title: Microdissected Mice Renal CCD, WT1_Vehicle, RNA-Seq, Transcriptome 02

city: Bethesda

description: Library name: Sample 2

value: Kidney

value: WT

value: Vehicle


title: S4-S5 Mutant, S4 Viewpoint, rep2

status: Public on Mar 04 2026

type: SRA

city: Mexico City

first: Angel

middle: Josue

last: Cerecedo-Castillo

state: Coyoacan

address: Circuito Exterior s/n Ciudad Universitaria

department: Molecular Genetics

country: Mexico

institute: Universidad Nacional Autonoma de Mexico

description: Library name: VP_S4_dS4S5_rep2

library_source: genomic

data_processing:
Pipe4C (v1.1.6) was utilized for preprocessing and analysis of all samples. The hg19 reference genome was used for all alignments. deepTools multiBamSummary was used to estimate scaling factors by viewpoint, which were then applied to generate bigWig files using bamCoverage.
Assembly: hg19
Supplementary files format and content: Normalized 4C counts and signal
Library strategy: 4C-Seq

molecule: genomic DNA

organism: Homo sapiens

source_name: Bone Marrow

growth_protocol: K562 cells were cultured in ISCOVE supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin. Cells were maintained at 37 °C in a humidified atmosphere with 5% CO₂.

extract_protocol:
Ten million cells were crosslinked with 2% formaldehyde for 10 min, followed by a 5-min quenching with glycine. Cells were washed once with PBS and then incubated for 20 min in lysis buffer (10 mM Tris-HCl pH 8, 10 mM NaCl, 0.2% Igepal) with 1× protease inhibitors. First, three rounds of digestion were carried out with DpnII (NEB R0543S) at 37 °C in a thermomixer at 500 rpm (100 U for 4 h, 100 U overnight, and 100 U for another 4 h); the restriction enzyme was inactivated by heating to 62 °C for 20 min while shaking at 500 rpm. Next, the first ligation was performed with 2000 U of T4 DNA ligase (NEB M0202L) at 16 °C in 7 mL of Milli-Q water overnight. Samples were then phenol-chloroform extracted and ethanol precipitated. The second digestion was performed overnight with 50 U of NlaIII (NEB R0125S) or CviQI (NEB R0639S). The second ligation was carried out in a total volume of 5 mL with 3000 U of T4 DNA ligase (NEB M0202L). The ligated material was purified with SPRI beads and quantified using a Qubit dsDNA Assay Kit.
The first round of PCR amplification with viewpoint-specific primers was performed using 4 × 50 µL PCR reactions with 200 ng of 4C template and 16 PCR cycles with Phusion polymerase (NEB M0530L). A second round of PCR with universal primers containing Illumina adapters was then performed, and the material was purified with SPRI beads. Two independent libraries per condition were sequenced on an Illumina HiSeq 4000 platform as single-end 150 bp reads.

tag: tissue

value: Bone Marrow

tag: cell line

tag: cell type

value: Chronic Myelogenous Leukemia

tag: genotype

value: S4-S5 mutant


title: S5 Mutant, S4 Viewpoint, rep2

description: Library name: VP_S4_dS5_rep2

value: S5 mutant


title: P4,mPOCs,Control,t1

city: Solna

first: Tianyi

last: Li

address: Bioclinicum NKS J5:20, Solnavägen 30

department: Oncology-Pathology

country: Sweden

institute: Karolinska Institute

description: Library name: P30458_1036_S93

library_source: transcriptomic

data_processing:
Fastq files were trimmed using TrimGalore (version 0.6.1) to remove the low-quality reads before mapping.
STAR aligner (version 2.7.11a) was used to map the trimmed fastq files to human genome hg38.
The bam files were aligned using featureCount function in subread package (version 2.0.3) and annotated using UCSC gtf file
Assembly: hg38
Supplementary files format and content: RawCounts.txt

molecule: total RNA

source_name: Ovary

extract_protocol:
RNA extraction was performed using the RNeasy Micro Kit (Qiagen, Germany) following the manufacturer’s instructions.
Libraries were prepared using the Illumina Stranded mRNA Prep Ligation protocol (Illumina, USA) according to the manufacturer’s instruction, with 10 ng of RNA used as input.

value: Ovary

value: Primary ovarian cells

tag: treatment

value: Control

tag: time

tag: type

value: mPOCs


title: Microdissected Mice Renal CCD, WT2_Vehicle, RNA-Seq, Transcriptome 01

first: Shuo-Ming

last: Ou

state: MD

address: 10 Center Dr

country: USA

institute: NHLBI

description: Library name: Sample 4

data_processing:
Sequenced reads were mapped to Ensembl mouse gene set using STAR v2.7.61
Transcript abundances in TPM were caculated by  RSEM/1.3.3
Assembly: GRCm39 (Ensembl)
Supplementary files format and content: Excel file includes TPM values for each sample

molecule: polyA RNA

organism: Mus musculus

source_name: Kidney

growth_protocol: Pathogen-free male C57BL/6 mice (Taconic) weighing 20-30 g had free access to ad libitum drinking water and normal rodent chow before experiment. The mice were housed one per cage, maintained on a 12:12-h light-dark cycle, and acclimated to the housing conditions for 3 days before the experimental procedures.

extract_protocol:
RNAs were extracted using Zymo kit and cDNAs were sythesized using SMART-Seq V4 Ultra Low Input RNA Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Ten-week-old WT and MUT (Thr551Ala/Ser552Ala at beta-catenin) mice were assigned to two groups without treatments


title: P4,mPOCs,Control,t24

description: Library name: P30458_1040_S97


title: High flow velocity_2

city: WUxi

first: Xin

last: Gao

country: China

institute: Nanjing Agricultural University

description: Library name: G_1

data_processing:
Firstly, Cutadapt were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). including the Q20, Q30 and GC-content of the clean data. All downstream analyses were based on clean data of high quality. De novo assembly of the transcriptome was performed with Trinity 2.4.0. Trinity groups transcripts into clusters based on shared sequence content. Such a transcript cluster is very loosely referred to as a 'gene'. The longest transcript in the cluster was chosen as the 'gene' sequence (aka Unigene).
All assembled Unigenes were aligned against the non-redundant (Nr) protein database (http://www.ncbi.nlm.nih.gov/), Gene ontology (GO)(http://www.geneontology.org), SwissProt(http://www.expasy.ch/sprot/), Kyoto Encyclopedia of Genes and Genomes (KEGG) (http://www.genome.jp/kegg/) and eggNOG (http://eggnogdb.embl.de/) databases using DIAMOND with a threshold of Evalue<0.00001.
Salmon was used to perform expression level for Unigenes by calculating TPM. The differentially expressed Unigenes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with FDR < 0.05) by R package edgeR.
hg18
Assembly: tab-delimited text files include TPM values for each Sample
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Triplophysa orientalis

source_name: muscle tissue

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: muscle tissue

value: skeletal muscle cells

value: Overexpressing


title: siPsmd13, Differentiated -2

city: Melbourne

first: Diji

last: Kuriakose

address: Clayton

country: Australia

institute: Monash University

description:
Library name: Sample6
Coulmn name in all_counts_Differentiated.txt Sample 6

data_processing:
Sequence libraries were filtered for adaptor contamination using the Cutadapt (v3.3) software tool.
Filtered reads were aligned to the mouse reference genome (mm10) using Bowtie (v.2.3.5)
Assembly: mm10
Supplementary files format and content: tab-delimited txt file

source_name: Hippocampus

growth_protocol: DMEM, 8mM HEPES, B27 supplement, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Bioruptor Plus sonication (Diagenode).
RNA librarries for small RNA-seq was prepared using Small RNA-seq Lib Prep Kit for Illumina V3-Abclonal according to the manufacturers instructions.

value: Hippocampus

value: Neural progenitor cells

value: primary cells

value: Psmd13 knockdown

value: Differentiated


title: High flow velocity_4

description: Library name: G_3


title: Normal flow velocity_4

description: Library name: A_4


title: siPsmd13, Dfferentiated -1

description:
Library name: Sample5
Coulmn name in all_counts_Differentiated.txt Sample 5


title: Normal flow velocity_5

description: Library name: A_5


title: S4 Mutant, S4 Viewpoint, rep2

description: Library name: VP_S4_dS4_rep2

value: S4 mutant


title: siControl, Undifferentiated -1

description:
Library name: Sample3
Coulmn name in all_counts_Undifferentiated.txt Sample 3

value: Undifferentiated


title: S4 Mutant, S4 Viewpoint, rep1

description: Library name: VP_S4_dS4_rep1

value: Bone Marrow

value: Chronic Myelogenous Leukemia


title: Normal flow velocity_3

description: Library name: A_3


title: siControl, Undifferentiated -2

description:
Library name: Sample4
Coulmn name in all_counts_Undifferentiated.txt Sample 4


title: S2 Mutant, S4 Viewpoint, rep2

description: Library name: VP_S4_dS2_rep2

value: S2 mutant


title: Normal flow velocity_1

description: Library name: A_1


title: siControl, Differentiated -1

description:
Library name: Sample7
Coulmn name in all_counts_Differentiated.txt Sample 7


title: Normal flow velocity_2

description: Library name: A_2


title: S5 Mutant, S4 Viewpoint, rep1

description: Library name: VP_S4_dS5_rep1

value: S5 mutant


title: Male 5×FAD Rapamycin 4

city: Chongqing

first: Kai

last: Guo

address: 1 Youyi Road, Yuzhong District

institute: Chongqing Medical University

description:
Library name: MR4
Column name in MR.txt: MR4

data_processing:
Raw FASTQ data were preprocessed using Trim Galore to remove low-quality reads (containing adapter sequences, reads with Phred scores <20, or N base proportions >10%), yielding high-quality clean reads for downstream analysis.
FastQC (v0.11.9) was used to assess the quality of raw sequencing reads
Trimmomatic (v0.39) was applied to remove adapter sequences and the first 10bp of each read were trimmed to eliminate potential bias. (sliding window: 4bp, minimum quality: 20, leading/trailing: 3bp, min length: 36bp)
Cleaned reads were aligned to the mouse reference genome (GRCm38/mm10) using HISAT2 (v2.2.1) with default parameters.
featureCounts(v2.0.3) was used to generate gene-level counts with the Ensembl annotation.
Assembly: GRCm38.p4
Supplementary files format and content: tab-delimited text file include raw counts for each sample
Supplementary files format and content: tab-delimited text file include raw counts for all samples

source_name: brain

extract_protocol:
Total RNA was isolated from mouse cortical tissues using TRIzol reagent (Cat. #15596026, Thermo Fisher Scientific) following homogenization and lysis.
cDNA fragments of 150–200 bp were size-selected using the AMPure XP system (Beckman Coulter, Beverly, USA). Adapter-ligated cDNA was treated with 3 µL of USER enzyme (NEB, USA) at 37°C for 15 min, followed by incubation at 95°C for 5 min prior to PCR amplification. PCR was performed using Phusion High-Fidelity DNA polymerase, universal PCR primers, and index (X) primers. The resulting PCR products were purified using the AMPure XP system, and library quality was assessed using the Agilent Bioanalyzer 2100 system. After passing quality control, libraries were pooled based on effective concentration and sequencing requirements, followed by paired-end sequencing (150 bp) on the Illumina HiSeq 2500 platform (Illumina, San Diego, USA) with unique index barcodes for sample identification.

value: brain

value: cortex tissue

value: Rapamycin diet

tag: Sex

value: Male

tag: batch


title: P4,cPOCs,Control,t24

description: Library name: P30458_1035_S92

value: Ovary

value: Primary ovarian cells

value: Control

value: cPOCs


title: siPsmd13, Undifferentiated -1

description:
Library name: Sample1
Coulmn name in all_counts_Undifferentiated.txt Sample 1

value: Hippocampus

value: Neural progenitor cells

value: primary cells


title: P4,cPOCs,Irradiated,t4

description: Library name: P30458_1033_S90

value: Irradiated


title: P3,mPOCs,Irradiated,t24

description: Library name: P30458_1029_S86

value: mPOCs


title: WT, S4 Viewpoint, rep2

description: Library name: VP_S4_WT_rep2

value: Bone Marrow

value: WT


title: P3,mPOCs,Control,t24

description: Library name: P30458_1030_S87


title: Male 5×FAD Rapamycin 3

description:
Library name: MR3
Column name in MR.txt: MR3


title: S2 Mutant, S4 Viewpoint, rep1

description: Library name: VP_S4_dS2_rep1

value: Chronic Myelogenous Leukemia

value: S2 mutant


title: WT, S4 Viewpoint, rep1

description: Library name: VP_S4_WT_rep1


title: WT_3

city: Guangzhou

first: Lipeng

last: Mao

state: Guangdong

address: No.601, West Huangpu Avenue

department: Department of Microbiology and Immunology

institute: Jinan University

data_processing:
Quality control of raw FastQ data is performed using FastQC and Trim Galore to filter and clean sequencing reads for RNAseq data from 12 mouse samples. Sequence alignment is done with HISAT2 using the mm10 mouse reference genome from the UCSC website, followed by BAM file conversion with Samtools. Gene quantification is carried out with featureCounts, generating FPKM values after normalizing raw counts for gene length and sequencing depth. Differential expression analysis between four mouse groups is conducted using DESeq2, identifying genes with significant expression changes based on adjusted p-values and fold changes.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: hippocampal

extract_protocol:
Total RNA was isolated from hippocampal tissues from WT, 5xFAD, 5xFAD;Ulk1OV and Ulk1OV mice. Agarose gel electrophoresis was applied to check RNA integrity and DNA contamination; RNA purity (as well as concentration) was checked by the NanoPhotomerer spectrophotometer (IMPLEN) and Bioanalyzer 2100 system (Agilent Technologies). Then cDNA libraries were constructed using ≥ 800 ng RNA per sample with the Illumina's NEBNext® UltraTM RNA Library Prep Kit following manufacturer’s recommendations. The effective concentration of the library was determined to be at least 2nM. Next-generation sequencing data (performed by the company Novogene, China) were obtained and analyzed. FastQC and trim galore were used to filter raw sequence data and the removal of adapters, N-containing reads, and low-quality reads (reads below Q20).
. The effective concentration of the library was determined to be at least 2nM. Next-generation sequencing data (performed by the company Novogene, China) were obtained and analyzed.
FastQC and trim galore were used to filter raw sequence data and the removal of adapters, N-containing reads, and low-quality reads (reads below Q20).

value: hippocampal


title: WT_2

treatment_protocol: Total RNA was isolated from hippocampal tissues from WT, 5xFAD, 5xFAD;Ulk1OV and Ulk1OV mice. Agarose gel electrophoresis was applied to check RNA integrity and DNA contamination; RNA purity (as well as concentration) was checked by the NanoPhotomerer spectrophotometer (IMPLEN) and Bioanalyzer 2100 system (Agilent Technologies). Then cDNA libraries were constructed using ≥ 800 ng RNA per sample with the Illumina's NEBNext® UltraTM RNA Library Prep Kit following manufacturer’s recommendations. The effective concentration of the library was determined to be at least 2nM. Next-generation sequencing data (performed by the company Novogene, China) were obtained and analyzed. FastQC and trim galore were used to filter raw sequence data and the removal of adapters, N-containing reads, and low-quality reads (reads below Q20).


title: siPsmd13, Undifferentiated -2

description:
Library name: Sample2
Coulmn name in all_counts_Undifferentiated.txt Sample 2

value: Psmd13 knockdown

value: Undifferentiated


title: P4,cPOCs,Control,t1

description: Library name: P30458_1031_S88


title: P4,cPOCs,Irradiated,t1

description: Library name: P30458_1032_S89


title: Male 5×FAD Rapamycin 2

description:
Library name: MR2
Column name in MR.txt: MR2

value: brain

value: cortex tissue

value: Rapamycin diet

value: Male


title: P4,cPOCs,Irradiated,t24

description: Library name: P30458_1034_S91

value: Ovary

value: Primary ovarian cells

value: cPOCs


title: S4-S5 Mutant, S2 Viewpoint, rep2

description: Library name: VP_S2_dS4S5_rep2

value: S4-S5 mutant


title: Male 5×FAD Rapamycin 1

description:
Library name: MR1
Column name in MR.txt: MR1


title: WT_1

value: primary cells


title: P3,mPOCs,Irradiated,t4

description: Library name: P30458_1028_S85

value: Irradiated

value: mPOCs


title: S5 Mutant, S2 Viewpoint, rep2

description: Library name: VP_S2_dS5_rep2

value: Bone Marrow

value: S5 mutant


title: Male 5×FAD Control 4

description:
Library name: MC4
Column name in MC.txt: MC4

value: Control diet


title: P3,mPOCs,Irradiated,t1

description: Library name: P30458_1027_S84


title: ULK1_2

value: hippocampal


title: P3,mPOCs,Control,t1

description: Library name: P30458_1026_S83

value: Control


title: ULK1_3


title: Male 5×FAD Control 3

description:
Library name: MC3
Column name in MC.txt: MC3


title: Male 5×FAD Control 2

description:
Library name: MC2
Column name in MC.txt: MC2


title: ULK1_1


title: S4 Mutant, S2 Viewpoint, rep1

description: Library name: VP_S2_dS4_rep1

value: Chronic Myelogenous Leukemia

value: S4 mutant


title: Female 5×FAD Rapamycin 5

description:
Library name: FR5
Column name in FR.txt: FR5

value: brain

value: cortex tissue

value: Female


title: P3,cPOCs,Irradiated,t24

description: Library name: P30458_1024_S81

value: Ovary


title: P3,cPOCs,Control,t24

description: Library name: P30458_1025_S82

value: Primary ovarian cells


title: S5 Mutant, S2 Viewpoint, rep1

description: Library name: VP_S2_dS5_rep1


title: S4 Mutant, S2 Viewpoint, rep2

description: Library name: VP_S2_dS4_rep2


title: FAD_ULK1_3


title: P3,cPOCs,Irradiated,t4

description: Library name: P30458_1023_S80

value: cPOCs


title: Male 5×FAD Control 1

description:
Library name: MC1
Column name in MC.txt: MC1

value: Male


title: Female 5×FAD Rapamycin 4

description:
Library name: FR4
Column name in FR.txt: FR4

value: Rapamycin diet


title: P3,cPOCs,Irradiated,t1

description: Library name: P30458_1022_S79

value: Irradiated


title: S4-S5 Mutant, S2 Viewpoint, rep1

description: Library name: VP_S2_dS4S5_rep1

value: S4-S5 mutant


title: FAD_ULK1_1

value: primary cells


title: FAD_ULK1_2


title: P3,cPOCs,Control,t1

description: Library name: P30458_1021_S78


title: S2 Mutant, S2 Viewpoint, rep2

description: Library name: VP_S2_dS2_rep2

value: Bone Marrow

value: S2 mutant


title: S2 Mutant, S2 Viewpoint, rep1

description: Library name: VP_S2_dS2_rep1


title: P2,mPOCs,Control,t24

description: Library name: P30458_1020_S77

value: mPOCs


title: FAD_1

value: hippocampal

value: FADgene


title: FAD_3


title: P2,mPOCs,Irradiated,t4

description: Library name: P30458_1018_S75


title: WT, S2 Viewpoint, rep2

description: Library name: VP_S2_WT_rep2

value: Chronic Myelogenous Leukemia

value: WT


title: FAD_2


title: P2,mPOCs,Irradiated,t24

description: Library name: P30458_1019_S76


title: Female 5×FAD Rapamycin 1

description:
Library name: FR1
Column name in FR.txt: FR1

value: brain

value: cortex tissue


title: Female 5×FAD Rapamycin 2

description:
Library name: FR2
Column name in FR.txt: FR2

value: Female


title: Female 5×FAD Control 4

description:
Library name: FC4
Column name in FC.txt: FC4

value: Control diet


title: ko_NC5_colon

city: Beijing

first: Li

last: Ji

address: No.1 Shuaifuyuan

department: Department of Gastroenterology

institute: Peking Union Medical College

description:
ko_NC5_colon
stringtie_fpkm_colon.csv

data_processing:
Adapter sequence, 5’ segment, 3’ segment, bases with quality <20 and reads with N >10% were trimmed.
Small fragments with length less than 25 bp after quality trimming were discarded.
Hisat2 (version 2.1.0, https://ccb.jhu.edu/software/hisat2/index.shtml) was used to align the clean data after quality control to the human reference genome.
Stringtie (version 1.3.3b, http://ccb.jhu.edu/software/stringtie/) calculates the fragments per kilobase of exon model per million mapped reads (FPKM) value of each gene / transcript in the sample according to the results in Hisat2, and used this value as the expression level of mRNA in the sample.
Assembly: mm39
Supplementary files format and content: stringtie_fpkm_lung.csv
Supplementary files format and content: stringtie_fpkm_colon.csv

source_name: colon

growth_protocol: The sequencing samples in this study included wild-type and Cd177 knock-out (KO) mice. RNA sequencing was performed to obtain the differentially expressed mRNAs (DEmRNAs).

extract_protocol:
Total RNA was extracted from cell samples using Trizol kit. Firstly, the mRNA was enriched and fragmented. Then, cDNA synthesis, terminal repair and connector linking were performed.
Polymerase chain reaction (PCR) reaction and product recovery were performed to complete the preparation of the library. Agilent 2100 BioAnalyzer was used to detect library quality. The Illumina novaseq 6000 platform was used to sequence cDNA library.

value: colon

tag: strain background

value: Cd177 KO mice

value: sham operation (Sham) group


title: S4-S5 Mutant, Notch1 Promoter Viewpoint, rep1

description: Library name: VP_promoter_dS4S5_rep1


title: Female 5×FAD Control 3

description:
Library name: FC3
Column name in FC.txt: FC3


title: S4-S5 Mutant, Notch1 Promoter Viewpoint, rep2

description: Library name: VP_promoter_dS4S5_rep2


title: P2,mPOCs,Irradiated,t1

description: Library name: P30458_1017_S74

value: Ovary

value: Primary ovarian cells

value: Irradiated


title: ko_NC3_colon

description:
ko_NC3_colon
stringtie_fpkm_colon.csv


title: Female 5×FAD Control 2

description:
Library name: FC2
Column name in FC.txt: FC2


title: S5 Mutant, Notch1 Promoter Viewpoint, rep1

description: Library name: VP_promoter_dS5_rep1

value: Bone Marrow

value: S5 mutant


title: VTA DO High Performer #2

city: New York

first: Priya

last: Rajasethupathy

state: NY

address: 1230 York Ave

institute: The Rockefeller University

description:
Library name: 88-EF-VTA
PPI-VTA-PFC_normalized_counts.csv

data_processing:
Sequencing reads were aligned to the mouse genome using STAR (v2.4.2a), quantified using Salmon (v0.8.2), and normalized counts were determined using DESeq2.
For differential expression analysis, different batches of RNAseq were included as a covariate in the DESeq2 model.
Assembly: mm10
Supplementary files format and content: Normalized counts files are comma separated value matrices containing the DESeq2 normalized counts for each of the samples.

source_name: Brain - VTA

extract_protocol:
Mice were sacrificed by cervical dislocation and immediately decapitated. The targeted brain regions were harvested from 1 mm brain slices, obtained by brain matrices (ZIVIC) using 1.0 mm tissue punches and transferred to a tube containing 300 µL of ice-cold lysis buffer and 3 µL ß-mercaptoethanol (Total RNA Purification kit, NORGEN; following the manufacturer’s protocol). Samples were then homogenized by passing a 25G insulin syringe six times and left on ice. For RNA extraction, the total RNA Purification kit was used according to the manufacturer’s instructions (NORGEN).
RNA libraries were prepared from 100ng of total RNA per sample using the TruSeq stranded mRNA LT kit (Cat# RS-122-2101, Illumina).

value: Brain - VTA

tag: mouse group

value: DO High Performing Mouse

value: male

tag: strain/line

value: Diversity Outbred


title: ko_NC4_colon

description:
ko_NC4_colon
stringtie_fpkm_colon.csv


title: P2,mPOCs,Control,t1

description: Library name: P30458_1016_S73

value: Control

value: mPOCs


title: WT, S2 Viewpoint, rep1

description: Library name: VP_S2_WT_rep1

value: Chronic Myelogenous Leukemia

value: WT


title: Female 5×FAD Control 1

description:
Library name: FC1
Column name in FC.txt: FC1

value: brain

value: cortex tissue

value: Control diet

value: Female


title: P2,cPOCs,Control,t24

description: Library name: P30458_1015_S72

value: Ovary

value: cPOCs


title: S5 Mutant, Notch1 Promoter Viewpoint, rep2

description: Library name: VP_promoter_dS5_rep2


title: P2,cPOCs,Irradiated,t24

description: Library name: P30458_1014_S71

value: Primary ovarian cells

value: Irradiated


title: ko_NC1_colon

description:
ko_NC1_colon
stringtie_fpkm_colon.csv

value: colon

value: Cd177 KO mice

value: sham operation (Sham) group


title: ko_AP5_colon

description:
ko_AP5_colon
stringtie_fpkm_colon.csv

value: AP group


title: S4 Mutant, Notch1 Promoter Viewpoint, rep2

description: Library name: VP_promoter_dS4_rep2

value: Bone Marrow

value: S4 mutant


title: S2 Mutant, Notch1 Promoter Viewpoint, rep2

description: Library name: VP_promoter_dS2_rep2

value: S2 mutant


title: P2,cPOCs,Irradiated,t4

description: Library name: P30458_1013_S70


title: ko_AP4_colon

description:
ko_AP4_colon
stringtie_fpkm_colon.csv


title: S4 Mutant, Notch1 Promoter Viewpoint, rep1

description: Library name: VP_promoter_dS4_rep1

value: Chronic Myelogenous Leukemia


title: TAMs, TRMT61A-KO-1

city: anonymity

first: anonymity

last: anonymity

state: anonymity

address: anonymity

department: anonymity

institute: anonymity

data_processing:
Raw reads were processed using Trimmomatic
The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference genome using hisat2.
FPKM value of each gene was calculated using cufflinks.
The read counts of each gene were obtained by htseq-count.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Tumor-associated macrophages

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

value: Tumor-associated macrophages

value: MC38 tumor injection


title: TAMs, TRMT61A-KO-2


title: P2,cPOCs,Control,t1

description: Library name: P30458_1011_S68

value: Control


title: ko_NC2_colon

description:
ko_NC2_colon
stringtie_fpkm_colon.csv


title: S2 Mutant, Notch1 Promoter Viewpoint, rep1

description: Library name: VP_promoter_dS2_rep1


title: P2,cPOCs,Irradiated,t1

description: Library name: P30458_1012_S69


title: TAMs, TRMT61A-WT-3


title: TAMs, TRMT61A-KO-3


title: ko_AP3_colon

description:
ko_AP3_colon
stringtie_fpkm_colon.csv


title: P1,mPOCs,Control,t24

description: Library name: P30458_1010_S67

value: mPOCs


title: TAMs, TRMT61A-WT-2


title: ko_AP1_colon

description:
ko_AP1_colon
stringtie_fpkm_colon.csv


title: WT, Notch1 Promoter Viewpoint, rep2

description: Library name: VP_promoter_WT_rep2

value: WT


title: WT, Notch1 Promoter Viewpoint, rep1

description: Library name: VP_promoter_WT_rep1


title: TAMs, TRMT61A-WT-1


title: LNCaP, R1881, pGIPZ, H3K4me2 ChIP

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University

description: Library name: M662

data_processing:
Reads were aligned to hg38 using bowtie2. Bigwig files were created using deeptools' bamCoverage.
Assembly: hg38
Supplementary files format and content: bigwig generated from bam files

source_name: Prostate

extract_protocol:
PCa cells were crosslinked with 1% formaldehyde for 10 min at room temperature with gentle rotation and then quenched for 5 min with 0.125 M glycine. Chromatin was sonicated to an average length of 200–600 bp using an E220 focused-ultrasonicator (Covaris).
ChIP–seq libraries were prepared from 3–5 ng of ChIPed DNA using NEBNext Ultra II DNA Library Prep Kit, according to the manufacturer’s instructions.

treatment_protocol: LNCaP cells were infected with control or HOXB13, FOXA1, GATA2 KD lentivirus and subjected to ChIP-seq assay

value: Prostate

value: LNCaP

value: Prostate cancer cell

value: pGIPZ

tag: antibody

value: H3K4me2 ChIP


title: ko_NC5_lung

description:
ko_NC5_lung
stringtie_fpkm_lung.csv

source_name: lung

value: lung

value: Cd177 KO mice


title: P1,mPOCs,Irradiated,t4

description: Library name: P30458_1008_S65

value: Ovary

value: Primary ovarian cells

value: Irradiated


title: ko_NC4_lung

description:
ko_NC4_lung
stringtie_fpkm_lung.csv

value: sham operation (Sham) group


title: P1,mPOCs,Irradiated,t1

description: Library name: P30458_1007_S64


title: H1563-48H-LMWH-S2

city: Hannover

first: Stephan

last: Immenschuh

state: Deutschland

address: Carl-Neuberg-Str. 1

department: Institute for Transfusion Medicine and Transplant Engineering

country: Germany

institute: Hannover Medical School

data_processing:
Sequencing was performed at the Genomics service (ISCIII) on a NextSeq 500 sequencer using 75 base read lengths in paired-end mode.
First quality control analysis was based on fastQC v0.11.3 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and any adapter sequences and low quality 3′ ends were removed using Trimmomatic v0.36.
High-quality reads were mapped against Hg38 human genome using STAR v2.4.0.1 and mapping quality control was performed using RseQC v2.6.4.
Transcriptome prediction and gene/isoform quantification was calculated using HT-seq v0.11.1 based on Hg38 RefSeq reference genes
Assembly: Hg38
Supplementary files format and content: Raw counts

source_name: H1563 cancer cell lines

growth_protocol: Four cancer cells lines (2106T, 2427T, H1437 and H1563) were cultured for 18 h.

extract_protocol:
The RNA was isolated with the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions and the RNA concentration was measured using the nanodrop (Thermo Fisher Scientific, Waltham, MA, USA).
The RNA sequencing was carried out in triplicates.  TruSeq Stranded mRNA Kit (Illumina Inc., USA) was used for library preparation according to the manufacturer protocol as described in our previous work.  The products were purified with Ampure XP Beads (Beckman Coulter, CA, USA) and enriched with 15 cycles of PCR to create the cDNA library. RNASeq libraries were prepared by using 200 ng RNA of each sample.

treatment_protocol: The culture is either in a complete growth medium without and with addition of LMWH (50 U/ml).

value: H1563 cancer cell lines

value: LMWH treated


title: ko_NC3_lung

description:
ko_NC3_lung
stringtie_fpkm_lung.csv


title: P1,mPOCs,Control,t1

description: Library name: P30458_1006_S63


title: P1,cPOCs,Control,t24

description: Library name: P30458_1005_S62

value: cPOCs


title: H1563-48H-LMWH-S1


title: ko_NC2_lung

description:
ko_NC2_lung
stringtie_fpkm_lung.csv


title: ko_NC1_lung

description:
ko_NC1_lung
stringtie_fpkm_lung.csv


title: LNCaP, R1881, plko.1, H3K4me3 ChIP

description: Library name: M487

value: H3K4me3 ChIP


title: LNCaP, R1881, shHOXB13, GATA2 ChIP

description: Library name: M346

value: GATA2 ChIP


title: H1563-48H-CONTROL-S3

value: control


title: LNCaP, R1881, pGIPZ, GATA2 ChIP

description: Library name: M345

value: Prostate


title: LNCaP, R1881, pGIPZ, H3K27ac ChIP

description: Library name: M452

value: LNCaP

value: H3K27ac ChIP


title: H1563-48H-LMWH-S3


title: H1563-48H-CONTROL-S2


title: P1,cPOCs,Irradiated,t24

description: Library name: P30458_1004_S61


title: ko_AP5_lung

description:
ko_AP5_lung
stringtie_fpkm_lung.csv

value: AP group


title: P1,cPOCs,Irradiated,t4

description: Library name: P30458_1003_S60


title: P1,mPOCs,Irradiated,t24

description: Library name: P30458_1009_S66

value: mPOCs


title: H1563-48H-CONTROL-S1


title: ko_AP3_lung

description:
ko_AP3_lung
stringtie_fpkm_lung.csv

value: lung


title: P1,cPOCs,Control,t1

description: Library name: P30458_1001_S58

value: Control


title: LNCaP, R1881, pGIPZ, FOXA1 ChIP

description: Library name: M343

value: Prostate cancer cell

value: pGIPZ

value: FOXA1 ChIP


title: LNCaP, R1881, pGIPZ, H3K4me1 ChIP

description: Library name: M658

value: H3K4me1 ChIP


title: H1437-48H-LMWH-S2

source_name: H1437 cancer cell lines

value: H1437 cancer cell lines


title: ko_AP2_lung

description:
ko_AP2_lung
stringtie_fpkm_lung.csv

value: Cd177 KO mice


title: ko_AP1_lung

description:
ko_AP1_lung
stringtie_fpkm_lung.csv


title: LNCaP, R1881, shHOXB13, AR ChIP

description: Library name: M342

value: AR ChIP


title: LNCaP, R1881, shHOXB13, FOXA1 ChIP

description: Library name: M344


title: ko_AP4_lung

description:
ko_AP4_lung
stringtie_fpkm_lung.csv


title: LNCaP, R1881, pGIPZ, AR ChIP

description: Library name: M341


title: H1437-48H-CONTROL-S3


title: H1437-48H-LMWH-S3

value: LMWH treated


title: hEGCLC_C5_P5

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

description: Library name: EG_C5_P5

data_processing:
WGS reads were processed using cutadapt v4.7 to remove Illumina adapters, to quality trim at Q20, and to filter read pairs containing N bases or where either read <31 bps.
Processed reads were aligned to the Human genome (GRCh38) using bowtie2 v2.5.1 and further analysed in R to using QDNAseq v1.42.0 setting options to count only properly paired reads and to exclude secondary alignments.
Assembly: GRCh38
Supplementary files format and content: TSV files containing DNA copy number estimated by QDNAseq

source_name: BTAG (Sasaki et al., 2015)

growth_protocol: hPSC lines were maintened in TeSR/E8 or Stemfit medium. They were cultured under feeder-free conditions on matrigel or Geltrex coated plates at 37°C, 5% CO2 and 5% O2.

extract_protocol:
Genomic DNA was extracted using the Monarch Genomic DNA Purification Kit (NEB #T3010) and following the manufacturer instructions. DNA samples were submitted to GENEWIZ for library preparation and sequencing
Library constuction (Illumina 2x150bp) was performed by GENEWIZ

treatment_protocol: hPGCLCs were induced from hPSCs based on the Sasaki et al., 2015 protocol. hEGCLCs were reprogrammed from hPGCLCs in our defined induction medium then gradually transitioned to conventional hPSCs medium.

value: BTAG (Sasaki et al., 2015)


title: NC5_colon

description:
NC5_colon
stringtie_fpkm_colon.csv

value: colon

value: WT mice

value: sham operation (Sham) group


title: H1437-48H-CONTROL-S2

value: control


title: P1,cPOCs,Irradiated,t1

description: Library name: P30458_1002_S59

value: Ovary

value: Primary ovarian cells

value: Irradiated

value: cPOCs


title: hEGCLC_C1_P5

description: Library name: EG_C1_P5


title: NC3_colon

description:
NC3_colon
stringtie_fpkm_colon.csv


title: CAR-iMACs-2

description: Library name: Sample 4

data_processing:
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
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.
Assembly: hg38
Supplementary files format and content: Matrix table with FPKM for every gene and every sample

source_name: human induced pluripotent stem cells (iPSCs)-derived macrophages (iMACs)

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.


title: NC4_colon

description:
NC4_colon
stringtie_fpkm_colon.csv


title: CAR-iMACs-1

description: Library name: Sample 3

value: human induced pluripotent stem cells (iPSCs)-derived macrophages (iMACs)


title: H1437-48H-LMWH-S1


title: Test 5

first: Rui

last: Xu

address: No. 1023-1063 Shatai South Road

institute: Southern Medical University

description: Library name: Sample 10

data_processing:
The sequencing data was filtered with SOAPnuke (v2.2.1).
The clean reads were mapped to the reference genome using HISAT2. After that, Ericscript (v0.5.5) and rMATS (V4.1.2) were used to detect fusion genes and differential splicing genes (DSGs), respectively.
mRNA expression level of gene was calculated by RSEM (v1.3.1).
Differential expression analysis was performed using the DEGseq, Q value≤ 0.05 (or FDR ≤0.001) to judge the significance of expression difference.
Assembly: NCBI GCF_000001215.4_Release_6_plus_ISO1_MT
Supplementary files format and content: XML files includes raw counts and FPKM values for each sample.

organism: Drosophila melanogaster

source_name: Whole body

extract_protocol:
Total RNA was extracted from tissues using TRIzol (Invitrogen, Carlsbad, California, USA) according to manual instruction. Total RNA was qualified and quantified using a Fragment Analyzer or Agilent 2100 Bioanalyzer (Agilent, CA, USA), or Qseq-400 (Bioptic, Taiwan, China).
Library preparation is performed using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China) following manufacturer's protocols.

value: Whole body

value: WT

value: HDM injection


title: Test 3

description: Library name: Sample 8


title: Test 1

description: Library name: Sample 6


title: 2427T-48H-LMWH-S3

source_name: 2427T cancer cell lines

value: 2427T cancer cell lines


title: NC2_colon

description:
NC2_colon
stringtie_fpkm_colon.csv


title: H1437-48H-CONTROL-S1

value: H1437 cancer cell lines


title: Test 2

description: Library name: Sample 7


title: Test 4

description: Library name: Sample 9


title: NC1_colon

description:
NC1_colon
stringtie_fpkm_colon.csv


title: 2427T-48H-LMWH-S2


title: hEGCLC_C2_P5

description: Library name: EG_C2_P5


title: TRMT61AOE-CAR-iMACs-1

description: Library name: Sample 1

value: human Trmt6 overexpression


title: TRMT61AOE-CAR-iMACs-2

description: Library name: Sample 2


title: AP5_colon

description:
AP5_colon
stringtie_fpkm_colon.csv

value: AP group


title: Control 5

description: Library name: Sample 5

value: PBS injection


title: AP4_colon

description:
AP4_colon
stringtie_fpkm_colon.csv

value: colon


title: hEGCLC1_P5_3

description: Library name: hEGCLC1_P5_3

data_processing:
Reads were processed using cutadapt v4.1 (Martin 2011) to remove Illumina adapters, trim, and filter on quality with the settings: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -n 1 -m 31 --nextseq-trim 20 --max-n 0
Processed reads were quantified against the GRCh38 transcriptome (Ensembl 107 annotations) by Salmon (Patro et al. 2017) with the following settings: -l A --softclip --softclipOverhangs --allowDovetail --seqBias --gcBias
Within DESeq2 v1.44.0 (Love, Huber, and Anders 2014), independent hypothesis weighting was conducted to optimise the power of p value filtering using IHW v1.32.0 (Ignatiadis et al. 2016) and log2 fold-change shrinkage was performed using ashr v2.2-63 (Stephens 2017). Multiple correction testing adjustments were optimised by passing FDR and log2FC thresholds at the point of results generation.
Assembly: GRCh38
Supplementary files format and content: Transcript-level expression estimates

extract_protocol:
Frozen pellets were submitted to GENEWIZ for RNA isolation
Library preparation with poly(A) selection and 150bp paired end sequencing on Illumina

value: BTAG (Sasaki et al., 2015)


title: 2427T-48H-CONTROL-S3


title: hEGCLC1_P5_2

description: Library name: hEGCLC1_P5_2


title: Control 3

description: Library name: Sample 3


title: Control 2

description: Library name: Sample 2


title: 2427T-48H-LMWH-S1

value: LMWH treated


title: AP3_colon

description:
AP3_colon
stringtie_fpkm_colon.csv

value: WT mice


title: Control 4

description: Library name: Sample 4


title: 2427T-48H-CONTROL-S1

value: control


title: 2106T-48H-LMWH-S3

source_name: 2106T cancer cell lines

value: 2106T cancer cell lines


title: AP2_colon

description:
AP2_colon
stringtie_fpkm_colon.csv


title: hEGCLC1_P5_1

description: Library name: hEGCLC1_P5_1


title: Control 1

description: Library name: Sample 1


title: AP1_colon

description:
AP1_colon
stringtie_fpkm_colon.csv


title: hEGCLC2_P5_3

description: Library name: hEGCLC2_P5_3


title: 2106T-48H-LMWH-S1


title: 2427T-48H-CONTROL-S2


title: NC2_lung

description:
NC2_lung
stringtie_fpkm_lung.csv

value: lung

value: sham operation (Sham) group


title: hEGCLC2_P5_2

description: Library name: hEGCLC2_P5_2


title: SKF5

city: Toon

first: Mohammed

middle: E

last: Choudhury

state: Ehime

address: 454 Shitsukawa

department: Anesthesia and Perioperative Medicine

country: Japan

institute: Ehime University Graduate School of Medicine

description: Library name: Sample 21

data_processing:
CLC Genomics Workbench Premium (QIAGEN) (ver 24.0.1), an ingenuity pathway analysis (IPA) (QIAGEN)
Assembly: mRatBN7.2
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include TPM values for each Sample

organism: Rattus norvegicus

source_name: Brain

extract_protocol:
Maxwell RSC simplyRNA Tissue/Cells Kit (Promega, Madison, WI, USA).
NEBNext® Poly(A) mRNA Magnetic Isolation Module (for PolyA selection), NEBNext® Ultra™ ll Directional RNA Library Prep Kit

value: Brain


title: 2106T-48H-LMWH-S2


title: SKF8

description: Library name: Sample 24


title: hEGCLC2_P5_1

description: Library name: hEGCLC2_P5_1


title: hEGCLC3_P5_1

description: Library name: hEGCLC3_P5_1


title: NC5_lung

description:
NC5_lung
stringtie_fpkm_lung.csv


title: 2106T-48H-CONTROL-S1


title: SKF7

description: Library name: Sample 23


title: hEGCLC3_P5_3

description: Library name: hEGCLC3_P5_3


title: hEGCLC3_P5_2

description: Library name: hEGCLC3_P5_2


title: SKF4

description: Library name: Sample 20


title: NC3_lung

description:
NC3_lung
stringtie_fpkm_lung.csv


title: NC4_lung

description:
NC4_lung
stringtie_fpkm_lung.csv


title: MDLBM

city: Philadelphia

first: Makarand

middle: V

last: Risbud

address: 1025 Walnut St.

institute: Thomas Jefferson University

description:
Library name: MDLBM
10X Genomics scRNA-seq CMO

library_source: transcriptomic single cell

data_processing:
Raw data were aligned to the mouse reference transcriptome (mm10-2020-A) and underwent preprocessing with Cell Ranger Multi v7.0.1. According to the authors ' recommended workflow, downstream processing was conducted using Seurat v4.3.0
Data were further analyzed and visualized using the scType and clusterProfiler packages in R.
Assembly: mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Bone Marrow

extract_protocol:
Splenocytes were collected from 24M BL6 mice by gently dissecting the spleen and diluted into an equal volume of Dulbecco’s PBS + 2% FBS (StemCell Technologies, 07905). Similarly Bone marrow cells were collected by flushing the femur and humerus bones with 1x PBS by a syringe. To facilitate removal of any remaining RBCs, a lysis step was performed (Biolegend, 420302). Briefly, lysis buffer (1X) was added to the cell suspension and incubated for 5 minutes, with periodic inversion. Cells were then centrifuged at 350 rcf for 10 minutes, and cells  were washed twice with PBS + 2% FBS.
Libraries were constructed according to manufacturer's specification for the 10X Genomics 3' single-cell gene expression analysis, with multiplexing

value: Bone Marrow

value: Bone Marrow cells

tag: strain

value: Mdl-800 IP 75mg/kg


title: SKF6

description: Library name: Sample 22


title: 2106T-48H-CONTROL-S3


title: 2106T-48H-CONTROL-S2


title: NC1_lung

description:
NC1_lung
stringtie_fpkm_lung.csv


title: AP5_lung

description:
AP5_lung
stringtie_fpkm_lung.csv


title: SKF3

description: Library name: Sample 19


title: hEGCLC1_P3_3

description: Library name: hEGCLC1_P3_3


title: hEGCLC1_P3_2

description: Library name: hEGCLC1_P3_2


title: VHBM

description:
Library name: VHBM
10X Genomics scRNA-seq CMO

value: Vehicle control DMSO IP 100uL


title: hEGCLC2_P3_3

description: Library name: hEGCLC2_P3_3


title: SKF1

description: Library name: Sample 17


title: hEGCLC2_P3_2

description: Library name: hEGCLC2_P3_2


title: SKF2

description: Library name: Sample 18


title: hEGCLC1_P3_1

description: Library name: hEGCLC1_P3_1


title: VHSPL

description:
Library name: VEHS1
10X Genomics scRNA-seq

source_name: Spleen

value: Spleen

value: Splenocytes


title: AP3_lung

description:
AP3_lung
stringtie_fpkm_lung.csv

value: AP group


title: MDLSPL

description:
Library name: MDLS1
10X Genomics scRNA-seq


title: Naive 4

city: Jerusalem

first: Inbar

last: Plaschkes

address: The Hebrew University of Jerusalem - Ein Kerem

department: The Faculty of Medicine - Ein Kerem

country: Israel

institute: HUJI

description: Library name: Yasmin_N4

data_processing:
Raw reads were processed for quality trimming and adaptors removal using fastx_toolkit v0.0.14 and cutadapt v2.10 (ref 1). The processed reads were aligned to the mouse transcriptome and genome version GRCm39 with annotations from Ensembl release 106 using TopHat v2.1.1. Counts per gene quantification was done with htseq-count v2.01. Normalization and differential expression analysis were done with the DESeq2 package v 1.36.0.
During the data exploratory analysis stage the PCA image clearly showed the existence of an unknown variability factor in this system, which might indicate the presence of attached tissue. In order to calculate differential expression while compensating for this source of variability, the statistical model included a “Batch” factor as well as the known biological condition (~ Batch + Condition). Batch-corrected normalized counts were obtained with the ‘ComBat’ function of the sva package for drawing images (e.g. heatmaps) with batch-corrected values.
Assembly: GRCm39 with annotations from Ensembl release 106
Supplementary files format and content: DESeq2_raw_norm_bcor.txt
Supplementary files format and content: Each row in the file contains a certain ensembl Gene ID, Symbol,  raw counts and DESEq2 normalized counts per sample and batch corrected normalized counts.

source_name: gingiva

extract_protocol:
Gingival tissues were incubated in 1 mL of 4 mg/ml Dispase in PBS + 2% FCS until fully distended for 30 minutes and epithelium was carefully separated using forceps and binocular microscope. Next, RNA was extracted using RNeasy mini kit (Qiagen) according to the manufacturer’s instructions, PolyA-selection.
mRNA libraries were prepared using KAPA Stranded mRNA kit with mRNA Capture Beads (KAPA Biosystems, KK8421). In brief, 1µg was used for the library construction; library was eluted in 20µl of elution buffer. All DNA samples libraries were pooled to 10nM sample. Multiplex samples Pool were loaded on NovaSeq 6000 (Illumina), using NovaSeq 6000 SP Reagent Kit v1.5 100 cycles (cat# 20028401), with 122 cycles

treatment_protocol: Mice were anesthetized, and silk ligatures (5/0, SMI, Belgium) were tied around both second maxillary molars as previously described (Abe and Hajishengallis 2013).

value: gingiva

value: epithelium

value: Naïve


title: Vehicle8

description: Library name: Sample 16


title: AP2_lung

description:
AP2_lung
stringtie_fpkm_lung.csv


title: Vehicle7

description: Library name: Sample 15


title: Vehicle6

description: Library name: Sample 14


title: hEGCLC2_P3_1

description: Library name: hEGCLC2_P3_1

value: BTAG (Sasaki et al., 2015)


title: Naive 3

description: Library name: Yasmin_N3


title: AP4_lung

description:
AP4_lung
stringtie_fpkm_lung.csv

value: WT mice


title: AP1_lung

description:
AP1_lung
stringtie_fpkm_lung.csv


title: p16KO_Old_4

city: Shanghai

first: tingting

middle: ting

last: Yang

address: 333 Nan Chen Road, Shanghai

institute: Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair

data_processing:
The transcriptome sequencing was performed on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the mm10 genome using HISAT2.
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
DESeq2 was used for gene expression analysis.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for all Samples
Supplementary files format and content: tab-delimited text files include RPKM values for all Samples

source_name: heart

growth_protocol: ~6 months and ~20 months post αMHC-Cre driven cardiomyocyte-specific knockout of p16INK4a（p16KO）and p16INK4a flox (Control) mice

extract_protocol:
Total RNAs were extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer's instructions.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

treatment_protocol: Pre-treatment with sh-Hmbox1 AAV9 or control AAV9 vectors via tail vein 1 week before I/R or sham surgery

value: heart

value: Old (20 months)


title: hEGCLC3_P3_3

description: Library name: hEGCLC3_P3_3


title: p16KO_Old_3


title: Naive 2

description: Library name: Yasmin_N2


title: Vehicle5

description: Library name: Sample 13


title: Vehicle4

description: Library name: Sample 12


title: Naive 1

description: Library name: Yasmin_N1


title: p16KO_Old_2


title: hEGCLC3_P3_1

description: Library name: hEGCLC3_P3_1


title: Control_Old_4

value: p16INK4a flox


title: Removal 4

description: Library name: Yasmin_R4

value: Removal


title: Vehicle2

description: Library name: Sample 10

value: Brain


title: hEGCLC2_P0

description: Library name: hEGCLC2_P0


title: p16KO_Old_1


title: Removal 3

description: Library name: Yasmin_R3


title: hEGCLC3_P3_2

description: Library name: hEGCLC3_P3_2


title: Control_Old_3


title: hEGCLC1_P0

description: Library name: hEGCLC1_P0


title: hEGCLC3_P0

description: Library name: hEGCLC3_P0


title: Control_Old_1


title: Vehicle3

description: Library name: Sample 11


title: Normal Control7

description: Library name: Sample 7


title: p16KO_Young_4

value: Young (6 months)


title: Normal Control8

description: Library name: Sample 8


title: Vehicle1

description: Library name: Sample 9


title: p16KO_Young_3


title: hPGCLC1

description: Library name: hPGCLC1

value: hPGCLC


title: Removal 2

description: Library name: Yasmin_R2


title: hIPSC1

description: Library name: hIPSC1

value: hIPSC


title: Normal Control6

description: Library name: Sample 6


title: hPGCLC2

description: Library name: hPGCLC2


title: Normal Control4

description: Library name: Sample 4


title: p16KO_Young_2


title: Control_Old_2


title: ligature 2

description: Library name: Yasmin_L2

value: ligature


title: Normal Control3

description: Library name: Sample 3


title: Removal 1

description: Library name: Yasmin_R1


title: hIPSC3

description: Library name: hIPSC3


title: hIPSC2

description: Library name: hIPSC2


title: Mouse heart, 192, T497A, 5 weeks after TAC surgery, 15 weeks old, rep3

city: Dallas

first: Lei

state: TX

address: 5323 Harry Hines Blvd

department: Department of Population and Data Sciences

institute: University of Texas Southwestern Medical Center

description:
Library name: Prkca-T497A-TAC-192
11-TT-Prkca-T497A-TAC-192_S11

data_processing:
Adaptors were trimmed using Trim Galore (v0.6.4). The trimmed reads were then aligned to the mouse genome (mm10) using STAR (2.7.3a). Gene expression was quantified using featureCounts of the Subread (v1.6.3) package. Low-expressed genes (genes with the expression value of 0 in more than 30% of samples) were removed before any subsequent analysis. Gene expression was normalized using the Voom method from the R package limma (v 3.50.3). Differentially expressed genes were identified using the same package. Gene Set Enrichment Analysis (GSEA) for the DEGs was performed using R package clusterProfiler (v4.2.2).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: left ventricle

extract_protocol:
Total RNA was extracted from murine cardiac tissue using the RNeasy Mini Kit  (74104, Qiagen, Hilden, Germany) following the manufacturer's instructions. RNA integrity was assessed using Agilent 2200 Tapestation and RNA Screentape (5067-5576, Agilent Technologies).
RNA-seq libraries were generated from total RNA using the KAPA  mRNA HyperPrep Kit (KK8581, Roche) according to the manufacturer's protocol.  Libraries were sequenced on an Illumina NextSeq500 platform using  single-end 75-cycle high-output mode.

treatment_protocol: WT and Prkca T497A mice were subjected to Sham or transverse aortic constriction (TAC) surgery using a 27-gauge needle at the age of 10 weeks .

value: left ventricle

value: cardiomyocyte

value: Prkca T497A

value: TAC surgery


title: Mouse heart, 201, T497A, 5 weeks after TAC surgery, 15 weeks old, rep3

description:
Library name: Prkca-T497A-TAC-201
12-TT-Prkca-T497A-TAC-201_S12


title: ligature 1

description: Library name: Yasmin_L1

value: gingiva

value: epithelium


title: ligature 3

description: Library name: Yasmin_L3


title: control MDAMB-231_2

city: Kyoto

first: Kenta

last: Yamamoto

address: Kajicho 465

department: Immunology

institute: Kyoto Prefectural University of Medicine

data_processing:
strand NGS was used.
Assembly: hg38
Supplementary files format and content: Raw read count values and normalized values for each sample.

source_name: mammary gland

growth_protocol: cultured in Dulbecco’s Modified Eagle Medium (DMEM, Nakalai Tesque) supplemented with 10% FBS, 100 U/mL penicillin, 100 mg/mL streptomycin, 1% sodium pyruvate, and 100 mM non-essential amino acids (complete DMEM) under the standard conditions

extract_protocol:
RNA was isolated using the ISOGENⅡ（NIPPON GENE CO., LTD） according to manufacturer’s instructions.
The sequencing libraries were prepared from the total RNA using the TruSeq Stranded mRNA Library Prep Kit in acordance with manifacturer's instructions.

treatment_protocol: BCCs and monocytes were cocultured for 48hours in 12-well plates at concentrations of 1.0E+4/well and 2.0E+4/well, respectively, under the standard conditions.

value: mammary gland

value: breast cancer

value: untreated


title: Control_Young_2

value: heart


title: Wild type Dicer

description: Library name: Wild type Dicer

data_processing:
Basecalls were performed using fastq for Illumina output.
ChIP-seq reads were trimmed with a cut-off quality score > 30, using the Trim galore software.
ChIP-seq reads were aligned to the UCSC mm10 genome using Bowtie version 2.3.5.
Peaks were called using MACS v3.0.0a5 with the significance cut-off q-value <=0.01.
Bedgraph files were generated using bdgpeakcall of MACS3. broadPeak files were generated using MACS v2 with default settings.
Assembly: mm10
Supplementary files format and content: Bedgraph files, narrowPeak/broadPeak (except for Input sample).

source_name: Hippocampus

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Bioruptor Plus sonication (Diagenode).
ChIP-seq libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina. 10 ng of DNA was used as starting material for input and IP samples. Libraries were amplified using 12 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using AMPure XP beads from Beckman Coulter. Libraries were validated using the Qubit High Sensitivity DNA Kit.

value: Hippocampus

value: Neural progenitor cells

value: primary cells

value: Wild type

value: not provided


title: Mouse heart, 149, T497A, 5 weeks after sham surgery, 15 weeks old, rep3

description:
Library name: Prkca-T497A-Sham-149
6-TT-Prkca-T497A-Sham-149_S6

value: Sham surgery


title: p16KO_Young_1

value: Young (6 months)


title: MDAMB-231 co-cultured with human monocytes_2

value: co-cultured with human monocytes for 48hours


title: Wild type Psmd13

description: Library name: Wild type Psmd13


title: Mouse heart, 67, T497A, 5 weeks after sham surgery, 15 weeks old, rep3

description:
Library name: Prkca-T497A-Sham-67
4-TT-Prkca-T497A-Sham-67_S4

value: left ventricle

value: cardiomyocyte


title: Normal Control5

description: Library name: Sample 5

value: Brain


title: Mouse heart, 151, WT, 5 weeks after TAC surgery, 15 weeks old, rep3

description:
Library name: WT-TAC-151
9-TT-WT-TAC-151_S9

value: WT

value: TAC surgery


title: siControl Undifferentiated

description: Library name: siControl Undifferentiated

value: siControl

tag: condition

value: Undifferentiated


title: Caco-2 cells, A_2

city: Tianjin

first: Yue

last: Dong

address: 154 Anshan Road, Heping District, Tianjin

institute: Tianjin Medical University General Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Assembly: mm8
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...

source_name: colon carcinoma

extract_protocol:
The cells in the culture plate were washed with PBS, and total RNA was extracted using an RNA isolater Total RNA Extraction Reagent (Vazyme, China).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: colon carcinoma

value: Caco-2 cells

value: Human colorectal cancer cells

value: proliferation with Desulfovibrio Vulgaris flagellin


title: Mouse heart, 80, WT, 5 weeks after sham surgery, 15 weeks old, rep3

description:
Library name: WT-Sham-80
2-TT-WT-Sham-80_S2


title: Mouse heart, 137, T497A, 5 weeks after TAC surgery, 15 weeks old, rep3

description:
Library name: Prkca-T497A-TAC-137
10-TT-Prkca-T497A-TAC-137_S10

value: Prkca T497A


title: Control_Young_3

value: heart

value: p16INK4a flox


title: Control_Young_4


title: Mouse heart, 64, WT, 5 weeks after TAC surgery, 15 weeks old, rep3

description:
Library name: WT-TAC-64
8-TT-WT-TAC-64_S8


title: MDAMB-231 co-cultured with human monocytes_1

value: mammary gland

value: breast cancer


title: Normal Control2

description: Library name: Sample 2


title: Caco-2 cells, B_1

value: proliferation without Desulfovibrio Vulgaris flagellin


title: BMDMs, TRMT61A-WT-2

data_processing:
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
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.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: bone marrow derived macrophages (BMDMs)

value: bone marrow derived macrophages (BMDMs)


title: Normal Control1

description: Library name: Sample 1


title: Mouse heart, 82, WT, 5 weeks after TAC surgery, 15 weeks old, rep3

description:
Library name: WT-TAC-82
7-TT-WT-TAC-82_S7

value: left ventricle

value: cardiomyocyte


title: Caco-2 cells, B_2

value: WT


title: siPsmd13 Differentiated

first: Diji

address: Clayton

institute: Monash University

description: Library name: siPsmd13 Differentiated

value: Hippocampus

value: Neural progenitor cells

value: primary cells

value: Differentiated

value: not provided


title: Control_Young_1

value: Young (6 months)


title: MG132 treated

description: Library name: MG132 treated


title: Input

description: Library name: Input


title: Caco-2 cells, B_3

value: colon carcinoma

value: Caco-2 cells

value: Human colorectal cancer cells


title: Caco-2 cells, A_3

value: proliferation with Desulfovibrio Vulgaris flagellin


title: BMDMs, TRMT61A-KO-3


title: BMDMs, TRMT61A-KO-2


title: Mouse heart, 79, T497A, 5 weeks after sham surgery, 15 weeks old, rep3

description:
Library name: Prkca-T497A-Sham-79
5-TT-Prkca-T497A-Sham-79_S5

value: Prkca T497A

value: Sham surgery


title: Mouse heart, 190, WT, 5 weeks after sham surgery, 15 weeks old, rep3

description:
Library name: WT-Sham-190
3-TT-WT-Sham-190_S3


title: BMDMs, TRMT61A-KO-1


title: BMDMs, TRMT61A-WT-3


title: 9SR44806A_B03

status: Public on Mar 03 2026

type: RNA

city: Tulsa

first: Dusti

last: Sloan

state: Oklahoma

address: 1111 West 17th Street

department: Pharmacology and Physiology

institute: Oklahoma State University Center for Health Sciences

description: Gene expression data from the PVN of Oil-treated rat

hyb_protocol: Thermofisher hyb protocol for Rat Clariom S Pico Assay (Applied Biosystems, 902937)

scan_protocol: Thermofisher scan protocol for Rat Clariom S Pico Assay (Applied Biosystems, 902937)

data_processing:
RNA was then sent to Thermo Fisher Scientific, Inc. for transcriptome assay services using the microarray, Rat Clariom S Pico Assay (Applied Biosystems, 902937).
Cell intensity (CEL) files were adjusted for background and normalized by Thermofisher. Processed output chip files (CHP) were subsequently processeed using the Transcriptome Analysis Console (TAC) software 4.0.

label: biotin

source_name: Oil-treated, paraventricular nucleus of the hypothalamus (PVN), biological replicate 2

label_protocol: Thermofisher label protocol for Rat Clariom S Pico Assay (Applied Biosystems, 902937)

growth_protocol: Adult, female Sprague-Dawley rats (90 days old, Charles River)

extract_protocol: A stereotaxic atlas (Paxinos and Watson, 1998) was used to identify the ARC, PVN, and nucleus of the solitary tract (NTS). Bilateral brain punches were acquired from frozen brains (1 x 3 mm tissue punch) and stored at -80C in RNAlater (Ambion, AM7020) until mRNA isolation. RNA was isolated using a Biorad Aurum Total RNA Mini kit (BioRad, 732-6820) per manufacturer’s instructions.

treatment_protocol: Ovariectomy followed by one-week recovery. Brain tissue from the arcuate nucleus (ARC), paraventricular nucleus (PVN), and nucleus of the solitary tract (NTS) was collected for microarray analysis on Day 4 of a 4-day treatment protocol:  Day 1: Subcutaneous injection of either 10 µg 17β-estradiol (EB, n = 3) in 0.1 mL oil vehicle or 0.1 mL oil vehicle (n = 3).  Day 2: Repeat injection of either 10 µg EB (n = 3) in 0.1 mL oil vehicle or 0.1 mL oil vehicle (n = 3).  Day 4: Tissue collection following euthanasia.Tissue frozen in liquid nitrogen and stored at -80C.

value: Sprague-Dawley

tag: gender

value: female

tag: age

value: adult, 90 days old

value: Oil

value: brain, PVN


title: control MDAMB-231_1

tag: tissue

value: mammary gland

value: breast cancer

value: untreated


title: 9SR44806A_A02

description: Gene expression data from the PVN of EB-treated rat

source_name: EB-treated, paraventricular nucleus of the hypothalamus (PVN), biological replicate 1

value: EB


title: siControl Differentiated

city: Melbourne

last: Kuriakose

description: Library name: siControl Differentiated

value: Hippocampus

tag: cell line

value: Neural progenitor cells

value: primary cells

value: siControl

value: Differentiated

value: not provided


title: Mouse heart, 65, WT, 5 weeks after sham surgery, 15 weeks old, rep3

last: Guo

description:
Library name: WT-Sham-65
1-TT-WT-Sham-65_S1

value: left ventricle

tag: cell type

value: cardiomyocyte

value: WT


title: Caco-2 cells, A_1

value: colon carcinoma

value: Caco-2 cells

value: Human colorectal cancer cells

tag: genotype

value: proliferation with Desulfovibrio Vulgaris flagellin


title: siPsmd13 Undifferentiated

description: Library name: siPsmd13 Undifferentiated

tag: treatment

value: Undifferentiated


title: 9SR44806A_B07

description: Gene expression data from the NTS of Oil-treated rat

source_name: Oil-treated, nucleus of the solitary tract (NTS), biological replicate 3

value: Sprague-Dawley

value: female

value: adult, 90 days old

value: Oil

value: brain, NTS


title: BMDMs, TRMT61A-WT-1

value: bone marrow derived macrophages (BMDMs)


title: ChIP_ubH2B_INPUT_mock

city: Leiden

first: Martijn

middle: S.

last: Luijsterburg

state: zuid-holland

address: Einthovenweg 20

department: Human Genetics

country: Netherlands

institute: LUMC

description: Library name: ChIP_ubH2B_INPUT_mock

library_source: other

data_processing:
Sequences were trimmed using TrimGalore (Version 0.6.5). Reads were aligned to the GRCh38.p14 primary assembly using bwa-mem tools (BWA (Version 0.7.17). Only uniquely mapping and high-quality reads (> q30) were included in the analyses. Duplicate reads were removed using Samtools (Version 1.11) with fixmate -m and markdup -r settings. Bam files were converted into TagDirectories (with fixed fragment length 150) and UCSC genome tracks using HOMER tools (Version 4.8.2). Example genome tracks were generated in IGV (Version 2.4.3).
A list of 49,948 gene-coordinates of GRCh38 was obtained from the UCSC genome database selecting the “knownCanonical” table containing the canonical transcription start sites per gene. To prevent contamination of binding profiles, genes from this list were selected to be non-overlapping with at least 2 kb between genes and a minimal size of 3 kb (n=9,944). The selected gene coordinates were updated to GRCh38.p14. From this, a set of 3,000 actively transcribed genes was selected by calculating read-densities of BrU-seq data in the first 3kb of the gene in WT cells, using the AnnotatePeaks.pl tool of HOMER with default settings. From these 3,000 actively transcribed genes, subselections of genes were defined based on gene size, as indicated per analysis. Read-density profiles around TSS coordinates were defined using the AnnotatePeaks.pl tool of HOMER, followed by normalizing the averaged metaprofiles to their internal maximum intensity (around the TSS). Individual datasets were subsequently processed into heatmaps or binding profiles using R (Version 4.3.1) and Rstudio (Version 1.1.423).
Assembly: Hg38
Supplementary files format and content: Averages_ubH2BChIP_-5to100kb200bin_Above50-100-150kb.xlsx: excel file containing average readcounts around the TSS (from -5kb to +50/100kb with 200bp bins); averaged are signals of genes with indicated genelength
Supplementary files format and content: GeneList_Details_TSSfiles.txt: TSS coordinates for 9,588 canonical genes selected for downstream analyses; table includes genelength and readcount of BrUseq signal in first 3kb of the genes
Supplementary files format and content: *_TagDir_norm.bw: all files ending on .bw are bigwig files of the indicated condition, ready to be visualized against Hg38

molecule: other

growth_protocol: Cell lines were cultured at 37°C in an atmosphere of 5% CO2 in DMEM GlutaMAX (Thermo Fisher Scientific) supplemented with penicillin/streptomycin (Sigma), and 8% fetal bovine serum (FBS; Bodinco BV or Thermo Fischer Scientific (Gibco)).

extract_protocol:
Chromatin was sonicated to approximately one nucleosome using the Bioruptor Pico (Diagenode), 10 cycles of 30s ON/30 s OFF in a 4°C water bath. ubH2B ChIP was performed using ~28 µg of chromatin with 3 µl of ubH2B antibody (Cell Signaling; #5546S) by overnight incubation at 4 °C. Protein-chromatin-pull down followed with a 1:1 mix of protein A and protein G Dynabeads (Thermo Fisher; 10001D, 10003D). ChIP samples were extensively washed and purified using Qiagen MinElute kit.
Sample libraries were prepared using Hifi Kapa sample prep kit and A-T mediated ligation of Nextflex adapters or xGen UDI-UMI adapters. Samples were sequenced using an Illumina NovaSeq X, using paired-end sequencing with 150 bp from each end.

treatment_protocol: Cells were grown to 80-90% confluency and crosslinked with 0.5 mg/mL disuccinimidyl glutarate (DSG; Thermo Fisher) in PBS for 45 min at room temperature. Cells were washed once with PBS followed by incubation with 1% FA for 20 min at RT. Fixation was stopped by the addition of glycine in PBS to a final concentration of 0.1 M for 3 min at RT. This was followed by washing with cold PBS and collection of the cells in 0.25% Triton X-100, 10 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0), and 20 mM Hepes (pH 7.6) in miliQ. Chromatin was pelleted by centrifugation for 5 min at 400 × g and incubated in 150 mM NaCl, 1 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0) and 50 mM Hepes (pH 7.6) in miliQ for 10 min at 4 °C. Chromatin was again pelleted by centrifugation and resuspended in ChIP-buffer (0.15 % SDS, 1 % Triton X-100, 150 mM NaCl, 1 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0) and 20 mM Hepes (pH 7.6) in miliQ) to a final concentration of 15 × 106 cells/mL.

value: hTERT-immortalized retinal pigment epithelial cells

value: RPE1 iCas9 p53/puro-dKO

value: mock


title: 9SR44806A_B05

description: Gene expression data from the ARC of Oil-treated rat

source_name: Oil-treated, arcuate nucleus of the hypothalamus (ARC), biological replicate 3

value: brain, ARC


title: 9SR44806A_A10

source_name: Oil-treated, arcuate nucleus of the hypothalamus (ARC), biological replicate 1


title: 9SR44806A_A04

description: Gene expression data from the ARC of EB-treated rat

source_name: EB-treated, arcuate nucleus of the hypothalamus (ARC), biological replicate 2

value: EB


title: ChIP_ubH2B_9J24h_rep3

description: Library name: ChIP_ubH2B_9J24h_rep3

value: UV-C 9J/m2, 24hours recovery


title: 9SR44806A_A08

source_name: EB-treated, paraventricular nucleus of the hypothalamus (PVN), biological replicate 3

value: brain, PVN


title: 9SR44806A_A09

description: Gene expression data from the NTS of EB-treated rat

source_name: EB-treated, nucleus of the solitary tract (NTS), biological replicate 3


title: ChIP_ubH2B_9J3h_rep1

description: Library name: ChIP_ubH2B_9J3h_rep1

value: UV-C 9J/m2, 3hours recovery


title: 9SR44806A_A05

source_name: EB-treated, paraventricular nucleus of the hypothalamus (PVN), biological replicate 2


title: ChIP_ubH2B_Mock_rep2

description: Library name: ChIP_ubH2B_Mock_rep2


title: ChIP_ubH2B_9J24h_rep2

description: Library name: ChIP_ubH2B_9J24h_rep2


title: 9SR44806A_A11

source_name: Oil-treated, paraventricular nucleus of the hypothalamus (PVN), biological replicate 1


title: 9SR44806A_B06

source_name: Oil-treated, paraventricular nucleus of the hypothalamus (PVN), biological replicate 3


title: ChIP_ubH2B_9J24h_rep1

description: Library name: ChIP_ubH2B_9J24h_rep1


title: ChIP_ubH2B_9J3h_rep2

description: Library name: ChIP_ubH2B_9J3h_rep2


title: Pla6T_r2 short-read RNAseq

city: Boston

first: Evan

middle: Michael

last: Appleton

state: MA

address: 75 Kneeland St.

institute: Colossal Biosciences

description:
Library name: PC-emC6-SV40_r2
Column name in countTable_hyrax.txt: SF_2

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

organism: Procavia capensis

source_name: Induced pluripotent stem cells

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

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

value: Induced pluripotent stem cells

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


title: ChIP_ubH2B_Mock_rep1

description: Library name: ChIP_ubH2B_Mock_rep1


title: pcF_r1 short-read RNAseq

description:
Library name: pcFib_WT_r1
Column name in countTable_hyrax.txt: WT_1

source_name: Fibroblasts

value: Fibroblasts

value: pcF


title: 9SR44806A_B01

source_name: Oil-treated, nucleus of the solitary tract (NTS), biological replicate 1

value: Sprague-Dawley

value: female


title: Embryo, Hpf40, Genotyping-only, rep1

city: Bergen

first: Jonas

middle: Maurice

last: Brandenburg

address: Thormolensgatan 55

department: Michael Sars Centre

country: Norway

institute: University of Bergen

description:
Library name: Hpf40
BRB-seq, demultiplexed

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

organism: Strongylocentrotus purpuratus

source_name: Embryo

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

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

value: Embryo


title: Embryo, Hpf72, Genotyping-only, rep1

description:
Library name: Hpf72
BRB-seq, demultiplexed


title: 9SR44806A_B02

source_name: Oil-treated, arcuate nucleus of the hypothalamus (ARC), biological replicate 2

value: adult, 90 days old

value: Oil


title: Embryo, Hpf20, Genotyping-only, rep1

description:
Library name: Hpf20
BRB-seq, demultiplexed


title: 9SR44806A_B04

source_name: Oil-treated, nucleus of the solitary tract (NTS), biological replicate 2

value: brain, NTS


title: 9SR44806A_A01

source_name: EB-treated, arcuate nucleus of the hypothalamus (ARC), biological replicate 1


title: pcF_r2 short-read RNAseq

description:
Library name: pcFib_WT_r2
Column name in countTable_hyrax.txt: WT_2


title: Embryo, Hpf15, Genotyping-only, rep2

description:
Library name: Hpf15_F4xM4
BRB-seq, demultiplexed


title: Embryo, Hpf4, Genotyping-only, rep1

description:
Library name: Hpf4_F1xM5
BRB-seq, demultiplexed


title: 9SR44806A_A07

source_name: EB-treated, arcuate nucleus of the hypothalamus (ARC), biological replicate 3


title: Embryo, Hpf12, Genotyping-only, rep1

description:
Library name: Hpf12_F1xM4
BRB-seq, demultiplexed


title: CD11c-KLRG1+CD127- CD8 T cells, rep1

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

description: Library name: AT_1_3

data_processing:
Illumina bcl2fastq software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using TopHat2 algorithm (v2.0.8b)
gene count measurements were obtained using HTSeq algorithm and using refseq annotation
Assembly: mm9
Supplementary files format and content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

source_name: Liver

extract_protocol:
RNA from sorted cells was isolated using RNeasy Micro Kit (QIAGEN) and quantified using nanodrop and Agilent bioanalyzer.
RNA-seq libraries were prepared according to SMART-seq2 protocol, with the following modifications: PCR preamplification to 10-12 cycles, two rounds beads cleanup with 1:1 ratio after cDNA synthesis, and 0.6-0.8 dual beads cleanup for Nextera XT DNA-seq library purification. Each library was bar-coded and then pooled for sequencing run with 50bp single-read sequencing protocol.

treatment_protocol: Male C57BL/6J mice, 6 weeks old, were treated with αCD137 antibody on day 0, 3 and 6 and single cell suspensions were isolated from the livers on day 8. Intrahepatic CD11c+KLRG1+CD127- and CD11c-KLRG1+CD127- CD8 T cells were sorted using BD FACSAria cell sorter (n=4/group).  CD8 T cells were defined as live CD45+MHCII-NK1.1-TCRβ+CD8α+CD4-.

value: Liver

value: CD11c-KLRG1+CD127- CD8 T cells


title: CD11c-KLRG1+CD127- CD8 T cells, rep2

description: Library name: AT_2_3

value: Male C57BL/6J mice, 6 weeks old, were treated with αCD137 antibody on day 0, 3 and 6 and single cell suspensions were isolated from the livers on day 8


title: Embryo, Hpf20, Hpf40, Hpf72

description:
Library name: scLate
10x Genomics


title: Embryo, Hpf5, Genotyping-only, rep1

description:
Library name: Hpf5_F3xM5
BRB-seq, demultiplexed


title: Embryo, Hpf8, Genotyping-only, rep1

description:
Library name: Hpf8_F6xM5
BRB-seq, demultiplexed


title: CD11c+KLRG1+CD127- CD8 T cells, rep4

description: Library name: AT_4_2

value: CD11c+KLRG1+CD127- CD8 T cells


title: 9SR44806A_A06

source_name: EB-treated, nucleus of the solitary tract (NTS), biological replicate 2

value: EB


title: CD11c+KLRG1+CD127- CD8 T cells, rep3

description: Library name: AT_3_2


title: Embryo, Hpf5, Genotyping-only, rep2

description:
Library name: Hpf5_F5xM5
BRB-seq, demultiplexed


title: Embryo, Hpf6, Genotyping-only, rep1

description:
Library name: Hpf6_F8xM5
BRB-seq, demultiplexed


title: ND8_2

city: New York City

first: Ze

state: New York

address: 430 East 29th Street

department: Microbioloy

institute: NYU Grossman School of Medicine

description: Library name: SAMPLE 46

data_processing:
The total RNA-sequencing reads were mapped to the human genome hg38 using STAR (v2.7.7a) with a 2-pass model. The hg38 reference sequence and RefSeq annotation were obtained from the UCSC table browser. The quantification of gene and transcript expression levels was performed using RSEM (v1.3.1), which generated gene-level raw counts and fragments per kilobase of transcript per million mapped reads (FPKM) results in table format. The RNA RSEM data was filtered to include genes with a median FPKM > 1 for downstream analyses. The expression change (Log2FC) of reversine- and AZ3146-treated hCECs compared to DMSO-treated hCECs were calculated using DESeqDataSetFromMatrix and DESeq functions in the R package DESeq2 (v1.34.0), which was used in Fig. 2D, 6C, and Fig. S3B, with the mean for the control being set to zero. For hCEC clones with different degrees of aneuploidy, the raw counts table was normalized using DESeqDataSetFromMatrix, estimateSizeFactors and counts functions in the R package DESeq2, followed by Log2 transformed. The log2-transformed normalized RNA levels were fitted by aneuploidy degrees of hCEC clones with a linear model as the following formula: RNA log2FC ~ β0+β1  × aneuploidy score The t-value of aneuploidy coefficient β1 was used to represent the association between RNA level and aneuploidy degree, as shown in Fig. 2F, 6E and Fig. S3C. A positive (negative) t-value represented the RNA expression of the certain gene increased (decreased) in hCEC clones with higher degree of aneuploidy.  The Log2FC of reversine/AZ3146-treated hCECs and the t-value of aneuploidy coefficient of hCEC clones were used in Fig. 5G, 6A and Fig. S5C-D. For PCA of RNA expression levels for lysosome or proteasome genes in hCEC clones shown in Fig. 5F, the raw count table of all genes obtained from RNAseq was pre-processed using the variance stabilizing transformation function in the DESeq2 package. Then 121 lysosome genes or 46 proteasome genes, as defined by the Kyoto Encyclopedia of Genes and Genomes (KEGG), were used to generate the PCA plot using the plotPCA function in the DESeq2 package. To assess the statistical significance of group separation in PCA plots, we performed permutation tests with 10,000 permutations. For each permutation, we calculated the mean Euclidean distance between groups in PC1-PC2 space as the test statistic. The p-value was determined as the fraction of permuted statistics that exceeded the observed test statistic. This analysis was implemented using custom R scripts with the vegan package (v2.6-4). The separation between diploid and aneuploid groups was considered significant when the permutation test p-value < 0.05.
Assembly: hg38
Supplementary files format and content: The total RNA-sequencing reads were mapped to the human genome hg38 using STAR (v2.7.7a)106 with a 2-pass model. The hg38 reference sequence and RefSeq annotation were obtained from the UCSC table browser. The quantification of gene and transcript expression levels was performed using RSEM (v1.3.1)107, which generated gene-level raw counts and fragments per kilobase of transcript per million mapped reads (FPKM) results in table format.

source_name: immortalized human colon epithelial cells (hCECs)

extract_protocol:
Cells were plated on 6-well plates one day before the collection. On the second day, the cells were examined to ensure their confluency level between 70% to 90%, with normal morphological characteristics. Then the cells were washed twice with PBS and promptly stored at –80°C. Total RNA was extracted using the PicoPure RNA Isolation kit (Life Technologies, Frederick, MD), which included an on-column RNase-free DNase I treatment (QIAGEN, Hilden, Germany), following the manufacturer’s recommendations. To further purify the RNA for sequencing, the QIAGEN RNeasy Mini Kit (QIAGEN, 74106) was used. The concentration and integrity of the RNA were assessed using a 2100 BioAnalyzer (Agilent, Santa Clara, CA).
Sequencing libraries were constructed using the TruSeq Stranded Total RNA Library Prep Gold mRNA kit (Illumina, San Diego, CA) with an input of 250 ng RNA and a 13-cycle final amplification. The resulting libraries were quantified using High Sensitivity D1000 ScreenTape on a 2200 TapeStation (Agilent) and the Qubit 1x dsRNA HS Assay Kit (Invitrogen, Waltham, MA). The samples were equimolarity pooled, and sequencing was carried out on an Illumina NovaSeq6000 SP 100 Cycle Flow Cell v1.5 in paired-end 50 reads mode.

value: TP53 Knockout

value: single-cell-derived clone after reversine treatment


title: Embryo, Hpf12, Genotyping-only, rep2

description:
Library name: Hpf12_F3xM4
BRB-seq, demultiplexed


title: Embryo, Hpf6, Genotyping-only, rep2

description:
Library name: Hpf6_F9xM5
BRB-seq, demultiplexed


title: Embryo, Hpf10, Genotyping-only, rep2

description:
Library name: Hpf10_F7xM4
BRB-seq, demultiplexed


title: CD11c-KLRG1+CD127- CD8 T cells, rep4

description: Library name: AT_4_3


title: CD11c-KLRG1+CD127- CD8 T cells, rep3

description: Library name: AT_3_3


title: Embryo, Hpf3, Genotyping-only, rep1

description:
Library name: Hpf3_F4xM5
BRB-seq, demultiplexed


title: ND8_1

description: Library name: SAMPLE 45

value: immortalized human colon epithelial cells (hCECs)


title: 9SR44806A_A03

description: Gene expression data from the NTS of EB-treated rat

source_name: EB-treated, nucleus of the solitary tract (NTS), biological replicate 1


title: Embryo, SLAMseq + Control, Hpf8, Hpf10 and Hpf24

description:
Library name: sc4sU
10x Genomics


title: Embryo, Hpf8, Genotyping-only, rep2

description:
Library name: Hpf8_F7xM5
BRB-seq, demultiplexed


title: D29_A

description: Library name: SAMPLE 39


title: Embryo, Hpf10, Genotyping-only, rep1

description:
Library name: Hpf10_F5xM4
BRB-seq, demultiplexed


title: ND5_1

description: Library name: SAMPLE 43


title: ND5_2

description: Library name: SAMPLE 44


title: CD11c+KLRG1+CD127- CD8 T cells, rep1

description: Library name: AT_1_2


title: D23_2

description: Library name: SAMPLE 37


title: D22_1

description: Library name: SAMPLE 34


title: D12_batch1_1

description: Library name: SAMPLE 30


title: D12_batch2_2

description: Library name: SAMPLE 33


title: D29_B

description: Library name: SAMPLE 40


title: D12_batch1_2

description: Library name: SAMPLE 31


title: D8_1

description: Library name: SAMPLE 41


title: D10_2

description: Library name: SAMPLE 29


title: D12_batch2_1

description: Library name: SAMPLE 32


title: D23_batch3_2

description: Library name: SAMPLE 38


title: A9_3

description: Library name: SAMPLE 28


title: D23_1

description: Library name: SAMPLE 36


title: A3_3

description: Library name: SAMPLE 25


title: D22_2

description: Library name: SAMPLE 35


title: A6_2

description: Library name: SAMPLE 27


title: D8_2

description: Library name: SAMPLE 42


title: A29_2

description: Library name: SAMPLE 24


title: A24_2

description: Library name: SAMPLE 21


title: A24_1

description: Library name: SAMPLE 20


title: A6_1

description: Library name: SAMPLE 26


title: A26_1

description: Library name: SAMPLE 22


title: A26_2

description: Library name: SAMPLE 23


title: A21_1

description: Library name: SAMPLE 19


title: A20_2

description: Library name: SAMPLE 18


title: A19_2

description: Library name: SAMPLE 16


title: A17_2

description: Library name: SAMPLE 14


title: A19_1

description: Library name: SAMPLE 15


title: C7_5AZ_4

description: Library name: SAMPLE 10


title: A17_1

description: Library name: SAMPLE 13


title: A12_2

description: Library name: SAMPLE 12


title: C7_5AZ_3

description: Library name: SAMPLE 9


title: C7_5AZ_2

description: Library name: SAMPLE 8


title: A12_1

description: Library name: SAMPLE 11


title: C7_Rev_4

description: Library name: SAMPLE 7

value: Reversine


title: C7_Rev_3

description: Library name: SAMPLE 6


title: C7_2

description: Library name: SAMPLE 1

value: untreated


title: C7_DMSO_2

description: Library name: SAMPLE 4

value: DMSO


title: C7_Rev_2

description: Library name: SAMPLE 5


title: MV411_SGI7079_03

city: Guangzhou

first: Peihong

last: Wang

address: No. 1, Panfu Road

department: Department of Hematology

institute: Guangzhou First People's Hospital

description:
Library name: MV411_SGI7079_03
MV411, SGI7079, replicate biosample 3

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: hg38
Supplementary files format and content: tab-delimited text files include FPKM and count 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.


title: C7_DMSO_1

description: Library name: SAMPLE 3


title: MV411_SGI7079_02

description:
Library name: MV411_SGI7079_02
MV411, SGI7079, replicate biosample 2


title: MV411_DMSO_02

description:
Library name: MV411_DMSO_02
MV411, DMSO, replicate biosample 2


title: MOLM13_SGI7079_03

description:
Library name: MOLM13_SGI7079_03
MOLM13, SGI7079, replicate biosample 3


title: MOLM13_DMSO_02

description:
Library name: MOLM13_DMSO_02
MOLM13, DMSO, replicate biosample 2


title: MOLM13_SGI7079_01

description:
Library name: MOLM13_SGI7079_01
MOLM13, SGI7079, replicate biosample 1


title: C7_3

description: Library name: SAMPLE 2


title: MOLM13_SGI7079_02

description:
Library name: MOLM13_SGI7079_02
MOLM13, SGI7079, replicate biosample 2


title: MV411_DMSO_01

description:
Library name: MV411_DMSO_01
MV411, DMSO, replicate biosample 1


title: MV411_DMSO_03

description:
Library name: MV411_DMSO_03
MV411, DMSO, replicate biosample 3


title: MOLM13_DMSO_03

description:
Library name: MOLM13_DMSO_03
MOLM13, DMSO, replicate biosample 3


title: A20_1

description: Library name: SAMPLE 17


title: BEAS2B,HDM+anti IL-6R,24h,6

city: BeiJing

first: Chun

last: Chang

address: 49 North Huayuan Road

institute: Peking University Third Hospital

description:
Library name: Sample18
IL6_6_1

data_processing:
Quality control: Raw reads were filtered using fastp (v0.19.7) to remove adapter contamination, low-quality bases (Qphred ≤ 5 exceeding 50% of read length), and reads containing ambiguous 'N' bases.
Alignment: Clean reads were aligned to the GRCh38 reference genome using HISAT2 (v2.0.5) with default parameters.
Quantification: Gene expression counts were obtained with featureCounts (v1.5.0-p3). FPKM values were calculated for expression normalization.
Differential expression: For samples with biological replicates, DESeq2 (v1.20.0) was used to identify differentially expressed genes (threshold: |log2FC| ≥ 1 & padj ≤ 0.05).
Functional enrichment: GO and KEGG enrichment analyses were performed using clusterProfiler (v3.8.1).
Assembly: The reference genome used was GRCh38 (Genome Reference Consortium Human Build 38), corresponding to the file ebi_39_homo_sapiens_grch38_primary_assembly.
Supplementary files format and content: gene_fpkm.txt: Table with FPKM-normalized expression values for each gene in all samples.

source_name: Lung

extract_protocol:
Total RNA was extracted from cultured cells using the Trizol reagent (Ambion/Invitrogen, USA) according to the manufacturer's instructions. RNA integrity was assessed using an Agilent 2100 Bioanalyzer.
Strand-specific RNA-seq libraries were constructed. mRNA was enriched from total RNA using Oligo(dT) beads and fragmented. First-strand cDNA was synthesized with random hexamers, followed by second-strand synthesis using dUTP instead of dTTP. After end repair, A-tailing, and adapter ligation, the second strand was digested with USER enzyme. The library was then amplified and purified.

value: Lung

value: bronchial epithelial cells


title: MV411_SGI7079_01

description:
Library name: MV411_SGI7079_01
MV411, SGI7079, replicate biosample 1


title: BEAS2B,HDM+anti IL-6R,24h,1

description:
Library name: Sample13
IL6_1_1


title: MOLM13_DMSO_01

description:
Library name: MOLM13_DMSO_01
MOLM13, DMSO, replicate biosample 1


title: BEAS2B,HDM+anti IL-6R,24h,2

description:
Library name: Sample14
IL6_2_1


title: BEAS2B,HDM,24h,3

description:
Library name: Sample9
H3_1

value: HDM


title: BEAS2B,Control,6

description:
Library name: Sample6
C6_1

value: WT


title: BEAS2B,HDM,24h,6

description:
Library name: Sample12
H6_1


title: BEAS2B,HDM,24h,5

description:
Library name: Sample11
H5_1


title: BEAS2B,HDM,24h,2

description:
Library name: Sample8
H2_1


title: BEAS2B,HDM+anti IL-6R,24h,4

description:
Library name: Sample16
IL6_4_1


title: BEAS2B,Control,5

description:
Library name: Sample5
C5_1


title: BEAS2B,HDM,24h,4

description:
Library name: Sample10
H4_1


title: BEAS2B,HDM+anti IL-6R,24h,5

description:
Library name: Sample17
IL6_5_1


title: BEAS2B,Control,4

description:
Library name: Sample4
C4_1


title: BEAS2B,HDM+anti IL-6R,24h,3

description:
Library name: Sample15
IL6_3_1


title: BEAS2B,Control,1

description:
Library name: Sample1
C1_1


title: BEAS2B,Control,3

description:
Library name: Sample3
C3_1