title: FG_ctl_rep1

city: Lausanne

first: Evarist

last: Planet

state: Vaud

address: Route Cantonale

country: Switzerland

institute: EPFL

data_processing:
Reads were mapped to the human (hg19) genome using Hisat2 for RNA-seq
Cell Ranger with default parameters was used for the single-cell
Assembly: hg19 for RNA-seq and hg38 for the single-cell
Supplementary files format and content: The .txt files contain read counts on genes or TEs

extract_protocol:
Total RNA from cell lines was isolated with NucleoSpin™ RNA Plus kit (Machery-Nagel). cDNA was prepared with Maxima Reverse Transcriptase (Thermo Scientific). Sequencing libraries were performed with Illumina Truseq Stranded mRNA LT kit
Illumina Truseq Stranded mRNA LT kit for RNA-seq and Chromium Single Cell Multiome ATAC + Gene Expression

treatment_protocol: H9 and H1 human ESC line were maintained in mTSER plus on Matrigel and were passaged using TryplE in single cells. Endodermal differentiation was performed as in 27. Briefly, hESC were passaged at 80k cells/cm2 density in 12-well Matrigel-coated plate. When cells reached 80 – 90% confluence at 48-76h post-splitting, endodermal differentiation was initiated with 100 ng/ml of Activin A for 3 days, 5 μM GSK-3 inhibitor (CHIR-99021) to activate the WNT pathway for the first day, and 0.5 μM for the second day. Pancreatic differentiation was performed accordingly to a Stem Cell TechnologyTM protocol (Catalog #05120) with harvest after 3 days of endodermal differentiation followed by 3 days of foregut differentiation. Gastruloid differentiation was performed as in 28. Briefly, hESC were passaged at 40,000 cells/cm2 in mTSER replaced 48-76h post-splitting by Nutristem media with 3 μM CHIR-99021. After 24h cells were split in single-cell passaging with TryplE, embryoid bodies were formed with 800 cells per well of low adherence 96-well plate Cell Star in E6 media supplemented with 3 μM CHIR-99021 and 10 μM Rock inhibitor for 18 hours, then replaced with E6 twice to be harvested at 72h.

value: Early Embryo

tag: culture media

value: mTSER Plus on matrigel

tag: status

value: hESC


title: LN3ADpos-S12

status: Public on Oct 31 2022

type: SRA

city: Philadelphia

first: Andrei

last: Thomas-Tikhonenko

state: PA

address: 3501 Civic Center Blvd, CTRB 4056

department: Children's Hospital of Philadelphia

country: USA

institute: Perelman School of Medicine at the University of Pennsylvania

library_source: transcriptomic

data_processing:
Paired-end reads were aligned using the RNA-seq aligner STAR (version 2.7.9a) with flags "--alignSJoverhangMin 8" and "--quantMode GeneCounts". For the geome reference and the subsequent gene quantification the gencode gene annotation for hg38 (version GRCh38.p13) was provided to STAR.
Assembly: hg38
Supplementary files format and content: SYY53_54_123_141_raw_counts.csv holds raw gene counts in csv format
Supplementary files format and content: Tonsil_raw_counts.csv holds raw gene counts in csv format
Supplementary files format and content: REH_controls_raw_counts.csv holds raw gene counts

molecule: total RNA

organism: Homo sapiens

source_name: normal tonsil cell subset

extract_protocol:
RNA was isolated using RNeasy Kit (Micro or Mini, Qiagen) or TRIzol and 1-bromo-3-chloropropane methods.
Library was constructed using NEBNext Ultra II RNA Library Prep Kit with Poly(A) selection.

tag: tissue

value: normal tonsil cell subset

tag: cell type

value: IgM+IgD+CD19+ normal tonsil B cells

tag: genotype

value: WT


title: FG_CRISPRi_rep1

molecule: polyA RNA

growth_protocol: H9 and H1 human ESC line were maintained in mTSER plus on Matrigel and were passaged using TryplE in single cells.

tag: cell line

value: Advance DMEM + CHIR + Activin

value: Endoderm-derived hESC expressing dCAS9-KRAB without sgRNA


title: FG_CRISPRi_rep2


title: Patient 10, rep 3

city: Edinburgh

first: Jose

middle: Ignacio

last: de las Heras

address: Max Born Crescent

department: Wellcome Trust Centre

country: United Kingdom

institute: University of Edinburgh

data_processing:
Mapping quality was assessed with FastQC v0.11.9, sequencing adaptors removed with Trimmomatic v0.35. Low quality and mitochondrial reads were removed
Alignment to Hg38 transcriptome performed with Salmon v.1.4.0
Normalisation of read counts and differential expression performed with DESeq2 v1.32.0 using healthy control samples as reference

source_name: myotubes

growth_protocol: Myoblasts isolated from muscle biopsies were grown in culture at 37oC and 5% CO2 using skeletal muscle growth medium (PELOBiotech #PB-MH-272-0090). When myoblasts reach confluency, differentiation was induced by changing to skeletal muscle cell differentiation medium (Cell Applications #151D-250) for six days, replacing the medium every 48 hours. Myotubes were selectively isolated by partial trypsinisation, where myotubes are gently detached in 0.1% Trypsin leaving myoblasts attached to the tissue culture dish.

extract_protocol:
Total RNA > 200nt was extracted using Qiagen RNeasy RNA extraction kit (#74134).
Sequencing libraries were prepared by Admera Health Inc. with the NEBNext Ultra II kit, with RiboZero rRNA depletion (NEB #E7103)

tag: individual

value: Patient 10

tag: condition

value: EDMD

tag: mutation

value: LMNA, p.R571S

tag: subgroup


title: FG_ctl_rep2


title: Patient 9, rep 2

value: Patient 9

value: LMNA, p.T528K


title: Patient 10, rep 1


title: ligamentum flavum , ossified IP,rep 3

city: Jinan

first: Dachuan

last: Wang

state: Shandong

address: Jingwu Weiqi Road NO.324

country: China

institute: Shandong provincial hospital

description:
treat 3
B03

data_processing:
Paired reads were harvested from Illumina HiSeq 4000 sequencer with quality controlled by Q30. After 3’ adaptor-trimming and the removal of low quality reads by Cutadapt software (v1.9.3), clean reads of all libraries were aligned to the reference genome (UCSC HG19) by Hisat2 software (v2.0.4). ExomePeak software was used for identifying RNA m6A-modified regions (m6A peaks) with FDR (false discovery rate) < 0.05. As previously reported, the common methylated RNAs (CMRs) were defined as RNAs containing at least one m6A peak in all samples, while the specific methylated RNAs (SMRs) were the RNAs with m6A modification only in one sample, and m6A peaks of SMRs were defined as specific m6A peaks. Biological process, molecular function and cellular component analysis were performed for the enrichment of differentially methylated genes, CMRs and SMRs.
Assembly: hg19  Supplementary files format and content: Number of raw junction read  Library strategy: m6A-Seq

source_name: ligamentum flavum

extract_protocol:
Trizol reagent (Invitrogen) was applied to extract total RNA.
MeRIP-Seq was performed by Cloudseq Biotech Inc. (Shanghai, China) according to the published procedure with proper adjustments. Briefly, the fragmented RNA was incubated with m6A polyclonal antibody (Synaptic Systems, 202003) in IPP buffer at 4°C for 2 hours. Then the mixture was immune-precipitated by incubation with protein-A beads (Thermo Fisher) at 4°C for an additional 2 hours. Then, bound RNA was eluted from the beads with N6-methyladenosine (BERRY & ASSOCIATES, PR3732) in IPP buffer and then extracted with Trizol reagent (Thermo Fisher) following the manufacturer's instruction. Purified RNA was used for RNA-seq library generation with NEBNext® UltraTM RNA Library Prep Kit (NEB). Both the input sample without immunoprecipitation and the m6A IP samples were subjected to 150 bp paired-end sequencing on Illumina HiSeq sequencer. In addition, the q-PCR was performed to detect the level of m6A using purified RNA fragments

value: ligamentum flavum

tag: antibody


title: Patient 9, rep 1


title: Patient 9, rep 3


title: Patient 8, rep 1

value: Patient 8

value: FHL1, p.V280M


title: Patient 8, rep 2


title: Patient 8, rep 3


title: Patient 6, rep 1

value: Patient 6


title: Patient 7, rep 2

value: Patient 7

value: FHL1, p.C224W


title: Patient 6, rep 3


title: Patient 4, rep 1

value: Patient 4


title: Patient 4, rep 2


title: Patient 3, rep 3

value: Patient 3


title: Patient 7, rep 3


title: Patient 2, rep 2

value: Patient 2

value: NET39, p.M92K


title: Patient 5, rep 2

value: Patient 5

value: EMD, p.S58Sfs*1


title: Patient 1, rep 1

value: Patient 1


title: Patient 5, rep 1

value: EDMD


title: Patient 1, rep 2


title: Patient 3, rep 2


title: Healthy control 2, rep 3

value: Healthy control 2

value: control


title: root nodules, MG136 Infected, rep 4

status: Public on Nov 01 2022

city: Barcelona

first: Lucas

middle: Esteban

last: Wange

address: Dr. Aiguader 88

department: Institut de Biologia Evolutiva

country: Spain

institute: Universitat Pompeu Fabra

description:
TACAAA
Lj_infection_raw_counts.rds
Lj_infection_filtered_normalised_counts.rds

data_processing:
demultiplexing, deML
adapter trimming, cutadapt, version 3.4
mapping and counting, zUMIs, version 2.5.4
normalisation and differential expression analysis, DESeq2
Assembly: L. japonicus Gifu v1.2
Supplementary files format and content: raw count matrix as generated by zUMIs
Supplementary files format and content: normalized count matrix as generated by DESeq2

organism: Lotus japonicus

source_name: root nodules

growth_protocol: Lotus japonicus seeds were surface sterilized with 1.2% NaClO, soaked with sterile water for 2 h, and germinated in 0.8% agar plates with ½ Gamborg B5 medium. Seeds were kept at 24 °C for 3 days in darkness, followed by 3 days under a long day photoperiod (16h:8h, light:dark).

extract_protocol:
Six biological replicates were collected for each accession (Infected: MG-70, MG-79, MG-136; Non-infected: MG-9, MG-112, MG-115). Each biological replicate comprised 20 nodules from at least 5 different plants. Nodules were harvested 5 wpi. Total RNA was extracted using the SpectrumTM Plant Total RNA kit (Sigma-Aldrich) according to the manufacturer’s instructions and treated with DNAse I (Ambion)
prime-seq RNA-sequencing
poly A enrichment, three prime counting

treatment_protocol: For phenotypic screening, 30 seedlings of each L. japonicus accession were transplanted into sterile Tulip-shaped Weck jars (WECK). Each jar contained 10 seedlings grown on 300 ml of a sand:vermiculite mixture (1:2) supplemented with 40 ml of FAB medium. Two days after transferring, seedlings were inoculated with 1 ml of a R. leguminosarum Norway-GFP suspension (OD600 = 0.005) previously washed with sterile water. Plants were grown under a long day photoperiod at 24 °C. Five weeks post inoculation (wpi) plants were harvested and phenotyped.

tag: accession

value: root nodules

tag: phenotype

value: Infected

tag: infection

value: sub-compatible Rhizobium strain


title: Healthy control 2, rep 1


title: Healthy control 1, rep 3

value: Healthy control 1


title: Patient 10, rep 2

value: Patient 10

value: LMNA, p.R571S


title: Patient 1, rep 3


title: Healthy control 1, rep 2


title: Patient 2, rep 1


title: Patient 7, rep 1

value: Patient 7

value: FHL1, p.C224W


title: Patient 4, rep 3

value: Patient 4


title: Healthy control 2, rep 2


title: Healthy control 1, rep 1


title: Patient 2, rep 3

value: Patient 2


title: patient 2; healthy skin

type: genomic

city: Muenster

first: Konstantin

last: Agelopoulos

address: Von-Esmarch-Str. 58

country: Germany

institute: Universitiy of Muenster

description:
Gene expression data from  healthy skin from healthy volunteer
K005

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to human Illumina Infinium EPIC arrays using standard Illumina protocol

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

data_processing:
GenomeStudio® Software 2011.1, Methylation  Module v1.9
Average Beta

label: Cy5 and Cy3

molecule: genomic DNA

source_name: human whole skin biopsy;  healthy skin

label_protocol: Standard Illumina protocol using the EZ-96 DNA Methylation Kit (Zymo Research)

extract_protocol: genomic DNA was extracted and purified from punch biopsies of human skin by means of Qiagens DNeasy kit

tag: Sex

value: male

tag: age (y)

value: skin


title: patient 3; healthy skin

description:
Gene expression data from  healthy skin from healthy volunteer
K007

value: female


title: Patient 3, rep 1

value: Patient 3


title: patient 5; healthy skin

description:
Gene expression data from  healthy skin from healthy volunteer
K011


title: patient 3; non pruritic, non lesional skin

description:
Gene expression data from  non pruritic, non lesional skin from prurigo nodularis patient
F007-2

source_name: human whole skin biopsy;  non pruritic, non lesional skin


title: Patient 5, rep 3

value: Patient 5

value: EDMD

value: EMD, p.S58Sfs*1


title: patient 2; non pruritic, non lesional skin

description:
Gene expression data from  non pruritic, non lesional skin from prurigo nodularis patient
F005-2


title: patient 1; non pruritic, non lesional skin

description:
Gene expression data from  non pruritic, non lesional skin from prurigo nodularis patient
F001-2


title: patient 5; pruritic lesional skin

description:
Gene expression data from  pruritic lesional skin from prurigo nodularis patient
F011-1

source_name: human whole skin biopsy;  pruritic lesional skin


title: patient 3; pruritic lesional skin

description:
Gene expression data from  pruritic lesional skin from prurigo nodularis patient
F007-1


title: patient 2; pruritic lesional skin

description:
Gene expression data from  pruritic lesional skin from prurigo nodularis patient
F005-1


title: patient 1; pruritic lesional skin

description:
Gene expression data from  pruritic lesional skin from prurigo nodularis patient
F001-1


title: patient 1; healthy skin

description:
Gene expression data from  healthy skin from healthy volunteer
K001


title: HCASMC-hTERT-FHL5_IgG_rep2

city: Charlottesville

first: Clint

middle: L

last: Miller

state: VA

department: Center for Public Health Genomics

institute: University of Virginia

library_source: genomic

data_processing:
The data was processed using the standard CUT&RUN Tools pipeline (Zhu et al. Genome Biology, 2019).
Adapters were trimmed from reads using Trimmomatic (v0.36), retaining only reads greater than 25bp in length.
Reads were mapped to the hg38 genome build using Bowtie2(v2.2.9), using the dove-tail option
Duplicates were marked and removed using Picard (v2.23.4) and samtools (v1.10).
Peaks were called using MACS2(v2.1.2) set to default parameters, using IgG samples as a background control.
Assembly: hg38
Supplementary files format and content: MACS2 narrowpeak files
Library strategy: CUT&RUN

source_name: HCASMC-hTERT

extract_protocol:
Genomic DNA  was released into the supernatant following antibody-guided MNase cleavage and purified by phenol-chloroform and ethanol precipitation.
CUT&RUN libraries were prepared as detailed on https://www.protocols.io/view/cut-amp-run-targeted-in-situ-genome-wide-profiling-14egnr4ql5dy/v3. Briefly, end repair and A tailing was performed at 12C for 15min, 37C for 15min, and 58C for 45min in a thermocycler. After Tru-seq adapter ligation, genomics DNA was purified using 2 rounds of Ampure Beads. Libraries were amplified through 14 cycles of PCR amplification and purified using 1.2X volume of Ampure XP beads.  The DNA concentration of each library was quantified using the Qubit and pooled for paired end sequencing on the Illumina Nextseq 2000 or Illumina Nextseq 500.

treatment_protocol: HCASMC-hTERT were immortalized via lentiviral mediated hTERT overexpression from the primary HCASMC cell line (Cell Signaling, Lot 2105). Cells were maintained in complete SmGM-2 Smooth Muscle Growth Medium-2 supplemented with hEGF, insulin, hFGF-B, 5% FBS and 1ug/mL of puromycin (Gibco, A1113803).

value: hTERT immortalized coronary artery smooth muscle cell

value: IgG (Abcam - ab46450)


title: HCASMC-hTERT-FHL5_H3K27ac_rep1

value: H3K27ac (Abcam - ab9110)


title: HCASMC-hTERT-FHL5_CREB_rep2

value: CREB (EMD Millipore - CS203204)


title: HCASMC-hTERT-FHL5_H3K4me3_rep2

value: H3K4me3 (Active Motifs - Cat#391159)


title: HCASMC-hTERT-FHL5_FHL5_rep1

value: FHL5 (Novus - NBP1- 32660)


title: Patient 6, rep 2

value: Patient 6


title: patient 4; healthy skin

description:
Gene expression data from  healthy skin from healthy volunteer
K008


title: HCASMC-hTERT-HA_FHL5_rep1


title: patient 4; non pruritic, non lesional skin

description:
Gene expression data from  non pruritic, non lesional skin from prurigo nodularis patient
F008-2


title: patient 4; pruritic lesional skin

description:
Gene expression data from  pruritic lesional skin from prurigo nodularis patient
F008-1


title: patient 5; non pruritic, non lesional skin

description:
Gene expression data from  non pruritic, non lesional skin from prurigo nodularis patient
F011-2


title: P16_DS_Rep2

city: New York

first: Michael

last: Rendl

state: NY

address: 1428 Madison Avenue

institute: Mount Sinai School of Medicine

description: Bulk RNA-sequencing of sorted populations from P16 back skin; raw data files contain all transcriptome information for DS, DP and DFs, and processed data file includes transcriptome information for DS, DP and DF populations used in this study.

data_processing:
Raw RNA sequencing reads were mapped to reference genome sequence GRCm39, transcript version M25 with Salmon v1.9.0.   Transcriptomes were then imported and assembled using the tximport and DESeq2 pipeline. Reads per kilobase per million reads (RPKM) for each gene were computed with DESeq2 1.28.1 using raw counts and avgTxLength.
Assembly: GRCm39
Supplementary files format and content: P16_FPKM_Table.xlsx: Tab separated file for all sequencing libraries combined, listing all genes (rows) and the number of Reads per kilobase per million reads (RPKM) for all samples. Column name indicates the sorted cell type (each sorted cell type has two biological replicates). The first column lists the gene ID, the second column the official gene symbol.

organism: Mus musculus

source_name: Dorsal skin

extract_protocol:
Total RNA was purified from sorted cells with the Absolutely RNA Nanoprep Kit (Agilent). RNA concentrations were measured with a NanoDrop spectrophotometer (Thermo), and quality was assessed with an Agilent Bio-analyzer. Samples with RNA integrity number score >8 were further processed. 6 ng of starting material was reverse transcribed and amplified with the RNA Ovation RNAseq System V2 (NuGEN).
From 100 ng of sheared amplified cDNA, sequencing libraries were generated with 6 unique barcoded adaptors, one for each sample (2 biological replicates x 3 populations) using the Ovation Ultralow DR Library System (NuGEN).

value: Dorsal skin

value: Mesenchymal Cells

tag: cell subtype

value: DS

tag: strain

value: Female


title: P16_DP_Rep2

value: DP


title: P16_DP_Rep1


title: P16_DS_Rep1


title: P16_DF_Rep2

value: DF


title: patient 4; healthy skin

type: RNA

description: Gene expression data from  healthy skin from healthy volunteer

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HuGene-1_0-st arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 1 using the module FSM1603 and protocol FS450_0007.

scan_protocol: GeneChips were scanned using theAffymetrix GeneArray Scanner M10.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA.

extract_protocol: total RNA was isolated from punch biopsies of human skin by means of Qiagens RNeasy kit

value: female

value: skin


title: patient 2; healthy skin

value: male


title: patient 5; healthy skin


title: patient 1; healthy skin


title: patient 3; healthy skin


description: Gene expression data from  non pruritic, non lesional skin from prurigo nodularis patient


title: patient 5; pruritic lesional skin

description: Gene expression data from  pruritic lesional skin from prurigo nodularis patient


title: patient 1; pruritic lesional skin


title: patient 2; pruritic lesional skin


title: patient 4; pruritic lesional skin


title: patient 3; pruritic lesional skin


title: hCoASMC +AdCMV Rep5

city: Lund

first: Sebastian

last: Albinsson

address: BMC D12

country: Sweden

institute: Lund University

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: This analysis was performed using the Expression Console Software v1.4.1.46. 3. Probe summarization and data normalization was done using Robust Multi-array Analysis (RMA).6. SAM analysis was performed to identify significantly differentially expressed genes between groups.

label: Biotin Allonamide Triphosphate

source_name: Cultured cells

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Primary human coronary artery smooth muscle cells (HCASMCs) were purchased from Gibco Life Technologies (#C-017-5C) and maintained in Medium 231 (Life Technologies, #M231500) supplemented with 5% smooth muscle growth supplement (Life Technologies, #S-007-25) and 1% penicillin/streptomycin (Biochrom, #A2212). Cells were cultured at 37°C in 5% CO2 and used until passage 8. Media was changed every other day.

extract_protocol: RNA was extracted using the RNeasy mini kit (Qiagen #74106) according to the manufacturer’s instructions. RNA quality was determined using a 2100 Bioanalyzer instrument (Agilent).

treatment_protocol: Cells were transduced 24 hours after seeding with 100 MOI of Ad-CMV-GATA6 (Vector Biolabs, #1027). Fresh media was added 96 hours after virus transduction for additional 48 hours. Ad-CMV-null (Vector Biolabs) was used as a control. (n=6 Ctrl and 6 Ad-GATA6)

value: Coronary artery smooth muscle

tag: construct

value: Ad-CMV-null


title: hCoASMC +AdCMV Rep6

tag: tissue

value: human coronary artery smooth muscle cells (HCASMCs)


title: P16_DF_Rep1

tag: cell type


title: hCoASMC +AdCMV Rep2


title: hCoASMC +AdGATA6 Rep5


title: Human MSD patient fibroblast line 6, tazarotene/bexarotene treatment, 6 days

city: Gottingen

first: Andre

last: Fischer

state: NS

address: Von Sieboldstr 3a

department: Epigenetic Mechanisms in Dementia

institute: German Center for Neurodegenerative Diseases (DZNE)

data_processing:
Base calling: bcl2fastq (v.2.20.0)
Read alignment: STAR (v.2.5.2b)
Read counting:  featureCounts/subread (v.1.5.1)
Differential expression: DESeq2 (v.1.22.2)
Assembly: hg38
Supplementary files format and content: All *exonCount.txt files contain read counts generated by featureCounts (subread) software. These files were used for doing differential expression analysis.

source_name: Human MSD patient fibroblast line 6

growth_protocol: Patient skin fibroblasts were grown in DMEM supplemented with 10% fetal calf serum and 1% penicillin/streptomycin under 5% CO2 at 37C

extract_protocol:
RNA was extracted using the Trizol/chloroform method and cleaned up using the Zymo RNA clean & concentrator-5 kit
RNA libraries for RNA-seq were prepared using TruSeq Stranded lotal RNA Library Prep following manufacturer's protocols.

treatment_protocol: Cells were treated at day 0 with 10 µM tazarotene and 20 µM bexarotene dissolved in DMSO or DMSO as control, medium and drugs were replenished at day 3, harvesting at day 6

value: Human MSD patient fibroblast line 6

value: Human MSD patient fibroblast line

tag: treatment

value: Tazarotene/Bexarotene


title: hCoASMC +AdGATA6 Rep6


title: Human MSD patient fibroblast line 6, DMSO treatment, 6 days

tag: cell line

value: DMSO


title: hCoASMC +AdCMV Rep1


title: Human MSD patient fibroblast line 5, tazarotene/bexarotene treatment, 6 days

source_name: Human MSD patient fibroblast line 5

value: Human MSD patient fibroblast line 5


title: Human MSD patient fibroblast line 5, DMSO treatment, 6 days


title: hCoASMC +AdCMV Rep3


title: Human MSD patient fibroblast line 4, DMSO treatment, 6 days

source_name: Human MSD patient fibroblast line 4

value: Human MSD patient fibroblast line 4


title: hCoASMC +AdCMV Rep4


title: Human MSD patient fibroblast line 2, tazarotene/bexarotene treatment, 6 days

source_name: Human MSD patient fibroblast line 2

value: Human MSD patient fibroblast line 2


title: Human MSD patient fibroblast line 4, tazarotene/bexarotene treatment, 6 days


title: Human MSD patient fibroblast line 1, tazarotene/bexarotene treatment, 6 days

source_name: Human MSD patient fibroblast line 1

value: Human MSD patient fibroblast line 1


title: Human control fibroblast line 4, DMSO treatment, 6 days

source_name: control fibroblast line 4

value: control fibroblast line 4

value: Human control fibroblast line


title: Human MSD patient fibroblast line 1, DMSO treatment, 6 days


title: Human control fibroblast line 5, tazarotene/bexarotene treatment, 6 days

source_name: control fibroblast line 5

value: control fibroblast line 5


title: Human MSD patient fibroblast line 3, DMSO treatment, 6 days

source_name: Human MSD patient fibroblast line 3

value: Human MSD patient fibroblast line 3


title: hCoASMC +AdGATA6 Rep4


title: Human MSD patient fibroblast line 2, DMSO treatment, 6 days


title: Human control fibroblast line 4, tazarotene/bexarotene treatment, 6 days


title: Human MSD patient fibroblast line 3, tazarotene/bexarotene treatment, 6 days


title: Human control fibroblast line 3, tazarotene/bexarotene treatment, 6 days

source_name: control fibroblast line 3

value: control fibroblast line 3


title: hCoASMC +AdGATA6 Rep1


title: Human control fibroblast line 5, DMSO treatment, 6 days


title: hCoASMC +AdGATA6 Rep2


title: Human control fibroblast line 3, DMSO treatment, 6 days


title: Human control fibroblast line 2, DMSO treatment, 6 days

source_name: control fibroblast line 2

value: control fibroblast line 2


title: Human control fibroblast line 2, tazarotene/bexarotene treatment, 6 days


title: Human control fibroblast line 1, DMSO treatment, 6 days

source_name: control fibroblast line 1

value: control fibroblast line 1


title: Human control fibroblast line 1, tazarotene/bexarotene treatment, 6 days


title: hCoASMC +AdGATA6 Rep3

value: Coronary artery smooth muscle


title: ‘Quanhong poplar’(QHP)，leaves 2

city: Guiyang

first: yunfeng

last: wei

address: Huaxi District, Guiyang City

institute: Guizhou University

data_processing:
After filtering out the adapter sequences and low quality sequence reads, the clean reads were were mapped to the poplar reference genome sequence (https://www.ncbi.nlm.nih.gov/data-hub/genome/GCA_015852605.2/) to obtain the unigenes using HISAT2 and StringTie software.
Eight databases, including NR, NR, GO, Swiss-Prot, COG, KOG, Pfam, and KEGG, were used to annotate the unigenes using BLAST (E <10−5).
The expression level of all unigenes were calculated and normalized to fragments per kilobase of transcript per million fragments mapped (FPKM).
Moreover, DEGs between two sample pairs were analyzed using the DESeq R package. The FDR (false discovery rate) of <0.05 and |log2(foldchange)| of ≥1 were applied to identify the significant DEGs.
In addition, GO annotations were conducted using the DAVID online tool on the screened DEGs. KEGG pathway analysis of DEGs was performed using the KOBAS online analysis database (available online: http://kobas.cbi.pku.edu.cn/).
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Populus deltoides

source_name: ‘Quanhong poplar’ ，leaf

extract_protocol:
Extraction of the total RNA from leaf samples was performed using the EAZY spin Plus Plant RNA Kit. The contaminated DNA was removed from the extracted RNA using DNase I (TAKARA).
The Dynabeads mRNA Purification Kit (Invitrogen) was used fot the total RNA to generate mRNA, which were furtehr fragmented and reverse transcribed into first strand cDNAs initiated by random hexamer priming.Then the double-stranded cDNAs (ds-cDNA) were generated by the NEBNext Ultra RNA Library Prep Kit (NEB), which were purified, end-repaired, and ligated to adaptors.
Finally, the dscDNAs with adding adaptors were further fragmented and enriched by PCR to construct the final cDNA libraries for Illumina paired-end sequencing. The cDNA library was sequenced using the Illumina NovaSeq 600

value: ‘Quanhong poplar’ ，leaf

tag: genotype

value: WT


title: ‘Quanhong poplar’(QHP)，leaves 1


title: the green leaf poplar (L2025)，leaves 1

source_name: the green leaf poplar，leaf

value: the green leaf poplar，leaf


title: the green leaf poplar (L2025)，leaves 3


title: the green leaf poplar (L2025)，leaves 2


title: ‘Quanhong poplar’(QHP)，leaves 3


title: ‘Zhongshanyuan poplar’（ZSY)，green-leaves 3

source_name: ‘Zhongshanyuan poplar’，leaf

value: ‘Zhongshanyuan poplar’，leaf


title: ‘Zhongshanyuan poplar’（ZSY)，green-leaves 1


title: ‘Zhongshanyuan poplar’（ZSY)，purple-leaves 3


title: ‘Zhongshanyuan poplar’（ZSY)，purple-leaves 2


title: ‘Zhongshanyuan poplar’（ZSY)，purple-leaves 1


title: A6w_Mcph1KO_RRBS

city: Shenzhen

first: Cao

last: Qiang

address: No. 66 Gongchang Road, Guangming District, Shenzhen

department: School of Medicine

institute: Sun Yat-sen University

data_processing:
The quality controls of all reads were checked using FastQC (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/).
Filter sequencing adapters and low-quality reads using TrimGalore (v0.6.6).
Cleaned reads were aligned to the mouse mm10 genome with Bismark (v0.19.0)
Assembly: GRCm38/mm10
Supplementary files format and content: Bismark coverage file

source_name: cerebral cortex

growth_protocol: standard growth condition

extract_protocol:
Every tissue in our study were chopped into small pieces, and half of homogenate from one tissues were used to extract the genomic DNA using the DNeasy Blood & Tissue Kits (Qiagen), and half of homogenate from one tissues were used to extract the total RNA using the Total RNA Extraction Kit (Omega).
Genomic DNA (100 ng) was used to construct the library of RRBS and oxRRBS [46]. RRBS and oxRRBS libraries were prepared by Ovation® RRBS Methyl-Seq with the TrueMethyl® oxBS kit (Tecan, Redwood City, CA, USA) according to the manufacturer’s instructions.

value: cerebral cortex

value: Mcph1 knockout

value: male

tag: developmental stage


title: A18w_Mcph1KO_RRBS


title: A6w_WT_oxRRBS

value: wild-type


title: A18w_WT_RRBS


title: A18w_Mcph1KO_oxRRBS


title: A6w_Mcph1KO_oxRRBS


title: A18w_WT_oxRRBS


title: A6w_WT_RRBS


title: P4_Mcph1KO_oxRRBS


title: P4_WT_oxRRBS


title: P4_Mcph1KO_RRBS


title: Pool of conrol samples

city: México.

first: Ruth

last: Ruiz-Esparza

address: Centro Médico Nacional Siglo XXI, IMSS, México,

department: Pediatría

country: Mexico

institute: Instituto Mexicano del Seguro Social

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: RMA data

source_name: Serum exosomas from padiatric patients with astrocytoma

label_protocol: Affymetrix protocol

extract_protocol: Blood serum samples from pediatric patients with Ast (PAst, n= 10, four boys and six girls; DAst, n= 13, five boys and eight girls) were collected from 2017 to 2020. All children included in this study were patients from the Hospital de Pediatría “Silvestre Frenk Freund”, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social (IMSS). The patient’s age range was 0-15 years with no history of relatives with cancer. All children’s relatives or tutors signed an informed consent.  Exosomes were isolated with the Total Isolation Exosome kit (from serum) (ThermoScientific) and the presence and integrity of exosomes was visualized by electron microscopy. For RNA isolation, exosomes were incubated for 15 h (4ºC) with TRIZOL® (this was to optimally resuspend exosomes) and later with 40 µL chloroform for 15 minutes at 4ºC. The aqueous phase (RNA) was transferred to a new tube and 500 µL isopropanol were added for RNA precipitation. Finally, RNA was washed three times with 75% ethanol and resuspended in 5 µL RNAse-free water. RNA quantification was performed by spectrophotometry (Nanodrop 1000, Thermo Fisher Scientific)

tag: disease state

value: control pediatric patients

value: serum


title: P4_WT_RRBS


title: Pool of Pilocitic astrocytoma

value: patients with pilocitic astroytoma grade I


title: E17.5_Mcph1KO_RRBS


title: E17.5_Mcph1KO_oxRRBS


title: E17.5_WT_oxRRBS


title: ‘Zhongshanyuan poplar’（ZSY)，green-leaves 2


title: Pool of Diffuse astrocytoma

value: patients with diffuse astroytoma grade II


title: E17.5_WT_RRBS


title: mESC_WT_oxRRBS

value: mouse embryonic stem cells


title: Lung, Control, rep3

city: Yokohama

first: Kentaro

last: Tojo

state: Kanagawa

address: 3-9, Fukuura, Kanazawa Ward

department: Department of Anesthesiology and Critical Care Medicine

country: Japan

institute: Yokohama City University School of Medicine

description: Sample 09

data_processing:
Sequence reads were quality checked and trimmed for adaptor sequence withTrim Galore version: 0.6.7 and Cutadapt version: 4.1.
Transcripts were quantified with Salmon version: 1.9.0.
Gene-level read counts were obtained with tximport R package version: 1.24.0.
Assembly: GRCm39
Supplementary files format and content: *_readcounts.tsv: Tab-delimited text files of raw count data.

source_name: Lung

extract_protocol:
Total RNA was extracted from lung tissues using FastGene RNA Premium Kit (Nippon Genetics).
mRNA libraries for RNA seq were prepared using TruSeq stranded mRNA (Illumina).

value: Lung

tag: age

value: 8 weeks

value: Male

value: PBS

tag: model

value: Control


title: Lung, Control, rep4

description: Sample 11


title: Lung, SARS-CoV-2 SP + Poly (I:C), rep3

description: Sample 08

value: SARS-CoV-2 SP and Poly (I:C)


title: Lung, Control, rep2

description: Sample 06


title: Lung, SARS-CoV-2 SP + Poly (I:C), rep2

description: Sample 05


title: Lung, Control, rep1

description: Sample 03


title: Lung, SARS-CoV-2 SP + Poly (I:C), rep1

description: Sample 02


title: WT Dorsal Hc, ASO control, rep1

first: Cesar

last: Sierra

address: C/ Dr Aiguader 88

institute: Centre for Genomic Regulation (CRG)

data_processing:
Trimmed reads were aligned using STAR (v.2.5.2a) to reference genome (GrCM38/mm10) with standard parameters and quantified using Rsubreads (v.1.26).
Assembly: mm10
Supplementary files format and content: Bam files with reads sorted by coordinate

source_name: Dorsal hippocampus

extract_protocol:
RNA was harvested by TRIzol extraction. 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA Library Prep kits following manufacturer's protocols.

value: Dorsal hippocampus

value: WT


title: WT Dorsal Hc, ASO Snhg11 rep1

value: Snhg11 KD


title: WT Dorsal Hc, ASO Snhg11 rep3


title: WT Dorsal Hc, ASO Snhg11 rep2


title: mESC_WT_RRBS


title: C57BL/6, S14

city: Ghent

first: Olga

last: Krysko

address: C. Heymanslaan 10

department: Department of Head and Skin

country: Belgium

institute: Ghent University

data_processing:
All fastq files passed quality control with FastQC v0.11.5.
Salmon v0.8.2 30 was used to align raw RNA-seq reads against Ensembl Mus musculus GRCm39 and get quantification estimates at the transcript level.
Assembly: mm39
Supplementary files format and content: quantification file with name (Name) of each transcript, its length (Length), effective length (EffectiveLength), and its abundance in terms of Transcripts Per Million (TPM) and estimated number of reads (NumReads) originating from this transcript.

source_name: bone marrow

extract_protocol:
RNA was harvested using RNAeasy kit (Qiagen)
The TruSeq Stranded mRNA kit (Illumina) was used to prepare a RNAseq library according to the manufacturer’s protocol.

value: bone marrow

value: mast cells


title: C57BL/6, S12


title: BALB/c, S11

value: BALB/c


title: BALB/c, S10


title: HepG2, R1274W, control

city: Huntsville

first: Chris

last: Partridge

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute

data_processing:
Fastq files were obtained from Illumina software and Discovery Life Sciences sequencing center pipeline.
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 2.3.4.3.
Peaks were called using SPP v.2.2.4 and IDR v.2.0.4.2 at .05.
Assembly: hg38
Supplementary files format and content: regionPeak

extract_protocol:
Crosslinking: 1% formaldehyde, 10 minutes, room temperature. See Meadows et al. (2020) "Epitope tagging ChIP-seq of DNA binding proteins using CETCh-seq"
ChIP-seq libraries were prepared using the ENCODE standardized protocol. 5-50 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 12 cycles on the thermocycler. Libraries were validated and quantified using KAPA library quantification kit.

tag: chip antibody

value: Sigma F1804 anti-FLAG


title: BALB/c, S9


title: HepG2, R1274W, variant


title: HepG2, R688H, variant


title: HepG2, R688H, control


title: Lung, SARS-CoV-2 SP + Poly (I:C), rep4

description: Sample 12


title: HepG2, CETCh-seq


title: ATAC-seq

first: Jimin

last: Tan

address: 435 E 30th St

institute: NYU Langone

data_processing:
Reads are subsampled to 40 million
Subsampled fastq are processed by Seq-N-Slide ATAC-seq pipeline described in https://igordot.github.io/sns/routes/atac.html
Assembly: hg38
Supplementary files format and content: bigwig

source_name: Peripheral blood

extract_protocol: Chromatin accessibility was accessed using the standard ATAC-seq protocol described in Buenrostro et al. 2015

value: Peripheral blood

value: T lymphoblast


title: 1_WT_ATAC

city: Hangzhou

first: Xinwei

last: Geng

address: 866 Yuhangtang Rd., Zijingang Campus, Zhejiang University, Hangzhou, China

institute: Zhejiang University School of Medicine

data_processing:
Basecalls performed using CASAVA version 1.4
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using trim_galore v0.6.4 with parameters -q 25 --phred33 --length 25 -e 0.1 --stringency 4
Reads were mapped to mm10 whole genome using bowtie2 v2.2.5 with default parameters, then duplicates were marked and removed using samtools v1.7  with default parameters
Bam files were transfered into bed files using bedtools v2.29.0 with deufault parameters, peaks were called from bed files using macs2 v2.1.3.3 with parameters -g mm --nomodel --shift -100 --extsize 200 --broad --broad-cutoff 0.05 --keep-dup all
Motifs were enriched using HOMER v4.11 with default parameters
Genome_build: mm10
Supplementary_files_format_and_content: trimmed fastq files
Supplementary_files_format_and_content: bam files, result file of alignment procedure
Supplementary_files_format_and_content: bed files, transfered from bam files
Supplementary_files_format_and_content: peak files

source_name: MEF cells

growth_protocol: MEF cells were generated from embryonic day 13.5 mouse embryos and reprogrammed with KOSM

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were extracted

treatment_protocol: transfected with lentivirus overexpressing KOSM

value: primary MEF cells


title: WT Dorsal Hc, ASO control, rep2


title: C57BL/6, S13


title: 2_KO_ATAC

value: PICH-KO


title: WT Dorsal Hc, ASO control, rep3


title: TS hippocampus, replicate 1, snRNAseq

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Hippocampus

extract_protocol:
Each hippocampus was dissected and placed in chilled Hanks’ Balanced Salt Solution. The, it was transferred to a new tube containing 500μL chilled EZ Lysis Buffer and homogenized using a sterile RNase-free douncer. The resulting homogenate was filtered using a 70μm strainer mesh to remove remaining chunks of tissue and centrifuged at 500g for 5 minutes at 4ºC. The pellet containing the nuclei was resuspended in 1.5mL EZ Lysis Buffer and centrifuged again. The supernatant was removed and 500μL of Nuclei Wash and Resuspension Buffer (NWRB, 1X PBS, 1% BSA and 0.2U/μL RNase inhibitor) were added without disturbing the pellet and incubated for 5 minutes. After incubation, 1mL of NWRB was added and the pellet resuspended. The nuclei suspension was centrifuged again and the washing step was repeated with 1.5mL of NWRB. After an additional centrifugation, nuclei were resuspended in 500μL of 1:1000 anti-NeuN antibody conjugated with AlexaFluor 647 in PBS and incubated in rotation for 15 minutes at 4ºC. After incubation, nuclei were washed with 500μL of NWRB and centrifuged again. Last, nuclei were resuspended in NWRB supplemented with DAPI and filtered with a 35μm cell strainer to obtain a single-nuclei suspension.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, 10.000 neuronal nuclei were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Hippocampus

value: Neurons

value: B6EiC3Sn a/A-Ts(1716)65Dn/J

value: 4 month old

value: TS


title: WT hippocampus, replicate 3, snRNAseq

description: 10x Genomics


title: TS hippocampus, replicate 2, snRNAseq

description: 10x Genomics


title: TS hippocampus, replicate 4, snRNAseq

description: 10x Genomics


title: TS hippocampus, replicate 3, snRNAseq

description: 10x Genomics


title: WT hippocampus, replicate 4, snRNAseq

description: 10x Genomics


title: WT hippocampus, replicate 1, snRNAseq

description: 10x Genomics


title: 1y_d_snRNAseq

city: Perth

first: Ryan

last: Lister

state: WA

address: 35 Stirling Highway

country: Australia

institute: The University of Western Australia

description:
RL2987
nuclear RNA
no paired snATAC data

data_processing:
cellranger mkfastq with Cellranger v3.1 to generate fastq files as inout for count pipeline.
cellranger count with Cellranger v3.1 to generate feature-barcode matrices of gene expression.
Assembly: hg19
Supplementary files format and content: Feature-barcode matrices in HDF5 format containing every barcode from the fixed list of known good barcode sequences that has at least 1 read for raw_feature files, or only containing detected cellular barcodes for filtered_feature files.

source_name: prefrontal cortex, BA9

extract_protocol:
Per sample, 50 mg of frozen brain tissue was lysed and nuclei extracted. Nuclei were then enriched by DAPI-positive FANS for single cell gene expression library generation.
10X Genomics 3' Single Cell Gene Expression v3.

value: brain


title: A549, RN7SK-KO, R3, rep3

city: Shanghai

first: Xin

last: Xu

address: West Huaihai Road No.241

institute: Shanghai Chest Hospital

data_processing:
Trimmomatic ver. 0.36,  Parameters: LEADING:3 TRAILING:3 ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10:8:true SLIDINGWINDOW:4:15 MINLEN:50
RseQC ver. 2.6.4
fastqc ver. 0.11.5
hisat2 ver. 2.2.1.0, Parameters :--rna-strandness rf --fr
stringtie2 ver. 1.3.3b, Parameters:--rf
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM and counts values for each Sample

extract_protocol:
Total RNA was extracted using TRIzol reagent
RNA library for RNA-seq were prepared using  mRNA-Seq Library Prep Kit following manufacture's protocols.

value: LUAD cell

value: RN7SK knockout


title: A549, control, N3, rep3

value: WT


title: A549, RN7SK-KO, R2, rep2


title: A549, control, N2, rep2


title: A549, RN7SK-KO, R1, rep1


title: 1y_c_snRNAseq

description:
RL2986
nuclear RNA
no paired snATAC data

source_name: prefrontal cortex, BA9, 46


title: WT hippocampus, replicate 2, snRNAseq

description: 10x Genomics


title: A549, control, N1, rep1


title: eCLIP_MOLM13_RBM10_Replicate_4

city: South San Francisco

first: Simon

middle: J

last: Hogg

state: California

address: 1000 Gateway Boulevard

department: Oncology Discovery Research

institute: AbbVie

data_processing:
Illumina Casava software was used for base calling.
The UCSC version GRCh38 (hg38) genome build and GENCODE Release 35 (GRCh38.p13) transcriptome build were used for mapping of eCLIP-seq reads.
Data processing was outsourced and performed by Eclipse Bioinnovations (San Diego, CA 92121).
Assembly: Hg38
Supplementary files format and content: BigWig files containing reads mapped to the positive (.pos.bw) and negative (.neg.bw) strands.

source_name: Acute Myelogenous Leukemia

growth_protocol: MOLM13 cells were grown under standard in vitro conditions in RPMI-1640 medium supplemented with fetal calf serumn and cultured at 37 °C with 5% CO2.

extract_protocol:
Extraction and Immunoprecipitation was outsourced and performed by Eclipse Bioinnovations (San Diego, CA 92121).
Library preparation and sequencing was outsourced and performed by Eclipse Bioinnovations (San Diego, CA 92121), which was performed using an Illumina NovaSeq with single-end 150 base-pair reads.

treatment_protocol: Aliquots of 20e6 MOLM13 cells were prepared in technical quadruplicate.

tag: index 1

value: CAAGCTAG

tag: index 2

value: ACGCACCT

tag: ip antibody

value: RBM10 antibody (Bethyl A301-006A)

tag: protocol

value: eCLIP


title: eCLIP_MOLM13_RBM10_Replicate_3

value: GCTTGTCA


title: eCLIP_MOLM13_RBM10_Replicate_2

value: GGACTTGG

value: TACTCATA


title: eCLIP_MOLM13_INPUT_Replicate_4

value: CGCTATGT


title: eCLIP_MOLM13_RBM10_Replicate_1

value: TTATAACC


title: eCLIP_MOLM13_INPUT_Replicate_3

value: ATCCACTG


title: eCLIP_MOLM13_INPUT_Replicate_2

value: TGGATCGA

value: GTATGTTC


title: eCLIP_MOLM13_INPUT_Replicate_1


title: eCLIP_MOLM13_Rabbit_IgG_IP

value: CTAGCGCT

value: Rabbit IgG (Thermo Fisher Scientific)


title: mESC WT IgG Control for H3K9me3  Rep 2

city: London

first: Helen

middle: M.

last: Rowe

state: --- Select a state ---

address: 4 Newark St, Whitechapel

department: Blizard Institute, Barts and The London School of Medicine and Dentistry

institute: Queen Mary University of London

description: WT conditions

data_processing:
Library strategy: CUT&TAG
RNA-Seq and CUT&RUN fastq files were trimmed for quality using TrimGalore v0.4.1
For RNA-Seq samples, alignment of trimmed reads to mm10 version of the mouse genome was performed with Tophat 2.1.0 using the --max-multihits 100 option. The number of read counts per gene and repeat family was calculated using the multi option from Tecount. Differential expression analysis was performed with DESeq2. For further details see Fernandes et al., 2022.
For CUT&RUN samples, trimmed reads were aligned with STAR with the following parameters: --outFilterMultimapNmax 5000 --outSAMmultNmax 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.06. Genomic coverage in form of bigwig files was calculated using the genomecov tool from bedtools using 10000000 / number_of_mapped_reads as a scaling factor.
For ChIP-Seq samples, reads were mapped to the mm10 version of the mouse genome using Bowtie2. ChIP-seq enriched peaks were called by MACS2 (v.2.1.2), and the common peaks were merged using bedtools
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files for genomic coverage normalised to number of mapped reads. Excel spreadsheet with results of differential expression analysis. Bed files with ChIP-Seq peaks

source_name: mESC

growth_protocol: ES3 mESCs were cultured in Glasgow Minimum Essential Medium (GMEM, Sigma) supplemented with 100 U/ml penicillin/streptomycin, 10% fetal calf serum (FCS, Life Technologies), 2mM L-glutamine (Gibco, Thermo Fisher Scientific), 1mM Sodium pyruvate (Sigma), 1x MEM non-essential amino acids (Gibco, Thermo Fisher), 0.1mM  2-Mercaptoethanol (Life Technologies) and 1,000 units/ml Leukaemia inhibitory factor (LIF, Chemicon) and grown at 5% CO2 at 37 °C. mESC lines were split 1:4 every 2 days using accutase or trypsin.

extract_protocol:
RNA-seq - Total RNA was extracted using RNeasy Micro kit columns (Qiagen) and DNase treated according to the manufacturer’s instructions (Ambion AM1907). RNA was quality checked on a 4200 Tapestation using the RNA ScreenTape assay (Agilent Technologies, Wokingham, UK) and the RNA concentration measured using a Qubit RNA Broad Range kit (Life Technologies, Paisley, UK)
CUT&RUN - We followed the EpiCypher® CUTANATM CUT&RUN Protocol (v1.6) (https://www.epicypher.com/resources/protocols/cutana-cut-and-run-protocol/). Briefly, CUT&RUN was performed using 100,000 sorted GFPBright cells (per antibody/sample combination). Cells were washed twice [20mM HEPES pH 7.5, 150mM NaCl, 0.5mM spermidine, 1× protease inhibitors (cOmplete™, Mini, EDTA-free, Roche)], attached to Concanavalin A beads (BioMag®Plus, Generon) which were pre-activated in activation buffer (20mM HEPES pH 7.9, 10mM KCl, 1mM CaCl2, 1mM MnCl2). Sample and bead slurry was resuspended in antibody buffer (20mM HEPES pH 7.5, 150mM NaCl, 0.5mM Spermidine, 1× protease inhibitors, 0.01% w/v digitonin, 2mM EDTA) containing primary antibody. 1ug of anti-H3K9me3 (Abcam, ab8898) or anti-H3K27ac (Abcam, ab4729) was incubated overnight at 4°C with gentle shaking. IgG control Ab (Millipore, 12-370) alone was used in parallel. The samples were washed 3x in cold digitonin buffer (20 mM HEPES pH 7.5, 150mM NaCl, 0.5mM Spermidine, 1× Roche complete protease inhibitors, 0.01% digitonin). pA-MNase (2.5μl per tube, CUTANA™ pAG-MNase, Epicypher) was added incubated with the bead-cell slurry at room temperature for 10min. The beads were washed twice and resuspended in cold digitonin buffer. The pA-MNase was activated by addition of 2mM CaCl2 (final) and incubating at 4°C for 2h. The reaction was quenched using stop buffer (340mM NaCl, 20mM EDTA, 4mM EGTA, 50μg/ml glycogen, 50μg/ml RNase A), vortexing and incubating for 10 min at 37°C. A magnetic rack was used to separate cells and beads from the supernatant which was purified with a MinElute PCR Purification Kit (Qiagen).
ChIP - ES3 mESCs were transduced with ZFP819 and ZFP809-expressing lentiviral vectors (pRRLSIN.cPPT.PGK-ZFP.WPRE vectors with a triple HA tag). Cells were washed twice (in PBS + 2% FCS), counted to normalize by cell number, cross-linked (10 min rotation in 1% formaldehyde), quenched with glycine (at 125 mM on ice), washed three times (PBS), and snap-frozen at 107 cells per tube. Cells were resuspended in sequential ChIP lysis buffers and then in 900ul of sonication buffer on ice (10 mM Tris at pH 8, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% NaDOC, 0.25% NLS, and protease inhibitors). Where a Covaris sonicator was used, 900ul was sonicated in one covaris glass tube with the settings: 20% duty cycle, intensity 5, 200 cycles/burst, 30 min. For sonication with a Bioruptor Pico, 300ul aliquots per 1.5ml tube were sonicated1. Immunoprecipitations were performed in duplicates as described2 using an HA Ab (Biolegend, 901501) and DNA extracted (Qiagen MinElute PCR purification kit, Cat. 28004) for PCR and sequencing. See Supplementary Information for primers.  1. Tie, C.H. et al. KAP1 regulates endogenous retroviruses in adult human cells and contributes to innate immune control. EMBO Rep 19(2018).  2. Robbez-Masson, L. et al. The HUSH complex cooperates with TRIM28 to repress young retrotransposons and new genes. Genome Res (2018).
RNA-seq - 500 ng per sample was processed using KAPA’s stranded RNA HyperPrep RiboErase kit and sequenced on a NextSeq 500 instrument (Illumina Cambridge, Chesterford, UK) after pooling libraries in equimolar quantities, using a 2x 151 bp paired-end run, resulting in over 15 million reads per sample.
CUT&RUN - Illumina sequencing libraries were prepared using a NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® and NEBNext® Multiplex Oligos for Illumina® (New England BioLabs). Enrichment of DNA fragments was achieved by PCR (12 cycles). Libraries pooled in equimolar quantities were sequenced on Novaseq6000 for 150 paired-end reads.
ChIP-seq - Libraries were prepared following the ChIP-Seq library preparation protocol (Illumina, IP-102-1001). Ligation products were purified on 2% E Gels Size Select (Invitrogen; fragments of 200 bp recovered), followed by enrichment of DNA fragments by PCR (18 cycles). Sequencing was performed with Illumina HiSeq 2500 in 100-bp single-end reads.

treatment_protocol: mESCs were transduced with shRNA expressing lentiviral vectors. Puromycin selection was performed 2 days post transduction overnight (and control cells verified to die) and samples harvested 5 days post selection. Cells tranduced with GFP shRNA expressing lentiviral vectors were sorted on day 2 post transduction and harvested 5 days later.

tag: antibodies

value: IgG control Ab (Millipore, 12-370)

tag: full name


title: mESC WT IgG Control for H3K9me3  Rep 1

description: WT conditions

tag: strain


title: eCLIP_MOLM13_Rabbit_IgG_INPUT

value: AAGTCCAA

value: CGTCTGCG


title: mESC WT H3K9me3 Rep 2

description: WT conditions

value: anti-H3K9me3 (Abcam, ab8898)


title: shTRIM28 H3K9me3 Rep 1

description: mESCs transduced with pLKO.1 (Addgene #10878) lentiviral vector expressing a shTRIM28 hairpin (see Fernandes et al., 2022 for shRNA sequences)

tag: transduction

tag: time-point

value: GFPBright cell were sorted as detailed in Fernandes et al., 2022


title: mESC WT H3K9me3 Rep 1

description: WT conditions


title: shTRIM28 H3K9me3 Rep 2


title: shTRIM28 IgG Control for H3K9me3 Rep 1


title: shZfp819 62 IgG Control for H3K9me3 Rep 2

description: mESCs transduced with pLKO.1 (Addgene #10878) lentiviral vector expressing a shZfp819 hairpin (known as shZfp819 62) (see Fernandes et al., 2022 for shRNA sequences)


title: shZfp819 62 IgG Control for H3K9me3 Rep 1


title: shZfp819 62 H3K9me3 Rep 1


title: shZfp819 59 H3K9me3 Rep 2

description: mESCs transduced with pLKO.1 (Addgene #10878) lentiviral vector expressing a shZfp819 hairpin (known as shZfp819 59) (see Fernandes et al., 2022 for shRNA sequences)


title: shZfp819 59 H3K9me3 Rep 1


title: shEmpty H3K9me3 Rep 2

description: mESCs transduced with empty pLKO.1 (Addgene #10878)  lentiviral vector (known as shControl) (see Fernandes et al., 2022 for shRNA sequences)

value: shEmpty


title: shZfp819 59 IgG Control for H3K9me3 Rep 2


title: shTRIM28  IgG Control for H3K27ac Rep 2

value: Samples collected 5 days post puromycin selection


title: shZfp819 59 IgG Control for H3K9me3 Rep 1


title: shZfp819 62 H3K9me3 Rep 2


title: shTRIM28 H3K27ac Rep 2

value: anti-H3K27ac (Abcam, ab4729)


title: shEmpty H3K9me3 Rep 1


title: shTRIM28  IgG Control for H3K27ac Rep 1


title: E4d13p3A1

first: Oskar

last: Rosmark

address: Sölvegatan 19

department: Experimental medical science

institute: Lund university

data_processing:
.bcl files generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq program version 2.20. One mismatch was allowed for index sequence identification.
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
Trimmed reads were mapped to the Homo sapiens reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted. Since a strand-specific library preparation was performed, the reads were strand-specifically counted.
Genome_build: hg38
Supplementary_files_format_and_content: tab delimted text files contains raw counts for each sample

source_name: Primary human alveolar epithelial cells in in vitro culture

growth_protocol: Cultured in decellualrized lung scaffolds in Small Airway Epithelial Cell Growth Medium with 1 % FBS

extract_protocol:
Samples were frozen RNA later and RNA was later extracted using QIAGEN RNeasy Plus Mini Kit used according to manufacurers instructions.
Strand-specific RNA sequencing library was prepared by using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA).

treatment_protocol: The TGF-ß1 group were treated with 2 ng/ml of recombiant TGF-ß1 added to the medium at medium changes day 7 and day 10 of culture.

value: Healthy

tag: experimental group

tag: cell donor key

tag: scaffold donor key

tag: time

value: 13 days of culture

tag: cell type

value: alveolar type II epithelial cells (AECII)


title: E4d13p3A2

tag: disease state


title: E4d13p3A4


title: shTRIM28 H3K27ac Rep 1


title: shZfp819 62 IgG Control for H3K27ac Rep 2


title: E4d13p2C4


title: shZfp819 62 IgG Control for H3K27ac Rep 1


title: E4d13p2B4


title: shTRIM28 IgG Control for H3K9me3 Rep 2


title: shZfp819 62 H3K27ac Rep 2


title: E4d13p2A4


title: shEmpty IgG Control for H3K9me3 Rep 1


title: shEmpty IgG Control for H3K9me3 Rep 2


title: E4d13p2B3


title: E4d13p2C2


title: E4d13p2B2


title: ChIP-seq_Input_W2

first: Fei

last: Li

address: 320 Yue-Yang Road Shanghai

institute: Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences

data_processing:
TrimGalore-0.5.0 was conducted for trimming raw fastq files to remove adaptors with the following parameter settings: -q 25 --phred33 --length 35 -e 0.1 --stringency 4. The trimmed fastq files were then mapped to the mm10 genome utilizing Bowtie2. Sambamba-0.6.6 was then used to remove duplicates. For IGV-2.3 visualization, deepTools-3.2.1 was performed using the “bamCoverage” function to generate normalized CPM.bw files. For peak calling, MACS2-2.1.1 was utilized with a -q 0.05 parameter setting. DeepTools was further applied for heatmap visualization with the functions “computeMatrix” and “plotHeatmap”. The “dba.peakset” function of the Diffbind-2.12.0 R package was further applied to identify overlap peaks on the basis of the peaks bound by both Foxa1 (early stage) and Foxa2 (late stage). To further identify Foxa1-specific and Foxa2-specific peaks, the “intersect” function of bedtools-2.25.0 was utilized as the following script: bedtools intersect -a -b -v. The links of ChIP-seq peaks and their related genes were established by the “annotatePeaks.pl” function in Homer. Motif enrichment analyses were performed using the “findMotifsGenome.pl” function in Homer, leading to Known enrichment results and de novo enrichment results, and the latter were chosen in this study. The “enrichGO” and “dotplot” functions of the clusterProfiler-3.12.0 R package were used to analyze and visualize pathway enrichment.
Genome_build: mm10
Supplementary_files_format_and_content: peak and bigWig

source_name: Mouse prostate tumor cells

extract_protocol: Three mouse prostates were dissected and minced with scissors in 5 ml cold DPBS with PMSF. Shredded tissue was fixed with 1% formaldehyde at room temperature for 10 min with rotation. Then, 125 mM glycine was added to quench the formaldehyde at room temperature for 5 min. 3ml of ice-cold lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl, 1× proteinase inhibitor) was added and incubated at 4 °C for 30 min with rotation. An 880 μL cell lysate was transferred into a Covaris milliTUBE 1 mL AFA Fiber vial and sheared in a Covaris S220 ultrasonicator (fill level: 10, duty cycle: 5, PIP: 140, cycles/BURST: 200, time: 15 min). Clarified samples were collected by centrifugation at 15,000 rcf for 15 min at 4 °C. After preclearing with 30 μL of protein G beads (Invitrogen, 10003D), 3 μL of anti-FOXA1 (Abcam ab23738)/FOXA2 (Abcam ab256493) antibody was added for immunoprecipitation overnight. To bind the anti-FOXA1/FOXA2 antibody, 100 μL of protein G beads was added and incubated with rotation for three hours at 4 °C. The beads were washed twice each with Low Salt Wash Buffer, High Salt Wash Buffer and LiCl Wash Buffer and resuspended in 100 μL of freshly prepared DNA Elution Buffer (50 mM NaHCO3 and 1% SDS). The ChIP sample beads were placed on a magnet, and the supernatant was collected into a new tube. The above elution step was repeated with another 100 μL of elution buffer. The samples were then digested with 10 μL of Proteinase K (Invitrogen, 25530049) with incubation at 65 °C for 5 h. DNA was purified with DNA Clean & ConcentratorTM-5 (Zymo Research, D4004). Two nanograms of eluted DNA was used as input for library construction with a TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD503). The libraries were sequenced with the Illumina NovaSeq sequencing system (PE 2×150 bp reads) at Berry Genomics.

value: Mouse prostate tumor cells

tag: treatment

value: treated with tamoxifen for 2 weeks


title: ChIP-seq_Foxa2_M6

tag: chip antibody

value: treated with tamoxifen for 6 months


title: ChIP-seq_Foxa2_W2


title: E4d7p1C4

value: 7 days of culture


title: ChIP-seq_Input_M6


title: E4d7p1C3


title: E4d7p1A4


title: E4d7p1A3


title: shEmpty H3K27ac Rep 2


title: E4d13p2A1


title: shEmpty IgG Control for H3K27ac Rep 2


title: shZfp819 62 H3K27ac Rep 1


title: ATAC_M6

data_processing:
In brief, after raw reads were trimmed by TrimGalore-0.5.0, Bowtie2 was used to map the reads to the mm10 genome. Samtools-1.4 was further utilized for bam file sorting and indexing. The “bamCoverage” function of deepTools was utilized to generate .bw files with counts per million (CPM) normalization.
Genome_build: mm10
Supplementary_files_format_and_content: peak and bigWig

extract_protocol: To reduce the amount of contaminating mitochondrial DNA, we performed an optimized ATAC-seq protocol. In brief, cells were collected and washed once with PBS. The cells were then lysed in ice-cold lysis buffer (10 mM Tris-HCl, pH 7.4; 10 mM NaCl; 3 mM MgCl2; 0.1% NP-40; 0.1% Tween 20; and 0.01% digitonin) for 3 min on ice. Immediately after lysis, nuclei were washed with 1 mL of wash buffer (10 mM Tris-HCl, pH 7.4; 10 mM NaCl; 3 mM MgCl2; and 0.1% Tween 20) and then centrifuged at 500 g for 10 min at 4 °C. To prepare sequencing libraries, a TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD501) was utilized for the following steps.


title: ATAC_W2


title: ChIP-seq_Foxa1_M6


title: E3d13p3A4

value: COPD


title: E4d7p1A1


title: E3d13p2A4


title: E3d13p3A3


title: ChIP-seq_Foxa1_W2


title: shEmpty IgG Control for H3K27ac Rep 1


title: shEmpty H3K27ac Rep 1


title: E3d13p2B3


title: E3d13p3A1


title: E4d13p2A2


title: E3d13p2C4


title: E3d13p2A3


title: E3d13p2C2


title: E3d13p2C1


title: E4d7p1A2


title: E3d13p2B2


title: E3d7p1A4


title: E3d13p2A1


title: E2d13p3A4


title: E3d7p1C2


title: E3d7p1A3


title: E2d13p3A2


title: E3d7p1A2


title: E3d7p1C4


title: E3d7p1C1


title: E2d13p2B4


title: E2d13p3A1


title: E2d13p2A2


title: E2d13p2C1


title: E2d13p2A3


title: E2d13p2B1


title: E2d7p1C4


title: E2d13p2A1


title: E2d13p2B3


title: mouse PBN chronic pain (SNL) rep1

city: Seattle

first: Xiaonan

last: Fu

address: 1705 NE Pacific St

department: Biochemistry

institute: University of Washington

description: SNL(16500,26000); Sham(29000,38500)

data_processing:
Library strategy: barcoded spatial sequencing
Index map: in house basecalling for spatial indices
Index & gene extraction: Pixel-seq reads include two parts of information: The UMIs and spatial indices sequences were extracted from Read 1 using cutadaptv3.3. The read 2 were aligned to the GRCm38 genome assembly using STARv2.7.8a with the default configurations, featureCountsv1.6.0 was used to assign gene name to each reads with Mus_musculus.GRCm38.101.gtf as reference. Then they were integrated into a fasta file with header for gene mapping information and sequences as spatial indices.
Mapped reads: The spatial barcode sequencing mapping was performed by bowtie allowing up to 2 mismatches reporting the top alignment.
Segmentation: A customized method V-seg (Volume-distance based segmentation of mapped transcripts) was used to aggregate the profile for cellular level analysis, implemented in R
Clustering: The DGE matrix of segmented cells was analyzed in the Seurat v4.0.2 package. The SCTransform was used for normalization. The UMAP Clustering was performed on PCA reductions and optimal resolution.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text file and seurat object file

source_name: C57BL/6 male mouse

growth_protocol: Standard Mouse rearing condition

extract_protocol:
Pixel-seq build pixel-level spatial indices map through in-house sequencing and place the tissue section onto the flow cell for spatial transcriptome quantification.
Illumina nextra kit

treatment_protocol: spinal nerve ligation (SNL)

tag: tissue

value: Mouse brain PBN region

tag: srtain

value: Wild-type


title: mouse PBN region_anterior

description: Anterior(16500,28000); middle(31000,43000);  posterior(45000,57500)


title: mouse PBN chronic pain (SNL) rep2

description: SNL(21000,31000); Sham(36000,47000)


title: E3d7p1A1


title: mouse Olfactory bulb sections_rep1

description: single section

value: Mouse brain Olfactory bulb


title: E2d7p1A3


title: E2d7p1C1


title: E2d13p2C3


title: E2d7p1A4


title: E1d13p2B3


title: E1d13p2B2


title: E1d13p2A2


title: E2d7p1C3


title: E2d7p1A2


title: E1d13p2B4


title: E1d13p3A3


title: E2d7p1A1


title: E1d13p3B1


title: E1d7p1A4


title: E1d13p2A1


title: E1d7p1C3


title: E1d13p2A4


title: E1d7p1C4


title: E1d13p2C2


title: E1d7p1A3


title: E1d7p1A2


title: E1d7p1C1


title: E1d7p1A1


title: 9mth_organoid_snRNAseq [RL2340]

data_processing:
cellranger mkfastq with Cellranger v3.1 to generate fastq files as inout for count pipeline.
cellranger count with Cellranger v3.1 to generate feature-barcode matrices of gene expression.
Genome_build: hg19
Supplementary_files_format_and_content: Feature-barcode matrices in HDF5 format containing every barcode from the fixed list of known-good barcode sequences that has at least 1 read for raw_feature files, or only containing detected cellular barcodes for filtered_feature files.

molecule: nuclear RNA

source_name: cerebral organoid

growth_protocol: Iefremova et al, Cell Rep 2019 (doi:10.1016/j.celrep.2017.03.047)

extract_protocol:
Per sample, 50 mg of frozen organoid material was lysed and nuclei extracted. Nuclei were then either enriched by DAPI-positive FANS for single cell gene expression library generation.
10X Genomics 3' Single Cell Gene Expression v3

tag: tissue/cell type

value: ESC-derived cell culture


title: 5mth_organoid_snRNAseq [RL2432]


title: HCASMC-hTERT-FHL5_H3K4me3_rep1

first: Clint

last: Miller

institute: University of Virginia

data_processing:
The data was processed using the standard CUT&RUN Tools pipeline (Zhu et al. Genome Biology, 2019).
Adapters were trimmed from reads using Trimmomatic (v0.36), retaining only reads greater than 25bp in length.
Reads were mapped to the hg38 genome build using Bowtie2(v2.2.9), using the dove-tail option
Duplicates were marked and removed using Picard (v2.23.4) and samtools (v1.10).
Peaks were called using MACS2(v2.1.2) set to default parameters, using IgG samples as a background control.
Assembly: hg38
Supplementary files format and content: MACS2 narrowpeak files
Library strategy: CUT&RUN

source_name: HCASMC-hTERT

extract_protocol:
Genomic DNA  was released into the supernatant following antibody-guided MNase cleavage and purified by phenol-chloroform and ethanol precipitation.
CUT&RUN libraries were prepared as detailed on https://www.protocols.io/view/cut-amp-run-targeted-in-situ-genome-wide-profiling-14egnr4ql5dy/v3. Briefly, end repair and A tailing was performed at 12C for 15min, 37C for 15min, and 58C for 45min in a thermocycler. After Tru-seq adapter ligation, genomics DNA was purified using 2 rounds of Ampure Beads. Libraries were amplified through 14 cycles of PCR amplification and purified using 1.2X volume of Ampure XP beads.  The DNA concentration of each library was quantified using the Qubit and pooled for paired end sequencing on the Illumina Nextseq 2000 or Illumina Nextseq 500.

tag: cell line

value: hTERT immortalized coronary artery smooth muscle cell

tag: antibody

value: H3K4me3 (Active Motifs - Cat#391159)


title: 12mth_organoid_snRNAseq [RL2290]


title: HCASMC-hTERT-FHL5_IgG_rep1

value: IgG (Abcam - ab46450)


title: E1d13p3A1


title: E1d13p2C4


title: 4_20_MUT_infected_ZIKV

city: Newcastle

last: Cockell

address: Framlington Place

institute: Newcastle University

data_processing:
Raw sequencing quality determined by FastQC (v0.11.9)
Transcript count tables were produced using Salmon (v0.14.1) and Gencode release 31
Transcript counts aggregated at the gene level using tximport
Assembly: Gencode release 31, GRCh38.p12 - Ensembl release 97
Supplementary files format and content: txt files with transcript level counts

source_name: iPS-macrophage

growth_protocol: iPS cells were differentiated to macrophages via embryoid bodies using AggreWells (Stem Cell Technologies) as previously described (PMID: 23951090).

extract_protocol:
RNA was extracted from iPS-macrophages at 24 hours post infection using BL buffer and ReliaPrepTM RNA Cell Miniprep System (Promega) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina (TruSeq) protocols

treatment_protocol: Samples were treated with ZIKV H/FP/2013 strain at multiplicity of infection 10 (ZIKV infection) or 0 (media only MOCK infection) for 24 hours before extraction.

value: negative

tag: zikv

value: ZIKV

tag: extraction date


title: 8_28_MUT_infected_ZIKV


title: 9_29_WT_uninfected_MOCK

value: positive

value: MOCK


title: 10_30_WT_infected_ZIKV


title: 12_32_MUT_infected_ZIKV


title: 6_26_WT_infected_ZIKV


title: 11_31_MUT_uninfected_MOCK


title: 7_27_MUT_uninfected_MOCK


title: 5_25_WT_uninfected_MOCK


title: 1_17_WT_uninfected_MOCK


title: 3_19_MUT_uninfected_MOCK


title: WT MoM1

city: High Education Mega Center, SCUT, Building B2, Room 404

first: min

last: ma

state: guangzhou

address: Panyu Square

department: medical division

institute: south china university of technology

data_processing:
Raw sequene data were processed on STAR_2.5.2b and mixcr-3.0.12
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: liver

extract_protocol:
Macrophages were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: monocyte-derived macrophages

tag: genotype

value: wild type


title: TG MoM 1

value: dnTGF[beta]RII


title: TG MoM 2


title: WT Kupffer 1

value: liver-resident Kupffer cells


title: WT MoM2


title: WT Kupffer 2


title: TG Kupffer 2


title: TG Kupffer 1


title: 2_18_WT_infected_ZIKV


title: Exosome_M0_Macrophage_Rep5

city: Kunming

first: Jiang-Tian

last: Hu

state: Yunnan

address: No. 1088 Middle Haiyuan Road

institute: Yunnan Stomatology Hospital

description: miRNA expression of M0 macrophage-derived exosomes

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Exosome, M0 Macrophage, replicate 4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the Versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Freshly drawn peripheral blood from healthy volunteers was irradiated, then diluted 1:1 with RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum.   The cultures were incubated for 6 or 24 hours at 37 ºC in a humidified incubator with 5% CO2.

value: M0 macrophage-derived exosomes


title: s_GV_D6Ertd527e_WT_r2.SE

status: Public on Oct 30 2022

city: Prague

first: Filip

last: Horvat

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the ASCR

data_processing:
All RNA-seq data were mapped onto indexed mm10 mouse genome using STAR 2.5.3a.
Read mapping coverage was visualized in the UCSC Genome Browser   by constructing bigWig tracks using the UCSC tools
Assembly: mm10
Supplementary files format and content: bigWig, coverage files of reads mapped to the genome, scaled to the library size in millions reads mapping to the parts of the genome annotated as anything but rDNA

source_name: fully-grown oocytes

growth_protocol: Fully grown, germinal vesicle (GV)-intact oocytes were obtained from superovulated C57Bl/6NCrl. Oocytes were collected in M2 medium (Sigma-Aldrich) and cultured in MEM medium (Sigma-Aldrich) supplemented with 0.2 mM 3-isobutyl-1-methyl-xanthine (IBMX; Sigma), sodium pyruvate (Sigma-Aldrich), 4 mg/ml bovine serum albumin (Sigma-Aldrich) and penicillin, streptomycin (100 U/ml: 100 mg/ml, Sigma-Aldrich) at 37 ºC in a 5% CO2 atmosphere. Animal experiments were approved by the Institutional Animal Use and Care Committees and were carried out in accordance with the law.  The deletion mutant model was produced in the Czech Centre for Phenogenomics at the Institute of Molecular Genetics ASCR using Cas9-mediated deletion of D6Ertd527e intron 1 and the protein-coding sequence of exon 2 (Fig. S1). Sequences of guide RNAs were sgRNA T5 5′ - CCTCGAGATGAGCCATCC -3′ and sgRNA E2 5′ - CTTAGGAAATCATTCCCA -3′. To produce guide RNAs, synthetic 128 nt guide RNA templates including T7 promoter, 18nt sgRNA and tracrRNA sequences were amplified using T7 and tracrRNA primers. Guide RNAs were produced in vitro using the Ambion mMESSAGE mMACHINE T7 Transcription Kit, and purified using the mirPremier™ microRNA Isolation Kit (Sigma). The Cas9 mRNA was synthesized from pSpCas9-puro plasmid using Ambion mMESSAGE mMACHINE T7 Transcription Kit, and purified using the RNeasy Mini kit (Qiagen). A sample for microinjection was prepared by mixing two guide RNAs in water (25 ng/μl for each) together with Cas9 mRNA (100 ng/μl). Five picoliters of the mixture were microinjected into male pronuclei of C57Bl/6 zygotes and transferred into pseudo-pregnant recipient mice. PCR genotyping was performed on tail biopsies from four-weeks-old animals. We obtained a positive founder which transmitted the mutant allele to F1 and after two generations of breeding with C57Bl/6NCrl animals, the heterozygotes were used for breeding D6Ertd527e1–/– animals for phenotype analysis.   For detection of the knock-out allele were used D6Ertd _gen_Fwd5: 5′ -CCTGACACTCAAGAGACACGGTCA and D6Ertd _1_Rev: 5′ -CACCTTTCTGTGCTTGTGCTGAAC giving a 877 bp (wild-type allele is absent, too long to amplify). For detecting the wild type allele were used D6Ertd _gen_Fwd5: 5′ -CCTGACACTCAAGAGACACGGTCA and D6Ertd _MTD_Rev4: 5′ -GAACTGCAAGCTGAGGCTCACAAG, yielding a 812 bp product.

extract_protocol:
Total RNA was extracted from 25 wild-type or D6Ertd527e1–/– fully-grown oocytes from 11-16 weeks old animals using PicoPure RNA Isolation Kit with on-column genomic DNA digestion according to the manufacturer’s instruction (Qiagen).
RNA-Seq libraries were constructed using the Ovation RNA-Seq system V2 (NuGEN) followed by Ovation Ultralow Library system (DR Multiplex System, NuGEN)

value: fully-grown oocytes

tag: animal age

value: 11-16 weeks

value: D6Ertd527e WT

tag: developmental stage

value: GV oocyte


title: s_GV_D6Ertd527e_KO_r3.SE

value: D6Ertd527e KO


title: Exosome_M0_Macrophage_Rep1

source_name: Exosome, M0 Macrophage, replicate 1


title: Exosome_M0_Macrophage_Rep2

source_name: Exosome, M0 Macrophage, replicate 2


title: Exosome_M0_Macrophage_Rep3

source_name: Exosome, M0 Macrophage, replicate 3


title: s_GV_D6Ertd527e_WT_r3.SE


title: s_GV_WT_ChHam_r1.PE

data_processing:
All RNA-seq data were mapped onto indexed criGriChoV2 chinese hamster genome using STAR 2.5.3a.
Read mapping coverage was visualized in the UCSC Genome Browser   by constructing bigWig tracks using the UCSC tools
Assembly: criGriChoV2
Supplementary files format and content: bigWig, coverage files of reads mapped to the genome, scaled to the library size in millions reads mapping to the parts of the genome annotated as anything but rDNA

organism: Cricetulus griseus

growth_protocol: Fully grown, germinal vesicle (GV)-intact oocytes from chinese hamster were collected using the same procedure as for isolation of mouse oocytes without superovulation (Nagy A, (2003) Manipulating the mouse embryo: a laboratory manual pp Cold Spring Harbor Laboratory Press). Resumption of meiosis during culture of GV oocytes was prevented with 0.2 mM 3-isobutyl-1-methyl-xanthine (IBMX, Sigma). Animal experiments were approved by the Institutional Animal Use and Care Committees and were carried out in accordance with the law.

extract_protocol:
Total RNA was extracted from 25 oocytes using PicoPure RNA Isolation Kit with on-column genomic DNA digestion according to the manufacturer’s instruction (Thermo Fisher Scientific).
Libraries were constructed using the Ovation RNA-Seq system V2 (NuGEN) followed by Ovation Ultralow Library system (DR Multiplex System, NuGEN). RNA-Seq libraries were pooled and sequenced by 250 bp paied-end reading using Illumina HiSeq

value: WT


title: Noncachexia5

status: Public on Oct 29 2022

first: Diya

last: Sun

address: Dongan Street

institute: Zhongshan Hospital Fudan University

data_processing:
Illumina CASAVA 1.7software was used for basecalling
Raw reads generated during high-throughput sequencing were fastq format sequences. In order to get high-quality reads that could be used for later analysis, raw reads needed to be further quality filtered. Trimmomatic version 0.36 software was first used for adpter removing, And then low-quality bases and N-bases or low-quality reads were filtered out. Finally, we got high-quality clean reads.
Using hisat2 version 2.2.1.0 to align clean reads to the reference genome of the experimental specie, the sample should be assessed by genomic and gene alignment.
Assembly: Genome Database GRCh38.p12
Supplementary files format and content: Table with raw gene counts or normalized abundance measurements for every gene and every sample

source_name: Adipose tissue

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA)
The libraries were constructed using TruSeq Stranded Total RNA with Ribo-Zero Gold according to the manufacturer’s instructions. Then these libraries were sequenced on the Illumina sequencing platform and 150 bp/125bp paired-end reads were generated.

value: Adipose tissue

tag: tumor stage

value: II stage

tag: gender

value: Male


title: Deadaptor Noncachexia4


title: Exosome_M2_Macrophage_Rep3

description: miRNA expression of M2 macrophage-derived exosomes

source_name: Exosome, M2 Macrophage, replicate 3

value: M2 macrophage-derived exosomes


title: s_GV_WT_ChHam_r2.PE


title: Exosome_M2_Macrophage_Rep1

source_name: Exosome, M2 Macrophage, replicate 1


title: Exosome_M2_Macrophage_Rep2

source_name: Exosome, M2 Macrophage, replicate 2


title: Noncachexia4


title: Exosome_M2_Macrophage_Rep5

source_name: Exosome, M2 Macrophage, replicate 4


title: s_GV_D6Ertd527e_KO_r2.SE


title: N14_ACE_2C_WT_rep2

status: Public on Oct 28 2022

city: Beijing

first: Fan

last: Guo

state: Beijing

address: 1 Beichen West Road, Chaoyang District

department: The State Key Laboratory of Stem Cell and Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

description: ACE-Seq sequencing data profiled by ACE-Seq

data_processing:
library strategy: ACE-seq
ACE-seq: Raw paired-end 150bp sequencing data of whole-genome ACE-seq were trimmed by using Trim Galore (v0.6.6) with default parameters. The low-quality reads and sequences of adapters were filtered and trimmed. Clean reads were further aligned to the mm9 mouse genome by using Bismark (v0.23.0) with the paired-end mode. For unmapped reads of Read1 and Read2, realignments were performed in single-end mode. Deduplications were then performed with sambamba markdup (v0.6.6). The deduplicated reads were used for downstream analysis. Cytosines in CpG, CHH, CHG sequence context were extracted and counted by using MethyDackel (v0.5.0). In this study, raw signals were defined as the percentage of C/(C+T) at each site.
Assembly: mm9
Supplementary files format and content: *bw: bigwig files

source_name: Mouse 2-Cell

extract_protocol:
To collect preimplantation embryos, 6-8week old females (C57BL/6) were super-ovulated by injection of PMSG and hCG. MII oocytes were collected at 14-15 hours after hCG injection. As to preimplantation embryos, superovulated female mice were mated with either C57BL/6 or PWK males. Embryos were collected at 25-26 h (zygotes), 42-43 h (2-cell), 56-57 h (4-cell), 70-71 h (8-cell), and 94-96 h (blastocysts) after hCG injection. To isolate pronuclei, mouse zygotes at PN3- PN4 stages were collected and pronucleus were isolated as previously described (Guo et al., 2014). Zygotes which were maternally deficient in Tet3 were obtained through Zp3-Cre mediated conditional knockout in oocytes as previously described (Guo et al., 2014). To inhibit DNA replication, zygotes were treated with aphidicolin until the collection of pronuclei (Guo et al., 2014). The inhibition of DNA replication in mouse zygotes was validated by EdU incorporation assay.
ACE-seq: The construction of ACE-seq libraries followed the published protocol (Schutsky et al., 2018), with minor modifications. Fragmented gDNA was first modified using UDP- glucose and T4 Phage β-glucosyltransferase at 37 °C for 1 h. Then 0.1 N NaOH was added to the modified gDNA for denaturation at 55 °C for 10 min. APOBEC enzyme was used to deaminate gDNA at 37°C for 3 hrs. After deamination, gDNA was purified using Ampure XP beads before library construction according to the TAILS procedure (Gu et al., 2019; Yan et al., 2021). Finally, the ACE-seq libraries were sequenced on a Novaseq sequencer for 150 bp paired-end sequencing. scBS-seq: The zona pellucida of MII oocytes and 2-cell embryos were firstly removed by Tyrode's Solution. Construction of the scBS-seq or scCOOL-seq libraries were performed as previously described (Guo et al., 2017a; Smallwood et al., 2014). DNA libraries were sequenced on a Novaseq sequencer for 150 bp paired-end sequencing. Single-cell RNA-seq: Single-cell RNA-seq of 2-cell embryos were conducted by using smart-seq2 protocol (Picelli et al., 2014). In brief, single cell was picked into lysis buffer and Poly(A)+ RNA was captured by Oligo(dT) primer. The first strand of cDNA was synthesized by reverse transcription, then amplified, purified and fragmented. Fragmented cDNA was processed to construct RNA-seq library by NEBNext UltraII DNA Library Prep Kit for Illumina.
ACE-seq, scBS-seq and scRNA-seq

value: Mouse 2-Cell

value: C57BL/6(mother) x PWK(father)


title: s_GV_D6Ertd527e_KO_r1.SE


title: Deadapator Cachexia6

value: III stage


title: Cachexia6


title: s_GV_D6Ertd527e_WT_r1.SE


title: Deadapator Cachexia4


title: Deadapator Cachexia5


title: DF3.ADAR Input Rep3

city: D

first: Kate

last: Meyer

state: NC

address: 307 Research Drive Box 3711

institute: Duke University School of Medicine

data_processing:
Raw sequencing reads from RNA-seq libraries were trimmed with Flexbar (v3.5.0) with the following parameters: --adapter-preset TruSeq --zip-output GZ -qf i1.8
Trimmed reads were aligned to the Ensembl GRCh38 (hg38) primary assembly, supplemented with the rat Apobec1 sequence, using STAR (v2.7.7) in paired-end mode with the following options: --runMode alignReads --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat --outSAMattributes All --outFilterMismatchNmax 20 --outFilterScoreMinOverLread 0.5 --outFilterMatchNminOverLread 0.5. Duplicate reads were then marked with STAR using the following options: --runMode inputAlignmentsFromBAM --bamRemoveDuplicatesType UniqueIdenticalNotMulti.
Editing sites for each YTHDF fusion proteins were identified in Gencode V36 annotated transcripts with Bullseye v1.3.0 using the following parameters: --minEdit 2.5 --maxEdit 99 --editFoldThreshold 1.5 --EditedMinCoverage 10 --ControlMinCoverage 10 --MinEditSites 3
Raw gene counts were calculated using featureCounts v2.0.1 with the following options: -O -M -p --ignoreDup -t exon -g gene_id. RNA enrichment in RIP samples over input was measured with DESeq2.
For TRIBE, an editing score defined as the cummulative some of editing frequency at each called editing site was calculated for each annotated ensembl transcript. Editing frequencies were used for fitting in a quasibinomial glm to calculate log2foldchange and wald statistic for each conditions.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample.
Supplementary files format and content: Result of DESeq2 analysis for enrichment in each YTHDF RIP samples
Supplementary files format and content: Tab separated file containing the result of differential editing analysis performed with Bullseye using a quasibinomial GLM.

source_name: Input

growth_protocol: Cells were grown in DMEM containing 10% Fetal bovine serum.

extract_protocol:
Cell lysates (25mM Tris-Cl pH7.4; 150mM NaCl; 2.5mM EDTA, 0.5mM DTT; 0.5% NP-50) were used for RIP using antibodies targeting the endogenous YTHDF1, YTHDF2 or YTHDF3 antibody. Total RNA was extracted from a fraction of the cell lysate (Input samples) or eluted from antibody coupled beads using 1mL of TRIZOL reagent (Thermo) and the RNA was extracts according to the manufacturer’s protocol. RNA was resuspended in Nuclease-Free water. Total RNA was extracted using TRIzol reagent. RNA was then subjected to DNaseI treatment to remove any contaminating DNA.
For each sample 150ng of total RNA was used for library preparation. Library construction was performed using the NEBNEXT Ultra II Directional RNA-Seq kit and the NEBNext rRNA Depletion Kit.

treatment_protocol: Expression of YTHDF-ADAR was induced by treating cells with 1 ug/mL of doxycycline for 24 h.

value: 1 µg/mL doxycycline 24h;

tag: rip antibody


title: DF3.ADAR_DF2.RIP Rep3

source_name: YTHDF2 RIP-seq


title: DF3.ADAR_Input Rep1


title: Deadaptor Noncachexia5


title: N14_ACE_2C_WT_rep1


title: Cachexia5


title: DF3.ADAR_DF3.RIP Rep3

source_name: YTHDF3 RIP-seq


title: N14_ACE_2C_KO_rep2

value: N14 maternal KO


title: DF3.ADAR_Input Rep2


title: DF3.ADAR_DF1.RIP Rep3

source_name: YTHDF1 RIP-seq


title: DF3.ADAR_DF1.RIP Rep2


title: N14_ACE_2C_KO_rep1


title: Cachexia4


title: DF2.ADAR_Input Rep3


title: DF3.ADAR_DF2.RIP Rep1


title: DF3.ADAR_DF1.RIP Rep1


title: DF2.ADAR_Input Rep1


title: DF2.ADAR_DF2.RIP Rep3


title: DF3.ADAR_DF3.RIP Rep1


title: DF2.ADAR_DF3.RIP Rep2


title: DF2.ADAR_DF1.RIP Rep3


title: DF2.ADAR_DF3.RIP Rep3


title: DF2.ADAR_DF2.RIP Rep2


title: DF2.ADAR_DF2.RIP Rep1


title: DF2.ADAR_DF3.RIP Rep1


title: DF3.ADAR_DF3.RIP Rep2


title: DF2.ADAR_DF1.RIP Rep2


title: DF1.ADAR_DF3.RIP Rep1


title: DF1.ADAR_Input Rep2


title: DF1.ADAR_DF2.RIP Rep2


title: DF1.ADAR_Input Rep3


title: DF2.ADAR_DF1.RIP Rep1


title: DF1.ADAR_Input Rep1


title: DF1.ADAR_DF1.RIP Rep1


title: DF1.ADAR_DF2.RIP Rep1


title: DF1.ADAR_DF3.RIP Rep3


title: DF2.ADAR_Input Rep2


title: DF1.ADAR_DF1.RIP Rep3


title: DF1.ADAR_DF3.RIP Rep2


title: DF3.ADAR_Polysome_Rep1

description: Polysome-associated RNA

data_processing:
Raw sequencing reads from RNA-seq libraries were trimmed with Flexbar (v3.5.0) with the following parameters: --adapter-preset TruSeq --zip-output GZ -qf i1.8
Trimmed reads were aligned to the Ensembl GRCh38 (hg38) primary assembly, supplemented with the rat Apobec1 sequence, using STAR (v2.7.7) in paired-end mode with the following options: --runMode alignReads --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat --outSAMattributes All --outFilterMismatchNmax 20 --outFilterScoreMinOverLread 0.5 --outFilterMatchNminOverLread 0.5. Duplicate reads were then marked with STAR using the following options: --runMode inputAlignmentsFromBAM --bamRemoveDuplicatesType UniqueIdenticalNotMulti.
Editing sites for each YTHDF fusion proteins were identified in Gencode V36 annotated transcripts with Bullseye v1.3.0 using the following parameters: --minEdit 2.5 --maxEdit 99 --editFoldThreshold 1.5 --EditedMinCoverage 10 --ControlMinCoverage 10 --MinEditSites 3
Raw gene counts were calculated using featureCounts v2.0.1 with the following options: -O -M -p --ignoreDup -t exon -g gene_id. RNA enrichment in RIP samples over input was measured with DESeq2.
For TRIBE, an editing score defined as the cummulative some of editing frequency at each called editing site was calculated for each annotated ensembl transcript. Editing frequencies were used for fitting in a quasibinomial glm to calculate log2foldchange and wald statistic for each conditions.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample.
Supplementary files format and content: Result of DESeq2 analysis for RNA enrichment in Polysome-associated RNAs.
Supplementary files format and content: Tab separated file containing the result of differential editing analysis performed with Bullseye using a quasibinomial GLM.

source_name: YTHDF3 HyperTRIBE

extract_protocol:
Cell lysate (10mM HEPES pH.7.4, 150mM KCl, 1mM MgCl2, 2% NP-40, 1mM DTT, 100 µg/mL cycloheximide, 40U/mL RNaseOUT, cOmplete Mini EDTA-free protease inhibitor (Roche)) was separated on a 10-50% linear sucrose gradient by centrifugation at 28.000g for 3h at 4C in a SW28Ti rotor (Beckman). Fractions containing polysomes (>2 ribosomes) were pooled and total RNA was precipitated with ethanol.
For each sample 150ng of total RNA was used for library preparation. Library construction was performed using the NEBNEXT Ultra II Directional RNA-Seq kit and the NEBNext rRNA Depletion Kit.

treatment_protocol: Expression of YTHDF-ADAR was induced by treating cells with 1 µg/mL of doxycycline for 24 h. Cells were treated with 100 µg/mL cycloheximide for 10 minutes at 37C.

value: 1 µg/mL doxycycline 24h; 100 µg/mL cycloheximide 10 min


title: DF3.ADAR_Polysome_Rep2

description: Polysome-associated RNA


title: DF3.ADAR_Polysome_Rep3

description: Polysome-associated RNA


title: DF1.ADAR_DF1.RIP Rep2


title: DF2.ADAR_Polysome_Rep2

description: Polysome-associated RNA

source_name: YTHDF2 HyperTRIBE


title: DF2.ADAR_Polysome_Rep3

description: Polysome-associated RNA


title: DF3.ADAR_Input_Rep1

description: total RNA


title: DF3.ADAR_Input_Rep3

description: total RNA


title: DF2.ADAR_Polysome_Rep1

description: Polysome-associated RNA


title: DF2.ADAR_Input_Rep3

description: total RNA


title: DF1.ADAR_DF2.RIP Rep3


title: DF1.ADAR_Input_Rep1

description: total RNA

source_name: YTHDF1 HyperTRIBE


title: DF2.ADAR_Input_Rep2

description: total RNA


title: DF1.ADAR_Polysome_Rep2

description: Polysome-associated RNA


title: DF1.ADAR_Polysome_Rep3

description: Polysome-associated RNA


title: DF1.ADAR_Input_Rep3

description: total RNA


title: DF2.ADAR_Input_Rep1

description: total RNA


title: DF1.ADAR_Polysome_Rep1

description: Polysome-associated RNA


title: APOBEC1.alone_Rep1

description: Negative control for STAMP

data_processing:
Raw sequencing reads from RNA-seq libraries were trimmed with Flexbar (v3.5.0) with the following parameters: --adapter-preset TruSeq --zip-output GZ -qf i1.8
Trimmed reads were aligned to the Ensembl GRCh38 (hg38) primary assembly, supplemented with the rat Apobec1 sequence, using STAR (v2.7.7) in paired-end mode with the following options: --runMode alignReads --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat --outSAMattributes All --outFilterMismatchNmax 20 --outFilterScoreMinOverLread 0.5 --outFilterMatchNminOverLread 0.5. Duplicate reads were then marked with STAR using the following options: --runMode inputAlignmentsFromBAM --bamRemoveDuplicatesType UniqueIdenticalNotMulti.
Editing sites for each YTHDF fusion proteins were identified in Gencode V36 annotated transcripts with Bullseye v1.3.0 using the following parameters: --minEdit 2.5 --maxEdit 99 --editFoldThreshold 1.5 --EditedMinCoverage 10 --ControlMinCoverage 10 --MinEditSites 3
For STAMP, editing sites found in at least 2 biological replicates and with at least 1.5 fold editing over cells expressing APOBEC1 alone are selected.
For TRIBE, editing sites found in at least 4 biological replicates for YTHDF1 and YTHDF2 or 3 replicates for YTHDF3, and with at least 3 fold editing over cells expressing ADAR alone  are selected.
Assembly: hg38
Supplementary files format and content: bed file with the position of editing sites identified in TRIBE-STAMP for each YTHDF protein fusion proteins

source_name: Cultured cells

extract_protocol:
Total RNA was extracted using TRIzol reagent. RNA was then subjected to DNAseI treatment to remove any contaminating DNA.
For each sample 500ng of total RNA was used for library preparation. Library construction was performed using the NEBNEXT Ultra II Directional RNA-Seq kit and the NEBNext Poly(A) mRNA Magnetic Isolation Module.

treatment_protocol: Expression of YTHDF-APOBEC1 was induced by treating cells with 1 ug/mL of doxycycline for 24 h. Cells were transfected with YTHDF1-, YTHDF2-, YTHDF3-ADAR, ADAR alone or APOBEC1 alone containing plasmids by lipofection using Fugene HD.

tag: cell type

value: HEK293T cells

tag: transfection

tag: library type

value: RNAseq


title: DF3.ADAR_DF3.APOBEC1_Rep2

description:
library was sequenced using 150bp paired-end (_151PE) and 250bp paired-end (_251PE) protocols.
DF3_ADAR.bed
DF3_APOBEC1.bed


title: DF3.ADAR_DF3.APOBEC1_Rep1


title: DF1.ADAR_Input_Rep2

description: total RNA

tag: treatment


title: DF3.ADAR_DF2.APOBEC1_Rep1

description:
library was sequenced using 150bp paired-end (_151PE) and 250bp paired-end (_251PE) protocols.
DF3_ADAR.bed
DF2_APOBEC1.bed


title: DF3.ADAR_DF1.APOBEC1_Rep2

description:
library was sequenced using 150bp paired-end (_151PE) and 250bp paired-end (_251PE) protocols.
DF3_ADAR.bed
DF1_APOBEC1.bed


title: ADAR.alone_Rep2

description: Negative control for TRIBE


title: DF2.ADAR_DF3.APOBEC1_Rep3

description:
library was sequenced using 150bp paired-end (_151PE) and 250bp paired-end (_251PE) protocols.
DF2_ADAR.bed
DF3_APOBEC1.bed


title: DF3.ADAR_Input_Rep2

description: total RNA


title: DF2.ADAR_DF3.APOBEC1_Rep2


title: DF3.ADAR_DF2.APOBEC1_Rep2


title: DF2.ADAR_DF2.APOBEC1_Rep3

description:
library was sequenced using 150bp paired-end (_151PE) and 250bp paired-end (_251PE) protocols.
DF2_ADAR.bed
DF2_APOBEC1.bed


title: DF3.ADAR_DF1.APOBEC1_Rep1


title: DF2.ADAR_DF3.APOBEC1_Rep1


title: DF2.ADAR_DF2.APOBEC1_Rep2


title: DF2.ADAR_DF2.APOBEC1_Rep1


title: DF2.ADAR_DF1.APOBEC1_Rep3

description:
library was sequenced using 150bp paired-end (_151PE) and 250bp paired-end (_251PE) protocols.
DF2_ADAR.bed
DF1_APOBEC1.bed


title: DF1.ADAR_DF2.APOBEC1_Rep3

description:
library was sequenced using 150bp paired-end (_151PE) and 250bp paired-end (_251PE) protocols.
DF1_ADAR.bed
DF2_APOBEC1.bed


title: DF1.ADAR_DF3.APOBEC1_Rep3

description:
library was sequenced using 150bp paired-end (_151PE) and 250bp paired-end (_251PE) protocols.
DF1_ADAR.bed
DF3_APOBEC1.bed


title: DF1.ADAR_DF2.APOBEC1_Rep2


title: DF2.ADAR_DF1.APOBEC1_Rep2


title: DF1.ADAR_DF3.APOBEC1_Rep2


title: APOBEC1.alone_Rep2

description: Negative control for STAMP


title: DF3.ADAR_DF2.RIP Rep2


title: DF1.ADAR_DF1.APOBEC1_Rep3

description:
library was sequenced using 150bp paired-end (_151PE) and 250bp paired-end (_251PE) protocols.
DF1_ADAR.bed
DF1_APOBEC1.bed


title: ADAR.alone_Rep1

description: Negative control for TRIBE


title: DF1.ADAR_DF3.APOBEC1_Rep1