title: CD45_MEKi_10 sample 33343

description:
Library name: Sample_33343
Low input bulk RNA-seq


title: Male Head,VAPP58SRepo, Day 5, Rep4

status: Public on Jun 27 2026

type: SRA

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 60

library_source: transcriptomic

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

molecule: total RNA

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

tag: tissue

value: Head

tag: cell line

tag: cell type

tag: genotype


title: CD45_MEKi_10 sample 33340

city: Newton

first: Matt

last: Kanke

state: MA - Massachusetts

address: 112 Harding Street

country: USA

institute: Amgen

description:
Library name: Sample_33340
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.

organism: Mus musculus

extract_protocol:
Rneasy
SMART-Seq mRNA LP Kit

value: KPC

tag: treatment

value: MEK inhibitor 10mpk


title: Male Head,VAPP58SRepo, Day 5, Rep3

description: Library name: Sample 59


title: HeLa, replicate 1

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

organism: Homo sapiens

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

value: WT


title: tissue_STDP8480016550BL_L01_99

city: Guangzhou

first: Tianshen

last: Jiang

state: Guangdong

address: Tianhe, South China University of Technology

country: China

institute: South China Univerisity of Technology

description: Library name: tissue_STDP8480016550BL_L01_99

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Raw sequencing data were processed using the Stereo-seq analysis pipeline.
Spatially resolved gene expression matrices were generated.
Assembly: RatBN7.2
Supplementary files format and content: Processed data include gene expression matrices in Matrix Market format (matrix.mtx.gz, barcodes.tsv.gz, features.tsv.gz) and an H5AD file containing expression matrices and cell annotations.
Library strategy: Spatial Transcriptomics

organism: Rattus norvegicus

source_name: knee cartilage

extract_protocol:
Single cells were harvested and total RNA was extracted following the single-cell RNA-seq workflow. Spatial transcriptomic libraries were prepared following the Stereo-seq workflow.
Single-cell RNA-seq libraries were prepared using a droplet-based single-cell RNA sequencing protocol.Spatial transcriptomic libraries were prepared using the Stereo-seq workflow.

value: knee cartilage


title: tissue_STDP8480016550BL_L01_98

description: Library name: tissue_STDP8480016550BL_L01_98


title: Female Gut, VAPP58S, Day 20, Rep4

description: Library name: Sample 56

source_name: Gut

value: Gut


title: tissue_STDP8480016550BL_L01_97

description: Library name: tissue_STDP8480016550BL_L01_97


title: CD45_MEKi_10 sample 33337

description:
Library name: Sample_33337
Low input bulk RNA-seq


title: Female Gut, VAPP58S, Day 20, Rep3

description: Library name: Sample 55


title: Male Head,VAPP58SRepo, Day 5, Rep2

description: Library name: Sample 58


title: tissue_STDP8480016550BL_L01_104

description: Library name: tissue_STDP8480016550BL_L01_104


title: Male Head,VAPP58SRepo, Day 5, Rep1

description: Library name: Sample 57


title: CD45_MEKi_3 sample 33334

description:
Library name: Sample_33334
Low input bulk RNA-seq

value: MEK inhibitor 3mpk


title: Female Gut, VAPP58S, Day 20, Rep2

description: Library name: Sample 54


title: CD45_MEKi_3 sample 33331

description:
Library name: Sample_33331
Low input bulk RNA-seq


title: Male Head, VAPP58S, Day 20, Rep4

description: Library name: Sample 24


title: tissue_STDP8480016550BL_L01_103

description: Library name: tissue_STDP8480016550BL_L01_103


title: Female Gut, VAPP58S, Day 20, Rep1

description: Library name: Sample 53


title: CD45_MEKi_3 sample 33328

description:
Library name: Sample_33328
Low input bulk RNA-seq


title: Male Head, VAPP58S, Day 20, Rep3

description: Library name: Sample 23


title: tissue_STDP8480016550BL_L01_102

description: Library name: tissue_STDP8480016550BL_L01_102


title: Female Gut, VAPP58S, Day 5, Rep4

description: Library name: Sample 52


title: Male Head, VAPP58S, Day 20, Rep2

description: Library name: Sample 22


title: tissue_STDP8480016550BL_L01_101

description: Library name: tissue_STDP8480016550BL_L01_101


title: CD45_MEKi_3 sample 33325

description:
Library name: Sample_33325
Low input bulk RNA-seq


title: Female Gut, VAPP58S, Day 5, Rep3

description: Library name: Sample 51


title: CD45_MEKi_3 sample 33322

description:
Library name: Sample_33322
Low input bulk RNA-seq


title: tissue_STDP8480016550BL_L01_100

description: Library name: tissue_STDP8480016550BL_L01_100


title: Female Gut, VAPP58S, Day 5, Rep2

description: Library name: Sample 50


title: Male Head, VAPP58S, Day 20, Rep1

description: Library name: Sample 21


title: CD45_AMG510 sample 33319

description:
Library name: Sample_33319
Low input bulk RNA-seq

value: KRAS G12C inhibitor


title: Male Head, VAPP58S, Day 15, Rep4

description: Library name: Sample 20


title: tissue_STDP8480016549BL_L01_99

description: Library name: tissue_STDP8480016549BL_L01_99


title: Female Gut, VAPP58S, Day 5, Rep1

description: Library name: Sample 49


title: CD45_AMG510 sample 33316

description:
Library name: Sample_33316
Low input bulk RNA-seq


title: Male Head, VAPP58S, Day 15, Rep3

description: Library name: Sample 19


title: tissue_STDP8480016549BL_L01_98

description: Library name: tissue_STDP8480016549BL_L01_98


title: CD45_AMG510 sample 33313

description:
Library name: Sample_33313
Low input bulk RNA-seq


title: Female Gut, VAPWT, Day 20, Rep4

description: Library name: Sample 48

value: VAPWT


title: tissue_STDP8480016549BL_L01_97

description: Library name: tissue_STDP8480016549BL_L01_97


title: Male Head, VAPP58S, Day 15, Rep2

description: Library name: Sample 18


title: Female Gut, VAPWT, Day 20, Rep3

description: Library name: Sample 47


title: CD45_AMG510 sample 33310

description:
Library name: Sample_33310
Low input bulk RNA-seq


title: Male Head, VAPP58S, Day 15, Rep1

description: Library name: Sample 17


title: tissue_STDP8480016549BL_L01_104

description: Library name: tissue_STDP8480016549BL_L01_104


title: Female Gut, VAPWT, Day 20, Rep2

description: Library name: Sample 46


title: CD45_AMG510 sample 33307

description:
Library name: Sample_33307
Low input bulk RNA-seq


title: Male Head, VAPP58S, Day 5, Rep4

description: Library name: Sample 16


title: tissue_STDP8480016549BL_L01_103

description: Library name: tissue_STDP8480016549BL_L01_103


title: Female Gut, VAPWT, Day 20, Rep1

description: Library name: Sample 45


title: tissue_STDP8480016549BL_L01_102

description: Library name: tissue_STDP8480016549BL_L01_102


title: Male Head, VAPP58S, Day 5, Rep3

description: Library name: Sample 15


title: CD45_veh sample 33304

description:
Library name: Sample_33304
Low input bulk RNA-seq

value: Vehicle


title: Female Gut, VAPWT, Day 5, Rep4

description: Library name: Sample 44


title: CD45_veh sample 33302

description:
Library name: Sample_33302
Low input bulk RNA-seq


title: tissue_STDP8480016549BL_L01_101

description: Library name: tissue_STDP8480016549BL_L01_101


title: Male Head, VAPP58S, Day 5, Rep2

description: Library name: Sample 14


title: Female Gut, VAPWT, Day 5, Rep3

description: Library name: Sample 43


title: CD45_veh sample 33298

description:
Library name: Sample_33298
Low input bulk RNA-seq


title: Male Head, VAPP58S, Day 5, Rep1

description: Library name: Sample 13


title: tissue_STDP8480016549BL_L01_100

description: Library name: tissue_STDP8480016549BL_L01_100


title: Female Gut, VAPWT, Day 5, Rep2

description: Library name: Sample 42


title: CD45_veh sample 33296

description:
Library name: Sample_33296
Low input bulk RNA-seq


title: Male Head, VAPWT, Day 20, Rep4

description: Library name: Sample 12


title: tissue_STDP8480016448BL_L01_99

description: Library name: tissue_STDP8480016448BL_L01_99


title: Female Gut, VAPWT, Day 5, Rep1

description: Library name: Sample 41


title: Male Head, VAPWT, Day 20, Rep3

description: Library name: Sample 11


title: CD45_veh sample 33292

description:
Library name: Sample_33292
Low input bulk RNA-seq


title: tissue_STDP8480016448BL_L01_98

description: Library name: tissue_STDP8480016448BL_L01_98


title: Female Head, VAPP58S, Day 20, Rep4

description: Library name: Sample 40


title: Xenium of sentinel lymph node / axillary lymph node 3-3SLN-ALN in treatment-naïve TNBC

type: RNA

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: FFPE lymph node Xenium sample. ID: 3-3SLN-ALN. Node annotation from sample name: sentinel lymph node / axillary lymph node.

hyb_protocol: Xenium Prime 5K probes were hybridised overnight at 50°C, followed by ligation at 37°C and rolling circle amplification.

scan_protocol: The Xenium Analyzer performed iterative probe hybridisation, decoding, and DAPI-based cell segmentation. Slides were then H&E stained and scanned at 40×.

data_processing: Xenium matrices were analysed with Scanpy v1.9.3, Seurat v5.0.3, and hoodscanR v1.0.0. Cells outside the 2nd-98th percentile were removed, BBKNN batch correction was applied, clustering used Louvain on PCA/UMAP/t-SNE, and SpatialDM v0.3.1 was used for ligand-receptor analysis.

label: Xenium probe set

source_name: lymph node

label_protocol: Xenium probe set

growth_protocol: Human surgical specimens; no in vitro growth step.

extract_protocol: tissue preparation protocol: FFPE sections (5 μm) were mounted on Xenium slides, deparaffinised, rehydrated, and permeabilised.

treatment_protocol: Treatment-naïve upfront surgery cohort. No neoadjuvant therapy was administered before tissue collection.

value: lymph node

tag: tissue preservation method

value: FFPE

value: treatment-naïve; no neoadjuvant therapy before surgery

value: not applicable


title: Male Head, VAPWT, Day 20, Rep2

description: Library name: Sample 10

value: Head


title: Female Head, VAPP58S, Day 20, Rep3

description: Library name: Sample 39


title: tissue_STDP8480016448BL_L01_97

description: Library name: tissue_STDP8480016448BL_L01_97


title: Male Head, VAPWT, Day 20, Rep1

description: Library name: Sample 9


title: Xenium of sentinel lymph node / axillary lymph node 3-1SLN-ALN in treatment-naïve TNBC

description: FFPE lymph node Xenium sample. ID: 3-1SLN-ALN. Node annotation from sample name: sentinel lymph node / axillary lymph node.


title: tissue_STDP8480016448BL_L01_104

description: Library name: tissue_STDP8480016448BL_L01_104


title: Female Head, VAPP58S, Day 20, Rep2

description: Library name: Sample 38


title: Xenium of sentinel lymph node / axillary lymph node 2-3ALN-SLN in treatment-naïve TNBC

description: FFPE lymph node Xenium sample. ID: 2-3ALN-SLN. Node annotation from sample name: sentinel lymph node / axillary lymph node.


title: Male Head, VAPWT, Day 15, Rep4

description: Library name: Sample 8


title: tissue_STDP8480016448BL_L01_103

description: Library name: tissue_STDP8480016448BL_L01_103


title: Female Head, VAPP58S, Day 20, Rep1

description: Library name: Sample 37


title: Male Head, VAPWT, Day 15, Rep3

description: Library name: Sample 7


title: Female Head, VAPP58S, Day 5, Rep4

description: Library name: Sample 36


title: Xenium of sentinel lymph node / axillary lymph node 2-2ALN-SLN in treatment-naïve TNBC

description: FFPE lymph node Xenium sample. ID: 2-2ALN-SLN. Node annotation from sample name: sentinel lymph node / axillary lymph node.


title: tissue_STDP8480016448BL_L01_102

description: Library name: tissue_STDP8480016448BL_L01_102


title: Xenium of sentinel lymph node 1-3SLN in treatment-naïve TNBC

description: FFPE lymph node Xenium sample. ID: 1-3SLN. Node annotation from sample name: sentinel lymph node.


title: tissue_STDP8480016448BL_L01_101

description: Library name: tissue_STDP8480016448BL_L01_101


title: Female Head, VAPP58S, Day 5, Rep3

description: Library name: Sample 35


title: Male Head, VAPWT, Day 15, Rep2

description: Library name: Sample 6


title: Male Head, VAPWT, Day 15, Rep1

description: Library name: Sample 5


title: Xenium of sentinel lymph node / axillary lymph node 1-2SLN-ALN in treatment-naïve TNBC

description: FFPE lymph node Xenium sample. ID: 1-2SLN-ALN. Node annotation from sample name: sentinel lymph node / axillary lymph node.


title: tissue_STDP8480016448BL_L01_100

description: Library name: tissue_STDP8480016448BL_L01_100


title: Osteoarthritic cartilage treated with coacervate, cells, and drug, rat (Age: 10 weeks), rep4

description: Library name: CCD_4

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: rn6
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: Isolate the osteoarthritic cartilage from rat treated with coacervate, cells, and drug (Age:10 weeks)


title: Female Head, VAPP58S, Day 5, Rep2

description: Library name: Sample 34


title: tissue_scRNA_Treated with pZCO-MSCs-DS

description: Library name: tissue_scRNA_treat_B1_cDNA

library_source: transcriptomic single cell

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Raw sequencing data were processed using the Stereo-seq analysis pipeline.
Spatially resolved gene expression matrices were generated.
Assembly: RatBN7.2
Supplementary files format and content: Processed data include gene expression matrices in Matrix Market format (matrix.mtx.gz, barcodes.tsv.gz, features.tsv.gz) and an H5AD file containing expression matrices and cell annotations.


title: Male Head, VAPWT, Day 5, Rep4

description: Library name: Sample 4


title: Female Head, VAPP58S, Day 5, Rep1

description: Library name: Sample 33


title: Male Head,VAPP58SRepo_KaySCR, Day 15, Rep3

description: Library name: Sample 87


title: Osteoarthritic cartilage treated with coacervate, cells, and drug, rat (Age: 10 weeks), rep3

description: Library name: CCD_3


title: Male Head, VAPWT, Day 5, Rep3

description: Library name: Sample 3


title: tissue_scRNA_Treated with HA-MSCs-DS

description: Library name: tissue_scRNA_treat_A1_cDNA


title: Female Head, VAPWT, Day 20, Rep4

description: Library name: Sample 32


title: Male Head, VAPWT, Day 5, Rep2

description: Library name: Sample 2


title: Osteoarthritic cartilage treated with coacervate, cells, and drug, rat (Age: 10 weeks), rep2

description: Library name: CCD_2


title: tissue_scRNA_Control

description: Library name: tissue_scRNA_Control_1_cDNA


title: Female Head, VAPWT, Day 20, Rep3

description: Library name: Sample 31


title: Osteoarthritic cartilage treated with coacervate, cells, and drug, rat (Age: 10 weeks), rep1

description: Library name: CCD_1


title: Male Head, VAPWT, Day 5, Rep1

description: Library name: Sample 1


title: Female Head, VAPWT, Day 20, Rep2

description: Library name: Sample 30


title: macro_scRNA_Treated with pZCO-MSCs-DS

description: Library name: macro_scRNA_Treated_c_cDNA

source_name: cultured macrophages

value: cultured macrophages

value: macrophage


title: Osteoarthritic cartilage treated with hyaluronic acid, cells, and drug, rat (Age: 10 weeks), rep4

description: Library name: HCD_4

value: Isolate the osteoarthritic cartilage from rat treated with hyaluronic acid, cells, and drug (Age:10 weeks)


title: 22Rv1 cells, JMC45-2,12 h

city: Shanghai

first: Weisong

last: Tan

state: Shanghai

address: No. 2005 Songhu Road

institute: Fudan University

description: Library name: Sample 4

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software.
Assembly: The mapped reads of each sample were assembled by StringTie in a reference-based approach.
Supplementary files format and content: csv files include TPM values for each sample

source_name: cell line

growth_protocol: 22Rv1 cells were cultured in Roswell Park Memorial Institute 1640 medium (RPMI 1640) supplemented with 10% fetal bovine serum, penicillin and streptomycin in a humidified incubator with an atmosphere containing 5% CO2 at 37 °C.

extract_protocol:
Total RNA was isolated with MagZol Reagent (Cat. No. R480102, Magen Biotechnology Co., Ltd.), according to the manufacturer's instructions. Then, RNA quality was determined by 5300 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample(OD260/280=1.8~2.2, OD260/230≥2.0, RQN≥6.5, 28S:18S≥1.0, >1μg) was used to construct sequencing library.
RNA purification, reverse transcription, library construction and sequencing were performed at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) according to the manufacturer’s instructions . The 22Rv1 RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep, Ligation (San Diego, CA) using 1μg of total RNA. Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers. Then the synthesized cDNA was subjected to end-repair, phosphorylation and adapter addition according to library construction protocol. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by Qubit 4.0, the sequencing library was performed on DNBSEQ-T7 platform(PE150) using DNBSEQ-T7RS Reagent Kit (FCL PE150) version.

treatment_protocol: 22RV1 cells were treated with the small molecule compound JMC45 (40 nM) targeting CDK9 and vehicle (DMSO) for 12 hours.

value: cell line

value: CRPC


title: macro_scRNA_Treated with IL4

description: Library name: macro_scRNA_Treated_b_cDNA


title: Female Head, VAPWT, Day 20, Rep1

description: Library name: Sample 29


title: Osteoarthritic cartilage treated with hyaluronic acid, cells, and drug, rat (Age: 10 weeks), rep3

description: Library name: HCD_3

value: knee cartilage


title: 22Rv1 cells, JMC45-1,12 h

description: Library name: Sample 3


title: macro_scRNA_Treated with IFN-γ and lipopolysaccharide(LPS)

description: Library name: macro_scRNA_Control_a_cDNA


title: Female Head, VAPWT, Day 5, Rep4

description: Library name: Sample 28


title: Osteoarthritic cartilage treated with hyaluronic acid, cells, and drug, rat (Age: 10 weeks), rep2

description: Library name: HCD_2


title: 22Rv1 cells, Vehicle-2,12 h

description: Library name: Sample 2


title: Osteoarthritic cartilage treated with hyaluronic acid, cells, and drug, rat (Age: 10 weeks), rep1

description: Library name: HCD_1


title: Female Head, VAPWT, Day 5, Rep3

description: Library name: Sample 27


title: 22Rv1 cells, Vehicle-1,12 h

description: Library name: Sample 1


title: RNA-sequencing of Xenorhabdus griffiniae HGB2511, conditon D, replicate 3

city: Pasadena

first: Elin

middle: Maria

last: Larsson

state: CA

address: 1200 E California Blvd

institute: California Institute of Technology

description:
Library name: 3D
Samples were Dnase treated with Invitrogen DNAse (RNAse free). Library preparation was performed using Illumina's Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp unique dual indices (UDI).

data_processing:
Transcript abundances were obtained using featureCounts.
foldchange tables were generated using DESeq2.
Assembly: GCF_037263165.1
Supplementary files format and content: tsv files contain transcript abundances
Supplementary files format and content: csv files contain log2foldchanges

organism: Xenorhabdus griffiniae

source_name: bacterial

growth_protocol: Grown for 24 hours at 25C in M9 medium with glucose (Teknova) with and without nematodes before sampling.

extract_protocol:
All standard RNA extractions at SeqCenter follow the ZymoBIOMICS™ Quick-RNA Miniprep Kit (Zymo Research, R1055). The preparation of cell and tissue sample types followed Zymo Research recommendations stated in the protocol. Samples were eluted into a final volume of 40ul. Final RNA concentrations were determined via Qubit.
Samples were Dnase treated with Invitrogen DNAse (RNAse free). Library preparation was performed using Illumina's Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp unique dual indices (UDI).

treatment_protocol: Treatments: bacteria grown without nematodes, with conventional (colonized) wildtype Steinernema hermaphroditum nematodes, axenic (gnobiotic) wildtype Steinernema hermaphroditum nematodes or daf-22 deficient axenic Steinernema hermaphroditum nematodes.

value: bacterial

value: WT

value: axenic daf-22 deficient Steinernema hermaphroditum nematodes

tag: time


title: Female Head, VAPWT, Day 5, Rep2

description: Library name: Sample 26

value: VAPWT


title: Female Head, VAPWT, Day 5, Rep1

description: Library name: Sample 25


title: Osteoarthritic cartilage, rat (Age: 10 weeks), rep3

description: Library name: PBS_3

value: Isolate the osteoarthritic cartilage from rat (Age:10 weeks)


title: RNA-sequencing of Xenorhabdus griffiniae HGB2511, condition D, replicate 2

description:
Library name: 2D
Samples were Dnase treated with Invitrogen DNAse (RNAse free). Library preparation was performed using Illumina's Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp unique dual indices (UDI).


title: Osteoarthritic cartilage, rat (Age: 10 weeks), rep2

description: Library name: PBS_2


title: PA1290 mutant, rep 3

city: Honolulu

first: Hung

last: Vo

state: Hawaii

address: 1800 East-West Road Life Sciences Building, Rm 318

department: Microbiology

institute: University of Hawaii at Manoa

description:
Library name: PA1290R3
RNA-seq of PA1290::Tn mutant in staticbiofilm formation growth, replication 3

data_processing:
Rockhopper version 2.03
Follow the protocol of Rockhopper
https://cs.wellesley.edu/~btjaden/Rockhopper/user_guide.html
Assembly: NC_002516.2
Supplementary files format and content: tab delimited text file include raw data of each sample
Supplementary files format and content: txt sample include RKPM value compared sample 1 and sample 2

organism: Pseudomonas aeruginosa

source_name: Bacteria

growth_protocol: The mutant PA1290::Tn and the wt PA01 strain were grown overnight in LB broth, diluted 100-fold into fresh LB broth, and grown in the same biofilm growth condition (30oC, no shake, 48 hours)

extract_protocol:
Bacteria were harvested, and total RNA was isolated using the Qiagen RNeasy Mini Kit (Qiagen), with on-column DNase I treatment; rRNA was depleted using RiboZero (Epicentre®)
Total mRNA was sent to TUCF (Tufts University Core Facility) for RNA-seq. Illumina® NGS libraries were created and sequenced at TUCF Genomics (http://tucf-genomics.tufts.edu/)

treatment_protocol: RNA-seq profiles of the mutant of regulator PA1290 compared to Pa wt PA01 in static biofilm condition

value: Bacteria

value: Psedomonas

value: aeruginosa

value: mutant PA1290::Tn

value: Static biofilm grow, 30 oC


title: RNA-sequencing of Xenorhabdus griffiniae HGB2511, condition D, replicate 1

description:
Library name: 1D
Samples were Dnase treated with Invitrogen DNAse (RNAse free). Library preparation was performed using Illumina's Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp unique dual indices (UDI).


title: Texo_3

city: Xi'an

first: Yang

last: Xinjie

address: No.127 Changle West Road, Xincheng District

department: Department of Head and Neck Oncology

institute: ir Force Medical University Institution: The Third Affiliated Hospital

description: SACC-83 cells treated with PBS, control group

hyb_protocol: Fragmented Cy3-labeled cRNA was hybridized to Agilent mRNA-lncRNA microarrays at 65 °C for 17 hours. Post-hybridization washing was performed following the manufacturer’s standard protocols.

scan_protocol: Microarrays were scanned using Agilent Scanner according to the official operating guidelines to acquire raw fluorescence images.

data_processing: Raw microarray images were processed with Agilent Feature Extraction software. Raw signal values were normalized using quantile normalization. Differentially expressed transcripts were screened with the threshold of P < 0.05.

label_protocol: First-strand and second-strand cDNA were synthesized using AffinityScript-RT Kit and Promoter Primer. cRNA was amplified by T7 RNA polymerase and labeled with Cy3 fluorescent dye. Fluorescently labeled cRNA was then purified and fragmented.

growth_protocol: SACC-83 cells were cultured in complete medium at 37 °C with 5% CO₂. Culture medium was refreshed regularly until cells reached the appropriate confluence for subsequent treatment.

extract_protocol: Total RNA was isolated from cell samples using TRIzol reagent (Invitrogen, USA). RNA purity and integrity were assessed by NanoDrop ND-2000 and Agilent 2100 Bioanalyzer respectively. Total RNA was further purified using QIAGEN RNeasy Kit before downstream experiments.

treatment_protocol: Cells were divided into two groups: control group treated with PBS, and experimental group treated with TAMs-derived exosomes. After incubation for the indicated time, cells were harvested for total RNA extraction.

value: SACC-83 Treatment

tag: group

value: PBS Group

value: Control


title: Osteoarthritic cartilage, rat (Age: 10 weeks), rep1

description: Library name: PBS_1


title: PA1290 mutant, rep 2

description:
Library name: PA1290R2
RNA-seq of PA1290::Tn mutant in staticbiofilm formation growth, replication 2


title: RNA-sequencing of Xenorhabdus griffiniae HGB2511, condition C, replicate 3

description:
Library name: 3C
Samples were Dnase treated with Invitrogen DNAse (RNAse free). Library preparation was performed using Illumina's Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp unique dual indices (UDI).

value: axenic WT Steinernema hermaphroditum nematodes


title: Texo_2


title: Texo_1


title: PA1290 mutant, rep 1

description:
Library name: PA1290R1
RNA-seq of PA1290::Tn mutant in staticbiofilm formation growth, replication 1


title: Healthy cartilage, rat (Age: 10 weeks), rep4

description: Library name: Sham_4

value: Isolate the cartilage from healthy rat (Age:10 weeks)


title: RNA-sequencing of Xenorhabdus griffiniae HGB2511, condition C, replcate 2

description:
Library name: 2C
Samples were Dnase treated with Invitrogen DNAse (RNAse free). Library preparation was performed using Illumina's Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp unique dual indices (UDI).


title: Healthy cartilage, rat (Age: 10 weeks), rep3

description: Library name: Sham_3


title: PA01 wt control, rep 3

description:
Library name: WTR3
RNA-seq of PA01 in staticbiofilm formation growth, replication 1

value: wild type PA01


title: Microcebus murinus, Vegetable fat-based diet, sample8

city: Saclay

first: Mohammed

last: TAOUIS

address: NeuroPSI

country: France

institute: CNRS

description:
Library name: Sample8
Sample8_Vegetable.fastq

data_processing:
Microcebus muronus genome (Mmur_3.0, Ensembl release 104) and miRBase v22.1.
Sequence reads were trimmed for adaptater sequences using Cutadapt v3.4 with following parameters : minimum reads 16nt quality threshold Q>20.
Timmed sequenc reads were aligned to the Microcebus murinus genome (mmur_3.0, Ensembl release 104) and miRBase v22.1. Known mature microRNA sequences were quantified and novel microRNA prediction were performed using default parametes (score threshold>5, signal-to-noise>10).
Assembly: Microcebus muronus genome (Mmur_3.0, Ensembl release 104) and miRBase v22.1.
Supplementary files format and content: Excel spreadsheet includes raw counts.

organism: Microcebus murinus

source_name: Plasma

growth_protocol: Microcebus murinus were housed in an adapted animal facilities.

extract_protocol:
Total plasma RNAs were extracted usin the miRNeasy Micro Kit (Qiagen, France) according to manufacturer's recommendation.
Librairies were prepared using the QIAseq miRNA library Kit (Qiagen, France) following the manufacturer's protocol.

treatment_protocol: Microcebus murinus were fed dairy fat-based or vegetable fat-based diet.

value: Plasma

value: Vegetable fat-based diet


title: RNA-sequencing of Xenorhabdus griffiniae HGB2511, condition C, replicate 1

description:
Library name: 1C
Samples were Dnase treated with Invitrogen DNAse (RNAse free). Library preparation was performed using Illumina's Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp unique dual indices (UDI).

value: bacterial

value: WT


title: Cexo_2

description: SACC-83 cells treated with TAMs-derived exosomes

value: TAMs-derived exosomes Group

value: Exosome treatment


title: PA01 wt control, rep 2

description:
Library name: WTR2
RNA-seq of PA01 in staticbiofilm formation growth, replication 1

value: Bacteria


title: Microcebus murinus, Vegetable fat-based diet, sample7

description:
Library name: Sample7
Sample7_Vegetable.fastq


title: Healthy cartilage, rat (Age: 10 weeks), rep2

description: Library name: Sham_2

value: knee cartilage


title: Microcebus murinus, Vegetable fat-based diet, sample6

description:
Library name: Sample6
Sample6_Vegetable.fastq


title: Cexo_1


title: RNA-sequencing of Xenorhabdus griffiniae HGB2511, condition B, replicate 3

description:
Library name: 3B
Samples were Dnase treated with Invitrogen DNAse (RNAse free). Library preparation was performed using Illumina's Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp unique dual indices (UDI).

value: conventional WT Steinernema hermaphroditum nematodes


title: PA01 wt control, rep 1

description:
Library name: WTR1
RNA-seq of PA01 in staticbiofilm formation growth, replication 1

value: Psedomonas

value: aeruginosa


title: Healthy cartilage, rat (Age: 10 weeks), rep1

description: Library name: Sham_1


title: RNA-sequencing of Xenorhabdus griffiniae HGB2511, conditon B, replicate 2

description:
Library name: 2B
Samples were Dnase treated with Invitrogen DNAse (RNAse free). Library preparation was performed using Illumina's Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp unique dual indices (UDI).


title: Microcebus murinus, Vegetable fat-based diet, sample5

description:
Library name: Sample5
Sample5_Vegetable.fastq


title: PA01 control, ChIP seq

description: Library name: PA01ChIPseq

data_processing:
ChIP-seq data were aligned to the Pa wt PA01 genome with Bowtie2 (Langmead, 2012), peaks called with MACS2 (Feng, 2012), and consensus binding regions determined with MEME (Bailey, 2009) (https://meme-suite.org/meme/).
Assembly: NC_002516.2
Supplementary files format and content: tab delimited text file include raw data of each sample
Supplementary files format and content: txt sample include -log10 of q value and Fold Enrichment compared between PA1290::Tn complement with 3xTY1 taq  and wild type control

extract_protocol:
The ChIP-seq assays were performed as previously described (Heacock-Kang, 2018). Briefly, the regulator mutant strain PA1290∷Tn containing IPlac-3xTY1-PA1290 was grown and induced by isopropyl β-D-1-thiogalactopyranoside (IPTG) (0.25 mM) in LB at 30 °C for 48h without shaking. After induction, bacterial cells were cross-linked with paraformaldehyde, harvested, and lysed by freezing and thawing. Supernatants containing the DNA-regulator complexes were sheared to an average size of 100–500 bp in a Roche® nebulizer. The TY1-tagged PA1290 regulator bound to its regulated DNA region/fragment was enriched and captured using TY1 mouse monoclonal antibody and DiaMag® anti-mouse IgG-coated magnetic beads (Diagenode®), respectively. Captured DNA-regulator complexes were reversed cross-linked and purified using the QIAquick PCR Purification Kit (QIAGEN).
Purified DNA fragments were used as a template for library construction according to the Illumina ChIP-seq sample preparation protocol and sequenced at TUCF Genomics, where DNA libraries were prepped and 50 bp single-end reads were sequenced with the Illumina HiSeq 2500.

treatment_protocol: ChIP-seq profile of PA1290::Tn complement with PA1290-TY1x3 in static biofilm growth with control is Pa wt PA01

value: Pseudomonas

value: PA01 wild type

value: static biofiilm growth


title: BMDMs, Tm and LPS

city: Suita

first: Tomohiko

last: Murakami

state: OSAKA

address: 1-8 Yamada-Oka

country: Japan

institute: Osaka University

description: Library name: Sample 4

library_source: genomic

data_processing:
Mapping and peak call were conducted by ENCODE ATAC-seq pipeline
Reads were mapped to the mm10 reference sequence using Bowtie2 (ver. 2.3.4.3), and duplicate reads were removed with Picard (ver. 2.20.7) and samtools (ver. 1.9).
Peak calling was performed using MACS2 (ver. 2.2.4) with default parameters
Assembly: mm10
Supplementary files format and content: BigWig, each sample

molecule: genomic DNA

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:
Cells were lysed and transposition reaction was performed with the Tn5 Transposase (Illumina) at 37 ℃ for 30 minutes.
The reaction liquid was purified with Smart Extract kit (DNAFORM). Then 5 cycles of PCR with custom Nextera PCR primers was conducted using NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs). Additional number of PCR cycles was determined by qPCR of the partly amplified products. The PCR products were purified with KAPA HyperPure Beads, using double size selection (left ratio: 1.8x, right ratio: 0.4x) according to the manufacturer’s protocol. Obtained libraries were converted by using DNBSEQ MGIEasy Universal Library Conversion Kit (MGI Tech).

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: RNA-sequencing of Xenorhabdus griffiniae HGB2511, condition B, replicate 1

description:
Library name: 1B
Samples were Dnase treated with Invitrogen DNAse (RNAse free). Library preparation was performed using Illumina's Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp unique dual indices (UDI).


title: Microcebus murinus, Dairy fat-based diet, sample4

description:
Library name: Sample4
Sample4_Dairy.fastq

value: Plasma

value: Dairy fat-based diet


title: PA1290 mutant complement, ChIP seq

description: Library name: PA1290ChIPSeq

value: PA1290::Tn complement with TY 1x3 tag


title: RNA-sequencing of Xenorhabdus griffiniae HGB2511, conditon A, replicate 3

description:
Library name: 3A
Samples were Dnase treated with Invitrogen DNAse (RNAse free). Library preparation was performed using Illumina's Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp unique dual indices (UDI).

value: bacterial

value: WT

value: no nematode


title: RNA-sequencing of Xenorhabdus griffiniae HGB2511, conditon A, replicate 2

description:
Library name: 2A
Samples were Dnase treated with Invitrogen DNAse (RNAse free). Library preparation was performed using Illumina's Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp unique dual indices (UDI).


title: Microcebus murinus, Dairy fat-based diet, sample2

description:
Library name: Sample2
Sample2_Dairy.fastq


title: Microcebus murinus, Dairy fat-based diet, sample3

description:
Library name: Sample3
Sample3_Dairy.fastq


title: 21E x 26P, STARR-seq, E-P-BC amplicon

city: Palo Alto

first: Jesse

last: Engreitz

address: 240 Pasteur Dr

department: Genetics

institute: Stanford University

description: Library name: 21E x 26P STARR-seq Dictionary Building

library_source: other

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.

molecule: other

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 26P, upstream, E-P-BC amplicon

description: Library name: 21E x 26P Upstream Dictionary Building


title: BMDMs, Control

description: Library name: Sample 1


title: BMDMs, Tm

description: Library name: Sample 3

value: Tm


title: RNA-sequencing of Xenorhabdus griffiniae HGB2511, conditon A, replicate 1

description:
Library name: 1A
Samples were Dnase treated with Invitrogen DNAse (RNAse free). Library preparation was performed using Illumina's Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp unique dual indices (UDI).


title: Microcebus murinus, Dairy fat-based diet, sample1

description:
Library name: Sample1
Sample1_Dairy.fastq


title: SAM24449928

status: Public on Jun 26 2026

city: Stanford

first: Tawaun

middle: Autry

last: Lucas

address: 1201 Welch Rd

description: Library name: LIB6230122

data_processing:
Single-end, 50 bp reads were generated on an Illumina HiSeq sequencer, aiming for approximately 30 million reads per sample. Raw sequencing reads were subjected to quality control using FastQC (version 0.12.0) to assess read quality, identify potential adaptor contamination, and evaluate sequence biases. Results were then aggregated using MultiQC (v1.9). Based on FastQC reports, adapter sequences and low-quality bases were trimmed from the 3' end of reads using fastp (v0.23.3) with default parameters. Post-trimming quality control was performed to ensure sufficient read quality for downstream analysis.
Trimmed reads were aligned to the mouse reference genome GRCm38 using HTSeqGenie (version 3.20). Reads were aligned, and gene-level counts were quantified based on "Ensembl GRCm38.97 annotations from BioMart.
Assembly: Ensembl GRCm38.97
Supplementary files format and content: h5ad

source_name: midbrain

extract_protocol:
Total RNA was isolated from the midbrain of 5 SPG11-/- mice and 5 SPG11+/+ littermate control brain tissue using the RNeasy Universal Mini Plus Kit (Qiagen)
RNA-seq libraries were prepared from 0.15-1 μg of total RNA per sample using the TruSeq RNA Sample Preparation Kit v2 (Illumina)

value: midbrain

value: SPG11 KO; A53T hemi 55 weeks midbrain


title: SAM24449927

description: Library name: LIB6230121


title: BMDMs, LPS

description: Library name: Sample 2

value: LPS


title: SAM24449926

description: Library name: LIB6230120


title: SAM24449925

description: Library name: LIB6230119


title: SAM24449924

description: Library name: LIB6230118


title: SAM24449923

description: Library name: LIB6230117

value: SPG11 WT; A53T hemi 55 weeks midbrain


title: SAM24449922

description: Library name: LIB6230116


title: SAM24449921

description: Library name: LIB6230115


title: SAM24449919

description: Library name: LIB6230113


title: SAM24427761

description: Library name: LIB5465868

value: Wildtype Midbrain


title: SAM24427759

description: Library name: LIB5465866


title: SAM24427760

description: Library name: LIB5465867


title: SAM24427756

description: Library name: LIB5465863

value: SPG11 KO Midbrain


title: SAM24427757

description: Library name: LIB5465864


title: SAM24427755

description: Library name: LIB5465862


title: SAM24427758

description: Library name: LIB5465865


title: SAM24427754

description: Library name: LIB5465861


title: SAM24427753

description: Library name: LIB5465860


title: SAM24449920

description: Library name: LIB6230114


title: SAM24427752

description: Library name: LIB5465859


title: Osteoarthritic cartilage, rat (Age: 10 weeks), rep4

description: Library name: PBS_4

value: knee cartilage

value: Isolate the osteoarthritic cartilage from rat (Age:10 weeks)


title: FgLH03+FaLH03 filtrate+DMSO 2d Bio. replicate4

city: Ottawa

first: Linda

middle: J

last: Harris

state: Ontario

address: 960 Carling Ave.

department: Eastern Cereal & Oilseed Research Centre

country: Canada

institute: Agriculture & Agri-Food Canada (AAFC)

hyb_protocol: The arrays were hybrized overnight in a Robbins Scientific Model 400 incubator and an Agilent Scientific G2530-60020 rotator. Hybridization was carried out as per manufacturer's protocol. Slides were washed as per protocol except omitting the 3rd wash (Stabilization and drying solution).

scan_protocol: Slides were scanned using the Agilent DNA Microarray Scanner (G2505C) at 5µ resolution.

data_processing: Data was extracted using the Agilent Feature Extraction software and imported in GeneSpring GX (Agilent Technologies) software. Data was normalized using Threshold raw signals to 1; Percentile target 75% and using the Baseline to median of all samples. Low-intensity features (intensity less than 50) were removed from analysis and retained samples where 40% of samples have values within range. A moderated T-test was performed keeping features with a fold-change > 2.0  and p-values < 0.05.

organism: Fusarium graminearum

source_name: F. graminearum strain DAOM242075

label_protocol: Total RNA was labelled using the One-Color Quick-Amp Labelling Kit (Agilent Technologies) using the manufacturer's instructions except using half the volumes of the reagents in Step 2 of the protocol.

growth_protocol: 4ml of 1st stage media was added to each well of eight 6-well plates. Each well was inoculated with 80µL of F. graminearum (Fg LH03, DAOM242075) spore stock for a final concentration of 1 million spores/mL. A sterile Miracloth circle was added to each well and plates sealed with AirPore tape (Qiagen). The plates were incubated at 28°C with agitation (170 rpm) for 2 days in the dark.

extract_protocol: Frozen biomass was ground using a mortar and pestle in liquid nitrogen. Total RNA was extracted using the Absolutely RNA Miniprep Kit (Agilent Technologies) or Rneasy Plant and Fungal Mini Kit (Qiagen). Total RNA was quantified using a Nanodrop instrument (Thermo Scientific) and qualified on the BioAnalyzer (Agilent Technologies). Total RNA was stored at -80°C until use.

treatment_protocol: Following the incubation, the 1st stage media was removed, the cultures were rinsed and replaced with 4mL fresh 2nd stage media (McCormick et al., 2004). 10µL of F. avenaceum filtrate resuspended in DMSO was added to half the wells. The other half were treated with 10µL DMSO. [To prepare the F. avenaceum filtrate, 250 mL flasks containing 50 mL media (3 g NH4CL, 2 g MgSO4-7H2O, 0.2 g of FeSO4-7H2O, 2 g KH2PO4, 2 g peptone, 2 g yeast extract, 2 g malt extract, and 20 g glucose in 1 liter distilled water)were inoculated with 2 million spores/mL of F. avenaceum FaLH27 (DAOM242378) or FaLH03 [DAOM242075] and the fungi were grown at 28°C, 170 rpm for 6 days in the dark, then transferred into 50 ml of either formulation 1 [1g NH4H2PO4, 3g KH2PO4, 0.2g MgSO4-7H2O), 5g NaCl, 40g sucrose, 10g glycerol + 1L of distilled water] or formulation 2 [0.5g NH4H2PO4 , 30mL 200nM glutamine, 3g KH2PO4, 0.2g MgSO4-7H2O, 5g NaCl, 40g sucrose, 10g glycerol + 970 ml of distilled water]. After thirteen days, the culture supernatants were run through a 20mg Bond Elute PLEXA column (Agilent Technologies, Inc.) and the 100% MeOH filtrate fractions collected, pooled and dried under vacuum. The mixed filtrate extracts were resuspended at a concentration of 81.8 mg/mL in DMSO.] The F. graminearum cultures in 6-well plates were covered with a fresh AirPore sheet and returned to the incubator (170rpm, 28°C in the dark). At each collection time point (6 hours and 2 days) the Miracloth with attached mycelia was removed, dried (using a Buchner funnel) and transfered to a scintillation vial. The scintillation vials were flash frozen in liquid N2 and stored at -80°C.

value: F. avenaceum  mixed filtrate extracts in DMSO

value: 2 days

tag: biological replicate


title: FgLH03+FaLH03 filtrate+DMSO 2d Bio. replicate3


title: FgLH03+FaLH03 filtrate+DMSO 6h Bio. replicate4

value: 6 hours


title: FgLH03+FaLH03 filtrate+DMSO 2d Bio. replicate1


title: FgLH03+FaLH03 filtrate+DMSO 6h Bio. replicate3


title: Cexo_3

description: SACC-83 cells treated with TAMs-derived exosomes

value: SACC-83 Treatment

value: TAMs-derived exosomes Group

value: Exosome treatment


title: FgLH03+FaLH03 filtrate+DMSO 6h Bio. replicate1


title: Healthy Donor 31

city: New Haven

first: Matthew

last: McConnell

state: Connecticut

address: PO Box 208019, 300 Cedar St

institute: Yale University

description: Library name: HD31

data_processing:
The sequencing reads for each of the samples were aligned to the GRCh38 human reference using HISAT2.   Gene-level read counts were generated using StringTie2 and its prepDE.py tool, based on annotations from the ENCODE v27 GTF file.  Sample and experiment quality metrics were generated using Picard, and TPM counts were generated using Ballgown
Assembly: GRCh38 human reference
Supplementary files format and content: comma separated variable, includes raw counts for each sample

source_name: primary cells

extract_protocol:
RNA was extracted using Trizol according to manufacturer instructions
RNA libraries for RNAseq were prepared using a Clontech Pico Input Mammalian Kit

value: primary cells

value: Platelets

tag: batch


title: FgLH03+FaLH03 filtrate+DMSO 6h Bio. replicate2


title: Healthy Donor 32

description: Library name: HD32


title: FgLH03+DMSO 2d Bio. replicate4

value: DMSO


title: FgLH03+DMSO 6h Bio. replicate3


title: Healthy Donor 35

description: Library name: HD35


title: FgLH03+DMSO 2d Bio. replicate2


title: FgLH03+DMSO 2d Bio. replicate1


title: FgLH03+DMSO 6h Bio. replicate2


title: Healthy Donor 4

description: Library name: HD4


title: FgLH03+DMSO 6h Bio. replicate1


title: Healthy Donor 3

description: Library name: HD3


title: Healthy Donor 2

description: Library name: HD2


title: Inpatient AH52

description: Library name: IP52


title: Inpatient AH 33

description: Library name: IP33


title: Inpatient AH 51

description: Library name: IP51


title: Healthy Donor 1

description: Library name: HD1


title: Inpatient AH 28

description: Library name: IP28


title: Inpatient AH 2

description: Library name: IP2


title: Inpatient AH 3

description: Library name: IP5


title: Inpatient AH 19

description: Library name: IP19


title: Inpatient AH 1

description: Library name: IP1


title: hiPSC-CMs, MYH7R663H, rep5

city: Paris

first: Jean-Sébastien

last: Hulot

address: Rue Leblanc

institute: Paris Centre de Recherche Cardiovasculaire

description: Library name: CM_MYH7R663H-2_DC108

data_processing:
Sequencing quality was assessed with FastQC (version 0.11.4). Analyses were performed with Galileo v1.0 by Integragen. STAR was used to obtain the number of reads associated to each gene in the Gencode v31 annotation (restricted to protein-coding genes, antisense and lincRNAs).
Raw counts for each sample were imported into R statistical software using the Bioconductor DESeq2 package.
Extracted count matrix was normalized for library size and coding length of genes to compute FPKM expression levels.
The Bioconductor edgeR package was used to import raw counts into R statistical software, and compute normalized log2 CPM (counts per millions of mapped reads) using the TMM (weighted trimmed mean of M-values) as normalization procedure.
Assembly: GRCh38
Supplementary files format and content: csv file contains the raw counts for all samples

molecule: polyA RNA

growth_protocol: hiPSCs were kept on stem cell-qualified Matrigel-coated with mTeSR Plus medium at 5% CO2, 37°C. Cardiac differentiation was carried out with 6 um CHIR-99021 and 5 um IWR-1. Cardiomyocytes were enriched by two rounds of glucose starvation and kept in RPMI-1640 medium with B27 supplement until day 35 post-differentiation.

extract_protocol:
Total RNA was extracted with a NucleoSpin RNA mini Kit (Macherey-Nagel).
Library was constructed with the 'NEBNext® UltraTM II mRNA-Seq' kit.

value: Human induced pluripotent stem cell-derived cardiomyocytes

value: MYH7 p.Arg663His


title: hiPSC-CMs, MYH7R663H, rep4

description: Library name: CM_MYH7R663H-2_DC32


title: hiPSC-CMs, MYH7R663H, rep3

description: Library name: CM_MYH7R663H-2_DC23


title: hiPSC-CMs, MYH7R663H, rep2

description: Library name: CM_MYH7R663H-2_DC13


title: hiPSC-CMs, MYH7R663H, rep1

description: Library name: CM_MYH7R663H-2_DC04


title: hiPSC-CMs, BRAFT599R, rep4

description: Library name: CM_BRAFT599R_34-2_DC34

value: BRAF p.Thr599Arg


title: hiPSC-CMs, BRAFT599R, rep5

description: Library name: CM_BRAFT599R_34-2_DC45


title: hiPSC-CMs, BRAFT599R, rep3

description: Library name: CM_BRAFT599R_34-2_DC25


title: hiPSC-CMs, healthy, rep5

description: Library name: CM_31_3_DC47

value: Healthy control


title: hiPSC-CMs, BRAFT599R, rep1

description: Library name: CM_BRAFT599R_34-2_20191014


title: hiPSC-CMs, BRAFT599R, rep2

description: Library name: CM_BRAFT599R_34-2_DC22


title: hiPSC-CMs, healthy, rep3

description: Library name: CM_31_3_DC31


title: hiPSC-CMs, healthy, rep1

description: Library name: CM_31_3_DC01


title: hiPSC-CMs, healthy, rep2

description: Library name: CM_31_3_DC03


title: Donor4, M2 Macrophages, XYLT2-knockdown

city: Bad Oeynhausen

first: Isabel

last: Faust-Hinse

state: NRW

address: Georgstraße 11

department: ILTM

country: Germany

institute: HDZ NRW, Institut für Laboratoriums- und Transfusionsmedizin, Universitätsklinik der Ruhr-Universität Bochum

description:
Library name: Sample 24
Coloum name in L160525BO2_01.read.counts.sampleIDs.detailed.txt: MB93_M2_siXYLT2

data_processing:
Raw sequencing data were processed and quality controlled by the sequencing provider (Alithea Genomics SA).
Low-count genes were filtered by retaining genes with a minimum count of 4 in at least three samples.
Differential gene expression analysis was performed in R (version 4.3.3) using the DESeq2 package with a generalized linear model (~ donor + condition) to account for paired donor effects.
Log2 fold changes were estimated and shrunk using the apeglm method. Genes with an adjusted p-value < 0.05 and absolute log2 fold change ≥ 0.5 were considered differentially expressed.
Gene annotation was performed using the org.Hs.eg.db package, and pathway enrichment analysis was conducted using ShinyGO with KEGG pathway mapping.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files containing raw count data for each gene and sample.
Supplementary files format and content: Normalized expression values (variance-stabilized counts or log2-transformed counts) for each gene across all samples.

source_name: primary macrophages

growth_protocol: Human primary monocytes were isolated from buffy coats of healthy donors and differentiated into macrophages by cultivation in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine, 1% penicillin–streptomycin–amphotericin, and 50 ng/mL M-CSF under standard conditions (37°C, 5% CO₂).

extract_protocol:
Total RNA was extracted from macrophages using the NucleoSpin RNA Mini Kit (Macherey-Nagel) according to the manufacturer’s instructions. RNA quality and quantity were assessed by spectrophotometry, and samples with appropriate purity  were used for downstream applications.
RNA sequencing libraries were prepared from total RNA using the MERCURIUS™ BRB-seq platform (Alithea Genomics SA) following the manufacturer’s protocol. Library preparation included mRNA enrichment, reverse transcription, barcoding, and amplification prior to sequencing on an Illumina platform.

treatment_protocol:
siRNA-mediated knockdown of XYLT2 was performed in adherent macrophages using Lipofectamine 2000. Cells were transfected with XYLT2-specific siRNA (siXYLT2) or non-targeting control siRNA (siNC) at a final concentration of 50 nM and incubated for 6 h, followed by recovery in complete medium.
Macrophage polarization was induced 24 h post-transfection. M1 macrophages were stimulated with IFNγ (50 ng/mL) and LPS (10 ng/mL), M2 macrophages with IL4 (20 ng/mL), while M0 macrophages were maintained without additional stimuli. Cells were cultured for 48 h prior to RNA isolation.

value: primary macrophages

value: XYLT2-siRNA-knockdown (siXYLT2)


title: Donor4, M0 Macrophages, XYLT2-knockdown

description:
Library name: Sample 22
Coloum name in L160525BO2_01.read.counts.sampleIDs.detailed.txt: MB93_M0_siXYLT2


title: Donor3, M1 Macrophages, XYLT2-knockdown

description:
Library name: Sample 20
Coloum name in L160525BO2_01.read.counts.sampleIDs.detailed.txt: HB62_M1_siXYLT2


title: Donor3, M0 Macrophages, XYLT2-knockdown

description:
Library name: Sample 19
Coloum name in L160525BO2_01.read.counts.sampleIDs.detailed.txt: HB62_M0_siXYLT2


title: Donor3, M2 Macrophages, XYLT2-knockdown

description:
Library name: Sample 21
Coloum name in L160525BO2_01.read.counts.sampleIDs.detailed.txt: HB62_M2_siXYLT2


title: Donor2, M2 Macrophages, XYLT2-knockdown

description:
Library name: Sample 18
Coloum name in L160525BO2_01.read.counts.sampleIDs.detailed.txt: MK65_M2_siXYLT2


title: Donor2, M1 Macrophages, XYLT2-knockdown

description:
Library name: Sample 17
Coloum name in L160525BO2_01.read.counts.sampleIDs.detailed.txt: MK65_M1_siXYLT2


title: Donor2, M0 Macrophages, XYLT2-knockdown

description:
Library name: Sample 16
Coloum name in L160525BO2_01.read.counts.sampleIDs.detailed.txt: MK65_M0_siXYLT2


title: Donor1, M2 Macrophages, control

description:
Library name: Sample 15
Coloum name in L160525BO2_01.read.counts.sampleIDs.detailed.txt: AWI96_M2_siNC

value: WT

value: non-targeting control (siNC)


title: Donor1, M0 Macrophages, control

description:
Library name: Sample 13
Coloum name in L160525BO2_01.read.counts.sampleIDs.detailed.txt: AWI96_M0_siNC


title: Donor4, M2 Macrophages, control

description:
Library name: Sample 12
Coloum name in L160525BO2_01.read.counts.sampleIDs.detailed.txt: MB93_M2_siNC


title: Donor1, M1 Macrophages, control

description:
Library name: Sample 14
Coloum name in L160525BO2_01.read.counts.sampleIDs.detailed.txt: AWI96_M1_siNC


title: Donor3, M2 Macrophages, control

description:
Library name: Sample 9
Coloum name in L160525BO2_01.read.counts.sampleIDs.detailed.txt: HB62_M2_siNC


title: Donor3, M1 Macrophages, control

description:
Library name: Sample 8
Coloum name in L160525BO2_01.read.counts.sampleIDs.detailed.txt: HB62_M1_siNC


title: Donor2, M2 Macrophages, control

description:
Library name: Sample 6
Coloum name in L160525BO2_01.read.counts.sampleIDs.detailed.txt: MK65_M2_siNC


title: Donor2, M0 Macrophages, control

description:
Library name: Sample 4
Coloum name in L160525BO2_01.read.counts.sampleIDs.detailed.txt: MK65_M0_siNC


title: Donor1, M1 Macrophages, XYLT2-knockdown

description:
Library name: Sample 2
Coloum name in L160525BO2_01.read.counts.sampleIDs.detailed.txt: AWI96_M1_siXYLT2


title: Donor1, M0 Macrophages, XYLT2-knockdown

description:
Library name: Sample 1
Coloum name in L160525BO2_01.read.counts.sampleIDs.detailed.txt: AWI96_M0_siXYLT2


title: A673, EWS-FLI1 parental control, replicate 3

city: Boston

first: Huy

last: Nguyen

state: MA

address: 450 Brookline Ave

department: Radiation Oncology

institute: Dana-Farber Cancer Institute

description: Library name: WT6

data_processing:
Kallisto (version 0.48.0) was used to map the raw RNA-seq reads against the GENCODE human reference gene annotation (Release 44) and generate raw transcript abundance estimates.
The tximport Bioconductor R package was used to summarize the transcript abundance estimates to produce gene-level estimated counts.
Assembly: hg38
Supplementary files format and content: tab-delimited file with matrix table of raw gene counts for every gene and every sample

source_name: Bone and soft tissue

growth_protocol: A673 EWS-FLI1 wildtype and knockout cells were grown in DMEM and supplemented with 10% fetal bovine serum (FBS) (Sigma-Aldrich).

extract_protocol:
RNA samples were prepared using RNeasy Mini Kit and RNase-Free DNase Set (QIAGEN). RNA samples were quantified using Qubit 2.0 Fluorometer, and the RNA integrity was checked with 4200 TapeStation.
NEBNext Ultra II RNA Library Prep Kit for Illumina was used following the manufacturer’s recommendations (New England BioLabs). Briefly, mRNAs were initially enriched with Oligo d(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3´ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing libraries were validated using Agilent TapeStation and quantified using Qubit 2.0 Fluorometer as well as by quantitative PCR (KAPA Biosystems). The sequencing libraries were clustered on flowcell lanes. After clustering, the flowcell was loaded on the Illumina NovaSeq instrument according to manufacturer’s instructions.

value: Bone and soft tissue

value: Ewing sarcoma cell

value: EWS-FLI1 wildtype


title: A673, EWS-FLI1 parental control, replicate 2

description: Library name: WT5


title: A673, EWS-FLI1 parental control, replicate 1

description: Library name: WT4


title: CAF#1-SC

city: Beijing

first: Xianglin

last: Yin

state: Other (Non U.S.)

address: No.1 Shuaifu garden, Dongcheng District

institute: Peking Union Medical College Hospital

description: Library name: S1

data_processing:
Raw reads of fastq format were firstly processed using fastp (v 0.20.0).
Pair-end sequencing raw data were firstly processed with Trimmomatic (v0.36)  for adapter trimming and low-quality bases removal. The clean reads were then subjected to Hisat2 (v2.1.0) for mapping back to human genome (v. hg38) and only uniquely mapped reads are kept for further peak calling.PCR duplicates were removed and mitochondrial reads were excluded. To improve the accuracy of transposase insertion sites, Tn5 shifting was applied to the paired-end alignments using deepTools (v3.5.6) alignmentSieve (--ATACshift).
Peaks were called for each sample using MACS2(v2.2.9.1).For differential accessibility analysis, fragment counts in each peak were quantified from the shifted BAM files using GenomicAlignments(v1.38.0)
peaks were annotated to genomic features and nearest genes using ChIPseeker(v1.38.0) with TxDb.Hsapiens.UCSC.hg38.knownGene and org.Hs.eg.db.
Assembly: hg38
Supplementary files format and content: bigWig

source_name: pancreas

extract_protocol:
A minimum of 5 × 104 of CAFs transfected with SC or HSF1-targeting siRNAs were harvested for ATAC-seq.Cells were pelleted at 500 g for 5 min, resuspended in lysis buffer, and incubated on ice for 5 min. After addition of wash buffer, nuclei were collected by centrifugation at 500 g for 5 min.
Briefly, nuclei were isolated and subjected to transposition using Tn5 transposase at 37 °C for 30 min. Following PCR amplification, libraries were purified with AMPure beads and quality was assessed using Qubit. Libraries were sequenced on an Illumina NovaSeq platform to generate 150-bp paired-end reads.

value: pancreas

value: primary cancer-associated fibroblasts

value: Control


title: imCAF#1-HSF1 KD

description: Library name: N2

value: HSF1 knockdown


title: imCAF#1-SC

description: Library name: N1


title: CAF#7, siALKBH5, (MeRIP)

description: Library name: 7-KD-IP

data_processing:
The quality of raw sequencing data was assessed using FastQC (version 0.11.3).
Data preprocessing was performed with Trimmomatic (version 0.36) to remove adapter sequences, trim low-quality bases (quality <3) from the start and end of reads, and discard reads shorter than 50 bases.
High-quality paired-end reads passing the quality control steps were aligned to the human reference genome (build 38) using Hisat2 (version 2.1.0).
Only uniquely mapped reads with mapping quality score >20 were retained for downstream analysis. The aligned reads were further filtered and sorted using Samtools (version 1.9), and gene-level read counts were quantified with the featureCounts from Subread R package (version1.32.4).
To identify m6A peaks, we employed the exomePeak R package (version 2.16.0), using a window width of 150 bp and a fragment length of 100 bp.
Assembly: hg38
Supplementary files format and content: BED12 files represent m6A peaks information generated by exomePeak from MeRIP-seq data, including genomic coordinates, scores, strand orientation, and exon block structures.
Library strategy: MeRIP-seq

extract_protocol:
RNA was harvested using TRIzol (Ambion).
RNA libraries for RNA-seq were prepared using SMARTer Stranded Total RNA-Seq Kit v2 (Takara, #634413) following manufacturer's protocols. At least 10 ng of total RNA was used for the construction of sequencing libraries.

value: pancreatic stellate cells

value: KD


title: CAF#7, Control (MeRIP)

description: Library name: 7-SC-IP

value: SC


title: CAF#7, siALKBH5, (input)

description: Library name: 7-KD-input


title: CAF#5, siALKBH5, (input)

description: Library name: 5-KD-input


title: CAF#7, Control (input)

description: Library name: 7-SC-input


title: CAF#5, siALKBH5, (MeRIP)

description: Library name: 5-KD-IP


title: CAF#5, Control (MeRIP)

description: Library name: 5-SC-IP


title: CAF#5, Control (input)

description: Library name: 5-SC-input


title: CAF#2, ATRA treatment (MeRIP)

description: Library name: 2-ATRA-IP

value: ATRA


title: CAF#2, ATRA treatment (input)

description: Library name: 2-ATRA-input


title: CAF#2, Control (input)

description: Library name: 2-con-input

value: con


title: CAF#1, ATRA treatment (MeRIP)

description: Library name: 1-ATRA-IP


title: imCAF#2, IP (ALKBH5-RIP)

description: Library name: 2-IP

data_processing:
The quality of raw sequencing data was assessed using FastQC (version 0.11.3).
Data preprocessing was performed with Trimmomatic (version 0.36) to remove adapter sequences, trim low-quality bases (quality <3) from the start and end of reads, and discard reads shorter than 50 bases.
High-quality paired-end reads passing the quality control steps were aligned to the human reference genome (build 38) using Hisat2 (version 2.1.0).
Only uniquely mapped reads with mapping quality score >20 were retained for downstream analysis. The aligned reads were further filtered and sorted using Samtools (version 1.9), and gene-level read counts were quantified with the featureCounts from Subread R package (version1.32.4).
We used the DESeq2 R package to identify transcripts combined with ALKBH5. Transcripts were considered significant based on the following criteria: RPKM (Reads Per Kilobase of Exon Model per Million Mapped Reads) > 1 for the Input sample, log2[fold change (IP vs Input)] >1, log2[fold change (IgG vs Input)] <1, P-value < 0.05, Input RPKM> 1.
Assembly: hg38
Supplementary files format and content: csv file includes raw counts for each sample

value: immortalized pancreatic stellate cells


title: imCAF#2, IgG (ALKBH5-RIP)

description: Library name: 2-IgG


title: imCAF#2, Input (ALKBH5-RIP)

description: Library name: 2-input


title: imCAF#1, IP (ALKBH5-RIP)

description: Library name: 1-IP


title: imCAF#1, IgG (ALKBH5-RIP)

description: Library name: 1-IgG


title: imCAF#1, Input (ALKBH5-RIP)

description: Library name: 1-input


title: CAF#1, CUT&Tag (HSF1)

description: Library name: S2

data_processing:
Raw reads of fastq format were firstly processed using fastp (v 0.20.0).
Index of the reference genome was built using BWA (v 0.7.12) and clean reads were aligned to the reference genome using BWA mem -k 32 -T 30 -t 4 -M. These reads were then filtered for high quality (MAPQ ≥ 13).
All peak calling was performed with MACS2 (v 2.1.0) using ‘macs2 -q 0.05 -f AUTO --callsummits --nomodel --shift -100 --extsize 200 --keep-dup all’. By default, peaks with q-value threshold of 0.05 was used for all data sets.
The position of peak summit around transcript start sites of genes can predict the interaction sites between protein and gene. ChIPseeker was used to retrieve the nearest genes around the peak and annotate genomic region of the peak.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

extract_protocol:
the cells are bound to Concanavalin A-coated magnetic beads, and the cell membrane is permeabilized by Digitonin. The enzyme pA-Tn5 Transposase precisely binds the DNA sequence near the target protein under the antibody guidance and results in factor-targeted tagmentation.
DNA sequence is tagmented, with adapters added at the same time at both ends, which can be enriched by PCR to form the sequencing-ready libraries(CUT&Tag_Novogene Kit). After the PCR reaction, libraries were purified with the AMPurebeads and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: primary pancreatic stellate cells

value: HSF1 overexpression


title: imCAF#1, CUT&Tag (HSF1)

description: Library name: S1


title: Spleen GEX 0723

city: San Francisco

first: Loukas

last: Diafos

address: 35 Medical Center Way

institute: UCSF

description:
Library name: Spleen2_GEX
10X Genomics Chromium Single Cell 5' v2 kit

data_processing:
Cellranger (v5.0.1) from 10x Genomics was used for data pre-processing. Bcl files were converted to fastq using cellranger mkfastq. Barcode correction and reference genome alignment (GRCh38-3.0.0) were done using cellranger count with default parameters.
Assembly: GRCh38-3.0.0 using Cellranger (v5.0.1)
Supplementary files format and content: The three files are the contents of the filtered_feature_bc_matrix of the corresponding sample.  This includes the features, barcodes, and matrix.  The first two are .tsv and the matrix is .mtx all being in the gzip file format

source_name: Spleen

extract_protocol:
To determine the molecular profile of brain T cells and examine their relationship to peripheral T cells from paired lymphoid and non-lymphoid organs, we performed single-cell RNA sequencing from 2 prenatal donors. We isolated T cells from paired brain, mesenteric lymph node (MLN), spleen and small intestine using gradient centrifugation, and sorting via FACS.  Briefly, we isolated CD3+ T cells from CD45+ single celll suspensions.
Tissue samples were processed for FACS sorting and isolated cells were collected in PBS + 0.5% BSA then captured for single cell RNA sequencing using the 10X Genomics Chromium Single Cell 5’ v2 kit per manufacturer’s instructions. 10,000 cells were targeted for captured and 12 cycles for each of the cDNA amplification and library amplification were performed. Libraries were sequenced per manufacturer recommendation on a NovaSeq S2 flow cell.

value: Spleen


title: Small Intestine TCR 0723

description:
Library name: Smal_intestine2_TCR
10X Genomics Chromium Single Cell 5' v2 kit

source_name: Small Intestine

value: Small Intestine


title: HBV HCMS, HepG2.2.15, HBV-gRNA4-EE4000, 2

status: Public on Jun 28 2026

first: Jennifer

last: Marlowe

state: Massachusetts

address: 201 Brookline Avenue

institute: nChroma Bio

description: Library name: NGSHC862

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: Small Intestine GEX 0723

description:
Library name: Small_intestine2_GEX
10X Genomics Chromium Single Cell 5' v2 kit


title: MLN TCR 0723

description:
Library name: MLN2_TCR
10X Genomics Chromium Single Cell 5' v2 kit

source_name: MLN

value: MLN


title: MLN GEX 0723

description:
Library name: MLN2_GEX
10X Genomics Chromium Single Cell 5' v2 kit


title: Brain TCR 0723

description:
Library name: Brain2_TCR
10X Genomics Chromium Single Cell 5' v2 kit

source_name: Brain

value: Brain


title: Brain GEX 0723

description:
Library name: Brain2_GEX
10X Genomics Chromium Single Cell 5' v2 kit


title: theta, rep2

city: London

first: Sofia

last: Peressotti

address: Exhibition Rd, South Kensington, London

country: United Kingdom

institute: Imperial College London

description: Library name: Stim2

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.

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: MCF7 Parent DMSO RNAseq replicate 2

city: Melbourne

first: Shom

last: Goel

state: Victoria

address: 305 Grattan St

country: Australia

institute: Peter MacCallum Cancer Centre

description: Library name: Sample 2

data_processing:
Adapters and low quality reads were removed using BBMap v38.90 bbduk.sh with the following parameters: ktrim=r k=23 mink=11 hdist=1 tpe tbo qtrim=r trimq=5 minlen=20
trimmed reads were aligned using STAR (v2.7.5b) to the human reference genome (hg38)
Aligned reads were counted using featurecounts (v2.0.1)  using annotations from GENCODE (gencode.v35.annotation.gtf )
Assembly: hg38
Supplementary files format and content: csv file include raw count (non-normalised) values for each sample

growth_protocol: RPMI-1640 supplemented with 10% FBS, 1% GlutaMax, and 1% HEPES, incubated at 37C at 5% CO2.

extract_protocol:
RNA was extracted using NucleoSpin RNA Plus kit (Macherey-Nagel).
Libraries were prepared using the QuantaSeq Lexogen 3’mRNA RW kit.

treatment_protocol: Abemaciclib 500 nM or equal volume of DMSO (control) for 5 days.

value: Parent

value: DMSO

tag: replicate


title: HBV HCMS, HepG2.2.15, HBV-gRNA2-EE4000, 1

description: Library name: NGSHC852


title: hiPSC-CMs, healthy, rep4

description: Library name: CM_31_3_DC35

value: Human induced pluripotent stem cell-derived cardiomyocytes

value: Healthy control


title: Donor4, M1 Macrophages, XYLT2-knockdown

description:
Library name: Sample 23
Coloum name in L160525BO2_01.read.counts.sampleIDs.detailed.txt: MB93_M1_siXYLT2

value: primary macrophages

value: XYLT2-siRNA-knockdown (siXYLT2)


title: Spleen TCR 0723

description:
Library name: Spleen2_TCR
10X Genomics Chromium Single Cell 5' v2 kit


title: Spleen TCR 0588

description:
Library name: Spleen_TCR
10X Genomics Chromium Single Cell 5' v2 kit


title: Spleen GEX 0588

description:
Library name: Spleen_GEX
10X Genomics Chromium Single Cell 5' v2 kit


title: Small Intestine GEX 0588

description:
Library name: Smal_intestine_GEX
10X Genomics Chromium Single Cell 5' v2 kit


title: Small Intestine TCR 0588

description:
Library name: Smal_intestine_TCR
10X Genomics Chromium Single Cell 5' v2 kit


title: MLN TCR 0588

description:
Library name: MLN_TCR
10X Genomics Chromium Single Cell 5' v2 kit


title: MLN GEX 0588

description:
Library name: MLN_GEX
10X Genomics Chromium Single Cell 5' v2 kit


title: Donor4, M0 Macrophages, control

description:
Library name: Sample 10
Coloum name in L160525BO2_01.read.counts.sampleIDs.detailed.txt: MB93_M0_siNC

value: non-targeting control (siNC)


title: Brain TCR 0588

description:
Library name: Brain_TCR
10X Genomics Chromium Single Cell 5' v2 kit


title: Brain GEX 0588

description:
Library name: Brain_GEX
10X Genomics Chromium Single Cell 5' v2 kit


title: Donor3, M0 Macrophages, control

description:
Library name: Sample 7
Coloum name in L160525BO2_01.read.counts.sampleIDs.detailed.txt: HB62_M0_siNC


title: Donor4, M1 Macrophages, control

description:
Library name: Sample 11
Coloum name in L160525BO2_01.read.counts.sampleIDs.detailed.txt: MB93_M1_siNC


title: Donor1, M2 Macrophages, XYLT2-knockdown

description:
Library name: Sample 3
Coloum name in L160525BO2_01.read.counts.sampleIDs.detailed.txt: AWI96_M2_siXYLT2


title: Donor2, M1 Macrophages, control

description:
Library name: Sample 5
Coloum name in L160525BO2_01.read.counts.sampleIDs.detailed.txt: MK65_M1_siNC


title: MCF7_TET3KO_TET3ChIP_rep2

city: Shanghai

first: Lu

last: Liu

address: 131 Dongan Road

institute: Fudan University

description: Library name: MCF7_TET3KO_TET3ChIP_rep2

data_processing:
Raw reads were trimmed using Trim_galore (v0.6.7) and aligned to the hg19 genome using Bowtie2 (v2.2.5) to report best alignment with mapping quality (MAPQ). Unique reads were filtered by MAPQ > 20. PCR duplicates were removed using Picard (v2.26.2). Genome coverage bigwig files were generated by deeptools bamCoverage with the parameter ‘--normalizeUsing RPKM --bs 5’.
Assembly: hg19
Supplementary files format and content: Genome coverage bigwig files

source_name: breast

growth_protocol: MCF7 cells were cultured in DMEM high glucose medium (Hyclone) containing 1% penicillin/streptomycin (Hyclone) and 10% fetal bovine serum FBS (ExCell Bio).

extract_protocol:
MCF7 cells were fixed with 1% formaldehyde (diluted in PBS) for 10 min at room temperature. 1 ml 1.25 M glycine was added and incubated for 5 min to stop the crosslinking reaction. Cells were collected and sonicated with Bioruptor. 10 ml cell lysates were preserved as input, 500 ml cell lysates were incubated overnight at 4°C with 5 mg anti-TET3 (CST, #99980) in ChIP Lysis Buffer (50 mM HEPE-NaOH pH 7.5, 300 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 0.05% SDS, 0.5mM PMSF, 1× cocktail). Pre-washed protein A/G beads (30 ml per reaction) were then used to capture the chromatin-antibody complexes. Captured complexes were washed three times with ChIP Lysis Buffer, twice with Low Salt Wash Buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% Na-deoxylcholate), and once with 10 mM Tris-HCl pH 8.0. Protein-DNA crosslinks were reversed in Elution Buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS) for 4 hours at 65°C. The samples were then treated with RNase A and Proteinase K (1 hour, 55°C), the released DNA was purified using the QIAGEN PCR extraction kit (#28006).
The sequencing libraries for ChIP-seq were prepared using the VAHTS Universal DNA Library Prep Kit for Illumina V3 (ND607-02, Vazyme) according to the manufacturer’s instructions.

value: breast

value: epithelial cell

value: TET3 KO


title: MCF7_TET3KO_input_rep2

description: Library name: MCF7_TET3KO_input_rep2


title: MCF7_WT_input_rep2

description: Library name: MCF7_WT_input_rep2


title: MCF7_TET3KO_TET3ChIP_rep1

description: Library name: MCF7_TET3KO_TET3ChIP_rep1


title: MCF7_WT_TET3ChIP_rep2

description: Library name: MCF7_WT_TET3ChIP_rep2


title: A673, EWS-FLI1 knockout, replicate 3

description: Library name: KO6

value: Bone and soft tissue

value: Ewing sarcoma cell

value: EWS-FLI1 knockout


title: A673, EWS-FLI1 knockout, replicate 2

description: Library name: KO5


title: MCF7_TET3KO_input_rep1

description: Library name: MCF7_TET3KO_input_rep1


title: MCF7_WT_input_rep1

description: Library name: MCF7_WT_input_rep1


title: MCF7_shTET3-2_mRNAseq_rep1

description: Library name: MCF7shTET3-2_mRNAseq_rep1

data_processing:
Raw reads were trimmed using Trim_galore (v0.0.6), then the reads were aligned to the hg19 or mm10 reference genomes using Tophat (v2.1.1) with default parameters. Genes FPKM (fragment per million mapped reads per kilobase exon) were calculated by FPKM_count.py (v2.6.4).
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include FPKM values of each Sample

growth_protocol: MCF7 and B16F10 cells were cultured in DMEM high glucose medium (Hyclone) containing 1% penicillin/streptomycin (Hyclone) and 10% fetal bovine serum FBS (ExCell Bio).

extract_protocol:
Total RNAs were extracted from cancer cells using the TRIzol reagent (Invitrogen, #15596018).
The sequencing libraries for RNA-seq were prepared using the VAHTS® Universal V6 RNA-seq Library Prep Kit (Vazyme) according to the manufacturer’s instructions.

value: TET3 KD


title: MCF7_shTET3-2_mRNAseq_rep2

description: Library name: MCF7shTET3-2_mRNAseq_rep2


title: MCF7_shTET3-1_mRNAseq_rep2

description: Library name: MCF7shTET3-1_mRNAseq_rep2


title: ZR-75-1 Parent DMSO RNAseq replicate 1

description: Library name: Sample 1

treatment_protocol: Abemaciclib 500 nM or equal volume of DMSO (control) for 4 days.


title: A673, EWS-FLI1 knockout, replicate 1

description: Library name: KO4


title: TetKO_D7_RNA_rep2

first: Marlet

last: Morales Franco

state: Île-de-France

address: 15 rue Hélène Brion

institute: Institut Jacques Monod, CNRS, Université Paris Cité

description: Library name: TetKO_D7_RNA_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 ‘ILLUMINACLIP:adapters.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:24’.
Processed reads were aligned to the mm10 genome using STAR (v2.7.9a) and default parameters.
BigWig files were generated using deepTools (v3.5.1) bamCoverage and parameters ‘--binSize 1 --smoothLength 0 --minMappingQuality 255 --normalizeUsing CPM --blackListFileName ENCFF547MET.bed --ignoreForNormalization chrX chrM chrY’. Blacklisted regions are those defined by Amemiya et al., 2019.
Assembly: mm10
Supplementary files format and content: Bigwig format. CPM-normalized counts of RNA signal.

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.

extract_protocol:
Total RNA was extracted from cell pellets using the NucleoSpin RNA kit (Macherey-Nagel).
Total RNA was sent to Novogene for poly(A) RNA library constructions.

value: epiblast like-cells

value: Tet1/2 DKO

value: EpiLC differentiation

value: Day 7


title: MCF7_WT_TET3ChIP_rep1

description: Library name: MCF7_WT_TET3ChIP_rep1

value: WT


title: MCF7_shscramble_mRNAseq_rep2

description: Library name: MCF7shscramble_mRNAseq_rep2

value: Control


title: MCF7_shTET3-1_mRNAseq_rep1

description: Library name: MCF7shTET3-1_mRNAseq_rep1


title: MCF7_shscramble_mRNAseq_rep1

description: Library name: MCF7shscramble_mRNAseq_rep1


title: CAF#1-HSF1 KD

description: Library name: S2

value: pancreas

value: primary cancer-associated fibroblasts

value: HSF1 knockdown


title: MCF7_TET3KO_mRNAseq_rep2

description: Library name: MCF7TET3KO_mRNAseq_rep2


title: MCF7_WT_mRNAseq_rep2

description: Library name: MCF7WT_mRNAseq_rep2


title: MCF7_WT_mRNAseq_rep1

description: Library name: MCF7WT_mRNAseq_rep1


title: u6-3

city: NANJING

first: XINYU

last: YAN

address: 文苑路1号

institute: NANJING NORMAL UNIVERSITY

description: Library name: Sample 6

data_processing:
The libraries were sequenced on an Illumina Novaseq 6000 platform and 150 bp paired-end reads were generated. 、The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count. PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples.
ASprofile [Florea L, Song L & Salzberg SL. Thousands of exon skipping events differentiate among splicing patterns in sixteen humantissues. F1000Research 2013; 2:188.] was used to analyse the alternatively splicing of differentially regulated transcripts isoforms or exons. SNPs and InDels were called using SAMtools, and the details were shown on SAMtools webpage(http://samtools.sourceforge.net/mpileup.shtml). Then SnpEff annotates and predicts the effects of variants on genes (such as amino acid changes).
Assembly: mm10
Supplementary files format and content: tab-delimited textfiles include splicing events for 2 genotypes of MCF-7

source_name: Breast

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
the libraries were constructed using VAHTS Universal V10 RNA-seq Library Prep Kit (Premixed Version) according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

value: Breast

value: Cancer cells

value: SRSF2 knockdown

value: no


title: MCF7_TET3KO_mRNAseq_rep1

description: Library name: MCF7TET3KO_mRNAseq_rep1

value: breast

value: epithelial cell

value: TET3 KO


title: u6-2

description: Library name: Sample 5


title: sh-3

description: Library name: Sample 3

value: control WT


title: sh-2

description: Library name: Sample 2


title: u6-1

description: Library name: Sample 4


title: sh-1

description: Library name: Sample 1