title: H3K27me3 AB CUT&Tag ProB cell Cfp1(fl/fl) Rag1(-/-) biol rep2

city: Shenzhen

first: Wanyu

last: Bai

address: 628 Zhenyuan Road

institute: The Seventh Affiliated Hospital of Sun Yat-Sen University

description: Library name: H3K27me3 AB CUT_Tag ProB cell Cfp1(fl/fl) Rag1(-/-) biol rep2

data_processing:
Raw sequenced reads were  trimmed for adapter sequences and quality filtered using Trim Galore (v20.04.6), and aligned to the GRCm38 (mm10) reference genome using BWA-MEM (v0.7.17). SAM files were converted and sorted into BAM format using Samtools (v1.10). Duplicate reads in the BAM files were marked and removed with Picard MarkDuplicates (v3.3.0). Deeptools (v3.5.1) was used for converting the sorted BAM files into bigWig format via bamCoverage with parameters --binSize 10 --normalizeUsing RPKM.
Assembly: mm10
Supplementary files format and content: bigWig file
Library strategy: CUT&Tag

source_name: bone marrow

extract_protocol:
CUT&Tag assays were performed on approximately 5 × 10^4 cells as previously described (Kaya-Okur et al., 2019). Cells were washed once with 500 μl of wash buffer and then bound to 10 μl of CaCl2-activated concanavalin A beads (ConA, Bang Laboratories, BP531) for 10 min at room temperature. After that, cells were incubated with 0.5 μl of anti-H3K27ac (Active Motif, 39133), anti-H3K4me1 (Abcam, Ab176877), or anti-H3K27me3 (Cell Signaling Technology, 9733) antibody in 50 μl of Antibody buffer for 2 h at room temperature with slow rotation. Following this, cells were incubated with 0.5 μl of anti-rabbit (Antibodies Online, ABIN101961) secondary antibody for 1 h at room temperature. Then cells were washed three times with DIG wash buffer and then incubated with hyperactive pA-Tn5 transposase (Vazyme, S603) at a final concentration of 0.04 μM in 50 μl of DIG 300 buffer for 1 h at room temperature. Afterwards, cells were washed three times with DIG 300 buffer, resuspended in tagmentation buffer and incubated at 37°C for 1 h. DNA was purified using phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation after terminating tagmentation.
DNA libraries were amplified by NEBNext HiFi 2 × PCR Master Mix (New England Biolabs, M0541) using the following parameters: 58°C for 5 min; 72°C for 5 min; 98°C for 30 s; 16 - 19 cycles of 98°C for 10 s and 63°C for 10 s; and 72°C for 1 min.

value: bone marrow

value: Pro-B cells (CD19+CD43+)

value: Cfp1(fl/fl) Rag1(-/-)


title: H3K27me3 AB CUT&Tag ProB cell Cfp1(fl/fl) Rag1(-/-) biol rep1

status: Public on Feb 08 2026

type: SRA

country: China

description: Library name: H3K27me3 AB CUT_Tag ProB cell Cfp1(fl/fl) Rag1(-/-) biol rep1

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: tissue

tag: cell type

tag: genotype


title: H3K27me3 AB CUT&Tag ProB cell Cfp1(fl/fl) Rag1(-/-) biol combined

description:
Library name: H3K27me3 AB CUT_Tag ProB cell Cfp1(fl/fl) Rag1(-/-) biol combined
BAM files of biological replicates were merged and then converted into bigWig format via bamCoverage.


title: H3K27me3 AB CUT&Tag ProB cell Cfp1(fl/fl) Mb1-Cre Rag1(-/-) biol rep1

description: Library name: H3K27me3 AB CUT_Tag ProB cell Cfp1(fl/fl) Mb1-Cre Rag1(-/-) biol rep1

value: Cfp1(fl/fl) Mb1-Cre Rag1(-/-)


title: H3K4me1 AB CUT&Tag ProB cell Cfp1(fl/fl) Rag1(-/-) biol combined

description:
Library name: H3K4me1 AB CUT_Tag ProB cell Cfp1(fl/fl) Rag1(-/-) biol combined
BAM files of biological replicates were merged and then converted into bigWig format via bamCoverage.


title: H3K27me3 AB CUT&Tag ProB cell Cfp1(fl/fl) Mb1-Cre Rag1(-/-) biol combined

description:
Library name: H3K27me3 AB CUT_Tag ProB cell Cfp1(fl/fl) Mb1-Cre Rag1(-/-) biol combined
BAM files of biological replicates were merged and then converted into bigWig format via bamCoverage.


title: H3K27me3 AB CUT&Tag ProB cell Cfp1(fl/fl) Mb1-Cre Rag1(-/-) biol rep2

description: Library name: H3K27me3 AB CUT_Tag ProB cell Cfp1(fl/fl) Mb1-Cre Rag1(-/-) biol rep2


title: H3K4me1 AB CUT&Tag ProB cell Cfp1(fl/fl) Rag1(-/-) biol rep2

description: Library name: H3K4me1 AB CUT_Tag ProB cell Cfp1(fl/fl) Rag1(-/-) biol rep2


title: H3K27ac AB CUT&Tag ProB cell Cfp1(fl/fl) Rag1(-/-) biol combined

description:
Library name: H3K27ac AB CUT_Tag ProB cell Cfp1(fl/fl) Rag1(-/-) biol combined
BAM files of biological replicates were merged and then converted into bigWig format via bamCoverage.


title: H3K4me1 AB CUT&Tag ProB cell Cfp1(fl/fl) Rag1(-/-) biol rep1

description: Library name: H3K4me1 AB CUT_Tag ProB cell Cfp1(fl/fl) Rag1(-/-) biol rep1


title: H3K27ac AB CUT&Tag ProB cell Cfp1(fl/fl) Rag1(-/-) biol rep1

description: Library name: H3K27ac AB CUT_Tag ProB cell Cfp1(fl/fl) Rag1(-/-) biol rep1


title: Ven/aza treated BM stroma cell multiplexing oligo data

city: LONDON

first: Giuseppe

middle: Alessandro

last: D'Agostino

state: ENGLAND

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

description:
Library name: Ven/aza_CMO
Bone marrow stroma from ven/aza-treated mice - CMO 303, 304, 305, 306. Cell Multiplexing Oligo library, R1 contains cell barcode and UMI, R2 contains CMO

library_source: transcriptomic single cell

data_processing:
FASTQ files were aligned, quantified and demultiplexed using Cellranger v. 7.0 in multi mode
Assembly: mm10 v.3.0.0 from 10X Genomics
Supplementary files format and content: H5 files of demultiplexed count matrices

molecule: polyA RNA

source_name: bone marrow stroma

growth_protocol: mice were culled 3 days following the end of treatment for ven/aza - vehicle treated groups for 'recovery 'single cell RNAseq timepoint, mice were culled 50 days post end of treatment

extract_protocol:
Bone marrow cells were isolated by centrifugal flushing at 2500g for 1 min. BM was enzymatically digested with collagenase-type I (3mg/ml) and dispase (neutral protease, grade 2: 4mg/ml). BM cells also underwent RBC lysis protocol. Stromal cells were sorted based on CD45-/CD71-/Ter119- gating strategy
scRNA-seq 10X 3' Gene Expression with Cell Multiplexing Oligo

value: bone marrow stroma

tag: library type

value: CMO

value: NBSG-S (NSG ckit41/41 with human SCF/IL3 and GM-CSF)

tag: treatment

value: ven/aza

tag: batch


title: Recovery BM stroma gene cell multiplexing oligo data

description:
Library name: Recovery_CMO
Bone marrow stroma from post-treatment recovery mice - CMO 306, 307, 308, 309. Cell Multiplexing Oligo library, R1 contains cell barcode and UMI, R2 contains CMO

treatment_protocol: mice were culled 3 days following the end of treatment for ven/aza - vehicle treated groups for 'recovery 'single cell RNAseq timepoint, mice were culled 50 days post end of treatment

value: ven/aza and recovery


title: Vehicle treated BM stroma gene expression data

description:
Library name: Vehicle_GEX
Bone marrow stroma from vehicle-treated mice - CMO 307, 308, 309. Gene expression library, R1 contains cell barcode and UMI, R2 contains transcript

value: mRNA

value: vehicle


title: Vehicle treated BM stroma cell multiplexing oligo data

description:
Library name: Vehicle_CMO
Bone marrow stroma from vehicle-treated mice - CMO 307, 308, 309. Cell Multiplexing Oligo library, R1 contains cell barcode and UMI, R2 contains CMO


title: Ven/aza treated BM stroma gene expression data

description:
Library name: Ven/aza_GEX
Bone marrow stroma from ven/aza-treated mice - CMO 303, 304, 305, 306. Gene expression library, R1 contains cell barcode and UMI, R2 contains transcript


description: Library name: Igh VDJ-Seq JH4 Pro-B cell Cfp1(fl/fl) Mb1-Cre biol rep1

data_processing:
For the VHDJH identification, we used the pipeline available at Bitbucket (https://bitbucket.org/adugduzhou/htgtsrep). HTGTSrep pipeline was used for generating the processed files with "pass.xls" ends.
For the DJH joins analysis, we used the standard HTGTS sequencing pipeline provided by Frederick W. Alt Lab, which is available at GitHub (https://robinmeyers.github.io/transloc_pipeline/thedocs.html). Linear amplification-mediated (LAM)-HTGTS pipeline was used for generating processed files with "tlx" ends.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include a V usage report for each sample
Supplementary files format and content: tab delimited text files contain filtered junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); the entire stitched paired end read sequence (Seq); the junction sequence(J_seq)

extract_protocol:
Genomic DNA of FACS-sorted pro-B cells (CD19+CD43+) was extracted using phenol-chloroform.
0.5-2 μg of genomic DNA extracted from FACS-sorted pro-B cells (CD19+CD43+) was sonicated into fragments ranging from 300 to1000 bp using M220 Focused-ultrasonicator (Covaris), and amplified by LAM-PCR with biotin-conjugated 5’ JH1 or JH4 primers. Biotinylated PCR products were captured by Dynabeads MyOne streptavidin C1 beads (Invitrogen, 65002) and ligated with bridge adapters on-bead. The ligated products were amplified by nested PCR using barcode primers, followed by a third round of PCR using P5-I5 and P7-I7 primers. PCR products ranging 300-1,000 bp were purified by gel separation and sequenced on the Illumina NovaSeq platform with 250 bp or the Illumina MiSeq platform with150 bp paired-end reads.

value: Cfp1(fl/fl) Mb1-Cre


description: Library name: Igh VDJ-Seq JH4 Pro-B cell Cfp1(fl/fl) biol rep1


title: H3K27ac AB CUT&Tag ProB cell Cfp1(fl/fl) Rag1(-/-) biol rep2

description: Library name: H3K27ac AB CUT_Tag ProB cell Cfp1(fl/fl) Rag1(-/-) biol rep2


description: Library name: Igh VDJ-Seq JH1 Pro-B cell Cfp1(fl/fl) biol rep2


description: Library name: Igh VDJ-Seq JH1 Pro-B cell Cfp1(fl/fl) biol rep3


description: Library name: Igh VDJ-Seq JH1 Pro-B cell Cfp1(fl/fl) Mb1-Cre biol rep3


description: Library name: Igh VDJ-Seq JH1 Pro-B cell Cfp1(fl/fl) Mb1-Cre biol rep2


description:
Library name: RNA-Seq Pro-B cell Cfp1(fl/fl) Mb1-Cre Rag1(-/-) biol combined
BAM files of biological replicates were merged and then converted into bigWig format via bamCoverage.

library_source: transcriptomic

data_processing:
Raw sequenced reads were trimmed for adapter sequences and quality filtered using Trim Galore (v20.04.6), and aligned to the GRCm38 (mm10) reference genome using Hisat2 (v2.2.0). Samtools (v1.10) was used for converting and sorting the SAM files into BAM format. Deeptools (v3.5.1) was used for converting the sorted BAM files into bigWig format via bamCoverage with parameters --binSize 10 --normalizeUsing BPM for total reads; or --binSize 10 --normalizeUsing BPM –filterRNAstrand forward/reverse for strand-specific reads. FeatureCounts (v2.0.0) was used to quantify reads mapped to genomic features, with parameters -p -s 2 -t exon -g gene_id, and the Gencode vM23 (Ensembl 98) annotation was used as the reference.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: bigWig file
Supplementary files format and content: bigWig for combined samples of the same genotype, forward strand
Supplementary files format and content: bigWig for combined samples of the same genotype, reverse strand

molecule: total RNA

extract_protocol:
Total RNA was extracted from pro-B cells (CD19+CD43+) via standard TRIzol extraction (Invitrogen, 15596026). 100 ng of total RNA was used as input, and rRNA was removed by Ribo-off rRNA Depletion Kit (Vazyme, N406).
RNA-seq libraries were prepared using the Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme, NR605) with the dUTP incorporation method.


description:
Library name: RNA-Seq Pro-B cell Cfp1(fl/fl) Rag1(-/-) biol combined
BAM files of biological replicates were merged and then converted into bigWig format via bamCoverage.


description: Library name: Igh VDJ-Seq JH1 Pro-B cell Cfp1(fl/fl) biol rep1


title: Recovery BM stroma gene expression data

description:
Library name: Recovery_GEX
Bone marrow stroma from post-treatment recovery mice - CMO 306, 307, 308, 309.  Gene expression library, R1 contains cell barcode and UMI, R2 contains transcript


description: Library name: Igh VDJ-Seq JH1 Pro-B cell Cfp1(fl/fl) Mb1-Cre biol rep1


description:
Library name: RNA-Seq Pro-B cell Cfp1(fl/fl) Mb1-Cre Rag1(-/-) biol rep1
Column name in All_featurecounts.txt: Cfp1_KO_1


title: CTCF AB CUT&Tag Pro-B cell Cfp1(fl/fl) Mb1-Cre Rag1(-/-) biol rep5

description: Library name: CTCF AB CUT_Tag Pro-B cell Cfp1(fl/fl) Mb1-Cre Rag1(-/-) biol rep5

extract_protocol:
CUT&Tag assays were performed on approximately 5 × 10^4 cells as previously described (Kaya-Okur et al., 2019). Cells were wash once with 500 μl of wash buffer, then bound to 10 μl of CaCl2-activated concanavalin A beads (ConA, Bang Laboratories, BP531) for 10 min at room temperature. After that, cells were incubated with 0.5 μl of anti-H3K4me3 (Milipore, 07-473), anti-CTCF (ABClonal, A19588), or anti-Pol II (Cell Signaling, 2629) antibodies in 50 μl of Antibody buffer for 2 h at room temperature with slow rotation. Following this, cells were incubated with 0.5 μl of anti-rabbit (Antibodies Online, ABIN101961) or anti-mouse IgG (Abcam, Ab46540) secondary antibodies for 1 h at room temperature. Then cells were washed three times with DIG wash buffer and then incubated with hyperactive pA-Tn5 transposase (Vazyme, S603) at a final concentration of 0.04 μM in 50 μl of DIG 300 buffer for 1 h at room temperature. Similarly, cells were washed three times with DIG 300 buffer, resuspended in tagmentation buffer and incubated at 37°C for 1 h. DNA was purified using phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation after terminating tagmentation.
DNA libraries were amplified by NEBNext HiFi 2 × PCR Master Mix (New England Biolabs, M0541) using the following parameters: 58°C for 5 min; 72°C for 5 min; 98°C for 30 s; 16 - 19 cycles of 98°C for 10 s and 63°C for 10 s; and 72°C for 1 min.


description:
Library name: RNA-Seq Pro-B cell Cfp1(fl/fl) Rag1(-/-) biol rep1
Column name in All_featurecounts.txt: CTRL_1


title: CTCF AB CUT&Tag Pro-B cell Cfp1(fl/fl) Mb1-Cre Rag1(-/-) biol rep4

description: Library name: CTCF AB CUT_Tag Pro-B cell Cfp1(fl/fl) Mb1-Cre Rag1(-/-) biol rep4


description:
Library name: RNA-Seq Pro-B cell Cfp1(fl/fl) Mb1-Cre Rag1(-/-) biol rep2
Column name in All_featurecounts.txt: Cfp1_KO_2


title: CTCF AB CUT&Tag Pro-B cell Cfp1(fl/fl) Mb1-Cre Rag1(-/-) biol rep1

description: Library name: CTCF AB CUT_Tag Pro-B cell Cfp1(fl/fl) Mb1-Cre Rag1(-/-) biol rep1


title: CTCF AB CUT&Tag Pro-B cell Cfp1(fl/fl) Rag1(-/-) biol rep2

description: Library name: CTCF AB CUT_Tag Pro-B cell Cfp1(fl/fl) Rag1(-/-) biol rep2


description:
Library name: RNA-Seq Pro-B cell Cfp1(fl/fl) Rag1(-/-) biol rep2
Column name in All_featurecounts.txt: CTRL_2


title: CTCF AB CUT&Tag Pro-B cell Cfp1(fl/fl) Mb1-Cre Rag1(-/-) biol rep2

description: Library name: CTCF AB CUT_Tag Pro-B cell Cfp1(fl/fl) Mb1-Cre Rag1(-/-) biol rep2


title: Pol II AB CUT&Tag Pro-B cell Cfp1(fl/fl) Mb1-Cre Rag1(-/-) biol combined

description:
Library name: Pol II AB CUT_Tag Pro-B cell Cfp1(fl/fl) Mb1-Cre Rag1(-/-) biol combined
BAM files of biological replicates were merged and then converted into bigWig format via bamCoverage.


title: CTCF AB CUT&Tag Pro-B cell Cfp1(fl/fl) Rag1(-/-) biol rep1

description: Library name: CTCF AB CUT_Tag Pro-B cell Cfp1(fl/fl) Rag1(-/-) biol rep1


title: CTCF AB CUT&Tag Pro-B cell Cfp1(fl/fl) Mb1-Cre Rag1(-/-) biol rep3

description: Library name: CTCF AB CUT_Tag Pro-B cell Cfp1(fl/fl) Mb1-Cre Rag1(-/-) biol rep3


title: H9 rep2

city: Hohhot

first: Chen

last: Yanglin

address: Xilin road

institute: Inner Mongolia University

description: Library name: H9_rep2

data_processing:
Adaptor sequences and low-quality base calls were trimmed using fastp with default parameters.
Trimmed reads were aligned to the rat reference genome (Rattus norvegicus.mRatBN7.2.109) or human reference genome (GRCh38) using STAR v2.7.7a in paired-end mode with default parameters
Gene level counts were generated using FeatureCounts from Subread v2.0.
Assembly: Rattus norvegicus.mRatBN7.2.109, GRCh38
Supplementary files format and content: comma-separated csv file include count value of each sample

organism: Homo sapiens

source_name: cell line

extract_protocol:
Total RNA was extracted from cultured cells using Rneasy mini kit (Qiagen). 1.5 ug of total RNA was used for the construction of sequencing libraries.
Library for RNA-seq were prepared using Illumina TruseqTM RNA sample prep Kit.

value: cell line

tag: cell line

value: Pluripotent stem cell

value: wildtype

value: PSCM


title: H9 rep1

description: Library name: H9_rep1


title: Pol II AB CUT&Tag Pro-B cell Cfp1(fl/fl) Mb1-Cre Rag1(-/-) biol rep2

description: Library name: Pol II AB CUT_Tag Pro-B cell Cfp1(fl/fl) Mb1-Cre Rag1(-/-) biol rep2


title: CTCF AB CUT&Tag Pro-B cell Cfp1(fl/fl) Mb1-Cre Rag1(-/-) biol combined

description:
Library name: CTCF AB CUT_Tag Pro-B cell Cfp1(fl/fl) Mb1-Cre Rag1(-/-) biol combined
BAM files of biological replicates were merged and then converted into bigWig format via bamCoverage.


title: H9 rep3

description: Library name: H9_rep3


title: Pol II AB CUT&Tag Pro-B cell Cfp1(fl/fl) Rag1(-/-) biol combined

description:
Library name: Pol II AB CUT_Tag Pro-B cell Cfp1(fl/fl) Rag1(-/-) biol combined
BAM files of biological replicates were merged and then converted into bigWig format via bamCoverage.


title: CTCF AB CUT&Tag Pro-B cell Cfp1(fl/fl) Rag1(-/-) biol combined

description:
Library name: CTCF AB CUT_Tag Pro-B cell Cfp1(fl/fl) Rag1(-/-) biol combined
BAM files of biological replicates were merged and then converted into bigWig format via bamCoverage.


title: Pol II AB CUT&Tag Pro-B cell Cfp1(fl/fl) Rag1(-/-) biol rep2

description: Library name: Pol II AB CUT_Tag Pro-B cell Cfp1(fl/fl) Rag1(-/-) biol rep2


title: NSC H9 rep3

description: Library name: NSC_H9_rep3

value: Neural Stem Cell

value: CHIR+LIF


title: NSC H9 rep2

description: Library name: NSC_H9_rep2


title: H3K4me3 AB CUT&Tag Pro-B cell Cfp1(fl/fl) Mb1-Cre Rag1(-/-) biol combined

description:
Library name: H3K4me3 AB CUT_Tag Pro-B cell Cfp1(fl/fl) Mb1-Cre Rag1(-/-) biol combined
BAM files of biological replicates were merged and then converted into bigWig format via bamCoverage.

value: bone marrow

value: Pro-B cells (CD19+CD43+)


title: NSC H9 rep1

description: Library name: NSC_H9_rep1


title: ANSC H9 rep3

description: Library name: ANSC_H9_rep3

value: CHIR+TTNPB


title: Pol II AB CUT&Tag Pro-B cell Cfp1(fl/fl) Rag1(-/-) biol rep1

description: Library name: Pol II AB CUT_Tag Pro-B cell Cfp1(fl/fl) Rag1(-/-) biol rep1

value: Cfp1(fl/fl) Rag1(-/-)


title: ANSC H9 rep2

description: Library name: ANSC_H9_rep2


title: ANSC H9 rep1

description: Library name: ANSC_H9_rep1


title: H3K4me3 AB CUT&Tag Pro-B cell Cfp1(fl/fl) Mb1-Cre Rag1(-/-) biol rep2

description: Library name: H3K4me3 AB CUT_Tag Pro-B cell Cfp1(fl/fl) Mb1-Cre Rag1(-/-) biol rep2

value: Cfp1(fl/fl) Mb1-Cre Rag1(-/-)


title: H3K4me3 AB CUT&Tag Pro-B cell Cfp1(fl/fl) Rag1(-/-) biol combined

description:
Library name: H3K4me3 AB CUT_Tag Pro-B cell Cfp1(fl/fl) Rag1(-/-) biol combined
BAM files of biological replicates were merged and then converted into bigWig format via bamCoverage.


title: PSC_H9_rep1

description: Library name: PSC_H9_rep1

data_processing:
Trimmed paired-end reads were mapped to a human GRCh38 genome reference genome with bowtie2 (parameter --very-sensitive).
Deduplication and read indexing: samtools (v1.10)
Normalized Coverage Computation: deepTools bamCoverage (v3.5.1)
Peak Calling: MACS2 (v3.0.0), parameters --scale-to-small --format BAMPE
Differential Peak Calling: DiffBind
Assembly: GRCh38
Supplementary files format and content: ANSC_H9_rep1.bw, bigWig,  normalised peaks per sample
Supplementary files format and content: ANSC_H9_rep2.bw, bigWig,  normalised peaks per sample
Supplementary files format and content: NSC_H9_rep1.bw, bigWig,  normalised peaks per sample
Supplementary files format and content: NSC_H9_rep2.bw, bigWig,  normalised peaks per sample
Supplementary files format and content: PSC_H9_rep1.bw, bigWig,  normalised peaks per sample
Supplementary files format and content: PSC_H9_rep2.bw, bigWig,  normalised peaks per sample

extract_protocol:
Utilizing the Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme TD711) for cell lysis and DNA extraction, cells were first digested with 0.25% trypsin at room temperature, then collected and counted. A total of 100,000 cells were resuspended in 50 μl of pre-chilled TW Buffer and centrifuged at 4°C, 2,300 rpm for 5 minutes, after which the supernatant was discarded. This washing process was repeated twice. The cells were then resuspended in 50 μl of pre-chilled Lysis Buffer, placed on ice for 5 minutes, and centrifuged again at 4°C, 2,300 rpm for 10 minutes, with the supernatant discarded. To each sample, 50 μl of pre-chilled Fragmentation Mix was added, and the mixture was gently pipetted 10 times to ensure homogeneity. The samples were then incubated at 37°C for 30 minutes. Post-reaction, the EP tubes were briefly centrifuged, and the contents were gently mixed by pipetting and transferred to a 200 μl PCR tube. Immediately after transfer, 5 μl of Stop Buffer was added to each sample, mixed gently by pipetting 10 times, and allowed to stand at room temperature for 5 minutes. The magnetic beads were equilibrated to room temperature, vortexed to mix the ATAC DNA Extract Beads, and 100 μl was added to 55 μl of the terminated sample, mixed thoroughly by pipetting 10 times, and incubated at room temperature for 5 minutes. The reaction tubes were briefly centrifuged and placed on a magnetic stand to separate the magnetic beads from the liquid, and the supernatant was carefully removed after approximately 5 minutes of clarification. The magnetic beads were washed twice with 200 μl of freshly prepared 80% ethanol, incubated at room temperature for 30 seconds, and the supernatant was carefully removed. The reaction tubes were kept on the magnetic stand and air-dried with the lid open for approximately 5 minutes. The tubes were then removed from the magnetic stand, and 26 μl of Nuclease-free ddH2O was added to elute the DNA, mixed thoroughly by pipetting 10 times, and incubated at room temperature for 5 minutes. Finally, the tubes were briefly centrifuged and placed on the magnetic stand to separate the magnetic beads from the liquid, and after approximately 5 minutes of clarification, 24 μl of the supernatant was carefully transferred to a new sterile PCR tube for direct proceeding to the next PCR amplification step.
The ATAC DNA Clean Beads were vortexed thoroughly, and 33 µl (0.55×) was transferred to 60 µl of PCR product. The mixture was homogenized by vortexing or pipetting 10 times and incubated at room temperature for 5 min. The reaction tube was briefly centrifuged and placed on a magnetic stand to separate the beads from the solution. After the supernatant cleared (~5 min), 88 µl of the supernatant (supernatant volume = total volume 93 µl – 5 µl) was carefully transferred to a new sterile PCR tube, and the beads were discarded. The ATAC DNA Clean Beads were vortexed again, and 72 µl (1.2×) was added to the supernatant, followed by thorough mixing via vortexing or pipetting 10 times and incubation at room temperature for 5 min. The tube was briefly centrifuged and placed on the magnetic stand until the solution cleared (~5 min), after which the supernatant was removed. While keeping the tube on the magnetic stand, the beads were washed twice with 200 µl of freshly prepared 80% ethanol, incubating for 30 sec each time before carefully removing the supernatant. The tube remained on the magnetic stand with the lid open for ~5 min to air-dry the beads. The tube was then removed from the stand, and 22 µl of nuclease-free ddH₂O was added for elution. The mixture was vortexed or pipetted 10 times to ensure complete resuspension and incubated at room temperature for 5 min. After brief centrifugation and placement on the magnetic stand, the cleared supernatant (~5 min) was collected, and 20 µl of the eluate was transferred to a new sterile PCR tube for storage at –30 to –15°C.

value: pluripotent stem cell


title: H3K4me3 AB CUT&Tag Pro-B cell Cfp1(fl/fl) Rag1(-/-) biol rep2

description: Library name: H3K4me3 AB CUT_Tag Pro-B cell Cfp1(fl/fl) Rag1(-/-) biol rep2


title: Pol II AB CUT&Tag Pro-B cell Cfp1(fl/fl) Mb1-Cre Rag1(-/-) biol rep1

description: Library name: Pol II AB CUT_Tag Pro-B cell Cfp1(fl/fl) Mb1-Cre Rag1(-/-) biol rep1


title: H3K4me3 AB CUT&Tag Pro-B cell Cfp1(fl/fl) Rag1(-/-) biol rep1

description: Library name: H3K4me3 AB CUT_Tag Pro-B cell Cfp1(fl/fl) Rag1(-/-) biol rep1


title: H3K4me3 AB CUT&Tag Pro-B cell Cfp1(fl/fl) Rag1(-/-) biol rep3

description: Library name: H3K4me3 AB CUT_Tag Pro-B cell Cfp1(fl/fl) Rag1(-/-) biol rep3


title: NSC_H9_rep1

description: Library name: NSC_H9_rep1


title: NSC_H9_rep2

description: Library name: NSC_H9_rep2


title: PSC_H9_rep2

description: Library name: PSC_H9_rep2


description: Library name: 4C-Seq iEm Pro-B cell Cfp1(fl/fl) Mb1-Cre Rag1(-/-) biol rep3

data_processing:
Libraries were normalized by randomly selecting the number of junctions matching the smallest library. BEDTools (v2.27.1) was used to convert junction coordinates to bedGraph format for visualization in IGV.
For joins analysis, we used the standard HTGTS sequencing pipeline provided by Frederick W. Alt Lab, which is available at GitHub (https://robinmeyers.github.io/transloc_pipeline/thedocs.html). Linear amplification-mediated (LAM)-HTGTS pipeline was used for generating processed files with "tlx" ends.
Assembly: mm9
Supplementary files format and content: bedGraph file
Supplementary files format and content: tab delimited text files contain filtered junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); the entire stitched paired end read sequence (Seq); the junction sequence(J_seq)
Library strategy: 4C-Seq

extract_protocol:
4C-HTGTS assays combined chromosome conformation capture via Low-input Capture-C teachniques (Oudelaar et al., 2017) with library preparation via HTGTS (Ba et al., 2020; Dong et al., 2015; Hu et al., 2016). Briefly, 12 × 10^4 FACS-sorted pro-B cells were collected, crosslinked with 2% formaldehyde (Sigma-Aldrich, F8775) for 10 min at room temperature and then quenched with glycine at a final concentration of 125 mM. The crosslinked cells were lysed in 0.5 ml of Lysis buffer (10mM Tris-HCl pH 8.0, 10 mM Nacl, 0.2% NP-40, 1 × protease inhibitors) and nuclei were digested with 9 μl of NlaIII enzyme (New England Biolabs, R0125L) in 191 μl of Digestion Mix buffer (1 × CutSmart Buffer, 0.29 % SDS, 1.68% Triton X-100) for 2 h at 37°C. An additional 7 μl of NlaIII enzyme was added for further digestion overnight at 37°C. After digestion, 100 U of T4 ligase (Thermo Scientific, EL0011) was added, and the reaction was incubated overnight at 16°C. The ligated DNA was de-crosslinked and purified.
0.5 μg of genomic DNA extracted from FACS-sorted pro-B cells (CD19+CD43+) was sonicated into fragments ranging from 300 to1000 bp using M220 Focused-ultrasonicator (Covaris), and amplified by LAM-PCR with biotin-conjugated iEμ bait primers. Biotinylated PCR products were captured by Dynabeads MyOne streptavidin C1 beads (Invitrogen, 65002) and ligated with bridge adapters on-bead. The ligated products were amplified by nested PCR using barcode primers, followed by a third round of PCR using P5-I5 and P7-I7 primers. were purified by gel separation and sequenced on the Illumina NovaSeq platform with 150 bp paired-end reads.


title: shNC_3, Day 7 CD8+ P14 T cells

city: Wuhan

first: Huafeng

last: Zhang

address: Hangkong Road #13

institute: Huazhong University of Science and Technology

description: Library name: noxPPP_shNC_3_lib

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
Assembly: GRCm39_release110（https://ftp.ensembl.org/pub/release-110/fasta/mus_musculus/dna/）

source_name: Spleen

extract_protocol:
Total RNA was extracted from CD8+ P14 T cells using RNeasy Mini Kit (Qiagen). mRNA was purified using oligo(dT) magnetic beads for poly(A) selection.
2 μg total RNAs were used for stranded RNA sequencing library preparation using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. The kit eliminates duplication bias in PCR and sequencing steps, by using unique molecular identifier (UMI) of 8 random bases to label the pre-amplified cDNA molecules. The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on DNBSEQ-T7 sequencer (MGI Tech Co., Ltd. China) with PE150 model.

treatment_protocol: CD8+P14 T cells were sorted from spleens of LCMV-Arm infected mice on 7 dpi.

value: Spleen

value: CD8+ P14 T cells

value: shNC


title: shTkt_1, Day 7 CD8+ P14 T cells

description: Library name: noxPPP_shTkt_1_lib

value: shTkt


title: shTkt_3, Day 7 CD8+ P14 T cells

description: Library name: noxPPP_shTkt_3_lib


title: shNC_2, Day 7 CD8+ P14 T cells

description: Library name: noxPPP_shNC_2_lib


description: Library name: 4C-Seq iEm Pro-B cell Cfp1(fl/fl) Mb1-Cre Rag1(-/-) biol rep2


description: Library name: 4C-Seq iEm Pro-B cell Cfp1(fl/fl) Mb1-Cre Rag1(-/-) biol rep1


title: shNC_1, Day 7 CD8+ P14 T cells

description: Library name: noxPPP_shNC_1_lib


title: ANSC_H9_rep1

description: Library name: ANSC_H9_rep1


title: H3K4me3 AB CUT&Tag Pro-B cell Cfp1(fl/fl) Mb1-Cre Rag1(-/-) biol rep1

description: Library name: H3K4me3 AB CUT_Tag Pro-B cell Cfp1(fl/fl) Mb1-Cre Rag1(-/-) biol rep1


title: ANSC_H9_rep2

description: Library name: ANSC_H9_rep2


title: PSC_ATAC-seq_rep2

description: Library name: PSC_rep2

data_processing:
Trimmed paired-end reads were mapped to a human GRCh38 genome reference genome with bowtie2 (parameter --very-sensitive).
Deduplication and read indexing: samtools (v1.10)
Normalized Coverage Computation: deepTools bamCoverage (v3.5.1)
Peak Calling: MACS2 (v3.0.0), parameters --scale-to-small --format BAMPE
Differential Peak Calling: DiffBind
Assembly: GRCh38
Supplementary files format and content: *bw, bigWig,  normalised peaks per sample


title: Cultured Pro-B cell Input

description: Library name: Cultured Pro-B cell Input

data_processing:
Raw sequenced reads were  trimmed for adapter sequences and quality filtered using Trim Galore (v20.04.6), and aligned to the GRCm38 (mm10) reference genome using BWA-MEM (v0.7.17). SAM files were converted and sorted into BAM format using Samtools (v1.10). Duplicate reads in the BAM files were marked and removed with Picard MarkDuplicates (v3.3.0). Deeptools (v3.5.1) was used for converting the sorted BAM files into bigWig format via bamCoverage with parameters --binSize 10 --normalizeUsing RPKM.
Assembly: mm10
Supplementary files format and content: bigWig file

growth_protocol: Cfp1f/fRag1-/- pro-B cells were cultured with 10 ng/ml IL-7 and 10 ng/ml SCF for 4 days.

extract_protocol:
ChIP assays were performed using the Sonication ChIP Kit (ABclonal, RK20258) according to the manufacturer’s protocol with minor modifications. 500 × 10^4 cultured pro-B cells (CD19+CD43+) were cross-linked with 1% formaldehyde (Sigma-Aldrich, F8775) for 10 min at room temperature and then quenched with glycine at a final concentration of 125 mM. After two washes with cold PBS, the cell pellets were frozen with liquid nitrogen and stored at -80°C overnight. The crosslinked cells were lysed in 500 μl of Cell Swelling Buffer and then digested by 2.5 U of MNase (Thermo Scientific, EN0181) in 250 μl of 1 × MNase reaction buffer (New England Biolabs, B0247SVIAL). The digestion was stopped by adding 25 μl of 0.5 M EDTA (pH8.0). The nuclei ware resuspended in 500 μl of ChIP Sonication Buffer and sonicated using a VCX 130 sonicator (Sonics) with a 3 mm microtip probe to shear chromatin into 300-500 bp fragments. 2.5% of samples was used as input and the remainder was incubated with 5 μg of anti-CFP1 (Abcam, ab198977) antibody at 4°C for 3 h, followed by incubated with 30 μl of Protein A/G Magnetic Beads (MedChemExpress, HY-K0202) at 4°C for 2 h. After incubation, the beads were washed sequentially with low salt wash buffer, high salt wash buffer, LiCl wash buffer and 1 × TE buffer. Immunoprecipitation (IP) DNA was de-crosslinked and purified using phenolchloroform.
Libraries were prepared using VAHTS Universal DNA library prep kit for Illumina (Vazyme, ND607) according to the manufacturer’s instructions.


description:
Library name: CFP1 AB ChIP-Seq Pro-B cell Cfp1(fl/fl) Rag1(-/-) biol combined
BAM files of biological replicates were merged and then converted into bigWig format via bamCoverage.


description: Library name: 4C-Seq iEm Pro-B cell Cfp1(fl/fl) Rag1(-/-) biol rep3


title: shTkt_2, Day 7 CD8+ P14 T cells

description: Library name: noxPPP_shTkt_2_lib


description: Library name: CFP1 AB ChIP-Seq Pro-B cell Cfp1(fl/fl) Rag1(-/-) biol rep4


description: Library name: CFP1 AB ChIP-Seq Pro-B cell Cfp1(fl/fl) Rag1(-/-) biol rep2


title: PSC_ATAC-seq_rep1

description: Library name: PSC_rep1


description: Library name: 4C-Seq iEm Pro-B cell Cfp1(fl/fl) Rag1(-/-) biol rep2


title: NSC_ATAC-seq_rep2

description: Library name: NSC_rep2


description: Library name: CFP1 AB ChIP-Seq Pro-B cell Cfp1(fl/fl) Rag1(-/-) biol rep1


description: Library name: CFP1 AB ChIP-Seq Pro-B cell Cfp1(fl/fl) Rag1(-/-) biol rep3


title: NSC_ATAC-seq_rep1

description: Library name: NSC_rep1


title: H3K4me3 AB CUT&Tag Macrophage WT biol rep2

description: Library name: H3K4me3 AB CUT_Tag Macrophage WT biol rep2

value: WT


title: H3K4me3 AB CUT&Tag Macrophage WT biol rep3

description: Library name: H3K4me3 AB CUT_Tag Macrophage WT biol rep3


title: ANSC_ATAC-seq_rep2

description: Library name: ANSC_rep2


title: ANSC_ATAC-seq_rep1

description: Library name: ANSC_rep1


title: H3K4me3 AB CUT&Tag CMP WT biol rep2

description: Library name: H3K4me3 AB CUT_Tag CMP WT biol rep2


title: 13 week spinal cord.  AR-97Q, AR-ASO rep2

city: Nagoya

first: Tomoki

last: Hirunagi

state: Aichi

address: 65 Tsurumai-cho, Showa-ku

department: Neurology

country: Japan

institute: Nagoya University GraduateSchool of Medicine

description:
Library name: 13wkARASO-02
ARASO_13week.txt.gz

data_processing:
Overall reads’ quality, total bases, total reads, GC (%) and basic statistics are calculated by FastQC and trimmed by Trimmomatic software.
Trimmed reads are mapped to reference genome with HISAT2.
Transcript is assembled by StringTie with aligned reads, and expression profiles are represented as TPM.
Assembly: mm10
Supplementary files format and content: text files include TPM values for each sample

source_name: Spinal cord

extract_protocol:
Total RNA was extracted from the spinal cord of WT and AR-97Q mice the RNeasy Mini Kit (QIAGEN). The quality and quantity of the RNA obtained were checked using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific) and analyzed with the Agilent 2100 Bioanalyzer system (Agilent Technologies Inc., Santa Clara, CA).
A library was independently prepared with 1ug of total RNA for each sample by Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina, Inc.).

treatment_protocol: AR-ASO or Rest4-ASO were intracerebroventricularly injected to AR-97Q mice at postnatal day 1 (P1).

value: Spinal cord

value: AR-ASO


title: 13 week spinal cord.  AR-97Q, AR-ASO rep1

description:
Library name: 13wkARASO-01
ARASO_13week.txt.gz


title: H3K4me3 AB CUT&Tag Macrophage WT biol rep1

description: Library name: H3K4me3 AB CUT_Tag Macrophage WT biol rep1


title: H3K4me3 AB CUT&Tag CMP WT biol rep3

description: Library name: H3K4me3 AB CUT_Tag CMP WT biol rep3


title: H3K4me3 AB CUT&Tag Mature B cell WT biol rep2

description: Library name: H3K4me3 AB CUT_Tag Mature B cell WT biol rep2

source_name: spleen

value: spleen

value: Mature B cells (CD19+CD43-CD3e-)


title: H3K4me3 AB CUT&Tag Mature B cell WT biol rep1

description: Library name: H3K4me3 AB CUT_Tag Mature B cell WT biol rep1


title: H3K4me3 AB CUT&Tag CMP WT biol rep1

description: Library name: H3K4me3 AB CUT_Tag CMP WT biol rep1


title: H3K4me3 AB CUT&Tag Mature B cell WT biol rep3

description: Library name: H3K4me3 AB CUT_Tag Mature B cell WT biol rep3


title: 13 week spinal cord.  AR-97Q, AR-ASO rep3

description:
Library name: 13wkARASO-03
ARASO_13week.txt.gz


title: P21OIR

city: Guangzhou

first: Yuan

last: Ma

address: No.7 Jinsui road

department: Zhongshan Ophthalmic Center

institute: Sun Yat-sen University

description: 10x Genomics

data_processing:
Cellranger was used to align the reads to the mouse reference genome and compute gene expression.
Assembly: mm11
Supplementary files format and content: Tab-separated values files and matrix files

source_name: retina

extract_protocol:
OIR mice models and normoxia  (NOX) mice at two different time points (P17 and P21) were chosen and sacrificed by an overdose of anesthetic (1% pentobarbital sodium 20 mL/kg). 12 retinas of 6 mice from each group were collected and cut into small pieces before being incubated in a 3 mL enzymatic hydrolysis system containing 2 mg/mL papain, 1 mg/mL collagenase, Type I, and 1 mg/mL DNase I. After enzymatic digestion at 37°C for 15min, single-cell suspensions were obtained and then filtered through a 30-μm filter and cytocentrifugated in 300 ×g for 7min at 4°C. According to the protocol of magnetic-activated cell sorting (MACS) Separation, the cells were resuspended with 180 μL MACS buffer (0.01 mM EDTA + 0.04% BSA + 1×PBS) and incubated with 20 μL CD11b Microbeads at 4°C for around 15min. Subsequently, CD11b+ cells were isolated and enriched after passing through the MACS sorting column.
The CD11b+ cells were then used for the generation of single-cell gel bead-in-emulsion (GEM). ScRNA-seq libraries were constructed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 according to the manufacturer’s instructions and sequenced on the Illumina NovaSeq 6000 platform.

value: retina

value: hyperoxia chamber (P7-P12)


title: ANSC_RNA-seq_rep2

description:
Library name: CT_rep2
CT-b

data_processing:
Adaptor sequences and low-quality base calls were trimmed using fastp with default parameters.
Trimmed reads were aligned to the Human reference genome (GRCh38) using STAR v2.7.7a in paired-end mode with default parameters
Gene level counts were generated using FeatureCounts from Subread v2.0.
Assembly: GRCh38
Supplementary files format and content: comma-separated csv file include count value of each sample

value: Neural Stem Cell

value: wildtype


title: H3K4me3 AB CUT&Tag Pre-B cell WT biol rep1

description: Library name: H3K4me3 AB CUT_Tag Pre-B cell WT biol rep1

value: bone marrow

value: Pre-B cells (CD19+c-Kit-CD25+)


title: P17OIR

description: 10x Genomics


title: ANSC_RNA-seq_rep1

description:
Library name: CT_rep1
CT-a

value: CHIR+TTNPB


title: H3K4me3 AB CUT&Tag Pre-B cell WT biol rep2

description: Library name: H3K4me3 AB CUT_Tag Pre-B cell WT biol rep2


description: Library name: 4C-Seq iEm Pro-B cell Cfp1(fl/fl) Rag1(-/-) biol rep1

value: Pro-B cells (CD19+CD43+)

value: Cfp1(fl/fl) Rag1(-/-)


title: H3K4me3 AB CUT&Tag Pre-B cell WT biol rep3

description: Library name: H3K4me3 AB CUT_Tag Pre-B cell WT biol rep3


title: ANSC_RNA-seq_rep3

description:
Library name: CT_rep3
CT-c


title: EXOSC10-AS1-siRNA 2#-3

city: weifang

first: Jiaqiu

last: Li

address: Baotong west street No.7166

institute: shandong second medical university

description:
Library name: siRNA 2-3
Column name in raw count siRNA2#

data_processing:
The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
The cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA).
After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min.
The average insert size for the final cDNA librarys were 300±50 bp.
At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.
Assembly: HG19
Supplementary files format and content: The Excel file contains raw counts for each gene and each sample.

source_name: HCT116 cell

growth_protocol: HCT116 was cultured in McCOY’s 5A medium supplemented with 10% bovine serum at 37ºC with 5% CO2.

extract_protocol:
After EXOSC10-AS1 knockdown, total RNA was isolated using Trizol reagent. Trizol extraction of total RNA was performed according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: HCT116 cell was transfected with EXOSC10-AS1 specific small interfering RNA (siRNA) using Lipofectamine RNAiMax (Invitrogen).

value: HCT116 cell

value: colorectal cancer cell

value: EXOSC10-AS1 knockdown

value: EXOSC10-AS1 siRNA2#

value: Day 3


title: H3K4me3 AB CUT&Tag CLP WT biol rep3

description: Library name: H3K4me3 AB CUT_Tag CLP WT biol rep3

value: CLP (Lin-IL-7Ra+Flt3+)

value: WT


title: P21NOX

description: 10x Genomics

value: room air


title: H3K4me3 AB CUT&Tag Pro-B cell WT biol rep1

description: Library name: H3K4me3 AB CUT_Tag Pro-B cell WT biol rep1

value: Pro-B cells (CD19+c-Kit+CD25-)


title: EXOSC10-AS1-siRNA 2#-2

description:
Library name: siRNA 2-2
Column name in raw count siRNA2#


title: P17NOX

description: 10x Genomics

value: retina


title: P7 spinal cord, AR-97Q, Rest4ASO, rep3

value: Spinal cord


title: H3K4me3 AB CUT&Tag Pro-B cell WT biol rep3

description: Library name: H3K4me3 AB CUT_Tag Pro-B cell WT biol rep3


title: H3K4me3 AB CUT&Tag Pro-B cell WT biol rep2

description: Library name: H3K4me3 AB CUT_Tag Pro-B cell WT biol rep2


title: H3K4me3 AB CUT&Tag CLP WT biol rep2

description: Library name: H3K4me3 AB CUT_Tag CLP WT biol rep2


title: EXOSC10-AS1-siRNA 1#-3

description:
Library name: siRNA 1-3
Column name in raw count siRNA1#

value: EXOSC10-AS1 siRNA1#


title: Pro-B cell Input

description: Library name: Pro-B cell Input

extract_protocol:
ChIP assays were performed using the Sonication ChIP Kit (ABclonal, RK20258) according to the manufacturer’s protocol with minor modifications. Briefly, 200 × 10^4 FACS-sorted pro-B cells (CD19+CD43+) were cross-linked with 1% formaldehyde (Sigma-Aldrich, F8775) for 10 min at room temperature and then quenched with glycine at a final concentration of 125 mM. The crosslinked cells were lysed in 200 μl of Cell Swelling Buffer and then digested by 1 U of MNase (Thermo Scientific, EN0181) in 100 μl of 1 × MNase reaction buffer (New England Biolabs, B0247SVIAL). The digestion was stopped by adding 10 μl of 0.5 M EDTA (pH8.0). The nuclei ware resuspended in 500 μl of ChIP Sonication Buffer and sonicated using a VCX 130 sonicator (Sonics) with a 3 mm microtip probe to shear chromatin into 300-500 bp fragments. 2.5% of samples was used as input and the remainder was incubated with 10 μl of anti-RAG2 (ABClonal, A12488) antibody at 4°C for 3 h, followed by incubated with 30 μl of Protein A/G Magnetic Beads (MedChemExpress, HY-K0202) at 4°C for 2 h. After incubation, the beads were washed sequentially with low salt wash buffer, high salt wash buffer, LiCl wash buffer and 1 × TE buffer. Immunoprecipitation (IP) DNA was de-crosslinked and purified using phenolchloroform.
Libraries were prepared using VAHTS Universal DNA library prep kit for Illumina (Vazyme, ND607) according to the manufacturer’s instructions.

value: bone marrow


description:
Library name: RAG2 AB ChIP-Seq Pro-B cell Cfp1(fl/fl) Mb1-Cre Rag1(-/-) biol combined
BAM files of biological replicates were merged and then converted into bigWig format via bamCoverage.

value: Cfp1(fl/fl) Mb1-Cre Rag1(-/-)


title: EXOSC10-AS1-siRNA 2#-1

description:
Library name: siRNA 2-1
Column name in raw count siRNA2#


title: P7 spinal cord, AR-97Q, Rest4ASO, rep1


description:
Library name: RAG2 AB ChIP-Seq Pro-B cell Cfp1(fl/fl) Rag1(-/-) biol combined
BAM files of biological replicates were merged and then converted into bigWig format via bamCoverage.


title: EXOSC10-AS1-siRNA 1#-1

description:
Library name: siRNA 1-1
Column name in raw count siRNA1#


description: Library name: RAG2 AB ChIP-Seq Pro-B cell Cfp1(fl/fl) Mb1-Cre Rag1(-/-) biol rep1


description: Library name: RAG2 AB ChIP-Seq Pro-B cell Cfp1(fl/fl) Mb1-Cre Rag1(-/-) biol rep2


title: EXOSC10-AS1-siRNA 1#-2

description:
Library name: siRNA 1-2
Column name in raw count siRNA1#


description: Library name: RAG2 AB ChIP-Seq Pro-B cell Cfp1(fl/fl) Rag1(-/-) biol rep2


title: P7 spinal cord, AR-97Q, scrambleASO, rep3

value: Scramble-ASO


title: P7 spinal cord, AR-97Q, scrambleASO, rep1


title: P7 spinal cord, AR-97Q, scrambleASO, rep2


description: Library name: RAG2 AB ChIP-Seq Pro-B cell Cfp1(fl/fl) Rag1(-/-) biol rep1

value: Pro-B cells (CD19+CD43+)


title: H3K4me3 AB CUT&Tag CLP WT biol rep1

description: Library name: H3K4me3 AB CUT_Tag CLP WT biol rep1


title: TAE-2

city: Suzhou

last: Jiang

address: No. 899, Pinghai Road, Gusu District

department: Department of Interventional Radiology

institute: The First Affiliated Hospital of Soochow University

description:
Library name: TAE-2
The experimental group underwent transarterial embolization, replicate biosample 2

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to DM 1-3 516 R44 (v6.1)  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mRatBN7.2
Supplementary files format and content: tab-delimited text file includes gene counts and fpkm for each sample

organism: Rattus norvegicus

source_name: liver

extract_protocol:
RNA was extracted from tissue using TRIzol reagent. Briefly, cells were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA (1 µg, RIN >7) was enriched for mRNA using poly(A) selection (for eukaryotes) or rRNA depletion (for prokaryotes). The RNA was fragmented (∼200–300 nt) and reverse-transcribed into cDNA using random hexamers and SuperScript IV. Second-strand synthesis was performed with dUTP incorporation (strand-specific libraries). The cDNA was end-repaired, A-tailed, and ligated to Illumina-compatible adapters. Post-ligation cleanup (AMPure XP beads) was followed by size selection (200–500 bp) and uracil digestion (for strand specificity). Library amplification (8–12 cycles) used indexed primers, and final quantification (Qubit) and quality control (Bioanalyzer/TapeStation) ensured optimal fragment size (∼300 bp) and concentration (>10 nM). Libraries were pooled and sequenced (Illumina platforms, 150 bp paired-end).

value: liver


title: 13 week spinal cord, AR-97Q, rep3


title: TAE-1

description:
Library name: TAE-1
The experimental group underwent transarterial embolization, replicate biosample 1


title: HCC-3

description:
Library name: HCC-3
the control group received no treatment, replicate biosample 3


title: TAE-3

description:
Library name: TAE-3
The experimental group underwent transarterial embolization, replicate biosample 3


title: NC-1

description:
Library name: NC-1
Column name in raw count NC

value: HCT116 cell

value: Control

value: control siRNA


title: P7 spinal cord, AR-97Q, Rest4ASO, rep2


title: Human PSC derived cardiomyocytes, doxorubicin treatment, replicate 3

city: Kyoto

first: Tomoya

last: Kitani

address: 465 Kajii-cho Kawaramachi-Hirokoji Kamigyo-ku

institute: Kyoto Prefectural University of Medicine

data_processing:
Raw FASTQ data were quantified and mapped onto the reference genome of GRCh38 using STAR software.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw count for each Sample

extract_protocol:
Total RNA was extracted from human PSC-CMs 24 h after treatment with 1 μM DOX using Direct-zol RNA MiniPrep (ZYMO Research), according to the manufacturer’s protocol.
Library preparation was performed using a TruSeq-stranded mRNA sample prep kit (Illumina), according to the manufacturer’s instructions.

value: pluripotent derived cardiomyocytes

value: doxorubicin


title: HCC-2

description:
Library name: HCC-2
the control group received no treatment, replicate biosample 2


title: 13 week spinal cord, AR-97Q, rep2


title: GZM-3

description:
Library name: GZM-3
the ZnS microsphere embolization group, replicate biosample 3


title: NC-3

description:
Library name: NC-3
Column name in raw count NC

value: colorectal cancer cell

value: Day 3


title: NC-2

description:
Library name: NC-2
Column name in raw count NC


title: GZM-1

description:
Library name: GZM-1
the ZnS microsphere embolization group, replicate biosample 1


title: Human PSC derived cardiomyocytes, doxorubicin treatment, replicate 2

value: WT


title: HCC-1

description:
Library name: HCC-1
the control group received no treatment, replicate biosample 1


title: GZM-2

description:
Library name: GZM-2
the ZnS microsphere embolization group, replicate biosample 2


title: 13 week spinal cord, WT, rep3


title: GM-3

description:
Library name: GM-3
the blank microsphere embolization group (control), replicate biosample 3


title: GM-2

description:
Library name: GM-2
the blank microsphere embolization group (control), replicate biosample 2


title: GM-1

description:
Library name: GM-1
the blank microsphere embolization group (control), replicate biosample 1


title: 13 week spinal cord, WT, rep2


title: primary_tumor3

city: Rehovot

first: Marina

last: Kizner

address: 234 Herzel st.

country: Israel

institute: Weizmann Institute of Science

description: Library name: primary_tumor3

data_processing:
Analysis was performed using the bioinformatics analysis pipeline User Friendly Transcriptomic Analysis Pipeline (UTAP) version 2.0
Reads were trimmed using cutadapt v4.1 (parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a “A{10}” -a “T{10}” -A “A{10}” -A “T{10}” –times 2 -q 20 -m 25)
Custom mouse genome (mm10) with Gencode annotations was supplemented with a chicken Ovalbumin and mCherry genes. Reads were mapped to the custom genome using STAR  v2.7.10a (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic).
Read counting was performed using STAR v2.7.10a
Counts normalization was performed using DESeq2 v1.36.0 with the parameters: betaPrior=True, cooksCutoff=FALSE, independentFiltering=FALSE.
Assembly: mm10
Supplementary files format and content: excel file include DESeq2 normalized values for each sample

source_name: Mammary fat pad tumor

extract_protocol:
106 OVA-RFP E0771 cells were introduced i.v., and 3 days later fluorescent cells were sorted from whole lungs using FACS Aria III Cell Sorter. Cells were collected in the presence of Actinomycin D (Sigma-Aldrich, cat. A1410) in order to minimize ex vivo RNA transcription. RNA was purified from the sorted cells using the QIAGEN Rneasy kit. A second experimental group consisted of 103 OVA- RFP E0771 cells implanted in mammary fat pads to generate primary tumors. Cells from primary tumors were similarly isolated and sorted on day 14 post implantation.
Libraries were prepared using a modified SMART-Seq2 (33). RNA lysate clean-up was performed using RNAClean XP beads (Agencourt), followed by reverse transcription with Maxima Reverse Transcriptase (Life Technologies) and wholetranscription amplification (WTA) with KAPA HotStart HIFI 2 × ReadyMix (Kapa Biosystems) for 18 cycles. WTA products were purified with Ampure XP beads (Beckman Coulter), quantified with Qubit dsDNA HS Assay Kit (ThermoFisher) and assessed with a high-sensitivity DNA chip (Agilent). RNA-seq libraries were constructed from purified WTA products using Nextera XT DNA Library Preperation Kit (Illumina). The libraries were sequenced on an Illumina NextSeq 500/550.

value: Mammary fat pad tumor

value: E0771 RFP-OVA

value: B-luminal-like cancer cell


title: 13 week spinal cord, AR-97Q, rep1

value: Spinal cord


title: 13 week spinal cord, WT, rep1


title: primary_tumor1

description: Library name: primary_tumor1

growth_protocol: 106 OVA-RFP E0771 cells were introduced i.v., and 3 days later fluorescent cells were sorted from whole lungs using FACS Aria III Cell Sorter. Cells were collected in the presence of Actinomycin D (Sigma-Aldrich, cat. A1410) in order to minimize ex vivo RNA transcription.


title: P7 spinal cord, AR-97Q, AR-ASO, rep3

value: AR-ASO


title: Human PSC derived cardiomyocytes, control treatment, replicate 1

value: DMSO


title: P7 spinal cord, AR-97Q, AR-ASO, rep2


title: Human PSC derived cardiomyocytes, control treatment, replicate 2


title: Ven/aza treated BM stroma cell multiplexing oligo data (NGO7013A35)

description:
Library name: NGO7013A35
Bone marrow stroma from ven/aza-treated mice. Cell Multiplexing Oligo library, R1 contains cell barcode and UMI, R2 contains CMO
feature_reference_2.csv
Venaza_2.filtered_feature_bc_matrix.h5

library_source: other

data_processing:
FASTQ files were aligned and quantified using Cell Ranger v. 9.0.0 using CMO as additional features
Assembly: mm10, refdata-gex-mm10-2020-A from 10X Genomics
Supplementary files format and content: H5 files of multiplexed count matrices

molecule: other

value: bone marrow stroma

value: CMO

value: NBSG-S (NSG ckit41/41 with human SCF/IL3 and GM-CSF)

value: ven/aza


title: Human PSC derived cardiomyocytes, doxorubicin treatment, replicate 1


title: lung_metastasis2

description: Library name: lung_metastasis2

source_name: Murine lungs

value: Murine lungs


title: Human PSC-derived cardiomyocyte, TAOK1 KO, replicate 3

value: TAOK1 knockout


title: Vehicle treated BM stroma gene expression data (NGO7013A28)

description:
Library name: NGO7013A28
Bone marrow stroma from vehicle-treated mice. Gene expression library, R1 contains cell barcode and UMI, R2 contains transcript
feature_reference_2.csv
Vehicle_2.filtered_feature_bc_matrix.h5

value: mRNA

value: vehicle


title: Vehicle treated BM stroma cell multiplexing oligo data (NGO7013A34)

description:
Library name: NGO7013A34
Bone marrow stroma from vehicle-treated mice. Cell Multiplexing Oligo library, R1 contains cell barcode and UMI, R2 contains CMO
feature_reference_2.csv
Vehicle_2.filtered_feature_bc_matrix.h5


title: P7 spinal cord, AR-97Q, AR-ASO, rep1


title: Ven/aza treated BM stroma gene expression data (NGO7013A29)

description:
Library name: NGO7013A29
Bone marrow stroma from ven/aza-treated mice. Gene expression library, R1 contains cell barcode and UMI, R2 contains transcript
feature_reference_2.csv
Venaza_2.filtered_feature_bc_matrix.h5


title: primary_tumor2

description: Library name: primary_tumor2


title: Human PSC-derived cardiomyocyte, wild type, replicate 3

value: pluripotent derived cardiomyocytes

value: doxorubicin


title: AR-24Q_8w_spinal cord

description:
Library name: AR-24Q-8
10xGenomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v9.0.1.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: h5 files

extract_protocol:
Mice were deeply anesthetized, and the entire spinal cord were dissected and snap-frozen in powdered CO2 in liquid nitrogen. Spinal cords from 4 mice for each condition were pooled for homogenization and nuclear isolation. Fresh frozen murine spinal cord was placed in a Dounce homogenizer (Kimble Chase 2 ml Tissue Grinder) containing ice-cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Igepal and 0.2 U/μl RNase inhibitor). After homogenizing, the lysate was diluted with 1.4 mL of lysis buffer and incubated for 5 minutes. The homogenate was passed over a 70 μm strainer (Fisher Scientific). The filtered lysate was centrifuged at 500 × g for 5 min at 4 °C. After centrifugation, the pellet was resuspended in 1.5 ml lysis buffer and incubated for 3 minutes on ice. Then, the pellet was centrifuged at 500 × g for 5 minutes and resuspended in 1500 µl of wash buffer (1× PBS with 1% BSA and RNase Inhibitor). The nuclei were washed and centrifuged at 500 × g for 5 minutes three times and filtered through a 40 µm cell strainer. The cell suspensions were processed according to the debris removal solution (Milteni Biotec) protocol. Cells were resuspended in cold PBS with 0.04% BSA and stained with DAPI. The nuclei were sorted with a FACS Aria instrument (Becton Dickson) with a 100 nm nozzle and 405 nm excitation laser. These nuclei were centrifuged, inspected for appearance, and concentrated for the next step.
The nulei per sample were run on the Chromium GEM-X Single Cell Gene Expression 3' v4 platform (10x Genomics, Pleasanton, CA). DAPI-positive nuclei were immediately loaded onto a Chromium Single Cell Processor (10x Genomics) to barcode the mRNA inside each nucleus. Sequencing libraries were constructed according to the manufacturer’s instructions, and the resulting cDNA samples were run on an Agilent Bioanalyzer using the High Sensitivity DNA Chip as a quality control to determine cDNA concentrations. The samples were run on NovaSeqX Ten with 150 bp paired end to obtain ≥20,000 reads per cell. A total of 22,093 and 18,372 cells with approximately 423 million and 541 million reads were sequenced for the AR-97Q and AR-24Q samples, respectively. Reads were aligned and assigned to Ensembl mm10 transcript definitions using the Cell Ranger v9.0.1 pipeline (10x Genomics). The gene barcode matrices for each sample were imported into R (version 4.4.3) using the Read10X function in the Seurat R package (version 5.3.0).

treatment_protocol: The spinal cord samples were obtained from AR-97Q and AR-24Q mice at 8 weeks of age.

tag: age

value: 8 weeks


title: lung_metastasis1

description: Library name: lung_metastasis1


title: P7 spinal cord, AR-97Q, Rest-ASO3, rep3

description: Library name: RestASO3-03

extract_protocol:
Total RNA was extracted from the mouse spinal cord using the RNeasy Mini Kit (QIAGEN). The quality and quantity of the RNA obtained were checked using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific) and analyzed with the Agilent 2100 Bioanalyzer system (Agilent Technologies Inc., Santa Clara, CA).
A library was independently prepared with 1ug of total RNA for each sample by Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina, Inc.).

treatment_protocol: Scramble-ASO or Rest4-ASO #3 (20 mg) was intracerebroventriculary administered AR-97Q mice at P1.


title: P7 spinal cord, AR-97Q, rep2


title: AR-97Q_8w_spinal cord

description:
Library name: AR-97Q-8
10xGenomics


title: P7 spinal cord, AR-97Q, Rest-ASO3, rep2

description: Library name: RestASO3-02


title: Human PSC derived cardiomyocytes, control treatment, replicate 3

value: WT


title: Human PSC-derived cardiomyocyte, TAOK1 KO, replicate 2


title: Human PSC-derived cardiomyocyte, TAOK1 KO, replicate 1


title: P7 spinal cord, AR-97Q, rep3


title: P7 spinal cord, AR-97Q, Rest-ASO3, rep1

description: Library name: RestASO3-01


title: P7 spinal cord, AR-97Q, Scramble-ASO, rep3

description: Library name: Scramble-03

value: Scramble-ASO


title: P7 spinal cord, AR-97Q, Scramble-ASO, rep2

description: Library name: Scramble-02


title: P7 spinal cord, AR-24Q, rep 3

description: Library name: AR24Q-03

value: NT


title: K562, lymphoblast, myelogenous leukemia, siGMNN (Geminin siRNA), FANCD2 (ChIP), Replicate 2

city: Seville

first: Andrés

last: Aguilera

address: Av. Américo Vespucio 24

department: Genome BIology

country: Spain

institute: CABIMER, Universidad de Sevilla

description: Library name: K562_siGMNN, Replicate 2, ChIP

data_processing:
Basecalling, quality control filtering, demultiplexing and adapter trimming were performed using the BaseSpace Seq Hub from Illumina.
ChIP-seq reads were mapped to the canonical version of human reference genome hg38 (H. sapiens, GRCh38 no-alt analysis set; https://bowtie-bio.sourceforge.net/bowtie2/manual.shtml) and PCR duplicates removed with SAMtools. Only properly-paired primary alignments with a mapping quality (MAPQ) > 20 were retained for downstream analysis.
To create ChIP-seq coverage plots and visualize data in the genome browser, ChIP-seq data was RPKM-normalized and formatted in bigwig format using deepTools. Coverage plots and analysis were also performed using deepTools package.
Peak calling was performed with MACS2 package allowing broad peak identification (--broad) and setting p-value and broad cutoffs < 0.05. Biological replicates were then intersected using BEDtools and only peaks detected in both biological replicates considered for further analysis. Comparative peak analysis was conducted using BEDtools to determine condition-specific peaks (only appearing in one condition).
Assembly: hg38
Supplementary files format and content: bigwig, bed

source_name: bone narrow

growth_protocol: RPMI, 10% Fetal Bovine Serum, 2mM Glutamine, 1x Penicilin/Streptomycin. Cells were cultured at 37ºC and 5%CO2 supply

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes and then quenched with 200mM glycine. After cell lysis, chromatin was sonicated using a Bioruptor Pico (Diagenode).
ChIP-seq libraries were prepared using ThruPLEX DNA-Seq Kit from Takara Bio. Libraries were end-repaired, adapter-ligated and PCR amplified according to manufacturer's instructions. Next, libraries underwent quality control using a Bioanalyzer with a High Sensitivity DNA chip to assess sample size distributions. Finally, samples were sequenced in a NextSeq550 Illumina platform using a 2x75bp flow cell.

treatment_protocol: K562 cells were transiently transfected with Silencer Select siRNAs (Thermo Fisher Scientific) against a non-targeting sequence (control) or targeting Geminin expression. Transfections were performed at a final concentration of 20 nM (48h) according to the manufacturer’s instructions

value: bone narrow

tag: disease state

value: myelogenous leukemia

value: lymphoblast

tag: Sex

value: female

value: siGMNN (Geminin siRNA)

tag: chip antibody


title: K562, lymphoblast, myelogenous leukemia, siGMNN (Geminin siRNA), FANCD2 (Input), Replicate 2

description: Library name: K562_siGMNN, Replicate 2, Input


title: P7 spinal cord, AR-24Q, rep 2

description: Library name: AR24Q-02

value: Spinal cord


title: P7 spinal cord, AR-97Q, Scramble-ASO, rep1

description: Library name: Scramble-01


title: P7 spinal cord, WT, rep3


title: E. coli wild type APEC94, mid-log phase (OD600=0.5), 3h, RNA-seq, replicate1

city: Shanghai

first: Lan

middle: fang

last: Kong

address: 518 Ziyue Road, Shanghai

institute: Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences

description:
Library name: APEC94_rep1
E. coli APEC94 grown in LB medium to mid-log phase (OD600=0.5). RNA extracted using TRIzol.

data_processing:
Raw RNA-seq reads were quality-checked using FastQC and trimmed with Trimmomatic v0.39 to remove adapters and low-quality bases. Clean reads were aligned to the reference genome using STAR v2.7.3a with default parameters. Gene-level read counts were quantified using featureCounts v1.6.4. TPM and count matrices were generated in R. Signal tracks (bigWig) were generated using deepTools bamCoverage with RPKM normalization. All analyses were performed using default settings unless otherwise noted.
Assembly: Escherichia coli K-12 MG1655 (U00096.3)
Supplementary files format and content: Processed data consist of gene expression matrices in Excel format (.xls). The file "gene_fpkm.xls" contains gene-level fpkm values, with genes as rows and samples as columns. Values were obtained after alignment with STAR and quantification using featureCounts.

organism: Escherichia coli K-12

source_name: Escherichia coli cells

growth_protocol: E. coli strains were grown in LB medium at 37°C with shaking at 200 rpm to mid-log phase (OD600 ~0.5).

extract_protocol:
Total RNA was extracted using TRIzol reagent according to the manufacturer’s instructions. RNA integrity was confirmed using Agilent Bioanalyzer.
Sequencing libraries were prepared using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer’s instructions. A total of 3 μg total RNA per sample was used as input. mRNA was enriched using poly-T oligo-attached magnetic beads. The purified RNA was fragmented under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5×). First-strand cDNA was synthesized using M-MuLV Reverse Transcriptase (RNase H–) and random hexamers, followed by second-strand cDNA synthesis using DNA Polymerase I and RNase H with dUTP substituted for dTTP to maintain directionality. After end repair and A-tailing, NEBNext adaptors with a hairpin loop were ligated. Size selection for ~150–200 bp fragments was performed using AMPure XP beads. The adaptor-ligated DNA was treated with USER enzyme at 37°C for 15 min and 95°C for 5 min. Libraries were PCR-amplified using Phusion High-Fidelity DNA Polymerase, universal primers, and index primers (X cycles according to kit recommendations). Final libraries were purified with AMPure XP beads and assessed using the Agilent 2100 Bioanalyzer. Library type: paired-end, directional (strand-specific).

value: Escherichia coli cells


title: NTDsSpine1

city: Taiyuan

first: lu

last: li

address: Xinjian South Road, Yingze District

institute: Shanxi Medical University

data_processing:
Raw Reads obtained by Illumina platform sequencing were eliminated by removing low quality sequences, splice contamination, etc  Cheng completed data processing to obtain high-quality sequences (Clean Reads).
Using a modified BWT algorithm (Siren et al. 2014),HISAT2-2.0.1 aligned the clean sequences at the paired ends to the reference genome.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene, Vonsidering the effect of sequencing depth and gene lenath for the reads count.
Assembly: mm10

source_name: embryonic development

growth_protocol: CD-1 mice (7–8 weeks old) were provided by Beijing Vital River laboratory Animal Technology Co., Ltd, China (no: 110011200105514958, 16–25 g). Male and female CD-1 mice were fed on low-folate diet for more than 8 weeks.

extract_protocol: On E9.5, pregnant mice were euthanized by cervical dislocation, and the phenotypes of the fetuses were observed under a microscope. All samples with NTDs clinical manifestations were collected for experiments.

treatment_protocol: Sexually matured individuals were mated overnight; vaginal plug was detected at 8:00 am in the following morning and was designated as E0.5 day. NTDs mouse models were induced by intraperitoneal injection with 1.5 mg/kg of MTX (Sigma–Aldrich, USA) on E7.5. On E9.5, pregnant mice were euthanized by cervical dislocation, and the phenotypes of the fetuses were observed under a microscope.

tag: strain

value: embryo

value: spine cell

value: folate deficiency (neural tube defects)


title: Human PSC-derived cardiomyocyte, wild type, replicate 2


title: P7 spinal cord, WT, rep2


title: P7 spinal cord, AR-97Q, testosterone, rep2

description: Library name: T-02

extract_protocol:
Total RNA was extracted from the spinal cord of WT, AR-97Q, and testosterone-treated AR-97Q mice using the RNeasy Mini Kit (QIAGEN). The quality and quantity of the RNA obtained were checked using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific) and analyzed with the Agilent 2100 Bioanalyzer system (Agilent Technologies Inc., Santa Clara, CA).
A library was independently prepared with 1ug of total RNA for each sample by Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina, Inc.).

treatment_protocol: Testosterone (20 mg) was subcutaneously adminstered to AR-97Q mice at postnatal day 1 (P1).

value: Testosterone


title: Venous thrombus in femoral vein of pig after 30 days, Specimen 1: 8/30

city: Chicago

first: Kenneth

last: Bader

address: 5835 S Cottage Grove Ave

country: USA

institute: University of Chicago

description: Library name: Clot 1

data_processing:
STAR
Reads were trimmed using Trim Galore and then mapped to the Sscrofa11.1 genome assembly
Quantification of gene counts was done using Salmon
FastQC and MultiQC were used for data quality checking
Assembly: Reads were trimmed using Trim Galore and then mapped to the Sscrofa11.1 genome assembly using STAR.
Supplementary files format and content: The data were processed to count tables normalized by library size, scaled by gene length, and log2 transformed to be used as the mixture file in CYBERSORTx.

organism: Sus scrofa domesticus

source_name: Chronic venous thrombus

growth_protocol: Thrombi were formed in the femoral vein of female mixed breed pigs via selective catheterization.

extract_protocol:
Selected regions were deparaffinized, digested with Proteinase K and crosslinks were reversed, and processed with RNeasy FFPE kit (QIAGEN Cat#73504) according to the manufacturer instructions
Strand-specific RNA-seq libraries were prepared using an TruSEQ total RNA-SEQ library protocol

value: Chronic venous thrombus

tag: breed

value: Mixed Breed Pig


title: P7 spinal cord, AR-97Q, rep1


title: E. coli lsrR deletion strain, mid-log phase (OD600=0.5), 3h, RNA-seq, replicate2

description:
Library name: lsrR deletion_rep1
E. coli lsrR deletion strain mutant grown in LB medium to mid-log phase (OD600=0.5). RNA extracted using TRIzol.

source_name: Escherichia coli lsrR deletion strain

value: Escherichia coli lsrR deletion strain

value: lsrR deletion strain


title: NTDsBrain1

value: brain cell


title: Human PSC-derived cardiomyocyte, wild type, replicate 1

value: pluripotent derived cardiomyocytes

value: WT

value: doxorubicin


title: K562, lymphoblast, myelogenous leukemia, siGMNN (Geminin siRNA), FANCD2 (ChIP), Replicate 1

description: Library name: K562_siGMNN, Replicate 1, ChIP

value: bone narrow

value: myelogenous leukemia

value: lymphoblast


title: K562, lymphoblast, myelogenous leukemia, siC (non-targeting siRNA), FANCD2 (Input), Replicate 2

description: Library name: K562_siC, Replicate 2, Input

value: female

value: siC (non-targeting siRNA)


title: P7 spinal cord, WT, rep1

value: Spinal cord


title: K562, lymphoblast, myelogenous leukemia, siC (non-targeting siRNA), FANCD2 (ChIP), Replicate 2

description: Library name: K562_siC, Replicate 2, ChIP


title: P7 spinal cord, AR-97Q, testosterone, rep3

description: Library name: T-03


title: Venous thrombus in femoral vein of pig after 30 days, Specimen 3: 11/13

description: Library name: Clot 3


title: HEK293T I1174N, rep3

city: Toronto

first: Haissi

last: Cui

address: 80 St George St

department: Chemistry

country: Canada

institute: University of Toronto

description:
Library name: I1174N-3
MSRseq

data_processing:
Sequencing data was analyzed as described by Frietze and Pan (61) with support from Trillium high performance computing, operated by the University of Toronto and Compute Canada. In brief, paired-end reads were merged, aligned to human tRNA sequences (61) with Bowtie2 (62), and reads at each nucleotide position were quantified using the pileup function of Samtools (63). Read counts per tRNA were quantified with Pysam as outlined by (61) and differential expression was assessed with DESeq2 (64).
Assembly: Human tRNA references were described in Frietze and Pan, 2025, and are available at https://github.com/Luke-F1875/MSRseq_data_processing_pipeline. tRNA sequences were derived from hg38.
Supplementary files format and content: count matrix

growth_protocol: HEK 293T cells were obtained from ATCC and confirmed by STR analysis. Cells were cultured at a density of 80-90% confluency and passaged on average twice per week. If not stated otherwise, cells were maintained in high glucose DMEM (Sigma-Aldrich), with 10% FBS (Corning), and 1% Penicillin/Streptomycin (Sigma-Aldrich). Cells were tested monthly for mycoplasma contamination and were consistently found negative. Experiments were performed before passage 30.

extract_protocol:
Multiplex small RNA sequencing (MSR-seq) libraries were prepared as described by Watkins et al. (42), with minor modifications. Total RNA was extracted from wild-type HEK293T and I1174N-9 HEK293T cells using TRIzol (Invitrogen™), and 1 µg of total RNA per sample was used as input. RNA was kept under acidic conditions to preserve aminoacylation status. To preserve tRNA aminoacylation information, only the acylated MSR-seq workflow was performed. Total RNA was subjected to one-pot periodate oxidation and β-elimination to selectively remove the terminal 3’ nucleotide from uncharged tRNAs, followed by 3′ end repair with T4 polynucleotide kinase (NEB).
Barcoded biotinylated capture hairpin oligonucleotides were ligated to RNA 3′ ends using T4 RNA ligase I (NEB), after which samples were pooled and immobilized on streptavidin-coated MyOne C1 Dynabeads (ThermoFisher). All subsequent steps were performed on-bead, including dephosphorylation, reverse transcription using SuperScript IV VILO (ThermoFisher) under extended incubation conditions, RNase H (NEB) digestion, periodate oxidation to inactivate unligated adapters, and second adapter ligation. Libraries were PCR-amplified using Q5 high-fidelity DNA polymerase (Q5), size-selected by 10% TBE-PAGE (Invitrogen™) to remove terminal transferase by-products, and purified by gel extraction followed by ethanol precipitation.  Final libraries were sequenced on a NovaSeq X using paired-end sequencing.

treatment_protocol: The PEA1-GFP plasmids were a gift from Paul Thomas (Addgene #171993) (41). Guide RNA (gRNA), repair template, and second nick gRNA were designed using Petal (41). Sequences are shown in Figure 1B. The plasmid was transfected into HEK293T cells using Calfectin (SignaGen). Successfully transfected cells were selected based on GFP expression by the Temerty Faculty of Medicine flow cytometry facility and sorted as individual cells into a 96-well plate.

value: cell line

value: immortalized cell line

value: IARS1 I1174N


title: Venous thrombus in femoral vein of pig after 30 days, Specimen 2: 10/2

description: Library name: Clot 2

value: Chronic venous thrombus


title: ConSpine1

value: embryo

value: spine cell

value: control


title: P7 spinal cord, AR-97Q, testosterone, rep1

description: Library name: T-01

value: Testosterone


title: P7 spinal cord, AR-24Q, rep 1

description: Library name: AR24Q-01

value: NT


title: ConBrain1

value: brain cell


title: shTaldo1_3, Day 7 CD8+ P14 T cells

description: Library name: noxPPP_shTaldo1_3_lib

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
Assembly: GRCm39_release110（https://ftp.ensembl.org/pub/release-110/fasta/mus_musculus/dna/）
Supplementary files format and content: Taldo_gene_expression.xlsx

extract_protocol:
Total RNA was extracted from CD8+ P14 T cells using RNeasy Mini Kit (Qiagen). mRNA was purified using oligo(dT) magnetic beads for poly(A) selection.
Library preparation is performed using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China).

value: Spleen

value: CD8+ P14 T cells


title: HEK293T I1174N, rep2

description:
Library name: I1174N-2
MSRseq


title: P7 spinal cord, AR-97Q, rep3

description: Library name: AR97Q-03


title: K562, lymphoblast, myelogenous leukemia, siGMNN (Geminin siRNA), FANCD2 (Input), Replicate 1

description: Library name: K562_siGMNN, Replicate 1, Input

value: bone narrow

value: myelogenous leukemia

value: siGMNN (Geminin siRNA)


title: shTaldo1_2, Day 7 CD8+ P14 T cells

description: Library name: noxPPP_shTaldo1_2_lib


title: P7 spinal cord, AR-97Q, rep2

description: Library name: AR97Q-02


title: HEK293T I1174N, rep1

description:
Library name: I1174N-1
MSRseq


title: P7 spinal cord, AR-97Q, rep1

description: Library name: AR97Q-01


title: HEK 293T wt, rep3

description:
Library name: IARS1_WT-3
MSRseq

value: wt


title: shNC_2, Day 7 CD8+ P14 T cells

description: Library name: noxPPP_shNC_2_lib

value: shNC


title: P7 spinal cord.  WT, rep 3

description: Library name: WT-03

value: Spinal cord

value: WT


title: K562, lymphoblast, myelogenous leukemia, siC (non-targeting siRNA), FANCD2 (Input), Replicate 1

description: Library name: K562_siC, Replicate 1, Input

value: lymphoblast

value: female

value: siC (non-targeting siRNA)


description: Library name: Igh VDJ-Seq JH4 Pro-B cell Cfp1(fl/fl) Mb1-Cre biol rep3

data_processing:
For the VHDJH identification, we used the pipeline available at Bitbucket (https://bitbucket.org/adugduzhou/htgtsrep). HTGTSrep pipeline was used for generating the processed files with "pass.xls" ends.
For the DJH joins analysis, we used the standard HTGTS sequencing pipeline provided by Frederick W. Alt Lab, which is available at GitHub (https://robinmeyers.github.io/transloc_pipeline/thedocs.html). Linear amplification-mediated (LAM)-HTGTS pipeline was used for generating processed files with "tlx" ends.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include a V usage report for each sample
Supplementary files format and content: tab delimited text files contain filtered junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); the entire stitched paired end read sequence (Seq); the junction sequence(J_seq)

extract_protocol:
Genomic DNA of FACS-sorted pro-B cells (CD19+CD43+) was extracted using phenol-chloroform.
0.5-2 μg of genomic DNA extracted from FACS-sorted pro-B cells (CD19+CD43+) was sonicated into fragments ranging from 300 to1000 bp using M220 Focused-ultrasonicator (Covaris), and amplified by LAM-PCR with biotin-conjugated 5’ JH1 or JH4 primers. Biotinylated PCR products were captured by Dynabeads MyOne streptavidin C1 beads (Invitrogen, 65002) and ligated with bridge adapters on-bead. The ligated products were amplified by nested PCR using barcode primers, followed by a third round of PCR using P5-I5 and P7-I7 primers. PCR products ranging 300-1,000 bp were purified by gel separation and sequenced on the Illumina NovaSeq platform with 250 bp or the Illumina MiSeq platform with150 bp paired-end reads.

value: bone marrow

value: Pro-B cells (CD19+CD43+)

value: Cfp1(fl/fl) Mb1-Cre


title: P7 spinal cord.  WT, rep 1

description: Library name: WT-01

value: NT


description: Library name: Igh VDJ-Seq JH4 Pro-B cell Cfp1(fl/fl) Mb1-Cre biol rep2


title: shTaldo1_1, Day 7 CD8+ P14 T cells

description: Library name: noxPPP_shTaldo1_1_lib


title: shNC_3, Day 7 CD8+ P14 T cells

description: Library name: noxPPP_shNC_3_lib


description: Library name: Igh VDJ-Seq JH4 Pro-B cell Cfp1(fl/fl) biol rep2


title: shNC_1, Day 7 CD8+ P14 T cells

description: Library name: noxPPP_shNC_1_lib


title: P7 spinal cord.  WT, rep 2

description: Library name: WT-02


title: VSMC- H_I3

status: Public on Feb 07 2026

city: Nanjing

first: po

last: hu

state: jiangsu

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

institute: 南京中医药大学

description:
Library name: sample3
H_I3_FPKM

data_processing:
Sequencing data contains a number of connectors, low-quality Reads, so we use fastp(0.22.0) software to filter the sequencing data to get high quality sequence (Clean Data) for further analysis .
The reference genome and gene annotation files were downloaded from genome website. The filtered reads were mapping to the reference genome using HISAT2 (v2.1.0).
Use HTSeq (v0.9.1) statistics to compare the Read Count values on each gene as the original expression of the gene, and then used FPKM to standardize the expression.
Assembly: Ensembl
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
Supplementary files format and content: xls file includes FPKM values for each Sample

source_name: cell

extract_protocol:
Total RNA was isolated using the Freezol Reagent (Invitrogen Life Technologies. Three micrograms of RNA were used as input material for the RNA sample preparations.
Firstly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in an Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and Super Script II. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities and the enzymes were removed. After adenylation of the 3′ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare forhybridization. To select cDNA fragments of the preferred 400-500 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter,Beverly, CA, USA).DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent).

value: cell

value: VSMC

value: Smooth Muscle Cell


title: VSMC- H2O21

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

description:
Library name: sample4
H2O21_FPKM

value: Isoliensinine


title: VSMC- H_I1

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

description:
Library name: sample1
H_I1_FPKM


title: K562, lymphoblast, myelogenous leukemia, siC (non-targeting siRNA), FANCD2 (ChIP), Replicate 1

description: Library name: K562_siC, Replicate 1, ChIP

value: bone narrow

value: myelogenous leukemia


title: PBMC, newly diagnosed NKTCL, 14

first: Xiaozhen

last: Liang

address: Life Science Research Building 320 Yueyang Road, Xuhui District

institute: Shanghai Institute of Materia Medica Chinese Academy of Sciences

description: Library name: patient14

data_processing:
Raw scRNA-seq data were initially pre-processed using CellRanger (version 8.0.1, 10x Genomics) to align reads to the human genome (GRCh38, 2024-A from 10x Genomics) and count the unique molecular identifiers (UMIs) for each gene to generate specific gene cell count tables. For each scRNA-seq sample, the count tables were filtered to retain the genes detected in at least 10 cells and cells with a minimum gene count of 300.
Assembly: GRCh38
Supplementary files format and content: barcodes, features, and matrix files for each samples

source_name: blood

extract_protocol:
Isolated PBMCs were loaded into a 10× Chromium Chip (v3.1 PN:1000120) and barcoded using a 10x Chromium Controller.
RNA from the barcoded cells was then reverse-transcribed, amplified, and prepared into sequencing libraries with the 10× Library Construction Kit (v3.1 PN:1000190) according to the manufacturer’s instructions.

value: blood

value: PBMCs

value: Peripheral blood immune cells


title: HEK 293T wt, rep2

description:
Library name: IARS1_WT-2
MSRseq

value: cell line

value: immortalized cell line

value: wt


title: VSMC- H2O22

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

description:
Library name: sample5
H2O22_FPKM


title: VSMC- H_I2

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

description:
Library name: sample2
H_I2_FPKM


title: PBMC, newly diagnosed NKTCL, 9

description: Library name: patient9


title: BJ5ta-StarveSpike

city: Knoxville

first: Rachel

middle: Patton

last: McCord

state: TN

address: 309 Mossman Bldg. 1311 Cumberland Ave

department: BCMB

institute: University of Tennessee

description:
Library name: Sample 2
Arima-HiC+ Kit (Mammalian Cell Lines A160134v01)

data_processing:
Sequencing reads were mapped to the human genome (hg19), filtered, binned, and iteratively corrected by Hi-CPro (https://github.com/nservant/Hi-C‐Pro)
Compartment analysis was performed by running principal component analysis using matrix2compartment.pl script in the cworld‐dekker pipeline available on GitHub (https://github.com/dekkerlab/cworld‐dekker). The PC1 value was then used to determine compartment identity for 250kb binned matrices.
Multiresolution cool files were created from the HiCPro validpair files using the cooler package https://github.com/open2c/cooler.
Assembly: hg19
Supplementary files format and content: Each .mcool file (see https://cooler.readthedocs.io/ for filetype information) contains the iteratively corrected contacts binned at multiple resolutions.  For human, resolutions include 10 kb, 20 kb, 40 kb, 100 kb, 250 kb, 1 Mb, and 2.5 Mb.    These .mcool files can be used for analysis with cooltools or loaded into HiGlass. See https://cooltools.readthedocs.io/ and https://github.com/higlass/higlass-docker
Supplementary files format and content: Each .tar.gz file contains raw and iteratively corrected (iced) matrix files in tabular format for all chromosomes for multiple bin resolutions.
Supplementary files format and content: Each .bedgraph file contains the result of A/B compartment analysis at 250 kb resolution for all chromosomes.  This is principal component 1 from compartment PCA analysis and corresponds to the data used to draw conclusions about compartment switch locations between conditions.

growth_protocol: BJ-5ta cells (from ATCC) were cultured in a complete medium (4:1 mixture of Dulbecco’s Modified Eagle’s Medium (DMEM, Corning, 10-013-CV) and Medium 199 (M199, Gibco, 11150-059), supplemented with 10% FBS, 1% Pen-Strep, 1% L-glutamine and 0.01 mg/ml hygromycin B) at 37°C supplied with 5% CO2.

extract_protocol:
~5 million BJ5ta cells were processed using the Arima-HiC+ Kit (Mammalian Cell Lines A160134v01) protocol. Nuceli were isolated and fixed with 2% formaldehyde and used in Arima Hi-C+ Kits
Biotinylated DNA was pulled down using streptavidin coated magnetic beads and prepared for multiplex sequencing on an Illumina platform using the NEBNext Ultra II kit (NEB). All end preparation, adaptor ligation, and PCR amplification steps were carried out on bead bound DNA libraries.

treatment_protocol: For migration, Transwell filters with 5µm pores were used. The bottom of each filter was coated with of 10ug/µL fibronectin for ~30 min. BJ-5ta cells in fully supplemented media were placed into the top well of the transwell with fully supplemented media in the bottom chamber. Cells were allowed to attach overnight. The following day both the top and bottom chamber’s media were replaced with a 4:1 ratio of DMEM and 1x Medium 199, but with 1% BSA instead of 10% FBS. Cells were starved overnight. The following day, the bottom chamber’s media was replaced with a 4:1 ratio of DMEM and Medium 199 supplemented with 20% FBS and 5 μg/mL of FGF.

value: Fibroblast

value: Starved overnight then Fibroblast Growth Factor (FGF) + 20% FBS Spiked Media


title: BJ5ta-BR1-96hr

description:
Library name: Sample 4
Arima-HiC+ Kit (Mammalian Cell Lines A160134v01)

value: Migrated once through 5 micron Transwell filter and then grown for 96 hours before fixation


title: RNA27

city: Hefei

first: Shuanghu

last: Yuan

address: No. 17 Lujiang Road

department: Department of Radiation Oncology,

institute: The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China

description: Library name: Sample 27

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > was sequenced run with Illumina Novaseq TM 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: Homo sapiens.GRCh38/hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Tumor tissue

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 10 ug of total RNA was extracted according to the RNA-Seq sample preparation kit for constructing sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Tumor tissue

tag: disease

value: esophageal squamous cell carcinoma


title: HEK 293T wt, rep1

description:
Library name: IARS1_WT-1
MSRseq

source_name: cell line


title: RNA24

description: Library name: Sample 24


title: BJ5ta-BR1-0hr

description:
Library name: Sample 3
Arima-HiC+ Kit (Mammalian Cell Lines A160134v01)

value: Cells collected immediately after migration through 5 micron Transwell filter


title: RNA26

description: Library name: Sample 26


title: RNA29

description: Library name: Sample 29


title: VSMC- H2O23

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

description:
Library name: sample6
H2O23_FPKM

value: cell

value: VSMC


title: RNA23

description: Library name: Sample 23


title: RNA25

description: Library name: Sample 25


title: PBMC, newly diagnosed NKTCL, 6

description: Library name: patient6


title: RNA22

description: Library name: Sample 22


title: RNA17

description: Library name: Sample 17


title: RNA20

description: Library name: Sample 20


title: BJ5ta-BR5

description:
Library name: Sample 5
Arima-HiC+ Kit (Mammalian Cell Lines A160134v01)

value: Migrated 5 rounds through 5 micron Transwell filters with proliferation time between each round and after final round before fixation


title: RNA18

description: Library name: Sample 18


title: RNA14

description: Library name: Sample 14


title: BJ5ta-Untreated

description:
Library name: Sample 1
Arima-HiC+ Kit (Mammalian Cell Lines A160134v01)

value: Untreated


title: RNA28

description: Library name: Sample 28


title: RNA15

description: Library name: Sample 15


title: NMIBC_888_URO_RNA_9

city: Yuseong-gu

first: Seung Woo

last: Baek

state: Daejeon

address: Gwahak-ro 125

country: South Korea

institute: Korea Research Institute Biology & Biotechnology

description: Library name: 888_URO_RNA_9

data_processing:
Reference genome indexing and read mapping of samples were performed using STAR software (ver. 2.6.1a).
FeatureCounsts (ver. 1.6.2) was used to calculate genereated binary alignment map (BAM) files.
The read counts per million fragments mapped (CPM) of each samples were used to estimate the expression level of each gene.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include CPM values for each Sample

source_name: Male

extract_protocol:
Total RNA was extracted from tissues using TRIzol reagent (Invitrogen, Carlsbad, CA) and stored at -80°C. RNA quality and integrity were assessed using the RNA Integrity Number (RIN) and the DV200 metric, which were determined with an RNA 6000 Nano Kit and an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
The sequencing library was prepared using the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA). Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNA. Adapters were ligated to the cDNA, and the fragments were amplified by polymerase chain reaction (PCR). Paired-end sequencing reads (2 x 100 bp) were obtained using the Novaseq platform (Illumina, San Diego, CA).

value: Male

value: Ta

tag: grade

value: low

value: No

tag: eortc-recur score


title: RNA16

description: Library name: Sample 16


title: RNA13

description: Library name: Sample 13


title: NMIBC_888_URO_RNA_88

description: Library name: 888_URO_RNA_88

value: high


title: RNA21

description: Library name: Sample 21


title: RNA19

description: Library name: Sample 19


title: NMIBC_888_URO_RNA_85

description: Library name: 888_URO_RNA_85

source_name: Female

value: Female


title: NMIBC_888_URO_RNA_84

description: Library name: 888_URO_RNA_84


title: RNA10

description: Library name: Sample 10


title: RNA11

description: Library name: Sample 11


title: NMIBC_888_URO_RNA_80

description: Library name: 888_URO_RNA_80


title: NMIBC_888_URO_RNA_81

description: Library name: 888_URO_RNA_81


title: RNA8

description: Library name: Sample 8


title: RNA9

description: Library name: Sample 9


title: RNA7

description: Library name: Sample 7


title: NMIBC_888_URO_RNA_79

description: Library name: 888_URO_RNA_79


title: RNA6

description: Library name: Sample 6


title: NMIBC_888_URO_RNA_76

description: Library name: 888_URO_RNA_76


title: RNA5

description: Library name: Sample 5


title: RNA4

description: Library name: Sample 4


title: NMIBC_888_URO_RNA_8

description: Library name: 888_URO_RNA_8


title: NMIBC_888_URO_RNA_71

description: Library name: 888_URO_RNA_71


title: NMIBC_888_URO_RNA_75

description: Library name: 888_URO_RNA_75


title: NMIBC_888_URO_RNA_74

description: Library name: 888_URO_RNA_74


title: RNA2

description: Library name: Sample 2


title: NMIBC_888_URO_RNA_70

description: Library name: 888_URO_RNA_70


title: NMIBC_888_URO_RNA_68

description: Library name: 888_URO_RNA_68


title: RNA1

description: Library name: Sample 1


title: NMIBC_888_URO_RNA_67

description: Library name: 888_URO_RNA_67


title: NMIBC_888_URO_RNA_66

description: Library name: 888_URO_RNA_66


title: Hacat cell, RR2

city: SHENZHEN

first: JIANGMING

last: ZHONG

address: Shennan rd 9996, 518000, Shenzhen, Guangdong, P.R. China.

institute: Shenzhen Hujia Technology Co., Ltd.

description: Library name: R-R2

data_processing:
The raw image data of the sequencing results were subjected to Base Calling using the software Bcl2fastq (v2.20.0.422), and preliminary quality analysis (during the sequencing process, Illumina's built-in software decides whether to retain or discard the read based on the quality of the first 25 bases of each sequencing segment, i.e., the read). Pass Filter Data, the result is stored in FASTQ file format, which contains the sequencing sequence information (line 2 of FASTQ format) and its corresponding sequencing quality information (line 4 of FASTQ format).
Filtering of low quality data using Cutadapt (version 1.9.1) to remove contamination and splice sequences.
The filtered sequencing Clean Data was compared and analyzed with the reference genome, and the selection of the appropriate reference genome is crucial to the success of the project information analysis, and the data comparison rate can reflect to a certain extent the similarity relationship between the experimentally sequenced samples and the selected reference genome.
Hisat2 (v2.2.1) software was used for the comparison of short reads with default parameters.
alternative splicing analysis of RNA-Seq data using rMATS (4.1.0)，Gene expression was calculated using Htseq software (V 0.6.1), which uses the FPKM (Fragments Per Kilo bases per Million reads) (Mortazavi, 2008) method for calculating gene expressions
Assembly: mm39
Supplementary files format and content: all.fpkm_anno.txt

source_name: Hacat

growth_protocol: Hacat cell were maitained in DMEM supplemented wth 10% fetal bovine serum(FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using TransZol Up Plus RNA Kit (Transgen).2 ug of total RNA was used for the construction of sequencing ibraries.
Library construction using the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina kit

value: Hacat

value: Human Keratinocyte cell

value: WT

value: UVB(50 mJ/cm2) and ROL with Rpalm treated


title: Hacat cell, RR1

description: Library name: R-R1