title: TetKO_D4_MCnT_H3K27ac_rep2

description: Library name: TetKO_D4_MCnT_H3K27ac_rep2

data_processing:
PCR duplicate reads were removed pre-alignment using BBmap Clumpify (v38.18) with parameters ‘dedupe=t k=19 passes=6 subs=(0.01 x readlength)’.
Sequencing adaptors and low-quality nucleotides were removed using Trimmomatic (v0.39) with parameters ‘HEADCROP:18 ILLUMINACLIP:adapters.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:24’.
Processed reads were aligned to the mm10 genome using Bismark (v0.23.1) and default parameters. Reads that lost their mate pair during read trimming and/or that could not be aligned in paired-end mode were kept and re-aligned as single-end reads. Aligned reads were deduplicated with ‘deduplicate_bismark’.
Methylation information of individual cytosines was extracted with ‘bismark_methylation_extractor’.
BigWig files were generated using deepTools (v3.5.1) bamCoverage and parameters ‘--binSize 1 --smoothLength 0 --minMappingQuality 10 --normalizeUsing CPM --blackListFileName ENCFF547MET.bed --ignoreForNormalization chrX chrM chrY’. Blacklisted regions are those defined by Amemiya et al., 2019.
BigWig files for 5mC levels were generated from Bismark's CpG report by extracting the coordinates and methylation percentage of Cs covered by at least five reads. The resulting file was transformed with bedGraphToBigWig (v4). For H3K27ac samples, only reads without CH methylation were used for this step.
Assembly: mm10
Supplementary files format and content: Bigwig format. CPM-normalized counts of H3K4me1 or H3K27ac signal.
Supplementary files format and content: Bigwig format. Percentage of methylated Cs at CpG dinucleotides covered by at least 5 reads.

extract_protocol:
Nuclei were prepared from 500,000 cells (H3K4me1) or 1,000,000 cells (H3K27ac) for each transposition reaction.
A transposome was assembled with methylated adaptors for transposition reaction. Tagmented purified DNA was either bisulfite converted (Zymo EZ DNA Methylation-Gold Kit) for H3K4me1, or submitted to Enzyme-Methyl kit (NEB) for H3K27ac. Converted DNA was amplified using KAPA HiFi HotStart Uracil+ ReadyMix.

value: Day 4

tag: antibody

value: H3K27ac (Active Motif, 39133)


title: TetKO_D4_MCnT_H3K27ac_rep1

status: Public on Jun 27 2026

type: SRA

city: Paris

first: Marlet

last: Morales Franco

state: Île-de-France

address: 15 rue Hélène Brion

country: France

institute: Institut Jacques Monod, CNRS, Université Paris Cité

description: Library name: TetKO_D4_MCnT_H3K27ac_rep1

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

growth_protocol: The ESCs were grown on 0.1% gelatin-coated flask in serum culture conditions using Glasgow medium (Gibco) supplemented with 15% Fetal bovine Serum (FBS), MEM non-essential amino acid, sodium pyruvate, l-glutamine, penicillin, streptomycin, 0.1 mM β-mercaptoethanol and leukemia inhibitory factor (LIF), and passed with trypsin. Before EpiLC differentiation, cells were transitioned from serum to 2i + Vitamin C (vitC) cell culture conditions for at least 7 days. For the 2i + vitC culture conditions, N2B27 medium (50% neurobasal medium, 50% DMEM) supplemented with N2, B27, l-glutamine, β-mercaptoethanol, penicillin, streptomycin, LIF and 2i (Gsk3, and MEK inhibitors) and ascorbic acid. To induce EpiLC differentiation, cells were replated on Fibronectin (10 μg/ml, Sigma)-coated plates in N2B27 medium supplemented with FGF2 and Activin A.

tag: cell line

tag: cell type

value: epiblast like-cells

tag: genotype

value: Tet1/2 DKO

tag: treatment

value: EpiLC differentiation

tag: time


title: TetKO_D2_MCnT_H3K27ac_rep2

description: Library name: TetKO_D2_MCnT_H3K27ac_rep2

value: Day 2


title: TetKO_D2_MCnT_H3K27ac_rep1

description: Library name: TetKO_D2_MCnT_H3K27ac_rep1


title: TetKO_D0_MCnT_H3K27ac_rep2

description: Library name: TetKO_D0_MCnT_H3K27ac_rep2

value: embryonic stem cells

value: 2i + vitamin C

value: Day 0


title: TetKO_D0_MCnT_H3K27ac_rep1

description: Library name: TetKO_D0_MCnT_H3K27ac_rep1


title: DnmtKO_D2_MCnT_H3K27ac_rep2

description: Library name: DnmtKO_D2_MCnT_H3K27ac_rep2

value: Dnmt1/3a/3b TKO


title: DnmtKO_D4_MCnT_H3K27ac_rep1

description: Library name: DnmtKO_D4_MCnT_H3K27ac_rep1


title: DnmtKO_D2_MCnT_H3K27ac_rep1

description: Library name: DnmtKO_D2_MCnT_H3K27ac_rep1


title: DnmtKO_D0_MCnT_H3K27ac_rep2

description: Library name: DnmtKO_D0_MCnT_H3K27ac_rep2


title: DnmtKO_D0_MCnT_H3K27ac_rep1

description: Library name: DnmtKO_D0_MCnT_H3K27ac_rep1


title: WT_D4_MCnT_H3K27ac_rep2

description: Library name: WT_D4_MCnT_H3K27ac_rep2

value: WT


title: WT_D2_MCnT_H3K27ac_rep2

description: Library name: WT_D2_MCnT_H3K27ac_rep2


title: WT_D2_MCnT_H3K27ac_rep1

description: Library name: WT_D2_MCnT_H3K27ac_rep1


title: WT_D0_MCnT_H3K27ac_rep1

description: Library name: WT_D0_MCnT_H3K27ac_rep1


title: TetKO_D4_MCnT_H3K4me1_rep1

description: Library name: TetKO_D4_MCnT_H3K4me1_rep1

value: H3K4me1 (Cell Signaling Technology, 5326)


title: TetKO_D2_MCnT_H3K4me1_rep2

description: Library name: TetKO_D2_MCnT_H3K4me1_rep2


title: TetKO_D2_MCnT_H3K4me1_rep1

description: Library name: TetKO_D2_MCnT_H3K4me1_rep1


title: TetKO_D0_MCnT_H3K4me1_rep2

description: Library name: TetKO_D0_MCnT_H3K4me1_rep2


title: TetKO_D0_MCnT_H3K4me1_rep1

description: Library name: TetKO_D0_MCnT_H3K4me1_rep1


title: DnmtKO_D4_MCnT_H3K4me1_rep1

description: Library name: DnmtKO_D4_MCnT_H3K4me1_rep1


title: DnmtKO_D4_MCnT_H3K4me1_rep2

description: Library name: DnmtKO_D4_MCnT_H3K4me1_rep2


title: DnmtKO_D0_MCnT_H3K4me1_rep2

description: Library name: DnmtKO_D0_MCnT_H3K4me1_rep2


title: DnmtKO_D0_MCnT_H3K4me1_rep1

description: Library name: DnmtKO_D0_MCnT_H3K4me1_rep1


title: WT_D4_MCnT_H3K4me1_rep2

description: Library name: WT_D4_MCnT_H3K4me1_rep2


title: WT_D4_MCnT_H3K4me1_rep1

description: Library name: WT_D4_MCnT_H3K4me1_rep1


title: WT_D2_MCnT_H3K4me1_rep2

description: Library name: WT_D2_MCnT_H3K4me1_rep2


title: WT_D2_MCnT_H3K4me1_rep1

description: Library name: WT_D2_MCnT_H3K4me1_rep1


title: WT_D0_MCnT_H3K4me1_rep2

description: Library name: WT_D0_MCnT_H3K4me1_rep2


title: WT_D0_MCnT_H3K4me1_rep1

description: Library name: WT_D0_MCnT_H3K4me1_rep1


title: TetKO_D4_MATAC_rep2

description: Library name: TetKO_D4_MATAC_rep2

data_processing:
PCR duplicate reads were removed pre-alignment using BBmap Clumpify (v38.18) with parameters ‘dedupe=t k=19 passes=6 subs=(0.01 x readlength)’.
Sequencing adaptors and low-quality nucleotides were removed using Trimmomatic (v0.39) with parameters ‘HEADCROP:18 ILLUMINACLIP:adapters.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:24’.
Processed reads were aligned to the mm10 genome using Bismark (v0.23.1) and default parameters. Reads that lost their mate pair during read trimming and/or that could not be aligned in paired-end mode were kept and re-aligned as single-end reads. Aligned reads were deduplicated with ‘deduplicate_bismark’.
Methylation information of individual cytosines was extracted with ‘bismark_methylation_extractor’.
BigWig files were generated using deepTools (v3.5.1) bamCoverage and parameters ‘--binSize 1 --smoothLength 0 --minMappingQuality 10 --normalizeUsing CPM --blackListFileName ENCFF547MET.bed --ignoreForNormalization chrX chrM chrY’. Blacklisted regions are those defined by Amemiya et al., 2019.
BigWig files for 5mC levels were generated from Bismark's CpG report by extracting the coordinates and methylation percentage of Cs covered by at least five reads. The resulting file was transformed with bedGraphToBigWig (v4).
Assembly: mm10
Supplementary files format and content: Bigwig format. CPM-normalized counts of ATAC signal.
Supplementary files format and content: Bigwig format. Percentage of methylated Cs at CpG dinucleotides covered by at least 5 reads.

extract_protocol:
Nuclei were prepared from 50,000 cells for each transposition reaction.
A transposome was assembled with methylated adaptors for transposition reaction. Tagmented purified DNA was bisulfite converted (Zymo EZ DNA Methylation-Gold Kit) and amplified using KAPA HiFi HotStart Uracil+ ReadyMix.


title: TetKO_D2_MATAC_rep2

description: Library name: TetKO_D2_MATAC_rep2


title: SSR_3

city: Changchun

first: Xiaohui

last: Dong

address: No. 1363, Shengtai Street, Jingyue High-tech Industrial Development Zone

department: Institute of Plant Protection

country: China

institute: Jilin Academy of Agricultural Sciences

description:
Library name: SSR_3
control, replicate biosample 3

library_source: transcriptomic

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to ASM14694v1  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: ASM14694v1
Supplementary files format and content: tab-delimited text files include gene count and fpkm value for each Sample

molecule: total RNA

organism: Sclerotinia sclerotiorum

source_name: hyphae

extract_protocol:
RNA was extracted from tissue using TRIzol reagent. Briefly, tissue samples were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA is enriched for small RNAs, followed by 3' and 5' adapter ligation. Reverse transcription generates cDNA, which is then PCR amplified with indexed primers. The final library is size-selected (typically ~150 bp) and validated by Bioanalyzer before sequencing on an Illumina flow cell.

tag: tissue

value: hyphae

value: control


title: TetKO_D2_MATAC_rep1

description: Library name: TetKO_D2_MATAC_rep1


title: SSR_2

description:
Library name: SSR_2
control, replicate biosample 2


title: WT_D4_5hmCseq_rep1

description: Library name: WT_D4_5hmCseq_rep1

data_processing:
Sequencing adaptors and low-quality nucleotides were removed using Trimmomatic (v0.39) with parameters ‘ILLUMINACLIP:adapters.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:36’.
Processed reads were aligned to the mm10 genome using Bismark (v0.23.1) and default parameters. Aligned reads were deduplicated with ‘deduplicate_bismark’.
Hydroxymethylation information of individual cytosines was extracted with ‘bismark_methylation_extractor’.
BigWig files for 5hmC levels were generated from Bismark's CpG report by extracting the coordinates and hydroxymethylation percentage of Cs covered by at least five reads. The resulting file was transformed with bedGraphToBigWig (v4).
Assembly: mm10
Supplementary files format and content: Bigwig format. Percentage of hydroxymethylated Cs at CpG dinucleotides covered by at least 5 reads.
Library strategy: EM-seq

extract_protocol:
Genomic DNA was extracted using NucleoSpin tissue kit (Macherey-Nagel ref. 740952) as per the manufacturer instructions and sonicated using covaris instrument.
Sonicated DNA was processed through the NEB Enzymatic 5hmC-seq complete kit as per the manufacturer instructions.


title: TetKO_D0_MATAC_rep2

description: Library name: TetKO_D0_MATAC_rep2


title: TetKO_D4_MATAC_rep1

description: Library name: TetKO_D4_MATAC_rep1


title: DnmtKO_D4_hMATAC

description: Library name: DnmtKO_D4_hMATAC

data_processing:
PCR duplicate reads were removed pre-alignment using BBmap Clumpify (v38.18) with parameters ‘dedupe=t k=19 passes=6 subs=(0.01 x readlength)’.
Sequencing adaptors and low-quality nucleotides were removed using Trimmomatic (v0.39) with parameters ‘HEADCROP:18 ILLUMINACLIP:adapters.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:24’.
Processed reads were aligned to the mm10 genome using Bismark (v0.23.1) and default parameters. Reads that lost their mate pair during read trimming and/or that could not be aligned in paired-end mode were kept and re-aligned as single-end reads. Aligned reads were deduplicated with ‘deduplicate_bismark’.
Hydroxymethylation information of individual cytosines was extracted with ‘bismark_methylation_extractor’.
BigWig files were generated using deepTools (v3.5.1) bamCoverage and parameters ‘--binSize 1 --smoothLength 0 --minMappingQuality 10 --normalizeUsing CPM --blackListFileName ENCFF547MET.bed --ignoreForNormalization chrX chrM chrY’. Blacklisted regions are those defined by Amemiya et al., 2019.
BigWig files for 5hmC levels were generated from Bismark's CpG report by extracting the coordinates and hydroxymethylation percentage of Cs covered by at least five reads. The resulting file was transformed with bedGraphToBigWig (v4).
Assembly: mm10
Supplementary files format and content: Bigwig format. CPM-normalized counts of ATAC signal.
Supplementary files format and content: Bigwig format. Percentage of hydroxymethylated Cs at CpG dinucleotides covered by at least 5 reads.

extract_protocol:
Nuclei were prepared from 50,000 cells for each transposition reaction.
A transposome was assembled with hydroxymethylated adaptors for transposition reaction. Tagmented purified DNA was submitted to 5hmC conversion module kit (NEB) as per the manufacturer instructions.


title: WT_D4_hMATAC_rep2

description: Library name: WT_D4_hMATAC_rep2


title: WT_D2_hMATAC_rep1

description: Library name: WT_D2_hMATAC_rep1


title: WT_D0_hMATAC_rep2

description: Library name: WT_D0_hMATAC_rep2


title: SSR_VV1_3

description:
Library name: SSR_VV1_3
After infection with virus BbrVV1, replicate biosample 3

value: After infection with virus BbrVV1


title: DnmtKO_D4_MATAC_rep2

description: Library name: DnmtKO_D4_MATAC_rep2


title: TetKO_D0_MATAC_rep1

description: Library name: TetKO_D0_MATAC_rep1


title: SSR_VV1_2

description:
Library name: SSR_VV1_2
After infection with virus BbrVV1, replicate biosample 2


title: DnmtKO_D4_MCnT_H3K27ac_rep2

description: Library name: DnmtKO_D4_MCnT_H3K27ac_rep2


title: DnmtKO_D4_MATAC_rep1

description: Library name: DnmtKO_D4_MATAC_rep1


title: SSR_VV1_1

description:
Library name: SSR_VV1_1
After infection with virus BbrVV1, replicate biosample 1


title: Transcriptiome of 30 hour Marchantia spores, 2nd biological replicate, lane 4

status: Public on Jun 29 2026

city: Rehovot

first: Zohar

last: Meir

state: Shfela

address: Herzl 234

department: Mathematics & CS

country: Israel

institute: Weizmann Institute of Science

description:
Library name: spores_30h_rep2_lane4
RNAseq derived from spores of six sporangia 30 hours after their culture on agar plates

data_processing:
Raw reads were returned as fastq.gz files.Reads passing quality control (Phred +33 quality score >30 assessed with FastQC) were trimmed by removing the first and last 10 bases, and adapters were removed using Trimmomatic (v0.32). Paired-end reads were interleaved. Residual bacterial rRNA sequences were filtered with SortMeRNA (v2.1b). Reads were error-corrected using BayesHammer within SPAdes (v3.10.1) and aligned to the Marchantia polymorpha reference genome JGI (v3.1) and its association gene annotations, using Salmon. Differential gene expression analysis was performed with DESeq2.Gene annotations were obtained from the Marchantia polymorpha reference genome (v3.1) (functional annotation downloaded from https://marchantia.info/download/v31/). Pairwise comparisons were conducted, with an adjusted p-value (padj) <0.05 considered significant. Genes with log2FoldChange <0 were classified as downregulated, >0 as upregulated, and NA indicated no significant change.
Assembly: Marchantia polymorpha Takaragaike-1 (MpTak1_v3.1)
Supplementary files format and content: Dataset1_DESeq2_output_annotated_2021.xlsx; Excel sheet; Shows pairwise differential expression analysis, genome-wide, based on Marchantia polymorpha JGI 3.1 reference genome and its associated gene predictions (v3.1), including Log2FoldChanges and statsitical significance values for per-gene comparisons between samples and conditions.
Supplementary files format and content: Normalized_Read_Counts_2_transcriptome_shared_final.xlsx; Excel sheet; Contains genome-wide read counts across all samples and biological replicates, normalized by sampling depth.

organism: Marchantia polymorpha

source_name: spores

growth_protocol: Wild type Marchantia polymorpha sporangia, derived from a cross of Tak-1 and Tak-2, were collected and surface-sterilized with 1% NaDCC, followed by washing three times with sterile water. The spore suspension was plated and maintained under continuous white light (PFD 50-60 µmol m⁻² s⁻¹) for the indicated durations.

extract_protocol:
For collection of samples, the cellophane with adhered spores was peeled from the medium, flash-frozen in liquid nitrogen, and ground to a fine powder using a mixer mill (RETSCH MM 400) at 30 Hz for 4 minutes. Total RNA was extracted using the RNeasy Plant Mini Kit (Qiagen) according to the manufacturer’s instructions, followed by Turbo DNase treatment to remove residual genomic DNA.
mRNA library preparation, RNA sequencing was performed at the Wellcome Trust Centre for Human Genetics, University of Oxford, using an Illumina HiSeq 4000 platform generating 75 bp paired-end reads. Each sample was sequenced in five technical replicates, with replicates distributed across five independent sequencing lanes.

treatment_protocol: Spores were grown under standard white light for 0, 15, or 30 hours after plating.

value: spores

value: spore

value: Takaragaike-1 (Tak-1, male) x Takaragaike-2 (Tak-2, female)

value: 30 hours

tag: batch


title: HEK293 cells, sorbitol+cycloheximide, improved RNA extraction, biol rep1

city: Suita

first: Tetsuro

last: Hirose

state: Osaka

address: 1-3 Yamadaoka

department: Graduate School of Frontier Biosciences

country: Japan

institute: The University of Osaka

description:
Library name: OSCHX_Impr_1
DoG regions are provided as BED files, and DoG expression levels (FPKM) are provided in all_dogs.fpkm.txt.

data_processing:
Adapter sequences were removed and low-quality reads were filtered using fastp (v0.25.0). Filtered reads were first aligned to human 45S rDNA (KY962518.1) using Bowtie2 (v2.5.4). Reads unmapped to rDNA were subsequently aligned to the human genome (GRCh38 primary assembly) with gene annotation GENCODE v49 using STAR (v2.7.11b) with --outFilterMultimapNmax 1 (unique mapping only). DoGs were detected from the alignments using ARTDeco with following parameters: -read-in-threshold -1 -read-in-fpkm 1 -min-dog-len 10000 -dog-window 5000 -min-dog-coverage 0.5. Two-group sample comparisons were performed using DESeq2 as implemented in ARTDeco. For unspliced RNA analysis, non-exonic regions derived from the GENCODE annotation were used.
Assembly: GRCh38 primary assembly
Supplementary files format and content: Processed data include (i) a DoG-level quantification table (all_dogs.fpkm.txt) containing FPKM values across all samples and (ii) BED files (n=16) describing DoG genomic regions linked to the DoG IDs in the FPKM table.

organism: Homo sapiens

growth_protocol: Cells were maintained in Dulbecco’s Modified Eagle Medium (DMEM; Nacalai Tesque, Kyoto, Japan) supplemented with 10% heat-inactivated fetal bovine serum (FBS; SIGMA, St. Louis, MO) at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
Cells were lysed in TRI Reagent (1 × 10⁶ cells per 1 mL; Molecular Research Center, Cincinnati, OH), followed by the addition of chloroform (200 µL per 1 mL lysate). After phase separation by centrifugation (15,000 rpm, 15 min, 4°C), the upper aqueous phase containing readily extractable RNAs was collected as the “SERIPH 1st-step fraction.” The interphase was then recovered and gently overlaid onto freshly phase-separated TRI Reagent/chloroform (1.0 mL per wash), followed by centrifugation; this wash step was repeated three times. The washed interphase was subsequently incubated at 55°C for 10 min, after which chloroform (200 µL) was added. Samples were vortexed and centrifuged at 15,000 rpm for 15 min at 4°C to perform the improved extraction. Highly viscous interphases were briefly sheared through a 20-gauge needle prior to heating, when necessary. The resulting aqueous phase constituted the seRNA-enriched “SERIPH 2nd-step fraction.” For comparison, "conventional extraction" and "improved extraction" were also performed as described in Chujo et al. (EMBO J., 2017)
Libraries were prepared from rRNA-depleted total RNA (100–500 ng for SERIPH 1st; 5–50 ng for SERIPH 2nd) using Illumina Stranded Total RNA Prep with Ribo-Zero Plus (illumina, San Diego, CA).

treatment_protocol: For OSCHX libraries, the medium was replaced with DMEM + 10% FBS containing 200 mM sorbitol (FUJIFILM Wako Pure Chemical Corporation, Osaka, Japan) and 100 µg/mL cycloheximide (CHX; Nacalai Tesque, Kyoto, Japan), and cells were incubated for an additional 9 h.

value: human embryonic kidney

value: 200 mM sorbitol + 100 µg/mL cycloheximide for 9h


title: DnmtKO_D2_MATAC_rep2

description: Library name: DnmtKO_D2_MATAC_rep2

value: epiblast like-cells

value: EpiLC differentiation


title: DnmtKO_D2_MATAC_rep1

description: Library name: DnmtKO_D2_MATAC_rep1

value: Day 2


title: HEK293 cells, sorbitol+cycloheximide, improved RNA extraction, biol rep2

description:
Library name: OSCHX_Impr_2
DoG regions are provided as BED files, and DoG expression levels (FPKM) are provided in all_dogs.fpkm.txt.


title: WT_D4_MCnT_H3K27ac_rep1

description: Library name: WT_D4_MCnT_H3K27ac_rep1

value: Day 4

value: H3K27ac (Active Motif, 39133)


title: DnmtKO_D0_MATAC_rep2

description: Library name: DnmtKO_D0_MATAC_rep2

value: embryonic stem cells

value: Dnmt1/3a/3b TKO

value: 2i + vitamin C

value: Day 0


title: WT_D0_MCnT_H3K27ac_rep2

description: Library name: WT_D0_MCnT_H3K27ac_rep2

value: WT


title: HEK293 cells, sorbitol+cycloheximide, conventional RNA extraction, biol rep2

description:
Library name: OSCHX_Conv_2
DoG regions are provided as BED files, and DoG expression levels (FPKM) are provided in all_dogs.fpkm.txt.


title: DnmtKO_D0_MATAC_rep1

description: Library name: DnmtKO_D0_MATAC_rep1


title: HEK293 cells, sorbitol+cycloheximide, conventional RNA extraction, biol rep1

description:
Library name: OSCHX_Conv_1
DoG regions are provided as BED files, and DoG expression levels (FPKM) are provided in all_dogs.fpkm.txt.


title: TetKO_D4_MCnT_H3K4me1_rep2

description: Library name: TetKO_D4_MCnT_H3K4me1_rep2

value: Tet1/2 DKO

value: H3K4me1 (Cell Signaling Technology, 5326)


title: WT_D4_MATAC_rep2

description: Library name: WT_D4_MATAC_rep2


title: HEK293 cells, sorbitol+cycloheximide, SERIPH2nd RNA fraction, improved RNA extraction, biol rep2

description:
Library name: OSCHX_Conv2nd_2
DoG regions are provided as BED files, and DoG expression levels (FPKM) are provided in all_dogs.fpkm.txt.


title: HEK293 cells, sorbitol+cycloheximide, SERIPH2nd RNA fraction, improved RNA extraction, biol rep1

description:
Library name: OSCHX_Conv2nd_1
DoG regions are provided as BED files, and DoG expression levels (FPKM) are provided in all_dogs.fpkm.txt.


title: WT_D2_MATAC_rep2

description: Library name: WT_D2_MATAC_rep2


title: HEK293 cells, sorbitol+cycloheximide, SERIPH1st RNA fraction, conventional RNA extraction, biol rep2

description:
Library name: OSCHX_Conv1st_2
DoG regions are provided as BED files, and DoG expression levels (FPKM) are provided in all_dogs.fpkm.txt.


title: WT_D4_MATAC_rep1

description: Library name: WT_D4_MATAC_rep1


title: WT_D2_MATAC_rep1

description: Library name: WT_D2_MATAC_rep1


title: HEK293 cells, sorbitol+cycloheximide, SERIPH1st RNA fraction, conventional RNA extraction, biol rep1

description:
Library name: OSCHX_Conv1st_1
DoG regions are provided as BED files, and DoG expression levels (FPKM) are provided in all_dogs.fpkm.txt.


title: WT_D0_MATAC_rep2

description: Library name: WT_D0_MATAC_rep2


title: WT_D0_MATAC_rep1

description: Library name: WT_D0_MATAC_rep1


title: HEK293 cells, control, improved RNA extraction, biol rep2

description:
Library name: Ctrl_Impr_2
DoG regions are provided as BED files, and DoG expression levels (FPKM) are provided in all_dogs.fpkm.txt.

value: no treatment


title: ko brown adipose tissue, fasted, 20 hours, rep3

city: Shanghai

first: Zhenyu

last: Xu

state: 枫林校区

address: Dongan Road

institute: Shanghai Medical College, Fudan University

description:
Library name: ko3
Ucp1-Bmp4knock-out mouse derived BAT

data_processing:
raw reads were quality-checked using FastQC and adapter-trimmed with Cutadapt (minimum length = 30 bp).
Clean reads were aligned to the mouse reference genome (GRCm38.102) using STAR aligner.
Assembly: Mouse mm10
Supplementary files format and content: xslx file includes count values for each sample
Supplementary files format and content: xslx file includes fpkm values for each sample

source_name: brown adipose tissue

extract_protocol:
Total RNA was extracted by VeZol (Vazyme, R411) and 500ng of total RNA was used for the construction of sequencing libraries.
RNA fragmentation was performed using the NEB Magnesium RNA Fragmentation Module at 94°C for 5-7 min. The cleaved fragments were then reverse transcribed into cDNA using SuperScript II Reverse Transcriptase (Invitrogen, 1896649), followed by second-strand cDNA synthesis with U-labeling employing E. coli DNA polymerase I, RNase H (both from NEB), and dUTP solution (Thermo Fisher, R0133). PCR amplification yielded a final cDNA library with an average insert size of 300±50 bp. The final RNA library was subjected to 2×150 bp paired-end sequencing (PE150) on an Illumina NovaSeq 6000 platform (Novogene Technology) following the manufacturer's protocol.

value: brown adipose tissue

value: Ucp1-Bmp4 knock-out

value: Fasted for 20 hours


title: HEK293 cells, control, improved RNA extraction, biol rep1

description:
Library name: Ctrl_Impr_1
DoG regions are provided as BED files, and DoG expression levels (FPKM) are provided in all_dogs.fpkm.txt.

value: human embryonic kidney


title: ko brown adipose tissue, fasted, 20 hours, rep2

description:
Library name: ko2
Ucp1-Bmp4knock-out mouse derived BAT


title: HEK293 cells, control, conventional RNA extraction, biol rep2

description:
Library name: Ctrl_Conv_2
DoG regions are provided as BED files, and DoG expression levels (FPKM) are provided in all_dogs.fpkm.txt.


title: HEK293 cells, control, conventional RNA extraction, biol rep1

description:
Library name: Ctrl_Conv_1
DoG regions are provided as BED files, and DoG expression levels (FPKM) are provided in all_dogs.fpkm.txt.


title: ko brown adipose tissue, fasted, 20 hours, rep1

description:
Library name: ko1
Ucp1-Bmp4knock-out mouse derived BAT


title: HEK293 cells, control, SERIPH2nd RNA fraction, improved RNA extraction, biol rep2

description:
Library name: Ctrl_Conv2nd_2
DoG regions are provided as BED files, and DoG expression levels (FPKM) are provided in all_dogs.fpkm.txt.


title: wt brown adipose tissue, fasted, 20 hours, rep3

description:
Library name: wt3
Ucp1-Bmp4fl/fl  mouse derived BAT


title: DnmtKO_D2_MCnT_H3K4me1_rep2

description: Library name: DnmtKO_D2_MCnT_H3K4me1_rep2

value: epiblast like-cells


title: HEK293 cells, control, SERIPH2nd RNA fraction, improved RNA extraction, biol rep1

description:
Library name: Ctrl_Conv2nd_1
DoG regions are provided as BED files, and DoG expression levels (FPKM) are provided in all_dogs.fpkm.txt.


title: HEK293 cells, control, SERIPH1st RNA fraction, conventional RNA extraction, biol rep2

description:
Library name: Ctrl_Conv1st_2
DoG regions are provided as BED files, and DoG expression levels (FPKM) are provided in all_dogs.fpkm.txt.


title: wt brown adipose tissue, fasted, 20 hours, rep2

description:
Library name: wt2
Ucp1-Bmp4fl/fl  mouse derived BAT


title: DnmtKO_D2_MCnT_H3K4me1_rep1

description: Library name: DnmtKO_D2_MCnT_H3K4me1_rep1

value: EpiLC differentiation


title: wt brown adipose tissue, fasted, 20 hours, rep1

description:
Library name: wt1
Ucp1-Bmp4fl/fl  mouse derived BAT


title: HEK293 cells, control, SERIPH1st RNA fraction, conventional RNA extraction, biol rep1

description:
Library name: Ctrl_Conv1st_1
DoG regions are provided as BED files, and DoG expression levels (FPKM) are provided in all_dogs.fpkm.txt.


title: Treat，AAV-Ly6d，rep2

city: Chongqing

first: Xiaohe

last: Luo

state: Chongqing

address: No. 165, Xincheng Road, Wanzhou District, Chongqing

department: Central lab

institute: Chongqing University Three Gorges Hospital

description:
Library name: Sample 5
Column name in ExpressionProfile.txt: L6_2

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample,  please see the ExpressionProfile.txt for details.

source_name: Liver

extract_protocol:
Retains were removed, flash frozen on dry ice, and RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
RNA libraries were prepared for sequencing using stantard Illumina protocols.

value: Liver

value: Ly6d overexpression


title: Treat，AAV-Ly6d，rep3

description:
Library name: Sample 6
Column name in ExpressionProfile.txt: L6_3


title: human pancreatic duct cells, ALDH3B2-infected

city: Boston

first: Jonathan

middle: M

last: Dreyfuss

state: MA

address: 1 Joslin Pl

department: Bioinformatics & Biostatistics Core

country: USA

institute: Joslin Diabetes Center

description:
Library name: Sample 2
10 x Genomics

library_source: transcriptomic single cell

data_processing:
We applied velocyto with the run10x command to obtain spliced and unspliced counts
Assembly: refdata-gex-GRCh38-2024-A
Supplementary files format and content: Loom file with spliced & unspliced counts

source_name: Pancreas

extract_protocol:
Purified human primary pancreatic ductal cells (HPPD) were immediately cultured in a low-attachment plate in RMPI DMEM/F12 medium (Gibco), supplemented with 10% FBS and penicillin/streptomycin. Lentivirus encoding a NT or ALDH3B2 gRNA together with a Cas9-mCherry reporter construct was added to the culture media.
After 6 days cells were harvested and live mCherry positive cells were isolated by FACS sorting, 40,000 cells per sample (10,000 cells each sample with unique barcode; four samples each group) were used for scRNAseq using the Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 (cat # PN-1000213; 10 x Genomics) according to manufactures’ instructions. Illumina NovaSeq 6000 with about 1.3 billion reads total was used for sequencing the purified 3’ gene expression library.

treatment_protocol: NTC or ALDH3B2 lentiviral infection

value: Pancreas

value: Duct cells


title: human pancreatic duct cells, NTC-infected

description:
Library name: Sample 1
10 x Genomics


title: HUDEP2 cells, sgH1-0 rep3, Day8

city: zhengzhou

first: Hengchao

last: Zhang

state: Henan

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

institute: zzu

description:
Library name: RNAseq_HUDEP2_sgH1-0_rep3
RNAseq_HUDEP2_raw_count.txt

data_processing:
The original data were filtered and compared with the reference genome, which can be downloaded from the Ensemble database (http://www.ensembl.org/index.html,human genome build GRCh38.87). Using HISAT2 version 2.2.1 (http://daehwankimlab.github.io/hisat2/) to read the counts for each gene in each sample and gene expression was assessed by StringTie (https://ccb.jhu.edu/software/stringtie/). TPM (Transcripts Per Kilobase of exon model per Million mapped reads) was calculated to evaluate the expression level. Differentially expressed genes (DEGs) were defined by p.adjust < 0.05 and fold change >1.2 using the DESeq2 version 1.38.3 (https://bioconductor.org/packages/release/bioc/html/DESeq2.html). Gene ontology (GO) enrichment analysis and visualization of DEGs was performed using the Metascape (www.metascape.org/) online tool with q < 0.05.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample

source_name: Cord blood

growth_protocol: CD34+ cells were puriﬁed from cord blood by positive selection using the magnetic-activated cell sorting magnetic beads system, according to the manufacturer’sinstructions. The purity of isolated CD34+ cells was 95% to 98%. The day of CD34+ cell harvest was recorded as day 0. The cell culture procedure consisted of 3 phases. The basic culture medium consisted of Iscove's Modified Dulbecco's Medium (IMDM), 2% human peripheral blood plasma, 3% human AB serum, 200 mg/mL human holo-transferrin, 3 IU/mL heparin and 10 μg/mL insulin. From day 0 to day 7, CD34+ cells were cultured at a concentration of 105/mL in the presence of 10 ng/mL stem cell factor (SCF), 1 ng/mL interleukin-3 (IL-3) and 3 IU/mL erythropoietin (EPO).  The cells were cultured at 37°C in the presence of 5% CO2. HUDEP-2 cells were cultured in expansion medium: StemSpan Serum-Free Expansion Medium (SFEM, 09650, Stemcell Technologies, Canada), 2% Penicillin Streptomycin solution (10,000 U/mL stock), 50 ng/mL recombinant human stem cell factor (SCF), 3 IU/mL Epoetin alfa, 0.4 μg/mL dexamethasone, 1 μg/mL doxycycline. To induce differentiation, HUDEP-2 cells were cultured in IMDM supplemented with FBS (10%), 5% plasma, 1 μg/mL doxycycline, EPO (3 IU/mL), transferrin 330µg/mL, hSCF (100 ng/mL), and L-glutamine1% for 5 days and then transferred them into IMDM supplemented with FBS (10%), 5% plasma, 1 μg/mL doxycycline, EPO (3 IU/mL), transferrin 330µg/mL, and L-glutamine1% for 5days.

extract_protocol:
Experiment procedure before sequencing: 2 million cells were collected and washed twice with PBS. RNA was extracted from cell culture using RNA extract kits (74104, Qiagen) according to the manufacturer’s instruction.
RNA was extracted and used as cDNA input, cDNA library was prepared by VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina ® (NR604-01,  Vazyme, China), and sequenced on Illumina NovaSeq 6000.

treatment_protocol: H1.0 shRNA/sgRNA lentivirus particles were transfected into human umbilical cord blood-derived CD34+ cells or HUDEP2 cells. Puromycin was added for selection of H1.0 shRNA transduced cells. GFP+ cells (transduced with H1.0-sgRNA1 or H1.0-sgRNA2) were sorted by FACS. The sorted cells were cultured under erythroid differentiation condition.

value: Cord blood

value: Human Umbilical cord blood-Derived Erythroid Progenitor-2 cell line

value: Erythroid cells


title: Treat，AAV-Ly6d，rep1

description:
Library name: Sample 4
Column name in ExpressionProfile.txt: L6_1


title: Control，AAV-GFP，rep3

description:
Library name: Sample 3
Column name in ExpressionProfile.txt: Control_3

value: WT

value: AAV-GFP


title: Control，AAV-GFP，rep2

description:
Library name: Sample 2
Column name in ExpressionProfile.txt: Control_2


title: HUDEP2 cells, sgH1-0 rep2, Day8

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description:
Library name: RNAseq_HUDEP2_sgH1-0_rep2
RNAseq_HUDEP2_raw_count.txt


title: HUDEP2 cells, sgH1-0 rep1, Day8

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description:
Library name: RNAseq_HUDEP2_sgH1-0_rep1
RNAseq_HUDEP2_raw_count.txt


title: Control，AAV-GFP，rep1

description:
Library name: Sample 1
Column name in ExpressionProfile.txt: Control_1


title: HUDEP2 cells, sgControl rep3, Day8

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description:
Library name: RNAseq_HUDEP2_sgControl_rep3
RNAseq_HUDEP2_raw_count.txt

value: sgControl


title: HUDEP2 cells, sgControl rep2, Day8

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description:
Library name: RNAseq_HUDEP2_sgControl_rep2
RNAseq_HUDEP2_raw_count.txt


title: BMDMs, Tm_LPS, rep3

first: Tomohiko

last: Murakami

state: OSAKA

address: 1-8 Yamada-Oka

institute: Osaka University

description: Library name: Sample 12

data_processing:
Illumina Casava1.8.2 software used for basecalling
Sequenced reads were mapped to mm10 using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
FPKMs was calculated using Cufflinks version 2.2.1.
Assembly: mm10
Supplementary files format and content: tsv file includes FPKM values for each sample

source_name: bone marrow derived macrophages (BMDMs)

growth_protocol: Bone marrow cells were cultured in RPMI with 10% FSC and MCSF for 7 days to induce differentiation into macrophages

extract_protocol:
Total RNA was isolated using  Nucleospin RNA Plus kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: BMDMs were pretreated with Tm (5 ug/ml) for 3h and then treated with LPS (1 ng/ml) for 3h

value: bone marrow derived macrophages (BMDMs)

value: macrophages

value: Tm and LPS


title: BMDMs, Tm_LPS, rep2

description: Library name: Sample 11


title: HUDEP2 cells, sgControl rep1, Day8

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description:
Library name: RNAseq_HUDEP2_sgControl_rep1
RNAseq_HUDEP2_raw_count.txt


title: HUDEP2 cells, H1-0-ΔN rep3, Day8

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description:
Library name: RNAseq_HUDEP2_H1-0-ΔN_rep3
RNAseq_HUDEP2_raw_count.txt


title: BMDMs, Tm, rep3

description: Library name: Sample 9

value: Tm


title: BMDMs, Tm_LPS, rep1

description: Library name: Sample 10


title: BMDMs, Tm, rep1

description: Library name: Sample 7


title: HUDEP2 cells, H1-0-ΔC rep3, Day8

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description:
Library name: RNAseq_HUDEP2_H1-0-ΔC_rep3
RNAseq_HUDEP2_raw_count.txt


title: HUDEP2 cells, H1-0-ΔN rep1, Day8

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description:
Library name: RNAseq_HUDEP2_H1-0-ΔN_rep1
RNAseq_HUDEP2_raw_count.txt


title: BMDMs, LPS, rep3

description: Library name: Sample 6

value: LPS


title: HUDEP2 cells, H1-0-ΔN rep2, Day8

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description:
Library name: RNAseq_HUDEP2_H1-0-ΔN_rep2
RNAseq_HUDEP2_raw_count.txt


title: HUDEP2 cells, H1-0-ΔC rep2, Day8

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description:
Library name: RNAseq_HUDEP2_H1-0-ΔC_rep2
RNAseq_HUDEP2_raw_count.txt


title: BMDMs, LPS, rep2

description: Library name: Sample 5


title: HUDEP2 cells, H1-0-ΔC rep1, Day8

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description:
Library name: RNAseq_HUDEP2_H1-0-ΔC_rep1
RNAseq_HUDEP2_raw_count.txt


title: BMDMs, Tm, rep2

description: Library name: Sample 8


title: BMDMs, LPS, rep1

description: Library name: Sample 4


title: Erythroid cells, shLuci rep3, Day15

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description:
Library name: RNAseq_CB_shLuci_rep3
RNAseq_CB_raw_count.txt

value: shLuci


title: BMDMs, Control, rep3

description: Library name: Sample 3


title: Erythroid cells, shLuci rep2, Day15

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description:
Library name: RNAseq_CB_shLuci_rep2
RNAseq_CB_raw_count.txt


title: BMDMs, Control, rep2

description: Library name: Sample 2


title: Erythroid cells, shLuci rep1, Day15

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description:
Library name: RNAseq_CB_shLuci_rep1
RNAseq_CB_raw_count.txt


title: BMDMs, Control, rep1

description: Library name: Sample 1


title: Erythroid cells, shH1-0 rep3, Day15

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description:
Library name: RNAseq_CB_shH1-0_rep3
RNAseq_CB_raw_count.txt


title: IGFBP1_OE rep 2

city: Aurora

first: Andrew

last: Goodspeed

state: CO

address: 12801 E 17th Ave, Mail Stop 8303

institute: University of Colorado Anschutz Medical Campus

data_processing:
Fastq files were processed using the nf-core/rnaseq pipeline (version 3.12.0, https://nf-co.re/rnaseq/3.12).
Sequencing adapters were removed using Cutadapt (version 3.4) as part of the trimgalore package (version 0.6.7).
Reads were aligned using STAR (version 2.7.9a) to the mouse transcriptome (GRCm39, gene annotation from Ensembl release 104).
Gene quantification was performed using Salmon (version 1.10.1).
Tables with transcript and gene counts were generated by the tximport R package (version 1.26.0) under R version 4.2.2.
Assembly: GRCm39
Supplementary files format and content: Txt file containg gene counts

source_name: skeletal muscle (quadriceps)

extract_protocol:
Total RNA from skeletal muscle (quadriceps) was isolated using the RNeasy Mini Kit (Qiagen)
Universal Plus mRNA-Seq library preparation kit with NuQuant (Nugen/Tecan)

treatment_protocol: Mice were infected with 10^12 vg/ml (in 200 ul sterile saline) of AAV8 constructs (Vector Builder) via tail vein and sacrificed after 54 days.

value: skeletal muscle (quadriceps)

tag: Sex

value: male

tag: strain

value: wild type


title: 21E x 500P, upstream, integrated, BC amplicon, DNA

city: Palo Alto

first: Jesse

last: Engreitz

state: CA

address: 240 Pasteur Dr

department: Genetics

institute: Stanford University

description: Library name: 21E x 500P upstream integrated DNA BC sequencing

data_processing:
Base calls were generated using bcl2fastq v2.20. Adapter sequences were trimmed with seqtk v1.3 (trimfq).
Enhancer-promoter barcode look-up table dictionaries were generated by first aligning paired-end reads to reference enhancer and promoter library sequences using bowtie2 v2.5.4 (--norc --no-discordant) and filtering for alignment quality (AS<-10) and low read count (n<2) before joining with barcode reads based on read IDs.
5'-end TSS mapping data was aligned to reference sequences of reporter constructs again with bowtie2 to identify which reads align with start position within the promoter sequence, which is reported as a fraction of total aligned reads.
Reporter barcode (BC) data is matched with the respective enhancer-promoter-BC dictionary and BC abundance of those that map within the dictionary is counted using the python package matcha v0.0.2 allowing for 1 mismatch in the 16 nt BC if the second best match has a mismatch of 2 or greater.
Assembly: Amplicons are derived from custom reference sequences and aligned to a synthetic reporter sequence. Sequences with human genomic origin are derived from hg19.
Supplementary files format and content: All processed files are tab-deliminted files. Enhancer-promoter-barcode (BC) look-up table dictionaries contain minimally enhancer, promoter, and BC variables. 5'-end TSS mapping counts include number of aligned reads and fraction of reads aligning to the promoter sequence for individual enhancer-promoter pairs or aggregated across enhancers first for larger enhancer-promoter libraries. BC count tables include enhancer and promoter columns as well as unnormalized BC abundances in the respective DNA and RNA samples.

extract_protocol:
gDNA samples from 5M cells each were harvested with NEB Monarch gDNA Spin Extraction Kit. Total RNA samples from 10M cells each were harvested with Qiagen RNeasy Plus Mini Kit. PolyA+ mRNA was enriched from total RNA with Invitrogen Poly(A) Purist MAG Kit.
Plasmid pool amplicons sequencing libraries were directly amplified from Gibson cloned plasmid pools with 12-17 cycles of PCR with 1 ng of input. Reporter barcode (BC) cDNA libraries were generated using the SuperScript IV First-Strand Synthesis System from Invitrogen. Reporter BC amplicons sequencing libraries were amplified from gDNA and cDNA using the same primers for 20 cycles and 13 cycles, respectively. Full length transcript cDNA was generated using the same reverse transcription kit but with an added template switch oligo. Then 3 steps of nested PCR on the full-length transcript cDNA were used to generated the final sequencing libraries.


title: 21E x 500P, upstream, integrated, BC amplicon, RNA

description: Library name: 21E x 500P upstream integrated RNA BC sequencing

molecule: polyA RNA


title: IGFBP1_OE rep 3


title: 203E x 78P, upstream, integrated, BC amplicon, DNA

description: Library name: 203E x 78P upstream integrated DNA BC sequencing


title: Erythroid cells, shH1-0 rep2, Day15

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description:
Library name: RNAseq_CB_shH1-0_rep2
RNAseq_CB_raw_count.txt


title: IGFBP1_OE rep 1


title: 203E x 78P, upstream, integrated, BC amplicon, RNA

description: Library name: 203E x 78P upstream integrated RNA BC sequencing


title: Erythroid cells, shH1-0 rep1, Day15

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description:
Library name: RNAseq_CB_shH1-0_rep1
RNAseq_CB_raw_count.txt


title: cells, Relapse after treatment 5

city: Jinan

first: Shuohui

address: Qilu Hospital, Shandong University, No.107, Wen Hua Xi Road, Jinan, Shandong, 250012, P.R. China

institute: Qilu Hospital of Shandong University

description:
Library name: QQX17Reg5
column AH in 1_genes_fpkm_expression.txt:QQX17Reg5

data_processing:
Raw sequencing reads were filtered using Cutadapt (version 1.9) to remove adapter-containing sequences, polyA/polyG-rich sequences, reads containing more than 5% unknown nucleotides (N), and low-quality reads (> 20% bases with Q-value ≤ 20). The clean read quality was confirmed using FastQC (version 0.11.9). Clean reads were aligned to the human reference genome (hg19) using HISAT2 (version 2.2.1), allowing up to two mismatches and multiple alignments per read (default, up to 20 alignments). StringTie (version 2.1.6) was used to assemble the mapped reads into transcripts and quantify transcript abundance, expressed as fragments per kilobase of transcript per million mapped reads. Differential gene expression analysis was performed using DESeq2 (version 1.10.1), with genes exhibiting an absolute fold change ≥ 2 and false discovery rate (FDR) < 0.05 defined as differentially expressed genes (DEGs). The resulting DEGs were subjected to Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis to identify significantly altered biological processes and metabolic pathways. Principal component analysis (PCA) and correlation analyses were performed to assess reproducibility and variance among samples.
Assembly: Homo_sapiens.GRCh38,EnsemblV112
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: PDX tumor

growth_protocol: To establish a patient-derived xenograft (PDX) model, tumor pieces mixed with Matrigel (Corning) were implanted subcutaneously into the interscapular fat pad of female NOG mice (Charles River Laboratories). Anesthesia and analgesia were administered using tribromoethanol (300 mg/kg) and meloxicam (4 mg/kg/day). After reaching generation 3, mice with tumors of 1,000 mm3 were sacrificed, and the tumors were minced and subsequently implanted subcutaneously into female NOD-SCID mice (Charles River Laboratories) for further experiments.

extract_protocol:
Total RNA was isolated from CRC cells in xenograft tumor samples using TRIzol reagent (Thermo Fisher Scientific), following the manufacturer’s instructions. RNA integrity and purity were assessed using the Bioanalyzer 2100 system and RNA 6000 Nano LabChip kit (Agilent Technologies), and samples with RNA integrity numbers (RIN) greater than 7.0 were selected for library construction.
First-strand complementary DNA (cDNA) was synthesized using SuperScript II Reverse Transcriptase (Invitrogen), followed by the synthesis of second-strand cDNA using Escherichia coli DNA polymerase I (New England Biolabs), RNase H (New England Biolabs), and a dUTP solution (Thermo Fisher Scientific). The blunt-ended cDNA fragments were subsequently adenylated at the 3′-ends to facilitate ligation with dual-index adapters containing T-overhangs. Size selection of adapter-ligated cDNA (~300 ± 50 bp) was performed using AMPure XP beads (Beckman Coulter), followed by digestion of U-labeled second strands with heat-labile UDG enzyme (New England Biolabs). Libraries were PCR-amplified (95℃ for 3 minutes, followed by 8 cycles of 98℃ for 15 s, 60℃ for 15 s, and 72℃ for 30 s, and a final extension at 72℃ for 5 minutes).

treatment_protocol: The FOLFOXIRI regimen was administered to NOD/SCID mice at the optimized doses of 10 mg/kg 5-FU, 20 mg/kg leucovorin, 2 mg/kg oxaliplatin, and 50 mg/kg CPT-11. This dosing strategy was established based on maximum tolerated dose studies and preliminary tumor response assessments. The primary adverse effects included transient reductions in leukocyte and thrombocyte counts, which were manageable and did not require treatment discontinuation. The PDX  models were treated with a single dose of FOLFOXIRI when the tumors reached a volume of 100 mm3. Tumor dimensions were measured using calipers every 3 days, and volumes were calculated using the formula: V = 0.52 × length × width2. Body weights were recorded every 3–5 days to monitor treatment-related toxicity.

value: PDX tumor

value: Primary CRC cell

value: tumor cell

value: Relapse after treatmen


title: 21E x 26P, downstream, integrated, BC amplicon, DNA, biol rep 3

description: Library name: 21E x 26P downstream integrated DNA BC sequencing rep 3


title: Control rep 4


title: 21E x 26P, downstream, integrated, BC amplicon, RNA, biol rep 3

description: Library name: 21E x 26P downstream integrated RNA BC sequencing rep 3


title: cells, Relapse after treatment 4

description:
Library name: QQX17Reg4
column AG in 1_genes_fpkm_expression.txt:QQX17Reg4


title: Control rep 3


title: 21E x 26P, downstream, integrated, BC amplicon, DNA, biol rep 2

description: Library name: 21E x 26P downstream integrated DNA BC sequencing rep 2


title: cells, Relapse after treatment 3

description:
Library name: QQX17Reg3
column AF in 1_genes_fpkm_expression.txt:QQX17Reg3


title: 21E x 26P, STARR-seq, integrated, BC amplicon, DNA, biol rep 3

description: Library name: 21E x 26P STARR-seq integrated DNA BC sequencing rep 3


title: 21E x 26P, downstream, integrated, BC amplicon, RNA, biol rep 2

description: Library name: 21E x 26P downstream integrated RNA BC sequencing rep 2


title: Control rep 2


title: 21E x 26P, STARR-seq, integrated, BC amplicon, RNA, biol rep 3

description: Library name: 21E x 26P STARR-seq integrated RNA BC sequencing rep 3


title: cells, Relapse after treatment 2

description:
Library name: QQX17Reg2
column AE in 1_genes_fpkm_expression.txt:QQX17Reg2


title: 21E x 26P, STARR-seq, integrated, BC amplicon, DNA, biol rep 2

description: Library name: 21E x 26P STARR-seq integrated DNA BC sequencing rep 2


title: Control rep 1


title: 21E x 26P, STARR-seq, integrated, BC amplicon, RNA, biol rep 2

description: Library name: 21E x 26P STARR-seq integrated RNA BC sequencing rep 2


title: cells, Relapse after treatment 1

description:
Library name: QQX17Reg1
column AD in 1_genes_fpkm_expression.txt:QQX17Reg1


title: 21E x 26P, upstream, integrated, BC amplicon, DNA, biol rep 3

description: Library name: 21E x 26P upstream integrated DNA BC sequencing rep 3


title: Nr, O, IP, rep3

city: Beijing

first: Lili

last: Ma

address: 50 Changhua Road, Haidian District

institute: Beijing Academy of Agriculture and Forestry Science

data_processing:
Briefly, Paired-end reads were harvested from Illumina Novaseq 6000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). Clean reads of all libraries were aligned to the reference genome by Hisat2 software (v2.0.4).
Methylated sites on RNAs (peaks) were identified by MACS software. Differentially methylated sites were identified by diffReps. These peaks identified by both softwares overlapping with exons of mRNA, LncRNA and circRNA were figured out and chosen by home-made scripts.
GO and Pathway enrichment analysis were performed by the differentially methylated protein coding genes, the associated genes of differentially methylated LncRNAs and the source genes of differentially methylated circRNAs separately.
Assembly: SL3.0
Supplementary files format and content: tab-demilited text file includes raw counts for each samples

organism: Solanum lycopersicum

source_name: tomato

extract_protocol:
Total RNA was extracted using Trizol reagent
Total RNA was subjected to immunoprecipitation with the GenSeq® m1A-IP Kit (GenSeq Inc.) by following the manufacturer’s instructions. Briefly, RNA was randomly fragmented to ~200 nt by RNA Fragmentation Reagents. Protein A/G beads were coupled to the m1A antibodies by rotating at room temperature for 1 h. The RNA fragments were incubated with the bead-linked antibodies and rotated at 4°C for 4 h. After incubation, the RNA/antibody complexes were washed for several times, and then, captured RNA was eluted from the complexes and purified. Induced m1A-to-m6A rearrangement was achieved by incubating the input and immunoprecipitation fragments in an alkaline buffer followed by column purification. Alkaline-treated IP/Input samples were subjected to library construction with GenSeq® Low Input Whole RNA Library Prep Kit (GenSeq, Inc.) by following the manufacturer’s instructions. Libraries were qualified using Agilent 2100 bioanalyzer and then sequenced in a NovaSeq platform (Illumina).

value: tomato


title: 21E x 26P, upstream, integrated, BC amplicon, RNA, biol rep 3

description: Library name: 21E x 26P upstream integrated RNA BC sequencing rep 3


title: cells, FOLFOXIRI treatment6

description:
Library name: QQX17DTP6
column AC in 1_genes_fpkm_expression.txt:QQX17DTP6

value: FOLFOXIRI treatment

value: FOLFOXIRI


title: 21E x 26P, upstream, integrated, BC amplicon, DNA, biol rep 2

description: Library name: 21E x 26P upstream integrated DNA BC sequencing rep 2


title: Nr, O, IP, rep2


title: 21E x 26P, upstream, integrated, BC amplicon, RNA, biol rep 2

description: Library name: 21E x 26P upstream integrated RNA BC sequencing rep 2


title: cells, FOLFOXIRI treatment5

description:
Library name: QQX17DTP5
column AB in 1_genes_fpkm_expression.txt:QQX17DTP5


title: 21E x 26P, downstream, plasmid, BC amplicon, DNA, biol rep 3

description: Library name: 21E x 26P downstream plasmid DNA BC sequencing rep 3


title: Nr, O, IP, rep1


title: 21E x 26P, downstream, plasmid, BC amplicon, RNA, biol rep 3

description: Library name: 21E x 26P downstream plasmid RNA BC sequencing rep 3


title: cells, FOLFOXIRI treatment4

description:
Library name: QQX17DTP4
column AA in 1_genes_fpkm_expression.txt:QQX17DTP4


title: 21E x 26P, downstream, plasmid, BC amplicon, DNA, biol rep 2

description: Library name: 21E x 26P downstream plasmid DNA BC sequencing rep 2


title: 21E x 26P, STARR-seq, plasmid, BC amplicon, DNA, biol rep 3

description: Library name: 21E x 26P STARR-seq plasmid DNA BC sequencing rep 3


title: cells, FOLFOXIRI treatment3

description:
Library name: QQX17DTP3
column Z in 1_genes_fpkm_expression.txt:QQX17DTP3


title: 21E x 26P, downstream, plasmid, BC amplicon, RNA, biol rep 2

description: Library name: 21E x 26P downstream plasmid RNA BC sequencing rep 2


title: Nr, G, IP, rep2


title: Nr, G, IP, rep3


title: 21E x 26P, STARR-seq, plasmid, BC amplicon, RNA, biol rep 3

description: Library name: 21E x 26P STARR-seq plasmid RNA BC sequencing rep 3


title: Nr, G, IP, rep1


title: cells, FOLFOXIRI treatment2

description:
Library name: QQX17DTP2
column Y in 1_genes_fpkm_expression.txt:QQX17DTP2


title: 21E x 26P, STARR-seq, plasmid, BC amplicon, DNA, biol rep 2

description: Library name: 21E x 26P STARR-seq plasmid DNA BC sequencing rep 2


title: 21E x 26P, STARR-seq, plasmid, BC amplicon, RNA, biol rep 2

description: Library name: 21E x 26P STARR-seq plasmid RNA BC sequencing rep 2


title: cells, FOLFOXIRI treatment1

description:
Library name: QQX17DTP1
column X in 1_genes_fpkm_expression.txt:QQX17DTP1


title: 21E x 26P, upstream, plasmid, BC amplicon, DNA, biol rep 3

description: Library name: 21E x 26P upstream plasmid DNA BC sequencing rep 3


title: AC, Br+6, IP, rep2


title: 21E x 26P, upstream, plasmid, BC amplicon, RNA, biol rep 3

description: Library name: 21E x 26P upstream plasmid RNA BC sequencing rep 3


title: 21E x 26P, upstream, plasmid, BC amplicon, DNA, biol rep 2

description: Library name: 21E x 26P upstream plasmid DNA BC sequencing rep 2


title: cells, Con6

description:
Library name: QQX17Con6
column W in 1_genes_fpkm_expression.txt:QQX17Con6

value: WT

value: Control


title: 21E x 26P, downstream, integrated, BC amplicon, DNA, biol rep 1

description: Library name: 21E x 26P downstream integrated DNA BC sequencing rep 1


title: 21E x 26P, upstream, plasmid, BC amplicon, RNA, biol rep 2

description: Library name: 21E x 26P upstream plasmid RNA BC sequencing rep 2


title: cells, Con5

description:
Library name: QQX17Con5
column V in 1_genes_fpkm_expression.txt:QQX17Con5


title: AC, Br+6, IP, rep3


title: AC, Br+6, IP, rep1


title: 21E x 26P, downstream, integrated, BC amplicon, RNA, biol rep 1

description: Library name: 21E x 26P downstream integrated RNA BC sequencing rep 1


title: cells, Con4

description:
Library name: QQX17Con4
column U in 1_genes_fpkm_expression.txt:QQX17Con4


title: HBV HCMS, HepG2.2.15, Untreated, 3

status: Public on Jun 28 2026

first: Jennifer

last: Marlowe

state: Massachusetts

address: 201 Brookline Avenue

institute: nChroma Bio

description: Library name: NGSHC882

data_processing:
The nf-core Methyl-Seq pipeline (v1.6.1) was used to map sequencing reads to a genotype specific HBV reference genome (dependant on sample) using the Bismark methylation extraction workflow, with default parameters except for the following: clip_r1 = 10, clip_r2 = 10, three_prime_clip_r1 = 10, three_prime_clip_r2 = 10, cytosine_report = true.
Assembly: Genotype D (GenBank Accession: U95551.1) or Genotype A (GenBank Accession: AF305422.1)
Supplementary files format and content: Bismark methylation bedgraph file
Supplementary files format and content: Bismark cytosine report file
Library strategy: EM-seq

source_name: HepG2.2.15 cells

growth_protocol: HepG2.2.15 cells were cultured in DMEM (Gibco, 11965092) with 10% fetal bovine serum (FBS) (Gibco, A5670501) and 1% Pen-Strep (Gibco, 15140122). One day prior to treatment, 20,000 cells/well were seeded in collagen type I-coated 96-well plates. Plates were maintained and subcultured (cell trypsinization every 3-4 days).  HepG2-NTCP cells were plated at 20,000 cells/well in collagen coated 96-well plates and infected 24 hours later with HBV Genotype D at 2,000 multiplicity of genome equivalents (MGE) using DMEM media supplemented with 4% PEG8000 and 2.5% DMSO. At 16 hours post-infection, media was removed, cells were washed with PBS and were maintained in DMEM media supplemented with 2.5% DMSO.  C57BL/6-HBV transgenic mice (Tg-HBV), 5-6 weeks old, carrying two copies per diploid host genome of the 1.28× Genotype A HBV genome were obtained from Beijing Vitalstar Biotechnology Co., Ltd.

extract_protocol:
HepG2.2.15, cell samples were collected at a timepoint 14 days after treatment. Nucleic acids were extracted using simultaneous RNA and DNA extraction protocols (Beckman Coulter) for methylation assessments.  cccDNA was extracted from HepG2-NTCP using a modified Hirt protocol, using the MasterPure Complete DNA and RNA Purification Kit (LucigenEpicentre) without the proteinase K digestion. Total DNA was digested using 10 U of T5 exonuclease per 1 ug of DNA for 30 mins at 37°C, followed by heat inactivation at 80°C for 20 minutes. One third of the extracted total DNA was not digested and used as a control. After digestion, all samples were concentrated using a standard sodium acetate DNA precipitation protocol.  Tg-HBV mice were euthanized, and liver samples were collected for methylation assessment.
Genomic or cccDNA was sheared to a target size of 350bp using a Covaris 96 AFA-Tube TPX plate. Sequencing libraries were then constructed from the sheared genomic DNA using the NEBNext Enzymatic Methyl-seq (EM-seq) kit plus NEBNext Multiplex Oligos for Enzymatic Methyl-seq. After methylation conversion, a custom panel targeting the appropriate HBV genome (genotype A for Tg-HBV mouse and genotype D for HepG2.2.15 cells and cccDNA) was used to enrich for regions of interest, following the recommended Twist protocol for 8-plex pools. Libraries were then amplified and sequenced using an Illumina NextSeq2000 running NextSeq1000/2000 Control software version 1.7.0.45751 with 2 x 150 bp reads to a sequencing depth of > 5 million read pairs per sample.

treatment_protocol: HepG2.2.15 cells were treated with 100 µL of fresh media supplemented with LNP-formulated epigenetic silencers at a dose of 0.5 µg/mL (or 1.0 µg/mL for CRMA-1001) and/or 1 µg/mL of rhApoE3. Untreated controls were also included for one study.  Infected HepG2-NTCP cells were treated with 1 µg/mL of CRMA-1001 or vehicle. Cells were washed with PBS and snap frozen on Day 7.  All Tg-HBV mice were acclimated for 10 days before receiving a single IV bolus administration of vehicle, or HBV-EE4000 (0.2, 0.5, 1 and 3 mg/kg).

value: HepG2.2.15 cells

value: HBV Genotype D


title: 21E x 26P, STARR-seq, integrated, BC amplicon, DNA, biol rep 1

description: Library name: 21E x 26P STARR-seq integrated DNA BC sequencing rep 1


title: AC, MG, IP, rep2


title: 21E x 26P, STARR-seq, integrated, BC amplicon, RNA, biol rep 1

description: Library name: 21E x 26P STARR-seq integrated RNA BC sequencing rep 1


title: SSR_1

description:
Library name: SSR_1
control, replicate biosample 1

value: hyphae

value: control


title: MK92-Day294-ART

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

description:
Library name: p24155-s002_MK92-Day294-ART
Column name in raw_count_p24155_Tomas_Processing.csv

data_processing:
Alignment was performed using STAR version 2.7.9a and transcripts were annotated using a composite genomic assembly and annotation of the Mmul10 Indian rhesus macaque and SIVsm804ECL757 (Accession MF370842). Transcript abundance estimates were calculated internal to the STAR aligner using the algorithm of htseq-count.
Assembly: Mmul10
Assembly: MF370842
Supplementary files format and content: csv files containing raw counts for each sample (in columns) and transcript (in rows)

organism: Macaca mulatta

source_name: Blood

extract_protocol:
CD4+ T-cells were lyse in 350 L of Buffer RLT and then extracted using the RNeasy Mini / kit (Qiagen) with on-column DNase digestion. RNA quality was assessed using a TapeStation 4200 (Agilent)
Ten nanograms of total RNA was used as input for cDNA synthesis using the SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) according to the manufacturer’s instructions. Amplified cDNA was fragmented and appended with dual-indexed barcodes using the Nextera XT DNA Library Preparation kit (Illumina). Libraries were validated by capillary electrophoresis on a TapeStation 4200 (Agilent), pooled at equimolar concentrations, and sequenced with PE100 reads on an Illumina NovaSeq 6000, yielding ~21 million reads per sample on average.

value: Blood

value: CD4+ T-cells

tag: timepoint

tag: venetoclax treatment

tag: anti-cd8a treatment


title: AC, MG, IP, rep1


title: 21E x 26P, upstream, integrated, BC amplicon, DNA, biol rep 1

description: Library name: 21E x 26P upstream integrated DNA BC sequencing rep 1


title: 21E x 26P, upstream, integrated, BC amplicon, RNA, biol rep 1

description: Library name: 21E x 26P upstream integrated RNA BC sequencing rep 1


title: 21E x 26P, downstream, plasmid, BC amplicon, DNA, biol rep 1

description: Library name: 21E x 26P downstream plasmid DNA BC sequencing rep 1


title: cells, Con3

description:
Library name: QQX17Con3
column T in 1_genes_fpkm_expression.txt:QQX17Con3


title: cells, Con2

description:
Library name: QQX17Con2
column S in 1_genes_fpkm_expression.txt:QQX17Con2


title: AC, MG, IP, rep3


title: cells, Con1

description:
Library name: QQX17Con1
column R in 1_genes_fpkm_expression.txt:QQX17Con1


title: Nr, O, Input, rep3


title: 21E x 26P, STARR-seq, plasmid, BC amplicon, DNA, biol rep 1

description: Library name: 21E x 26P STARR-seq plasmid DNA BC sequencing rep 1


title: 21E x 26P, downstream, plasmid, BC amplicon, RNA, biol rep 1

description: Library name: 21E x 26P downstream plasmid RNA BC sequencing rep 1


title: 21E x 26P, STARR-seq, plasmid, BC amplicon, RNA, biol rep 1

description: Library name: 21E x 26P STARR-seq plasmid RNA BC sequencing rep 1


title: cells, Relapse after treatment5

description:
Library name: QQX09Reg5
column AF in 1_genes_fpkm_expression.txt:QQX09Reg3


title: 21E x 26P, upstream, plasmid, BC amplicon, DNA, biol rep 1

description: Library name: 21E x 26P upstream plasmid DNA BC sequencing rep 1


title: 21E x 26P, upstream, plasmid, BC amplicon, RNA, biol rep 1

description: Library name: 21E x 26P upstream plasmid RNA BC sequencing rep 1


title: Nr, O, Input, rep2


title: 21E x 500P, upstream, full-length transcript 5'-end

description: Library name: 21E x 500P upstream integrated 5_-end TSS mapping


title: Nr, O, Input, rep1


title: 21E x 26P, upstream, full-length transcript 5'-end

description: Library name: 21E x 26P upstream integrated 5_-end TSS mapping


title: cells, Relapse after treatment4

description:
Library name: QQX09Reg4
column AE in 1_genes_fpkm_expression.txt:QQX09Reg2


title: 21E x 500P, upstream, P-BC amplicon

description: Library name: 21E x 500P upstream Dictionary Building (P-BC)

library_source: other

molecule: other


title: cells, Relapse after treatment3

description:
Library name: QQX09Reg3
column AD in 1_genes_fpkm_expression.txt:QQX09Reg1


title: cells, Relapse after treatment2

description:
Library name: QQX09Reg2
column AC in 1_genes_fpkm_expression.txt:QQX09DTP6


title: 21E x 500P, upstream, E-BC amplicon

description: Library name: 21E x 500P upstream Dictionary Building (E-BC)


title: Nr, G, Input, rep3


title: 203E x 78P, upstream, full-length transcript 5'-end

description: Library name: 203E x 78P upstream integrated 5_-end TSS mapping


title: Nr, G, Input, rep2


title: 203E x 78P, upstream, P-BC amplicon

description: Library name: 203E x 78P upstream Dictionary Building (P-BC)


title: cells, Relapse after treatment1

description:
Library name: QQX09Reg1
column AB in 1_genes_fpkm_expression.txt:QQX09DTP5


title: 21E x 26P, downstream, P-BC amplicon

description: Library name: 21E x 26P downstream Dictionary Building (P-BC)


title: 203E x 78P, upstream, E-BC amplicon

description: Library name: 203E x 78P upstream Dictionary Building (E-BC)


title: Nr, G, Input, rep1


title: 21E x 26P, downstream, E-BC amplicon

description: Library name: 21E x 26P downstream Dictionary Building (E-BC)


title: cells,FOLFOXIRI treatment5

description:
Library name: QQX09DTP5
column AA in 1_genes_fpkm_expression.txt:QQX09DTP4


title: AC, Br+6, Input, rep3


title: NCA3-3

city: Fuzhou

first: Kunqi

last: Chen

address: Fujian Medical University

institute: Fujian Medical University

description: Library name: sample6

data_processing:
Base calling was performed using Illumina CASAVA software (v1.8.2) with default parameters. Raw FASTQ files were processed with in-house Perl scripts to remove reads containing adapter sequences, reads with >10% poly-N, and low-quality reads (Q-score < 20 in more than 50% of bases). Quality metrics (Q20, Q30, GC content, and sequence duplication levels) were calculated using FASTQC (v0.11.9).
Clean reads were aligned to the Homo sapiens reference genome (GRCh38) using HISAT2 (v2.0.5) with default parameters (--rna-strandness RF). Only reads with perfect matches or up to one mismatch were retained.
Transcripts were assembled and quantified using StringTie (v1.3.3) with default settings. Gene expression levels were calculated as fragments per kilobase of transcript per million mapped reads (FPKM).
Alignment files were sorted and duplicates removed using Picard tools (v1.41) and SAMtools (v0.1.18).
Assembly: GRCh38.110
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: liver

growth_protocol: HepG2 cells were cultured in DMEM supplemented with 10% fetal bovine serum(FBS) under the following conditions: 37°C, 5% CO2 incubator.

extract_protocol:
After 48 h of treatment, total RNA was extracted using Trizol and subjected to RNA sequencing.
RNA libraries for RNA-seq were prepared using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: HepG2 cells were seeded at 5×10⁵ cells/well in 6-well plates and cultured to 70–80% confluence. Transfection with siRNA targeting SF3A3 (siSF3A3-2, experimental group) or negative control siRNA (NC, control group) was performed using Lipofectamine 3000 at a final siRNA concentration of 50 nM according to the manufacturer's instructions. Cells were harvested 48 hours post-transfection for subsequent assays.

value: liver

value: epithelial cells

value: Wild type

value: Knockdown of SF3A5 gene


title: cells,FOLFOXIRI treatment4

description:
Library name: QQX09DTP4
column Z in 1_genes_fpkm_expression.txt:QQX09DTP3

value: PDX tumor

value: Primary CRC cell

value: tumor cell


title: AC, Br+6, Input, rep2

value: tomato


title: cells,FOLFOXIRI treatment3

description:
Library name: QQX09DTP3
column Y in 1_genes_fpkm_expression.txt:QQX09DTP2

value: FOLFOXIRI treatment

value: FOLFOXIRI


title: NCA3-2

description: Library name: sample5

value: Knockdown of SF3A4 gene


title: D36 KLRG1-TdTomato+ biol rep 2

city: San Antonio

first: Nu

state: TX

address: 7703 Floyd Curl Drive

department: Department of MIMG

institute: UT Health San Antonio

description:
Library name: Sample3
Cloumn name: V3

data_processing:
Raw sequencing reads were quantified using kallisto (v0.48.0) against a custom Mus musculus GRCm39 transcriptome derived from the Ensembl mouse cDNA reference. The reference transcriptome was supplemented with custom transgene sequences encoding TdTomato and Cre_P2A_EBFP.
Transcript abundances were estimated using pseudoalignment with default kallisto parameters. Transcript-level abundance estimates were imported into R using the tximport package and summarized to gene-level counts.
Downstream analyses were performed in R using DESeq2(v1.50.2). Size factor normalization and differential expression analyses were carried out using the median-of-ratios method implemented in DESeq2. Variance-stabilizing transformation (VST) was used for visualization and heatmap generation.
Gene expression values are provided as raw counts and normalized counts.
Assembly: GRCm39
Supplementary files format and content: csv file includes raw counts for each Sample
Supplementary files format and content: csv file includes normal counts for each Sample

source_name: Spleen and Lymph Nodes

extract_protocol:
RNA was harvested using Rneasy Micro Kit.
Library was constructed by Novogene

value: Spleen and Lymph Nodes

value: CD8+ T cells

value: p14 transgenic

value: LCMV Armstrong infected


title: D36 KLRG1-TdTomato- biol rep 2

description:
Library name: Sample4
Cloumn name: V4


title: AC, Br+6, Input, rep1


title: NCA3-1

description: Library name: sample4

value: Knockdown of SF3A3 gene


title: theta, rep1

city: London

first: Sofia

last: Peressotti

address: Exhibition Rd, South Kensington, London

country: United Kingdom

institute: Imperial College London

description: Library name: Stim1

data_processing:
The hisat2 software (2.0.5) was used with default parameters to map the data to the reference genome: mRatBN7.2 from Ensembl. Stringtie (1.3.3b) was used for the assembly (transcripts of class code type 'u'). featureCounts (1.5.0-p3) was used for the qunatification with default parameters. The data quality control was performed using a base calling error rate distribution of Q30 (99.9%), a GC content distribution control (with cut-off at 50%), and non-clean reads were removed from the analysis (defined as containing adapter contamination, a percentage of uncertain nucleotides >10%, and a percentage of low-quality nucleotides >50%).
Assembly: Ensembl mRatBN7.2
Supplementary files format and content: All .bam files contain the raw data. The gene_count.xlsx file contains the gene count for each sample and the gene_fpkm.xls contains the corresponding FPKM values for each sample.

organism: Rattus norvegicus

source_name: ventral mesencephalon embryonic day 14

growth_protocol: Primary neurogprogenitor cells were plated in 24-well plates at a density of 60,000 cells/cm2 with 0.75 ml of proliferation medium (DMEM)/F12 supplemented with 33 mM D-glucose, 1% L-glutamine, 1% penicillin/streptomycin (P/S), 2% B27, 1% fetal bovine serum (FBS), 20 ng/ml EGF, 20 ng/ml FGF). The cultures were then gradually transitioned from proliferation medium to differentiation medium: Dulbecco’s modified Eagle’s medium (DMEM)/F12 supplemented with 33 mM D-glucose, 1% L-glutamine, 1% penicillin/streptomycin (P/S), 50 mg/ml BSA, 1% N2. 75% of the medium was replaced every 2 days, increasing the ratio of differentiation medium by a third at every first medium change, until the transition was complete. Cells were grown for 10 days in total.

extract_protocol:
The mRNA was extracted using a commercial RNeasy Micro Kit (Cat. 74004, Quiagen) following the manufacturer protocol. Only samples with a purity ratio above 1.9 were included in the dataset.
Poly(A) enrichment was utilised for library preparation followed by 150 bp paired-end (40 million reads) sequencing using an Illumina Sequencing PE150 system.

treatment_protocol: Cells were stimulated in vitro with a temporal interference protocol (10 Hz amplitude modulation, 1 kHz frequency, 2 s on-2 s off, 2 mA peak-to peak, 300-500 mV/mm) for 3 days (day in vitro 7,8,9), 6 h per day. RNA extraction was performed at day in vitro 10.

value: ventral mesencephalon embryonic day 14

value: embryonic neuroprogenitor cells

value: WT

value: theta TI stimulation


title: cells,FOLFOXIRI treatment2

description:
Library name: QQX09DTP2
column X in 1_genes_fpkm_expression.txt:QQX09DTP1


title: D36 KLRG1-TdTomato- biol rep 1

description:
Library name: Sample2
Cloumn name: V2


title: NCNC-3

description: Library name: sample3

value: liver

value: epithelial cells

value: Wild type

value: Control


title: AC, MG, Input, rep3

value: tomato


title: cells,FOLFOXIRI treatment1

description:
Library name: QQX09DTP1
column W in 1_genes_fpkm_expression.txt:QQX09Con6

value: PDX tumor

value: Primary CRC cell

value: tumor cell

value: FOLFOXIRI treatment


title: D36 KLRG1-TdTomato+ biol rep 1

description:
Library name: Sample1
Cloumn name: V1

value: Spleen and Lymph Nodes

value: CD8+ T cells


title: AC, MG, Input, rep2


title: NCNC-2

description: Library name: sample2


title: cells,Con5

description:
Library name: QQX09Con5
column V in 1_genes_fpkm_expression.txt:QQX09Con5


title: AC, MG, Input, rep1


title: NCNC-1

description: Library name: sample1


title: cells,Con4

description:
Library name: QQX09Con4
column U in 1_genes_fpkm_expression.txt:QQX09Con4


title: dendritic_MEKi_10 sample 33377

city: Newton

first: Matt

last: Kanke

state: MA - Massachusetts

address: 112 Harding Street

institute: Amgen

description:
Library name: Sample_33377
Low input bulk RNA-seq

data_processing:
Fastqs were aligned using a modified OmicSoft Sequence Aligner pipeline.
Raw gene level counts were determined using Omicsoft’s RSEM implementation and relying on the Omicsoft GENCODE v34 gene model.
Differential gene expression analysis was performed in R (v4.2.1) using DESeq2 (v1.38.3).
Assembly: GRCm39
Supplementary files format and content: Count table containing gene level counts.

source_name: dendritic

extract_protocol:
Rneasy
SMART-Seq mRNA LP Kit

value: dendritic

value: KPC

value: MEK inhibitor 10mpk


title: dendritic_MEKi_10 sample 33378

description:
Library name: Sample_33378
Low input bulk RNA-seq


title: Male Head,VAPP58SRepo_KaySCR, Day 15, Rep4

city: Pune

first: Girish

last: Ratnaparkhi

state: Maharashtra

address: NCL Colony, Dr. Homi Bhabha Road

department: Biology

country: India

institute: IISER-Pune

description: Library name: Sample 88

data_processing:
Done with Kangooroo Beta, a web-based interactive platform for RNA-Seq data analysis for males and Bluebee platform for females
Assembly: Drosophila melanogaster genome (dm6)
Supplementary files format and content: csv files containing raw counts for male data
Supplementary files format and content: csv files containing counts per million for female data

organism: Drosophila melanogaster

source_name: Head

extract_protocol:
RNA was manually extracted using phenol-choloroform extraction.
RNA libraries for RNA-Seq were prepared using 3‘ mRNA-Seq V2 Library Prep Kit FWD with Unique Dual Indices (12nt) for males following manufacturer's protocol
QuantSeq 3' mRNA-Seq Library Prep Kit FWD for females following manufacturer's protocol

value: Head


title: Sample10-ALN axillary lymph node scRNA-seq

city: jinan

first: pengfei

last: qiu

address: 440 Jiyan Rd, Jinan, P.R. China

institute: Shandong First Medical University and Shandong Academy of Medical Sciences

description:
Library name: Sample10-ALN
Fresh frozen axillary lymph node sample from a patient with triple-receptor negative breast cancer collected at Shandong Cancer Hospital on 2024-06-06 for single-cell RNA sequencing after immune cell sorting.

data_processing:
Raw base call files were converted to FASTQ files and processed with Cell Ranger v7.0.0.
Reads were aligned to the human reference genome GRCh38 and feature-barcode matrices were generated using Cell Ranger v7.0.0.
Quality control filtering excluded cells with fewer than 200 genes, more than 7,500 genes, more than 50,000 UMIs, or more than 10% mitochondrial reads.
Seurat v5.0.3 was used for log-normalization, dimensionality reduction, clustering, and annotation based on marker gene expression.
This GEO submission contains processed single-cell expression matrices and per-sample cell metadata tables. Raw FASTQ data were deposited separately in the Genome Sequence Archive (GSA) for human data, and the GSA ID is HRA010347.
Assembly: GRCh38
Supplementary files format and content: Per-sample processed files include compressed filtered feature-barcode matrices exported from Cell Ranger.
Supplementary files format and content: Additional processed files include per-sample cell-level metadata tables in tab-delimited text format.

source_name: axillary lymph node

growth_protocol: Fresh primary tumor and lymph node tissues were obtained from treatment-naive female patients with triple-negative breast cancer who underwent upfront surgery at Shandong Cancer Hospital and Institute. No in vitro growth step was involved.

extract_protocol:
Fresh tissues were rinsed in cold PBS, minced into approximately 1 mm3 pieces, incubated in PBS containing DNase I (100 μg/mL) for 5 min at room temperature, mechanically dissociated through 100-μm strainers, subjected to red blood cell lysis, washed in PBS with 0.04% BSA, filtered, and enriched for CD45+ immune cells by fluorescence-activated cell sorting using a BD FACSAria III with a 70-μm nozzle. Cell viability was assessed by trypan blue staining on a Countess II FL counter; samples with viability >85% were used for library preparation, or dead cells were removed using a Miltenyi Biotec kit.
Single-cell libraries were generated using the 10x Genomics Chromium Single Cell 3' v3 platform, targeting approximately 8,000 cells per sample. Reverse transcription and cell barcoding were performed in GEMs, followed by cDNA amplification, fragmentation, adaptor ligation, and enrichment according to the manufacturer's protocol. Libraries were quality-controlled using an Agilent Bioanalyzer.

treatment_protocol: No treatment was applied before tissue collection. All samples were obtained from treatment-naive patients at the time of surgery.

value: axillary lymph node

value: immune cells


title: cells,Con3

last: Dong

description:
Library name: QQX09Con3
column T in 1_genes_fpkm_expression.txt:QQX09Con3

value: WT


title: dendritic_MEKi_10 sample 33376

description:
Library name: Sample_33376
Low input bulk RNA-seq


title: Sample10-SLN sentinel lymph node scRNA-seq

description:
Library name: Sample10-SLN
Fresh frozen sentinel lymph node sample from a patient with triple-receptor negative breast cancer collected at Shandong Cancer Hospital on 2024-06-06 for single-cell RNA sequencing after immune cell sorting.

source_name: sentinel lymph node

value: sentinel lymph node


title: cells,Con2

description:
Library name: QQX09Con2
column S in 1_genes_fpkm_expression.txt:QQX09Con2


title: dendritic_MEKi_3 sample 33375

description:
Library name: Sample_33375
Low input bulk RNA-seq

value: MEK inhibitor 3mpk


title: Sample10-Tumor primary tumor scRNA-seq

description:
Library name: Sample10-Tumor
Fresh frozen breast tumor sample from a patient with triple-receptor negative breast cancer collected at Shandong Cancer Hospital on 2024-06-06 for single-cell RNA sequencing after immune cell sorting.

source_name: breast tumor

value: breast tumor


title: Male Head,VAPP58SRepo_KaySCR, Day 15, Rep2

description: Library name: Sample 86


title: cells,Con1

description:
Library name: QQX09Con1
column R in 1_genes_fpkm_expression.txt:QQX09Con1

value: Control


title: dendritic_MEKi_3 sample 33374

description:
Library name: Sample_33374
Low input bulk RNA-seq


title: Sample9-ALN axillary lymph node scRNA-seq

description:
Library name: Sample9-ALN
Fresh frozen axillary lymph node sample from a patient with triple-receptor negative breast cancer collected at Shandong Cancer Hospital on 2024-05-10 for single-cell RNA sequencing after immune cell sorting.


title: Male Head,VAPP58SRepo_KaySCR, Day 15, Rep1

description: Library name: Sample 85


title: KD-nCALs, subacute stage 202135B

city: suzhou

first: xiaoling

last: li

state: State...

address: 100 Chongwen Road, Suzhou Industrial Park, Jiangsu Province, China

institute: suzhou func biotec inc.

description: KD-nCALs, subacute stage

data_processing:
the quality of raw reads were be checked using FastQC/fastp, remove low-quality reads and ribosomal RNA,adapter were be removed by trimmomatic
clean reads were mapped to GRCh38 using hisat,the generated BAM file were be handled with samtools
read count extraction  were performed using stringtie
raw counts were used for differential expression analysis using DESeq2.(A statistical cutoff of fold change >2 and p-adjusted value <0.05 was used to find DEGs)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file that contains sequence alignment data
Supplementary files format and content: binary version of a SAM file that is used to represent aligned sequences
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file include FPKM/TPM value for each sample

source_name: PBMC

extract_protocol:
This protocol utilizes total RNA extracted from PBMCs by TRIzol extraction.
Total RNA sequencing libraries were constructed using the Illumina TruSeq RNA Access kit (Illumina, USA)

value: PBMC


title: Sample9-SLN sentinel lymph node scRNA-seq

description:
Library name: Sample9-SLN
Fresh frozen sentinel lymph node sample from a patient with triple-receptor negative breast cancer collected at Shandong Cancer Hospital on 2024-05-10 for single-cell RNA sequencing after immune cell sorting.


title: Male Head,VAPP58SRepo_KaySCR, Day 5, Rep4

description: Library name: Sample 84


title: KD-nCALs, subacute stage 202134B

description: KD-nCALs, subacute stage


title: dendritic_MEKi_3 sample 33372

description:
Library name: Sample_33372
Low input bulk RNA-seq


title: Male Head,VAPP58SRepo_KaySCR, Day 5, Rep3

description: Library name: Sample 83


title: Sample9-Tumor primary tumor scRNA-seq

description:
Library name: Sample9-Tumor
Fresh frozen breast tumor sample from a patient with triple-receptor negative breast cancer collected at Shandong Cancer Hospital on 2024-05-10 for single-cell RNA sequencing after immune cell sorting.


title: dendritic_MEKi_3 sample 33371

description:
Library name: Sample_33371
Low input bulk RNA-seq


title: KD-nCALs, subacute stage 202131B

description: KD-nCALs, subacute stage


title: Sample8-ALN axillary lymph node scRNA-seq

description:
Library name: Sample8-ALN
Fresh frozen axillary lymph node sample from a patient with triple-receptor negative breast cancer collected at Shandong Cancer Hospital on 2024-04-07 for single-cell RNA sequencing after immune cell sorting.


title: Male Head,VAPP58SRepo_KaySCR, Day 5, Rep2

description: Library name: Sample 82


title: KD-nCALs, subacute stage 202129B

description: KD-nCALs, subacute stage


title: dendritic_MEKi_3 sample 33370

description:
Library name: Sample_33370
Low input bulk RNA-seq


title: Male Head,VAPP58SRepo_KaySCR, Day 5, Rep1

description: Library name: Sample 81


title: Sample8-SLN sentinel lymph node scRNA-seq

description:
Library name: Sample8-SLN
Fresh frozen sentinel lymph node sample from a patient with triple-receptor negative breast cancer collected at Shandong Cancer Hospital on 2024-04-07 for single-cell RNA sequencing after immune cell sorting.


title: KD-nCALs, subacute stage 202104B

description: KD-nCALs, subacute stage


title: dendritic_AMG510 sample 33369

description:
Library name: Sample_33369
Low input bulk RNA-seq

value: KRAS G12C inhibitor


title: Male Head,VAPP58SRepo_KayWT, Day 15, Rep4

description: Library name: Sample 80


title: Sample8-Tumor primary tumor scRNA-seq

description:
Library name: Sample8-Tumor
Fresh frozen breast tumor sample from a patient with triple-receptor negative breast cancer collected at Shandong Cancer Hospital on 2024-04-07 for single-cell RNA sequencing after immune cell sorting.


title: KD-nCALs, subacute stage 202102B

description: KD-nCALs, subacute stage


title: dendritic_AMG510 sample 33368

description:
Library name: Sample_33368
Low input bulk RNA-seq


title: Male Head,VAPP58SRepo_KayWT, Day 15, Rep3

description: Library name: Sample 79


title: Sample7-ALN axillary lymph node scRNA-seq

description:
Library name: Sample7-ALN
Fresh frozen axillary lymph node sample from a patient with triple-receptor negative breast cancer collected at Shandong Cancer Hospital on 2024-03-06 for single-cell RNA sequencing after immune cell sorting.


title: KD-nCALs, acute stage 202135A

description: KD-nCALs, acute stage


title: dendritic_AMG510 sample 33367

description:
Library name: Sample_33367
Low input bulk RNA-seq


title: Male Head,VAPP58SRepo_KayWT, Day 15, Rep2

description: Library name: Sample 78


title: Sample7-SLN sentinel lymph node scRNA-seq

description:
Library name: Sample7-SLN
Fresh frozen sentinel lymph node sample from a patient with triple-receptor negative breast cancer collected at Shandong Cancer Hospital on 2024-03-06 for single-cell RNA sequencing after immune cell sorting.


title: KD-nCALs, acute stage 202134A

description: KD-nCALs, acute stage


title: Male Head,VAPP58SRepo_KayWT, Day 15, Rep1

description: Library name: Sample 77


title: dendritic_AMG510 sample 33366

description:
Library name: Sample_33366
Low input bulk RNA-seq


title: Sample7-Tumor primary tumor scRNA-seq

description:
Library name: Sample7-Tumor
Fresh frozen breast tumor sample from a patient with triple-receptor negative breast cancer collected at Shandong Cancer Hospital on 2024-03-06 for single-cell RNA sequencing after immune cell sorting.


title: KD-nCALs, acute stage 202131A

description: KD-nCALs, acute stage


title: dendritic_AMG510 sample 33365

description:
Library name: Sample_33365
Low input bulk RNA-seq


title: Male Head,VAPP58SRepo_KayWT, Day 5, Rep4

description: Library name: Sample 76


title: Sample6-ALN axillary lymph node scRNA-seq

description:
Library name: Sample6-ALN
Fresh frozen axillary lymph node sample from a patient with triple-receptor negative breast cancer collected at Shandong Cancer Hospital on 2024-02-27 for single-cell RNA sequencing after immune cell sorting.


title: KD-nCALs, acute stage 202129A

description: KD-nCALs, acute stage


title: dendritic_AMG510 sample 33364

description:
Library name: Sample_33364
Low input bulk RNA-seq


title: Male Head,VAPP58SRepo_KayWT, Day 5, Rep3

description: Library name: Sample 75


title: KD-nCALs, acute stage 202104A

description: KD-nCALs, acute stage


title: dendritic_veh sample 33363

description:
Library name: Sample_33363
Low input bulk RNA-seq

value: Vehicle


title: Male Head,VAPP58SRepo_KayWT, Day 5, Rep2

description: Library name: Sample 74


title: Sample6-SLN sentinel lymph node scRNA-seq

description:
Library name: Sample6-SLN
Fresh frozen sentinel lymph node sample from a patient with triple-receptor negative breast cancer collected at Shandong Cancer Hospital on 2024-02-27 for single-cell RNA sequencing after immune cell sorting.


title: KD-nCALs, acute stage 202102A

description: KD-nCALs, acute stage


title: Sample6-Tumor primary tumor scRNA-seq

description:
Library name: Sample6-Tumor
Fresh frozen breast tumor sample from a patient with triple-receptor negative breast cancer collected at Shandong Cancer Hospital on 2024-02-27 for single-cell RNA sequencing after immune cell sorting.


title: Sample5-ALN axillary lymph node scRNA-seq

description:
Library name: Sample5-ALN
Fresh frozen axillary lymph node sample from a patient with triple-receptor negative breast cancer collected at Shandong Cancer Hospital on 2024-01-26 for single-cell RNA sequencing after immune cell sorting.


title: dendritic_veh sample 33362

description:
Library name: Sample_33362
Low input bulk RNA-seq


title: KD-CALs, subacute stage 202141B

description: KD-CALs, subacute stage


title: Male Head,VAPP58SRepo_KayWT, Day 5, Rep1

description: Library name: Sample 73


title: Male Head,VAPP58SRepo_KayKD, Day 15, Rep4

description: Library name: Sample 72


title: dendritic_veh sample 33361

description:
Library name: Sample_33361
Low input bulk RNA-seq


title: Sample5-SLN sentinel lymph node scRNA-seq

description:
Library name: Sample5-SLN
Fresh frozen sentinel lymph node sample from a patient with triple-receptor negative breast cancer collected at Shandong Cancer Hospital on 2024-01-26 for single-cell RNA sequencing after immune cell sorting.


title: KD-CALs, subacute stage 202140B

description: KD-CALs, subacute stage


title: dendritic_veh sample 33360

description:
Library name: Sample_33360
Low input bulk RNA-seq


title: Male Head,VAPP58SRepo_KayKD, Day 15, Rep3

description: Library name: Sample 71


title: KD-CALs, subacute stage 202138B

description: KD-CALs, subacute stage


title: Sample5-Tumor primary tumor scRNA-seq

description:
Library name: Sample5-Tumor
Fresh frozen breast tumor sample from a patient with triple-receptor negative breast cancer collected at Shandong Cancer Hospital on 2024-01-26 for single-cell RNA sequencing after immune cell sorting.


title: dendritic_veh sample 33359

description:
Library name: Sample_33359
Low input bulk RNA-seq


title: Male Head,VAPP58SRepo_KayKD, Day 15, Rep2

description: Library name: Sample 70


title: Sample4-ALN axillary lymph node scRNA-seq

description:
Library name: Sample4-ALN
Fresh frozen axillary lymph node sample from a patient with triple-receptor negative breast cancer collected at Shandong Cancer Hospital on 2023-11-17 for single-cell RNA sequencing after immune cell sorting.


title: dendritic_veh sample 33358

description:
Library name: Sample_33358
Low input bulk RNA-seq


title: KD-CALs, subacute stage 202136B

description: KD-CALs, subacute stage


title: Male Head,VAPP58SRepo_KayKD, Day 15, Rep1

description: Library name: Sample 69


title: Sample4-SLN sentinel lymph node scRNA-seq

description:
Library name: Sample4-SLN
Fresh frozen sentinel lymph node sample from a patient with triple-receptor negative breast cancer collected at Shandong Cancer Hospital on 2023-11-17 for single-cell RNA sequencing after immune cell sorting.


title: dendritic_veh sample 33357

description:
Library name: Sample_33357
Low input bulk RNA-seq


title: KD-CALs, subacute stage 202109B

description: KD-CALs, subacute stage


title: Male Head,VAPP58SRepo_KayKD, Day 5, Rep4

description: Library name: Sample 68


title: Sample4-Tumor primary tumor scRNA-seq

description:
Library name: Sample4-Tumor
Fresh frozen breast tumor sample from a patient with triple-receptor negative breast cancer collected at Shandong Cancer Hospital on 2023-11-17 for single-cell RNA sequencing after immune cell sorting.


title: KD-CALs, subacute stage 202108B

description: KD-CALs, subacute stage


title: dendritic_veh sample 33356

description:
Library name: Sample_33356
Low input bulk RNA-seq


title: Male Head,VAPP58SRepo_KayKD, Day 5, Rep3

description: Library name: Sample 67


title: Sample3-SLN sentinel lymph node scRNA-seq

description:
Library name: Sample3-SLN
Fresh frozen sentinel lymph node sample from a patient with triple-receptor negative breast cancer collected at Shandong Cancer Hospital on 2023-08-03 for single-cell RNA sequencing after immune cell sorting.


title: KD-CALs, acute stage 202141A

description: KD-CALs, acute stage


title: dendritic_veh sample 33355

description:
Library name: Sample_33355
Low input bulk RNA-seq


title: Male Head,VAPP58SRepo_KayKD, Day 5, Rep2

description: Library name: Sample 66


title: Sample3-Tumor primary tumor scRNA-seq

description:
Library name: Sample3-Tumor
Fresh frozen breast tumor sample from a patient with triple-receptor negative breast cancer collected at Shandong Cancer Hospital on 2023-08-03 for single-cell RNA sequencing after immune cell sorting.


title: KD-CALs, acute stage 202140A

description: KD-CALs, acute stage


title: dendritic_MEKi_3 sample 33373

description:
Library name: Sample_33373
Low input bulk RNA-seq


title: dendritic_veh sample 33354

description:
Library name: Sample_33354
Low input bulk RNA-seq


title: Sample2-ALN axillary lymph node scRNA-seq

description:
Library name: Sample2-ALN
Fresh frozen axillary lymph node sample from a patient with triple-receptor negative breast cancer collected at Shandong Cancer Hospital on 2023-07-14 for single-cell RNA sequencing after immune cell sorting.


title: Male Head,VAPP58SRepo_KayKD, Day 5, Rep1

description: Library name: Sample 65


title: dendritic_veh sample 33353

description:
Library name: Sample_33353
Low input bulk RNA-seq


title: KD-CALs, acute stage 202138A

description: KD-CALs, acute stage


title: Male Head,VAPP58SRepo, Day 15, Rep4

description: Library name: Sample 64


title: Sample2-SLN sentinel lymph node scRNA-seq

description:
Library name: Sample2-SLN
Fresh frozen sentinel lymph node sample from a patient with triple-receptor negative breast cancer collected at Shandong Cancer Hospital on 2023-07-14 for single-cell RNA sequencing after immune cell sorting.


title: KD-CALs, acute stage 202136A

description: KD-CALs, acute stage


title: dendritic_veh sample 33352

description:
Library name: Sample_33352
Low input bulk RNA-seq


title: Sample2-Tumor primary tumor scRNA-seq

description:
Library name: Sample2-Tumor
Fresh frozen breast tumor sample from a patient with triple-receptor negative breast cancer collected at Shandong Cancer Hospital on 2023-07-14 for single-cell RNA sequencing after immune cell sorting.


title: Male Head,VAPP58SRepo, Day 15, Rep3

description: Library name: Sample 63


title: KD-CALs, acute stage 202109A

description: KD-CALs, acute stage


title: CD45_MEKi_10 sample 33349

description:
Library name: Sample_33349
Low input bulk RNA-seq


title: Sample1-SLN sentinel lymph node scRNA-seq

description:
Library name: Sample1-SLN
Fresh frozen sentinel lymph node sample from a patient with triple-receptor negative breast cancer collected at Shandong Cancer Hospital on 2023-06-29 for single-cell RNA sequencing after immune cell sorting.


title: Male Head,VAPP58SRepo, Day 15, Rep2

description: Library name: Sample 62


title: KD-CALs, acute stage 202108A

description: KD-CALs, acute stage


title: CD45_MEKi_10 sample 33348

description:
Library name: Sample_33348
Low input bulk RNA-seq


title: Male Head,VAPP58SRepo, Day 15, Rep1

description: Library name: Sample 61


title: Sample1-Tumor primary tumor scRNA-seq

description:
Library name: Sample1-Tumor
Fresh frozen breast tumor sample from a patient with triple-receptor negative breast cancer collected at Shandong Cancer Hospital on 2023-06-29 for single-cell RNA sequencing after immune cell sorting.


title: HeLa, replicate 2

city: Warsaw

first: Damian

last: Graczyk

address: ul. Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics Polish Academy of Sciences

description: RNA-seq

data_processing:
Raw sequencing reads were mapped to human genome reference assembly GRh38/hg38 using STAR (version 2.7.10a) in the paired-end mode. bigWig signal files (counts per million normalised) were generated using deeptools (version 3.5.1). Duplicate reads were removed.
Assembly: hg38
Supplementary files format and content: bigWig

source_name: Cervical cancer

growth_protocol: Cells were cultured in HyClone DMEM with high glucose, 4 mM L-glutamine, and sodium pyruvate (Cytiva) supplemented with 10% FBS (Gibco) at 37°C in an atmosphere of 5% CO2

extract_protocol:
Total cellular RNA was isolated using TRI Reagent (Sigma) according to the manufacturer's instructions. RNA samples were treated with TURBO DNase (Thermo Scientific). The RNA was then purified by phenol:chloroform extraction, precipitated with ethanol, resuspended in water and the concentration was measured in a NanoDrop ND2000 spectrophotometer (Thermo Scientific). Two micrograms of purified total RNA was subjected to depletion of nuclear-encoded rRNA using the Ribo-Zero rRNA Removal Kit (Illumina) according to the manufacturer's instructions.
Library preparation was performed using KAPA RNA HyperPrep Kit (Kapa Biosciences) according to the manufacturer's recommendations. To estimate the number of library PCR amplification, the KAPA Library Quantification Kit (Kapa Biosciences) was used following the manufacturer's recommendations. The final amplification products (cDNA libraries) were purified using beads included in the KAPA RNA HyperPrep Kit and subjected to an additional purification step with the AMPure XP beads (Beckman Coulter), and then analysed with the 2100 Bioanalyzer using the High Sensitivity DNA Kit (Agilent).

treatment_protocol: No treatment

value: Cervical cancer

value: HeLa Flp-In T-Rex

value: Epithelial cells