembly: HGhg38
Supplementary files format and content: raw counts; .txt
Supplementary files format and content: lcpm; .txt

source_name: Retroperitoneal Sarcoma

extract_protocol:
Qiagen Rneasy microRNA kit with Dnase treatment
Libraries were prepared according to Lexogen's instructions accompanying the Kit (QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina)

value: Retroperitoneal Sarcoma

tag: type of_material

value: FFPE


title: LD47

description: Library name: LD47


title: NCM460 cells,input,linear pcDNA3.1-neo,rep2 (ChIP-seq)

city: Hong Kong

first: yicen

last: zhou

address: Block 2, To Yuen Building, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, China

department: Department of Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

library_source: genomic

molecule: genomic DNA


title: LD49

description: Library name: LD49


title: NCM460 cells,input,linear pcDNA3.1-neo,rep1 (ChIP-seq)


title: 5LRV_CD8_Empty_CCTAAGAC_TACTCCTT


title: 5LRV_CD8_Empty_CGATCAGT_TACTCCTT


title: UPF2_KD, NPC, Rep6


title: LD43

description: Library name: LD43


title: UPF2_iKO, NPC, Rep5


title: NCM460 cells,H3K27ac,linear pcDNA3.1-neo,rep3 (ChIP-seq)

value: Acetyl-Histone H3-K27 Rabbit mAb


title: 5LRV_CD8_Empty_ACTGAGCG_TACTCCTT


title: UPF2_KD, NPC, Rep5


title: LD41

description: Library name: LD41


title: UPF2_KD, NPC, Rep4


title: 5LRV_CD8_anti-TRAIL_TAGCGCTC_TACTCCTT

value: Control


title: 5LRV_CD8_anti-TRAIL_ATGCGCAG_TACTCCTT


title: NCM460 cells,H3K27ac,linear pcDNA3.1-neo,rep2 (ChIP-seq)


title: LD19

description: Library name: LD19


title: NCM460 cells,input,pcDNA3.1-neo,rep3 (ChIP-seq)

value: transfected with pcDNA3.1-neo plasmid


title: LD39

description: Library name: LD39


title: NCM460 cells,input,pcDNA3.1-neo,rep2 (ChIP-seq)


title: LD37

description: Library name: LD37


title: NCM460 cells,input,pcDNA3.1-neo,rep1 (ChIP-seq)


title: UPF2_KD, NPC, Rep1


title: 5LRV_CD8_anti-TRAIL_TACGCTGC_TACTCCTT


title: 5LRV_CD8_anti-TRAIL_CGGAGCCT_TACTCCTT


title: UPF2_KD, NPC, Rep3


title: Ctrl, NPC, Rep6

value: Ctrl


title: LD15

description: Library name: LD15


title: LD13

description: Library name: LD13


title: 5LRV_CD4_Empty_GCGTAGTA_TACTCCTT

value: CD4 T Cells


title: 5LRV_CD4_Empty_GGAGCTAC_TACTCCTT


title: NCM460 cells,H3K27ac,linear pcDNA3.1-neo,rep1 (ChIP-seq)


title: 5LRV_CD4_Empty_ACTCGCTA_TACTCCTT


title: Ctrl, NPC, Rep4


title: KW98

description: Library name: KW98


title: NCM460 cells,H3K27ac,pcDNA3.1-neo,rep3 (ChIP-seq)


title: Ctrl, NPC, Rep5


title: UPF2_KD, NPC, Rep2


title: LD10

description: Library name: LD10


title: KW81

description: Library name: KW81


title: NCM460 cells,H3K27ac,pcDNA3.1-neo,rep1 (ChIP-seq)


title: NCM460 cells,H3K27ac,pcDNA3.1-neo,rep2 (ChIP-seq)


title: Ctrl, NPC, Rep3


title: NCM460 cells,input,control,rep3 (ChIP-seq)

value: control


title: 5LRV_CD4_Empty_TGCAGCTA_TATGCAGT


title: Ctrl, NPC, Rep1


title: Ctrl, NPC, Rep2


title: KW73

description: Library name: KW73


title: KW78

description: Library name: KW78


title: 5LRV_CD4_anti-TRAIL_ACTGAGCG_TATGCAGT


title: 5LRV_CD4_anti-TRAIL_CGATCAGT_TATGCAGT


title: NCM460 cells,input,control,rep2 (ChIP-seq)

value: human normal adult colon mucosal epithelial cell


title: KW75

description: Library name: KW75


title: 5LRV_CD4_anti-TRAIL_CCTAAGAC_TATGCAGT


title: UPF2_iKO_KD, ESC, Rep6

growth_protocol: Cells were cultured in StemFlexTM medium (Gibco) on plates coated with hESC-qualified Matrigel (Corning).


title: UPF2_iKO_KD, ESC, Rep4


title: NCM460 cells,input,control,rep1 (ChIP-seq)


title: KW54

description: Library name: KW54


title: UPF2_iKO_KD, ESC, Rep5


title: NCM460 cells,H3K27ac,control,rep3 (ChIP-seq)


title: 5LRV_CD4_anti-TRAIL_TAGCGCTC_TATGCAGT


title: KW70

description: Library name: KW70


title: UPF2_iKO_KD, ESC, Rep2


title: KW49

description: Library name: KW49


title: NCM460 cells,H3K27ac,control,rep2 (ChIP-seq)


title: HeLa cells,input,linear pcDNA3.1-neo,rep3 (ChIP-seq)

source_name: HeLa

value: HeLa

value: human cervical adenocarcinoma cell

value: transfected with linear pcDNA3.1-neo plasmid


title: 5LRV_CD4_Empty_TCGACGTC_TATGCAGT

value: Female

value: 8 week

value: Brain


title: UPF2_iKO_KD, ESC, Rep3

value: human embryonic stem cells


title: HeLa cells,input,linear pcDNA3.1-neo,rep2 (ChIP-seq)


title: NCM460 cells,H3K27ac,control,rep1 (ChIP-seq)


title: UPF2_iKO_KD, ESC, Rep1


title: KW45

description: Library name: KW45


title: Monocytes_sgTrail - 5OLJ_ACTCGCTA_TCTTACGC

value: Monocytes

value: TRAIL Knockdown by sgRNA


title: Monocytes_sgTrail - 5OLJ_GGAGCTAC_TCTTACGC


title: Monocytes_sgTrail - 5OLJ_TCGACGTC_ACTCTAGG


title: Monocytes_Scramble - 5OLJ_CGATCAGT_ACTCTAGG


title: KW47

description: Library name: KW47

value: Retroperitoneal Sarcoma

value: FFPE


title: Monocytes_sgTrail - 5OLJ_TGCAGCTA_ACTCTAGG


title: UPF2_iKO, ESC, Rep5


title: HeLa cells,input,linear pcDNA3.1-neo,rep1 (ChIP-seq)


title: KW43

description: Library name: KW43


title: HeLa cells,H3K27ac,linear pcDNA3.1-neo,rep3 (ChIP-seq)

value: Acetyl-Histone H3-K27 Rabbit mAb


title: UPF2_iKO, ESC, Rep4


title: KW41

description: Library name: KW41


title: Monocytes_Scramble - 5OLJ_ACTGAGCG_ACTCTAGG

value: Control


title: UPF2_iKO, ESC, Rep3


title: KW20

description: Library name: KW20


title: KW24

description: Library name: KW24


title: Monocytes_Scramble - 5OLJ_TAGCGCTC_ACTCTAGG


title: HeLa cells,H3K27ac,linear pcDNA3.1-neo,rep2 (ChIP-seq)


title: HeLa cells,input,pcDNA3.1-neo,rep3 (ChIP-seq)

value: transfected with pcDNA3.1-neo plasmid


title: UPF2_iKO, ESC, Rep2


title: Monocytes_Scramble - 5OLJ_ATGCGCAG_ACTCTAGG


title: KW14

description: Library name: KW14


title: UPF2_iKO, ESC, Rep1


title: KW11

description: Library name: KW11


title: Microglia_sgTrail - 5OLJ_TACGCTGC_ACTCTAGG

value: Microglia


title: HeLa cells,input,pcDNA3.1-neo,rep2 (ChIP-seq)


title: UPF2_iKO, ESC, Rep6


title: HeLa cells,input,pcDNA3.1-neo,rep1 (ChIP-seq)


title: UPF2_KD, ESC, Rep6


title: KU93

description: Library name: KU93


title: Microglia_sgTrail - 5OLJ_CGGAGCCT_ACTCTAGG


title: UPF2_KD, ESC, Rep5


title: HeLa cells,H3K27ac,pcDNA3.1-neo,rep3 (ChIP-seq)


title: Monocytes_Scramble - 5OLJ_CCTAAGAC_ACTCTAGG


title: Microglia_sgTrail - 5OLJ_GCGTAGTA_ACTCTAGG


title: UPF2_KD, ESC, Rep4


title: KU91

description: Library name: KU91


title: HeLa cells,H3K27ac,pcDNA3.1-neo,rep2 (ChIP-seq)


title: HeLa cells,H3K27ac,linear pcDNA3.1-neo,rep1 (ChIP-seq)


title: Microglia_sgTrail - 5OLJ_GGAGCTAC_ACTCTAGG


title: HeLa cells,H3K27ac,pcDNA3.1-neo,rep1 (ChIP-seq)


title: KU87

description: Library name: KU87


title: HeLa cells,input,control,rep3 (ChIP-seq)

value: control


title: Microglia_sgTrail - 5OLJ_ACTCGCTA_ACTCTAGG


title: KU85

description: Library name: KU85


title: Microglia_Scramble - 5OLJ_TCGACGTC_AGCTAGAA


title: UPF2_KD, ESC, Rep2


title: UPF2_KD, ESC, Rep1


title: HeLa cells,input,control,rep2 (ChIP-seq)


title: HeLa cells,input,control,rep1 (ChIP-seq)


title: KU81

description: Library name: KU81


title: Microglia_Scramble - 5OLJ_CGATCAGT_AGCTAGAA


title: Ctrl, ESC, Rep6

value: Ctrl


title: Microglia_Scramble - 5OLJ_TGCAGCTA_AGCTAGAA


title: KU83

description: Library name: KU83


title: Ctrl, ESC, Rep5


title: HeLa cells,H3K27ac,control,rep3 (ChIP-seq)

value: HeLa


title: Microglia_Scramble - 5OLJ_CCTAAGAC_AGCTAGAA


title: HeLa cells,H3K27ac,control,rep2 (ChIP-seq)

value: human cervical adenocarcinoma cell


title: KU63

description: Library name: KU63


title: Ctrl, ESC, Rep4


title: KR30

description: Library name: KR30


title: KU61

description: Library name: KU61


title: KU89

description: Library name: KU89


title: Ctrl, ESC, Rep3


title: Cultured_mm55_pathogen,RAN-seq rep3

city: Yokohama

first: Imad

last: Abugessaisa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: IMS

country: Japan

institute: RIKEN

data_processing:
The quality of the raw reads was assessed using FastQC . We returned 152,647,712 total tags for M. mycetomatis samples.
M. mycetomatis raw reads mapped against M. mycetomatis genome assembly ASM127576v2
for each of the M. mycetomatis libraries on average 43.8 million reads mapped, of these on average 75.8% uniquely mapped.
We used STAR Aligner version 2.7.1a with default settings.
Assembly: GCA_001275765.2
Supplementary files format and content: tab-seperated valuess file include TSS gene expression level values for each Sample

organism: Madurella mycetomatis

extract_protocol: RNA-Seq libraries were prepared using 1 ug of total RNA with TruSeq Stranded mRNA Library Prep kit (Illumina) following the manufacturer's instructions.

value: Culture


title: UPF2_KD, ESC, Rep3


title: Microglia_Scramble - 5OLJ_ACTGAGCG_AGCTAGAA

value: Female


title: HeLa cells,H3K27ac,control,rep1 (ChIP-seq)


title: CD8_sgTrail - 5OLJ_TAGCGCTC_AGCTAGAA

value: 8 week

value: CD8 T Cells


title: Cultured_mm55_pathogen,RNA-seq rep2


title: CD8_sgTrail - 5OLJ_ATGCGCAG_AGCTAGAA

value: Brain


title: KR24

description: Library name: KR24


title: Ctrl, ESC, Rep1

value: human embryonic stem cells


title: KR27

description: Library name: KR27


title: Cultured_mm55_pathogen,RNA-seq rep1


title: pUPF1, NPC, Rep3

data_processing:
Reads were filtered for quality and aligned with STAR (2.5.2b) against the GRCh38 (Ensembl version 106).
Low quality reads were discarded by requiring the minimum quality threshold of 30 and at least 50% of bases in a read above this quality threshold. PCR duplication was removed using BEDTools.
After removal of PCR duplicates, the reads were re-aligned and peak calling was performed on a gene-by-gene basis using the CLAM program. Motifs were identified by using Homer. Track screen shots were produced in IGV (version2.6.2).
Assembly: GRCh38
Supplementary files format and content: Tab-delimited txt file including identified peaks

growth_protocol: Cells were cultured in plates coated with poly-ornithine/Laminin in DMEM/F12 media supplemented with N2 (1:200; Gemini), Gem21 (1:100; Gemini), and 20 ng/mL bFGF (Sigma).

extract_protocol:
Cellular RNAs bound by p-UPF1 were immunoprecipitated using anti-p-UPF1 [Millipore, anti-phospho-Upf1(Ser1127)] and Dynabeads protein A magnetic beads (Thermo Fisher Scientific). The RNA in bead-bound RNA–p-UPF1 complexes was digested by incubation for 20 min at 4°C with 1 U/μl RNase I (Ambion). To prepare RNA for cDNA library construction, after extensive washing, bound complexes were eluted using immunoprecipitation elution buffer (125 mM Tris-HCl [pH 6.8], 4% SDS, 20% glycerol, 0.1% bromophenol blue, 10% 2-mercaptoethanol). RNAs were purified using TRIzol reagent followed by ethanol precipitation. In parallel, control immunoprecipitations using rIgG were performed. Additional control samples (input) were prepared without immunoprecipitation.
Purified RNA fragments were used to make the library using the NEBNext Ultra II Directional Library Prep Kit (New England Biolabs), as per manufacturer's instructions. Libraries were sequenced (pair-end reads) with an Illumina NovaSeq 6000 platform for 100 cycles at the UCSD IGM core.

treatment_protocol: Before collection, cells were incubated in 50 nM okadaic acid for 3 hr.

value: Neural progenitor cells

tag: antibody

value: pUPF1 (Millipore, #07-1016)


title: CD8_sgTrail - 5OLJ_TACGCTGC_AGCTAGAA

value: TRAIL Knockdown by sgRNA


title: KR09

description: Library name: KR09

value: Retroperitoneal Sarcoma

value: FFPE


title: Cultured_mm55_pathogen, LQ-ssCAGE rep3

data_processing:
After performing base calling for all samples, we returned 68,428,840 total tags for the M. mycetomatis samples
For each of the M. mycetomatis libraries on average 22.8 million reads mapped, of these on average 35.0% uniquely mapped to ASM127576v2 genome
Using LQ-ssCAGE  a genome wide map of Transcription start site (TSS) was established
We used STAR Aligner version 2.7.1a with default settings.
Using LQ-ssCAGE  a genome wide map of Transcription start site (TSS) was established for both the Galleria mellonella larvae
Assembly: GCA_001275765.2
Supplementary files format and content: tab-seperated valuess file include TSS gene expression level values for each Sample


title: CD8_sgTrail - 5OLJ_CGGAGCCT_AGCTAGAA


title: Cultured_mm55_pathogen, LQ-ssCAGE rep2


title: KR07

description: Library name: KR07


title: CD8_sgTrail - 5OLJ_GCGTAGTA_AGCTAGAA


title: CD8_Scramble - 5OLJ_GGAGCTAC_AGCTAGAA

value: Control


title: IgG, NPC, Rep3

value: rIgG (Abcam, #ab171870 )

value: Before collection, cells were incubated in 50 nM okadaic acid for 3 hr.


title: Cultured_mm55_pathogen, LQ-ssCAGE rep1


title: KR03

description: Library name: KR03


title: Ctrl, ESC, Rep2

value: Ctrl


title: CD8_Scramble - 5OLJ_ACTCGCTA_AGCTAGAA


title: MDCK_stretch_replicate_4

city: Utrecht

first: Martijn

last: Gloerich

state: Utrecht

address: Universiteitsweg 100

department: Center for Molecular Medicine

country: Netherlands

institute: University Medical Center Utrecht

description: Library name: 8-STRETCH

data_processing:
Quality control on the sequence reads from the raw FASTQ files was done with FastQC (v0.11.8). TrimGalore (v0.6.5) was used to trim reads based on quality and adapter presence after which FastQC was again used to check the resulting quality. rRNA reads were filtered out using SortMeRNA (v4.3.3) after which the resulting reads were aligned to the reference genome CanFam4_GSD_1.0 using the STAR (v2.7.3a) aligner. Follow-up quality control on the mapped (bam) files was done using Sambamba (v0.7.0), RSeQC (v3.0.1) and PreSeq (v2.0.3). Readcounts were then generated using the Subread FeatureCounts module (v2.0.0).
Assembly: CanFam4_GSD_1.0
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Canis lupus familiaris

source_name: Kidney

growth_protocol: Madin-Darby Canine Kidney (MDCK) GII cells and derivatives were cultured at 37°C and 5% CO2 in low glucose Dulbecco’s Modified Eagle Medium (DMEM) (Sigma, D5523) containing 10% fetal bovine serum, 1 g/L sodium bicarbonate and 1% penicillin/streptomycin.

extract_protocol:
cell lysis and RNA isolation were performed using the NucleoSpin RNA mini kit for RNA purification (Macherey-Nagel, 740955.250) with DNase treatment. cDNA was synthesized using the iScript cDNA synthesis kit (Bio-Rad, 1708891). The quality and quantity of the RNA was measured using NanoDrop 2000 spectrophotometer (Thermo Scientific).
Truseq RNA stranded polyA

treatment_protocol: 6-well stretch devices were adapted from designs described by Simmons et al., (Simmons et al., 2011) and generated by attaching a stretchable polydimethylsiloxane (PDMS) membrane (0.25 mm thickness) to a custom made polymethylmethacrylate (PMMA) 6-well plate containing circular apertures, using polypropylene double-sided adhesive tape. The PDMS membrane was subsequently plasma treated to enable surface coating. The center of each well was coated with 0.05 mg/mL rat tail Collagen Type 1  in 0.1% (v/v) acetic acid, using a stainless steel ring (Ø 17 mm) placed in the center of each well and plates were sterilized by 1-minute exposure to UV light. Cells were plated onto the stretch devices in 400 µL drops of cell suspension at 1.7 × 105 cells/cm2. To optimize homogeneity in cell density, MDCK cells were plated in low-calcium (50 µM) DMEM. For all cell types, seeding medium was replaced by regular culture medium 1-2 hours after plating. Cells were cultured overnight, before application of stretch according to Simmons et al. (Simmons et al., 2011). In brief, the cell plate was placed on top of a 6-well PMMA baseplate containing 3 flat-bottom wells and three wells with a central pillar surrounded by a pneumatic compartment. Equi-biaxial in-plane strains of 18% in the cell monolayer were achieved by vacuum application to the pneumatic compartment using a pressure controler. Technical quadruplets were randomly divided over seperate 6-well stretch devices to prevent potential positional bias. The samples were isolated for further processing after 2 hours of strain application.

value: Kidney

value: MDCK GII

value: Epithelial kidney cells

value: Stretch


title: CD8_Scramble - 5OLJ_TCGACGTC_CTAGTCGA

value: Female

value: 8 week


title: IgG, NPC, Rep2


title: MDCK_stretch_replicate_3

description: Library name: 7-STRETCH


title: KR01

description: Library name: KR01


title: IgG, NPC, Rep1


title: MDCK_stretch_replicate_2

description: Library name: 6-STRETCH


title: KQ99

description: Library name: KQ99


title: KQ97

description: Library name: KQ97


title: Input, NPC, Rep3


title: CD8_Scramble - 5OLJ_CGATCAGT_CTAGTCGA

value: Brain

value: CD8 T Cells


title: pUPF1, NPC, Rep2

value: Neural progenitor cells


title: CD8_Scramble - 5OLJ_TGCAGCTA_CTAGTCGA


title: MDCK_stretch_replicate_1

description: Library name: 5-STRETCH


title: pUPF1, NPC, Rep1

value: pUPF1 (Millipore, #07-1016)


title: MDCK_control_replicate_4

description: Library name: 4-CTRL


title: KQ80

description: Library name: KQ80


title: Input, NPC, Rep1


title: CD4_sgTrail - 5OLJ_ACTGAGCG_CTAGTCGA

value: CD4 T Cells

value: TRAIL Knockdown by sgRNA


title: KR05

description: Library name: KR05

value: Retroperitoneal Sarcoma

value: FFPE


title: CD4_sgTrail - 5OLJ_CCTAAGAC_CTAGTCGA


title: MDCK_control_replicate_3

description: Library name: 3-CTRL

value: Control


title: KQ78

description: Library name: KQ78


title: pUPF1, ESC, Rep3

value: human embryonic stem cells

value: Before collection, cells were incubated in 50 nM okadaic acid for 3 hr.


title: CD4_sgTrail - 5OLJ_TAGCGCTC_CTAGTCGA


title: pUPF1, ESC, Rep2


title: KQ76

description: Library name: KQ76


title: KQ73

description: Library name: KQ73


title: CD4_sgTrail - 5OLJ_ATGCGCAG_CTAGTCGA


title: MDCK_control_replicate_1

description: Library name: 1-CTRL

value: Kidney


title: KQ67

description: Library name: KQ67


title: mads9 knockout replicate 3, 37

city: Beijing

first: Xueyan

last: Hu

state: Beijing

address: 38 Xueyuan Rd, Haidian District

country: China

institute: Peking University Health Science Center

data_processing:
For RNA-seq, adapters and low-quality segments were trimmed from the raw sequencing data. The cleaned data were aligned to the PM1 reference genome40 using HISAT2, and gene expression TPM (Transcripts per million) matrices were generated with StringTie2, correcting for sequencing depth and gene length. Differential expressed genes (DEGs) were identified by DESeq2 package with FDR < 0.05 and |log2(FC)| > 1. Functional enrichment of genes were preformed using ClusterProfiler package. For ChIP-seq, The clean reads generated by ChIP-seq were evaluated using FastQC (https://github.com/s-andrews/FastQC) and aligned to the reference PM1 genome with Bowtie2. Samtools was then used to sort and index BAM files and uniquely mapped reads were extracted using Sambamba. MACS2 was employed to call peaks for each sample, using input DNA as a control. ChIP-seq peaks were annotated, compared and visualized using ChIPseeker package, and motif analysis was conducted using MEME.
Assembly: PRJNA967827
Supplementary files format and content: RNA-seq_mads_count.txt (RNA-seq expression matrix)

molecule: polyA RNA

organism: Talaromyces marneffei

source_name: Talaromyces marneffei

growth_protocol: The wild-type Talaromyces marneffei strain PM1, isolated from a patient with culture-documented talaromycosis in Hong Kong, was utilized in this study. All strains (both mutants and wild type) were cultured on Sabouraud Dextrose Agar (SDA, Oxoid, Cambridge, UK) at 25°C for seven days to facilitate conidia collection and phenotypic observation, and at 37°C for an additional seven days for further observation. For total RNA extraction, all strains were grown in Sabouraud Dextrose Broth (SDB, Oxoid, Cambridge, UK) at 25°C or 37°C for three days.

extract_protocol:
Total RNA of strains was extracted using the E.Z.N.A. fungal RNA kit (Omega Bio-Tek), following the manufacturer’s instructions with DNase I digestion to eliminate genomic DNA. The RNA concentration was measured using Nanodrop (Thermo Fisher Scientific Inc. GorUSA), and the quality was assessed using Qsep1 (BiOptic, Inc., New Taipei City, Taiwan). RNA with a RIN > 8 was selected and stored at -80℃ until downstream preparation.  For ChIP-seq, Strains were collected and frozen by immersion in liquid nitrogen. Frozen samples were ground and cross-linked with 1% formaldehyde for 10 min at room temperature with gentle rotation. Cross-linking was stopped by adding 200 mM final concentration of glycine solution in PBS and cells were rotated at room temperature for 5 min. Fixed cells were pelleted at 1500 ×g for 10 min at 4℃ and washed twice with 10 mL of ice-cold PBS and pelleted at 1500 ×g for 10 min at 4℃ each time. Washed cell pellet was then stored at -80℃ until further processing.
RNA-seq library was performed and sequenced on the Illumina XTEN platform at the Novogene Bioinformatics Institute (Beijing, China), generating paired-end 150 bp reads. ChIP-seq was performed using Anti-FLAG (DYKDDDDK Tag Rabbit mAb, CST #14793) at the Boyun Huakang Gene Technology Ltd (Beijing, China).

value: Talaromyces marneffei

value: mads9 KO

value: 37 degree Celsius


title: Input, NPC, Rep2


title: KQ49

description: Library name: KQ49


title: IgG, ESC, Rep2

value: rIgG (Abcam, #ab171870 )


title: CD4_Scramble - 5OLJ_CGGAGCCT_CTAGTCGA

value: Female

value: 8 week


title: KQ47

description: Library name: KQ47


title: mads9 knockout replicate 2, 37


title: CD4_Scramble - 5OLJ_GCGTAGTA_CTAGTCGA

value: Brain


title: mads9 knockout replicate 1, 37


title: KQ45

description: Library name: KQ45


title: IgG, ESC, Rep1


title: CD4_Scramble - 5OLJ_GGAGCTAC_CTAGTCGA


title: Input, ESC, Rep3


title: mads9 knockout replicate 2, 25

value: 25 degree Celsius


title: KQ41

description: Library name: KQ41


title: CD4_Scramble - 5OLJ_ACTCGCTA_CTAGTCGA


title: mads9 knockout replicate 3, 25


title: MDCK_control_replicate_2

description: Library name: 2-CTRL

value: MDCK GII

value: Epithelial kidney cells


title: Input, ESC, Rep2


title: KQ39

description: Library name: KQ39


title: CD4_Scramble - 5OLJ_TACGCTGC_CTAGTCGA

value: CD4 T Cells


title: Input, ESC, Rep1


title: pUPF1, ESC, Rep1

value: pUPF1 (Millipore, #07-1016)


title: KQ36

description: Library name: KQ36

value: Retroperitoneal Sarcoma

value: FFPE


title: mads9 knockout replicate 1, 25


title: CFA40_12_Trail_positive - 5ADB_TACGCTGC_AGAGGATA

value: Brain Cells

value: TRAIL Positive Sorted


title: madsA knockout replicate 3, 37

value: madsA KO


title: IgG, ESC, Rep3

value: human embryonic stem cells

value: Before collection, cells were incubated in 50 nM okadaic acid for 3 hr.


title: KQ19

description: Library name: KQ19


title: MSC,3D cultured,rep3

city: Seoul

first: Jung-Woong

last: Kim

address: 84 Heuksuk-ro Dongjak-ku

department: Life Science

country: South Korea

institute: Chung-Ang University

data_processing:
Raw sequence reads were trimmed for adaptor sequence and masked for low-quality sequences using Trimgalore (ver. 0.6.6).
RNA-Seq reads were aligned using STAR (ver. 2.7.1a) by reads aligned to GRCh38.p13.103.
The counts values of transcripts were estimated by RSEM (ver. 1.3.3).
The FPKM values were calculated using 'fpkm' function from DESeq2 (ver. 1.32.0) that processes on the robust median ratio method.
To analyze a transcript as differentially expressed, EdgeR (ver. 3.36.0) calculates the results based on the normalized counts from entire sequence alignments.
Assembly: GRCh38.p13.103
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: Whole bone marrow

growth_protocol: Human bone marrow MSCs were derived from whole bone marrow from independent human donors (commercially available by AllCells, Alameda, CA, USA). For 2D culture, cells were cultured in Modified Eagle Medium-a (MEM-a, Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 20% fetal bovine serum (FBS, GW Vitek, Geumcheon-gu, Seoul, Korea), and 1% penicillin/streptomycin (Thermo Fisher Scientific) in a humidified atmosphere of 5% CO2 at 37°C. For 3D culture of MSCs, the bottom was coated with 4% pluronic F-127 (Sigma-Aldrich, St. Louis, MO, USA) for at least 16 h to prevent the cells from adhering to the bottom. 3D medium was prepared by supplementing MEM-a with 0.05% (v/v) FCeM Advance preparation kit. (Nissan Chemical Corporation, Tokyo, Japan) according to the manufacturer’s instruction. Cells were seeded at a density of 50,000 cells/well using 2D or 3D medium in 24-well plates and then cultured for 24 h.

extract_protocol:
Total RNA was extracted from 2D and 3D cultured MSCs using the RNeasy kit (Qiagen, Hilden, Germany) according to the manufacturer’s instruction and quantified with UV/VIS Nano spectrophotometer (Nabi, MicroDigital Co.,Ltd., Bundang-gu, Seongnam-si, Gyeonggi-do, Korea). Reverse transcription of RNA was performed using a Maxima First Strand cDNA Synthesis Kit (Thermo Fisher Scientific).
The construction of RNA-sequencing library was performed using Truseq RNA Sample preparation kit v2 (Illumina, Inc., San Diego, CA, USA, RS-122-2002).

value: Whole bone marrow

value: Mesenchymal Stem Cells

value: 3D cultured


title: CFA40_10_Trail_negative - 5ADB_CGGAGCCT_AGAGGATA

value: Female

value: 8 week

value: TRAIL Negative Sorted


title: KQ16

description: Library name: KQ16


title: MSC,3D cultured,rep2


title: CFA40_10_Trail_positive - 5ADB_GCGTAGTA_AGAGGATA

value: Brain


title: madsA knockout replicate 1, 37

value: Talaromyces marneffei

value: 37 degree Celsius


title: madsA knockout replicate 2, 37


title: KJ70

description: Library name: KJ70


title: CFA40_8_Trail_negative - 5ADB_GGAGCTAC_AGAGGATA


title: madsA knockout replicate 3, 25

value: 25 degree Celsius


title: KJ68

description: Library name: KJ68

value: Retroperitoneal Sarcoma


title: MSC,2D cultured,rep2

value: 2D cultured


title: madsA knockout replicate 2, 25


title: CFA40_8_Trail_positive - 5ADB_ACTCGCTA_AGAGGATA

value: Brain Cells


title: CFA40_12_Trail_negative - 5ADB_ATGCGCAG_AGAGGATA


title: madsA knockout replicate 1, 25


title: CFA40_1_Trail_negative - 5ADB_TCGACGTC_ATAGAGAG


title: MSC,2D cultured,rep1


title: mads9 overexpression replicate 3, 37

value: mads9 OE


title: KJ64

description: Library name: KJ64

value: FFPE


title: KJ62

description: Library name: KJ62


title: OxL2HG_9

city: Jerusalem

first: Inbar

last: Plaschkes

address: The Hebrew University of Jerusalem - Ein Kerem

department: The Faculty of Medicine - Ein Kerem

country: Israel

institute: HUJI

data_processing:
Raw reads were processed for quality trimming and adaptors removal using fastx_toolkit v0.0.14 and cutadapt v2.10 (ref 1). The processed reads were aligned to the mouse transcriptome and genome version WBcel235 with annotations from Ensembl release 106 using TopHat v2.1.1 (ref 2). Counts per gene quantification was done with htseq-count v2.01 (ref. 3). Normalization and differential expression analysis were done with the DESeq2 package v 1.36.0 (ref 4.).
Assembly: GRCm39
Supplementary files format and content: txt table with DESeq2 normalized and batch corrrected counts per gene (rows) per sample (column)

source_name: Testis

growth_protocol: Cells were incubated for 24 hours in MEM Eagle medium  (Ref # 01-040-1A from BI) supplemented with 2 mM glutamine, 5mM sodium lactate, 5mM sodium pyruvate, 15mM HEPES, 1% antibiotic-antimycotic (Thermo Scientific, 15240096) and  v/v, 5% dialyzed serum.

extract_protocol:
RNA was harvested using Triazol and RNeasy mini kit (74104) Qiagen
PolyA-selection, mRNA libraries were prepared using KAPA Stranded mRNA kit with mRNA Capture Beads (KAPA Biosystems, KK8421). In brief, 1µg was used for the library construction; library was eluted in 20µl of elution buffer. All DNA samples libraries were pooled to 10nM sample. Multiplex samples Pool were loaded on NovaSeq 6000 (Illumina), using NovaSeq 6000 SP Reagent Kit v1.5 100 cycles (cat# 20028401), with 122 cycles

treatment_protocol: During the above incubation period either vehicle (DMSO 0.15%) or 24 mM oxamate  with DMSO  0.15% or 24 mM oxamate (ChemCruz, sc-215880) and 0.3 mM octyl-L2HG (Cayman, 16367) dissolved in DMSO (final DMSO 0.15%) was added.

value: Testis

value: Round spermatids

value: WT

value: 24 mM oxamate +0.3 mM octyl-L2HG


title: CFA40_1_Trail_positive - 5ADB_TGCAGCTA_ATAGAGAG

value: TRAIL Positive Sorted


title: mads9 overexpression replicate 2, 37


title: KJ44

description: Library name: KJ44


title: mads9 overexpression replicate 1, 37


title: OxL2HG_7


title: OxL2HG_8


title: KJ40

description: Library name: KJ40


title: MSC,3D cultured,rep1

value: Whole bone marrow

value: Mesenchymal Stem Cells

value: 3D cultured


title: MSC,2D cultured,rep3


title: mads9 overexpression replicate 2, 25


title: Ox_6

value: 24 mM oxamate


title: Ox_5


title: mads9 overexpression replicate 3, 25

value: Talaromyces marneffei


title: KJ38

description: Library name: KJ38


title: KJ66

description: Library name: KJ66


title: KJ36

description: Library name: KJ36


title: KJ34

description: Library name: KJ34


title: mads9 overexpression replicate 1, 25


title: Ctr_3

value: vehicle


title: madsA overexpression replicate 2, 37

value: madsA OE

value: 37 degree Celsius


title: KJ32

description: Library name: KJ32

value: Retroperitoneal Sarcoma


title: Ctr_2


title: madsA overexpression replicate 3, 37


title: madsA overexpression replicate 1, 37


title: KJ42

description: Library name: KJ42


title: KJ14

description: Library name: KJ14


title: madsA overexpression replicate 3, 25

value: 25 degree Celsius


title: KJ11

description: Library name: KJ11


title: madsA overexpression replicate 2, 25


title: KH82

description: Library name: KH82


title: Ctr_1


title: KH79

description: Library name: KH79


title: madsA overexpression replicate 1, 25


title: wild type replicate 2, 37

value: wild type


title: KH58

description: Library name: KH58

value: FFPE


title: Ox_4

value: Testis


title: wild type replicate 3, 37


title: KH55

description: Library name: KH55


title: KH76

description: Library name: KH76


title: 24h after PHx -Liver macrophages 3 [M24_3]

city: Hangzhou

first: Yiyuan

last: Chen

state: Zhejiang

address: Huansha Road 261#

institute: Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province

data_processing:
Illumina Casava 1.8 software used for basecalling.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: Mus_musculus_Ensemble_106
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Liver macrophages

growth_protocol: Liver macrophages  were isolated using  BD Aria III

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

value: Liver macrophages

value: 24h after PHx


title: wild type replicate 1, 37


title: 24h after PHx -Liver macrophages 1 [M24_1]


title: wild type replicate 2, 25


title: 0h after PHx -Liver macrophages 2 [M0_2]

value: 0h after PHx


title: wild type replicate 3, 25


title: KH52

description: Library name: KH52


title: 48h after PHx -Liver macrophages 3 [M48_3]

value: 48h after PHx


title: Sh_luciferase(CTL) replicate 5

city: Freiburg

first: Tanja

last: Vogel

address: Albertstr. 23

country: Germany

institute: University of Freiburg

data_processing:
The all sequences of the raw BCL Basecall files where demultiplexed and converted into the Fastq file format using the Bcl2fastq conversion software v2.20.
Reads trimmed using Cutadapt (Galaxy Version 1.16.5)
Reads aligned using RNASTAR (Galaxy Version 2.6.0b-2)
Reads summarized using featureCounts (Galaxy Version 1.6.3+galaxy2)
Genome_build: mm10 ensembl
Supplementary_files_format_and_content: Differental gene expression was calculated using DESeq (Galaxy Version 2.11.40.6)

source_name: hippocampal neurons

growth_protocol: Grassi et al., 2017. (E18.5 hippocampal embryos were dissected, and cells cultivated for 7 days (DIV7).At DIV2 the hippocampal neurons were transduced with lentiviral particles containing specific short-hairpin RNA (ShRNA) to knock down the targeted gene).

extract_protocol:
Vezzali et al., 2016
NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer’s instructions (#E7530S/L, NEB, Frankfurt, Germany)

treatment_protocol: Grassi et al., 2017 (cells were treated with AraC at DIV4 and I applied Puromycin for selecting only infected cells)

value: hippocampal neurons DIV 7

value: Wild type (BL6 mouse)

tag: developmental stage

value: E18.5 embryos

value: Control


title: KH46

description: Library name: KH46


title: 48h after PHx -Liver macrophages 2 [M48_2]


title: 0h after PHx -Liver macrophages 1 [M0_1]


title: KH24

description: Library name: KH24


title: Primary hepatocyes1+4-Octyl Itaconate-3 [ITA3]

source_name: Primary hepatocyes

growth_protocol: Hepatocytes were seeded at a density of 2X10^6 cells  or 5 X10^6 cells  in DMEM with Earle salts , supplemented with 10 g/ml of streptomycin, 100 units/ml of penicillin. After cell attachment (4 h), the medium was replaced by fresh DMEM for 24 h

treatment_protocol: Treated with Remodelin hydrobromide or not then treated with Bobcat339, 4-Octyl Itaconate or DMSO.

value: Primary hepatocyes

value: 4-Octyl Itaconate


title: 48h after PHx -Liver macrophages 1 [M48_1]


title: mads9 overexpression replicate 5, 37, ChIP

data_processing:
For RNA-seq, adapters and low-quality segments were trimmed from the raw sequencing data. The cleaned data were aligned to the PM1 reference genome40 using HISAT2, and gene expression TPM (Transcripts per million) matrices were generated with StringTie2, correcting for sequencing depth and gene length. Differential expressed genes (DEGs) were identified by DESeq2 package with FDR < 0.05 and |log2(FC)| > 1. Functional enrichment of genes were preformed using ClusterProfiler package. For ChIP-seq, The clean reads generated by ChIP-seq were evaluated using FastQC (https://github.com/s-andrews/FastQC) and aligned to the reference PM1 genome with Bowtie2. Samtools was then used to sort and index BAM files and uniquely mapped reads were extracted using Sambamba. MACS2 was employed to call peaks for each sample, using input DNA as a control. ChIP-seq peaks were annotated, compared and visualized using ChIPseeker package, and motif analysis was conducted using MEME.
Assembly: PRJNA967827
Supplementary files format and content: FLAG-mads9-M-1_peaks.narrowPeak
Supplementary files format and content: FLAG-mads9-M-2_peaks.narrowPeak
Supplementary files format and content: FLAG-madsA-M-1_peaks.narrowPeak
Supplementary files format and content: FLAG-mads9-Y-1_peaks.narrowPeak
Supplementary files format and content: FLAG-madsA-Y-1_peaks.narrowPeak

value: Anti-FLAG

value: Talaromyces marneffei

value: mads9 OE


title: Sh_luciferase(CTL) replicate 4


title: mads9 overexpression replicate 4, 37, ChIP

value: 37 degree Celsius


title: 24h after PHx -Liver macrophages 2 [M24_2]


title: KH20

description: Library name: KH20

value: Retroperitoneal Sarcoma


title: Sh_luciferase(CTL) replicate 2


title: Sh_luciferase(CTL) replicate 3


title: KH22

description: Library name: KH22

value: FFPE


title: Primary hepatocyes1+4-Octyl Itaconate-2 [ITA2]


title: mads9 overexpression replicate 5, 25, ChIP

value: 25 degree Celsius


title: 0h after PHx -Liver macrophages 3 [M0_3]

value: Liver macrophages


title: Primary hepatocyes1+4-Octyl Itaconate-1 [ITA1]


title: KH49

description: Library name: KH49


title: mads9 overexpression replicate 4, 25, ChIP


title: KH16

description: Library name: KH16


title: wild type replicate 1, 25

value: wild type


title: Primary hepatocyes+Bobcat339-3 [BC3]


title: Sh_Foxg1 replicate 5

value: Knock-down Foxg1


title: madsA overexpression replicate 5, 37, ChIP

value: madsA OE


title: VCaP_BRD4_DexDHT_ChIP-seq_rep2

city: Kuopio

first: Ville

last: Paakinaho

address: Yliopistonranta 8

department: School of Medicine

country: Finland

institute: University of Eastern Finland

data_processing:
Basecalls performed using CASAVA, and FASTX-toolkit was used to trim low quality reads.
The reads were aligned to human reference genome version hg38 by using Bowtie2 software version 2.3.4.1. with end-to-end sensitive mode allowing no mismatches.
Peaks were called using HOMER program version 4.10. using findPeaks with style factor, FDR<0.01, >25 tags, >4-fold over control sample and local background. Corresponding EtOH sample was used as the control sample. AR and SMARCA4 ChIP-seq in EtOH and DHT treated VCaP cells were from GSE136016. FOXA1 ChIP-seq in EtOH (rep2), Dex (rep2) and DHT exposed VCaP cells were from GSE214757.
Assembly: hg38
Supplementary files format and content: bedGraph (HOMER makeUCSCfile command) from alignment file.

source_name: VCaP

growth_protocol: VCaP cells were grown in DMEM medium supplemented with 10% fetal bovine serum, 1 U/µl penicillin and 1 µg/ml streptomycin. All cells were kept at 37 °C in a humidified 95% air/ 5% CO2 incubator.

extract_protocol:
For ChIP-seq, after 1% formaldehyde crosslinking, cells were harvested, chromatin was sonicated to 100-300 bp fragments, and protein-DNA complexes were isolated with specified antibody.
ChIP-seq libraries were prepared with NEBNext Ultra II DNA Library Prep Kit according to instructions.

treatment_protocol: VCaP cells were treated with vehicle (EtOH) or 100 nM of Dexamethasone (Dex) or 100 nM of dihydrotestosterone (DHT) or Dex and DHT  for 1 h before the start of ChIPs.

value: VCaP

value: Vertebral Cancer of the Prostate

tag: dex treatment

tag: dht treatment

value: BRD4 (Bethyl Laboratories, A301-985A)


title: Primary hepatocyes+Bobcat339-2 [BC2]


title: Primary hepatocyes+Bobcat339-1 [BC1]


title: madsA overexpression replicate 4, 37, ChIP


title: VCaP_BRD4_DexDHT_ChIP-seq_rep1


title: Sh_Foxg1 replicate 3

value: hippocampal neurons DIV 7

value: Wild type (BL6 mouse)

value: E18.5 embryos


title: VCaP_BRD4_DHT_ChIP-seq_rep2


title: Primary hepatocyes3 [PH3]

value: Primary hepatocyes

value: DMSO


title: madsA overexpression replicate 5, 25, ChIP

value: Anti-FLAG

value: Talaromyces marneffei


title: madsA overexpression replicate 4, 25, ChIP


title: Primary hepatocyes2 [PH2]


title: VCaP_BRD4_DHT_ChIP-seq_rep1


title: mads9 overexpression replicate 5, 37

value: mads9 OE

value: 37 degree Celsius


title: Primary hepatocyes1 [PH1]


title: Sh_Purb replicate 5

value: Knock-down Purb


title: mads9 overexpression replicate 4, 37


title: VCaP_BRD4_Dex_ChIP-seq_rep1


title: Sh_Foxg1 replicate 1


title: VCaP_BRD4_EtOH_ChIP-seq_rep2


title: VCaP_BRD4_Dex_ChIP-seq_rep2


title: tpp 38C∆ 42AB∆_3

city: Kumamoto

first: Shingo

last: Usuki

address: 2-2-1 Honjo, Chuo-ku

department: Institute of Molecular Embryology and Genetics (IMEG)

institute: Kumamoto University

data_processing:
Adaptor trimming and QC were done using Trim galore (v0.6.5).
Mapping of the trimmed reads on the reference was done using STAR (v2.7.9a).
Calculating CPM were performed using SAMtools(v1.15)
Assembly: Drosophila melanogaster BDGP6.48
Supplementary files format and content: tab-delimited text file includes CPM values for each sample

organism: Drosophila melanogaster

source_name: ovary

growth_protocol: Fly lines were maintained at 25℃ on standard cornmeal agar medium.

extract_protocol:
Total RNA was extracted from dissected ovaries using Isogen2 (Nippon Gene, Tokyo, Japan).
Sequencing libraries were prepared using illumina TruSeq Stranded mRNA Library Prep Kit

value: ovary

value: tpp[fs4] 38Cdelta 42ABdelta/Df(2L)BSC110 38Cdelta 42ABdelta


title: mads9 overexpression replicate 5, 25

value: 25 degree Celsius


title: tpp 38C∆ 42AB∆_2


title: mads9 overexpression replicate 4, 25


title: Sh_Foxg1 replicate 4

value: Knock-down Foxg1


title: Sh_Purb replicate 4


title: Sh_Purb replicate 3


title: madsA overexpression replicate 5, 37

value: madsA OE


title: VCaP_BRD4_EtOH_ChIP-seq_rep1

value: VCaP

value: Vertebral Cancer of the Prostate


title: VCaP_FOXA1_DexDHT_ChIP-seq_rep2

value: FOXA1 (Abcam, ab23738)


title: tpp 38C∆ 42AB∆_1


title: Sh_Purb replicate 1

value: hippocampal neurons DIV 7

value: Wild type (BL6 mouse)


title: madsA overexpression replicate 4, 37


title: Sh_Purb replicate 2

value: E18.5 embryos


title: 38C∆ 42AB∆_3

value: 38Cdelta 42ABdelta


title: 38C∆ 42AB∆_2


title: madsA overexpression replicate 5, 25


title: sh_Pantr1 replicate 5

value: Knock-down Pantr1


title: VCaP_FOXA1_DexDHT_ChIP-seq_rep1


title: Sh_Foxg1 replicate 2


title: VCaP_FOXA1_Dex_ChIP-seq_rep1


title: 38C∆ 42AB∆_1


title: madsA overexpression replicate 4, 25

value: Talaromyces marneffei


title: tpp_3


title: MpDELLAmiRNA_Mpvih_2_3

city: Bangalore

first: Debabrata

last: Laha

address: C V Raman Institute

institute: Indian Institute of Science

data_processing:
The sequencing reads were proceesed using FastQC and adapter content was removed using Trim-Galore (v0.6.6). rRNA reads were removed using RiboDetector (v0.2.7).
Reads were mapped against M. polymorpha reference genome MpTak v6.1r2 (https://marchantia.info/) using Salmon v1.4.0.
Differential gene expression analysis was performed using Deseq2 v1.36.0. Gene ontology analysis was carried out using Fuzzy Gene Ontology (GO) (2021) annotation using blast2go algorithm 18.
GO enrichment analysis was conducted using the biological process terms topGO.
Assembly: MpTak_v6.1r2 release of Marchantia polymorpha
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Marchantia polymorpha

source_name: Thallus

growth_protocol: M. polymorpha plants were grown on half-strength Gamborg’s B5 medium (HIMEDIA # PT127) containing 1% phytagel (Merck # P8169) at 22°C in long day condition with a period of 16 h light (50-60 µmolm-2sec-1) and 8 h dark in a Percival growth chamber (AR-41L3).

extract_protocol:
Total RNA was extracted from 1-month-old M. polymorpha genotypes thalli using a Qiagen RNeasy Plant Mini Kit (Cat. #74904).
RIN (RNA integrity number) values of each RNA samples was profiled through tapestation 4150 and RNA samples with RIN>6 was considered for the library preparation.
Library preparation was carried out using TruSeq Stranded Total RNA Library Prep plant kit (Illumina #20020611) following the manufacturer protocol.

treatment_protocol: No treatment were given to plants, prior to RNA extraction.

value: Thallus

value: Plant cell

value: MpDELLA knockdown line in Mpvih knockout background


title: VCaP_SMARCA4_DexDHT_ChIP-seq_rep2

value: SMARCA4 (Abcam, ab110641)


title: VCaP_FOXA1_EtOH_ChIP-seq_rep1


title: tpp_2

value: ovary


title: sh_Pantr1 replicate 3


title: sh_Pantr1 replicate 2


title: VCaP_SMARCA4_DexDHT_ChIP-seq_rep1


title: tpp_1


title: MpDELLAmiRNA_Mpvih_2_2


title: MpDELLAmiRNA_Mpvih_2_1


title: sh_Pantr1 replicate 1


title: VCaP_SMARCA4_Dex_ChIP-seq_rep2


title: Sh_luciferase(CTL) replicate 1

value: Control


title: aub_3

value: aub[QC/HK]


title: MpDELLAmiRNA_Mpvih_1_3


title: HD_cg_3

city: London

first: Stephen

last: Sturzenbaum

address: 150 Stamford Street

department: Analytical, Environmental and Forensic Sciences

country: United Kingdom

institute: King's College London

data_processing:
Original image data file from high-throughput sequencing (like Illumina) was transformed into sequenced reads (Raw Data or Raw Reads) by CASAVA base recognition (Base Calling).  Adapter and quality trimming were performed on the raw reads to remove possible adapter sequences and poor quality reads.
Clean reads were de novo assembled by Trinity to obtain the assembly transcriptome. Then Corset performed Hierarchical Clustering to remove redundence. A minimum contig length of  150 base pairs was required.
After performing the de novo transcriptome assembly with Trinity, gene hit counts and FPKM values were calculated by mapping the trimmed sequence reads to the newly assembled transcriptome
After mapping and total gene hit counts calculation, the total gene hit counts table was used for downstream differential expression analysis using DESeq2
Genes with adjusted p-value < 0.05 and Log2Fold change >1 were defined as differentially expressed genes for each comparison
Assembly: Trinity.fasta
Supplementary files format and content: MS Excel files containing raw counts for each comparison.
Supplementary files format and content: MS Excel files containing FPKM values for each comparison.

organism: Dendrobaena veneta

source_name: Cerebral ganglion

growth_protocol:
No additional food was added to the soil during the exposure time to control the uptake of drugs
Adult animals were cleaned with deionized water and transferred to plastic containers containing topsoil with /without carbamazepine until further processing

extract_protocol:
Total RNA was extracted from gut and cerebral ganglion tissues, using first Trizol reagent then followed by the Quick-RNA™ MiniPrep kit (Zymo Research, Irvine, USA) according to manufacturer's protocol
Libraries were prepared according to Illumina's instructions. Briefly, mRNAs were purified using Poly(A) selection from total RNA and then fragmented. First strand cDNA was synthesized using random priming, followed by the synthesis of the second strand. The resulting double-strand cDNA was end repaired, phosphorylated and A-tailed. Adapter ligation and PCR amplification were performed, rendering the library ready for Illumina flow cell clustering and sequencing on an Illumina HiSeq  X Ten following the manufacturer's protocols.

treatment_protocol: The adult worms were transferred to moist soil (top soil, spiked with 10 mg/kg carbamazepine and allowed to settle for 48 h prior to use), stored in well-ventilated plastic boxes in the dark at 15°C (± 0.2°C) for 28 days

value: Cerebral ganglion

value: High dose cerebral ganglion (4 week 10 mg/kg carbamazepine soil exposure, cerebral ganglion tissue)


title: MpDELLAmiRNA_Mpvih_1_2


title: aub_2


title: VCaP_SMARCA4_Dex_ChIP-seq_rep1

value: VCaP

value: Vertebral Cancer of the Prostate


title: aub_1


title: HD_cg_1


title: MpDELLAmiRNA_Mpvih_1_1


title: HD_cg_2


title: VCaP_AR_DexDHT_ChIP-seq_rep1

value: AR (rabbit antiserum; Karvonen et al. 1997)


title: VCaP_AR_DexDHT_ChIP-seq_rep2


title: yw_3

value: yw


title: sh_Pantr1 replicate 4

value: hippocampal neurons DIV 7

value: Wild type (BL6 mouse)

value: E18.5 embryos


title: Mpvih_2_3

value: MpVIH Knock out line


title: HD_gut_2

source_name: Gut

value: Gut

value: High dose gut (4 week 10 mg/kg carbamazepine soil exposure, gut tissue)


title: Mpvih_2_1

value: Thallus

value: Plant cell


title: VCaP_GR_DexDHT_ChIP-seq_rep1

value: GR (Santa Cruz Biotechnology, sc-1003)


title: VCaP_GR_DexDHT_ChIP-seq_rep2


title: Non-Tumor_6

description: Library name: HJWHHDRXY.TCCTGAGC

data_processing:
The raw sequences from all the samples were aligned to the GRCm38/GRCh38 reference genome and quantified using Drop-Seq pipeline.
Assembly: GRCm38/GRCh38 reference genome
Supplementary files format and content: h5 files of the Count matrix of these sequencing runs.

source_name: Brain

extract_protocol:
Briefly, frozen tissue was minced with a razor blade and mechanically homogenized in Nuclei EZ Lysis Buffer (Sigma-Aldrich). After incubation for 5 min, the homogenate was filtered through a 70µm strainer mesh. Two washing steps were performed with a 1% solution of bovine serum albumin (BSA) (Sigma-Aldrich, A3294-100G) in phosphate buffered saline (PBS) (Thermo Fisher Scientific, 14190250), with addition of 0.2U/µL of RNase Inhibitor (Lucigen, 30281-2). Centrifugation occurred at 500xg for 5 minutes at 4°C. To separate nuclei from cell debris, nuclei suspensions were incubated for 10 min with 10µg/mL 4',6-Diamidin-2-phenylindol (DAPI) (Sigma, #D9542) in wash buffer to stain DNA. Subsequently, DAPI+ nuclei were sorted via fluorescence activated cell sorting (FACS) and utilized for Drop-Seq as described below. When Aldh1l1Cre-ERT2/TdTomato astrocyte reporter mice (The Jackson Laboratory, #031008 and #007909) were used, 200mg/kg Tamoxifen (Sigma-Aldrich, T5648) diluted in corn oil (Sigma-Aldrich, C8267) was administered intraperitoneally 2-4 weeks before starting the experiment and TdTomato induction was confirmed by flow cytometry at the time of measurement. 1 x 105 GL261-Luc2 cells (ATCC) were implanted intracranially. GL261 cells with passage number < 10 were detached using Accutase (Stemcell Technologies) and cell suspensions prepared in serum-free DMEM. The surgical procedure was performed following IACUC guidelines for survival surgery. Briefly, a small animal stereotaxic frame (David Kopf Instruments) was placed within a laminar flow cabinet and a sterile field containing all surgical instruments and tools was established. An activated charcoal filter (VetEquip) was connected to the outflow to adsorb Isoflurane. Mice were individually placed in an anesthesia induction chamber and a flow of Isoflurane (Patterson Veterinary) at 2.5-3 L/h mixed with oxygen at 2.5 L/h was initiated. The top of the skull was shaved and disinfected using isopropyl swabs (Becton Dickinson) and application of the antiseptic Betadine (Purdue Products). For intracranial injection, the mouse skull was fixed on the stereotaxic frame using ear bars and a mouthpiece for incisor fixation and gas supplementation. Sufficient depth of anesthesia was confirmed by a toe pinch, and mouse vital signs were monitored throughout the procedure. Following a 2cm incision on the scalp, the injection coordinates were determined from bregma. A hole was drilled at the +1.8 mm (lateral) and +0.5 mm (anterior) position. A 25µl glass syringe (Hamilton) was inserted until -3.5 mm depth and slowly retracted 0.5 mm to the final injection site at -3mm depth. 3µL of GL261 cell suspension were gradually injected at a rate of 1 µl/ min. Control mice received a sham injection of 3µL DMEM. Astrocyte sorting from Aldh1l1Cre-ERT2/TdTomato astrocyte reporter mice was performed by gating Live+ CD45- CD11b- TdTomato+. Drop-Seq113 was used for scRNA-seq via co-encapsulation of uniquely barcoded beads and single cells in nanoliter droplets prior to cell/nucleus lysis and transcriptome capture. Following the protocol developed by Macosko et al.113, barcoded MACOSKO-2011-10 B beads (Chemgenes) linked to 108 uniquely barcoded oligonucleotides (5’-Bead–Linker-TTTTTTTAAGCAGTGGTATCAACGCAGAGTACJJJJJJJJJJJJNNNNNNNNTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT-3’) were resuspended in a wash solution made of 10 mM Tris pH 8.0 (Sigma-Aldrich, T3038), 1 mM EDTA (Amresco, E177-100ML) and 0.01% Tween‐20 (Sigma-Aldrich, P9416) (TE-TW) at a density of 3 x 105/mL and stored at 4°C. Immediately prior to use, beads were centrifuged at 1000xg and resuspended in 1mL of lysis buffer composed of 570µL OptiPrep (Sigma-Aldrich, D1556-250ML), 120µL 20% Ficoll PM‐400 (Cytiva, 17-0300-10), 20µL 10% Sarkosyl (Sigma-Aldrich, L7414-50ML), 40µL 0.5M EDTA (Amresco, E177-100ML), 200µL 1M Trizma hydrochloride solution pH 8.0 (Sigma-Aldrich, T2663-1L), 50µL 1M dithiothreitol (Thermo Fisher Scientific, P2325) (DTT). Sorted cells or nuclei were taken up in 16% OptiPrep at a concentration of 2.5x105/mL in 1mL. If fewer cells or nuclei were available, Fluorinert FC-40 (Sigma Aldrich, F9755-250ML) was used as a backflow liquid. If fewer than 1x105 cells were available, bead concentrations were doubled to 6x105/mL to increase the capture rate, which follows a Poisson distribution. Beads and cells were taken up in a 3mL syringe (BD), adding a magnetic disk (VP Scientific, 772DP-N42-5-2) and using a magnetic stirrer (VP Scientific) to homogenize bead suspensions. QX200 Droplet Generation Oil for EvaGreen (BioRad, 1864006) was taken up in a 10mL syringe (BD). Three Legato 100 syringe pumps (KD Scientific) were loaded with oil, cell, and bead syringes, and PE/2 polyethylene microtubing (Scientific Commodities Inc., BB31695-PE/2) was used to connect them to the device input holes of PDMS devices placed on an inverted light microscope with an attached Fire-i 830b camera (Unibrain). Fire-i (Unibrain) was used to visualize rapidly flowing droplets with lowest shutter speed and highest exposure and gain settings. The device was initially primed with oil, prior to connecting cell and lastly bead flows at flow rates of 4500, 1500 and 1500 µL/h, respectively. Output flow containing droplets was collected for 20-25min or until the cell suspension was used up. For droplet breakage, approximately 1/3 of excess oil volume was added as 97% 1H,1H,2H,2H-Perfluoro-1-octanol (Sigma-Aldrich, 370533), along with 30mL of 6X sodium chloride-sodium citrate (SSC) buffer (National Diagnostics, EC-873). Emulsions were shaken a few times and centrifuged at 1000xg for 1min, resulting in a visible bead layer floating at the interface of oil and SSC. In the following steps, as much of the oil and SSC as possible was removed, while topping up with fresh SSC and centrifuging to wash the beads prior to reverse transcription (RT) into cDNA. Beads were washed in 300µL of 1x RT buffer (Thermo Fisher Scientific, EP0742) prior to incubation in 200µL RT mix composed of 75µL H2O, 40µL 5x RT buffer, 40µL 20% Ficoll PM-400 (Cytiva, 17-0300-10), 20µL 1mM dNTPs (Thermo Fisher Scientific, R0194), 5µL RNase Inhibitor (Lucigen, 30281-2), 10µL 50µM Template Switch Oligo (AAGCAGTGGTATCAACGCAGAGTGAATrGrGrG, IDT) and 10µL (with 2000U) Maxima H Minus Reverse Transcriptase (Thermo Fisher Scientific, EP0742) for 30 min at room temperature and 90 min at 42°C (with rotation in both cases). Reaction mixtures were then washed with 1mL of a solution containing 10mM Tris pH 8.0, 1mM EDTA and 0.5% sodium dodecyl sulfate (Sigma-Aldrich, L3771-100G) (TE-SDS), twice with 1mL of TE-TW, and once with 1mL 10mM Tris pH 8.0. To remove bead-linked oligonucleotides that had not captured an mRNA molecule, beads were incubated in a mix of 20µL 10x Exonuclease I buffer (Thermo Fisher Scientific, EN0581), 170µL H2O and 10µL (with 200U) Exonuclease I (Thermo Fisher Scientific, EN0581) for 45min at 37°C with rotation. After washing once with TE-SDS, twice with TE-TW and once with 1mL H2O beads were counted using a hemocytometer chamber and divided into 4000 beads per aliquot in PCR tubes. A PCR mix containing 24.6µL H2O, 0.4µL 100µM SMART PCR primer (AAGCAGTGGTATCAACGCAGAGT) (IDT) and 25µL 2x Kapa HiFi Hotstart Readymix (Kapa Biosystems, 7958927001) were added. PCR was performed in a thermocycler with the following program to amplify cDNA molecules: 95°C (3 min); 4 cycles of: 98°C (20 s), 65°C (45 s), 72°C (3 min); 9 cycles of: 98°C (20 s), 67°C (20 s), 72°C (3 min); 72°C (5 min); 4°C hold. PCR products were purified using AMPure XP beads (Beckman Coulter, A63881) at a 0.6x ratio according to manufacturer's protocol, eluting all samples in 50µL molecular grade H2O (Thermo Fisher Scientific, AM9937). At this point, the distribution of fragment sizes within cDNA libraries was quantified using a 2100 Bioanalyzer (Agilent) instrument with High Sensitivity DNA Kit (Agilent, 5067-4626). Library concentration and quality was assessed by a rounded curve with average sizes around 700 bp. In cases where DNA concentration was not sufficient, additional PCR cycles with the following conditions were added as needed: 98°C (20 s), 67°C (20 s), 72°C (3 min). 600pg of cDNA library in 5µL were used for fragmentation and addition of sample tags by means of the Nextera XT DNA Library Prep Kit (Illumina, FC-131-1096). cDNA was added to 10µL of Nextera Tagment DNA buffer and 5µL of Amplicon Tagment Mix. After incubation for 5min at 55°C, 5µL of Neutralize Tagment buffer was added. After 5 min at room temperature, a mix containing 15µL Nextera PCR Mix, 8µL H2O, 1µL 10µM New-P5-SMART PCR hybrid oligo (AATGATACGGCGACCACCGAGATCTACACGCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGT*A*C) (IDT), and 1µL of a 10µM sample-specific Nextera indexing oligonucleotide (Illumina, FC-121-1011). Samples underwent PCR with the following program: 95°C (30 s); 12 cycles of: 95°C (10 s), 55°C (30 s), 72°C (30 s); 72°C (5 min); 4°C hold. cDNA was purified AMPure XP beads at a 0.6x ratio and eluted in 10µL H2O. Library distribution was analyzed using a 2100 Bioanalyzer and the molarity-weighted average fragment size was calculated. The Library Quantification Kit (Kapa Biosystems) was used to determine library concentrations by qPCR according to standard protocol. Finally, 4µL samples were pooled at an equimolar ratio of 5nM. Finally, samples were sequenced using NovaSeq S2 at with a Custom Read 1 primer (GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC), estimating around 25,000 reads per STAMP. STAMPs were estimated by multiplying the cell number used (determined by flow rate, run time and concentration) with the co-encapsulation probability (given by the product of the encapsulation probability of either cells or beads). The co-encapsulation probability of single units follows a Poisson distribution as a function of droplet volume and cell or bead concentration and was 2.5% for mouse samples and on average 1.4% for human nuclei.
Library was constructed using Drop-Seq protocols

value: Brain

value: Astrocytes


title: HD_gut_3


title: Mpvih_1_3


title: LD_cg_3

treatment_protocol: The adult worms were transferred to moist soil (top soil, spiked with 0.6 mg/kg carbamazepine and allowed to settle for 48 h prior to use), stored in well-ventilated plastic boxes in the dark at 15°C (± 0.2°C) for 28 days

value: Cerebral ganglion

value: Low dose cerebral ganglion (4 week 0.6 mg/kg carbamazepine soil exposure, cerebral ganglion tissue)


title: VCaP_GR_Dex_ChIP-seq_rep2

value: VCaP


title: yw_2

value: ovary


title: HD_gut_1


title: Mpvih_2_2


title: LD_cg_2


title: yw_1


title: VCaP_GR_EtOH_ChIP-seq_rep2

value: Vertebral Cancer of the Prostate


title: Mpvih_1_2


title: Non-Tumor_5

description: Library name: HJWHHDRXY.CGTACTAG


title: Mpvih_1_1


title: LD_cg_1


title: Tumor_5

description: Library name: HJWHHDRXY.CGAGGCTG


title: Tak2_WT-Gemma_3

value: WT plant


title: LD_gut_3

value: Low dose gut (4 week 0.6 mg/kg carbamazepine soil exposure, gut tissue)


title: VCaP_ATAC_DexDHT_rep2

data_processing:
Basecalls performed using CASAVA, and FASTX-toolkit was used to trim low quality reads.
The reads were aligned to human reference genome version hg38 by using Bowtie2 software version 2.3.4.1. with end-to-end sensitive mode allowing no mismatches.
Peaks were called using HOMER program version 4.10. using findPeaks with style factor, FDR<0.01, >25 tags, >4-fold over control sample and local background. Transposase treated naked DNA sample was used as the control sample (GSE214757).
Assembly: hg38
Supplementary files format and content: bedGraph (HOMER makeUCSCfile command) from alignment file.

extract_protocol:
For ATAC-seq, 100 000 isolated nuclei were treated with 2.5 µl Tn5 Transposase loaded with sequencing adapters.
ATAC-seq libraries were prepared with loaded Diagenode Tagmentase (#C01070012) according to instructions.

treatment_protocol: VCaP cells were treated with vehicle (EtOH) or 100 nM of Dexamethasone (Dex) or 100 nM of dihydrotestosterone (DHT) or Dex and DHT  for 1 h before the start of nuclei extraction.


title: LD_gut_2


title: Tak2_WT-Gemma_2


title: Tumor_4

description: Library name: HJWHHDRXY.AGGCAGAA


title: VCaP_GR_Dex_ChIP-seq_rep1


title: VCaP_ATAC_DexDHT_rep1


title: Non-Tumor_4

description: Library name: HJWHHDRXY.AAGAGGCA


title: CON_cg_3

treatment_protocol: The adult worms were transferred to moist soil (top soil, spiked with MeOH and allowed to evaporate for 48 h prior to use), stored in well-ventilated plastic boxes in the dark at 15°C (± 0.2°C) for 28 days

value: Control cerebral ganglion (4 week MeOH spiked soil exposure, cerebral ganglion tissue)


title: VCaP_ATAC_DHT_rep2


title: Non-Tumor_2

description: Library name: TACGCTGC


title: LD_gut_1


title: VCaP_ATAC_DHT_rep1


title: Tumor_3

description: Library name: GGAGCTAC


title: CON_cg_2


title: Non-Tumor_3

description: Library name: TAGCGCTC


title: oldmouse2

city: beijing

first: Wei

last: Ying

state: beijing

address: beijing

institute: Peking union medical college

data_processing:
Raw reads were processed using Trimmomatic.The reads containing ploy-N and the low quality reads were removed to obtain the clean reads and the clean reads were mapped to reference genome using hisat2.
FPKM value of each gene was calculated using cufflinks and the read counts of each gene were obtained by htseq-count. DEGs were identified using the DESeq (2012) R package functions estimateSizeFactors and nbinomTest.
FPKM and read counts value of each transcript (protein_coding) was calculated using bowtie2 and eXpress and DEGs were identified using. the DESeq[6] (2012) functions estimateSizeFactors and nbinomTest
The reads were reassembled using StringTie.Then gene structure extension and novel transcripts identification were performed by comparing the reference genome and the known annotated genes using cuffcompare software
Hierarchical cluster analysis of DEGs was performed to explore genes expression pattern. GO enrichment and KEGG pathway enrichment analysis of DEGs were respectively performed using R based on the hypergeometric distribution
The alternatively splicing analysis of differentially regulated transcripts isoforms or exons was performed using ASprofile.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: heart

extract_protocol:
Total RNA was harvested using mirVana™ miRNA ISOlation Kit and was stored at -70.
RNA libraries for RNA-seq were prepared usingTruSeq Stranded mRNA LTSample Prep Kit following manufacturer's protocols.

value: heart

tag: group

value: old

value: WT

value: no treatment


title: Tak2_WT-Gemma_1

value: Thallus


title: oldmouse3


title: CON_cg_1


title: VCaP_ATAC_Dex_rep1


title: VCaP_GR_EtOH_ChIP-seq_rep1


title: VCaP_ATAC_Dex_rep2


title: Tumor_6

description: Library name: HJWHHDRXY.TAAGGCGA


title: Non-Tumor_1

description: Library name: GCGTAGTA


title: Tumor_2

description: Library name: CGGAGCCT


title: Tumor_1

description: Library name: ATGCGCAG


title: VCaP_ATAC_EtOH_rep1


title: CON_gut_2

value: Gut

value: Control gut (4 week MeOH spiked soil exposure, gut tissue)


title: VCaP_ATAC_EtOH_rep2


title: youngmouse2

value: young


title: youngmouse1


title: CON_gut_1


title: GB_LT_Patient-17

status: Public on May 20 2025

city: Kaunas

first: Giedrius

last: Steponaitis

address: Eiveniu str. 4

department: Neuroscience Institute

country: Lithuania

institute: Lithuanian University of Health Sciences

description: Library name: GB_322058

data_processing:
Fast5 files were base-called with high accuracy mode using Guppy (v5.0.11), applying a configuration file for dRNA-seq ("rna_r9.4.1_70bps_hac.cfg"): guppy_basecaller -i ${FAST5_INPUT} -s ${FASTQ_OUTPUT} -c ${CONFIG} --fast5_out --disable_pings --num_callers 16
Base-called fast5 files were processed with Poreplex (ver.: 0.5) to demultiplex fast5 files:  poreplex -i ${FAST5_INPUT} -o ${FASTQ_OUTPUT} --barcoding --trim-adapter --fast5 --parallel 16
FASTQ files were alligned to the full Ensembl reference transcriptome (GRCh38.p13; ver.: 105, cDNA + ncRNA) using Minimap2 software (ver. 2.17-r941), sorted and indexed with Samtools (ver.: 1.15.1): minimap2 -ax map-ont -p 0 -N 10 -t 50 ${Ref_index} ${Reads_fq} | samtools sort -o ${BAM} -@ 50 -l 9
RNA expression assessed using NanoCount (ver. 1.0.0.post6): NanoCount --alignment_file ${BAM} --count_file ${NANOCOUNT_OUT} --filter_bam_out ${FILTERED_BAM} --min_alignment_length 50 --min_query_fraction_aligned 0.5 --sec_scoring_value alignment_score --sec_scoring_threshold 0.95 --convergence_target 0.005 --max_em_rounds 100
m6A modifications assessed using EpiNano (ver.: ) python3 Epinano_Variants.py --number_cpus 32 --reference $REF_FILE --bam $BAM_FILE --sam2tsv misc/sam2tsv.jar --type t; awk -F ',' '{ if ($5 > 2) print }' $SAMPLE.plus_strand.per.site.csv > $SAMPLE.plus_strand.per.site.csv; python3 Slide_Variants.py $SAMPLE.plus_strand.per.site.csv 5; awk 'NR==1; /[GA][GA]AC[ACT]/{print}' $SAMPLE.plus_strand.per.site.csv.per_site.5\mer.csv > $SAMPLE.plus.per_site.cov_2.5\mer.RRACH.csv; python3 Epinano_Predict.py --model models/rrach.q3.mis3.del3.linear.dump --predict  $SAMPLE.plus.per_site.cov_2.5\mer.RRACH.csv --columns 8,13,23 --out_prefix $SAMPLE.cov_2.m6A
Assembly: Full Ensembl reference transcriptome (GRCh38.p13; ver.: 105, cDNA + ncRNA)
Supplementary files format and content: Processed file NAT_lnc.csv contains calculated tpm for each sample: lncRNA and overlapping gene are provided in one row

source_name: Glioma surgical sample

extract_protocol:
RNA isolated with TRIzol (cat. no.: 15596026; protocol no.: MAN0001271 Rev. C.0). Poly-A enrichment using Dynabeads mRNA DIRECT purification kit (cat. no.: 61012; protocol no.: June 2012 Rev. 009)
Libraries prepared applying Direct RNA sequencing kit (cat. no.: SQK-RNA002; protocol no.: DRS_9080_v2_revO_14Aug2019) from 600 ng of poly-A enriched RNA. Maunifacturer's protocol was adjusted for multiplexing according to directions made by the Poreplex author (https://github.com/hyeshik/poreplex)

value: Glioma surgical sample

tag: disease

value: Glioblastoma

tag: overal survival_(days)

tag: overal survival_status

value: Alive

value: Female

tag: cause of_death

tag: diagnosis (icd-10_code)

tag: diagnosis (notation)

tag: year of_surgery

tag: mgmt promoter_methylation_status

value: unmethylated

tag: idh1 mutation_status

value: wild type

tag: column names_for_"tpm_all_samples.csv"


title: GB_LT_Patient-13

description: Library name: GB_306058

tag: tissue

value: Dead

tag: Sex

value: methylated


title: GB_LT_Patient-15

description: Library name: GB_308090


title: GB_LT_Patient-16

description: Library name: GB_311816

value: Male


title: GB_LT_Patient-11

description: Library name: GB_304634


title: GB_LT_Patient-14

description: Library name: GB_306218


title: GB_LT_Patient-10

description: Library name: GB_304627


title: oldmouse1

value: heart

tag: genotype

tag: treatment


title: GB_LT_Patient-9

description: Library name: GB_303989


title: GB_LT_Patient-12

description: Library name: GB_304641


title: GB_LT_Patient-7

description: Library name: GB_301251


title: youngmouse3


title: GB_LT_Patient-8

description: Library name: GB_303132


title: CON_gut_3


title: GB_LT_Patient-2

description: Library name: GB_233651


title: GB_LT_Patient-3

description: Library name: GB_238328


title: GB_LT_Patient-1

description: Library name: GB_231473


title: GB_LT_Patient-4

description: Library name: GB_295604


title: LGG_LT_Patient-9

description: Library name: LGG_311687

value: Low Grade Glioma

value: mutation


title: GB_LT_Patient-6

description: Library name: GB_301220


title: LGG_LT_Patient-8

description: Library name: LGG_228930


title: LGG_LT_Patient-7

description: Library name: LGG_227728


title: GB_LT_Patient-5

description: Library name: GB_269360


title: LGG_LT_Patient-5

description: Library name: LGG_211642


title: LGG_LT_Patient-6

description: Library name: LGG_211697


title: LGG_LT_Patient-3

description: Library name: LGG_208673


title: LGG_LT_Patient-1

description: Library name: LGG_102940


title: LGG_LT_Patient-2

description: Library name: LGG_200189


title: LGG_LT_Patient-4

description: Library name: LGG_211529


title: MOS_mutant_M2_replicate_1

city: Hanover

first: Brittany

last: Goods

state: New Hampshire

address: 15 Thayer Dr.

institute: Dartmouth College

description:
Library name: scO_B1_S28
Smart-seq2

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were downsampled to 10 million reads per sample to make sequencing depth uniform across samples. Data were demultiplexed and aligned to the GRCm38 genome using STAR aligner and count matrices generated with HTSeq.
Cells expressing less than 200 genes were excluded from further analysis and genes were filtered to contain only those that were protein coding. In order to account for the effects of integrating data from multiple sequencing runs, the Harmony package was used (Korsunsky et al., 2019) to correct for batch effect."
Assembly: GRCm38/mm10
Supplementary files format and content: count matrix

source_name: Oocyte

extract_protocol:
Ovaries were dissected, and germinal vesicle (GV) oocytes were isolated in minimal essential medium supplemented with 2.5μM milrinone to prevent meiotic resumption.  To induce synchronous meiotic progression, oocytes were then cultured in milrinone-free Chatot, Ziomek, and Bavister (CZB) medium in a humidified incubator at 37°C with 5% CO₂. For chemical activation, wildtype oocytes were matured in CZB for 15-16 hours after germinal vesicle breakdown, then incubated for 2 hours in calcium-free CZB containing 10 mM strontium chloride. Following activation, the eggs were washed and maintained in CZB.
scRNA-seq libraries were generated using SMART-Seq2 protocol (Trombetta et al., 2014). Briefly, cDNA was reversed transcribed from single cells using SuperScript III (Thermo Fisher Scientific) and whole transcriptome amplification (WTA) was performed. WTA products were purified using the Agencourt AMPure XP beads (Beckman Coulter, IN, USA) and used to prepare paired-end libraries with Nextera XT  (Illumina, CA, USA).

tag: cell type

value: Oocyte

tag: batch


title: MOS_mutant_M3_replicate_1

description:
Library name: scO_A7_S37
Smart-seq2


title: MOS_mutant_M1_replicate_6

description:
Library name: scO_A8_S40
Smart-seq2


title: MOS_mutant_M1_replicate_7

description:
Library name: scO_B10_S3
Smart-seq2


title: MOS_mutant_M1_replicate_9

description:
Library name: scO_B4_S39
Smart-seq2


title: MOS_mutant_M3_replicate_3

description:
Library name: scO_B6_S27
Smart-seq2


title: MOS_WT_replicate_4

description:
Library name: scO_A5_S29
Smart-seq2


title: MOS_mutant_M3_replicate_2

description:
Library name: scO_B5_S22
Smart-seq2


title: MOS_WT_replicate_3

description:
Library name: scO_A3_S19
Smart-seq2


title: MOS_treated_replicate_17

description:
Library name: Plate4_SC_B8_S46
Smart-seq2


title: MOS_WT_replicate_1

description:
Library name: scO_A1_S11
Smart-seq2


title: MOS_treated_replicate_15

description:
Library name: Plate4_SC_B6_S34
Smart-seq2


title: MOS_treated_replicate_12

description:
Library name: Plate4_SC_B3_S14
Smart-seq2


title: MOS_treated_replicate_10

description:
Library name: Plate4_SC_B1_S4
Smart-seq2


title: MOS_treated_replicate_16

description:
Library name: Plate4_SC_B7_S40
Smart-seq2


title: MOS_WT_replicate_2

description:
Library name: scO_A2_S15
Smart-seq2


title: MOS_mutant_M2_replicate_2

description:
Library name: scO_B3_S36
Smart-seq2


title: MOS_treated_replicate_6

description:
Library name: Plate4_SC_A5_S27
Smart-seq2


title: MOS_treated_replicate_3

description:
Library name: Plate4_SC_A12_S68
Smart-seq2


title: MOS_mutant_M1_replicate_8

description:
Library name: scO_B2_S33
Smart-seq2


title: MOS_treated_replicate_11

description:
Library name: Plate4_SC_B2_S7
Smart-seq2


title: MOS_treated_replicate_14

description:
Library name: Plate4_SC_B5_S28
Smart-seq2


title: MOS_treated_replicate_8

description:
Library name: Plate4_SC_A7_S39
Smart-seq2


title: MOS_WT_replicate_5

description:
Library name: scO_A6_S34
Smart-seq2


title: MOS_treated_replicate_9

description:
Library name: Plate4_SC_A8_S45
Smart-seq2


title: MOS_treated_replicate_5

description:
Library name: Plate4_SC_A4_S20
Smart-seq2


title: MOS_treated_replicate_7

description:
Library name: Plate4_SC_A6_S33
Smart-seq2


title: MOS_treated_replicate_4

description:
Library name: Plate4_SC_A3_S13
Smart-seq2


title: MOS_WT_replicate_50

description:
Library name: Plate3_WT_D2_S94
Smart-seq2


title: MOS_treated_replicate_1

description:
Library name: Plate4_SC_A1_S3
Smart-seq2


title: MOS_WT_replicate_47

description:
Library name: Plate3_WT_B7_S115
Smart-seq2


title: MOS_WT_replicate_51

description:
Library name: Plate3_WT_D3_S101
Smart-seq2


title: MOS_WT_replicate_46

description:
Library name: Plate3_WT_B6_S109
Smart-seq2


title: MOS_WT_replicate_45

description:
Library name: Plate3_WT_B5_S103
Smart-seq2


title: MOS_WT_replicate_48

description:
Library name: Plate3_WT_B8_S121
Smart-seq2


title: MOS_WT_replicate_43

description:
Library name: Plate3_WT_B3_S89
Smart-seq2


title: MOS_WT_replicate_42

description:
Library name: Plate3_WT_B2_S82
Smart-seq2


title: MOS_WT_replicate_37

description:
Library name: Plate3_WT_A7_S114
Smart-seq2


title: MOS_WT_replicate_38

description:
Library name: Plate3_WT_A8_S120
Smart-seq2


title: MOS_WT_replicate_44

description:
Library name: Plate3_WT_B4_S96
Smart-seq2


title: MOS_treated_replicate_13

description:
Library name: Plate4_SC_B4_S21
Smart-seq2


title: MOS_WT_replicate_41

description:
Library name: Plate3_WT_B12_S145
Smart-seq2


title: MOS_WT_replicate_36

description:
Library name: Plate3_WT_A6_S108
Smart-seq2


title: MOS_treated_replicate_2

description:
Library name: Plate4_SC_A10_S57
Smart-seq2


title: MOS_WT_replicate_39

description:
Library name: Plate3_WT_B10_S133
Smart-seq2


title: MOS_WT_replicate_40

description:
Library name: Plate3_WT_B11_S139
Smart-seq2


title: MOS_WT_replicate_31

description:
Library name: Plate3_WT_A12_S144
Smart-seq2


title: MOS_mutant_M1_replicate_26

description:
Library name: Plate2_mut_C8_S44
Smart-seq2


title: MOS_mutant_M1_replicate_27

description:
Library name: Plate2_mut_C9_S50
Smart-seq2


title: MOS_WT_replicate_32

description:
Library name: Plate3_WT_A2_S81
Smart-seq2


title: MOS_WT_replicate_33

description:
Library name: Plate3_WT_A3_S88
Smart-seq2


title: MOS_WT_replicate_34

description:
Library name: Plate3_WT_A4_S95
Smart-seq2


title: MOS_mutant_M3_replicate_21

description:
Library name: Plate2_mut_C4_S19
Smart-seq2


title: MOS_mutant_M1_replicate_23

description:
Library name: Plate2_mut_C3_S12
Smart-seq2


title: MOS_mutant_M2_replicate_17

description:
Library name: Plate2_mut_C11_S61
Smart-seq2


title: MOS_mutant_M1_replicate_21

description:
Library name: Plate2_mut_C12_S67
Smart-seq2


title: MOS_WT_replicate_28

description:
Library name: Plate3_WT_A1_S74
Smart-seq2


title: MOS_WT_replicate_29

description:
Library name: Plate3_WT_A10_S132
Smart-seq2


title: MOS_WT_replicate_35

description:
Library name: Plate3_WT_A5_S102
Smart-seq2


title: MOS_WT_replicate_49

description:
Library name: Plate3_WT_B9_S127
Smart-seq2


title: MOS_mutant_M3_replicate_18

description:
Library name: Plate2_mut_B7_S37
Smart-seq2


title: MOS_mutant_M3_replicate_20

description:
Library name: Plate2_mut_B9_S49
Smart-seq2


title: MOS_mutant_M3_replicate_15

description:
Library name: Plate2_mut_B12_S66
Smart-seq2


title: MOS_mutant_M2_replicate_16

description:
Library name: Plate2_mut_B4_S18
Smart-seq2


title: MOS_mutant_M3_replicate_14

description:
Library name: Plate2_mut_B11_S60
Smart-seq2


title: MOS_mutant_M1_replicate_24

description:
Library name: Plate2_mut_C6_S32
Smart-seq2


title: MOS_mutant_M2_replicate_18

description:
Library name: Plate2_mut_C5_S26
Smart-seq2


title: MOS_mutant_M1_replicate_22

description:
Library name: Plate2_mut_C2_S23
Smart-seq2


title: MOS_mutant_M1_replicate_20

description:
Library name: Plate2_mut_C10_S56
Smart-seq2


title: MOS_mutant_M1_replicate_19

description:
Library name: Plate2_mut_C1_S2
Smart-seq2


title: MOS_mutant_M3_replicate_13

description:
Library name: Plate2_mut_A9_S48
Smart-seq2


title: MOS_mutant_M3_replicate_19

description:
Library name: Plate2_mut_B8_S43
Smart-seq2


title: MOS_mutant_M1_replicate_16

description:
Library name: Plate2_mut_A8_S42
Smart-seq2


title: MOS_mutant_M2_replicate_14

description:
Library name: Plate2_mut_A6_S30
Smart-seq2


title: MOS_mutant_M2_replicate_13

description:
Library name: Plate2_mut_A5_S24
Smart-seq2


title: MOS_mutant_M3_replicate_10

description:
Library name: Plate2_mut_A1_S9
Smart-seq2


title: MOS_mutant_M3_replicate_17

description:
Library name: Plate2_mut_B6_S31
Smart-seq2


title: MOS_mutant_M1_replicate_18

description:
Library name: Plate2_mut_B3_S11
Smart-seq2


title: MOS_mutant_M2_replicate_10

description:
Library name: Plate1_mut_C3_S86
Smart-seq2


title: MOS_WT_replicate_30

description:
Library name: Plate3_WT_A11_S138
Smart-seq2


title: MOS_mutant_M1_replicate_25

description:
Library name: Plate2_mut_C7_S38
Smart-seq2


title: MOS_mutant_M3_replicate_9

description:
Library name: Plate1_mut_B9_S124
Smart-seq2


title: MOS_mutant_M1_replicate_17

description:
Library name: Plate2_mut_B10_S55
Smart-seq2


title: MOS_mutant_M3_replicate_7

description:
Library name: Plate1_mut_B2_S78
Smart-seq2


title: MOS_mutant_M2_replicate_15

description:
Library name: Plate2_mut_A7_S36
Smart-seq2


title: MOS_mutant_M3_replicate_12

description:
Library name: Plate2_mut_A4_S17
Smart-seq2


title: MOS_mutant_M2_replicate_6

description:
Library name: Plate1_mut_A8_S117
Smart-seq2


title: MOS_mutant_M2_replicate_5

description:
Library name: Plate1_mut_A5_S98
Smart-seq2


title: MOS_mutant_M2_replicate_4

description:
Library name: Plate1_mut_A4_S91
Smart-seq2


title: MOS_mutant_M3_replicate_11

description:
Library name: Plate2_mut_A3_S10
Smart-seq2


title: MOS_mutant_M2_replicate_3

description:
Library name: Plate1_mut_A3_S84
Smart-seq2


title: MOS_mutant_M1_replicate_11

description:
Library name: Plate1_mut_A2_S77
Smart-seq2


title: MOS_mutant_M2_replicate_11

description:
Library name: Plate2_mut_A11_S59
Smart-seq2


title: MOS_mutant_M1_replicate_15

description:
Library name: Plate2_mut_A10_S54
Smart-seq2


title: MOS_mutant_M2_replicate_12

description:
Library name: Plate2_mut_A12_S65
Smart-seq2


title: LN2A cells, rep 3

city: Chapel Hill

first: Office of Genomics Research

last: UNC Lineberger Comprehensive Cancer Center

state: NC

address: 125 Mason Farm Road, CB #7599 5105-5106 Marsico Hall

institute: University of North Carolina at Chapel Hill

description:
Library name: LN2A_3_1
LN2A_3_1_57956826

data_processing:
Libraries were run on the NextSeq2000 machine generating paired-end 50bp reads.
Raw reads were aligned to GRCm38.p6 mouse genome annotated with the GENCODE vM transcriptome via STAR (v2.7.6.a). Transcripts were counted with Salmon (v1.4.0).
Assembly: GRCm38.p6
Supplementary files format and content: tab delimited file contains raw counts for all samples

extract_protocol:
RNA was isolated from JH716-18, JH716-18-LN1A, and JH716-18-LN2A cell lines using the Quick-RNA MicroPrep kit (Zymo Research, R1051). Purified RNA was quantified using QuBit RNA BR Assay (Thermo Fisher, Q10210).
Libraries were made using Illumina TruSeq Stranded mRNA kit

tag: cell line

tag: genetic background


title: LN2A cells, rep 2

description:
Library name: LN2A_2_1
LN2A_2_1_57956826


title: MOS_mutant_M3_replicate_16

description:
Library name: Plate2_mut_B5_S25
Smart-seq2


title: MOS_mutant_M3_replicate_4

description:
Library name: Plate1_mut_A1_S70
Smart-seq2


title: MOS_mutant_M2_replicate_8

description:
Library name: Plate1_mut_B8_S118
Smart-seq2


title: LN1A cells, rep 3

description:
Library name: LN1A_3_1
LN1A_3_1_57956826


title: MOS_mutant_M1_replicate_14

description:
Library name: Plate1_mut_C9_S125
Smart-seq2


title: MOS_mutant_M2_replicate_7

description:
Library name: Plate1_mut_B1_S71
Smart-seq2


title: LN1A cells, rep 1

description:
Library name: LN1A_1_1
LN1A_1_1_57956826


title: MOS_mutant_M1_replicate_13

description:
Library name: Plate1_mut_C2_S79
Smart-seq2


title: MOS_mutant_M2_replicate_9

description:
Library name: Plate1_mut_C1_S72
Smart-seq2


title: MOS_mutant_M3_replicate_8

description:
Library name: Plate1_mut_B3_S85
Smart-seq2


title: Library 4 ref rep4

city: Boston

first: Wei-Chien

last: Yuan

state: MA

address: 1 Blackfan Circle

institute: Boston Children's Hospital

data_processing:
Barcode sequences were parsed and trimmed from FASTQs using custom python scripts
Paired-end reads were aligned to mm10 using bowtie or STAR.
Duplicate reads were removed using picard.
Peaks were called using MACS2
For the CRISPR screen, reads were trimmed and then mapped to a custom-built index of the library using bowtie 2. The mapped counts were first normalized within each library (total counts = 10E6 reads), averaged across experimental replicates, and then divided by the average normalized reads of the respective sequenced plasmid libraries (BC1-BC4) to calculate the final fold-enrichment for each guide in each mouse.
Genome_build: mm10
Supplementary_files_format_and_content: For RNA-seq, gene count was generted using featurecounts. For bulk ATAC-seq and ChIP-seq, algined reads are converted to bigwig tracks. For scATAC, peak-cell matrix is generated using ChromVAR. For the CRISPR-screening, processed data are tab separated text files for each mouse (biological replicate), showing, for each sgRNA, the fold enrichment over its abundance in the corresponding plasmid library (BC1-BC4).

organism: Escherichia coli

source_name: plasmid

extract_protocol:
plamids exctrct from E coli
Plasmids were used as a template for a PCR using primers targeting the common sgRNA scaffold and containing Illumina TruSeq adapter sequences, with the following parameters: 98ºC 5’, 30 cycles of (98ºC 30’’, 58ºC 30’’, 72ºC 30’’). The number of cycles was optimized by DNA quantification to stop in the middle of the linear amplification phase. Illumina i5 and i7 adapters were added by performing an additional 10-12 PCR cycles with TruSeq adapter primers

value: plasmid


title: MOS_mutant_M1_replicate_10

description:
Library name: Plate1_mut_A12_S141
Smart-seq2


title: Library 4 ref rep2


title: MOS_mutant_M1_replicate_12

description:
Library name: Plate1_mut_B12_S142
Smart-seq2


title: GFP_liver_PBS_C4

city: Morgantown

first: Gangqing

state: WV

address: 64 Medical Center Drive

institute: West Virginia University

description: Library name: Robinson_3GEX_02_C4

data_processing:
Subsequent data QC, normalization, scaling, variable gene identification and clustering were performed using the Seurat R package v5 and custom R code. Cell data were quality controlled and filtered based on cellular complexity (number of genes per cell) and mitochondrial reads. Viable cells were selected by filtering for cells with UMI count comprised between 500 and 2500. Cells with over 200 genes, and mitochondrial percent reads less than 40 were kept for analysis. Following quality control analysis and data filtering, there were 622 control cells and 1,016 infected cells. After data normalisation and scaling, Principal-component (PC) analysis (RunPCA) was performed on the 2,000 most variable genes, identified by the function FindVariableFeatures. We used the RunHarmony function from the harmony R package for potential batch-effect correction.The Harmony embeddings were used to define the dimensionality of our dataset and the resulting number of PCs were used in the RunUMAP function for reduction into two dimensions as well as for nearest neighbor graph (SNN) creation (FindNeighbors). We used the Clustree R package to compute the optimal resolution for clustering (res=1.1),  number which was then supplied to the FindClusters function. Differential gene expression between infected and control cells was calculated with FindMarkers. Cluster specific gene signatures were obtained with the function FindAllMarkers. Cells were annotated using the Cell Typist with the Healthy_Mouse_Liver model and Majority Voting mode ON.
Assembly: GRCm38
Supplementary files format and content: *.filtered_feature_bc_matrix.h5 : Filtered feature barcode matrix stored as a Compressed Sparse Column (CSC) sparse matrix in hdf5 format. The rows consist of all the gene features concatenated together (identical to raw feature barcode matrix) and the columns are restricted to those barcodes that are identified as cells.

source_name: Liver, Female

extract_protocol:
Neonatal livers were dissociated using the same instrument with the “37C_m_LIDK_1” protocol and the Miltenyi Biotec murine liver dissociation kit. Following dissociation, tissues were pelleted at 350 x g for 5 min at 4˚C and ACK lysed for 4 min at room temperature. ACK was neutralized with 10% FBS in RPMI and pelleted at 350 x g for 5 min. Cell debris was removed by putting cells through 40 µm strainer in a 50 mL conical tube and pelleted. Cells were counted and assessed for viability using the ThermoFisher Scientific Countess 3 Automated Cell Counter (Waltham, MA, USA).
Downstream steps were performed according to the 10X Genomics manufacturer recommendations for the 10X Genomics Chromium Next GEM Single Cell 3' Kit v3.1 (Product 1000269). The library was prepared using the 10X Genomics Chromium Controller available in the WVU FCSCCF by the WVU Genomics Core Facility.

value: Liver

value: PBS Control


title: GFP_liver_infected_Ec1

description: Library name: Robinson_3GEX_03_Ec1

value: E. coli infected


title: MOS_mutant_M3_replicate_6

description:
Library name: Plate1_mut_A9_S123
Smart-seq2


title: GFP_liver_PBS_C2

description: Library name: Robinson_3GEX_01_C2

source_name: Liver, Male


title: LN2A cells, rep 1

description:
Library name: LN2A_1_1
LN2A_1_1_57956826


title: MOS_mutant_M3_replicate_5

description:
Library name: Plate1_mut_A11_S135
Smart-seq2


title: JH716-18 cells, rep 2

description:
Library name: JH716-18_2_1
JH716-18_2_1_57956826


title: Library 4 ref rep3


title: Library 2 ref rep2


title: i3N_ASO_Control_RNAseq_rep1

city: Houston

first: Benxia

state: Texas

address: 431 Fannin

institute: University of Texas Health Science Center at Houston

data_processing:
RNA-seq
RNA-seq data analysis: Basecalls were performed using bcl2fastq v2.19.0.316 for NextSeq 550 output.  We used FastQC to check the quality of RNA-seq raw reads.  RNA-seq clean reads were aligned to the human reference genome (hg19) from the UCSC database using HISAT2 with -k 1 --no-discordant --rna-strandness RF.  StringTie was implemented to assemble and quantify transcripts based on gencode.v19.annotation.gtf.
MeRIP-seq data analysis: Basecalls were performed using bcl2fastq v2.19.0.316 for NextSeq 550 output. We used FastQC to check the quality of RNA-seq raw reads.  RNA-seq clean reads were aligned to the human reference genome (hg19) from the UCSC database using HISAT2 with -k 1 --no-discordant --rna-strandness RF.  We used MACS3 with --nomodel --extsize 100 to call m6A peaks.The high-confidence m6A peaks were retained based on q value ≤ 10−5 and fold change ≥ 5. We used bedtools to get intersected m6A peaks detected in at least 3 samples. We used ChIPseeker to annotate the genomic region of a m6A peak as TSS, exon, 5′ UTR, 3′ UTR, intronic or intergenic. The ‘gencode.v19.annotation.gtf’ was used as the transcript database.
Assembly: hg19
Supplementary files format and content: bigwig. bigwig file incldue the coverage of reads in genome region

growth_protocol: WTC11-Ngn2 iPSCs were utilized to generate i3Neuron following a previously established protocol.  For pre-differentiation, WTC11-Ngn2 iPSCs were cultured with 2 μg ml−1 doxycycline in knockout DMEM/F12 medium supplemented with 1× N2, 1× NEAA, 1 μg ml−1 mouse laminin, 10 ng ml−1 brain-derived neurotrophic factor (BDNF) and 10 ng ml−1 NT3 for three days. ROCK inhibitor(10 μM) was included in the predifferentiation media for the first day, and the medium was replaced daily. During the maturation phase, predifferentiated neural cells were dissociated into single cells using accutase and plated on Poly-L-Ornithine-coated plates in maturation medium containing equal parts DMEM/F12 and Neurobasal-A with 2 μg ml−1 doxycycline, 0.5× B-27, 0.5× N-2, 1× NEAA, 0.5× GlutaMax, 1 μg ml−1 mouse laminin, 10 ng ml−1 BDNF and 10 ng ml−1 NT3. Doxycycline was only added to the maturation medium on the first day and omitted thereafter. Half of the medium was replaced weekly for the first 2 weeks, and the medium volume was doubled on week 3. Subsequently, one third of the medium was replaced weekly until 8 weeks for further treatment.

extract_protocol:
Total cellular RNAs were extracted by TRIzol (Thermo Fisher) or Zymo RNA miniprep kit (Zymo Research).  RNA-seq and MeRIP-seq were performed according to our previous report with some modifications (Xiong et al. 2021. PMID: 34108665). Total RNA (5 μg) was fragmented at 70 °C for 6 min in the fragmentation buffer (10 mM ZnCl2, 10 mM TrisHCl pH7.4), following precipitation the RNA were resuspended with ice-cold IP buffer (10 mM Tris-HCl, pH 7.4, 150 mM NaCl, 0.1% NP-40, 20 U/mL Superase-In, 1× Protease Inhibitor) to a ﬁnal volume of 1050 μL. Of this, 50 μL of diluted RNA was utilized for RNA-seq (5% input for m6A IP) and the remaining 1000 μL was reserved for MeRIP-seq (Methylated RNA immunoprecipitation sequencing). To prepare anti-m6A antibody conjugated beads, 20 μL of Dynabeads Protein G beads (Thermo Fisher) was washed 3 times with 1ml IP buffer and then incubated with 1 μg of m6A antibody (Synaptic Systems, Cat 202-003) at room temperature for 30min. The conjugated anti-m6A-Dynabeads were washed in 1ml IP buffer 3 times. Subsequently, the RNA sample was mixed with the beads and rotated at 4 °C for 3 hours. The beads were then washed in the IP buffer 5 times. The immunoprecipitated RNAs were extracted from the beads by TRIzol-LS (Thermo Fisher). The extracted RNA was subjected to the next generation sequencing library preparation for RNA-seq and MeRIP-seq, as well as qPCR, to quantify the m6A levels.
RNA samples were collected by one of two methods: lysis in TRIzol reagent (Thermo Fisher) for RNA-seq and MeRIP-seq, followed by standard phenol-chloroform extraction methods; alternatively, lysis was performed using Zymo Research Quick-RNA MiniPrep kit (Genesee Scientific) for regular qPCR following the manufacturer protocol. Libraries for RNA-Seq and MeRIP-Seq were made with NEBNext Ultra Directional Library Prep Kit for Illumina (NEB, E7760) following the manufacturer’s instructions. Ribosome RNA was depleted with NEBNext rRNA Depletion Kit (NEB, E6301S). The generated libraries were quantified using the Qubit-3 system and/or qPCR. In some cases (such as Chip-seq), the libraries were examined by TBE PAGE gel and Bioanalyzer 2100. Sequencing of the libraries was performed using a NextSeq 550 platform (Illumina) with paired-end sequencing.

treatment_protocol: Knockdown experiments were performed using antisense oligonucleotides (ASOs) with modifications by Affinity Plus nucleic acids. ASOs were specifically designed and synthesized by IDT for the knockdown of MAPT-paRNA.  An unrelated scrambled ASO (Scr ASO) was used as a control.  ASOs was dissolved in TE buffer (10 mM Tris-HCl, pH 7.4, 1 mM EDTA) and directly added to the i3Neuron culture without any transfection reagent (termed gymnosis) at a final concentration of 10µM. After 3 days of ASOs treatment, cells were harvested for downstream analysis.

value: iPSC-derived Neurons

value: ASO Control


title: JH716-18 cells, rep 1

description:
Library name: JH716-18_1_1
JH716-18_1_1_57956826