title: COLO320DM_in_vitro,  DMSO, 48hr, rep3 [21--3]

city: Cambridge

first: YaGuang

last: Si

address: 30 Acorn Park Dr

institute: Fogpharma

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.39
The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.7.7a
Unique gene hit counts were calculated by using featureCounts from the R Subread package v.2.4.2
Read filtering, normalization, and differential expression analysis with respect to biological variation was performed with the edgeR package v.4.0.2 in R
Assembly: GRCh38
Supplementary files format and content: readcounts_CPM_allsamples_invitro.xls
Supplementary files format and content: CPM from EdgeR for all samples in EXCEL format

extract_protocol:
RNA estraction was performed by GENEWIZ, LLC. (South Plainfield, NJ) with RNeasy Plus Universal mini kit following manufacture's instructions (QIAGEN, Hilden, Germany)
Library preparation and sequencing reactions were conducted at GENEWIZ, LLC. (South Plainfield, NJ). The RNA-seq libraries were prepared using the Illumina TruSeqstranded Total RNA protocol with subsequent PolyA enrichment

value: Colorectal adenocarcinoma

value: DMSO

tag: biol replicate


title: HepG2, GLORI, sgTAF7

status: Public on Oct 21 2025

type: SRA

city: Beijing

first: Jun

last: Liu

address: Haidian District

department: School of Life Sciences

country: China

institute: Peking University

description:
Library name: HepG2_GLORI_sgTAF7
HepG2_sgTAF7

library_source: transcriptomic

data_processing:
Reads were firstly trimmed by Trim Galore (v0.6.7)96 to remove adapters and low-quality bases with command as follows: "trim_galore -q 20 --stringency 1 -e 0.3 --length 35".
Seqkit (v.2.8.2) was then used to deduplicate PCR based on the 10-base-pair UMI at the 5′ end of reads R2 with parameters as follows: "seqkit rmdup -s".
Finally, FASTX-Toolkit (v.0.0.14) was used to remove UMI in the deduplication reads with parameters as follows: "fastx_trimmer -f 15".
For the downstream analysis we used GLORI-tools (https://github.com/liucongcas/GLORI-tools) with default parameters.
Assembly: hg38
Supplementary files format and content: csv files include m6A site ratio for each Sample

molecule: polyA RNA

organism: Homo sapiens

extract_protocol:
Cells were harvested and total RNA was extracted using TRIZOL reagent (Invitrogen) following the manufacturer’s protocols. To isolate mRNA from total RNA, the Dynabeads® mRNA Purification Kit (Invitrogen) was used following the manufacturer’s protocols. The RNA concentration was determined using Nanodrop (Invitrogen) by measuring the UV absorbance at 260 nm.
Library preparation was then performed using SMARTer Stranded Total RNA-Seq kits v3 Pico Input mammalian (Takara, 634487)

tag: cell line

tag: cell type

value: human hepatocellular carcinoma (HCC) cell line

tag: genotype

tag: treatment

value: sgRNA transfection


title: HepG2, GLORI, sgCTRL

description:
Library name: HepG2_GLORI_sgCTRL
HepG2_sgCTRL


title: HeLa, totalRNA, MeRIP, rep2

description:
Library name: HeLa_totalRNA_MeRIP_rep2
HeLa_totalRNA_MERIP_rep2

library_source: other

data_processing:
Basecalls were performed using bcl-convert.
Low-quality bases and adapters were trimmed using Trim Galore (v0.6.7), then trimmed reads mapping to ribosomal RNAs were removed by Bowtie2 (v2.2.5).
The remaining reads were aligned to the human genome (hg38) using HISAT2 (v2.2.1) with ‘--rna-strandness RF’ parameters.
Strand-specific reads were separated using samtools view (v1.18) with flags 99,147,83,163. m6A peak calling was performed using macs2 (v2.2.7.1) with ‘--keep-dup 5 -q 0.01 --nomodel’ parameters.
Assembly: hg38
Supplementary files format and content: narrowPeak (except for Input sample)

molecule: other

source_name: HeLa

extract_protocol:
Total RNA was isolated from chromatin-associated fraction of SMMC-7721, HepG2, HCT116 and HeLa cells. To isolate mRNA from total RNA, the Dynabeads® mRNA Purification Kit (Invitrogen) was used following the manufacturer’s protocols. Non-ribosome RNA was enriched from total RNA by using RiboMinus transcriptome isolation kit (Invitrogen). 1 μL 1:1000 diluted m6A spike-in from EpiMark N6-Methyladenosine Enrichment Kit (NEB #E1610S) was added to 1 μg polyA or non-ribosome RNA, followed by fragmentation according to previously published protocols. m6A-IP was performed using EpiMark N6-Methyladenosine Enrichment Kit following the manufacturer’s protocols.
Library preparation was performed by using SMARTer Stranded Total RNA-Seq Kit (Takara) v2 following manufacturer's protocols.

value: HeLa

value: human cervical cancer (CC) cell line

value: WT

tag: m6a antibody


title: COLO320DM_in_vitro,  DMSO, 48hr, rep2 [21--2]

state: MA

country: USA

tag: time


title: HCT116, caRNA, MeRIP, rep2

description:
Library name: HCT116_caRNA_MeRIP_rep2
HCT116_caRNA_MERIP_rep2

value: human colorectal cancer (CRC) cell line

value: EpiMark N6-Methyladenosine Enrichment Kit


title: COLO320DM_in_vitro,  DMSO, 48hr, rep1 [21--1]


title: HCT116, caRNA, Input, rep1

description:
Library name: HCT116_caRNA_Input_rep1
HCT116_caRNA_Input_rep1


title: SMMC-7721, GLORI, sgTAF7

description:
Library name: SMMC7721_GLORI_sgTAF7
SMMC7721_sgTAF7


title: HCT116, GLORI, sgCTRL

description:
Library name: HCT116_GLORI_sgCTRL
HCT116_sgCTRL


title: SMMC-7721, GLORI, sgCTRL

description:
Library name: SMMC7721_GLORI_sgCTRL
SMMC7721_sgCTRL


title: COLO320DM_in_vitro, Helicon 4-neg,  1uM, 48hr, rep3 [20--3]

value: Helicon 4-neg

tag: dose


title: COLO320DM_in_vitro, Helicon 4-neg,  1uM, 48hr, rep2 [20--2]


title: Male breast cancer-associated fibroblast, 1362236

city: Rende

first: Rosamaria

last: Lappano

state: Cs

address: via P. Bucci

country: Italy

institute: University of Calabria

description: Library name: Sample 6

data_processing:
Reads preprocessing was performed by using fastp v0.20.0 applying specific parameters to remove residual adapter sequences and to keep only high-quality data (qualified_quality_phred=20, unqualified_percent_limit=30, average_qual=25, low_complexity_filter=True, complexity_threshold=30). The percentage of uniquely mapped reads resulted high with the mean value of 89% (mean value for sample: unmapped reads 6%, quality base >q30 90%). Then, passing filter reads were mapped to the genome reference (Homo sapiens) using STAR v2.7.0 with standard parameters, except for sjdbOverhang option set on read length. Genome and transcript annotations provided as input were downloaded from v105 of the Ensembl repository. Alignments were then elaborated by RSEM v1.3.3, to estimate transcript and gene abundances. Subsequently, the sample-specific gene-level abundances were merged into a single raw expression matrix by applying a dedicated RSEM command (rsem-generate-data-matrix). Genes with at least 10 counts in N samples were then selected, where N corresponds to the sample number in the smallest experimental group.
Assembly: Homo sapiens
Supplementary files format and content: tab-delimited includes raw counts for each sample

molecule: total RNA

extract_protocol:
RNA integrity for library preparation was determined by analysis of extracted total RNA using a 2100 Bioanalyzer (Agilent Technologies) with RNA 6000 NanoChip. RNA concentrations were measured using Qubit RNA Assay Kit. Libraries were prepared from total RNA according to manufacturer instructions with Illumina Stranded mRNA Prep kit. Libraries quality was evaluated by size analysis on 2100 Bioanlyzer (Chip DNA HS) and concentrations were determined using Qubit DNA HS assay kit (Thermo Fisher Scientific).
RNA-seq

treatment_protocol: Total RNA was extracted using RNeasy mini kit (Qiagen).


title: Male breast cancer-associated fibroblast, 1362235

description: Library name: Sample 5


title: Female breast cancer-associated fibroblast, 1362233

description: Library name: Sample 3


title: COLO320DM_in_vitro, Helicon 4-neg,  1uM, 48hr, rep1 [20--1]


title: COLO320DM_in_vitro, Helicon 4-neg,  3uM, 48hr, rep3 [19--3]


title: COLO320DM_in_vitro, Helicon 4-neg,  3uM, 48hr, rep2 [19--2]


title: Female breast cancer-associated fibroblast, 1362232

description: Library name: Sample 2


title: COLO320DM_in_vitro, Helicon 4-neg,  3uM, 48hr, rep1 [19--1]


title: Male breast cancer-associated fibroblast, 1362234

description: Library name: Sample 4


title: COLO320DM_in_vitro, Helicon 4-neg,  10uM, 48hr, rep2 [18--2]


title: Female breast cancer-associated fibroblast, 1362231

description: Library name: Sample 1


title: SBC5_RGFP2

city: Toronto

first: Benjamin

middle: H

last: Lok

state: ON

address: 101 College Street, PMCRT, 13-307

country: Canada

institute: Princess Margaret Cancer Centre

library_source: genomic

data_processing:
Reads were aligned to human genome hg38 using Bowtie2 (v. 2.4.5) and filtered to remove multimapping reads using Sambamba (v. 0.7.0).
Samtools (v. 1.14) was used to shift the read start sites (forward reads +4 bases, reverse reads -5 bases) to adjust for overhangs generated by the Tn5 transposon
Duplicate reads were flagged and removed using Picard MarkDuplicates (v. 2.10.9).
Peaks were called using MACS2 (v. 2.2.7.1) using a q-value cutoff of 0.01.
Bigwig files were generated using deeptools bamCoverage (v. 3.5.1) normalizing to reads per kilobase per million (RPKM) and a bin size of 10 bases.
Assembly: hg38
Supplementary files format and content: MACS2 narrowPeak files
Supplementary files format and content: RPKM-normalized bigwig files for each sample and mean coverage for each condition.

molecule: genomic DNA

growth_protocol: SBC5 cells were cultured in Roswell Park Memorial Institute (RPMI) 1640 1X, (Wisent Bioproducts, catalog # 350-000-CL) and 10% FBS.

extract_protocol:
For each submitted sample, 60 000 viable cells were pelleted at 500 x g for 5 minutes at 4oC, resuspended in 50 µL of fully supplemented ATAC-seq resuspension buffer (RSB) containing 0.1% NP-40, 0.1% Tween-20, and 0.01% digitonin, and incubated on ice for 3 minutes. Following lysis, 1 mL of ATAC-seq RSB containing 0.1% Tween-20 (without NP-40 or digitonin) was added and the tubes were inverted to mix. Nuclei were then centrifuged at 500 x g for 10 minutes at 4oC, followed by careful aspiration of all supernatant and resuspension of pellet with 50 µL of transposition master mix (25 µL 2x TD buffer, 2.5 µL transposase, 16.5 µL PBS, 0.5 µL 1% digitonin, 0.5 µL 10% Tween-20, and 5 µL water).
Transposition reactions were incubated at 37oC for 30 minutes in a thermomixer with shaking at 1000 rpm. Reactions were cleaned up with MinElute columns (Qiagen, catalog # 28204), followed by library amplification, where the appropriate number of PCR cycles was determined by qPCR. PCR product purification and size selection were achieved using AMPure XP Beads (Beckman Coulter, catalog # A63882).

treatment_protocol: shHDAC3 cells were generated using lentiviral transduction and three independent shRNA constructs agains HDAC3. RGFP966 treatment was used by dissolving RGFP966 in DMSO and diluting in a vehihcle of 40% (v/v) polyethylene glycol 300 (TCI Chemicals # H0543), 5% (v/v) TWEEN 80 (Sigma-Aldrich # P1754), and 45% (v/v) saline (Baxter # JF7123) to a final DMSO concentration of 10% (v/v).

value: Small cell lung cancer


title: SBC5_RGFP5


title: HepG2, totalRNA, MeRIP, rep2

description:
Library name: HepG2_totalRNA_MeRIP_rep2
HepG2_totalRNA_MERIP_rep2


title: COLO320DM_in_vitro, Helicon 4,  1uM, 48hr, rep2 [17--2]

value: Helicon 4


title: SBC5_WT

value: CTRL


title: SBC5_SCR


title: COLO320DM_in_vitro, Helicon 4,  3uM, 48hr, rep3 [16--3]


title: COLO320DM_in_vitro, Helicon 4-neg,  10uM, 48hr, rep1 [18--1]


title: SBC5_SH2

value: RNAi


title: SMMC-7721, sgCTRL, rep2

data_processing:
Basecalls were performed using bcl-convert.
Low-quality bases and adapters were trimmed using Trim Galore (v0.6.7), then trimmed reads mapping to ribosomal RNAs were removed by Bowtie2 (v2.2.5).
The remaining reads were aligned to the human genome (hg38) using HISAT2 (v2.2.1) with ‘--rna-strandness RF’ parameters.
Gene expression was analyzed using featureCounts (v2.0.1) with the annotation file (hg38) from UCSC table browser (https://genome.ucsc.edu/). Differential gene expression analysis was performed by DESeq2 (v1.42.0) R package.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include gene counts for each Sample

extract_protocol:
Cells were harvested and total RNA was extracted using TRIZOL reagent (Invitrogen) following the manufacturer’s protocols. To isolate mRNA from total RNA, the Dynabeads® mRNA Purification Kit (Invitrogen) was used following the manufacturer’s protocols. The RNA concentration was determined using Nanodrop (Invitrogen) by measuring the UV absorbance at 260 nm.
RNA libraries for RNA-seq were prepared using VAHTS Stranded mRNA-seq Library Prep Kits (Vazyme) following manufacturer's protocols.


title: COLO320DM_in_vitro, Helicon 4,  1uM, 48hr, rep3 [17--3]


title: COLO320DM_in_vitro, Helicon 4,  10uM, 48hr, rep2 [15--2]


title: COLO320DM_in_vitro, Helicon 4,  3uM, 48hr, rep1 [16--1]


title: COLO320DM_in_vitro, Helicon 4,  10uM, 48hr, rep1 [15--1]


title: COLO320DM_in_vitro, Helicon 4,  1uM, 48hr, rep1 [17--1]


title: SMMC-7721, sgCCNT1, rep1


title: SMMC-7721, sgCCNT1, rep2


title: SMMC-7721, sgCBX4, rep2


title: COLO320DM_in_vitro, Helicon 4-neg,  10uM, 48hr, rep3 [18--3]


title: SBC5_SH1


title: COLO320DM_in_vitro,  DMSO, 24hr, rep3 [14--3]


title: SMMC-7721, sgCBX4, rep1


title: COLO320DM_in_vitro, Helicon 4-neg,  1uM, 24hr, rep3 [13--3]


title: SMMC-7721, sgEP300, rep2


title: SMMC-7721, sgEP300, rep1


title: COLO320DM_in_vitro, Helicon 4-neg,  1uM, 24hr, rep2 [13--2]


title: SMMC-7721, sgCTRL, rep1


title: COLO320DM_in_vitro, Helicon 4,  3uM, 48hr, rep2 [16--2]


title: SMMC-7721, sgSETD5, rep2


title: COLO320DM_in_vitro, Helicon 4,  10uM, 48hr, rep3 [15--3]


title: SMMC-7721, sgTAF7, rep2


title: SMMC-7721, sgING5, rep1


title: COLO320DM_in_vitro, Helicon 4-neg,  3uM, 24hr, rep1 [12--1]


title: SMMC-7721, sgJADE2, rep2


title: COLO320DM_in_vitro, Helicon 4-neg,  10uM, 24hr, rep3 [11--3]


title: COLO320DM_in_vitro, Helicon 4-neg,  3uM, 24hr, rep3 [12--3]


title: COLO320DM_in_vitro, Helicon 4-neg,  1uM, 24hr, rep1 [13--1]


title: COLO320DM_in_vitro, Helicon 4-neg,  3uM, 24hr, rep2 [12--2]


title: SMMC-7721, sgING5, rep2


title: COLO320DM_in_vitro,  DMSO, 24hr, rep1 [14--1]


title: COLO320DM_in_vitro, Helicon 4-neg,  10uM, 24hr, rep1 [11--1]


title: COLO320DM_in_vitro, Helicon 4,  1uM, 24hr, rep3 [10--3]


title: SMMC-7721, sgMSL1, rep1


title: COLO320DM_in_vitro, Helicon 4,  3uM, 24hr, rep3 [9--3]


title: COLO320DM_in_vitro, Helicon 4,  1uM, 24hr, rep2 [10--2]


title: COLO320DM_in_vitro, Helicon 4-neg,  10uM, 24hr, rep2 [11--2]


title: COLO320DM_in_vitro, Helicon 4,  3uM, 24hr, rep1 [9--1]


title: SMMC-7721, sgEHMT1, rep2


title: SMMC-7721, sgMSL1, rep2


title: SMMC-7721, sgEHMT1, rep1


title: SMMC-7721, sgTAF7, rep1


title: SMMC-7721, sgTAF4, rep1


title: COLO320DM_in_vitro, Helicon 4,  10uM, 24hr, rep3 [8--3]


title: SMMC-7721, sgKCTD1, rep2


title: COLO320DM_in_vitro, Helicon 4,  3uM, 24hr, rep2 [9--2]


title: SMMC-7721, sgKCTD1, rep1


title: COLO320DM_in_vitro, Helicon 4,  10uM, 24hr, rep2 [8--2]


title: COLO320DM_in_vitro, Helicon 4,  10uM, 24hr, rep1 [8--1]


title: SMMC-7721, sgINTS11, rep1


title: SMMC-7721, sgINTS11, rep2


title: SMMC-7721, sgSETD1B, rep2


title: SMMC-7721, sgTAF4, rep2


title: COLO320DM_in_vitro,  DMSO, 6hr, rep3 [7--3]


title: COLO320DM_in_vitro, Helicon 4,  1uM, 24hr, rep1 [10--1]


title: COLO320DM_in_vitro,  DMSO, 6hr, rep2 [7--2]


title: SMMC-7721, sgSETD1B, rep1


title: SMMC-7721, sgSETD5, rep1


title: SMMC-7721, caRNA, MeRIP, rep2

description: SMMC-7721_caRNA_m6A_rep2_pos_peaks.narrowPeak

data_processing:
Basecalls were performed using bcl-convert.
Low-quality bases and adapters were trimmed using Trim Galore (v0.6.7), then trimmed reads mapped to ribosomal RNAs were removed by Bowtie2 (v2.2.5).
The remaining reads were aligned to the human genome along with spike-in genomes, which included two control RNAs (one with m6A modification and one without), using HISAT2 (v2.2.1) with ‘--rna-strandness RF’ parameters.
Strand-specific reads were separated using samtools view (v1.18) with flags 99,147,83,163. m6A peak calling was performed using macs2 (v2.2.7.1) with ‘--keep-dup 5 -q 0.01 --nomodel’ parameters.
Assembly: hg38
Supplementary files format and content: narrowPeak (except for Input sample)
Library strategy: MeRIP-Seq

molecule: nuclear RNA

extract_protocol:
Total RNA was isolated from chromatin-associated fraction of SMMC-7721 cells. Non-ribosome RNA was further enriched from total RNA by using RiboMinus transcriptome isolation kit (Invitrogen). 1 μL 1:1000 diluted m6A spike-in from EpiMark N6-Methyladenosine Enrichment Kit (NEB #E1610S) was added to 1 μg non-ribosome RNA, followed by fragmentation according to previously published protocols. m6A-IP was performed using EpiMark N6-Methyladenosine Enrichment Kit following the manufacturer’s protocols.
Library preparation was performed by using SMARTer Stranded Total RNA-Seq Kit (Takara) v2 following manufacturer's protocols.


title: COLO320DM_in_vitro,  DMSO, 6hr, rep1 [7--1]


title: SMMC-7721, caRNA, MeRIP, rep1

description: SMMC-7721_caRNA_m6A_rep1_pos_peaks.narrowPeak


title: SMMC-7721, caRNA, Input, rep2


title: COLO320DM_in_vitro, Helicon 4-neg,  1uM, 6hr, rep2 [6--2]


title: COLO320DM_in_vitro, Helicon 4-neg,  1uM, 6hr, rep3 [6--3]


title: SMMC-7721, caRNA, Input, rep1


title: COLO320DM_in_vitro, Helicon 4-neg,  1uM, 6hr, rep1 [6--1]


title: SMMC-7721, sgJADE2, rep1


title: SMMC-7721, sgCTRL, Input, rep2

data_processing:
Basecalls were performed using bcl-convert.
Low-quality bases and adapters were trimmed using Trim Galore (v0.6.7).
Then trimmed reads were aligned to the human genome (hg38) and Drosophila melanogaster (dm6) genome using Bowtie2 (v2.2.5). PCR duplicates were removed using picard (v2.26.0) (http://broadinstitute.github.io/picard/) MarkDuplicates.
Peaks were called using macs2 (v2.2.7.1) callpeak and only peaks overlapped in two biological replicates were used for downstream analysis.
Assembly: hg38
Supplementary files format and content: bigwig
Supplementary files format and content: narrowPeak (except for Input sample)

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 15 min at room temperature, and then 0.125 M glycine was added to stop the reaction.
Library preparation was performed by using VAHTS Universal Pro DNA Library Prep Kit with spike-in Chromatin (Active Motif) and spike-in Antibody (Active Motif) following the manufacturer’s protocols.

tag: antibody


title: SMMC-7721, sgCTRL, H3K4me3, rep1

value: rabbit anti-Histone H3 (tri methyl K4) (ab8580, Abcam)


title: COLO320DM_in_vitro, Helicon 4-neg,  3uM, 6hr, rep2 [5--2]


title: SMMC-7721, sgCTRL, Input, rep1


title: SMMC-7721, sgKCTD1, H3K4me3, rep2


title: SMMC-7721, sgCTRL, H3K4me3, rep2


title: COLO320DM_in_vitro, Helicon 4-neg,  10uM, 6hr, rep3 [4--3]


title: COLO320DM_in_vitro, Helicon 4,  1uM, 6hr, rep2 [3--2]


title: COLO320DM_in_vitro, Helicon 4-neg,  3uM, 6hr, rep3 [5--3]


title: SMMC-7721, sgKCTD1, Input, rep1


title: COLO320DM_in_vitro, Helicon 4,  1uM, 6hr, rep1 [3--1]


title: COLO320DM_in_vitro, Helicon 4-neg,  10uM, 6hr, rep1 [4--1]


title: COLO320DM_in_vitro, Helicon 4,  1uM, 6hr, rep3 [3--3]


title: SMMC-7721, sgKCTD1, H3K4me3, rep1


title: SMMC-7721, sgINTS11, H3K4me3, rep2


title: COLO320DM_in_vitro, Helicon 4,  3uM, 6hr, rep3 [2--3]


title: SMMC-7721, sgINTS11, Input, rep2


title: SMMC-7721, sgKCTD1, Input, rep2


title: COLO320DM_in_vitro, Helicon 4,  3uM, 6hr, rep2 [2--2]


title: SMMC-7721, sgINTS11, H3K4me3, rep1


title: SMMC-7721, sgINTS11, Input, rep1


title: COLO320DM_in_vitro, Helicon 4,  3uM, 6hr, rep1 [2--1]


title: COLO320DM_in_vitro, Helicon 4,  10uM, 6hr, rep3 [1--3]


title: COLO320DM_in_vitro, Helicon 4-neg,  3uM, 6hr, rep1 [5--1]


title: COLO320DM_in_vitro, Helicon 4,  10uM, 6hr, rep2 [1--2]


title: COLO320DM_in_vitro, Helicon 4-neg,  10uM, 6hr, rep2 [4--2]


title: SMMC-7721, sgSETD1B, H3K4me3, rep1


title: SMMC-7721, sgSETD1B, H3K4me3, rep2


title: SMMC-7721, sgSETD1B, Input, rep2


title: SMMC-7721, sgSETD1B, Input, rep1


title: p20169.s203_203_PT031

city: Boston

first: Dan

last: Barouch

address: 3 Blackfan Cir

department: CVVR

institute: Beth Israel Deaconess Medical Center

data_processing:
Transcript abundance estimates were calculated internal to the STAR aligner using the algorithm of htseq-count(2). DESeq2 was used for normalization(3), producing a normalized read count.
Assembly: GRCh38
Supplementary files format and content: airis_countMatrix.csv
Supplementary files format and content: raw count matrix

source_name: Blood

extract_protocol:
PBMCs were lysed in 700 L of Trizol and then extracted using the miRNeasy Mini kit (Qiagen) with on-column DNase digestion. RNA quality was assessed using a TapeStation 4200 (Agilent) and then ten nanograms of total RNA was used as input for cDNA synthesis using the Clontech SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) according to the manufacturer’s instructions.
Amplified cDNA was fragmented and appended with dual-indexed barcodes using the Nextera XT DNA Library Preparation kit (Illumina). Libraries were validated by capillary electrophoresis on a TapeStation 4200 (Agilent), pooled at equimolar concentrations, and sequenced with PE100 reads on an Illumina NovaSeq 6000, yielding ~30 million reads per sample on average. Alignment was performed using STAR version 2.7.3a(1)and transcripts were annotated using a composite genome reference which included GRCh38 Ensembl release 100 and SARS-CoV-2 (GCF_009858895.2, ASM985889v3, MN985325.1).

tag: tissue

value: Blood

tag: pasc severity

value: critical


title: Zebrafish,control-2

city: Nantong City

first: Xin

last: Wang

state: Jiangsu Province

address: No.9, Seyuan Road

institute: Nantong University

data_processing:
Raw sequencing BCL data base-calling using bcl2fastq v2.20.0.422;
Data filtering using fastp v0.23.2 (--cut_front --cut_tail --cut_mean_quality 20 --length_required 35) followed by rRNA filtering using SortMeRNA v4.3.2 with default parameters;
Read alignment using STAR v2.7.10a (--quantMode TranscriptomeSAM --twopassMode Basic );
Quantify using Salmon v1.9.0 with default parameters;
Differential expression analysis using R DESeq2 package, significant genes cutoff: fold change > 2 and adjusted p-value < 0.05;
Assembly: Danio rerio GRCz11;
Supplementary files format and content: tab-delimited text file incldues raw counts for each sample
Supplementary files format and content: tab-delimited text file incldues gene counts for each sample

organism: Danio rerio

source_name: larvae

growth_protocol: Zebraﬁsh was raised at 28.5C in recirculated water under a 14h light:10 h dark cycle. Stages were determined according to time postfertilization and characteristics described in the zebraﬁsh book

extract_protocol:
RNA was enriched using VAHTS mRNA Capture Beads kit following manufacturer's protocol.
RNA libraries for RNA-seq were prepared using VAHTS Universal V8 RNA-seq Library Prep Kit following manufacturer's protocol.

treatment_protocol: At 3dpf, Larvae were treated with 2.5uM 4-octyl itaconate(MedChemExpress) for 48h.

value: larvae

value: Control


title: Zebrafish,control-3


title: COLO320DM_in_vitro, Helicon 4,  10uM, 6hr, rep1 [1--1]

value: Colorectal adenocarcinoma


title: p20169.s202_201_PT10009


title: Zebrafish,control-1


title: Zebrafish, 4-octyl itaconate-3

value: 4-octyl itaconate


title: p20169.s201_196_PT10016


title: p20169.s199_187_PT103


title: Zebrafish, 4-octyl itaconate-1


title: Zebrafish, 4-octyl itaconate-2


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 96

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

description:
Lsk.DNDP.96
Fluidigm C1

data_processing:
Data analyses were performed as in PMID: 32494068.
Assembly: mm10
Supplementary files format and content: RSEM transcript per million estimates text file

organism: Mus musculus

source_name: Bone Marrow

extract_protocol:
Fluidigm C1 captures were performed as described in PMID: 32494068.
Library preperation was performed as described in PMID: 32494068.
Library strategy was performed as described in PMID: 32494068.

value: Bone Marrow

tag: protocol

value: paired-end


title: p20169.s196_173_PT10061


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 95

description:
Lsk.DNDP.95
Fluidigm C1

value: WT


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 93

description:
Lsk.DNDP.93
Fluidigm C1


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 92

description:
Lsk.DNDP.92
Fluidigm C1


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 91

description:
Lsk.DNDP.91
Fluidigm C1


title: p20169.s190_164_PT006


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 90

description:
Lsk.DNDP.90
Fluidigm C1


title: p20169.s188_158_PT036


title: p20169.s189_163_PT090


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 88

description:
Lsk.DNDP.88
Fluidigm C1


title: p20169.s186_154_PT070


title: p20169.s185_151_PT006


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 86

description:
Lsk.DNDP.86
Fluidigm C1


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 87

description:
Lsk.DNDP.87
Fluidigm C1


title: p20169.s198_181_PT070


title: p20169.s200_190_PT10013


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 83

description:
Lsk.DNDP.83
Fluidigm C1


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 84

description:
Lsk.DNDP.84
Fluidigm C1


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 85

description:
Lsk.DNDP.85
Fluidigm C1


title: p20169.s197_174_PT10068


title: 293T-Uli-epic-BIDSeq-1ng-input1

city: shanghai

first: Xu

last: Chu

address: Dong'an Road

institute: Fudan University Shanghai Cancer Center

description: Library name: Sample 7

data_processing:
Reads were trimmed using Cutadapt
HEK293T mapped to hg38  use STAR, sperm and NSC mapped to mm10  use STAR
Assembly: hg38 or mm10
Supplementary files format and content: tab-delimited text file include Ψ sites and level for each Sample
Library strategy: Uli-Epic BID-seq

growth_protocol: HEK 293T cells were cultured in DMEM high glucose (GIBCO) supplemented with 10% heat-inactivated FBS, 100 U/mL penicillin and 100 μg/mL of streptomycin. Cells were kept under standard 37 ℃ and 5% CO2 conditions. Sperm were collected from the cauda epididymis of 10-12 week old mice. NSC were isolated from embryonic 17.5 Nestin-GFP mice.

extract_protocol:
HEK293T total RNA was extracted by Trizol in accordance with the manufacturer’s protocol. mRNA were purified by VAHTS mRNA capture beads (Vazyme).    Sperm were collected from the cauda epididymis of 10-12 week old mice and released into 2 mL of phosphate-buffered saline (PBS) maintained at 37°C for a 20-minute incubation. Following incubation, the suspension was filtered through a 40 µm cell strainer to remove tissue debris. Subsequently, the sperm were treated with 10 mL somatic cell lysis buffer (0.1% SDS, 0.5% Triton X-100) on ice for 40 minutes to eliminate somatic cell contamination. The purity of the sperm sample was confirmed via microscopic examination. The sperm pellet was washed twice in 5 mL of PBS, followed by centrifugation at 1000g for 5 minutes. The sperm pellet was resuspended in TRIzol reagent (Invitrogen), homogenized, and subjected to RNA extraction. The hippocampi were isolated from embryonic 17.5 Nestin-GFP mice and dissociated using the Neural Tissue Dissociation Kit P (Miltenyi Biotec, 130-092-628). Following enzymatic digestion, the solution was diluted by adding 9 mL of Hibernate™-A medium (Invitrogen, A1247501) and centrifuged at 250 × g for 8 minutes. The cell pellets were then resuspended in 0.5 mL of 1× red blood cell lysis buffer (Biogems, 64010-00-100) and incubated for 1 minute. Subsequently, 5 mL of Hibernate™-A medium was added, and the mixture was centrifuged again at 250 × g for 6 minutes. The cells were resuspended in FACS sorting medium (0.5% BSA in Hibernate™-A), incubated with DAPI (Solarbio, C0060) at a 1:1,000 dilution for 5 minutes to label dead cells, and passed through a cell strainer. Finally, the cells were sorted using a BD FACS Aria II cell sorter. Total RNAs were isolated from sorting cells by using TRIzol reagent (Invitrogen) and MaXtractTM High Density (Qiagen).
Uli-Epic BID-seq steps are combined steps of our uli-epic and reported bulk BID-seq. 1 ng or 100 pg 293T mRNA and were fragmented using 0.1M NaHCO3 pH 9.2 and incubate at 95 °C for 5 min, then add 3M NaOAc pH 5.2 to neutralize pH. RNA was 3’ end-repaired by T4 polynucleotide kinase (PNK) (catalog no. M0201, NEB). Then add poly (A) tailing to the 3’ end of RNA by E. coli Poly(A) Polymerase (NEB, M0276L). Carrier DNA was added to poly (A) RNA and was purified by Oligo Clean & Concentrator（Zymo Research，D4061), eluting with 7 µl RNase-free water. A 1.5 µl aliquot of the purified RNA was saved for ‘Input’ library construction, 5 µl was subjected to BID-seq optimized bisulfite treatment, as the ‘Treated’ sample. The 5 µl RNA was mixed with 45 µl freshly prepared BID-seq BS reagent (2.4 M Na2SO3 and 0.36 M NaHSO3, prepared by dissolving 270 mg Na2SO3 and 34 mg NaHSO3 in 850 µl RNase-free water) and incubated at 70 °C for 3 h. Then, 100 µl RNase-free H2O, 250 µl RNA binding buffer (RNA Clean and Concentrator), and 400 µl ethanol were added to the reaction mixture, which was mixed well and loaded on a RNA Clean and Concentrator-5 column. After spinning and washing once with 200 µl RNA wash buffer (RNA Clean and Concentrator), 200 µl RNA Desulphonation Buffer (catalog no. R5001-3-40, Zymo Research) was added to the column and incubated at room temperature for 1 h. This was followed by spinning and washing twice with 700 µl RNA wash buffer (RNA Clean and Concentrator), followed by eluting RNA with 10.5 µl RNase-free water. Reverse transcription and template switching were performed with template switching RT enzyme mix (NEB, M0466L)、 T7 primer (sequence: 5’-GCCGCGAAATTAATACGACTCACTATAGGGATAATGAGCAGACGTGTGCTCTTCCGATCTTTTTTTTTTTTTTTTTTTTTVN-3’) and Template switch oligo (TSO: 5’Biotin-GCTAATCATTGCACACGACGCTCTTCCGATCTrGrGrG-3’) at 42 °C for 90 min. Then RNA template was degradation by E. coli RNase H (NEB, M0297L), followed by second strand cDNA were synthesized by Q5 Hot Start High Fidelity Master Mix (NEB #M0494). The excess T7 primer was digested by exonuclease I (NEB, M0293S). The double strand cDNA was purified by Oligo Clean & Concentrator (Zymo Research，D4061). In vitro transcription was carried out with double strand cDNA by T7 High Yield RNA Transcription Kit, vazyme. At the end of in vitro transcription, DNase I was added to digest double strand cDNA. RNA was purified by 1.8 × SPRIselect beads (Beckman, B23318). Then the RNA was subjected to reverse transcription with RT primer (sequence: 5’- ACACGACGCTCTTCCGATCT -3’) by SuperScript™ III (Thermo Fisher Scientific, cat. no.18080051). cDNA was purified with 1.8 × SPRIselect beads (Beckman, B23318). Library were constructed with single index primers (NEB, E7335S).

value: Human embryonic kidney


title: p20169.s177_123_PT10042

value: moderate


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 82

description:
Lsk.DNDP.82
Fluidigm C1


title: p20169.s195_172_PT10006


title: p20169.s176_122_PT109

value: asymptomatic


title: p20169.s173_119_PT062


title: p20169.s193_171_PT10003


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 80

description:
Lsk.DNDP.80
Fluidigm C1


title: 293T-Uli-epic-GLORI-rep1

data_processing:
Reads were trimmed using Cutadapt
HEK293T mapped to hg38  use STAR, sperm and NSC mapped to mm10  use STAR
Assembly: hg38 or mm10
Supplementary files format and content: tab-delimited text file include m6A sites and level for each Sample
Library strategy: Uli-Epic GLORI

extract_protocol:
HEK293T total RNA was extracted by Trizol in accordance with the manufacturer’s protocol. mRNA were purified by VAHTS mRNA capture beads (Vazyme).    Sperm were collected from the cauda epididymis of 10-12 week old mice and released into 2 mL of phosphate-buffered saline (PBS) maintained at 37°C for a 20-minute incubation. Following incubation, the suspension was filtered through a 40 µm cell strainer to remove tissue debris. Subsequently, the sperm were treated with 10 mL somatic cell lysis buffer (0.1% SDS, 0.5% Triton X-100) on ice for 40 minutes to eliminate somatic cell contamination. The purity of the sperm sample was confirmed via microscopic examination. The sperm pellet was washed twice in 5 mL of PBS, followed by centrifugation at 1000g for 5 minutes. The sperm pellet was resuspended in TRIzol reagent (Invitrogen), homogenized, and subjected to RNA extraction. The hippocampi were isolated from embryonic 17.5 Nestin-GFP mice and dissociated using the Neural Tissue Dissociation Kit P (Miltenyi Biotec, 130-092-628). Following enzymatic digestion, the solution was diluted by adding 9 mL of Hibernate™-A medium (Invitrogen, A1247501) and centrifuged at 250 × g for 8 minutes. The cell pellets were then resuspended in 0.5 mL of 1× red blood cell lysis buffer (Biogems, 64010-00-100) and incubated for 1 minute. Subsequently, 5 mL of Hibernate™-A medium was added, and the mixture was centrifuged again at 250 × g for 6 minutes. The cells were resuspended in FACS sorting medium (0.5% BSA in Hibernate™-A), incubated with DAPI (Solarbio, C0060) at a 1:1,000 dilution for 5 minutes to label dead cells, and passed through a cell strainer. Finally, the cells were sorted using a BD FACS Aria II cell sorter. Total RNAs were isolated from sorting cells by using TRIzol reagent (Invitrogen) and MaXtractTM High Density (Qiagen).
Uli-Epic GLORI steps are combined steps of our uli-epic and reported bulk GLORI. In brief, 10ng 293T mRNA or 10ng mouse sperm ribo-depletion RNA or 10ng mouse NSC ribo-depletion RNA was added into 40 μL of reaction buffer containing 6 μL of glyoxal solution (Sigma-Aldrich, 50649), 20 μL of DMSO and nuclease-free water. The mixture was incubated at 50 °C for 30 min. Then 10 μL of saturated H3BO3 (Sigma-Aldrich, B0394) solution was added and the incubation continued at 50 °C for 30 min followed by cooling on ice for further use. The 50 μL of reaction mixture was added to premixed deamination buffer and gently mixed. The tubes were incubated for 8 h at 16 °C. RNA was purified by Oligo Clean & Concentrator (Zymo Research，D4061). Then RNA were dissolved by 50 μL deprotection buffer(文献). The mixture was incubated at 95 °C for 10 min. RNA was purified with Oligo Clean & Concentrator（Zymo Research，D4061）, and then end-repaired by PNK (NEB, M0201S) to free the 3’ OH. Then add poly (A) tailing to the 3’ end of RNA by E. coli Poly(A) Polymerase (NEB, M0276L). RNA was purified by Oligo Clean & Concentrator（Zymo Research，D4061). Reverse transcription and template switching were performed with template switching RT enzyme mix (NEB, M0466L)、 T7 primer (sequence: 5’GCCGCGAAATTAATACGACTCACTATAGGGATAATGAGCAGACGTGTGCTCTTCCGATCTTTTTTTTTTTTTTTTTTTTTVN-3’) and Template switch oligo (TSO: 5’Biotin-GCTAATCATTGCACACGACGCTCT TCCGATCTrGrGrG-3’) at 42 °C for 90 min. Then RNA template was degradation by E. coli RNase H (NEB, M0297L), followed by second strand cDNA were synthesized by Q5 Hot Start High Fidelity Master Mix (NEB #M0494). The excess T7 primer was digested by exonuclease I (NEB, M0293S). The double strand cDNA was purified by Oligo Clean & Concentrator (Zymo Research，D4061). In vitro transcription was carried out with double strand cDNA by T7 High Yield RNA Transcription Kit, Vazyme. At the end of in vitro transcription, DNase I was added to digest double strand cDNA. RNA was purified by 1.8 × SPRIselect beads (Beckman, B23318). Then the RNA was subjected to reverse transcription with RT primer (sequence: 5’- ACACGACGCTCTTCCGATCT -3’) by SuperScript™ III (Thermo Fisher Scientific, cat. no.18080051). cDNA was purified with 1.8 × SPRIselect beads (Beckman, B23318). Library were constructed with single index primers (NEB, E7335S).


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 89

description:
Lsk.DNDP.89
Fluidigm C1


title: 293T-Uli-epic-GLORI-rep2


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 76

description:
Lsk.DNDP.76
Fluidigm C1


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 79

description:
Lsk.DNDP.79
Fluidigm C1


title: 293T-Uli-epic-BIDSeq-1ng-rep2


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 77

description:
Lsk.DNDP.77
Fluidigm C1


title: 293T-Uli-epic-BIDSeq-1ng-input2

description: Library name: Sample 8


title: p20169.s170_105_PT025


title: p20169.s169_98_PT124

value: severe


title: 293T-Uli-epic-BIDSeq-1ng-rep1


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 74

description:
Lsk.DNDP.74
Fluidigm C1


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 72

description:
Lsk.DNDP.72
Fluidigm C1


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 75

description:
Lsk.DNDP.75
Fluidigm C1


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 71

description:
Lsk.DNDP.71
Fluidigm C1


title: p20169.s168_96_PT109


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 70

description:
Lsk.DNDP.70
Fluidigm C1


title: 293T-Uli-epic-BIDseq-100pg-rep2


title: p20169.s167_95_PT106


title: 293T-Uli-epic-BIDSeq-100pg-rep1


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 81

description:
Lsk.DNDP.81
Fluidigm C1


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 69

description:
Lsk.DNDP.69
Fluidigm C1


title: 293T-Uli-epic-BIDSeq-100pg-input2


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 67

description:
Lsk.DNDP.67
Fluidigm C1


title: p20169.s165_91_PT081


title: p20169.s166_93_PT084


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 66

description:
Lsk.DNDP.66
Fluidigm C1


title: 293T-Uli-epic-BIDSeq-100pg-input1


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 65

description:
Lsk.DNDP.65
Fluidigm C1


title: p20169.s163_89_PT018


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 64

description:
Lsk.DNDP.64
Fluidigm C1


title: 293T-bulk-BIDseq-input-rep2


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 63

description:
Lsk.DNDP.63
Fluidigm C1


title: p20169.s162_88_PT025


title: 293T-bulk-BIDseq-input-rep1


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 62

description:
Lsk.DNDP.62
Fluidigm C1


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 61

description:
Lsk.DNDP.61
Fluidigm C1


title: p20169.s161_82_PT074


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 60

description:
Lsk.DNDP.60
Fluidigm C1


title: 293T-bulk-BIDseq-20ng-rep2


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 59

description:
Lsk.DNDP.59
Fluidigm C1


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 68

description:
Lsk.DNDP.68
Fluidigm C1


title: p20169.s158_77_PT095


title: COLO320DM_in_vitro,  DMSO, 24hr, rep2 [14--2]

value: DMSO


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 57

description:
Lsk.DNDP.57
Fluidigm C1


title: 293T-bulk-BIDseq-20ng-rep1


title: THP-1 cell line, WT, RNA-seq, rep3

city: Yangzhou

first: Cui

last: Du

state: Jiangsu

address: NO.88 University South Road

institute: Yangzhou University

data_processing:
Raw reads were trimmed with Trim Galore v0.6.4
Clean reads were aligned to the reference genome (GRCh38) using STAR v2.7.3
Obtaining gene-level read counts using the featureCount function from subread v2.0.0
calculated TPM/FPKM value for each gene using RSEM v1.3.2
differentially expressed genes were identified with FDR<0.05 and fold change>1 using DESeq2 v1.36.0
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM and FPKM values for each Sample

source_name: THP-1 cell line

growth_protocol: The culture medium for THP-1 cells consists of RPMI-1640 supplemented with 10% fetal bovine serum (FBS), 0.05 mM β-mercaptoethanol, and 1% penicillin/streptomycin (P/S). Culturing is performed in a constant-temperature incubator at 37°C with 5% CO2.

extract_protocol:
Total RNA was isolated from three biological replicates using TRIzol (Invitrogen, Cat#350508), and RNA integrity and concentration were assessed by the Qubit dsDNA HS Assay (Invitrogen).
RNA-Seq libraries were sequenced as 150 bp paired-end reads with the DNBSEQ (MGI-Shenzhen, China) platform.

value: THP-1 cell line

value: human monocyte


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 55

description:
Lsk.DNDP.55
Fluidigm C1


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 56

description:
Lsk.DNDP.56
Fluidigm C1


title: p20169.s160_79_PT051


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 54

description:
Lsk.DNDP.54
Fluidigm C1


title: THP-1 cell line, WT, RNA-seq, rep2


title: p20169.s157_75_PT095


title: p20169.s156_74_PT093


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 52

description:
Lsk.DNDP.52
Fluidigm C1


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 53

description:
Lsk.DNDP.53
Fluidigm C1


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 51

description:
Lsk.DNDP.51
Fluidigm C1


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 50

description:
Lsk.DNDP.50
Fluidigm C1


title: p20169.s155_73_PT051


title: THP-1 cell line, SPI1 knockdown, RNA-seq, rep3

value: SPI1 knockdown


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 49

description:
Lsk.DNDP.49
Fluidigm C1


title: p20169.s154_72_PT088

value: Blood

value: mild


title: p20169.s153_71_PT086


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 47

description:
Lsk.DNDP.47
Fluidigm C1


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 46

description:
Lsk.DNDP.46
Fluidigm C1


title: THP-1 cell line, SPI1 knockdown, RNA-seq, rep1


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 48

description:
Lsk.DNDP.48
Fluidigm C1


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 58

description:
Lsk.DNDP.58
Fluidigm C1


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 45

description:
Lsk.DNDP.45
Fluidigm C1


title: THP-1 cell line, SPI1 knockdown, RNA-seq, rep2


title: p20169.s152_70_PT084


title: THP-1 cell line, WT, input, ChIP-seq, rep1

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
Raw reads were trimmed with Trim Galore v0.6.5.
Clean reads were aligned to the reference genome (GRCh38) using Bowtie v2.3.5 with default settings.
The PCR duplicates for each dataset were removed using the rmdup function of samtools v1.2. The data reproducibility between biological replicates was confirmed, then reads from replicates were pooled together for further analysis
Peak calling was performed with MACS v2.2.7.1 with --keep-dup all. The called peaks were further cleaned by removing those overlap ENCODE Blacklist V2 regions.
Differential binding analysis was performed using v3.4.11 with settings: minOverlap= 1, summits= 250, method=DBA_EDGER. Overlap of peaks were performed using the window function from BEDTools v2.29.2.
Assembly: GRCh38
Supplementary files format and content: narrowPeak (except for Input sample)

extract_protocol:
After the cells were transinfection for 48 hours, 10000000 cells were used per immunoprecipitation. At first, the cells were fixed with 1% formaldehyde (Sigma-Aldrich, 252549) at room temperature for 10 min. A final concentration of 0.2 M glycine was added to quench the fixation. Nuclear lysates were fragmented by Covaris S220 (Adaptive Focused Acoustics®). For each tissue, 3 μg of H3K27ac (Abcam Cat# ab177178) antibodies were mixed with 25 μL Protein A/G Dynabeads (Selleck. cn, B23201), with rotation at 4°C for 4 h. For per immunoprecipitation, about 50 μg of chromatin was incubated with antibody–bead complexes overnight at 4 °C. Chip-DNA was purificated by MinElute PCR Purification kit (QIAGEN, Cat# 28004 ).
ChIP-seq libraries were constructed using the MGIEasy DNA library prep kit (1000006985, BGI-Shenzhen, China), and sequenced as 100 bp paired-end reads with the DNBSEQ (MGI-Shenzhen, China) platform.


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 44

description:
Lsk.DNDP.44
Fluidigm C1


title: p20169.s151_68_PT081

value: critical


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 41

description:
Lsk.DNDP.41
Fluidigm C1


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 42

description:
Lsk.DNDP.42
Fluidigm C1


title: THP-1 cell line, WT, H3K27ac, ChIP-seq, rep2

value: SPI1(Santa Cruz, sc-390405)


title: p20169.s150_67_PT051


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 40

description:
Lsk.DNDP.40
Fluidigm C1


title: THP-1 cell line, WT, RNA-seq, rep1


title: p20169.s148_59_PT115


title: THP-1 cell line, SPI1 knockdown, input, ChIP-seq, rep1


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 39

description:
Lsk.DNDP.39
Fluidigm C1


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 37

description:
Lsk.DNDP.37
Fluidigm C1


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 38

description:
Lsk.DNDP.38
Fluidigm C1


title: p20169.s147_54_PT018


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 36

description:
Lsk.DNDP.36
Fluidigm C1


title: THP-1 cell line, SPI1 knockdown, H3K27ac, ChIP-seq, rep2


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 34

description:
Lsk.DNDP.34
Fluidigm C1


title: p20169.s145_45_PT007


title: THP-1 cell line, SPI1 knockdown, H3K27ac, ChIP-seq, rep1


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 32

description:
Lsk.DNDP.32
Fluidigm C1


title: RNAseq_WT_PreselectionDP_rep2

city: Shanghai

first: Haiqiang

last: Dai

address: 320 Yue Yang Road

institute: Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell  Science

description: Library name: sample4

data_processing:
Adapter sequences were first trimmed from sequencing reads using Cutadapt (v4.1) with the parameters “-e 0.1 -O 3 -m 55 -j 8 --quality-cutoff 25”. The trimmed reads were then aligned to the mouse genome (mm10) using STAR (v2.5.2b). Differential gene expression was analyzed using the Bioconductor package DESeq2 (v1.46.0), with significance thresholds set at adjusted P ≤ 0.05 and |log₂ fold change| ≥ 1.
Assembly: mm10
Supplementary files format and content: bw

source_name: Thymus

extract_protocol:
Total RNA was extracted with the TRIzol kit (15596018CN, ThermoFisher).
Poly(A) mRNA was isolated using Oligo(dT) beads, fragmented with divalent cations at high temperature, and reverse-transcribed with random primers. Double-stranded cDNA was synthesized, end-repaired, A-tailed, and adaptor-ligated. Adaptor-ligated DNA was size-selected with DNA Clean Beads and amplified with P5/P7 primers. Indexed libraries were validated, multiplexed, and sequenced on an Illumina HiSeq 6000 (2×150 bp paired-end).

value: Thymus

value: Preselection DP thymocytes

value: Wapl f/-


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 43

description:
Lsk.DNDP.43
Fluidigm C1

value: Bone Marrow

value: paired-end


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 31

description:
Lsk.DNDP.31
Fluidigm C1

value: WT


title: p20169.s144_40_PT002


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 30

description:
Lsk.DNDP.30
Fluidigm C1


title: RNAseq_WT_PreselectionDP_rep1

description: Library name: sample3


title: THP-1 cell line, WT, H3K27ac, ChIP-seq, rep1


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 29

description:
Lsk.DNDP.29
Fluidigm C1


title: RNAseq_KO_PreselectionDP_rep2

description: Library name: sample2

value: Cd4-cre Wapl f/-


title: p20169.s142_34_PT018


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 25

description:
Lsk.DNDP.25
Fluidigm C1


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 26

description:
Lsk.DNDP.26
Fluidigm C1


title: p20169.s143_36_PT025


title: RNAseq_KO_PreselectionDP_rep1

description: Library name: sample1


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 35

description:
Lsk.DNDP.35
Fluidigm C1


title: p20169.s140_15_PT025


title: Ly6D CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D+) cell 96

description:
Sept4_x_x_311_Cell_96
Fluidigm C1


title: p20169.s146_53_PT022


title: Ly6D CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D+) cell 94

description:
Sept4_x_x_311_Cell_94
Fluidigm C1


title: Ly6D CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D+) cell 95

description:
Sept4_x_x_311_Cell_95
Fluidigm C1


title: Ly6D CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D+) cell 93

description:
Sept4_x_x_311_Cell_93
Fluidigm C1


title: Day 6 EPS-embryoids-2

first: Ruoqi

last: Cheng

state: Beijing

address: NO.5, Yiheyuan Road, Haidian District

description:
Library name: Sample 2
10x Genomics

library_source: transcriptomic single cell

data_processing:
The clean single-cell RNA-seq reads were mapped to mouse reference genome mm10 using Cell Ranger v5.0.1.
Assembly: mm10
Supplementary files format and content: gz archives contain Cell Ranger output (barcodes.tsv, features.tsv, matrix.mtx).

source_name: synthetic-embryo

extract_protocol:
EPS-derived embryoids were digested by 0.05% trypsin/TripLE into single cells, then washed and resuspended in 1X PBS (calcium and magnesium free) containing 2% FBS.  Cell suspensions were filtered through a 40 μm cell strainer.Cell viability was determined by Count Star, and the density of living cells were adjusted to 300-600 living cells per microliter. Cell suspension was loaded onto the Chromium single cell controller (10x Genomics). Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 (10x Genomics) and Chromium Single Cell B Chip Kit (10x Genomics) were used to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol. In short, single cells were suspended in PBS containing 0.04% BSA. About 6,000 cells were added to each channel, and the target cells were recovered (about 3,000 cells). Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs. Reverse transcription was performed on a S1000TM Touch Thermal Cycler (Bio Rad) at 53°C for 45 min, followed by 85°Cfor 5 min, and hold at 4°C. The cDNA was generated and then amplified, and quality assessed using an Agilent 4200.
Single-cell RNA-seq libraries were constructed using Single Cell 3’ Library and Gel Bead Kit V3.1 according to the manufacture’s introduction. The libraries were finally sequenced using an IlluminaNovaseq6000 sequencer with a sequencing depth of at least 100,000 reads per cell with pair-end 150 bp (PE150) reading strategy.

value: synthetic-embryo

value: TD-EPS

value: Day 6 EPS-embryoids


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 33

description:
Lsk.DNDP.33
Fluidigm C1


title: p20169.s139_13_PT051


title: Ly6D CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D+) cell 92

description:
Sept4_x_x_311_Cell_92
Fluidigm C1


title: E18.5

city: Bethesda

first: Sergey

last: Leikin

state: Maryland

department: NICHD

institute: National Institutes of Health

description: Library name: SL_ftest_S2

data_processing:
Raw sequencing data were processed using the 10X Genomics Space Ranger 3.0.1 pipeline.
Sequences were aligned to mm10-3.0.0 mouse genome using Space Ranger's default settings.
UMI counts for Refseq coding genes were quantified using Space Ranger's default settings.
CytAssist tissue image was replaced with high resolution H&E image using Visium Image Alignment protocol in 10X Genomics Loupe Browser 8.0.0
Assembly: mm10-3.0.0
Supplementary files format and content: filtered_feature_bc_matrix.h5: gene count matrix in h5 format
Supplementary files format and content: tissue_hires_image.png: high resolution H&E image
Supplementary files format and content: tissue_lowres_image.png: low resolution H&E image
Supplementary files format and content: tissue_positions.parquet: tisue positions in parquet format
Supplementary files format and content: scalefactors_json.json: scale factors in json format
Supplementary files format and content: detected_tissue_image.jpg: image of automatically detected tissue
Supplementary files format and content: cytassist_image.tiff: CytAssist image
Supplementary files format and content: aligned_tissue_image.jpg: Image of aligned tissue
Supplementary files format and content: aligned_fiducials.jpg: image of aligned fiducials
Supplementary files format and content: E18_tibia.cloupe: Loupe browser file with selected growth plate chondrocytes
Supplementary files format and content: web_summary.html
Library strategy: Spatial Transcriptomics

source_name: tibia

growth_protocol: C57BL/6J (stock #000664) mice were purchased from the Jackson Laboratory (Bar Harbor, ME, USA) and maintained on the C57BL/6J background. Animal care and experiments were performed in accordance with a protocol approved by the Eunice Kennedy Shriver National Institute of Child Health and Human Development Animal Care and Use Committee.

extract_protocol:
5 um FFPE sections were cut and mounted on a positively chaged glass slide. Three sections from the same tibia were placed on the slide within 6.5x6.5 mm area, stained with Hematoxylin and Eosin, imaged on a Nikon Ti2-E inverted microscope with a 20X/0.8NA objective.
The sections were processed, transferred onto Visium HD slide, and further processed to prepare cDNA library using 10X Genomics CytAssist instrument and 10X Genomics Visium HD slide and reagents kit according to the manufacturer's protocol.

value: tibia

value: wild type


title: p20169.s138_9_PT029

value: severe


title: Ly6D CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D+) cell 91

description:
Sept4_x_x_311_Cell_91
Fluidigm C1


title: Day 6 EPS-embryoids-1

description:
Library name: Sample 1
10x Genomics


title: p20169.s137_6_PT037

value: Blood


title: Ly6D CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D+) cell 90

description:
Sept4_x_x_311_Cell_90
Fluidigm C1


title: Ly6D CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D+) cell 89

description:
Sept4_x_x_311_Cell_89
Fluidigm C1


title: DNDP (LSK CD48-CD150- & LSK CD48+CD150+) cell 27

description:
Lsk.DNDP.27
Fluidigm C1


title: TES2-P21 rep2

description:
Library name: Sample 34
column name in counts.csv: TES2-P21-2

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low quality data by Trimmomatic v0.39, then mapped to mm10 whole genome using STAR v2.7.10b and annotated using gencode vm25 gtf file.
sam file generated by STAR was converted to bam and counts were generated using featureCounts v2.0.6.
Assembly: mm10
Supplementary files format and content: csv file with raw gene counts for every gene and every sample.

source_name: TD-EPS

extract_protocol:
Total RNA was isolated from cells using the RNeasy Mini Kit
RNA sequencing libraries were constructed by using magnetic beads with oligo (DT) enriched mRNA. After that, fragment buffer was added to break the mRNA into short segments. Using mRNA as template, a strand of cDNA was synthesized using six base random primers. Then buffer, dNTPs, DNA polymer I and RNase H were added to synthesize a two strand cDNAs, which were purified using AMPURE XP beads. The purified double stranded cDNAs were repaired, a-tailed and sequenced, and then the fragment size was selected by AMPURE XP beads. Finally, PCR amplification was carried out and PCR products were purified with AMPURE XP beads to obtain the final library. The fragmented and randomly primed 2 × 150- bp paired-end libraries were sequenced using an Illumina NovaSeq 6000.

tag: cell definition

value: mouse trophectoderm like cell P21

value: Mouse TELCs derived from EPS cells cultured in TE-S2 medium for 21 passages.


title: Ly6D CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D+) cell 87

description:
Sept4_x_x_311_Cell_87
Fluidigm C1


title: Ly6D CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D+) cell 86

description:
Sept4_x_x_311_Cell_86
Fluidigm C1


title: Ly6D CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D+) cell 85

description:
Sept4_x_x_311_Cell_85
Fluidigm C1


title: TES2-P21 rep1

description:
Library name: Sample 33
column name in counts.csv: TES2-P21-1


title: TES2-P6 rep2

description:
Library name: Sample 32
column name in counts.csv: TES2-P6-2

value: mouse trophectoderm like cell P6

value: Mouse TELCs derived from EPS cells cultured in TE-S2 medium for 6 passages.


title: Ly6D CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D+) cell 84

description:
Sept4_x_x_311_Cell_84
Fluidigm C1


title: p20169.s133_202_PT10011


title: Ly6D CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D+) cell 83

description:
Sept4_x_x_311_Cell_83
Fluidigm C1


title: Ly6D CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D+) cell 81

description:
Sept4_x_x_311_Cell_81
Fluidigm C1


title: TES2-P6 rep1

description:
Library name: Sample 31
column name in counts.csv: TES2-P6-1


title: Ly6D CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D+) cell 82

description:
Sept4_x_x_311_Cell_82
Fluidigm C1


title: p20169.s132_200_PT10064


title: p20169.s131_198_PT10059


title: Ly6D CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D+) cell 79

description:
Sept4_x_x_311_Cell_79
Fluidigm C1


title: TES2-P3 rep1

description:
Library name: Sample 29
column name in counts.csv: TES2-P3-1

value: mouse trophectoderm like cell P3

value: Mouse TELCs derived from EPS cells cultured in TE-S2 medium for 3 passages.


title: Ly6D CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D+) cell 77

description:
Sept4_x_x_311_Cell_77
Fluidigm C1

value: Bone Marrow


title: Ly6D CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D+) cell 80

description:
Sept4_x_x_311_Cell_80
Fluidigm C1

value: paired-end


title: Ly6D CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D+) cell 78

description:
Sept4_x_x_311_Cell_78
Fluidigm C1

value: WT


title: TES2-P1 rep2

description:
Library name: Sample 28
column name in counts.csv: TES2-P1-1

value: mouse trophectoderm like cell P1

value: Mouse TELCs derived from EPS cells cultured in TE-S2 medium for 4 days.


title: Ly6D CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D+) cell 76

description:
Sept4_x_x_311_Cell_76
Fluidigm C1


title: p20169.s130_194_PT10015


title: p20169.s129_186_PT10072


title: Ly6D CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D+) cell 74

description:
Sept4_x_x_311_Cell_74
Fluidigm C1


title: Ly6D CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D+) cell 75

description:
Sept4_x_x_311_Cell_75
Fluidigm C1


title: Ly6D CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D+) cell 73

description:
Sept4_x_x_311_Cell_73
Fluidigm C1


title: p20169.s136_3_PT007

value: critical


title: TES2-P1 rep1

description:
Library name: Sample 27
column name in counts.csv: TES2-P1-1

value: TD-EPS


title: p20169.s127_183_PT072


title: Ly6D CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D+) cell 72

description:
Sept4_x_x_311_Cell_72
Fluidigm C1


title: p20169.s134_205_PT076


title: TES1 rep2

description:
Library name: Sample 26
column name in counts.csv: TES1-2

value: mouse extended pluripotent stem cell EPS treated with TE-S1 medium

value: Mouse  EPS cells treated with TE-S1 medium for 3 days.


title: p20169.s125_179_PT10005


title: Ly6D CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D+) cell 71

description:
Sept4_x_x_311_Cell_71
Fluidigm C1


title: Ly6D CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D+) cell 69

description:
Sept4_x_x_311_Cell_69
Fluidigm C1


title: p20169.s124_178_PT10019


title: Ly6D CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D+) cell 68

description:
Sept4_x_x_311_Cell_68
Fluidigm C1


title: TES1 rep1

description:
Library name: Sample 25
column name in counts.csv: TES1-1


title: OG-PE rep2

description:
Library name: Sample 24
column name in counts.csv: OG-PE-2

source_name: OG-EPS

value: OG-EPS

value: mouse Oct4-GFP-PrE

value: Mouse  OG-EPS cells treated with PrE induction medium for 3 days.


title: Ly6D CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D+) cell 66

description:
Sept4_x_x_311_Cell_66
Fluidigm C1


title: Ly6D CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D+) cell 65

description:
Sept4_x_x_311_Cell_65
Fluidigm C1


title: OG-PE rep1

description:
Library name: Sample 23
column name in counts.csv: OG-PE-1


title: Ly6D CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D+) cell 64

description:
Sept4_x_x_311_Cell_64
Fluidigm C1


title: TES2-P3 rep2

description:
Library name: Sample 30
column name in counts.csv: TES2-P3-2


title: p20169.s123_176_PT10002

value: Blood


title: p20169.s122_175_PT10008


title: Ly6D CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D+) cell 63

description:
Sept4_x_x_311_Cell_63
Fluidigm C1


title: OG-EPS rep2

description:
Library name: Sample 22
column name in counts.csv: OG-EPS-2

value: mouse Oct4-GFP-EPS

value: Mouse  EPS cells were cultured in LCDM medium.


title: Ly6D CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D+) cell 62

description:
Sept4_x_x_311_Cell_62
Fluidigm C1


title: p20169.s121_168_PT027


title: OG-EPS rep1

description:
Library name: Sample 21
column name in counts.csv: OG-EPS-1


title: Ly6D CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D+) cell 60

description:
Sept4_x_x_311_Cell_60
Fluidigm C1


title: p20169.s119_165_PT001


title: Ly6D CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D+) cell 59

description:
Sept4_x_x_311_Cell_59
Fluidigm C1


title: OG-BLES rep2

description:
Library name: Sample 20
column name in counts.csv: OG-BLES-2

value: mouse Oct4-GFP-PrE/EPI bilineage structures

value: EPI/PrE bilineage structures derived from OG-EPS cells.


title: Ly6D CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D+) cell 58

description:
Sept4_x_x_311_Cell_58
Fluidigm C1

value: Bone Marrow


title: Ly6D CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D+) cell 70

description:
Sept4_x_x_311_Cell_70
Fluidigm C1

value: paired-end


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 9

description:
Sept4_x_x_250_Cell_9
Fluidigm C1

value: WT


title: OG-BLES rep1

description:
Library name: Sample 19
column name in counts.csv: OG-BLES-1


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 8

description:
Sept4_x_x_250_Cell_8
Fluidigm C1


title: p20169.s112_138_PT10065

value: mild


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 7

description:
Sept4_x_x_250_Cell_7
Fluidigm C1


title: FBS-TS rep2

description:
Library name: Sample 18
column name in counts.csv: FBS-TS-2

source_name: 1641/serum-TS cells

value: 1641/serum-TS cells

value: mouse trophoblast stem cell

value: Mouse  TSC cells cultured in serum-containing 1640/serum-TSC medium.


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 57

description:
Sept4_x_x_250_Cell_57
Fluidigm C1


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 56

description:
Sept4_x_x_250_Cell_56
Fluidigm C1


title: FAXY-TS rep2

description:
Library name: Sample 16
column name in counts.csv: FAXY-TS-2

source_name: FAXY-TS cells

value: FAXY-TS cells

value: Mouse  TSC cells cultured in serum-free FAXY-TSC medium.


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 55

description:
Sept4_x_x_250_Cell_55
Fluidigm C1


title: p20169.s106_127_PT083


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 54

description:
Sept4_x_x_250_Cell_54
Fluidigm C1


title: p20169.s101_99_PT123

value: severe


title: FAXY-TS rep1

description:
Library name: Sample 15
column name in counts.csv: FAXY-TS-1


title: Ly6D CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D+) cell 61

description:
Sept4_x_x_311_Cell_61
Fluidigm C1


title: p20169.s098_92_PT105

value: critical


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 52

description:
Sept4_x_x_250_Cell_52
Fluidigm C1


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 53

description:
Sept4_x_x_250_Cell_53
Fluidigm C1


title: EPS-C20 rep2

description:
Library name: Sample 14
column name in counts.csv: C20-2

value: TD-EPS

value: mouse extended pluripotent stem cell EPS + 20 µM CHIR 99021

value: Mouse  EPS cells treated with 20 µM CHIR 99021 for 3 days.


title: p20169.s097_86_PT031

value: Blood


title: EPS-C20 rep1

description:
Library name: Sample 13
column name in counts.csv: C20-1


title: p20169.s118_162_PT069


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 5

description:
Sept4_x_x_250_Cell_5
Fluidigm C1


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 50

description:
Sept4_x_x_250_Cell_50
Fluidigm C1


title: EPS-C10 rep2

description:
Library name: Sample 12
column name in counts.csv: C10-2

value: mouse extended pluripotent stem cell EPS + 10 µM CHIR 99021

value: Mouse  EPS cells treated with 10 µM CHIR 99021 for 3 days.


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 49

description:
Sept4_x_x_250_Cell_49
Fluidigm C1

value: Bone Marrow


title: p20169.s096_84_PT061


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 6

description:
Sept4_x_x_250_Cell_6
Fluidigm C1

value: paired-end


title: FBS-TS rep1

description:
Library name: Sample 17
column name in counts.csv: FBS-TS-1

source_name: 1640/serum-TS cells

value: 1640/serum-TS cells

value: WT


title: p20169.s095_80_PT054


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 48

description:
Sept4_x_x_250_Cell_48
Fluidigm C1


title: EPS-C10 rep1

description:
Library name: Sample 11
column name in counts.csv: C10-1


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 46

description:
Sept4_x_x_250_Cell_46
Fluidigm C1


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 47

description:
Sept4_x_x_250_Cell_47
Fluidigm C1


title: p20169.s107_131_PT10049

value: asymptomatic


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 45

description:
Sept4_x_x_250_Cell_45
Fluidigm C1


title: p20169.s094_66_PT080


title: EPS-C6 rep2

description:
Library name: Sample 10
column name in counts.csv: C6-2

value: mouse extended pluripotent stem cell EPS + 6 µM CHIR 99021

value: Mouse  EPS cells treated with 6 µM CHIR 99021 for 3 days.


title: p20169.s093_65_PT054


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 51

description:
Sept4_x_x_250_Cell_51
Fluidigm C1


title: EPS-C6 rep1

description:
Library name: Sample 9
column name in counts.csv: C6-1


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 43

description:
Sept4_x_x_250_Cell_43
Fluidigm C1


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 41

description:
Sept4_x_x_250_Cell_41
Fluidigm C1


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 42

description:
Sept4_x_x_250_Cell_42
Fluidigm C1


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 40

description:
Sept4_x_x_250_Cell_40
Fluidigm C1


title: p20169.s091_61_PT118

value: mild


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 4

description:
Sept4_x_x_250_Cell_4
Fluidigm C1


title: p20169.s090_58_PT113


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 39

description:
Sept4_x_x_250_Cell_39
Fluidigm C1


title: EPS-C3 rep1

description:
Library name: Sample 7
column name in counts.csv: C3-1

value: mouse extended pluripotent stem cell EPS + 3 µM CHIR 99021

value: Mouse  EPS cells treated with 3 µM CHIR 99021 for 3 days.


title: p20169.s089_57_PT113

value: critical


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 37

description:
Sept4_x_x_250_Cell_37
Fluidigm C1


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 38

description:
Sept4_x_x_250_Cell_38
Fluidigm C1


title: EPS-N rep2

description:
Library name: Sample 6
column name in counts.csv: EPS-2-N

value: TD-EPS

value: a new batch of mouse extended pluripotent stem cell

value: Mouse  EPS cells were cultured in LCDM medium.


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 36

description:
Sept4_x_x_250_Cell_36
Fluidigm C1


title: p20169.s087_50_PT010

value: Blood

value: severe


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 35

description:
Sept4_x_x_250_Cell_35
Fluidigm C1


title: p20169.s086_48_PT019


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 34

description:
Sept4_x_x_250_Cell_34
Fluidigm C1


title: mESC Tet1/2/3 TKO, Input, mock, clone29

city: Mainz

first: Alexandr

last: Gopanenko

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology gGmbH (IMB)

description: Library name: FIBo_seq_31

data_processing:
Raw read data were quality-assessed by FastQC (v.0.11.9) and aligned to reference genome using STAR (v. 2.7.10a) with the following relaxed parameters to map short overlapping reads containing C-to-T mismatches: outFilterScoreMinOverLread 0.1, --outFilterMatchNminOverLread 0.1 and --outFilterMismatchNoverReadLmax 0.05.
exomePeak2 (v. 1.10.0) was utilized for peak calling from input and RIP samples. The following parameters were applied to scan the gene coding part of the genome (mode = "exon") using a DESeq2 for statistical testing (test_method = "DESeq2", p_cutoff = 0.001, bin_size = 25, step_size = 25). Unstranded library type was taken into account (strandness = "unstrand"). Fragment length parameter was estimated as the average insert size for all samples. The peaks were filtered using the following criteria: FDR < 0.01, RPM.input > 10, RPM.IP > 50, log2FC > 3.32.
deepTools (v. 3.5.1) was used to generate bigWig tracks.
Assembly: GRCm39 (mm39)
Supplementary files format and content: bigWig; tracks for RIP-seq experiment

source_name: mouse embryonic stem cells

growth_protocol: mESC clones were cultured on tissue culture plates coated with 0.1% gelatin solution in 2i medium (50% Neurobasal and 50% DMEM/F-12 medium, supplemented with 1x N2, 1x B27, 2 mM L-Glutamine, 1000 U/ml Leukemia inhibitory factor, 100 U/ml Pen-Strep, 1 µM PD0325901, 3 µM CHIR99021 and 50 µg/ml BSA) at 37 °C in 5% CO2 and 20% O2.

extract_protocol:
Total RNA was isolated from cultured cells using QIAzol Lysis Reagent (Qiagen) according to the manufacturer’s protocol followed by TURBO DNase (Invitrogen) treatment and another round of QIAzol purification. RNA was chemically fragmented to 120-180 nt-long fragments followed by immunoprecipitation with an anti-f5C-antibody (1 µg anti-f5C-antibody/ 5 µg RNA; #61227, Active Motif). Samples were incubated in 900 mM pyridine borane in 600 mM sodium acetate (pH 5.2) at 37°C for 24 hours. For mock treated samples, water was added instead of pyridine borane. Ribosomal RNA was depleted from samples using the NEBNext rRNA Depletion Kit v2 (Human/Mouse/Rat) (NEB) following the manufacturer’s protocol. RNA was T4 PNK (NEB) treated before library construction.
FIBo-seq library construction was performed with the NEXTFLEX Small RNA-Seq Kit V4 with UDIs (PerkinElmer) using the NEXTFLEX small RNAseq PreArrayed UDI Barcode primers. Libraries were prepared with a starting volume of 4 µl for the f5C-RIP samples (~ 0.823 ng) and a starting amount of 0.823 ng RNA for the input samples following Step A to Step F of Perkin Elmer`s standard protocol (V23.04). Step A (NEXTFLEX 3` 4N Adenylated Adapter Ligation) was performed overnight at 16°C and Step F (PCR amplification) with 24 PCR cycles. Thereafter, the no size selection option in the protocol was followed. Libraries were profiled in a High Sensitivity DNA Chip on a 2100 Bioanalyzer (Agilent technologies) and quantified using the Qubit dsDNA HS Assay Kit, in a Qubit 2.0 Fluorometer (Life technologies) and pooled together in equimolar ratio. The pool was purified by running a 3% agarose gel cassette on a PippinHT (Sage Science) and size-selected for library fragments in 175-250 bp size range (adapter size + insert size).

value: mouse embryonic stem cells

value: Tet1/2/3 TKO

tag: rip antibody


title: EPS rep4

description:
Library name: Sample 4
column name in counts.csv: EPS-4

value: mouse extended pluripotent stem cell


title: mESC Tet1/2/3 TKO, Input, mock, clone26

description: Library name: FIBo_seq_30


title: p20169.s085_47_PT009


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 44

description:
Sept4_x_x_250_Cell_44
Fluidigm C1

value: Bone Marrow

value: paired-end


title: mESC Tet1/2/3 TKO, Input, PyBo, clone29, rep3

description: Library name: FIBo_seq_29


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 33

description:
Sept4_x_x_250_Cell_33
Fluidigm C1

value: WT


title: EPS rep3

description:
Library name: Sample 3
column name in counts.csv: EPS-3


title: p20169.s084_46_PT008


title: EPS-C3 rep2

description:
Library name: Sample 8
column name in counts.csv: C3-2


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 32

description:
Sept4_x_x_250_Cell_32
Fluidigm C1


title: p20169.s083_39_PT031


title: mESC Tet1/2/3 TKO, Input, PyBo, clone29, rep2

description: Library name: FIBo_seq_28


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 31

description:
Sept4_x_x_250_Cell_31
Fluidigm C1


title: mESC Tet1/2/3 TKO, Input, PyBo, clone29, rep1

description: Library name: FIBo_seq_27


title: p20169.s082_38_PT087

value: moderate


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 30

description:
Sept4_x_x_250_Cell_30
Fluidigm C1


title: EPS-N rep1

description:
Library name: Sample 5
column name in counts.csv: EPS-1-N


title: liver cells from adult offspring with intrauterine hyperglycemia mother

first: Jiahang

last: Mo

address: No.131 Dong'an Road

department: Institute of Reproduction and Development

institute: Obstetrics and gynecology Hospital of Fudan University

description: Library name: Sample 4

data_processing:
The raw data were quantified by Cell Ranger. Analyses were conducted using the Seurat program. For quality control, we removed cells for which fewer than 500 UMIs. Simultaneous data normalization/scaling and variable feature detection was performed using “LogNormalize”. Cells were integrated by canonical correlation analysis (CCA). Cells were clustered via Seurat’s shared nearest neighbor clustering algorithm (“FindNeighbors” and “FindClusters”) using the the top 10 PCs and a resolution of 0.5. The top 10 most variable PCs were used for subsequent clustering. The clustering was visualized using 2-dimensional Uniform Manifold Approximation and Projection (UMAP) algorithm.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: liver

extract_protocol:
Fetal male offspring at E18.5 were obtained by caesarean section. Adult male offspring at 8 w were sacrificed for liver scRNA-seq after portal vein perfusion. Samples were pooled from three pregnant mice and adult individuals, respectively. Mice livers were digested in a mixed enzyme system containing collagenase IV (1 mg/ml; Worthington), collagenase I (0.5 mg/ml;Worthington), DNase I (0.02 mg/ml; Yeasen), hyaluronidase (30 U/ml, Sigma-Aldrich), 0.6% bovine serum albumin (BSA; Sigma-Aldrich), and 5% fetal bovine serum (FBS; Gibco) at 37 ℃ for 30 min. Then, the digestive system was filtered and centrifuged at 300×g for 5 min. After discarding the upper fluid, 2 ml erythrocyte lysate was added to remove the erythrocytes within 5 min. The cracking reaction was terminated by cleaning resolusion. Centrifuged 300×g for 5 min, then resuspended and counted the liver cells.
Single-cell libraries were generated using a GemCode single-cell instrument and a 10x Genomics Single Cell 3′ Library & Gel Bead Kit v2 and Chip Kit according to the kit manufacturer’s protocol (Ou Yi Bio, Shanghai). Brieﬂy, liver cells were suspended in 0.04% BSA–PBS and then counted with a Countess® II Automated Cell Counter. The cell concentration was adjusted to the desired concentration of 1×106/mL. Approximately 8000 cells were added to each channel. Nanoliter-scale gel beads in emulsion (GEMs) containing barcode information were generated and then reverse transcribed in a C1000 Touch Thermal Cycler (Bio-Rad). PCR ampliﬁcation was performed using cDNA as a template. Subsequently, the ampliﬁed cDNA was fragmented into approximately 200–300 bp fragments by a Bioruptor sonication device, and the traditional second generation sequencing process was followed, including, for example, sequencing linker P5 and sequencing primer R1. Finally, the DNA library was ampliﬁed by PCR.

value: liver

tag: Sex

value: male

tag: age

value: 8 weeks

value: adult offspring from intrauterine hyperglycemia model


title: mESC Tet1/2/3 TKO, Input, PyBo, clone26, rep3

description: Library name: FIBo_seq_26


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 3

description:
Sept4_x_x_250_Cell_3
Fluidigm C1


title: p20169.s080_31_PT063


title: p20169.s081_32_PT064


title: mESC Tet1/2/3 TKO, Input, PyBo, clone26, rep2

description: Library name: FIBo_seq_25


title: Iiver cells from adult offspring with control mother

description: Library name: Sample 3

value: adult offspring from control model


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 29

description:
Sept4_x_x_250_Cell_29
Fluidigm C1


title: p20169.s079_30_PT031

value: critical


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 28

description:
Sept4_x_x_250_Cell_28
Fluidigm C1


title: liver cells from fetal offspring with intrauterine hyperglycemia mother

description: Library name: Sample 2

value: fetal offspring from intrauterine hyperglycemia model


title: Iiver cells from fetal offspring with control mother

description: Library name: Sample 1

value: fetal offspring from control model


title: p20169.s078_28_PT024

value: Blood


title: mESC Tet1/2/3 TKO, Input, PyBo, clone26, rep1

description: Library name: FIBo_seq_24


title: mESC Tet1/2/3 TKO, RIP, mock, clone29

description: Library name: FIBo_seq_23

value: f5C antibody (# 61227, Active Motif)


title: EPS rep2

description:
Library name: Sample 2
column name in counts.csv: EPS-2

value: TD-EPS

value: Mouse  EPS cells were cultured in LCDM medium.


title: EPS rep1

description:
Library name: Sample 1
column name in counts.csv: EPS-1

value: mouse extended pluripotent stem cell


title: CD45+ cells, PBS, Csf2rb KO

first: Chen

last: Dong

institute: Tsinghua University

description: Library name: Sample 3

data_processing:
The raw scRNA-seq data were aligned to mm10 mouse reference CeleScope v3.0.1 (Singleron kit V2) following the standard pipeline and subsequent analysis was performed with R package Seurat v.4.1.2 (Hao et al., 2021).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: CD45+ cells

extract_protocol:
Lungs from uninfected or HCoV-OC43-infected WT or Csf2rb-/- mice were collected and digested into single-cell suspensions, and CD45+ cells were sorted. Cell viability was assessed using Trypan Blue staining.
Single-cell suspensions at a concentration of 2×10^5 cells/mL in PBS were loaded onto a microwell chip using the Singleron Matrix® Single Cell Processing System. Barcoding Beads were collected from the microwell chip, and mRNA captured by the Barcoding Beads was reversely transcribed to obtain cDNA, followed by PCR amplification. The amplified cDNA was then fragmented and ligated with sequencing adapters. scRNA-seq libraries were constructed using the GEXSCOPE® Single Cell RNA Library Kits (Singleron). Individual libraries were diluted to 4 nM, pooled and sequenced on an Illumina novaseq 6000 with 150 bp paired-end reads.

value: CD45+ cells

value: Csf2rb KO


title: CD45+ cells, HCoV-OC43, Csf2rb KO

description: Library name: Sample 4


title: mESC Tet1/2/3 TKO, RIP, mock, clone26

description: Library name: FIBo_seq_22

value: mouse embryonic stem cells

value: Tet1/2/3 TKO


title: p20169.s077_26_PT061


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 27

description:
Sept4_x_x_250_Cell_27
Fluidigm C1

value: Bone Marrow

value: WT

value: paired-end


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 26

description:
Sept4_x_x_250_Cell_26
Fluidigm C1


title: mESC Tet1/2/3 TKO, RIP, PyBo, clone29, rep3

description: Library name: FIBo_seq_21


title: p20169.s076_24_PT019


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 25

description:
Sept4_x_x_250_Cell_25
Fluidigm C1


title: p20169.s075_21_PT024

value: severe


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 24

description:
Sept4_x_x_250_Cell_24
Fluidigm C1


title: CD45+ cells, HCoV-OC43, WT

description: Library name: Sample 2


title: mESC Tet1/2/3 TKO, RIP, PyBo, clone29, rep2

description: Library name: FIBo_seq_20


title: CD45+ cells, PBS, WT

description: Library name: Sample 1


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 22

description:
Sept4_x_x_250_Cell_22
Fluidigm C1


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 23

description:
Sept4_x_x_250_Cell_23
Fluidigm C1


title: p20169.s074_20_PT019


title: mESC Tet1/2/3 TKO, RIP, PyBo, clone26, rep3

description: Library name: FIBo_seq_18


title: mESC Alkbh1 KO, mock, clone10

description:
Library name: sample_30
total RNA, rRNA-depleted

data_processing:
Raw read data were quality-assessed by FastQC (v.0.11.9, https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Alignment to the reference genome was performed using STAR (v. 2.7.10a) allowing soft-clipping with non-default parameters: --outFilterScoreMinOverLread 0.33, --outFilterMatchNminOverLread 0.33 and --outFilterMismatchNoverReadLmax 0.02, that ensure mapping of overlapping reads and allowed for up to 2% of mismatches. The reference (GRCm39.dna_sm.primary_assembly.fa) was taken from https://ftp.ensembl.org/pub/release-107 and the genome index was generated using M.mus.GRCm39.107.gtf for annotation and --sjdbOverhang 99 (read length - 1).
C-to-T events were identified using JACUSA2 (v.2.0.4) applying 2 conditions mode (call-2, PyBo/Mal vs mock), scanning only positions with coverage >5 reads (-c 5), minimum base quality > 20 (-q 20) and mapping quality > 20 (-m 20), taking into account rev-strand specificity of the libraries (P RF-FIRSTSTRAND) and using bam files with only uniquely mapped reads as an input. Shortly, to identify PyBo/Mal-induced C-to-T events for Tet1/2/3 or Alkbh1 CTRL samples, we applied the following filtering criteria for raw JACUSA2 output files: 1) JACUSA2 score >2, 2) C-to-T conversion level > 5% in each of 3 replicate of PyBo/Mal-treated sample, 3) ≥ 5 reads (average of 3 replicates) supporting mismatched T in PyBo/Mal-treated samples, and 4) C-to-T conversion level < 2% in each of 3 replicate of mock-treated samples, and less <5 reads (average of 3 replicates) supporting mismatched T in mock-treated samples. The C-to-T events that passed filtering were annotated with hiAnnotator (v. 1.34.0) using Mus_musculus.GRCm39.107.gtf as a gene model. In cases when the C-to-T site overlapped with multiple transcripts, we employed the following strategy to clarify the transcript annotation. Firstly, the gene with the correct orientation for the C-to-T site and the highest expression level was selected. Secondly, the transcript variant was selected with the following prioritization: (1) highest expression (2) marked as canonical and (3) the longest transcript variant. The transcript expression level was determined using kallisto (v. 0.44.0).
Assembly: GRCm39 (mm39)
Supplementary files format and content: bedGraph; shared C-to-T events observed in CTRL samples detected by PyBo-assisted RNA-seq

extract_protocol:
Total RNA was isolated from cultured cells using QIAzol Lysis Reagent (Qiagen) according to the manufacturer’s protocol followed by TURBO DNase (Invitrogen) treatment and another round of QIAzol purification.
Ribosomal RNA was depleted using the NEBNext rRNA Depletion Kit v2 (human/Mouse/Rat) (NEB) following the manufacturer’s protocol and purified using the RNA Clean & Concentrator kit (Zymo Research). For PyBo-seq, 200 ng of RNA was incubated in 900 mM pyridine borane in 600 mM sodium acetate (pH 5.2) at 37°C for 24 hours. For Mal-seq, 200 ng of RNA was incubated in 150 mM malononitrile in 1x TE buffer (pH 7.4) at 37°C for 24 hours. For mock treated samples, water was added instead of chemicals.
For PyBo-seq of ribosomal RNA, total RNA was chemically fragmented to 120-180 nt-long fragments and PyBo-treated as described above.
RNA library preparation was performed using the TruSeq Stranded mRNA Library Prep kit (20020594, Illumina), entering the protocol at the RNA fragmentation step and excluding the poly(A) enrichment. 10 ng RNA was used as starting amount. Libraries were size-selected for >100 bp fragments.
Library construction of rRNA was done with the NEXTFLEX Small RNA-Seq Kit V3 (Bioo Scientific) following Step A to Step G of Bioo Scientific`s standard protocol (V19.01) using the NEXTFLEX 3’ SR Adaptor and 5’ SR Adaptor. Step A (NEXTFLEX 3` 4N Adenylated Adapter Ligation) was performed overnight at 20°C and for step F (Bead Cleanup) the modified protocol was used to retain small RNAs. Libraries were prepared with a starting amount of 1.4 ng RNA and amplified in 21 PCR cycles. Libraries were size-selected for 18 – 362 nt insert size.

value: Alkbh1 KO

value: mock


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 21

description:
Sept4_x_x_250_Cell_21
Fluidigm C1


title: mESC Tet1/2/3 TKO, RIP, PyBo, clone29, rep1

description: Library name: FIBo_seq_19


title: mESC Alkbh1 KO, mock, clone5

description:
Library name: sample_29
total RNA, rRNA-depleted


title: mESC Tet1/2/3 TKO, RIP, PyBo, clone26, rep2

description: Library name: FIBo_seq_17


title: mESC Alkbh1 KO, Mal, clone10

description:
Library name: sample_27
total RNA, rRNA-depleted

value: malononitrile


title: p20169.s071_10_PT009

value: critical


title: mESC Alkbh1 KO, mock, clone3

description:
Library name: sample_28
total RNA, rRNA-depleted


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 20

description:
Sept4_x_x_250_Cell_20
Fluidigm C1


title: mESC Alkbh1 KO, Mal, clone5

description:
Library name: sample_26
total RNA, rRNA-depleted


title: mESC Tet1/2/3 CTRL, Input, mock, clone4

description: Library name: FIBo_seq_14

value: Tet1/2/3 wildtype


title: p20169.s069_5_PT035

value: Blood


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 18

description:
Sept4_x_x_250_Cell_18
Fluidigm C1


title: mESC Alkbh1 KO, Mal, clone3

description:
Library name: sample_25
total RNA, rRNA-depleted


title: p20169.s068_4_PT033


title: p20169.s072_11_PT054


title: mESC Tet1/2/3 CTRL, Input, PyBo, clone6, rep3

description: Library name: FIBo_seq_13


title: p20169.s070_7_PT039

value: mild


title: mESC Tet1/2/3 TKO, RIP, PyBo, clone26, rep1

description: Library name: FIBo_seq_16

value: f5C antibody (# 61227, Active Motif)


title: p20169.s067_2_PT009


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 17

description:
Sept4_x_x_250_Cell_17
Fluidigm C1


title: mESC Alkbh1 KO, PyBo, clone10

description:
Library name: sample_24
total RNA, rRNA-depleted


title: mESC Tet1/2/3 CTRL, Input, mock, clone6

description: Library name: FIBo_seq_15


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 16

description:
Sept4_x_x_250_Cell_16
Fluidigm C1


title: p20169.s066_199_PT10056


title: p20169.s065_197_PT10014


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 15

description:
Sept4_x_x_250_Cell_15
Fluidigm C1


title: mESC Tet1/2/3 CTRL, Input, PyBo, clone4, rep3

description: Library name: FIBo_seq_10


title: mESC Alkbh1 KO, PyBo, clone5

description:
Library name: sample_23
total RNA, rRNA-depleted


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 14

description:
Sept4_x_x_250_Cell_14
Fluidigm C1


title: mESC Tet1/2/3 CTRL, Input, PyBo, clone6, rep1

description: Library name: FIBo_seq_11


title: mESC Tet1/2/3 CTRL, Input, PyBo, clone4, rep2

description: Library name: FIBo_seq_9


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 13

description:
Sept4_x_x_250_Cell_13
Fluidigm C1


title: mESC Alkbh1 CTRL, mock, clone3

description:
Library name: sample_21
total RNA, rRNA-depleted

value: Alkbh1 wildtype


title: p20169.s063_193_PT10017


title: p20169.s062_192_PT10069


title: p20169.s064_195_PT10063


title: mESC Alkbh1 KO, PyBo, clone3

description:
Library name: sample_22
total RNA, rRNA-depleted


title: mESC Tet1/2/3 CTRL, Input, PyBo, clone4, rep1

description: Library name: FIBo_seq_8


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 19

description:
Sept4_x_x_250_Cell_19
Fluidigm C1


title: p20169.s061_191_PT10010


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 12

description:
Sept4_x_x_250_Cell_12
Fluidigm C1


title: mESC Alkbh1 CTRL, mock, clone1

description:
Library name: sample_19
total RNA, rRNA-depleted


title: mESC Alkbh1 CTRL, mock, clone2

description:
Library name: sample_20
total RNA, rRNA-depleted


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 11

description:
Sept4_x_x_250_Cell_11
Fluidigm C1


title: mESC Tet1/2/3 CTRL, RIP, mock, clone6

description: Library name: FIBo_seq_7


title: mESC Alkbh1 CTRL, Mal, clone3

description:
Library name: sample_18
total RNA, rRNA-depleted


title: mESC Tet1/2/3 CTRL, Input, PyBo, clone6, rep2

description: Library name: FIBo_seq_12


title: p20169.s060_189_PT10004


title: mESC Tet1/2/3 CTRL, RIP, mock, clone4

description: Library name: FIBo_seq_6


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 10

description:
Sept4_x_x_250_Cell_10
Fluidigm C1


title: mESC Alkbh1 CTRL, Mal, clone2

description:
Library name: sample_17
total RNA, rRNA-depleted


title: mESC Tet1/2/3 CTRL, RIP, PyBo, clone6, rep3

description: Library name: FIBo_seq_5


title: CLP (Lin-CD117+Sca1+CD127+CD135+Ly6D-) cell 1

description:
Sept4_x_x_250_Cell_1
Fluidigm C1


title: mESC Tet1/2/3 CTRL, RIP, PyBo, clone6, rep2

description: Library name: FIBo_seq_4


title: p20169.s059_188_PT10001


title: LK Gfi1-tdTomato intermediate Csf1r- cell 79

description:
LK.Gfi_int_Csf1r_neg.CD150-.79
Fluidigm C1


title: p20169.s056_177_PT10007


title: p20169.s055_170_PT10057


title: mESC Alkbh1 CTRL, PyBo, clone3

description:
Library name: sample_15
total RNA, rRNA-depleted


title: LK Gfi1-tdTomato intermediate Csf1r- cell 78

description:
LK.Gfi_int_Csf1r_neg.CD150-.78
Fluidigm C1


title: mESC Alkbh1 CTRL, Mal, clone1

description:
Library name: sample_16
total RNA, rRNA-depleted


title: mESC Tet1/2/3 CTRL, RIP, PyBo, clone6, rep1

description: Library name: FIBo_seq_3


title: mESC Alkbh1 CTRL, PyBo, clone2

description:
Library name: sample_14
total RNA, rRNA-depleted


title: p20169.s053_160_PT065


title: mESC Alkbh1 CTRL, PyBo, clone1

description:
Library name: sample_13
total RNA, rRNA-depleted


title: p20169.s049_149_PT119


title: mESC Tet1/2/3 CTRL, RIP, PyBo, clone4, rep2

description: Library name: FIBo_seq_2


title: mESC Tet1/2/3 TKO, mock, rep3

description:
Library name: sample_12
total RNA, rRNA-depleted


title: mESC Tet1/2/3 TKO, mock, rep2

description:
Library name: sample_11
total RNA, rRNA-depleted


title: p20169.s044_130_PT004


title: LK Gfi1-tdTomato intermediate Csf1r- cell 75

description:
LK.Gfi_int_Csf1r_neg.CD150-.75
Fluidigm C1


title: mESC Tet1/2/3 CTRL, RIP, PyBo, clone4, rep1

description: Library name: FIBo_seq_1


title: PDX UPS2236 Wk4 UPS

city: New York

first: Jonathan

last: Rub

state: NY

address: 417 E 68th St

department: Cancer Biology and Genetics

institute: MSKCC

description:
Library name: PDX_UPS2236_Wk3_UPS
10x Genomics

data_processing:
Raw sequencing data from cDNA and multiplexed libraries was demultiplexed and aligned with the 10X Genomics Cell Ranger pipeline (v.7.2.0).
Assembly: For mouse experiments, data was aligned to a custom GRCm38/mm10 reference genome including the tdTomato transgene used in this study.
Assembly: For human PDX experiments, data was aligned to a combined human (GRCh38) 2020-A and GRCm38/mm10 reference genome.
Supplementary files format and content: Tab-separated values files, matrix files, and h5ad scanpy files

organism:
Homo sapiens
Mus musculus

source_name: Undifferentiated Pleomorphic Sarcoma

growth_protocol: Autochthonous tumors were induced in KrasLSL-G12D/+; Trp53flox/flox; Rosa26tdtomato/+ (KPT) mice with 9x10^7 plaque-forming units (PFU) of AdCMV-Cre (Iowa Viral Vector Core) as previously described, in mice that were between 9-24 weeks of age. Immunocompromised NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (aka NSG mice)  (The Jackson Laboratory, catalog #005557) mice were used for transplantation of patient-derived xenografts (PDXs).

extract_protocol:
For isolation of tumor cells from KPT mice and PDXs, mice were euthanized at the indicated time points. Dissected tumors were dissociated with a mixture of Dispase II, Collagenase Type IV, and DNase I for 1 hr. The dissociated cells were filtered using a 100 µm filter and spun at 1000 rpm for 10 min at 4 °C. The supernatant was removed by aspiration and red blood cell lysis was performed using BD Pharm Lyse for 1 minute on ice. Cells were then washed with sterile media containing 2% heat inactivated FBS, passed through a 40 µm filter, and pelleted at 300 g for 5 min at 4 °C. The supernatant was removed and cells were resuspended in Fluorescence-Activated Cell Sorting (FACS) buffer media (2% heat-inactivated FBS in PBS) and counted for use in FACS.
Single cell suspensions from UPS tumors were prepared and stained as above. Live sorted cells were collected by flow cytometry, washed once with PBS containing 2% heat inactivated FBS (HI-FBS) and resuspended to a final concentration of 700–1,300 cells per μl of SMEM + 2% HI-FBS. The viability of cells in all experiments was confirmed to be above 80% by 0.2% (w/v) Trypan Blue staining (Invitrogen, Countess II) and processed by droplet based scRNA-seq using the 10X genomics Chromium Single Cell 3’ Library & Gel bead Kit >=V3 according to manufacturer’s protocol. Following reverse transcription and cell barcoding in droplets, emulsions were broken, and cDNA purified using Dynabeads MyOne SILANE followed by PCR amplification as per manufacturer’s instructions. Between 10,000 to 30,000 cells were targeted for each droplet formulation lane using Chromium. Samples were multiplexed using the TotalSeq B cell hashing protocol (Biolegend). Final libraries were sequenced on Illumina NovaSeq S4 platform (R1 – 28 cycles, i7 – 8 cycles, R2 – 90 cycles).

treatment_protocol: Mice were treated with intraperitoneal Doxorubicin (0.9-1 mg/kg) twice a week for up to 4 weeks. NSG mice bearing UPS2236 PDXs were harvested at 3 weeks, approximately 1 week earlier than the preplanned endpoint of 4 weeks due to tumor growth constraints.

value: Undifferentiated Pleomorphic Sarcoma

value: Doxorubicin


title: LK Gfi1-tdTomato intermediate Csf1r- cell 76

description:
LK.Gfi_int_Csf1r_neg.CD150-.76
Fluidigm C1


title: mESC Tet1/2/3 TKO, mock, rep1

description:
Library name: sample_10
total RNA, rRNA-depleted

value: mouse embryonic stem cells


title: PDX UPS2236 Veh and Wk1 UPS

description:
Library name: PDX_UPS2236_Veh_Wk1_UPS
10x Genomics


title: LK Gfi1-tdTomato intermediate Csf1r- cell 74

description:
LK.Gfi_int_Csf1r_neg.CD150-.74
Fluidigm C1


title: p20169.s040_117_PT092

value: asymptomatic


title: p20169.s041_124_PT089


title: LK Gfi1-tdTomato intermediate Csf1r- cell 73

description:
LK.Gfi_int_Csf1r_neg.CD150-.73
Fluidigm C1

value: Bone Marrow


title: mESC Tet1/2/3 TKO, PyBo, rep3

description:
Library name: sample_9
total RNA, rRNA-depleted

value: Tet1/2/3 TKO


title: PDX MFH9 Veh, Wk1, and Wk4 UPS

description:
Library name: PDX_MFH9_Veh_Wk1_Wk4_UPS
10x Genomics


title: p20169.s039_116_PT023


title: p20169.s038_114_PT043


title: LK Gfi1-tdTomato intermediate Csf1r- cell 77

description:
LK.Gfi_int_Csf1r_neg.CD150-.77
Fluidigm C1

value: WT

value: paired-end


title: LK Gfi1-tdTomato intermediate Csf1r- cell 71

description:
LK.Gfi_int_Csf1r_neg.CD150-.71
Fluidigm C1


title: mESC Tet1/2/3 TKO, PyBo, rep1

description:
Library name: sample_7
total RNA, rRNA-depleted


title: mESC Tet1/2/3 CTRL, mock, rep3

description:
Library name: sample_6
total RNA, rRNA-depleted


title: LK Gfi1-tdTomato intermediate Csf1r- cell 70

description:
LK.Gfi_int_Csf1r_neg.CD150-.70
Fluidigm C1


title: GDF11 3H treatment 1

city: Zhengzhou

first: Jung-Chien

state: Henan

address: 40, Daxue Road

institute: The First Affiliated Hospital of Zhengzhou University

description: Library name: Sample 4

data_processing:
RNA sequencing was performed by Shanghai Majorbio Bio-Pharm Biotechnology.
The raw paired end reads were trimmed and quality controlled by fastpwith defaultparameters.
Clean reads were separately aligned to reference genome with orientation modeusing HISAT2 software.
The mapped reads of each sample were assembled by StringTie in a reference-based approach.
To identify DEGs between two different samples, the expression level of each transcript was calculated according to the TPM method.
RSEM was used to quantify gene abundances. Essentially, differential expression analysis was performed using the DESeq2 or DEGseq.
DEGs with |log2FC| ≧ 1 and FDR≤ 0.05 (DESeq2 ) or FDR ≤0.001 (DEGseq) were considered to be significantly different expressed genes.
Assembly: GRCh38/hg38
Supplementary files format and content: A tab-delimited file containing the raw counts for each sample.

source_name: Placenta

extract_protocol:
Total RNA from each sample was extracted using TRIzol, and 1 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the Illumina Stranded mRNA Prep Ligation kit (Illumina) following the manufacturer’s protocol.

value: Placenta

value: Extravillous trophoblast cell

value: Treated with 30 ng/mL GDf-11 for 3 hours


title: LK Gfi1-tdTomato intermediate Csf1r- cell 72

description:
LK.Gfi_int_Csf1r_neg.CD150-.72
Fluidigm C1


title: p20169.s036_111_PT116

data_processing:
Transcript abundance estimates were calculated internal to the STAR aligner using the algorithm of htseq-count(2). DESeq2 was used for normalization(3), producing a normalized read count.
Assembly: GRCh38
Supplementary files format and content: airis_countMatrix.csv
Supplementary files format and content: raw count matrix

source_name: Blood

extract_protocol:
PBMCs were lysed in 700 L of Trizol and then extracted using the miRNeasy Mini kit (Qiagen) with on-column DNase digestion. RNA quality was assessed using a TapeStation 4200 (Agilent) and then ten nanograms of total RNA was used as input for cDNA synthesis using the Clontech SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) according to the manufacturer’s instructions.
Amplified cDNA was fragmented and appended with dual-indexed barcodes using the Nextera XT DNA Library Preparation kit (Illumina). Libraries were validated by capillary electrophoresis on a TapeStation 4200 (Agilent), pooled at equimolar concentrations, and sequenced with PE100 reads on an Illumina NovaSeq 6000, yielding ~30 million reads per sample on average. Alignment was performed using STAR version 2.7.3a(1)and transcripts were annotated using a composite genome reference which included GRCh38 Ensembl release 100 and SARS-CoV-2 (GCF_009858895.2, ASM985889v3, MN985325.1).

value: critical


title: GDF11 3H treatment 3

description: Library name: Sample 6


title: p20169.s037_112_PT052


title: Control 3

description: Library name: Sample 3

value: Untreated


title: LK Gfi1-tdTomato intermediate Csf1r- cell 69

description:
LK.Gfi_int_Csf1r_neg.CD150-.69
Fluidigm C1


title: Control 2

description: Library name: Sample 2


title: LK Gfi1-tdTomato intermediate Csf1r- cell 68

description:
LK.Gfi_int_Csf1r_neg.CD150-.68
Fluidigm C1


title: mESC Tet1/2/3 CTRL, mock, rep2

description:
Library name: sample_5
total RNA, rRNA-depleted

value: Tet1/2/3 wildtype

value: mock


title: p20169.s035_109_PT117

value: Blood


title: mESC Tet1/2/3 CTRL, mock, rep1

description:
Library name: sample_4
total RNA, rRNA-depleted


title: Control 1

description: Library name: Sample 1


title: p20169.s033_104_PT052


title: LK Gfi1-tdTomato intermediate Csf1r- cell 67

description:
LK.Gfi_int_Csf1r_neg.CD150-.67
Fluidigm C1


title: mESC Tet1/2/3 CTRL, PyBo, rep3

description:
Library name: sample_3
total RNA, rRNA-depleted


title: p20169.s032_103_PT020

value: severe