title: Embryo, Hpf24, Genotyping-only, rep2

city: Bergen

first: Jonas

middle: Maurice

last: Brandenburg

address: Thormolensgatan 55

department: Michael Sars Centre

country: Norway

institute: University of Bergen

description:
Library name: Hpf24_2_4sU
TrueSeq

data_processing:
The raw reads were trimmed for TSO and polyA tails using cutadapt (v1.18).
Trimmed reads were aligned and counted using Cellranger v6.0.2 (10x Genomics).
Individual biological samples were assigned based on genotyping using cellsnp-lite and vireo ( v0.5.7)
Filtering of cells based on counts per cells, genes detected per cells and the fraction mitochondrial reads per cells was performed in seurat v3, prior to merging all samples in a combined r object.
Assembly: Spur_5.0
Supplementary files format and content: RDS file with the filtered objects for each library. Note: for a fully processed data object, please refer to the merged_scRNA.rds in the common section.
Supplementary files format and content: Tsv file with donors assigned by Vireo based ont the geneotypes of the individual cells.

organism: Strongylocentrotus purpuratus

source_name: Embryo

growth_protocol: Sea urchin embryos (Strongylocentrotut purpuratus) were obtained by in vitro fertilization and maintained at 15C for the indicated time. Libraries sc4sU and scEarly were incubated in presence of 250ug 4-thiouridine (4sU, except for the no 4sU control).

extract_protocol:
Staged embryos were pelleted at 150g at 4°C for 5 minutes, washed with calcium-free artificial sea water (CFSW) [454mM NaCl, 9mM KCl, 48mM MgSO4, 6mM NaHCO3; pH adjusted to 8.2], and incubated in hyaline extraction medium (HEM) supplemented with BSA [NaCl 300mM, KCl 10mM, MgSO4 10mM, Glycine 300mM, Tris 10mM, EGTA 2mM; pH adjusted to 8.2; supplemented with BSA 2mg/mL] on ice for 5 minutes. Embryos were dissociated by gentle trituration with a 25ml serological pipet until reaching >95% single cells. Dissociated cells were then washed twice in CFSW and remaining clumps of cells were filtered out using a 40μm cell strainer. Cell viability was assessed using propidium iodine (Sigma Aldrich) staining. Only samples with > 90% viability were processed further. Cells were then diluted to 5x106 cells/ml in CFSW and fixed by adding ice-cold MeOH (to 90%) dropwise while gently vortexing and stored at -20°C until processing.
Fixed cells were rehydrated prior to library preparation. Therefore, cells were spun down (1000g, 5min at 4°C) and hydrated by two washes in CFSW with 0.1% BSA and 1x SUPERaseIn RNase inhibitor (both Fisher scientific). Rehydrated cells were diluted in Hanks balances salt solution (HBSS) with 0.04% BSA, followed by library preparation according to manufacturer’s instructions (10x Genomics). For scSLAM-seq, single cells were incubated with 10mM iodoacetamide overnight in 80% MeOH in CFSW at room temperature with gentle rotation and rehydrated in presence of 100mM DTT.

value: Embryo


title: AF9 rep3

status: Public on Mar 03 2026

type: SRA

city: Beijing

first: Huida

last: Ma

address: No. 30 Shuangqing Road, Haidian District

country: China

institute: Tsinghua University

description: Library name: AF9_B3

library_source: genomic

data_processing:
1. We used BWA (v0.7.15) with parameters "mem -k 18" to map the paired-end 150bp reads to hg38. 2. We used Samtools (v1.3.1) for handling SAM and BAM files. Records with mapping quality less than 20 was filtered. 3. We used Picard (v1.107) to remove duplicates. 4. We used bamCoverage from deepTools (v3.3.0) to make a normalized bigwig with RPKM normalization and a bin size of 10bp. ENCODE blacklist regions were excluded. 5. We used MACS2 (v2.1.2) to call peaks with parameters "--nomodel --shift 100 --extsize 200"
Assembly: hg38
Supplementary files format and content: narrowPeak
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Homo sapiens

extract_protocol:
The hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD903-1) was used for the test.
CUT&Tag seq libraries were prepared using the hyperactive Universal CUT&Tag Assay Kit (Vazyme, TD903-1). Libraries were amplified 13 cycles and validated by Qubit, AATI and qPCR.

tag: cell line

tag: cell type

value: Mammary epithelial cell


title: CTRL_INPUT_2

city: Fukuoka

first: Mitsutoki

last: Hatta

state: Fukuoka

address: 2-15-1 Tamura Sawara-ku

country: Japan

institute: Fukuoka Dental College

description: Library name: HaCaT_CTRL_INPUT_rep2

data_processing:
Next-generation sequencing was carried out on the Illumina NovaSeq 6000 (Illumina, San Diego, California), utilizing paired-end 150 base-read options.
ChIP-seq reads were trimmed using fastp (version 0.23.2) and subsequently mapped to the human reference genome (GRCh38) using Bowtie2 (version 2.4.5).
Peaks were called using findPeaks from HOMER (version 4.10). Super-enhancers were identified using the ROSE algorithm.
Duplicate sample data underwent irreproducibility discovery rate (IDR) analysis to assess the consistency of the peaks.
Bigwig files were generated using bamCoverage from deepTools (version 3.5.1).
Assembly: GRCh38
Supplementary files format and content: BigWig

source_name: HaCaT

growth_protocol: DMEM, 10% fetal bovine serum, 50 U/mL penicillin, and 50 µg/mL streptomycin. Cells were cultured at 37°C with 5% CO2.

extract_protocol:
Cells were fixed with 0.5% formaldehyde for 5 minutes. After quenching and nuclear extraction, chromatin was digested using microccoccal nuclease.
Library preparation was performed with the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA)

treatment_protocol: HaCaT cells were treated with 5 ng/ml of human recombinant TGF-β1 for 48 h to induce the EMT phenotype.

value: HaCaT

tag: treatment


title: Embryo, Hpf24, Genotyping-only, rep1

description:
Library name: Hpf24_1_4sU
TrueSeq

library_source: transcriptomic

molecule: total RNA

tag: tissue


title: TGFb_H3K27ac_1

description: Library name: HaCaT_TGFβ1_H3K27ac_rep1


title: Flag-AF9WT rep1

description: Library name: Flag-AF9WT_B1


title: pre-iPSC_r1 short-read RNAseq

city: Boston

first: Evan

middle: Michael

last: Appleton

state: MA

address: 75 Kneeland St.

country: USA

institute: Colossal Biosciences

description:
Library name: emPRC_r1
Column name in countTable_elemax2.txt: PreiPSC_1

data_processing:
We performed analysis using an Expression Analysis RNASeq workflow. Reads were trimmed using TrimGalore (V0.6.7), to remove low quality (qual < 25) ends of reads and remove reads < 35bp. Trimmed reads are aligned to a reference genome using STAR (default) or HiSAT2. BAMs from the same sample generated by multiple runs were merged using Samtools. The abundance of transcripts and genes were assessed using FeatureCount to generate raw gene counts, StringTie to generate FPKM and Salmon to generate raw transcript counts. Sample comparisons and differential gene/transcript expression analysis were performed using EdgeR, DESeq2 and IsoformSwitchAnalyzeR. Variant calling was called with DeepVariant and Freebayes. MA plots were generated with DESeq2 (v3.18) and ggpubr (v0.6.0).
Assembly: GCF_024166365.1_mEleMax1_primary_haplotype_genomic.fna
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Elephas maximus

source_name: Partially-reprogrammed induced pluripotent stem cells

growth_protocol: emiPSCs were grown in highly customized growth conditions as defined in the manuscript. Elephant primary endothelial cells were grown in 30% FBS/1% antibiotic/antimycotic /1% Non-essential AA/ EGM-2 media.

extract_protocol:
RNeasy Plus Universal Mini Kit (Qiagen 73404)
Proprietary to Novogene, Inc.

value: Chemical reprogramming

value: pre-iPSC


title: Eem6TH_r2 short-read RNAseq

description:
Library name: C2-emC6-SV40_r2
Column name in countTable_elemax.txt: C2_comb17_D_1

source_name: Induced pluripotent stem cells

value: Induced pluripotent stem cells

value: TF-overexpression of elephant OSKMNL and SV40 T-antigen


title: TGFb_H3K27ac_2

description: Library name: HaCaT_TGFβ1_H3K27ac_rep2


title: WT Cu428 cells, FLV treated for Input

city: Hefei

first: Zhengyu

last: Luo

address: huanshang

institute: USTC

description: Library name: Sample29

data_processing:
RNA-seq library adapters were trimmed using cutadapt v4.3, then the trimmed reads were mapped to MAC.v5 genome using hisat v2 2.2.1.
ATAC-seq library adapters were trimmed using cutadapt v4.3. The trimmed reads were mapped to MAC.v5 genome using bowtie2 v2.5.0 with the following parameters: -X 2000. PCR duplication was removed using samtools v1.17. bigwig files were generated by bamCoverage in deeptools v3.5.3.
ChIP-seq library adapters were trimmed using cutadapt v4.3. The trimmed reads were mapped to MAC.v5 genome using bowtie2 v2.5.0 and PCR duplication was removed using samtools v1.17. bigwig files were generated by bamCoverage in deeptools v3.5.3.
RNAseq raw counts were generated by featureCounts in subread v1.6.4.
Assembly: MAC.v5
Supplementary files format and content: RNAseq: tsv files includes raw counts for each sample.
Supplementary files format and content: ATACseq: bigwig files. ChIPseq: bigwig files

organism: Tetrahymena thermophila

growth_protocol: T. thermophila WT strains (SB210 and Cu428) were obtained from the Tetrahymena Stock Center. Cells were cultured at 30℃ in 1x SPP medium (10 g protease peptone, 2 g dextrose, 1 g yeast extract, 0.03 g Sequestrene (Fe-EDTA), adding water to final 1 L and autoclave prior to use).

extract_protocol:
For ATAC-seq, native cells were used for lysis and Tn5 treatment. For ChIP-seq, cells were fixed with 1% FA for 10 mins, then cell lysis and sonication were performed. For RNA-seq, cell pellets were resuspend in TRIZOL.
The RNA-seq library was generated by Sequencing company. ATAC-seq: After Tn5 treated, DNA were purified with FastPure Gel DNA Extraction Mini Kit, then amplified by PCR and purify with VAHTS DNA Clean Beads. ChIP-seq: the DNA were reverse crosslink at 65C overnight, then the DNA were purified and the library was generated by end-repair, dA-tailing, adapter ligation, after adapter ligation, PCR amplification and size select were performed similar to ATAC-seq library.

treatment_protocol: Flavopiridol (MedChemExpress, HY-10005) was prepared as a stock solution in DMSO at a concentration of 50 mM, the stock solution was diluted to final concentrations of 100 µM with 1x SPP medium. The cells treated with flavopiridol were then incubated at 30℃ for 6 hours before following experiments.

value: wild type cells

value: FLV


title: emEC1_r1 short-read RNAseq

description:
Library name: emEC_C1_WT_r1
Column name in countTable_elemax.txt: C1_control_1

source_name: Endothelial cells

value: Endothelial cells


title: Embryo, SLAMseq, Hpf3 to Hpf15

description:
Library name: scEarly
10x Genomics

library_source: transcriptomic single cell


title: Embryo, Hpf8, Genotyping-only, rep3

description:
Library name: Hpf8_1_4sU
TrueSeq


title: emEC1_r2 short-read RNAseq

description:
Library name: emEC_C1_WT_r2
Column name in countTable_elemax.txt: C1_control_2


title: WT Cu428 cells, DMSO control for Input

description: Library name: Sample27

value: DMSO


title: WU999_TCR1

city: St. Louis

first: Jacqueline

last: Payton

state: MO

address: 660 S. Euclid Ave

department: Pathology and Immunology

institute: Washington University School of Medicine

description:
Library name: TWDS-80075999-999PB040716-lib2
10x Genomics Chromium TCR

data_processing:
Alignment and gene counting were performed using the Cell Ranger pipeline (10x Genomics, v3.0, Pleasanton, CA). Genes found in fewer than 15 cells in each sample were removed. For each patient, gene counts and cells were pooled into a single Seurat (v5.1.0)(Butler et al., 2018; Hao et al., 2024; Stuart et al., 2019) object, and cells containing fewer than 200 or more than 3000-3750 expressed genes, more than 8-10% mitochondrial reads, fewer than 300 or more than 10000UMIs, or classification as a doublet by the R package scDblFinder(Germain et al., 2022) with parameters dims = 30, clust.method = “fast_greedy” were removed. In total, 118,608 cells were sequenced, with 92,496 passing initial QC filters after removing dead cells, empty droplets, and suspected multiplets.
Assembly: GRCh38/hg38
Supplementary files format and content: tab separated values files and matrix files

source_name: peripheral blood

extract_protocol: For each of the PBMC samples, 10,000 to 20,000 viable cells were submitted for processing using the 10x Genomics Chromium Controller and the Chromium Single Cell 5′ Library & Gel Bead Kit v2 (PN-1000006) following the manufacturer’s protocols. cDNA was prepared after the GEM generation and barcoding, followed by the GEM-RT reaction and bead cleanup steps. Purified cDNA was amplified for 10-14 cycles before being cleaned up using SPRIselect beads. Samples were then run on a Bioanalyzer to determine the cDNA concentration. TCR target enrichments were performed on the full-length cDNA. GEX and Enriched TCR libraries were prepared as recommended by the 10x Genomics Chromium Single Cell V(D)J Reagent Kits (v1.0 Chemistry) user guide with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. For sample preparation on the 10x Genomics platform, the Chromium Single Cell 5’ Library and Gel Bead Kit v2 (PN-1000006), Chromium Single Cell A Chip Kit (PN-1000152), Chromium Single Cell V(D)J Enrichment Kit, Human, Tcell (96rxns)(PN-1000005), and Chromium Single Index Kit T (PN-1000213) were used. The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer's protocol (KAPA Biosystems/Roche) to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument. Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 151x10x10x151 sequencing recipe according to manufacturer protocol. A median sequencing depth of 50,000 reads/cell was targeted for each sample.

treatment_protocol: Peripheral blood mononuclear cells were subjected to CD4+ enrichment (EasySep Human CD4 Positive Selection Kit or CD4+ staining and FACS) and/or monocyte depletion (RosetteSep Human Monocyte (CD36) Depletion Cocktail) and viable cells sorted using a 7-AAD viability stain on a Sony iCyt Synergy SY3200.

value: peripheral blood

value: peripheral blood mononuclear cells


title: emEC2_r1 short-read RNAseq

description:
Library name: emEC_C2_WT_r1
Column name in countTable_elemax.txt: C2_control_1


title: WU999_RNA1

description:
Library name: TWDS-80075999-999PB040716-lib1
10x Genomics Chromium 5' GEM


title: WT Cu428 x B2086, conjugation 12 hpm for RNAseq rep2

description:
Library name: Sample24
RNA.tt.12hpm.rep2

molecule: polyA RNA


title: WT Cu428 x B2086, conjugation 24 hpm for RNAseq rep2

description:
Library name: Sample25
RNA.tt.24hpm.rep2


title: WT Cu428 x B2086, Refeeding 24 hours after conjugation for RNAseq rep2

description:
Library name: Sample26
RNA.tt.Refeed.rep2


title: Eem4THsh_Ectoderm_r1 short-read RNA-seq

description:
Library name: Eem4THsh_Ectoderm_r1
Column name in countTable_txo_EB_TL.txt: EM_3
countTable_txo_TL_EB.txt

growth_protocol: Elephant primary cells, rock hyrax primary cells, emiPSCs, and pciPSCs were grown in highly customized growth conditions as detailed in the manuscript. These cell lines were also differentiated with a variety of different protocols as detailed in the manuscript. Please see the methods section of the manuscript for details.

value: Ectoderm

value: STEMdiff™ Trilineage Differentiation Kit ectoderm media differentiation for 7 days


title: TGFb_INPUT_1

description: Library name: HaCaT_TGFβ1_INPUT_rep1


title: Eem6TH_r1 short-read RNAseq

description:
Library name: C2-emC6-SV40_r1
Column name in countTable_elemax.txt: C2_comb17_D_1


title: WT Cu428 x B2086, conjugation 1.5 hpm  for RNAseq rep2

description:
Library name: Sample21
RNA.tt.1.5hpm.rep2


title: WU999_TCR2

description:
Library name: TWDS-80075999-999PB022119-lib2
10x Genomics Chromium TCR


title: WT Cu428 cells, DMSO control for ChIP-seq

description: Library name: Sample28


title: WT Cu428 cells, FLV treated for ChIP-seq

description: Library name: Sample30


title: Ela4T_r2 short-read RNA-seq

description:
Library name: C1-loxC4-SV40_r2
Column name in countTable_elemax.txt: CB2_i1_2

value: Chemical reprogramming, TF-overexpression of elephant OSKM and SV40 T-antigen


title: WT Cu428 x B2086, conjugation 24 hpm for RNAseq rep1

description:
Library name: Sample17
RNA.tt.24hpm.rep1


title: Embryo, Hpf10, Genotyping-only, rep3

description:
Library name: Hpf10_1_4sU
TrueSeq


title: WU1181_TCR2

description:
Library name: TWDS-800751181-1181PB101918-lib2
10x Genomics Chromium TCR


title: WT Cu428 x B2086, Refeeding 24 hours after conjugation for RNAseq rep1

description:
Library name: Sample18
RNA.tt.Refeed.rep1


title: WT Cu428 x B2086, conjugation 1.5 hpm  for RNAseq rep1

description:
Library name: Sample13
RNA.tt.1.5hpm.rep1


title: Ela6sh_r2 short-read RNA-seq

description:
Library name: C1-loxC6-TP53shRNA2_r2
Column name in countTable_elemax.txt: CB2_s3_2

value: Chemical reprogramming, TF-overexpression of elephant OSKMNL and shTP53


title: WT Cu428 cells, genomic DNA

description:
Library name: Sample31
purified gDNA treated with Tn5


title: WU1181_RNA2

description:
Library name: TWDS-800751181-1181PB101918-lib1
10x Genomics Chromium 5' GEM


title: WT Cu428 x B2086, conjugation 3 hpm for RNAseq rep1

description:
Library name: Sample14
RNA.tt.3hpm.rep1


title: CTRL_INPUT_1

description: Library name: HaCaT_CTRL_INPUT_rep1


title: WT Cu428 x B2086, conjugation 12 hpm for RNAseq rep1

description:
Library name: Sample16
RNA.tt.12hpm.rep1


title: Eem4TH_r1 short-read RNAseq

description:
Library name: C2-emC4-SV40_r1
Column name in countTable_elemax.txt: C2_comb5_D_1

value: TF-overexpression of elephant OSKM and SV40 T-antigen


title: Eem4TH_r2 short-read RNAseq

description:
Library name: C2-emC4-SV40_r2
Column name in countTable_elemax.txt: C2_comb5_D_2


title: CTRL_H3K27ac_1

description: Library name: HaCaT_CTRL_H3K27ac_rep1


title: WT Cu428 cells, vegetative growth for RNAseq rep2

description:
Library name: Sample19
RNA.tt.log.rep2


title: Ela6T_r2 short-read RNA-seq

description:
Library name: C1-loxC6-SV40_r2
Column name in countTable_elemax.txt: CB2_i3_2

value: Chemical reprogramming, TF-overexpression of elephant OSKMNL and SV40 T-antigen


title: WT Cu428 x B2086, conjugation 8 hpm for RNAseq rep2

description:
Library name: Sample23
RNA.tt.8hpm.rep2


title: WT Cu428 cells, FLV treated

description: Library name: Sample10


title: Ela6T_r1 short-read RNA-seq

description:
Library name: C1-loxC6-SV40_r1
Column name in countTable_elemax.txt: CB2_i3_1


title: WT Cu428 x B2086, Refeeding 24 hours after conjugation

description: Library name: Sample8


title: CTRL_H3K27ac_2

description: Library name: HaCaT CTRL_H3K27ac_rep2

value: HaCaT


title: WT Cu428 x B2086, conjugation 3 hpm for RNAseq rep2

description:
Library name: Sample22
RNA.tt.3hpm.rep2


title: Ela4sh_r1 short-read RNA-seq

description:
Library name: C1-loxC4-TP53shRNA2_r1
Column name in countTable_elemax.txt: CB2_s1_1

value: Chemical reprogramming, TF-overexpression of elephant OSKM and shTP53


title: Ela4T_r1 short-read RNA-seq

description:
Library name: C1-loxC4-SV40_r1
Column name in countTable_elemax.txt: CB2_i1_1


title: Ela4sh_r2 short-read RNA-seq

description:
Library name: C1-loxC4-TP53shRNA2_r2
Column name in countTable_elemax.txt: CB2_s1_2


title: WU999_RNA2

description:
Library name: TWDS-80075999-999PB022119-lib1
10x Genomics Chromium 5' GEM


title: WT Cu428 x B2086, conjugation 8 hpm for RNAseq rep1

description:
Library name: Sample15
RNA.tt.8hpm.rep1


title: WT Cu428 x B2086, conjugation 12 hpm

description: Library name: Sample6


title: WT Cu428 cells, DMSO control

description: Library name: Sample9


title: WT Cu428 cells, starvation 20 hours

description: Library name: Sample2


title: Ela4sh_r2 ATACseq

description: Library name: C1-loxC4-TP53shRNA2_r2

data_processing:
Reads were trimmed using TrimGalore (V0.6.7), to remove low-quality (qual < 25) ends of reads and remove reads < 35bp. Trimmed reads are aligned to a reference genome using minimap2 version 2.28. Duplicate reads were marked using Picard MarkDuplicates. BAMs from the same sample generated by multiple runs are merged using Samtools. Alignment quality was assessed using FastQC, Samtools, and Bedtools. Peak calling was run with MACS3. Alignments are converted to BigWIG files. This deepTool computeMatrix was used to calculate scores per genome region and prepares an intermediate file that is used with plotHeatmap and plotProfiles.
Assembly: GCF_024166365.1_mEleMax1_primary_haplotype_genomic.fna
Supplementary files format and content: BAM files after alignments were used directly to visualize mapping of reads to the genome

extract_protocol:
Libraries were prepared with a ActiveMotif kits (ActiveMotif 53150) following instructions from the manufacturer
Libraries were prepared with a ActiveMotif kits (ActiveMotif 53150) following instructions from the manufacturer

value: Chemical reprogramming, TF-overexpression of elephant OSKM and shTP54


title: WT Cu428 cells, starvation 20 hours for RNAseq rep2

description:
Library name: Sample20
RNA.tt.star20.rep2


title: Ela6sh_r1 short-read RNA-seq

description:
Library name: C1-loxC6-TP53shRNA2_r1
Column name in countTable_elemax.txt: CB2_s3_1

value: Induced pluripotent stem cells


title: WT Cu428 cells, starvation 20 hours for RNAseq rep1

description:
Library name: Sample12
RNA.tt.star20.rep1


title: WU1181_RNA1

description:
Library name: TWDS-800751181-1181PB022317-lib1
10x Genomics Chromium 5' GEM


title: SADB19_HighComplexityMainReplicate-3

city: San Francisco

first: David

last: Shin

state: CA

address: 1651 4th Street Room 521A

department: Neurosurgery

institute: University of California, San Francisco

description: Library name: SADB19_HighComplexityMainReplicate-3

library_source: other

data_processing:
Output fastqs from sequenced rabies barcode libraries were filtered and processed using the custom script barcode_processing.sh. The bbduk (v39.01) package (BBMap, Bushnell B.; sourceforge.net/projects/bbmap/) was used to discard any reads with average quality (maq) below 20. Reads were then trimmed down to individual RVdG barcodes, UMIs, and cell barcodes (for transcriptome-matched datasets). RVdG barcodes were aligned to a custom reference white list (Supplementary Table 1) with bowtie2, allowing for one base pair mismatch. After sorting output files with samtools, the RVdG barcodes, UMIs, and cell barcodes were merged on read IDs. The command line package UMI-tools (v1.1.2) was then used to quantify the number of UMIs per cell barcode and rabies barcode combination. A UMI collapsing threshold was set at 1 to collapse any UMIs with only one base pair difference into a single UMI count.
Assembly: Barcode whitelist in Supplemental Figure 1 in the associated manuscript
Supplementary files format and content: TSV format. Contains STICR barcode sequence and UMI-reduced read abundance.

molecule: other

organism: Lyssavirus rabies

source_name: rescued in HEKGT and pseudotyped in BHK21

extract_protocol:
phenol-chloroform extraction to extract viral RNA genomes; gigaprep to extract plasmid DNA
To quantify plasmid barcode library diversity, 50 ng of plasmid DNA was tagmented using seqWell’s Tagify UMI reagent, in order to tag each barcode-containing plasmid DNA fragment with a UMI and partial Illumina Read1 adapter. Tagmented fragments were purified using a 1× left-sided size selection using SPRIselect beads according to the manufacturer’s protocol. Sample indexing PCR was subsequently performed using custom sample index primers that bind to the BFP primer site sequence immediately proximal to the barcode sequence and to the TruSeq P5 PCR handle generated during Tn5 tagmentation (Primers 3 and 4, Key Resource Table). The library was sequenced using a target of 100 million reads. To quantify viral barcode library diversity, EnvA-pseudotyped barcoded RVdG was concentrated by ultracentrifugation as described above and RNA was isolated by phenol-chloroform extraction, the procedure for which is described as follows. The viral pellet was resuspended in 1 mL of Trizol (Invitrogen 15596026), and incubated at room temperature for five minutes to permit dissociation of rabies proteins from viral RNA. Subsequently, 200 μL of chloroform (Fisher 60047878) was added and vortexed for 30 seconds, followed by spin at 12000xg for 15 minutes at 4°C. 600 μL of the upper aqueous phase was collected and RNA was precipitated by mixing with 500 μL of isopropanol and 1 μL of Glycoblue (Invitrogen AM9515) and incubating for 10 minutes. Precipitated RNA was pelleted by centrifugation at 12000xg for 10 minutes at 4°C, washed twice with 80% ethanol, air dried for 2 minutes, and resuspended in 10 μL of nuclease-free water. Reverse transcription was performed on 1-5 μg of RNA using SuperScript IV (ThermoFisher 18090010) and 1 μL of 50 mM custom RT primer targeting a sequence distal to the barcode relative to the negative stranded viral genome, in order to generate cDNA containing barcodes from viral genome RNA but not from contaminant mRNA. RT primer also contained an overhanging sequence carrying an 8 bp randomer, which functions as a UMI to correct for PCR amplification bias after sequencing, and a binding site for Illumina sample index primer. The resulting cDNA (5 uL, or 25% of the RT reaction) was amplified using 10-12 cycles of PCR with KAPA HotStart PCR ReadyMix (Roche KK2601) and custom sample index primers, one of which is specific to an overhang introduced by the RT primer to facilitate viral genome-specific amplification. Each library was sequenced using at least 10 million reads.

tag: genotype

value: SAD B19


title: WU1181_TCR1

description:
Library name: TWDS-800751181-1181PB022317-lib2
10x Genomics Chromium TCR


title: WT Cu428 cells, vegetative growth for RNAseq rep1

description:
Library name: Sample11
RNA.tt.log.rep1

value: wild type cells


title: SADB19_HighComplexityMainReplicate-2

description: Library name: SADB19_HighComplexityMainReplicate-2

value: rescued in HEKGT and pseudotyped in BHK21


title: Ela4sh_r1 ATACseq

description: Library name: C1-loxC4-TP53shRNA2_r1


title: WU1181_TCR3

description:
Library name: TWDS-800751181-1181PB022119-lib2
10x Genomics Chromium TCR


title: Eem6TH_r2 ATACseq

description: Library name: C2-emC6-SV40_r2

value: TF-overexpression of elephant OSKMNL and SV40 T-antigen


title: Ela4T_r2 ATACseq

description: Library name: C1-loxC4-SV40_r2


title: WT Cu428 x B2086, conjugation 24 hpm

description: Library name: Sample7


title: WT Cu428 cells, vegetative growth

description: Library name: Sample1


title: Liver high NAFLD Activity Score + Ar1260 exposure, Replicate 1

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

description: Library name: Aro_HighNAS_1_9

data_processing:
Primary analysis of raw data to HiFi reads was performed on-instrument.
Following sequencing, the resulting flnc.bam files were aligned to the mouse genome version GRCm39.fa using the PBMM2 (V1.10.0) aligner.
IsoSeq3 (v4.0.0) “collapse” was used to collapse isoforms and get isoform abundance using the option “—do-not-collapse-extra-5exons” as recommended for bulk IsoSeq samples. The maximum allowed 3’ difference is 100 bases on the same exon. The maximum allowed 5’ difference is 1000 bases on the same exon.
Pigeon (v1.0.0) “sort” was used to sort the collapsed annotation file (GFF), “classify” was used to classify the isoforms in the individual files, and “filter” was used to filter isoforms for primers annealing to downstream A-rich regions (IntraPriming), isoforms containing a single exon (Mono-Exonic), artifacts of reverse transcriptase template switching (RTSwitching), and low sample coverage for splice sites that are not in the known “canonical” set of splice sites (LowCoverage/Non-Canonical).
A fasta file was generated for filtered isoforms using “gffread” (v0.12.6) and converted to sam format using minimap2 (v2.24), then converted to md tagged sam files using samtools (v1.3). All md tagged same files were added to a Talon SQLite database (TALON.db). Twelve sample files were added to the database, duplicates removed, and a combined annotation file was created for all genes and isoforms.
A unified count matrix was created with a customized R script by separating the results for each sample and merging the abundance using the PacBio IDs. An aggregate function in R was used to sum over duplicate transcripts and create one count sum for each unique transcript. These counts were then merged for each replicate to produce a single count matrix that was further filtered to include only transcripts with a sum of counts greater than or equal to 10 across the 12 samples.
After normalization, SQANTI3 (v3.3) classification was performed on filtered annotations and DTU analysis was performed using DRIMseq (V1.32.0). To overcome a known issue with DRIMseq when one experimental group has all zero counts for a transcript, but sufficient counts from the other experimental group and sufficient counts for the gene, a pseudocount of 0.1 was added to counts for genes with either experimental group in a comparison having zero counts. DRIMseq analysis was followed by an analysis in StageR (V1.26.0) to control overall error rate when dealing with both genes and transcripts.
Assembly: GRCm39
Supplementary files format and content: merged_counts_all.tsv.gz -- gzipped Tab-delimited isoform counts for all samples
Supplementary files format and content: Isoseq_combined_talon_observedOnly.gtf -gzipped text file for gene descriptions across all samples

organism: Mus musculus

source_name: liver

growth_protocol: The animal protocol was ratified by the University of Louisville Institutional Animal Care and Use Committee (Approval code 21871 on 15 July 2021). All mice were fed ad libitum a normal, low-fat diet (LFD, 20%, 69.8%, and 10.2% of total calories from protein, carbohydrate, and fat, respectively; TekLad 06416, (Envigo, Indianapolis, IN, USA).

extract_protocol:
Prior to euthanasia, mice were fasted for 6 h. Liver tissue was rapidly excised from each mouse and weighed to record any changes in organ weight. Immediately following excision, tissue samples were flash-frozen in liquid nitrogen and preserved in RNAlater Stabilization Solution (ThermoFisher, Waltham, MA).  Total RNA was isolated using TRIzol (ThermoFisher).
Barcoded cDNA was prepared from 300ng total RNA utilizing the IsoSeq Express 2.0 Kit (PacBio, 103-071-500) according to manufacturer. Barcoded Kinnex Array libraries were prepared from 56ng equimolar pooled barcoded cDNA according to “Preparing Kinnex Libraries using the Kinnex full-length RNA kit, 103-238-700, Rev03 (MAR2024)” utilizing the Kinnex PCR 8-Fold kit (PacBio, 103-071-600) and Kinnex concatenation kit (PacBio, 103-071-800). 150pM of the library was prepared for sequencing following calculations generated with SMRT Link v13.1 software (PacBio) for Kinnex full-length RNA library type and applications. Briefly, the library was annealed to the Kinnex sequencing primer and bound to polymerase prior to purification with SMRTbell cleanup beads (PacBio, 100-265-900) utilizing the Revio Polymerase Kit (102-739-100, PacBio). Sequencing was performed on a 25M SMRT cell on a Revio platform (PacBio) and data collected over a 24 hour movie with adaptive loading enabled.

treatment_protocol: After two weeks, Ar1260 was administered via a single oral gavage at a dose of 20 mg/kg. The duration of exposure, due to entero-hepatic PCB recycling, extended 34 weeks.

value: liver

tag: Sex

value: male

tag: strain

tag: diet

value: low fat

tag: age

value: 6-8 weeks

tag: rin

tag: body weight_(g)

tag: liver weight_(g)

tag: nas score

tag: pacbio library

value: IsoSeq


title: Liver low NAFLD Activity Score + Ar1260 exposure, Replicate 4

description: Library name: Aro_LowNAS_5_8


title: WU1181_RNA3

description:
Library name: TWDS-800751181-1181PB022119-lib1
10x Genomics Chromium 5' GEM

value: peripheral blood

value: peripheral blood mononuclear cells


title: WT Cu428 x B2086, conjugation 8 hpm

description: Library name: Sample5


title: WU1137_TCR1

description:
Library name: TWDS-800751137-1137PB121416-lib2
10x Genomics Chromium TCR


title: WT Cu428 x B2086, conjugation 3 hpm

description: Library name: Sample4


title: Eem4TH_r1 ATACseq

description: Library name: C2-emC4-SV40_r1

value: TF-overexpression of elephant OSKM and SV40 T-antigen


title: WT Cu428 x B2086, conjugation 1.5 hpm

description: Library name: Sample3


title: WU1137_RNA1

description:
Library name: TWDS-800751137-1137PB121416-lib1
10x Genomics Chromium 5' GEM


title: WU1137_TCR2

description:
Library name: TWDS-800751137-PB011719-lib2
10x Genomics Chromium TCR


title: Liver DMSO Control, Replicate 2

description: Library name: Control_2_2

value: DMSO control


title: WU1126_RNA3

description:
Library name: TWDS-800751126-PB110718-lib1
10x Genomics Chromium 5' GEM


title: Ela6T_r1 ATACseq

description: Library name: C1-loxC6-SV40_r1

value: Chemical reprogramming, TF-overexpression of elephant OSKMNL and SV40 T-antigen


title: Liver low NAFLD Activity Score + Ar1260 exposure, Replicate 2

description: Library name: Aro_LowNAS_3_6


title: Liver DMSO Control, Replicate 1

description: Library name: Control_1_1


title: WU1137_RNA2

description:
Library name: TWDS-800751137-PB011719-lib1
10x Genomics Chromium 5' GEM


title: WU1135_TCR2

description:
Library name: TWDS-800751135-1135PB120916_Tcell-lib2
10x Genomics Chromium TCR


title: SADB19_HighComplexityMainReplicate-1

description: Library name: SADB19_HighComplexityMainReplicate-1


title: HEK-TVA_Uninfected_08

description: Library name: HEK-TVA_Uninfected_08

source_name: rescued in HEKGT, pseudotyped in BHK21, collected from HEK-TVA


title: Liver high NAFLD Activity Score + Ar1260 exposure, Replicate 3

description: Library name: Aro_HighNAS_3_11


title: Liver high NAFLD Activity Score + Ar1260 exposure, Replicate 2

description: Library name: Aro_HighNAS_2_10


title: WU1135_RNA2

description:
Library name: TWDS-800751135-1135PB120916_Tcell-lib1
10x Genomics Chromium 5' GEM


title: HEK-TVA_Uninfected_07

description: Library name: HEK-TVA_Uninfected_07

value: rescued in HEKGT, pseudotyped in BHK21, collected from HEK-TVA


title: Liver high NAFLD Activity Score + Ar1260 exposure, Replicate 4

description: Library name: Aro_HighNAS_6_12


title: v1_CD4P_Untreated

description:
Library name: v1_CD4P_Untreated
counts_vstCTCL2018donorSpecimen.txt

data_processing:
Basecalling and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read allowed. RNA-seq reads were then aligned to the Human Ensembl GRCh38.76 assembly with STAR version 2.7.9a44. Gene counts were obtained from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.345. Isoform expression of known Ensembl transcripts were quantified with Salmon version 1.5.246. Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected. Ribosomal genes and genes not expressed in the smallest group size minus one sample greater than one count-per-million were excluded from further analysis. All RNAseq datasets were imported and normalized using variance stabilizing transformation (VST) in the DESeq2 R package version 1.45.047.
Assembly: GRCh38.76
Supplementary files format and content: VST normalized .txt (tab delimited)

source_name: PBMC

extract_protocol:
RNA was extracted from skin, lymph node, and purified PBMC samples processed as described above using the RNeasy Plus Mini kit (Qiagen).
Libraries were prepared by the WU GTAC@MGI using 10ng of total RNA with a Bioanalyzer RIN score greater than 8.0. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases. A subset of samples had previously been subjected to RNAseq using the following methods: Takara Bio SMARTer cDNA synthesis followed by library preparation according to manufacturer’s protocol (Takara), indexed, pooled, and sequenced (1x150 bp SE) on an Illumina HiSeq 3000 instrument according to the manufacturer’s instructions.

value: PBMC


title: WU1135_TCR1

description:
Library name: TWDS-800751135-1135PB120916_All-lib2
10x Genomics Chromium TCR


title: Eem6TH_r1 ATACseq

description: Library name: C2-emC6-SV40_r1

value: Induced pluripotent stem cells


title: v3_CD4P_Untreated

description:
Library name: v3_CD4P_Untreated
counts_vstCTCL2018donorSpecimen.txt


title: Ela6sh_r2 ATACseq

description: Library name: C1-loxC6-TP53shRNA2_r2

value: Chemical reprogramming, TF-overexpression of elephant OSKMNL and shTP54


title: HEK-TVA_Uninfected_05

description: Library name: HEK-TVA_Uninfected_05


title: Ela6sh_r1 ATACseq

description: Library name: C1-loxC6-TP53shRNA2_r1

value: Chemical reprogramming, TF-overexpression of elephant OSKMNL and shTP53


title: Ela4T_r1 ATACseq

description: Library name: C1-loxC4-SV40_r1

value: Chemical reprogramming, TF-overexpression of elephant OSKM and SV40 T-antigen


title: WU1135_RNA1

description:
Library name: TWDS-800751135-1135PB120916_All-lib1
10x Genomics Chromium 5' GEM


title: Liver low NAFLD Activity Score + Ar1260 exposure, Replicate 3

description: Library name: Aro_LowNAS_4_7


title: Liver low NAFLD Activity Score + Ar1260 exposure, Replicate 1

description: Library name: Aro_LowNAS_2_5


title: WU1126_TCR3

description:
Library name: TWDS-800751126-PB110718-lib2
10x Genomics Chromium TCR


title: HEK-TVA_Uninfected_01

description: Library name: HEK-TVA_Uninfected_01


title: WU1126_TCR4

description:
Library name: TWDS-800751126-1126PB021419-lib2
10x Genomics Chromium TCR


title: Liver DMSO Control, Replicate 4

description: Library name: Control_5_4


title: CTCL1196_CD4P_NoHDACi

description:
Library name: CTCL1196_CD4P_NoHDACi
counts_vstCTCL2018donorSpecimen.txt


title: Ela6T_r2 ATACseq

description: Library name: C1-loxC6-SV40_r2


title: Liver DMSO Control, Replicate 3

description: Library name: Control_4_3


title: CTCL1200_CD4P_OW

description:
Library name: CTCL1200_CD4P_OW
counts_vstCTCL2018donorSpecimen.txt


title: HEK-TVA_Infected_11

description: Library name: HEK-TVA_Infected_11


title: WU1126_TCR1

description:
Library name: TWDS-800751126-1126PB091417-lib2
10x Genomics Chromium TCR


title: CTCL1235_CD4P_POST

description:
Library name: CTCL1235_CD4P_POST
counts_vstCTCL2018donorSpecimen.txt


title: WU1084_TCR1

description:
Library name: TWDS-800751084-1084PB101118-lib2
10x Genomics Chromium TCR


title: WU1126_RNA1

description:
Library name: TWDS-800751126-1126PB091417-lib1
10x Genomics Chromium 5' GEM


title: v2_CD4P_Untreated

description:
Library name: v2_CD4P_Untreated
counts_vstCTCL2018donorSpecimen.txt


title: HEK-TVA_Infected_08

description: Library name: HEK-TVA_Infected_08


title: WU1126_TCR2

description:
Library name: TWDS-800751126-1126PB082318-lib2
10x Genomics Chromium TCR


title: WU1084_RNA1

description:
Library name: TWDS-800751084-1084PB101118-lib1
10x Genomics Chromium 5' GEM


title: HEK-TVA_Uninfected_06

description: Library name: HEK-TVA_Uninfected_06


title: HEK-TVA_Uninfected_04

description: Library name: HEK-TVA_Uninfected_04


title: WU1126_RNA2

description:
Library name: TWDS-800751126-1126PB082318-lib1
10x Genomics Chromium 5' GEM


title: HEK-TVA_Uninfected_02

description: Library name: HEK-TVA_Uninfected_02


title: HEK-TVA_Uninfected_03

description: Library name: HEK-TVA_Uninfected_03


title: HEK-TVA_Infected_05

description: Library name: HEK-TVA_Infected_05


title: HEK-TVA_Infected_15

description: Library name: HEK-TVA_Infected_15


title: HEK-TVA_Infected-16

description: Library name: HEK-TVA_Infected-16


title: CTCL992_CD4P_CD7N_PRE

description:
Library name: CTCL992_CD4P_CD7N_PRE
counts_vstCTCL2018donorSpecimen.txt

value: CD4P CD7N


title: HEK-TVA_Infected_13

description: Library name: HEK-TVA_Infected_13


title: HEK-TVA_Infected_14

description: Library name: HEK-TVA_Infected_14


title: WU1084_TCR3

description:
Library name: TWDS-800751084-PB112918-lib2
10x Genomics Chromium TCR


title: HEK-TVA_Infected_03

description: Library name: HEK-TVA_Infected_03


title: HEK-TVA_Infected_02

description: Library name: HEK-TVA_Infected_02


title: CTCL1145_CD4P_VOR_POST

description:
Library name: CTCL1145_CD4P_VOR_POST
counts_vstCTCL2018donorSpecimen.txt


title: CTCL1043_CD4P_CD7N_PRE

description:
Library name: CTCL1043_CD4P_CD7N_PRE
counts_vstCTCL2018donorSpecimen.txt


title: HEK-TVA_Infected_12

description: Library name: HEK-TVA_Infected_12


title: WU1084_RNA3

description:
Library name: TWDS-800751084-PB112918-lib1
10x Genomics Chromium 5' GEM


title: WU1126_RNA4

description:
Library name: TWDS-800751126-1126PB021419-lib1
10x Genomics Chromium 5' GEM


title: CTCL1084_CD4P_CD7N_PRE

description:
Library name: CTCL1084_CD4P_CD7N_PRE
counts_vstCTCL2018donorSpecimen.txt


title: HEK-TVA_Infected_10

description: Library name: HEK-TVA_Infected_10


title: HEK-TVA_Infected_09

description: Library name: HEK-TVA_Infected_09


title: CTCL992_CD4P_CD7N_OW

description:
Library name: CTCL992_CD4P_CD7N_OW
counts_vstCTCL2018donorSpecimen.txt


title: HEK-TVA_Infected_01

description: Library name: HEK-TVA_Infected_01


title: CTCL1200_CD4P_PRE

description:
Library name: CTCL1200_CD4P_PRE
counts_vstCTCL2018donorSpecimen.txt


title: WU999_cd4

description:
Library name: 999-110118_cd4.CATTCGCAGT-CTTCTCAGAG
CTCL999_110118_cd4
counts_vstCTCL2021donorSpecimen.txt


title: HEK-TVA_Infected_07

description: Library name: HEK-TVA_Infected_07


title: CVSN2c_Clone3-1

description: Library name: CVSN2c_Clone3-1

value: rescued in HEKGT and pseudotyped in BHK21


title: CVSN2c_Clone2-2

description: Library name: CVSN2c_Clone2-2


title: CTCL1125_CD4P_VOR_OT

description:
Library name: CTCL1125_CD4P_VOR_OT
counts_vstCTCL2018donorSpecimen.txt


title: CVSN2c_Clone2-1

description: Library name: CVSN2c_Clone2-1


title: HEK-TVA_Infected_06

description: Library name: HEK-TVA_Infected_06


title: CVSN2c_Clone1-1

description: Library name: CVSN2c_Clone1-1


title: WU1084_TCR2

description:
Library name: TWDS-800751084-1084PB012419-lib2
10x Genomics Chromium TCR


title: WU1084_RNA2

description:
Library name: TWDS-800751084-1084PB012419-lib1
10x Genomics Chromium 5' GEM


title: WU1787_skin

description:
Library name: 1787-022020_skin.AGGTATGAGA-AGTGCCGATG
CTCL1787_022020_skin
counts_vstCTCL2021donorSpecimen.txt

source_name: skin

value: skin


title: CVSN2c_HighComplexityMainReplicate-1

description: Library name: CVSN2c_HighComplexityMainReplicate-1


title: CVSN2c_Parental-2

description: Library name: CVSN2c_Parental-2


title: v5_normalcd4

description:
Library name: v5_normalcd4.CGCACTGGTA-CTGTGCATTA
v5_normalcd4
counts_vstCTCL2021donorSpecimen.txt


title: CTCL1024_SKIN_CD4P_CD7N_POST

description:
Library name: CTCL1024_SKIN_CD4P_CD7N_POST
counts_vstCTCL2018donorSpecimen.txt


title: Randomer_HighComplexityMainReplicate

description: Library name: Randomer_HighComplexityMainReplicate


title: CVSN2c_Parental-1

description: Library name: CVSN2c_Parental-1


title: CTCL079_CD4P_CD26N_PRE

description:
Library name: CTCL079_CD4P_CD26N_PRE
counts_vstCTCL2018donorSpecimen.txt

value: CD4P CD26N


title: v4_normalcd4

description:
Library name: v4_normalcd4.AGAACCGCTA-ATCTCTGGTA
v4_normalcd4
counts_vstCTCL2021donorSpecimen.txt


title: CVSN2c_Clone4-2

description: Library name: CVSN2c_Clone4-2


title: CTCL1008_SKIN_CD4P_PRE

description:
Library name: CTCL1008_SKIN_CD4P_PRE
counts_vstCTCL2018donorSpecimen.txt


title: HEK-TVA_Infected_04

description: Library name: HEK-TVA_Infected_04


title: CVSN2c_Clone4-1

description: Library name: CVSN2c_Clone4-1


title: Day_4_differentiated_4HT_treated_rep2

type: RNA

city: Faro

first: Rui Sotero

last: Rodrigues Machado

address: Campus de Gambelas

country: Portugal

institute: Universidade do Algarve

description: ESC differentiated for 4 days using the hanging drop method with 4-hydroxytamoxifen treatment for the first 48 h

hyb_protocol: Standard Affymetrix Protocol

scan_protocol: Standard Affymetrix Protocol

data_processing: Summarized probe data set was obtained using R, through a package called Oligo using default parameters suggested by the tool.

label: biotin

source_name: embryonic stem cell

label_protocol: Standard Affymetrix Protocol

growth_protocol: C2fl/fl[Cre] ESC maintained in conditions sustaining the undifferentiated state were treated with 1 μM 4HT for 48 h or ethanol (vehicle) were collected. C2fl/fl[Cre] ESC were also differentiated for 4 days using the hanging drop method, with 4HT or ethanol treatment for the first 48 h,

extract_protocol: Total RNA was also isolated from ESC using a commercial kit (NZYtech, MB13402)


title: Day_0_ETOH_treated_rep2

description: ESC maintained in conditions sustaining the undifferentiated state were treated with ethanol for 48 h

treatment_protocol: C2fl/fl[Cre] ESC maintained in conditions sustaining the undifferentiated state were treated with 1 μM 4HT for 48 h or ethanol (vehicle) were collected. C2fl/fl[Cre] ESC were also differentiated for 4 days using the hanging drop method, with 4HT or ethanol treatment for the first 48 h,


title: CTCL1137_CD4P_PRE

description:
Library name: CTCL1137_CD4P_PRE
counts_vstCTCL2018donorSpecimen.txt


title: CVSN2c_Clone3-2

description: Library name: CVSN2c_Clone3-2


title: CTCL1024_SKIN_CD4P_CD7N_PRE

description:
Library name: CTCL1024_SKIN_CD4P_CD7N_PRE
counts_vstCTCL2018donorSpecimen.txt


title: WU1728_skin

description:
Library name: 1728-120519_skin.CCGAATTGTG-GCCGTCATAA
CTCL1728_120519_skin
counts_vstCTCL2021donorSpecimen.txt


title: WU1599_skin1

description:
Library name: 1599-060619_skin.AATTGGAGTC-ATGTGCCGTC
CTCL1599_060619_skin
counts_vstCTCL2021donorSpecimen.txt


title: CTCL1084_CD4P_CD7N_OW

description:
Library name: CTCL1084_CD4P_CD7N_OW
counts_vstCTCL2018donorSpecimen.txt


title: CTCL1160_CD4P_OW

description:
Library name: CTCL1160_CD4P_OW
counts_vstCTCL2018donorSpecimen.txt


title: CVSN2c_Clone1-2

description: Library name: CVSN2c_Clone1-2


title: CVSN2c_HighComplexityMainReplicate-2

description: Library name: CVSN2c_HighComplexityMainReplicate-2


title: CTCL1137_CD4P_OW

description:
Library name: CTCL1137_CD4P_OW
counts_vstCTCL2018donorSpecimen.txt


title: WU1663_skin

description:
Library name: 1663-081519_skin.CGCGGAGATT-GCAACATTGG
CTCL1663_081519_skin
counts_vstCTCL2021donorSpecimen.txt


title: CTCL1043_CD4P_CD7N_POST

description:
Library name: CTCL1043_CD4P_CD7N_POST
counts_vstCTCL2018donorSpecimen.txt


title: WU1645_skin

description:
Library name: 1645-071819_skin.TCGGATGAGG-GATCATCGTC
CTCL1645_071819_skin
counts_vstCTCL2021donorSpecimen.txt


title: WU1535_cd4

description:
Library name: 1535-112918_cd4.AGCTATCTTC-ATCACCAACA
CTCL1535_112918_cd4
counts_vstCTCL2021donorSpecimen.txt


title: emEC1_r2 ATACseq

description: Library name: emEC_WT_r2

value: Endothelial cells


title: WU1646_skin

description:
Library name: 1646-071819_skin.TGACGTGGTT-TTCCACCTGG
CTCL1646_071819_skin
counts_vstCTCL2021donorSpecimen.txt


title: WU1599_skin3

description:
Library name: 1599-092619_skin.TGACAATGAC-ATACCGCAAG
CTCL1599_092619_skin
counts_vstCTCL2021donorSpecimen.txt


title: WU1535_skin

description:
Library name: 1535-081519_skin.CATAAGCGAC-CTTCTAACCG
CTCL1535_081519_skin
counts_vstCTCL2021donorSpecimen.txt


title: WU1599_skin2

description:
Library name: 1599-071819_skin.GTACCTGGCT-ATACAGGTGT
CTCL1599_071819_skin
counts_vstCTCL2021donorSpecimen.txt


title: CTCL992_CD4P_FU

description:
Library name: CTCL992_CD4P_FU
counts_vstCTCL2018donorSpecimen.txt


title: HPE-100uM PQ_Rep3

city: Mumbai

first: Amitesh

last: Anand

state: Maharashtra

address: Homi Bhabha Road

department: DBS

country: India

institute: TIFR

description: Library name: Sample 24

data_processing:
Raw sequencing reads were mapped to the reference genome (NC_000913.3) using bowtie v1.1.2
Maximum insert size of 1000 and two maximum mismatches after trimming 3 bp at the 3' ends.
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments packageintersection mode
The dispersion and differential expression level of each gene were estimated using DESeq2
Transcripts per Million (TPM) were calculated by DESeq2
Assembly: NC_000913.3
Supplementary files format and content: csv, TPM counts

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Whole cell

extract_protocol:
Bacteria were grown in M9 minimal medium supplemented with 4 g/L glucose, with respective paraquat concentration, till their mid-exponential phase. The culture was harvested and immediately processed for RNA isolation. The cells were dissolved in TRIzol and incubated at 65oC for 15 min. RNA was obtained in an aqueous layer upon the addition of chloroform, which was then precipitated using chilled isopropanol. This RNA pellet was washed with alcohol and finally resuspended in RNase-free water. RNA was quantified using a nano spectrophotometer before being frozen at -80°C for later use.
RNA sequencing libraries were prepared using the QIAseq FastSelect rRNA depletion system (5S/16S/23S) in combination with the QIAseq RNA library preparation enzymes and buffers, following the manufacturer’s protocols. After library construction, final library concentrations were quantified using the Qubit dsDNA High Sensitivity assay, and library size distribution and quality were assessed with the Agilent high-sensitivity NGS fragment analysis system. Libraries were normalized and pooled at equimolar concentrations prior to sequencing, and the pooled libraries were sequenced on an Illumina NextSeq 2000 platform.

value: Whole cell


title: Day_4_differentiated_ETOH_treated_rep2

description: ESC differentiated for 4 days using the hanging drop method with ethanol treatment for the first 48 h


title: WU1351_skin

description:
Library name: 1351-040419_skin.AATTGTCGTG-TGGCACATTG
CTCL1351_040419_skin
counts_vstCTCL2021donorSpecimen.txt


title: CTCL079_CD4P_CD26N_OW

description:
Library name: CTCL079_CD4P_CD26N_OW
counts_vstCTCL2018donorSpecimen.txt


title: Yet3 deletion repeat #3

city: Rehovot

first: Naama

last: Barkai

state: --- Select a state ---

address: Herzl St 234

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

description: Library name: RNA-yet3-async-C.mat

data_processing:
Different samples were demultiplexed based on R2 barcode
Umi was extracted from R2 and added to R1 title
polyA tails and adapters were removed using cutadapt
remaining sequences were aligned to yeast genome and coverage over each gene (3') calculated
duplicates were removed using umi_tools
Assembly: R64-3-1
Supplementary files format and content: A table of genes with their correpsonidng reads in each sample

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: Cells were grown in SD medium

extract_protocol: RNA was extracted as described in Zung et al. 2025

treatment_protocol: no special treatment

value: yeast cells

value: HISDel1 LEU2Del0 MET15Del0 URA3Del0, DelYET3::NATR

value: exp. growth


title: Day_4_differentiated_4HT_treated_rep1

description: ESC differentiated for 4 days using the hanging drop method with 4-hydroxytamoxifen treatment for the first 48 h


title: Yet3 deletion repeat #2

description: Library name: RNA-yet3-async-B.mat


title: Day_0_ETOH_treated_rep3

description: ESC maintained in conditions sustaining the undifferentiated state were treated with ethanol for 48 h


title: Day_4_differentiated_ETOH_treated_rep1


title: Day_4_differentiated_4HT_treated_rep3


title: Day_0_ETOH_treated_rep1


title: CTCL1234_SKIN_CD4P_POST

description:
Library name: CTCL1234_SKIN_CD4P_POST
counts_vstCTCL2018donorSpecimen.txt


title: emEC1_r1 ATACseq

description: Library name: emEC_WT_r1


title: CTCL1024_CD4P_CD7N_OW

description:
Library name: CTCL1024_CD4P_CD7N_OW
counts_vstCTCL2018donorSpecimen.txt


title: HPE_Rep3

description: Library name: Sample 21


title: WU1548_skin

description:
Library name: 1548-060619_skin.TCTACAGCTA-TGTGAATTGG
CTCL1548_060619_skin
counts_vstCTCL2021donorSpecimen.txt


title: Day_0_4HT_treated_rep3

description: ESC maintained in conditions sustaining the undifferentiated state were treated with 1 μM 4HT for 48 h


title: CTCL1182_CD4P_NoTx

description:
Library name: CTCL1182_CD4P_NoTx
counts_vstCTCL2018donorSpecimen.txt


title: Day_0_4HT_treated_rep2


title: Day_4_differentiated_ETOH_treated_rep3


title: CTCL409_CD4P_POST

description:
Library name: CTCL409_CD4P_POST
counts_vstCTCL2018donorSpecimen.txt


title: WU1222_cd4

description:
Library name: 1222-100418_cd4.CATACCGCTG-TTAACACGCT
CTCL1222_100418_cd4
counts_vstCTCL2021donorSpecimen.txt


title: CTCL1159_CD4P_VOR_POST

description:
Library name: CTCL1159_CD4P_VOR_POST
counts_vstCTCL2018donorSpecimen.txt


title: LPE-100uM PQ_Rep3

description: Library name: Sample 18


title: CTCL1024_SKIN_CD4P_CD7N_OW

description:
Library name: CTCL1024_SKIN_CD4P_CD7N_OW
counts_vstCTCL2018donorSpecimen.txt


title: HPE-100uM PQ_Rep2

description: Library name: Sample 23


title: Day_0_4HT_treated_rep1


title: WU1350_skin

description:
Library name: 1350-111617_skin.GTAATCACGC-TATACCAGGA
CTCL1350_111617_skin
counts_vstCTCL2021donorSpecimen.txt


title: Control repeat #2

description: Library name: RNA-nat-async-B.mat

value: HISDel1 LEU2Del0 MET15Del0 URA3Del0, HO::NATR


title: Female normal protein (NP, F), RNAseq, rep 3

city: Charlottesville

first: Jennifer

last: Charlton

address: 409 Lane Rd. Room 2035

institute: University of Virginia

description: Library name: S19

data_processing:
After removing low-quality sequencing reads that failed the quality check and after trimming adapter sequences, the obtained sequences were aligned to the mouse GRCm39 reference genome and quantified gene expression by transcript counting (GENCODE release M36) using the STAR aligner.
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Kidney

extract_protocol:
RNA was extracted from a quarter of the left kidney that was stored in RNAlaterTM Stabilization solution using TRIZOL (Invitrogen™, 15596018).  The RNA was cleaned with RNeasy MinElute Cleanup Kit (Qiagen, 74204) with RNase-Free DNase Set (Qiagen, 79254). The RNA was reconstituted with RNase-free water to a final volume of 50 μl and stored at – 80 degrees.  RNA concentration and quality were measured with a NanoDrop™ One/OneC Microvolume UV–Vis Spectrophotometer (Thermo Fisher Scientific) and RIN were obtained from the Genome Analysis and Technology Core at UVA using an Agilent 4200 TapeStation system.  Bulk RNA-Seq was performed by Novogene.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: Kidney

value: Female

value: WT

value: Normal Protein


title: Female normal protein (NP, F), RNAseq, rep 2

description: Library name: S17


title: CTCL1135_CD4P_POST

description:
Library name: CTCL1135_CD4P_POST
counts_vstCTCL2018donorSpecimen.txt

value: PBMC


title: HPE-100uM PQ_Rep1

description: Library name: Sample 22


title: WU1269_ln

description:
Library name: 1269-112217_ln.GTCATCAGTA-CTTCCTAGGC
CTCL1269_112217_ln
counts_vstCTCL2021donorSpecimen.txt

source_name: lymph node

value: lymph node


title: WU1269_skin

description:
Library name: 1269-111419_skin.GCTTGAGACG-ACGCAAGAAG
CTCL1269_111419_skin
counts_vstCTCL2021donorSpecimen.txt


title: Yet3 deletion repeat #1

description: Library name: RNA-yet3-async-A.mat


title: HPE_Rep2

description: Library name: Sample 20


title: Yet3 Overexpression repeat #3

description: Library name: RNA-pTef2Yet3-async-C.mat

value: HISDel1 LEU2Del0 MET15Del0 URA3Del0, NATR::TEFpr-YET3


title: WU1161_cd4

description:
Library name: 1161-101118_cd4.GTATGACTTC-ATACGCTAGA
CTCL1161_101118_cd4
counts_vstCTCL2021donorSpecimen.txt


title: panicle, OsSh1_2, Input

first: He

last: wei

state: Beijing

address: China agriculture university

institute: China agriculture university

data_processing:
Use STAR (2.5.3a) to locate clean reading segments to the reference genome
Assembly: Os-Nipponbare-Reference-IRGSP-1.0, MSU7
Supplementary files format and content: bigwig

organism: Oryza sativa

source_name: panicle

growth_protocol: All plants were grown in field conditions in Beijing or Sanya, Hainan province, China

extract_protocol:
Chromatin was isolated from the samples using sucrose gradient centrifugation and sonicated to produce DNA fragments using Bioruptor Plus sonication device (UCD-300)
Immunoprecipitation was performed with anti-GFP (Abcam) or IgG as described by He et al. (2013)
2g SH1-GFP transgene lines were harvested and washed them three times with distilled water
30 ml of 1% formaldehyde was added and the sample was fixed in vacuum for 5 minutes, released from vacuum, and fixed for 8 minutes
performed routine ChIP experiments with Anti GFP tag antibody (ab290)
sequenced the immunoprecipitated DNA on the Illumina Novaseq6000 platform.

value: panicle

tag: chip antibody


title: Male normal protein (NP, M), RNAseq, rep 5

description: Library name: S15

value: Male


title: WU1161_skin

description:
Library name: 1161-011917_skin.CCAAGCACAA-GATGCCGAAC
CTCL1161_011917_skin
counts_vstCTCL2021donorSpecimen.txt

value: skin


title: WU1222_skin

description:
Library name: 1222-100418_skin.CCATCTGGAA-ATCCTCCGAC
CTCL1222_100418_skin
counts_vstCTCL2021donorSpecimen.txt


title: panicle, OsSh1_2, GFP, ChIP

value: GFP antibody


title: LPE-10uM PQ_Rep1

description: Library name: Sample 13


title: Male normal protein (NP, M), RNAseq, rep 3

description: Library name: S13


title: CTCL1126_CD4P_POST

description:
Library name: CTCL1126_CD4P_POST
counts_vstCTCL2018donorSpecimen.txt


title: LPE-10uM PQ_Rep2

description: Library name: Sample 14


title: HPE_Rep1

description: Library name: Sample 19


title: LPE_Rep3

description: Library name: Sample 12


title: Yet3 Overexpression repeat #1

description: Library name: RNA-pTef2Yet3-async-A.mat


title: WU1159_skin2

description:
Library name: 1159-020220_skin2.GTCAACACCA-GCAGTGTATC
CTCL1159_020220_skin2
counts_vstCTCL2021donorSpecimen.txt


title: Yet3 Overexpression repeat #2

description: Library name: RNA-pTef2Yet3-async-B.mat


title: panicle, OsSh1_1, GFP, ChIP


title: Control repeat #3

description: Library name: RNA-nat-async-C.mat


title: WU1211_cd4

description:
Library name: 1211-102518_cd4.AAGGCAAGTT-GACAATGCGG
CTCL1211_102518_cd4
counts_vstCTCL2021donorSpecimen.txt


title: LPE-100uM PQ_Rep2

description: Library name: Sample 17


title: Male normal protein (NP, M), RNAseq, rep 2

description: Library name: S12


title: WU1145_cd4

description:
Library name: 1145-101818_cd4.AATGTCGGTT-ACGTAGCTCA
CTCL1145_101818_cd4
counts_vstCTCL2021donorSpecimen.txt


title: WU1211_skin

description:
Library name: 1211-092117_skin.TCCTGTACAC-GACTCTAGTT
CTCL1211_092117_skin
counts_vstCTCL2021donorSpecimen.txt


title: LPE-100uM PQ_Rep1

description: Library name: Sample 16


title: Control repeat #1

description: Library name: RNA-nat-async-A.mat


title: WU1159_skin1

description:
Library name: 1159-020220_skin1.TCCGTTCCAC-ATGAGCTACA
CTCL1159_020220_skin1
counts_vstCTCL2021donorSpecimen.txt


title: Female normal protein (NP, F), RNAseq, rep 1

description: Library name: S16


title: LPE-10uM PQ_Rep3

description: Library name: Sample 15


title: WT_100uM PQ_Rep2

description: Library name: Sample 8


title: WU1159_cd4

description:
Library name: 1159-091919_cd4.TCCGTAGGTA-TGTTGCACTA
CTCL1159_091919_cd4
counts_vstCTCL2021donorSpecimen.txt


title: Female low protein (LP, F), RNAseq, rep 4

description: Library name: S9

value: Low Protein


title: G3_J365_p20-3_912345_2_1

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

hyb_protocol: Agilent-026655 Whole Mouse Genome Microarray 4x44K v2 were scanned on an Agilent G2505B scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version V.10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

source_name: leukemia cells

label_protocol: manufacturer's instructions

growth_protocol: 1 million of B16F1-GFP-M, B16F1-GFP-D, B16F1-GFP-DB#1,  B16F1-GFP-DB#2 and B16F1-GFP-DB#3 melanoma cells were cultured in DMEM 10% FBS medium.

extract_protocol: Total RNA extracted using manufacturer's instructions

treatment_protocol: The cells were rinsed twice with sterile PBS. Total RNA extraction was performed following the manufacturer's protocol (RNeasy Kit, Qiagen, Courtaboeuf, France) with optional DNase treatment.

value: leukemia cells


title: Female low protein (LP, F), RNAseq, rep 3

description: Library name: S8


title: Male normal protein (NP, M), RNAseq, rep 4

description: Library name: S14


title: panicle, OsSh1_1, Input


title: LPE_Rep2

description: Library name: Sample 11

value: Whole cell


title: G1_J365-p20-1_912432_1_3


title: WU1181_cd4

description:
Library name: 1181-110118_cd4.CCGTATTAAG-ACCTCCGCTA
CTCL1181_110118_cd4
counts_vstCTCL2021donorSpecimen.txt


title: WU1126_cd4

description:
Library name: 1126-100518_cd4.AACACGGTGA-TAGCGCAATA
CTCL1126_100518_cd4
counts_vstCTCL2021donorSpecimen.txt


title: Male normal protein (NP, M), RNAseq, rep 1

description: Library name: S11


title: G0_J365-p20_912346_2_2


title: WT_10uM PQ_Rep3

description: Library name: Sample 6


title: LPE_Rep1

description: Library name: Sample 10


title: WU1008_skin

description:
Library name: 1008-042116_skin.AACACGCTTG-TATCATGTCG
CTCL1008_042116_skin
counts_vstCTCL2021donorSpecimen.txt


title: F2_M0-p20-2_912432_2_4


title: WT_10uM PQ_Rep2

description: Library name: Sample 5


title: WT_Rep3

description: Library name: Sample 3


title: Female low protein (LP, F), RNAseq, rep 5

description: Library name: S10


title: WU1137_skin

description:
Library name: 1137-092619_skin.CCATCAAGGA-CTGCCTCATC
CTCL1137_092619_skin
counts_vstCTCL2021donorSpecimen.txt


title: F0_M0-p20_912346_1_4


title: WU1137_ln

description:
Library name: 1137-052620_ln.AGACGCTGTG-ACCGTGCTTC
CTCL1137_052620_ln
counts_vstCTCL2021donorSpecimen.txt


title: Female low protein (LP, F), RNAseq, rep 2

description: Library name: S7


title: WT_100uM PQ_Rep1

description: Library name: Sample 7


title: BGLT3 OE DRIP input rep2

first: Zhongyang

last: Chen

address: No.5, Dongdan Santiao, Dongcheng District

institute: School of Basic Medicine, Peking Union Medical College (PUMC)

data_processing:
(Sample 43-50) For analyses, all reads were aligned to reference Homo sapiens genome (Ensembl GRCh38.92) using STAR, and uniquely mapped reads were retained.
Peaks of each sample were then called using MACS2 against its corresponding input with configurations: "-g 3.2e9 -p 1e-5".
Assembly: GRCh38
Supplementary files format and content: peak text file, bw file
Library strategy: DRIP-Seq

growth_protocol: (Sample 43-50) For DRIP-seq BGLT3 overexpression in K562 cell line: Human erythroleukemia cell line K562 was maintained in RPMI1640 supplemented with 10% FBS (Gibco, Carlsbad, CA, USA).

extract_protocol:
The harvested viral particles were added into the K562 cells plus with 8 µg/ml polybrene for 12 hours. Then the cells were replaced with fresh complete medium and subjected to the following experiments.
About 2×107 K562 cells were crosslinked by 1% formaldehyde followed by sonication. Lysates were clarified from sonicated chromatin and RNA-DNA complexes were isolated by S9.6 antibody on Protein A Dynabeads according to the protocol published by Sanz, L.A., et al., 2019. Then the DNA was purified for subsquential processes.
Libraries were prepared according to NEB's instructions accompanying the NEBNext Ultra II DNA Library Prep Kit (E7103S) and NEBNext Multiplex Oligos for Illumina (E7335S).


title: WT_Rep1

description: Library name: Sample 1


title: Male low protein (LP, M), RNAseq, rep 2

description: Library name: S2


title: F2_M0-p20-3_912346_1_1


title: E1_B16-D-739-1_912346_2_3

source_name: melanoma cells

value: melanoma cells


title: E2_B16-D-739-2_912345_1_4


title: WU1126_skin

description:
Library name: 1126-110118_skin.CGACTAACGT-CTCTATACTG
CTCL1126_110118_skin
counts_vstCTCL2021donorSpecimen.txt


title: WT_100uM PQ_Rep3

description: Library name: Sample 9


title: d7DBZ TTchem-seq R2

city: London

first: Folkert

last: van Werven

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

description: Library name: d7DBZ TTchem-seq R2

data_processing:
TT-TSS-seq and Poly(A)-TSS-seq read demultiplexing was performed using Ultraplex with parameters “--phredquality 15 --min_length 0”. Adaptor trimming was performed using Cutadapt with parameters “--minimum-length 20”. Bowtie 2 was used for pre-mapping to ribosomal and small RNAs. Genome mapping was performed using STAR, for mouse samples with Ensembl GRCm38 (mm10) release-89 annotation. Umitools was used for deduplication. BEDTools was used to identify the 5’-most nucleotide (tag) and for genome-wide comparative analyses.
RNA-seq and TT-chem-seq time course analysis read processing using nf-core/rnaseq (3.13.2). Adaptor and quality trimming were performed using Trim Galore! (minimum trimmed read threshold: 10,000). Genome mapping was performed using STAR with Ensembl GRCm38 (mm10) release-89 annotation (minimum uniquely mapped read threshold: 5%). Transcript assembly was performed using StringTie.
Assembly: GRCm38 (mm10)
Supplementary files format and content: processed files are higher bigwig or bedgraphs

growth_protocol: mESCs (HM-1) cells that had been passaged at least twice post-thawing were used for differentiation. The protocol for spinal cord motor neuron differentiation was adapted. Cells were lifted and resuspended in N2B27 (49% DMEM/F12-/- (Gibco), 49% Neurobasal (Gibco), 1X N2 (Gibco), 1X B27 (Gibco), 0.05 mM 2-Mercaptoethanol (Gibco), 2mM L-Glutamine (Gibco)) with bFGF (10 ng/ml, Bio-Techne, 3139-FB-025) before 85,000 cells were plated on Geltrex- (or Matrigel-) coated 6-well plates in N2B27 with bFGF (10 ng/ml). 48 hours later the media was changed to N2B27 with bFGF (10ng/ml), CHIR99021 (5μM, Axon MedChem, 1386), SB 431542 (10uM, Cambridge Bioscience S0400) and DMH1 (2uM, Cambridge Bioscience, 16679). 20 hours later the media was changed to N2B27 with 100 nM RA (Sigma Aldrich, R2625) and 100 nM SAG (Merck, 566660). After this, the media was replaced every 24 hours for up to 7 days of total differentiation. Treatment with 10 µg/ml notch inhibitor DBZ (Tocris 4889) occurred from day 5 onwards.

extract_protocol:
RNA was extracted from mESCs and NIH/3T3 fibroblasts by the standard TRIzol extraction procedure (Thermo Fisher). rDNase (Qiagen) digestion was carried out, and purification was performed by spin column (Qiagen) or by phenol: chloroform extraction and ethanol precipitation.  4SU labelling was carried out as detailed previously, with a few modifications. Cell culture media was removed, filtered, and 1 mM 4SU (Glentham Life Sciences) was added. The cells were returned to the incubator and labelled with 4SU for 15 minutes before medium aspiration and TRIzol addition. 1/5 volume of chloroform was added, followed by isopropanol precipitation. The pellet was then washed with 85% ethanol, dried, and resuspended. RNA integrity was checked for a selection of samples using Bioanalyzer (Agilent Technologies). 4SU incorporation was assessed using a slot blot. RNA clean-up was performed by phenol/chloroform/isoamyl alcohol, and precipitation by isopropanol. The pellet was washed with 85% ethanol, dried, and resuspended.
The TT-TSS-seq and Poly(A)-TSS-seq methods were previously described in detail. In short, total RNA was dephosphorylated with quickCIP (NEB, 1.2 U/µg RNA. RNA was extracted using phenol/chloroform/isoamyl alcohol. RNA was treated with mRNA decapping enzyme (NEB, 0.7 U/µg RNA) followed by purification by phenol/chloroform/isoamyl alcohol. RNA and the 5’ adaptor ligation was performed T4 RNA ligase I (30 U). RNAClean XP (1.8X ratio, Beckman Coulter) was used to remove unligated adaptors, according to the manufacturer’s instructions. Poly(A)+ RNA was enriched using Dynabeads Oligo(dT)25 (Thermo Fisher), or 4SU+ RNA was purified as detailed in the TT-chem-seq protocol. RNA was fragmented, and 3’ ends were fixed by quickCIP treatment (NEB, 30 U). Pre-adenylated 3’ adaptor (2 µM) were denatured and ligation was carried out by T4 Rnl2tr (NEB,200 U). Reverse transcription was carried out by SuperScript III (2 µl, Invitrogen). AMPure XP beads (Agencourt, Beckman Coulter) were used to clean up the cDNA. cDNA pre-amplification was performed with i5_s and i7_s (300 nM each) primers and Phusion HF PCR Mastermix (Thermo Fisher). 6 PCR cycles were carried. ProNex beads (Promega) with a 1:2.95 ratio to sample were used to remove sequences less than 55 nt (including primer dimers). Final amplification was carried out with NEBNext i50 and i70 primers (500 nM each) and Phusion HF PCR Mastermix, for 8 cycles. Amplification was checked by using Novex 6% TBE (Tris/Borate/EDTA) gel and staining with SYBR Green.For RNA-seq, libraries were prepared using NEB ultra II, with poly(A)+ purification, according to the manufacturer's protocol. Sequencing was performed on NovaSeq 6000 (Illumina) using 100 bp paired-end reads.  For TTchem-seq, at least 10 ng of eluted RNA was used for library preparation with NEBNext Ultra II Directional Poly(A) mRNA, according to the manufacturer’s protocol for fragmented RNA. Libraries were sequenced using NovaSeq 6000 (Illumina) as 100 bp paired-end reads.

value: mESC

value: day 7 DBZ


title: BGLT3 KD rep1, Day8

description: Library name: Sample 13

data_processing:
(Sample 1-6) The raw reads were trimmed low quality reads and adapter sequence using Trimmomatic  with “ILLUMINACLIP: ~/adapters/TruSeq3-PE-2.fa:2:30:10:5:true SLIDINGWINDOW:4:15 MINLEN:50”. Then trimmed reads were aligned to reference Homo sapiens genome (Ensembl GRCh38.92) using STAR. For sample 1-2, uniquely mapped reads were retained for calculating gene counts by FeatureCounts  with default parameter.
(Sample 3-4) Uniquely mapped reads were retained for calculating gene counts by FeatureCounts  with two parameters separately: “-t exon -C -J” (for exon reads and exon–exon junction reads) and “-t gene -C -J” (for all exon and intron reads). The SRRM2 protein-bound transcripts were identified by DESeq2  with P-value < 0.05 and Enrichment (IP versus Input) > 1.2. The splicing efficiency(SE) metric was computed as the fraction of exon counts over intron + exon (total) counts, and the transcripts with SE ≤1.01 and SE > 0.99 were considered as mature transcripts.
(Sample 5-6) Uniquely mapped reads were retained for calculating gene counts by FeatureCounts  with default parameter. The NPAT protein-bound transcripts were identified with Padj-value < 0.05 and Enrichment (IP versus Input) > 2.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
(Sample 7-10) All reads were aligned to reference Homo sapiens genome (Ensembl GRCh38.92) using STAR , and uniquely mapped reads were retained for calculating gene counts by FeatureCounts  with default parameter. Differential gene expression analyses was conducted using DESeq2  with the P-value < 0.05 and |FoldChange| (BGLT3 KD versus Control) > 1.2.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
(Sample 11-14) All reads were aligned to reference Homo sapiens genome (Ensembl GRCh38.92) using STAR , and uniquely mapped reads were retained for calculating gene counts by FeatureCounts  with two parameters separately: “-t exon -C -J” (for exon reads and exon–exon junction reads) and “-t gene -C -J” (for all exon and intron reads).The splicing efficiency(SE) metric was computed as the fraction of exon counts over intron + exon (total) counts, and the transcripts with SE ≤1.01 and SE > 0.99 were considered as mature transcripts. The differentially spliced genes were defined as |FoldChange| (BGLT3 KD versus Control) > 0.3.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: HSPC

growth_protocol:
(Sample 1-6) For UV RIP-seq on day 8 of erythroid differentiation: CD34+ cells cultured in IMDM medium supplemented with 20% BIT,5ng/ml IL-3, 100 ng/ml hSCF ,1 μM Hydrocortisone and 3 U/ml human hEPO for 8 days.
(Sample 7-10) For GRO-seq on day 8 of erythroid differentiation: CD34+ cells cultured in IMDM medium supplemented with 20% BIT,5ng/ml IL-3, 100 ng/ml hSCF ,1 μM Hydrocortisone and 3 U/ml human hEPO for 8 days.
(Sample 11-14) For RNA-seq on day 8 of erythroid differentiation: CD34+ cells cultured in IMDM medium supplemented with 20% BIT,5ng/ml IL-3, 100 ng/ml hSCF ,1 μM Hydrocortisone and 3 U/ml human hEPO for 8 days.

extract_protocol:
The cells were collected and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.
Total RNA was extracted according to the manufacturer’s protocol. Fragmentation of the extracted total RNA was performed using RNA Fragmentation Reagents. To Purify the Fragmented NRO-RNA Through p-30 RNase-free Spin Column. Newly synthesized BrdU-labeled RNA was immunopurified using agarose Beads conjugated BrdU antibody. Fragmented RNA underwent end repair, 3’ adapter ligation, reverse transcription, and 5’ adapter ligation using the Illumina TruSeq Small RNA kit. The resulting cDNA libraries were amplified by PCR, purified, and size-selected (typically 150-300 bp) using agarose gel electrophoresis.
Small RNA libraries were prepared using the TruSeq Small RNA Sample Preparation Kit (Illumina, Cat. No. RS-200-0048) according to the manufacturer's instructions.
The cells were collected and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: HSPC


title: DA_B16-D-735-1_912345_2_2


title: Female low protein (LP, F), RNAseq, rep 1

description: Library name: S6

value: Kidney

value: Female


title: F1_M0-p20-1_912345_2_3


title: BGLT3 DRIP input rep2


title: WU1137_cd4

description:
Library name: 1137-073020_cd4.AATACACGGA-TAGGTGATCT
CTCL1137_073020_cd4
counts_vstCTCL2021donorSpecimen.txt


title: plko rep1, Day8

description: Library name: Sample 11


title: D0_B16-D-735_912346_1_3


title: runon BGLT3 KD rep2, Day8

description: Library name: Sample 10

molecule: nuclear RNA


title: BGLT3 DRIP rep2


title: Male low protein (LP, M), RNAseq, rep 4

description: Library name: S4

value: WT


title: Male low protein (LP, M), RNAseq, rep 5

description: Library name: S5


title: d6 TTchem-seq R2

description: Library name: d6 TTchem-seq R2

value: day 6


title: WU1008_cd4

description:
Library name: 1008-010517_cd4.AGATAGCACA-ATGGCGTACG
CTCL1008_010517_cd4
counts_vstCTCL2021donorSpecimen.txt

value: PBMC


title: BGLT3 DRIP rep1


title: Male low protein (LP, M), RNAseq, rep 3

description: Library name: S3


title: C7_B16-D-733-1_23-02-2017_912432_2_2


title: C0_B16-D-733_912346_1_2


title: WT_Rep2

description: Library name: Sample 2


title: B9_B16-D-3_23-02-2017_912432_1_1


title: BGLT3 OE DRIP input rep1


title: NPAT IP rep2, Day8

description: Library name: Sample 6


title: d5 TTchem-seq R1

description: Library name: d5 TTchem-seq R1

value: day 5


title: E0_B16-D-739_912432_1_2


title: Male low protein (LP, M), RNAseq, rep 1

description: Library name: S1


title: WT_10uM PQ_Rep1

description: Library name: Sample 4


title: BGLT3 OE DRIP rep2


title: BGLT3 KD rep2, Day8

description: Library name: Sample 14


title: d4 TTchem-seq R2

description: Library name: d4 TTchem-seq R2

value: day 4


title: SNHG3 even rep1

data_processing:
(Sample 17-42) For all datasets, reads were aligned to reference Homo sapiens genome (Ensembl GRCh38.92) using Bowtie2. Only reads with mapping quality score >30 were retained for further analyses by SAMtools. And per-base coverage was normalized in accordance with previous studies(Chu et al., 2011). For each base pair of the genome, true coverage of this base in this sample was defined as the minimum coverage of the even lane and odd lane and a SAM file was generated for peak calling.
(Sample 17-28) For BGLT3 and BGLT3-KD IP and Input datasets, parameters used for peak calling were “--bw 200 -m 10 50 -g hs”. The peaks of increased or unchanged enrichment of BGLT3-KD binding and BGLT3 binding at the same location of the genome were filtered out, which was considered as background noise caused by non-specificity.
(Sample 29-42) For AC024267.1, SNHG1 and SNHG3 IP and Input datasets, peaks of each sample were then called using MACS2 against its corresponding input with following configurations: "--bw 200 -m 10 50 -g hs -p 1e-5".
(Sample 17-42) We filtered for peaks with substantial correlation of the raw data profile, and high coverage across the peaks were accepted. For all ChIRP-seq samples, thresholds of average coverage >2, fold enrichment >3 and peak correlation >0.5.
These peaks were annotated by HOMER and the enrichment of RNA binding sites on the genomic region was calculated by HOMER 'annotatePeaks.pl'. The peaks used in the further analysis were extended 150bp from the center of the standard peak upstream and downstream respectively.
Assembly: GRCh38
Supplementary files format and content: peak text file, bw file
Library strategy: ChIRP-Seq

growth_protocol: (Sample 17-42) For ChIRP-seq in K562 cell line: Human erythroleukemia cell line K562 was maintained in RPMI1640 supplemented with 10% FBS (Gibco, Carlsbad, CA, USA).

extract_protocol:
About 2×107 K562 cells were crosslinked by 1% glutaraldehyde followed by sonication. Lysates were clarified from sonicated chromatin and RNA-DNA complexes were isolated by antisense biotinylated oligos on streptavidin beads according to the protocol published by Chu et al., 2011. Then the DNA was purified by PhOH:Chloroform: Isoamyl for subsquential processes.
Libraries were prepared according to NEB's instructions accompanying the NEBNext Ultra II DNA Library Prep Kit (E7103S) and NEBNext Multiplex Oligos for Illumina (E7335S).


title: NPAT IP rep1, Day8

description: Library name: Sample 5


title: BGLT3 OE DRIP rep1


title: B0_16D_912345_1_2


title: D2_B16-D-735_912432_2_1


title: d3 TTchem-seq R2

description: Library name: d3 TTchem-seq R2

value: day 3


title: d7DBZ TTchem-seq R1

description: Library name: d7DBZ TTchem-seq R1


title: A2_B16-M-2_912345_1_3


title: SNHG1 odd rep1


title: d2 TTchem-seq R2

description: Library name: d2 TTchem-seq R2

value: day 2


title: plko rep2, Day8

description: Library name: Sample 12


title: UV-RIP input rep1, Day8

description: Library name: Sample 1


title: A0_B16-M_912432_2_3


title: SNHG1 even rep1


title: BGLT3 DRIP input rep1


title: SNHG1 even rep2


title: d7 TTchem-seq R1

description: Library name: d7 TTchem-seq R1

value: day 7


title: C9_B16-D-733-1_23-02-2017_912432_1_4


title: d0 TTchem-seq R2

description: Library name: d0 TTchem-seq R2

value: day 0


title: C8_B16-D-733-2_23-02-2017_912345_1_1


title: d7 TTchem-seq R2

description: Library name: d7 TTchem-seq R2


title: AC024267.1 odd rep2


title: runon BGLT3 KD rep1, Day8

description: Library name: Sample 9


title: runon plko rep2, Day8

description: Library name: Sample 8


title: runon plko rep1, Day8

description: Library name: Sample 7


title: d6 TTchem-seq R1

description: Library name: d6 TTchem-seq R1


title: SNHG3 odd rep2


title: d5 TTchem-seq R2

description: Library name: d5 TTchem-seq R2


title: d7DBZ RNA-seq R2

description: Library name: d7DBZ RNA-seq R2


title: SNHG3 odd rep1


title: ML2 R shRNA  TAZ #1 n3

city: Lyon

first: Kevin

last: Geistlich

address: 28 rue Laennec

institute: CRCL

description: Library name: shTAZ1_3

data_processing:
Galaxy US
shTAZ1_3 has been concatenated with the use of "concatenate multiple datasets" module from Galaxy US. Sequences were trimmed using Trim Galore! (parameters: Remove N bp from the 3' end of read 1 and read 2 = 15 ; Remove N bp from the 5' end of read 1 and read 2 = 15)
Sequences were mapped to Human (Homo sapiens) (b38): hg38 with RNA-seq aligner STAR (parameters: Elements to use from the gene model to use for splice junctions = exon ; Length of the genomic sequence around annotated junctions = 100 ; MAPQ value for unique mappers = 60)
Read count extraction was performed using featureCounts
Normalization was performed using DESeq2 (parameters: fit type = parametric ; Alpha value for MA-plot = 0.1)
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Peripheral Blood

extract_protocol:
Cell lines were lysed in TRI Reagent (Sigma, T9424) and RNA was extracted with Direct-zol RNA MicroPrep kit (Ozyme, ZR2062).
Libraries were prepared with Novogene poly A enrichment strategy. cDNA double strands have been synthetized, then ligation of adaptors and library amplification have been added to the sequences.

value: Peripheral Blood

value: ML2 Resistant

value: acute myelomonocytic leukemia


title: AC024267.1 even rep1


title: B8_B16-D-2_23-02-2017_912346_2_1

value: melanoma cells


title: SNHG3 even rep2


title: Lnc ChIRP input rep2


title: B7_B16-D-1_23-02-2017_912345_2_4


title: Hs374_GFP

city: Malmö

first: Jones

middle: K

last: Ofori

address: Jan Waldenströms gata 35

department: Department of Clinical Sciences

country: Sweden

institute: Lund University

description: Gene expression data from human islets

hyb_protocol: 2.3 µg of fragmented and labelled sscDNA target was hybridized to Clariom™ S Human/Rat Arrays for 16 h at 45°C under rotation in Affymetrix Gene Chip Hybridization Oven 645 (ThermoFisher Scientific)

scan_protocol: The fluorescent intensities were determined with Affymetrix GeneChip Scanner 3000 7G (ThermoFisher Scientific)

data_processing: Data were processed using the Transcriptome Analysis Console (TAC) and the SST-RMA analysis method including log2-transformation, quantile normalization, background correction and summarization. Annotations are based on build hg38/GRCh38 and were collected from TAC

source_name: Human pancratic islets

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5.5 ug total RNA

growth_protocol: 100-200 handpicked human islets were seeded in culture dishes containing RPMI 1640 media (#11879020, ThermoFisher Scientific) with 5mM glucose, 10% FBS, 200mM L-glutamine

extract_protocol: Total RNA was extracted from human islets after overexpressiong ONECUT2  (N=6 donors) using the miRNeasy isolation kit (QIAGEN) according to the manufacturer’s recommendations

treatment_protocol: For overexpression experiments, lentiviral plasmids containing the human phosphoglycerate kinase 1 promoter in front of cDNA of human ONECUT2  or the cDNA for GFP, were cloned by Genscript (Piscataway, NJ, USA)

value: Male


title: d7 RNA-seq R2

description: Library name: d7 RNA-seq R2

value: mESC


title: d7DBZ RNA-seq R1

description: Library name: d7DBZ RNA-seq R1

value: day 7 DBZ


title: Hs373_ONECUT2

description: Gene expression data from human islets


title: d4 TTchem-seq R1

description: Library name: d4 TTchem-seq R1


title: SRRM2 IP rep2, Day8

description: Library name: Sample 4

value: HSPC


title: SRRM2 IP rep1, Day8

description: Library name: Sample 3


title: Hs373_GFP

description: Gene expression data from human islets


title: SNHG1 odd rep2


title: d3 TTchem-seq R1

description: Library name: d3 TTchem-seq R1

value: WT


title: ML2 R shRNA  control n3

description: Library name: shCtl_3


title: UV-RIP input rep2, Day8

description: Library name: Sample 2


title: BGLT3 KD ChIRP input rep2


title: A1_B16-M-1_912346_2_4


title: Hs371_ONECUT2

description: Gene expression data from human islets

value: Female


title: d7 RNA-seq R1

description: Library name: d7 RNA-seq R1


title: d6 RNA-seq R2

description: Library name: d6 RNA-seq R2

value: day 6


title: Hs375_ONECUT2

description: Gene expression data from human islets


title: d2 TTchem-seq R1

description: Library name: d2 TTchem-seq R1


title: ML2 R shRNA  TAZ #2 n3

description: Library name: shTAZ2_3


title: BGLT3 KD odd rep2


title: BGLT3 KD odd rep1


title: Knockout

first: Clair

last: Crewe

address: 660 S Euclid Avenue

institute: Washington Univeristy in St. Louis

description: Library name: Knockout

data_processing:
The demultiplexing, barcoded processing, gene counting were made using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Mouse mm10
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: subcutaneous white adipose

extract_protocol:
12 week-old male mice were fed chow diet supplemented with 600 mg/kg doxycycline for 2 weeks and SVF cells were isolated from sWAT as described above. SVF was harvested from sWAT as described above. After centrifugation the cells were resuspended in 2% FBS in PBS containing propidium iodide (PI; 1:400) for 15 min incubation on ice. After washing, the cells were resuspended in 2% FBS in PBS for sorting of viable cells, PI- cells. FACS was conducted with a BD Bioscience FACSAria cytometer at the Flow Cytometry Core Facility at UT Southwestern.
Single-cell RNA-seq libraries were prepared using the 10x Genomics Chromium Single Cell 3′ Gene Expression v3.1 (Dual Index) kit according to the manufacturer’s protocol and sequenced on an Illumina NextSeq 2000 with paired-end reads (28 bp Read 1, 90 bp Read 2; 10 bp i7 and 10 bp i5).

value: subcutaneous white adipose

value: stromal vascular fraction

value: adiponectin rtTA, TRE Cre, Smpd3 flox


title: BGLT3 KD even rep2


title: ML2 R shRNA  control n1

description: Library name: shCtl_1


title: AC024267.1 odd rep1


title: ML2 R shRNA  TAZ #2 n2

description: Library name: shTAZ2_2


title: Hs369_ONECUT2

description: Gene expression data from human islets


title: GSCs, shSCD5-4, Day4

first: Hayk

last: Mnatsakanyan

address: 149 13th Street Charlestown

department: Neurology

institute: Massachusetts General Hospital

description: Library name: shscd5_4

data_processing:
Subread alignment (Subjunc)
ENTREZ annotation
FeatureCount was used for quantifying the number of reads
R DESeq2 package for differential gene expression
Assembly: GRCh38
Supplementary files format and content: txt processed_data file contains raw counts data

extract_protocol:
Quick-RNA Miniprep (Zymo)
NEBNext Ultra II RNA Library Prep Kit for Illumina/NEBNext Poly(A) mRNA Magnetic Isolation Module

value: Glioma stem cells


title: BGLT3 KD even rep1


title: Hs375_GFP

description: Gene expression data from human islets


title: Control

description: Library name: Control

value: adiponectin rtTA, Smpd3 flox


title: d0 TTchem-seq R1

description: Library name: d0 TTchem-seq R1

value: day 0


title: Hs369_GFP

description: Gene expression data from human islets


title: GSCs, shSCD5-2, Day4

description: Library name: shscd5_2


title: d3 RNA-seq R2

description: Library name: d3 RNA-seq R2

value: day 3


title: ML2 R shRNA  TAZ #2 n1

description: Library name: shTAZ2_1

value: Peripheral Blood

value: ML2 Resistant


title: Hs368_NC

description: Gene expression data from human islets

extract_protocol: Total RNA was extracted from human islets after silencing ADCY9 using siADCY9 (N=5 donors) using the miRNeasy isolation kit (QIAGEN) according to the manufacturer’s recommendations

treatment_protocol: Human islets were then transfected in a final volume of 2.5 mL per dish containing serum free Opti-MEM, 6.25 μL of Lipofectamine RNAiMAX, 50nM of Silencer® Select Pre-Designed siRNA against ADCY9 (s1037)


title: Hs367_NC

description: Gene expression data from human islets


title: AC024267.1 even rep2


title: Hs374_ONECUT2

description: Gene expression data from human islets


title: BGLT3 odd rep1


title: ML2 R shRNA  TAZ #1 n1

description: Library name: shTAZ1_1

value: acute myelomonocytic leukemia


title: ML2 R shRNA  TAZ #1 n2

description: Library name: shTAZ1_2


title: d0 RNA-seq R2

description: Library name: d0 RNA-seq R2


title: Lnc ChIRP input rep1


title: BGLT3 KD ChIRP input rep1


title: ML2 R shRNA  control n2

description: Library name: shCtl_2


title: Hs370_ONECUT2

description: Gene expression data from human islets

value: Male


title: d6 RNA-seq R1

description: Library name: d6 RNA-seq R1

value: mESC


title: d7DBZ TT-TSS-seq R2

description: Library name: d7DBZ TT-TSS-seq R2

value: day 7 DBZ


title: Hs365_NC

description: Gene expression data from human islets


title: d5 RNA-seq R2

description: Library name: d5 RNA-seq R2

value: day 5


title: Hs370_GFP

description: Gene expression data from human islets


title: Hs371_GFP

description: Gene expression data from human islets


title: d5 RNA-seq R1

description: Library name: d5 RNA-seq R1

value: WT


title: d4 RNA-seq R2

description: Library name: d4 RNA-seq R2

value: day 4


title: d4 RNA-seq R1

description: Library name: d4 RNA-seq R1


title: EKLF rep1, Day8

data_processing:
(Sample 9-16) For analysis, the raw reads were trimmed low quality reads and adapter sequence using Trimmomatic with “ILLUMINACLIP: ~/adapters/NexteraPE-PE.fa:2:30:10:1:true SLIDINGWINDOW:4:15 MINLEN:50”.
Then trimmed reads were aligned to reference Homo sapiens genome (Ensembl GRCh38.92) using STAR, and uniquely mapped reads were retained.
For peak calling, parameters used were MACS2 callpeak with “-t bam_file -p 1e-5 -keep-dup all”. These peaks were annotated by HOMER and the enrichment of RNA binding sites on the genomic region was calculated by HOMER 'annotatePeaks.pl'.
Assembly: GRCh38
Supplementary files format and content: peak text file, bw file
Library strategy: CUT&Tag

growth_protocol: (Sample 9-16) For CUT&Tag on day 8 of erythroid differentiation: CD34+ cells cultured in IMDM medium supplemented with 20% BIT,5ng/ml IL-3, 100 ng/ml SCF ,10^-6 M Hydrocortisone and 3 U/ml human EPO for 8 days.

extract_protocol:
1 × 105 HSPC cells were harvested freshly. The cells were enriched by ConA Beads and antibody. Then the beads were washed for 3 times using antibody buffer and then incubated with proteinA/G-Tn5 transposome for 1 h and washed for 3 times by ChiTaq buffer. Cells were resuspended in 50 µL Tagmentation buffer (10 mM MgCl2 in ChiTaq Buffer) and incubated at 37 °C for 1 h. The incubation was stopped by adding 10 µL 10% SDS at 55 °C for 10 min. The DNA fragments were extracted by Tagment DNA extract beads and amplified using 5× AmpliMix. Then the DNA was re-extracted by DNA clean beads for sequencing.
cDNA libraries were prepared as described (Nat Commun. 2019 Apr 29;10(1):1930) and sequenced with Novaseq-PE250 platform.

value: HSPC


title: GSCs, shSCD5-3, Day4

description: Library name: shscd5_3


title: GSCs, shControl-3, Day4

description: Library name: scr3


title: Hs368_ADCY9

description: Gene expression data from human islets

value: Female


title: BGLT3 ChIRP input rep2


title: Hs364_NC

description: Gene expression data from human islets


title: Hs364_ADCY9

description: Gene expression data from human islets


title: BGLT3 ChIRP input rep1


title: BGLT3 odd rep2


title: GSCs, shSCD5-1, Day4

description: Library name: shscd5_1


title: d2 RNA-seq R2

description: Library name: d2 RNA-seq R2

value: day 2


title: d3 RNA-seq R1

description: Library name: d3 RNA-seq R1


title: GSCs, shSCD1-4, Day4

description: Library name: shscd1_4


title: d7 TT-TSS-seq R2

description: Library name: d7 TT-TSS-seq R2

value: day 7


title: GATA1 rep2, Day8


title: Hs367_ADCY9

description: Gene expression data from human islets


title: H2122_AR30_rep2

city: Osaka-Sayama

first: Toshiyuki

last: Takehara

state: Osaka

address: 377-2, Ohno-Higashi

department: Faculty of Medicine

institute: Kindai Universty Hospital

description: gene expression data from H2122 AR30

hyb_protocol: Following fragmentation, 2.3 mg of fragmented and labeled ss-cDNA were hybridized for 16 hr at 45℃ on GeneChip Clariom S array, human. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Gene chip Scanner 7G, affymetrix.

data_processing: The data were analyzed with Transcriptome Analysis Console using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Restitance clone of sotorasib-sensitive KRASG12C-mutant NSCLC cell lines NCI-H2122 AR30

label_protocol: Biotinylated ss-cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Gene Chip WT PLUS Reagent kit, Affymetrix).

growth_protocol: The KRASG12C-mutant NSCLC cell lines NCI-H2122 were obtained from American Type Culture Collection (Manassas, VA). H2122 cells were cultured under a humidified atmosphere of 5% CO2 at 37°C in RPMI 1640 (Sigma-Aldrich, St. Louis, MO) supplemented with 10% FBS and 1% penicillin-streptomycin.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: Lung


title: d2 RNA-seq R1

description: Library name: d2 RNA-seq R1


title: wild-type; NSPC; Aph + ART558; lamhtgts; chr14; theta collection; rep4

city: Heidelberg

first: Pei-Chi

last: Wei

state: Baden-Württemberg

address: Im Neuenheim Feld 280

department: Structural and functional genomics

country: Germany

institute: German Cancer Research Center

description: Library name: wt-aph-lamhtgts-ipolq-chr14-LC219-rep4

data_processing:
*library strategy: linear amplification (LAM)-High-throughput Genome-wide Translocation Sequencing (HTGTS)
LAM-HTGTS: a sigularity package https://github.com/brainbreaks/HTGTS
Repli-seq: a sigularity pacakge https://github.com/brainbreaks/HighRes_RepliSeq
Assembly: mm10
Supplementary files format and content: GRO-seq: bigwig files for plus and minus strands.
Supplementary files format and content: LAM-HTGTS: tlx files contain LAM-HTGTS bait and prey junction, sequneces, start, end, and direction (Strand).
Supplementary files format and content: Repli-seq: log2 smoothed ratio file for early and late fractions.

source_name: Primary NSPC

growth_protocol: Mouse neural progenitor cells and primary neural stem/progenitor cells were cultured in NBBG medium (NeralBasalA, 2% B27 supplement without RA, 0.5 mM Glutamax, 10ng/ml human EGF, 10ng/ml mouse FGFb). Neural progenitor cells were then collected for nucleofection (LAM-HTGTS), GRO-seq, or Repli-seq experiments. For Aph treated cells, these cells were treated with 0.5 uM Aph for 72 hours and 0.25 uM for 24 hours. For PolQ inhibition, cells were incubated with 5uM ART558 for 72 hours then with 2.5 uM for 24 hours.

extract_protocol:
Genomic DNA for LAM-HTGTS: cells were lyzed in proteinase K digestion buffer, and genomic DNA were extraced with a standard phenol/chlorofomr protocol. RNA were removed by treating samples with RNAseA prior phenol/chlroform extraction. Genomic DNA for Repli-seq: cells were lyzed in proteinase K digestion buffer, fragmented by a Covaris fragmentation device to 200 bp, and nacent DNA were pulldowned by using an BrdU-specific antiboty.
We follow the published protocol, as indicated below, to construct the libraries. Repli-seq: https://www.nature.com/articles/nprot.2017.148 LAM-HTGTS: https://www.nature.com/articles/nprot.2016.043

treatment_protocol: Cells were treated with indicated concentration of aphidicolin or the veichle control DMSO for the indicated period.

value: Primary NSPC

value: Wild-type

value: ATR558 plus aphidicolin


title: d6 TT-TSS-seq R1

description: Library name: d6 TT-TSS-seq R1

value: day 6


title: GSCs, shSCD1-3, Day4

description: Library name: shscd1_3

value: Glioma stem cells


title: BGLT3 even rep2

city: Beijing


title: wild-type; NSPC; Aph + ART558; lamhtgts; chr14; theta collection; rep3

description: Library name: wt-aph-lamhtgts-ipolq-chr14-LC218-rep3


title: GSCs, shSCD1-2, Day4

description: Library name: shscd1_2


title: Hs366_ADCY9

description: Gene expression data from human islets


title: GATA1 rep1, Day8


title: Pol II rep1, Day8


title: wild-type; NSPC; Aph + ART558; lamhtgts; chr14; theta collection; rep2

description: Library name: wt-aph-lamhtgts-ipolq-chr14-LC217-rep2


title: Hs366_NC

description: Gene expression data from human islets


title: wild-type; NSPC; Aph + ART558; lamhtgts; chr14; theta collection; rep1

description: Library name: wt-aph-lamhtgts-ipolq-chr14-LC216-rep1


title: BGLT3 even rep1


title: H2122_rep2

description: gene expression data from H2122

source_name: The KRASG12C-mutant NSCLC cell lines NCI-H2122


title: Hs365_ADCY9

description: Gene expression data from human islets


title: d4 TT-TSS-seq R2

description: Library name: d4 TT-TSS-seq R2


title: d0 RNA-seq R1

description: Library name: d0 RNA-seq R1

value: day 0


title: d4 TT-TSS-seq R1

description: Library name: d4 TT-TSS-seq R1


title: H2122_rep1

description: gene expression data from H2122


title: wild-type; NSPC; Aph; lamhtgts; chr14; theta collection; rep3

description: Library name: wt-aph-lamhtgts-chr14-LC214-rep3

value: APH


title: GSCs, shSCD1-1, Day4

description: Library name: shscd1_1


title: d3 TT-TSS-seq R2

description: Library name: d3 TT-TSS-seq R2

value: mESC

value: day 3


title: EKLF rep2, Day8


title: GSCs, shControl-4, Day4

description: Library name: scr4