title: 123449-1

first: Hui

last: Yang

address: 320 Yueyang Road

institute: CAS Center for Excellence in Brain Science and Intelligence Technology

description:
CasRx + RPL4 sgRNA2 rep1
CasRx_RPL4_g2_1

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data from the sequencer were first underwent quality control using FastQC.
Next, reads are treated using trim_galore, where illumina adapter sequence and low quality (phred score <20) at the 3’ end were trimmed, and the paired reads were removed if any of the two reads doesn’t meet the minimum length (20bp).
After that, the filtered reads were aligned to human genome using hisat2. For each sample, we count the reads hitted on each transcript using htseq-count.
Genome_build: grch38
Supplementary_files_format_and_content: Matrix table with FPKM values for every gene and every sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: human embryonic kidneys

growth_protocol: HEK293T cell lines were cultured with DMEM (Gibco) supplemented with 10% fetal bovine serum (Gibco), 1% penicillin/streptomycin (Thermo Fisher Scientific) and 0.1 mM non-essential amino acids (Gibco) in an incubator at 37°C with 5% CO2.

extract_protocol:
Cell were collected and  RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: When cells reached 90% confluence, HEK293T cells were passaged at a ratio of 1:4 to 12-well plates. After 12 hrs, 2 μg/well plasmids expressing casRx and gRNA were introduced into cells with Lipofectamine 3000 (Thermo Fisher Scientific) using the standard protocol. EGFP and mCherry positive cells were then collected for RNA sequencing two days later.

value: CasRx + RPL4 sgRNA2


title: wild-type strain T=30 min (pH 8.0), replicate 1

status: Public on Sep 02 2025

type: SRA

city: CERDANYOLA DEL VALLES

first: JOAQUIN

last: ARINO

state: Barcelona

address: ED. IBB

department: Biochemistry & Mol. Biol.

country: Spain

institute: UNIVERSITAT AUTONOMA BARCELONA

description: Library name: WT_T30_rep1

library_source: transcriptomic

data_processing:
Mapping of fastq files to generate SAM files was carried out with the Bowtie2 software (Langmead & Salzberg, 2012) in local / sensitive mode against the GCA_000027005.1 assembly (an average of 92.3% of mapped reads).
The SeqMonk software v1.48.1 (https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/) was employed to analyze the SAM files. Mapped reads were counted using the RNA-Seq pipeline on gene features and differentially expressed genes with respect to time zero were identified using the built-in EdgeR package
Assembly: GCA_000027005.1
Supplementary files format and content: file "All_Datasets_RPKM.xlsx", excel file with "Reads Per Kilobase Million" data for each sample.
Supplementary files format and content: file "Table S3 full Transcriptomics TC.xlsx", excel file conaining the diferentially expressed genes for each condition as defined by the EdgeR package (fold-change log2 >1 or <-1 and p-value < 0.01) plus functional annotations

molecule: total RNA

organism: Komagataella phaffii

source_name: whole cell

growth_protocol: K. phaffii X-33 and its isogenic PJA-001 (crz1) and PJA-007 (rim101) derivatives were grown at 28 °C in YP medium (10 g/L yeast extract, 20 g/L peptone) supplemented with a 20 g/L of glycerol (YP-Gly)

extract_protocol:
Total RNA was extracted with the Ribo Pure™-Yeast kit (Ambion) following the manufacturer’s instructions. The quality was assessed by capillary electrophoresis in a Bioanalyzer equipment and RNA amounts quantified by measuring the A260 in a Nanodrop ND-1000 Spectrophotometer.
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dTTP (non-directional library). The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification, and was checked by Qubit™ assay (Thermofisher) and real-time PCR for quantification and size distribution monitored with a Bioanalyzer.

treatment_protocol: For the analysis of the transcriptional response of K. phaffii to alkalinization of the medium cells were grown overnight on YP-Gly medium, and then cultures were diluted in 100 ml of fresh medium at OD600=0.2 and grown until the OD600 of the cultures reached around 0.6. Then two 50 ml-aliquots were centrifuged (5 min at 1000xg). One aliquot was resuspended in the same volume of  fresh YPGly medium plus 50 mM TAPS pH 5.5 (control cells) or in YPGly supplemented with 50 mM TAPS adjusted to pH 8.0 (stressed cells). Samples (15 ml) were taken immediately after resuspension in medium at pH 5.5 (time=0) and, for each stressed culture, after 15, 30 and 60 min. In all cases samples were placed on ice and immediately centrifuged at 4 °C.

tag: tissue

value: whole cell

tag: cell line

tag: genotype

value: wild-type


title: 123448-3

city: Shanghai

state: Shanghai

country: China

description:
CasRx + RPL4 sgRNA1 rep3
CasRx_RPL4_g1_3

organism: Homo sapiens

tag: treatment

value: CasRx + RPL4 sgRNA1


title: male wt input, rep1

first: Guofeng

last: Cheng

address: #500, Zhennan Road, Shanghai

institute: Tongji University

description: Library name: 28d-M-1-input

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trim_galore (parameters -q 25 --paired --length 50 --trim-n)
Trimmed sequence reads were mapped to S. japonicum reference genome (Assembly PRJNA520774) using STAR (parameters --outFilterMultimapNmax 30 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --genomeLoad NoSharedMemory --sjdbOverhang 140).Then, reads that mapped to ribosomal RNA (rRNA) were excluded.
Assembly: S. japonicum reference genome (Assembly PRJNA520774)
Supplementary files format and content: bed
Library strategy: MeRIP-Seq

molecule: polyA RNA

organism: Schistosoma japonicum

source_name: Anhui

extract_protocol:
regular method for RNA isolation
regular protocol for library construction

tag: Sex

value: male

value: wt


title: Metastatic lymph node, patient 5

city: Turku

first: Diana

last: Lehotina

address: Tykistökatu 6A

country: Finland

institute: University of Turku

description:
Library name: Lymph node 4
Fresh Frozen Spatial transcriptome sequencing

data_processing:
The resulting sequencing data were processed using the Space Ranger HD pipeline (10x Genomics) with the GRCh38 human genome as a reference.
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors_json.json.gz: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv.gz: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: aligned_tissue_image.ipj: the alignment results of tissue images
Supplementary files format and content: cytassist_image.tiff: fluorescence image
Library strategy: Spatial Transcriptomics

source_name: lymph node

extract_protocol:
Human fresh tissue samples were frozen and stored in OCT at −80 °C until use. Sections of 10 μm thickness were obtained using a cryostat and processed according to the manufacturer’s manual (10x Genomics Visium HD Fresh Frozen Tissue Preparation Handbook, CG000763, revision D).
Gene expression libraries were prepared according to the manufacturer’s manual (Visium HD Spatial Gene Expression Reagent Kits User Guide, CG000685, revision B) by using human-specific probes (1000675, 10x Genomics, Pleasanton, CA, USA).

value: lymph node

value: female

tag: metastasis

value: yes


title: male wt input, rep3

description: Library name: 28d-M-3-input


title: Distant lymph node, patient 5

description:
Library name: Lymph node 3
Fresh Frozen Spatial transcriptome sequencing

value: no


title: wild-type strain T=15 min (pH 8.0), replicate 1

description: Library name: WT_T15_rep1


title: male kd, rep2

description: Library name: siMettl3-M26-2B

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trim_galore (parameters -q 25 --paired --length 50 --trim-n)
Trimmed sequence reads were mapped to S. japonicum reference genome (Assembly PRJNA520774) using STAR (parameters --outFilterMultimapNmax 30 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --genomeLoad NoSharedMemory --sjdbOverhang 140).Then, reads that mapped to ribosomal RNA (rRNA) were excluded.
Assembly: S. japonicum reference genome (Assembly PRJNA520774)
Supplementary files format and content: tab-delimited text files including TPM values for each Sample

value: mettl3 KD


title: 123448-1

description:
CasRx + RPL4 sgRNA1 rep1
CasRx_RPL4_g1_1


title: Myelin-Treated-4

city: Indianapolis

first: Joshua

last: Kulas

state: IN

address: 1210 Waterway Blvd Ste. 2000

country: USA

institute: IBRI

description: Library name: Myelin4

data_processing:
Fastq files were aligned with STAR version 2.7.11a and quantified by the featureCounts program from Subread version 2.0.4. Ensembl IDs were converted to gene symbols wih biomaRt. DEGs were found by using the R package DESeq2.
Assembly: GRCh38
Supplementary files format and content: a text file containing the raw counts matrix, csv files containing the relevant DESeq2 results tables with average normalized counts, log2FoldChange, and p-value

source_name: blood

extract_protocol:
Zymo Research Quick-RNA miniprep kit (Zymo Research, R1054, R1055)
Clontech SMARTer Stranded Total RNA-Seq Kit v3 – Pico

value: blood

value: IMG

tag: cell type

value: microglia differentiated from iPSC-derived HPCs


title: male kd, rep1

description: Library name: siMettl3-M26-1B


title: male control, rep2

description: Library name: siCont-M26-2B

value: siCont


title: 123449-3

description:
CasRx + RPL4 sgRNA2 rep3
CasRx_RPL4_g2_3


title: 123370-3

description:
CasRx + LacZ sgRNA rep2
NT_2

value: CasRx + LacZ sgRNA


title: wild-type strain T=0 (pH 5.5), replicate 3

description: Library name: WT_T0_rep3


title: 123449-2

description:
CasRx + RPL4 sgRNA2 rep2
CasRx_RPL4_g2_2


title: Distant lymph node, patient 3

description:
Library name: Lymph node 1
Fresh Frozen Spatial transcriptome sequencing


title: Canis lupus familiaris, retina, rep1

city: guangzhou

first: Zhibin

last: Li

address: tianhe road 600

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

library_source: transcriptomic single cell

data_processing:
Raw data were filtered using a custom script in Cell Ranger v3.0.2 (10X Genomics) and Seurat.
Assembly: GRCh38.p14,MFA1912RKSv2,F.catus_Fca126_mat1.0,UU_Cfam_GSD_1.0,CU_Pguttatus_1,ASM1899790v1,HZGC01,Bangor_MerUng_6.1,serCan2020,bMelUnd1.mat.Z,ASM2559416v1,ASM1176430v1.1,mEriEur2.1,mRatBN7.2,bGalGal1.mat.broiler.GRCg7b,Oreochromis_mossambicus_EIV1,ZJU1.0,GRCm39,Sscrofa11.1,pvi1.1,CAS_Tse_1.0,Cavpor3.0,BCM_Maur_2.0,AmbMex60DD.
Supplementary files format and content: Tab-separated values files and matrix files.

molecule: nuclear RNA

organism: Canis lupus familiaris

source_name: Retina

extract_protocol:
Eyeballs were excised and preserved in ice-cold, oxygenated Hanks Balanced Salt Solution (HBSS). Using fine scissors, the cornea was removed with a circular incision along the ora serrata. The lens and vitreous body were then extracted as thoroughly as possible. The detachment of the retina from the scleral cup was performed using ophthalmic forceps, followed by the careful removal of any retinal pigment epithelium (RPE) adhering to the retina. The isolated retina was washed once with fresh HBSS and immediately frozen in liquid nitrogen. For subsequent dissociation, the samples were transported on dry ice. The dissociated retinal tissue was washed with phosphate-buffered saline (PBS) and cut into smaller pieces, followed by the addition of 100 μL of precooled 0.1 × Lysis Buffer, thorough mixing, and incubation on ice for 5 min. The sample was then washed with 1 mL of precooled wash buffer, and cell debris and larger tissues were removed using 40-μm MACS Smart Strainer filtration. The sample was then centrifuged at 4 °C and 500 ×g for 5 min, after which the supernatant without nuclear particles was discarded. The sample underwent three wash cycles with wash buffer. The pellet was resuspended on ice in cooled, diluted nuclei buffer. Nuclear concentration was determined using a Countess II FL automatic cell counter, ensuring the nuclear suspension concentration was within the appropriate range.
The human retinal cells underwent library construction using a 10X Chromium Single-Cell 3’ Library Kit v3 (PN-1000078) following the guidelines provided by the manufacturer.The other 24 retina cells underwent library construction using DNBelab C4.

value: Retina


title: male control, rep1

description: Library name: siCont-M26-1B


title: wild-type strain T=0 (pH 5.5), replicate 2

description: Library name: WT_T0_rep2


title: wild-type strain T=0 (pH 5.5), replicate 1

description: Library name: WT_T0_rep1


title: 123370-1

description:
CasRx + LacZ sgRNA rep1
NT_1


title: wild-type strain T=15 min (pH 8.0), replicate 2

description: Library name: WT_T15_rep2


title: G3970_high_1

status: Public on Sep 01 2025

city: Dallas

first: Jialiang

last: Wang

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

description: Library name: Sample 7

data_processing:
Sequenced libraries were evaluated with FastQC.
Sequencing reads were mapped to the mouse reference genome (mm10/GRCm38) using STAR (v2.7.2b) and quantified with HTSeq (v0.6.0).
Differential expression analysis was performed using DESeq2 package based on the criteria of false discovery rates (FDR) < 0.05 and log2|FC| ≥ 1.
Assembly: mm10
Supplementary files format and content: genes.results files include transcripts per million mapped reads for each sample.

organism: Mus musculus

extract_protocol:
Ocy454 cells were treated with GLPG3970 for 4 hours at various concentrations. Cells were then washed with ice-cold 1x PBS and collected in RLT lysis buffer with freshly added beta-mercaptoethanol and RNA purification was performed according to the manufacturer's instructions (RNeasy Qiagen kit, Qiagen, Hilden, Germany).
RNA-sequencing was conducted using the BGISEQ-500 platform. RNA samples with RNA integrity values greater than 8.0 were used for mRNA isolation by PAGE, adaptor ligation, and reverse transcription with PCR amplification. PCR products were re-purified by PAGE and dissolved in EB solution, then were heat-denatured and circularized using splint oligo sequences. The library was amplified using phi29 to generate DNA nanoballs which were used for PE50 sequencing.

value: Osteocyte


title: G3970_low_3

description: Library name: Sample 6


title: G3970_high_2

description: Library name: Sample 8


title: 123448-2

description:
CasRx + RPL4 sgRNA1 rep2
CasRx_RPL4_g1_2


title: Ctrl_3

description: Library name: Sample 3

value: Control


title: G3970_low_1

description: Library name: Sample 4


title: G3970_high_3

description: Library name: Sample 9


title: Ctrl_2

description: Library name: Sample 2


title: Ctrl_1

description: Library name: Sample 1


title: G3970_low_2

description: Library name: Sample 5


title: mouse liver, G14.5, 10x Genomics

city: Beijing

first: Cheng-ran

last: Xu

address: NO.5 YIHEYUAN ROAD HAIDIAN DISTRICT, BEIJING, P.R.CHINA

department: School of Basic Medical Sciences

institute: Peking University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cellranger toolkit (v3.1.0; https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) with default settings.
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: liver

extract_protocol:
Mice were anesthetized by intraperitoneal injection of 2,2,2-Tribromoethanol, and then perfused with 10mL pre-warmed (37°C) phosphate-buffered saline (PBS) buffer containing 1 mM EGTA through the inferior vena cava. At the start of perfusion, the portal vein was cut to allow blood to be rinsed off. Subsequently, the liver was perfused and digested using 10mL of pre-warmed 1 mg/ml collagenase IV (Sigma‒Aldrich, C5138) in RIPM 1640 medium (Gibco, 21870076). The digested liver tissues were collected into PBS buffer and filtered using a 70μm cell strainer. The resulting cell suspension was centrifuged at 50 × g for 2 minutes at 4 °C, and the cell pellets were resuspended in RIPM 1640 medium supplemented with 1% fetal bovine serum (FBS). To enrich for viable hepatocytes, Percoll (GE, 17-0891-09) diluted in PBS was added to the cell suspension, followed by centrifugation at 50 × g for 2 minutes. The resulting cell pellets were collected, washed once, and resuspended in RIPM 1640 medium supplemented with 1% FBS.
10x Genomics scRNA-seq; cDNA preparation and library construction were conducted using the Single Cell 3’ Reagent Kit v3 according to the manufacturer’s instructions.

value: liver

value: liver cell

tag: strain


title: Kidney High Fat Diet ZT20 Replicate 3

city: irvine

first: Siwei

last: Chen

state: CA

address: 66304 Verano Road South

department: Computer Science

institute: University of California, Irvine

description:
Kidney harvested at ZT20 ad libitum high fat diet feeding
HFK.tsv: ZT_20_REP_2

data_processing:
Basecalling performed using RTA version 1.18.64
Demultiplexing performed using CASAVA version 1.8.2
Alignment to reference assembly mm10 with Tuxedo bowtie
Mapping results filtering performed using Tuxedo cuffquant
Read counting for each gene and normalization to FPKM values performed using Tuxedo cuffnorm
Assembly: mm10
Supplementary files format and content: FPKM value for each gene in tsv format

source_name: Kidney

extract_protocol:
Total RNA was extracted from kidney with TRIzol (Invitrogen), followed by precipitation with isopropanol and ethanol.
RNA libraries for each group were prepared as described in the TruSeq RNA Sample Preparation v2 Guide (Illumina).

value: Kidney

tag: time of harvest

value: 16 weeks

value: Wild-type

tag: treatment at zt3

value: Ad Libitum High Fat Diet


title: Kidney High Fat Diet ZT20 Replicate 4

description:
Kidney harvested at ZT20 ad libitum high fat diet feeding
HFK.tsv: ZT_20_REP_3


title: Kidney High Fat Diet ZT20 Replicate 1

description:
Kidney harvested at ZT20 ad libitum high fat diet feeding
HFK.tsv: ZT_20_REP_1


title: Kidney High Fat Diet ZT16 Replicate 3

description:
Kidney harvested at ZT16 ad libitum high fat diet feeding
HFK.tsv: ZT_16_REP_2


title: Kidney High Fat Diet ZT12 Replicate 5

description:
Kidney harvested at ZT12 ad libitum high fat diet feeding
HFK.tsv: ZT_12_REP_3


title: Kidney High Fat Diet ZT12 Replicate 4

description:
Kidney harvested at ZT12 ad libitum high fat diet feeding
HFK.tsv: ZT_12_REP_2


title: Kidney High Fat Diet ZT16 Replicate 4

description:
Kidney harvested at ZT16 ad libitum high fat diet feeding
HFK.tsv: ZT_16_REP_3


title: Metastatic lymph node, patient 3

description:
Library name: Lymph node 2
Fresh Frozen Spatial transcriptome sequencing

value: lymph node

value: female

value: yes


title: Kidney High Fat Diet ZT12 Replicate 2

description:
Kidney harvested at ZT12 ad libitum high fat diet feeding
HFK.tsv: ZT_12_REP_1


title: Kidney High Fat Diet ZT8 Replicate 2

description:
Kidney harvested at ZT8 ad libitum high fat diet feeding
HFK.tsv: ZT_8_REP_2


title: Kidney High Fat Diet ZT8 Replicate 1

description:
Kidney harvested at ZT8 ad libitum high fat diet feeding
HFK.tsv: ZT_8_REP_1


title: Kidney High Fat Diet ZT4 Replicate 3

description:
Kidney harvested at ZT4 ad libitum high fat diet feeding
HFK.tsv: ZT_4_REP_1


title: Kidney High Fat Diet ZT0 Replicate 4

description:
Kidney harvested at ZT0 ad libitum high fat diet feeding
HFK.tsv: ZT_0_REP_3


title: Kidney Normal Chow ZT16 Replicate 4

description:
Kidney harvested at ZT16 ad libitum normal chow feeding
NCK.tsv: ZT_16_REP_2

value: Ad Libitum Normal Chow Diet


title: Kidney Normal Chow ZT20 Replicate 1

description:
Kidney harvested at ZT20 ad libitum normal chow feeding
NCK.tsv: ZT_20_REP_1


title: Kidney High Fat Diet ZT0 Replicate 3

description:
Kidney harvested at ZT0 ad libitum high fat diet feeding
HFK.tsv: ZT_0_REP_2


title: Kidney Normal Chow ZT20 Replicate 3

description:
Kidney harvested at ZT20 ad libitum normal chow feeding
NCK.tsv: ZT_20_REP_2


title: Kidney Normal Chow ZT16 Replicate 5

description:
Kidney harvested at ZT16 ad libitum normal chow feeding
NCK.tsv: ZT_16_REP_3


title: Kidney High Fat Diet ZT0 Replicate 1

description:
Kidney harvested at ZT0 ad libitum high fat diet feeding
HFK.tsv: ZT_0_REP_1


title: Kidney Normal Chow ZT12 Replicate 2

description:
Kidney harvested at ZT12 ad libitum normal chow feeding
NCK.tsv: ZT_12_REP_1


title: Kidney Normal Chow ZT20 Replicate 5

description:
Kidney harvested at ZT20 ad libitum normal chow feeding
NCK.tsv: ZT_20_REP_3


title: mouse liver, G0, 10x Genomics

description: 10x Genomics


title: Kidney Normal Chow ZT12 Replicate 5

description:
Kidney harvested at ZT12 ad libitum normal chow feeding
NCK.tsv: ZT_12_REP_3


title: Kidney Normal Chow ZT12 Replicate 3

description:
Kidney harvested at ZT12 ad libitum normal chow feeding
NCK.tsv: ZT_12_REP_2


title: Kidney Normal Chow ZT4 Replicate 2

description:
Kidney harvested at ZT4 ad libitum normal chow feeding
NCK.tsv: ZT_4_REP_1


title: Kidney Normal Chow ZT0 Replicate 5

description:
Kidney harvested at ZT0 ad libitum normal chow feeding
NCK.tsv: ZT_0_REP_3


title: Kidney Normal Chow ZT0 Replicate 1

description:
Kidney harvested at ZT0 ad libitum normal chow feeding
NCK.tsv: ZT_0_REP_1


title: Kidney Normal Chow ZT8 Replicate 5

description:
Kidney harvested at ZT8 ad libitum normal chow feeding
NCK.tsv: ZT_8_REP_3


title: Kidney High Fat Diet ZT4 Replicate 5

description:
Kidney harvested at ZT4 ad libitum high fat diet feeding
HFK.tsv: ZT_4_REP_3


title: Kidney High Fat Diet ZT4 Replicate 4

description:
Kidney harvested at ZT4 ad libitum high fat diet feeding
HFK.tsv: ZT_4_REP_2


title: Kidney Normal Chow ZT8 Replicate 4

description:
Kidney harvested at ZT8 ad libitum normal chow feeding
NCK.tsv: ZT_8_REP_2


title: Kidney High Fat Diet ZT8 Replicate 5

description:
Kidney harvested at ZT8 ad libitum high fat diet feeding
HFK.tsv: ZT_8_REP_3


title: Kidney Normal Chow ZT4 Replicate 4

description:
Kidney harvested at ZT4 ad libitum normal chow feeding
NCK.tsv: ZT_4_REP_3


title: Kidney Normal Chow ZT16 Replicate 1

description:
Kidney harvested at ZT16 ad libitum normal chow feeding
NCK.tsv: ZT_16_REP_1


title: Kidney Normal Chow ZT0 Replicate 4

description:
Kidney harvested at ZT0 ad libitum normal chow feeding
NCK.tsv: ZT_0_REP_2


title: A375 xenograft tumors, ZLD1039 treatment, Day 27, 3

city: Cheng Du

first: Yongxia

last: Zhu

state: Si Chuan

address: Ren Min Road Numer 17

institute: Sichuan Cancer Hospital

data_processing:
CLC Genomics Workbench v 11.0.1
The original image data of the sequencing results were identified using the Bcl2fastq software (v2.17.1.14) for image base recognition, and the original sequencing data were obtained after a preliminary quality analysis.
We utilized the Htseq software (V 0.6.1) to calculate gene expression using fragments per kilobase per million reads.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: A375 cells were propagated in DMEM medium supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
mRNA was extracted from A375 xenograft tumors treated with ZLD1039 (100 mg/kg) or vehicle (n = 3), using the RNeasy pure mRNA bead kit (180244, Qiagen, Hilden, Germany), and screened for quality.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol:
A 100 μL suspension of 1×107 A375 cells in a serum-free medium was injected into the right flanks of BALB/c nude mice via subcutaneous implantation.
When the tumor volume reached approximately 100 mm3, the mice were randomly divided into two groups (n = 5)—the vehicle group and the ZLD1039-treated (100 mg/kg) group. Vehicle or ZLD1039 (10 mg/mL) was administered once daily via oral gavage for 27 d.

value: Melanoma cells

value: WT

value: ZLD1039 treatment

tag: time

value: Day 27


title: Kidney Normal Chow ZT4 Replicate 3

description:
Kidney harvested at ZT4 ad libitum normal chow feeding
NCK.tsv: ZT_4_REP_2


title: HUVEC, siPARK7, 2day, rep3

first: Jian

address: 180 Fenglin Road

institute: Zhongshan hospital

description: Library name: HUVEC_siPARK7_3

data_processing:
For RNA-seq, raw data of FASTQ format were firstly processed through in-house perl scripts and obtained clean data. Then, map the clean reads to the silva database to remove the rRNA. Paired-end clean reads were aligned to the reference genome using Hisat2. Featurecount] was used to count the reads numbers mapped to each gene. EdgeR was used for differential expression analysis.
Assembly: hg38
Supplementary files format and content: For RNA-seq, csv file of FPKM of genes in all samples was provided.

source_name: HUVEC

extract_protocol:
Total RNA was extracted from sorted endothelial cells or HUVECs using TRIzol reagent, with quality assessed by NanoDrop 2000 and Agilent 2100/4200.
For RNA-seq, libraries were constructed by enriching mRNA with polyT, synthesizing cDNA, adding adapters, and amplifying via PCR.

tag: transfection

value: HUVEC


title: A375 xenograft tumors, ZLD1039 treatment, Day 27, 2


title: A375 xenograft tumors, Vehicle, Day 27, 3

value: Vehicle


title: HUVEC, siNC, 2day, rep3

description: Library name: HUVEC_NC3

value: siNC


title: Kidney Normal Chow ZT8 Replicate 1

description:
Kidney harvested at ZT8 ad libitum normal chow feeding
NCK.tsv: ZT_8_REP_1


title: HUVEC, siNC, 2day, rep2

description: Library name: HUVEC_NC2


title: HUVEC, siNC, 2day, rep1

description: Library name: HUVEC_NC1


title: A375 xenograft tumors, Vehicle, Day 27, 2


title: F/B extract_rep2

first: Fuwen

last: Yuan

state: 上海

address: Cailun Road #1200, Pudong New area

institute: Shanghai University of Traditional Chinese Medicine

description:
Library name: Sample 5
AGS_14_10_2

data_processing:
Majorbio Cloud Platform, https://cloud.majorbio
Sequence reads were trimmed for adaptor sequence/low quality sequece (Quality lomit : 0.5)
Trimmed sequence reads were mapped to GRCh38.p13 (parameters-mismatch cost: 2 insertion cost: 3 deletion cost 3 legtn faction: 0.8 semilarity fractions: 0.8)
Read count extraction and normalization were performed using Majorbio Cloud Platform
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text file includes raw counts, TPM for each sample

growth_protocol: A549 cells were mantined in RMPI-1640 supplemented with 10% fetal bovine serum (FBS) in humidified atmshpore with 5% CO2 at 37℃.

extract_protocol:
The total RNA was isolated using the FastPure Cell/Tissue Total RNA Isolation Kit V2 (Vazyme RC112-01; China). The RNA quality was assessed using a Bioanalyzer 2100 (Agilent, USA), 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-seq Library Prep Kit fellowing manufaturer's protocols.

treatment_protocol: Cells were treated with F/B extract or vehicle and cluture for 24 h followed with RNA extraction and sequencing.

value: lung cancer

value: F/B extract


title: F/B extract_rep1

description:
Library name: Sample 4
AGS_14_10_1


title: A375 xenograft tumors, Vehicle, Day 27, 1


title: HUVEC, siPARK7, 2day, rep2

description: Library name: HUVEC_siPARK7_2


title: HUVEC, siPARK7, 2day, rep1

description: Library name: HUVEC_siPARK7_1


title: vehilce_rep2

description:
Library name: Sample 2
AGS_con_2

value: DMSO


title: LHON-RO_1_Day35

city: Gifu

first: Kota

last: Aoshima

state: Gifu

address: 1-25-4 Daigaku-nishi

department: Biofunctional Evaluation

country: Japan

institute: Gifu Pharmaceutical University

description: Library name: Sample 4

data_processing:
bcl2fastq2 v2.20
Assembly: Genome assembly GRCh38 (hg38)
Supplementary files format and content: Tab-delimited text files include RPM values for each sample.

source_name: retinal organoid

growth_protocol: A modified protocol for generating normal ROs was used (Capowski et al., 2019).

extract_protocol:
RNA was extracted using NucleoSpin RNA ІІ (Takara Bio Inc., Kusatsu, Japan).
RNA libraries for RNA-seq were prepared using IDT for Illumina - DNA/RNA UD Indexes, Tagmentation, Nextera XT DNA Library Prep Kit and SMART-Seq mRNA following manufacture's protocols.

value: retinal organoid

value: mtDNA G11778A

value: RO differentiation


title: P6_pre_GEX

city: Seoul

first: Junha

last: Cha

address: Yonsei-Ro 50

department: Department of Biotechnology

country: South Korea

institute: Yonsei University

description:
Library name: P6_pre_GEX
10X Genomics

data_processing:
The barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GEX: GRCh 1.2.0 (TCR: GRCh38-alts-ensembl-3.1.0)
Supplementary files format and content: Tab separated value files and matrix files

source_name: Oropharynx

extract_protocol:
We collected fresh tumor tissues on the day of surgery, which were mechanically and enzymatically dissociated using a gentleMACS dissociator (Miltenyi Biotec, Gladbach Bergisch, Germany, Cat#130-093-235) and the Human Tumor Dissociation Kit (Miltenyi Biotec, Cat#130-095-929), following the manufacturer's instructions. After incubation for 1 hour at 37℃, the resuspended samples were filtered through a 70-µm MACS SmartStrainer (Miltenyi Biotec, Cat#130-098-462) into RPMI-1640 medium (Corning, Inc., Corning, NY, USA) supplemented with 10% fetal bovine serum (Biowest, Riverside, MO, USA) and centrifuged at 300 × g for 10 minutes. The pellet was suspended in PBS containing 2% fetal bovine serum. Tissue-infiltrating lymphocytes were enriched using a Ficoll gradient (Sigma-Aldrich), and the resulting single-cell suspensions were subsequently counted using trypan blue.
Libraries were constructed using the Chromium controller, adhering to the protocol described in the 10x Chromium Next GEM Single Cell 5′ v2 Cell Surface Protein User Guide (CG000330). Initially, cell suspensions were diluted with nuclease-free water to achieve a target cell count of 10,000. These suspensions were then combined with a master mix and loaded with Single Cell 5′ Gel Beads and Partitioning Oil into a Next GEM Chip K. Within the droplets, RNA transcripts from individual cells were uniquely barcoded and reverse-transcribed. Following this, the cDNA molecules were pooled and subjected to PCR enrichment. The amplified cDNA underwent size selection for the 5′ Gene Expression libraries, V(D)J Enriched Libraries, and Cell Surface Protein libraries. For the Cell Surface Protein Library, the cDNA pool was enriched through index PCR. In the case of the V(D)J Enriched Library, the enriched cDNA pool was amplified through two rounds using specific primers. For the 5′ Gene Expression Library, the cDNA pool underwent end repair, addition of a single 'A' base, and ligation of adapters, followed by purification and PCR enrichment. The purified libraries were quantified using qPCR in accordance with the qPCR Quantification Protocol Guide (KAPA) and assessed for quality using the Agilent Technologies 4200 TapeStation. Finally, the libraries were sequenced on the HiSeq platform (Illumina) following the specified read length outlined in the user guide.

treatment_protocol: Patients who were pathologically diagnosed with head and neck cancer and underwent surgical resection at Severance Hospital (Seoul, Republic of Korea) between January 2019 and December 2020 were enrolled. Patients received a single cycle of either intravenous D (1,500 mg) or D+T (1,500 mg + 75 mg) before curative surgical resection. Surgery was planned within 2 to 8 weeks after administration. Radiologic evaluations were conducted at baseline and after neoadjuvant immunotherapy using CT or MRI, prior to surgical resection. All patients underwent surgical resection based on the original clinical and radiological extent of the disease. Adjuvant chemoradiotherapy was planned based on the multidisciplinary team's assessment. Clinical and radiologic surveillance, including physical examinations and cross-sectional imaging, was performed every 3 months for the first 2 years after surgical resection, and then every 6 months. Dose reduction was not permitted for neoadjuvant D+/-T or adjuvant D.

value: Oropharynx

tag: hpv p16

value: negative

tag: ici duration_days

value: D


title: Control-RO_2_Day35

description: Library name: Sample 2


title: F/B extract_rep3

description:
Library name: Sample 6
AGS_14_10_3


title: Jejunum, Unaffected, Rep 4

city: Portland

first: Zheng

last: Xia

state: Oregon

address: 2720 S. Moody Avenue

institute: OREGON HEALTH & SCIENCE UNIVERSITY

description: Library name: TC_60089

data_processing:
Sequence reads were mapped to mm10 and hg38 using STAR_2.7.10b.
Read counts extraction and normalization were performed using RSEM_v1.3.1.
Assembly: GENCODE vM25, GENCODE 41
Supplementary files format and content: .txt (Raw counts)

source_name: jejunum

extract_protocol:
Mouse tissues were harvested 54 days from the last tamoxifen injection. RNA was isolated from mouse and human samples using RNeasy Fibrous Tissue Mini Kit (QIAGEN, cat# 74104). 250ng of RNA was used to prepare sequencing libraries
RNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA library preparation kit and following manufacturers' protocol

treatment_protocol: Mice were injected daily with 70uL of 20mg/mL Tamoxifen for eight consecutive days

value: jejunum

value: Male

tag: age


title: Jejunum, Unaffected, Rep 1

description: Library name: TC_60086


title: Jejunum, DM1, Rep 2

description: Library name: TC_60080


title: vehilce_rep3

description:
Library name: Sample 3
AGS_con_3

value: WT


title: Jejunum, DM1, Rep 1

description: Library name: TC_60079


title: Colon, Unaffected, Rep6

description: Library name: TC_60077

source_name: colon, transverse

value: colon, transverse


title: Colon, Unaffected, Rep7

description: Library name: TC_60078

value: Female


title: vehilce_rep1

description:
Library name: Sample 1
AGS_con_1


title: A375 xenograft tumors, ZLD1039 treatment, Day 27, 1

value: Melanoma cells

value: ZLD1039 treatment

value: Day 27


title: LHON-RO_3_Day35

description: Library name: Sample 6


title: Colon, Unaffected, Rep4

description: Library name: TC_60075

source_name: colon, sigmoid

value: colon, sigmoid


title: Kidney High Fat Diet ZT16 Replicate 1

description:
Kidney harvested at ZT16 ad libitum high fat diet feeding
HFK.tsv: ZT_16_REP_1

value: Kidney

value: 16 weeks

value: Wild-type

value: Ad Libitum High Fat Diet


title: Control-RO_3_Day35

description: Library name: Sample 3

value: retinal organoid

value: RO differentiation


title: Colon, DM1, Rep 7

description: Library name: TC_60071

source_name: colon

value: colon


title: Jejunum, Unaffected, Rep 6

description: Library name: TC_58340_60091


title: Colon, DM1, Rep 5

description: Library name: TC_60069


title: Jejunum, Unaffected, Rep 5

description: Library name: TC_58339_60090


title: Jejunum, Unaffected, Rep 3

description: Library name: TC_60088


title: Blastema_head_5dpa_scATAC-seq, rep1

city: kaifeng

first: Hao

state: Hainan

address: Jinming

institute: Henan University

description:
Library name: scATAC_5dpa_rep1
ATAC: read1 contains cell barcode and UMl; read2 contains ATAC sequences

library_source: genomic single cell

data_processing:
Raw sequencing data were processed using the 10x Genomics Cell Ranger-atac pipeline to generate peak-barcode matrices. The matrices were loaded into Signac for future analyses.
Assembly: DJ_genome_v1
Supplementary files format and content: fragments.tsv.gz and feature_bc_matrix.h5

molecule: genomic DNA

organism: Dugesia japonica

source_name: Head blastema

extract_protocol:
Nuclei were prepared according to the 10X Genomics Chromium single-cell ATAC-seq solution protocol (Nuclei Isolation from Tissue for Single Cell ATAC Sequencing). In brief, amputated heads or blastema were transferred to 1.5 mL tubes, resuspended in 1xLysis Buffer and chopped to small pieces, and lysed on ice for 5 min. Lysed nuclei were diluted into the Wash Buffer and passed through a 40 µm filter. Nuclei was collected by centrifugation at 500 g for 5 min, resuspended in the Diluted Nuclei Buffer, and counted. Finally, nuclei were loaded on a Chromium Controller targeting 7,000 nuclei per sample.
ScATAC-seq libraries were prepared for sequencing following the 10X Genomics single-cell ATAC–seq protocol and sequenced using PE50 sequencing on an Illumina NovaSeq 6000.

value: Head blastema


title: Colon, Unaffected, Rep1

description: Library name: TC_60072


title: Jejunum, DM1, Rep 6

description: Library name: TC_60085

value: jejunum


title: Jejunum, DM1, Rep 5

description: Library name: TC_60083


title: Jejunum, DM1, Rep 4

description: Library name: TC_60082


title: Control-RO_1_Day35

description: Library name: Sample 1


title: Colon, DM1, Rep 2

description: Library name: TC_60064

value: Male


title: Jejunum, DM1, Rep 3

description: Library name: TC_60081


title: Colon, DM1, Rep 1

description: Library name: TC_60063


title: scRNA_DjTcf4_RNAi_trunk

description:
Library name: scRNA_DjTcf4
10x Genomics

data_processing:
Raw sequencing data were processed using the 10x Genomics Cell Ranger pipeline to generate gene expression matrix. The matrices were loaded into Seurat for future analyses.
Assembly: DJ_genome_v1
Supplementary files format and content: barcodes.tsv.gz: list of cell barcodes
Supplementary files format and content: features.tsv.gz: list of gene lDs
Supplementary files format and content: matrix.mtx.gz: gene expresion count data in Matrix Market Exchange Format

source_name: Trunk

extract_protocol:
The Control and DjTcf4 RNAi treatment in 5 dpa trunk fragment samples were collected in a batch experiment. Singular cells were prepared from the pooled tissues and analyzed for single cell transcriptome sequencing.
The libraries were constructed using the Chromium platform and Chromium Single Cell 3’ v3 chemistry. Sequencing was performed using an Illumina nova 6000 sequencer.

value: Trunk

value: RNAi


title: Colon, Unaffected, Rep5

description: Library name: TC_60076

source_name: colon, ascending

value: colon, ascending

value: Female


title: Colon, Unaffected, Rep3

description: Library name: TC_60074


title: Colon, Unaffected, Rep2

description: Library name: TC_58336_60073


title: DjTcf4_RNAi_5dap_rep3

description:
Library name: DjTcf4_RNAi_5dap_rep3
Column name in Gene_expression.txt: DjTcf4_5dpa_3_count

data_processing:
Bowtie2 was used to first remove ribosome RNA reads. Paired-end clean reads were mapped to the D. japonica genome using HISAT2. For each transcribed region, a FPKM value was calculated to quantify the expression levels using RSEM software. The R package DESeq2 was used to identify differentially expressed genes with cutoff values of read counts > 10, FDR < 0.2, and |log2 Fold of Change| > 0.5.
Assembly: DJ_genome_v1
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
RNA was extracted from groups of Control or DjTcf4 RNAi animals using standard Trizol isolation.
The mRNA was captured using Oligo-dT beads. The mRNA was reverse transcribed to synthesize cDNA that was modified by end repairing, A-tailing and adapter ligation. The NGSTM DNA Selection Beads were used to purify target fragments. PCR library amplification was then performed, and sequencing was carried out using the Illumina Novaseq X Plus with a PE150 dual-indexed setup.

tag: sample group


title: Jejunum, Unaffected, Rep 2

description: Library name: TC_60087


title: hiPSC-CMs, micropattern, rep7

city: Paris

first: Jean-Sébastien

last: Hulot

address: Rue Leblanc

country: France

institute: Paris Centre de Recherche Cardiovasculaire

description: Library name: CM-WT-upattern-7

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

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

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

treatment_protocol: 18 mm round micropatterned coverslips were purchased from 4Dcell with custom shape (repeated lines of 30 µm-width separated with a cell repellent). Cells were seeded on day 35 post-differentiation and incubated for one more week before measurements.

value: Human induced pluripotent stem cell-derived cardiomyocytes

value: Wildtype

value: Micropattern

tag: batch


title: Blastema_head_5dpa_scRNA

description:
Library name: scRNA_5dpa
10x Genomics

extract_protocol:
The intact and the 5 dpa head cell samples were collected in a batch experiment. Fifty heads from intact animals and ninety heads from 5 dpa animals were separately collected. Singular cells were prepared from the pooled tissues and analyzed for single cell transcriptome sequencing.
The libraries were constructed using the Chromium platform and Chromium Single Cell 3’ v3 chemistry. Sequencing was performed using an Illumina nova 6000 sequencer.

tag: tissue

value: WT


title: DjTcf4_RNAi_5dap_rep1

description:
Library name: DjTcf4_RNAi_5dap_rep1
Column name in Gene_expression.txt: DjTcf4_5dpa_1_count


title: Blastema_head_intact_scRNA

description:
Library name: scRNA_intact
10x Genomics

source_name: Head

value: Head


title: Colon, DM1, Rep 6

description: Library name: TC_60070


title: Blastema_head_5dpa_scATAC-seq, rep2

description:
Library name: scATAC_5dpa_rep2
ATAC: read1 contains cell barcode and UMl; read2 contains ATAC sequences


title: scRNA_Control_RNAi_trunk

description:
Library name: scRNA_Control
10x Genomics


title: LHON-RO_2_Day35

description: Library name: Sample 5

tag: cell line

value: mtDNA G11778A


title: hiPSC-CMs, micropattern, rep4

description: Library name: CM-WT-upattern-4

tag: genotype


title: Control_RNAi_5dap_rep4

description:
Library name: Control_RNAi_5dap_rep4
Column name in Gene_expression.txt: Control_5dpa_4_count

tag: treatment


title: Control_RNAi_5dap_rep3

description:
Library name: Control_RNAi_5dap_rep3
Column name in Gene_expression.txt: Control_5dpa_3_count


title: Intact_head_5dpa_scATAC-seq, rep2

description:
Library name: scATAC_intact_rep2
ATAC: read1 contains cell barcode and UMl; read2 contains ATAC sequences

source_name: Head intact

value: Head intact


title: Colon, DM1, Rep 3

description: Library name: TC_60067

tag: Sex


title: Colon, DM1, Rep 4

description: Library name: TC_60068


title: hiPSC-CMs, micropattern, rep1

description: Library name: CM-WT-upattern-1


title: Intact_head_5dpa_scATAC-seq, rep1

description:
Library name: scATAC_intact_rep1
ATAC: read1 contains cell barcode and UMl; read2 contains ATAC sequences


title: DjTcf4_RNAi_5dap_rep4

description:
Library name: DjTcf4_RNAi_5dap_rep4
Column name in Gene_expression.txt: DjTcf4_5dpa_4_count


title: hiPSC-CMs, micropattern, rep8

description: Library name: CM-WT-upattern-8


title: DjTcf4_RNAi_intact_rep3

description:
Library name: DjTcf4_RNAi_intact_rep3
Column name in Gene_expression.txt: DjTcf4_intact_3_count

source_name: Intact

value: Intact


title: hiPSC-CMs, nopattern, rep6

description: Library name: CM-WT-nopattern-6


title: hiPSC-CMs, micropattern, rep5

description: Library name: CM-WT-upattern-5


title: hiPSC-CMs, micropattern, rep3

description: Library name: CM-WT-upattern-3


title: hiPSC-CMs, micropattern, rep2

description: Library name: CM-WT-upattern-2


title: Control_RNAi_5dap_rep1

description:
Library name: Control_RNAi_5dap_rep1
Column name in Gene_expression.txt: Control_5dpa_1_count


title: hiPSC-CMs, nopattern, rep5

description: Library name: CM-WT-nopattern-5


title: hiPSC-CMs, micropattern, rep6

description: Library name: CM-WT-upattern-6


title: DjTcf4_RNAi_intact_rep2

description:
Library name: DjTcf4_RNAi_intact_rep2
Column name in Gene_expression.txt: DjTcf4_intact_2_count


title: hiPSC-CMs, nopattern, rep3

description: Library name: CM-WT-nopattern-3


title: DjTcf4_RNAi_intact_rep1

description:
Library name: DjTcf4_RNAi_intact_rep1
Column name in Gene_expression.txt: DjTcf4_intact_1_count


title: hiPSC-CMs, nopattern, rep7

description: Library name: CM-WT-nopattern-7


title: hiPSC-CMs, nopattern, rep8

description: Library name: CM-WT-nopattern-8


title: hiPSC-CMs, nopattern, rep2

description: Library name: CM-WT-nopattern-2


title: Control_RNAi_intact_rep4

description:
Library name: Control_RNAi_intact_rep4
Column name in Gene_expression.txt: Control_intact_4_count


title: Control_RNAi_intact_rep1

description:
Library name: Control_RNAi_intact_rep1
Column name in Gene_expression.txt: Control_intact_1_count


title: hiPSC-CMs, nopattern, rep4

description: Library name: CM-WT-nopattern-4


title: Control_RNAi_intact_rep3

description:
Library name: Control_RNAi_intact_rep3
Column name in Gene_expression.txt: Control_intact_3_count


title: Control_RNAi_intact_rep2

description:
Library name: Control_RNAi_intact_rep2
Column name in Gene_expression.txt: Control_intact_2_count


title: DjTcf4_RNAi_intact_rep4

description:
Library name: DjTcf4_RNAi_intact_rep4
Column name in Gene_expression.txt: DjTcf4_intact_4_count


title: hiPSC, nopattern, rep4

description: Library name: iPS-WT-4

value: Human induced pluripotent stem cells


title: Control_RNAi_5dap_rep2

description:
Library name: Control_RNAi_5dap_rep2
Column name in Gene_expression.txt: Control_5dpa_2_count


title: Pseudomonas qingdaonensis strain S-1(dam+) [MSPT]

first: Lili

last: Liu

address: 301 Yanchang Middle Road

institute: Shanghai Tenth People's Hospital, Tongji University School of Medicine

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: Pseudomonas
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

organism: Pseudomonas qingdaonensis

source_name: Pseudomonas qingdaonensis strain S-1

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: Pseudomonas qingdaonensis strain S-1

value: bacteria

value: transformation of  gene dam cluster

value: no


title: Pseudomonas qingdaonensis strain S-1(dnd+dam+) [MDPT]

value: transformation of  gene dam and dnd cluster


title: Pseudomonas qingdaonensis strain S-1(dnd+) [DPT]

value: transformation of  pf0-1 dnd cluster


title: hiPSC-CMs, nopattern, rep1

description: Library name: CM-WT-nopattern-1


title: hiPSC, nopattern, rep3

description: Library name: iPS-WT-3


title: Pseudomonas qingdaonensis strain S-1 [SPT]


title: hiPSC, nopattern, rep5

description: Library name: iPS-WT-5


title: hiPSC, nopattern, rep1

description: Library name: iPS-WT-1


title: iWAT_p28_SW_F_65

city: Oslo

first: Damien

last: Dufour

address: Sognsvannsvein 9

country: Norway

institute: University of Oslo

description:
Library name: 8-21-SW-F-56_S65_L003
21-SW-F-56_S65

data_processing:
Reads were filtered with fastp, aligned to the mm10 genome with hisat2 and counted using featureCounts.
Differential expression was performed using the DESeq2 package version 1.38.3.
Assembly: mm10
Supplementary files format and content: csv file represents normaliSed read count for every sample and every gene and comparisons between conditions with log2FC, p-values, adjusted p-values

source_name: inguinal white adipose tissue

extract_protocol:
Gene expression profile was analysed for subcutaneous inguinal white adipose tissue from four p21 mice, four delayed-weaning p28 mice and four standard-weaning p28 mice of each sex. RNA extraction was performed using RNeasy Lipid Tissue micro-Kit (Qiagen) following manufacturer instructions.
Sequencing libraries were prepared using the KAPA mRNA HyperPrep kit (Roche). Sequencing was performed on NovaSeqXPlus sequencer (Illumina) with a 25B flow cell using NovaSeqXPlus System Suite: 1.2.0.28691 and BCL Convert: 4.1.23.

value: inguinal white adipose tissue

value: female

tag: group

value: SW

tag: ID


title: RP-3

city: Wuhan

first: Jinzhou

state: Hubei

address: Jiefang Avenue

institute: Tongji Hospital

description: Library name: RP-3

data_processing:
The libraries were sequenced on an Illumina Novaseq 6000  platform and 150 bp paired-end reads were generated.
The clean reads were mapped to the reference genome  using HISAT2 . FPKM  of each gene was calculated and the read counts of each gene were obtained by HTSeq-count .
Assembly: GRCh38.p13
Supplementary files format and content: txt file with FPKM values for each sample

extract_protocol:
Total RNA was extracted using the TRIzol reagent  (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

treatment_protocol: 5% PBS/OH2 intervention for 24 hours

tag: cell type

value: Protate cancer


title: iWAT_p28_SW_F_55

description:
Library name: 7-21-SW-F-55_S64_L003
21-SW-F-55_S64


title: iWAT_p28_SW_M_78

description:
Library name: 9-28-SW-M-78_S66_L003
28-SW-M-78_S66

value: male


title: hiPSC, nopattern, rep2

description: Library name: iPS-WT-2

value: Wildtype


title: RP-2

description: Library name: RP-2

value: WT


title: iWAT_p28_SW_F_36

description:
Library name: 6-21-SW-F-36_S63_L003
21-SW-F-36_S63


title: iWAT_p28_SW_F_30

description:
Library name: 5-21-SW-F-30_S62_L003
21-SW-F-30_S62


title: iWAT_p28_SW_M_54

description:
Library name: 4-21-SW-M-54_S61_L003
21-SW-M-54_S61


title: RP-1

description: Library name: RP-1


title: R5-3

description: Library name: R5-3


title: R5-1

description: Library name: R5-1


title: CP1

description: Library name: CP1


title: CP2

description: Library name: CP2


title: iWAT_p28_DW_F_76

description:
Library name: 21-28-DW-F-76_S78_L003
28-DW-F-76_S78

value: DW


title: iWAT_p28_SW_F_81

description:
Library name: 20-28-SW-F-81_S77_L003
28-SW-F-81_S77


title: iWAT_p28_SW_M_53

description:
Library name: 3-21-SW-M-53_S60_L003
21-SW-M-53_S60


title: CP3

description: Library name: CP3


title: R5-2

description: Library name: R5-2


title: iWAT_p28_SW_F_75

description:
Library name: 19-28-SW-F-75_S76_L003
28-SW-F-75_S76


title: C51

description: Library name: C51


title: iWAT_p28_DW_F_83

description:
Library name: 24-28-DW-F-83_S81_L003
28-DW-F-83_S81


title: iWAT_p28_DW_F_82

description:
Library name: 23-28-DW-F-82_S80_L003
28-DW-F-82_S80


title: iWAT_p28_SW_F_74

description:
Library name: 18-28-SW-F-74_S75_L003
28-SW-F-74_S75


title: iWAT_p28_DW_F_77

description:
Library name: 22-28-DW-F-77_S79_L003
28-DW-F-77_S79


title: SEAM eye organoid, 60 days differentiation

city: Kgs. Lyngby

first: Anne

middle: Zebitz

last: Eriksen

address: Produktions Torvet 423

department: Health Technology

country: Denmark

institute: Technical University of Denamrk

description:
Library name: SEAM46
10X Genomics

data_processing:
Reads were aligned to the GRCh38 (hg38) human reference genome using the Cell Ranger Single-Cell Software Suite (v3.1).
Assembly: GRCh38 (hg38)
Supplementary files format and content: 3 integrated analysis files, processed through the Seurat packege in R. 2 .Rdata-files, 1 .rds file and coresponding R notebook files for each analysis.

source_name: Eye organoid

growth_protocol: SEAM Ocular Culture Differentiation To generate SEAM cultures, hESCs were seeded onto Matrigel-coated dishes at 500 cells/cm². Cultures were maintained in mTeSR1 media for 7-10 days to form colonies. Differentiation was initiated by switching to SEAM differentiation media: GMEM (Life Technologies) with 10% knockout serum replacement (KSR), 1X L-Glutamine, 1X MEM Non-Essential Amino Acids Solution, 1X Penicillin-Streptomycin (10,000 U/mL), 100 mM Sodium Pyruvate, and 55 µM 2-mercaptoethanol. Media changes were performed three times per week, starting with partial changes in the first week, followed by full changes. SEAM structures matured within 4–7 weeks and were analyzed or harvested when pigmented.

extract_protocol:
Frozen vials of freshly isolated adult human iris and SEAM ocular culture (week 7 of differentiation) were used. Viability of single cells was assessed using Trypan Blue staining, and only debris-free suspensions with >80% viability were processed. Cell suspensions were prepared for 10X Genomics Chromium controller.
Cells were processed using the 10X Genomics Chromium controller v3.16 and the Chromium Single Cell 3’ Library and Gel Bead Kit v3.0 with ~10,000 cells as input. Gel beads and cells were partitioned into GEMs, and reverse transcription was performed to tag cDNA with cell barcodes and UMIs. GEMs were broken, and cDNA was amplified and quantified using Agilent Bioanalyzer High Sensitivity chip and Qubit analysis. Libraries were sequenced on a Novaseq 6000 Illumina sequencer (S4 flow cell, 100 bp paired-end reads, 50,000–100,000 reads per cell).

value: Eye organoid


title: iWAT_p28_SW_M_38

description:
Library name: 2-21-SW-M-38_S59_L003
21-SW-M-38_S59


title: iWAT_p28_DW_M_87

description:
Library name: 16-28-DW-M-87_S73_L003
28-DW-M-87_S73


title: C53

description: Library name: C53


title: Adult human iris, Age 64

description:
Library name: IRIS94
10X Genomics

source_name: Iris

value: Iris

value: whole tissue


title: SEAM eye organoid, 55 days differentiation

description:
Library name: SEAM48
10X Genomics


title: SEAM eye organoid, 70 days differentiation

description:
Library name: SEAM42
10X Genomics


title: Adult human iris, Age 50

description:
Library name: IRIS92
10X Genomics


title: iWAT_p28_DW_M_80

description:
Library name: 14-28-DW-M-80_S71_L003
28-DW-M-80_S71


title: iWAT_p28_DW_M_79

description:
Library name: 13-28-DW-M-79_S70_L003
28-DW-M-79_S70


title: iWAT_p28_SW_M_124

description:
Library name: 12-28-SW-M-124_S69_L003
28-SW-M-124_S69


title: Adult human iris, age 74

description:
Library name: IRIS91
10X Genomics


title: PF-201, 30 µM, rep 5

city: Montreal

first: Bernard

last: Robaire

address: 3655 Prom. Sir-William-Osler

country: Canada

institute: McGill University

description:
Library name: N5PF
All chemicals (TGSA, D-8, and PF-201) were compared to DMSO samples. Therefore, DMSO's processed data files are the same as the files for other chemicals. I.e. within each processed file, all 5 biological replicates of DMSO are included.

data_processing:
After library quality control, different libraries were pooled based on the effective concentration and targeted data amount, then subjected to Illumina sequencing. The basic principle of sequencing is "Sequencing by Synthesis", where fluorescently labeled dNTPs, DNA polymerase, and adapter primers are added to the sequencing flow cell for amplification. As each sequencing cluster extends its complementary strand, the addition of each fluorescently labeled dNTP releases a corresponding fluorescence signal. The sequencer captures these fluorescence signals and converts them into sequencing peaks through computer software, thereby obtaining the sequence information of the target fragment.
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 1 reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
For DESeq2 with biological replicates: Differential expression analysis for two conditions/groups was performed using the DESeq2 R package (1.20.0). DESeq2 provides statistical programs for determining differential expression in digital gene expression data using models based on negative binomial distribution. The resulting P-value is adjusted using the Benjamini and Hochberg’s methods to control the error discovery rate. The corrected P-value ≤ 0.05 & |log2(foldchange)| ≥ 1 was set as the threshold of significant differential expression.
Assembly: GRCh38/hg38
Supplementary files format and content: Matrix table containing raw count, FPKM value, and normalized abundance output (from DESeq2) of each gene for each sample and each treatment group

source_name: Ovary

growth_protocol: KGN human granulosa cells were cultured in DMEM/F-12 medium supplemented with 10% fetal bovine serum (FBS) and 0.5% penicillin-streptomycin in a humidified atmosphere at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted using the Rneasy Plus Mini kit (Qiagen). The concentration and purity of extracted RNA was assessed using a NanoDrop 2000 spectrophotometer.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

treatment_protocol: KGN cells were exposed to vehicle control (DMSO) or 30 µM of TGSA, D-8, or PF-201 for 48 hours.

value: Ovary

value: KGN

value: granulosa-like tumor cell


title: C52

description: Library name: C52


title: iWAT_p28_SW_M_37

description:
Library name: 1-21-SW-M-37_S58_L003
21-SW-M-37_S58


title: PF-201, 30 µM, rep 3

description:
Library name: N3PF
All chemicals (TGSA, D-8, and PF-201) were compared to DMSO samples. Therefore, DMSO's processed data files are the same as the files for other chemicals. I.e. within each processed file, all 5 biological replicates of DMSO are included.


title: PF-201, 30 µM, rep 4

description:
Library name: N4PF
All chemicals (TGSA, D-8, and PF-201) were compared to DMSO samples. Therefore, DMSO's processed data files are the same as the files for other chemicals. I.e. within each processed file, all 5 biological replicates of DMSO are included.


title: iWAT_p28_SW_M_85

description:
Library name: 11-28-SW-M-85_S68_L003
28-SW-M-85_S68


title: D-8, 30 µM, rep 5

description:
Library name: N5D8
All chemicals (TGSA, D-8, and PF-201) were compared to DMSO samples. Therefore, DMSO's processed data files are the same as the files for other chemicals. I.e. within each processed file, all 5 biological replicates of DMSO are included.


title: PF-201, 30 µM, rep 1

description:
Library name: N1PF
All chemicals (TGSA, D-8, and PF-201) were compared to DMSO samples. Therefore, DMSO's processed data files are the same as the files for other chemicals. I.e. within each processed file, all 5 biological replicates of DMSO are included.


title: PF-201, 30 µM, rep 2

description:
Library name: N2PF
All chemicals (TGSA, D-8, and PF-201) were compared to DMSO samples. Therefore, DMSO's processed data files are the same as the files for other chemicals. I.e. within each processed file, all 5 biological replicates of DMSO are included.


title: iWAT_p28_SW_M_84

description:
Library name: 10-28-SW-M-84_S67_L003
28-SW-M-84_S67


title: D-8, 30 µM, rep 2

description:
Library name: N2D8
All chemicals (TGSA, D-8, and PF-201) were compared to DMSO samples. Therefore, DMSO's processed data files are the same as the files for other chemicals. I.e. within each processed file, all 5 biological replicates of DMSO are included.


title: C2C12 myoblasts treated with 6 micromolar PFOS rep 4

city: Clemson

first: William

last: Baldwin

state: SC

address: 132 Long Hall

institute: Clemson University

description: Library name: PFOS_6_4

data_processing:
PE150 strategy by Novogene. HISAT2 was used to map clean reads.
Assembly: GRCm39
Supplementary files format and content: Excel file containing raw counts performed by Novogene named "gene_count_C2C12_PFOS.xls"

extract_protocol:
Cells were grown to 100% confluency in petri dishes and treated with 0, 2, or 6 micromolar PFOS for 24 hours. RNA was extracted with TRIzol (Life Technology, Carlsbad, CA USA) and chloroform. Quality was checked via Nanodrop.
Library construction was performed by Novogene (Sacramento, CA USA) using messenger RNA purified from total RNA. Quality was checked with Qubit (Thermo Fisher Scientific, Walkham, MA USA).


title: D-8, 30 µM, rep 1

description:
Library name: N1D8
All chemicals (TGSA, D-8, and PF-201) were compared to DMSO samples. Therefore, DMSO's processed data files are the same as the files for other chemicals. I.e. within each processed file, all 5 biological replicates of DMSO are included.


title: iWAT_p28_SW_F_73

description:
Library name: 17-28-SW-F-73_S74_L003
28-SW-F-73_S74


title: iWAT_p28_DW_M_86

description:
Library name: 15-28-DW-M-86_S72_L003
28-DW-M-86_S72


title: C2C12 myoblasts treated with 6 micromolar PFOS rep 2

description: Library name: PFOS_6_2


title: TGSA, 30 µM, rep 5

description:
Library name: N5TGSA
All chemicals (TGSA, D-8, and PF-201) were compared to DMSO samples. Therefore, DMSO's processed data files are the same as the files for other chemicals. I.e. within each processed file, all 5 biological replicates of DMSO are included.

value: 30 µM TGSA


title: C2C12 myoblasts treated with 2 micromolar PFOS rep 3

description: Library name: PFOS_2_3


title: C2C12 myoblasts treated with 6 micromolar PFOS rep 3

description: Library name: PFOS_6_3


title: D-8, 30 µM, rep 3

description:
Library name: N3D8
All chemicals (TGSA, D-8, and PF-201) were compared to DMSO samples. Therefore, DMSO's processed data files are the same as the files for other chemicals. I.e. within each processed file, all 5 biological replicates of DMSO are included.


title: C2C12 myoblasts treated with 6 micromolar PFOS rep 1

description: Library name: PFOS_6_1


title: C2C12 myoblasts treated with 2 micromolar PFOS rep 2

description: Library name: PFOS_2_2


title: TGSA, 30 µM, rep 4

description:
Library name: N4TGSA
All chemicals (TGSA, D-8, and PF-201) were compared to DMSO samples. Therefore, DMSO's processed data files are the same as the files for other chemicals. I.e. within each processed file, all 5 biological replicates of DMSO are included.


title: C2C12 myoblasts treated with 2 micromolar PFOS rep 4

description: Library name: PFOS_2_4


title: C2C12 myoblasts treated with 2 micromolar PFOS rep 1

description: Library name: PFOS_2_1


title: TGSA, 30 µM, rep 3

description:
Library name: N3TGSA
All chemicals (TGSA, D-8, and PF-201) were compared to DMSO samples. Therefore, DMSO's processed data files are the same as the files for other chemicals. I.e. within each processed file, all 5 biological replicates of DMSO are included.


title: C2C12 myoblasts treated with 0 micromolar PFOS rep 4

description: Library name: PFOS_0_4


title: Control, rep 4

description:
Library name: N4DMSO
All chemicals (TGSA, D-8, and PF-201) were compared to DMSO samples. Therefore, DMSO's processed data files are the same as the files for other chemicals. I.e. within each processed file, all 5 biological replicates of DMSO are included.

value: DMSO


title: D-8, 30 µM, rep 4

description:
Library name: N4D8
All chemicals (TGSA, D-8, and PF-201) were compared to DMSO samples. Therefore, DMSO's processed data files are the same as the files for other chemicals. I.e. within each processed file, all 5 biological replicates of DMSO are included.


title: C2C12 myoblasts treated with 0 micromolar PFOS rep 2

description: Library name: PFOS_0_2


title: TGSA, 30 µM, rep 1

description:
Library name: N1TGSA
All chemicals (TGSA, D-8, and PF-201) were compared to DMSO samples. Therefore, DMSO's processed data files are the same as the files for other chemicals. I.e. within each processed file, all 5 biological replicates of DMSO are included.


title: C2C12 myoblasts treated with 0 micromolar PFOS rep 1

description: Library name: PFOS_0_1


title: TGSA, 30 µM, rep 2

description:
Library name: N2TGSA
All chemicals (TGSA, D-8, and PF-201) were compared to DMSO samples. Therefore, DMSO's processed data files are the same as the files for other chemicals. I.e. within each processed file, all 5 biological replicates of DMSO are included.


title: Control, rep 5

description:
Library name: N5DMSO
All chemicals (TGSA, D-8, and PF-201) were compared to DMSO samples. Therefore, DMSO's processed data files are the same as the files for other chemicals. I.e. within each processed file, all 5 biological replicates of DMSO are included.


title: amygdala, female, batch 2

city: Murcia

first: Elena

last: Garcia-Calero

address: Avda. Buenavista

institute: University of Murcia

description:
Library name: AF_2
10x Genomics

data_processing:
The demultiplexing, barcoded processing and gene counting were made using the Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Mouse GRCm39-2024-A
Supplementary files format and content: Hierarchical Data Format (HDF5 or H5). H5 is a binary format that can compress and access data much more efficiently than text formats such as MEX, which is especially useful when dealing with large datasets. H5 files are supported in both R and Python.

source_name: neural tissue

extract_protocol:
Nuclei were isolated using the Minute™ single nucleus isolation kit designed for neuronal tissue/cells (Cat# BN-020, Invent Biotechnologies)
Chromium Single Cell products: Chromium Next GEM Single Cell 3' Kit v3.1 (Cat#1000269), Chromium Next GEM Chip G Single Cell Kit (Cat# 1000127), Dual Index Kit TT Set A, (GEX Library; Cat# 1000215). The four library constructions were performed according to the manufacturer’s instructions. The final libraries were quantified using Qubit 4 fluorometer (Invitrogen).

value: neural tissue

value: telencephalon

value: glia, neurons

value: no treatment


title: Control, rep 2

description:
Library name: N2DMSO
All chemicals (TGSA, D-8, and PF-201) were compared to DMSO samples. Therefore, DMSO's processed data files are the same as the files for other chemicals. I.e. within each processed file, all 5 biological replicates of DMSO are included.


title: amygdala, female, batch 1

description:
Library name: AMM_A
10x Genomics


title: Control, rep 3

description:
Library name: N3DMSO
All chemicals (TGSA, D-8, and PF-201) were compared to DMSO samples. Therefore, DMSO's processed data files are the same as the files for other chemicals. I.e. within each processed file, all 5 biological replicates of DMSO are included.


title: amygdala, male, batch 3

description:
Library name: AM_3
10x Genomics


title: Control, rep 1

description:
Library name: N1DMSO
All chemicals (TGSA, D-8, and PF-201) were compared to DMSO samples. Therefore, DMSO's processed data files are the same as the files for other chemicals. I.e. within each processed file, all 5 biological replicates of DMSO are included.


title: amygdala, male, batch 2

description:
Library name: AM_2
10x Genomics


title: G-G_Case28_0W

city: Nagoya

first: Yoshifumi

last: Kanayama

address: 1 kawasumi, Mizuho-cho, Mizuho-ku

institute: Nagoya City University Graduate school of Medical Sciences

description: Library name: G-G_Case28_0W

data_processing:
Fastq files were processed using an RNA-seq integrative pipeline, ikra (v2.0.1).
Assembly: GRCh38
Supplementary files format and content: CSV files include scaledTPM values for each sample

source_name: periheral blood

extract_protocol:
Total RNA extraction using Trizol reagent
RNA libraries for RNA-seq were prepared using SMART-Seq v4 Ultra Low Input RNA Kit, Nextera XT DNA Library Prep Kit.

treatment_protocol: Guselkumab 100 mg is given subcutaneously at Week 0 and again at Week 4, followed by a maintenance phase where 100 mg is administered subcutaneously every 8 weeks. Peripheral blood sampling was performed before treatment and at Weeks 4 and 12.

value: periheral blood

value: Lymphocyte


title: G-G_Case27_12W

description: Library name: G-G_Case27_12W

value: Guselkumab


title: G-G_Case27_4W

description: Library name: G-G_Case27_4W


title: mouse hepatocyte,P4L,Acss2HMKO,CUT&RUN,rep1

first: Cheng-ran

address: NO.5 YIHEYUAN ROAD HAIDIAN DISTRICT, BEIJING, P.R.CHINA

institute: Peking University

description: Library name: P4L_Acss2KO_H3K27ac_rep1

library_source: genomic

data_processing:
The quality of CUT&RUN sequencing data (R1 and R2 fastq files) was assessed using FastQC (v0.11.3) with default parameters. The index, primer, and adapter sequences were trimmed using Trimmomatic (v0.38) with the command “java jar trimmomatic-0.38.jar PE -phred33 fasq1.file fastq2.file ILLUMINACLIP: fasta.file:2:30:10 LEADING:3 TAILING:3 SLIDINGWINDOW:4:15 MINLEN:36”. The trimmed fastq data were aligned to the reference genome mm10 using Bowtie2 (v2.2.5) with default parameters. Only reads with a mapping quality >= 30 were retained for further analysis using SAMtools (v1.3.1). Duplicate PCR reads were excluded using the command “samtools sort in.bam|samtools rmdup -s -out bam”. For downstream analyses, we used Homer (v4.6) to calculate tags per 10 million (TP10M) values with the parameters “makeUCSCfile out_dir –o out.bdg –name sample_name –fragLength 150 –avg -fsize 1e20” and stored the resulting data in bedGraph format.The peaks for H3K27ac and STAT3 CUT&RUN were called using MACS (v1.4.2) with the parameter “-p 1e-3”.Regions overlapping with ENCODE blacklisted genomic regions or located in the mitochondrial or Y chromosome were excluded from the subsequent analyses.
Assembly: mm10
Supplementary files format and content: bedgraph(.bedGraph.gz) and bed(.nbl.bed)
Library strategy: CUT&Run

source_name: liver

extract_protocol:
Mouse hepatocytes isolation was performed as previously reported. Mice were anesthetized by intraperitoneal injection of 2,2,2-tribromoethanol and then perfused through the inferior vena cava with 10 mL of pre-warmed (37°C) phosphate-buffered saline (PBS) containing 1 mM EGTA. The portal vein was cut at the start of perfusion to allow blood clearance. The liver was then perfused and digested with 10 mL of pre-warmed 1 mg/mL collagenase IV (Sigma-Aldrich, C5138) in RPMI 1640 medium (Gibco, 21870076). The digested liver tissue was collected into PBS and filtered through a 70 μm cell strainer. The cell suspension was centrifuged at 50 × g for 2 minutes at 4°C, and the cell pellets were resuspended in RPMI 1640 medium supplemented with 1% fetal bovine serum (FBS). To enrich for viable hepatocytes, Percoll (GE, 17-0891-09) diluted in PBS was added to the cell suspension, followed by centrifugation at 50 × g for 2 minutes. The cell pellets were then collected, washed once, and resuspended in RPMI 1640 medium supplemented with 1% FBS. Smart-seq3xpress scRNA-seq experiments was performed according to the published procedure(Hagemann-Jensen et al., 2022). Briefly, purified single hepatocytes were manually picked with a microcapillary pipette under a microscope and transferred into the 384-well PCR plates containing 0.3 μL of lysis buffer and 3 μL of silicone oil (Merck, 317667). The mRNA was reverse transcribed into cDNA using 0.2 μL of dispensed RT mix. The cDNA was then amplified using 0.6 μL PCR mix. The library of each cell was constructed separately using the TruePrep DNA Library Prep Kit (Vazyme, TD501)
CUT&RUN experiments were performed following the protocol of Skene et al.(PMID: 29651053). Approximately 10,000–20,000 cells were collected per reaction and incubated with antibodies against STAT3 (Active Motif, #39133, 1 µL per reaction) and H3K27ac (Cell Signaling Technology, #12640, 1 µL per reaction). DNA libraries were prepared using the KAPA Hyper Prep Kit (Kapa Biosystems, #KK8502) and purified using VAHTS DNA Clean Beads (Vazyme, #N411-03).

value: liver

value: hepatocyte

tag: strain

tag: Stage

value: female


title: mouse hepatocyte,P4L,Acss2HMKO,CUT&RUN,rep2

description: Library name: P4L_Acss2KO_H3K27ac_rep2


title: G-G_Case28_4W

description: Library name: G-G_Case28_4W


title: G-G_Case28_12W

description: Library name: G-G_Case28_12W


title: mouse hepatocyte,P4L,WT,CUT&RUN,rep1

description: Library name: P4L_Acss2WT_H3K27ac_rep1


title: G-G_Case27_0W

description: Library name: G-G_Case27_0W


title: G-G_Case26_12W

description: Library name: G-G_Case26_12W


title: C2C12 myoblasts treated with 0 micromolar PFOS rep 3

description: Library name: PFOS_0_3


title: mouse hepatocyte,G14.5,Il6stHMKO,CUT&RUN,rep2

description: Library name: G14.5_Il6stKO_Stat3_rep2


title: Multiplex of heart cells from eoEAM model

city: Cincinnati

first: Nives

last: Zimmermann

state: OH

address: 231 Albert Sabin Way, CVC Room 1925

department: Pathology and Laboratory Medicine

institute: University of Cincinnati

description:
Library name: Sample 1
BC001= control peptide= a790; BC002 and BC003= myocarditic peptide= a614; BC004= unchallenged= "control sample"

data_processing:
Raw FASTQ files were processed using Cell Ranger v7.1.0 (10x Genomics). The pipeline used the mouse reference transcriptome refdata-gex-mm10-2020-A and a custom probe set (Chromium_Mouse_Transcriptome_Probe_Set_v1.0.1_mm10-2020-A.csv). Chemistry was automatically detected, and background probe filtering was enabled . Each sample was demultiplexed using its associated probe barcodes, with sample a614 with BC002 and BC003, sample a790 with BC001, and sample control with BC004. Cell Ranger generated raw and filtered feature-barcode matrices in HDF5 format, which contain UMI counts per gene (row) and per cell-associated barcode (column).
Assembly: Mouse mm10 (refdata-gex-mm10-2020-A)
Supplementary files format and content: HDF5 files containing raw and filtered feature-barcode matrices generated by 10x Genomics Cell Ranger

source_name: heart

extract_protocol:
The heart single cell suspensions were prepared as per 10X genomics single cell protocol (CG00053 Rev C). Briefly, the hearts were cut into halves using 4-chamber cut, and half a heart was saved for histology, while the other half for preparation of single cell suspension. Heart tissue was minced, followed by enzymatic digestion (2.2mg/mL Collagenase IV and 1.5mg/mL Dispase II) at 37°C for 45 minutes. Subsequently, samples were filtered through a 40µm filter, and red blood cells were lysed (eBioscience RBC Lysis Buffer). Cells were then resuspended in RPMI supplemented with 10%FBS and filtered through 30 µm MACS cell strainer. The cells were counted to determine concentration and viability using a hemocytometer after which they were subsequently fixed for chromium fixed RNA profiling. The fixation was done following 10X genomics Fixation of Cells & Nuclei for Chromium Fixed RNA Profiling protocol (CG000478 | Rev C). Briefly, the heart single cell suspensions were centrifuged at 400g and resuspended in Fixation Buffer, followed by storage at 4°C for 16-24 hours. Following a spin at 850g for 5 minutes at room temperature (22°C), the sample pellet is resuspended in chilled Quenching Buffer, and cell concentration is determined. Pre-warmed Enhancer and glycerol are added prior to storing cells -80°C.
Library construction was performed using the Chromium Fixed RNA Profiling Reagent Kit (10x Genomics) according to the manufacturer’s protocol (User Guide CG000527). Fixed cells were hybridized overnight with mouse transcriptome probe pairs and labeled with CMOs (BC001–BC004). Following CMO-based barcoding, cells were pooled and subjected to GEM (gel bead-in-emulsion) generation using the Chromium X instrument. Within each GEM, gel beads dissolved to release barcoded primers, and fixed cells lysed to expose hybridized RNA. Probe ligation and incorporation of barcoding primers occurred within GEMs. The primers included Illumina Read 1 (Read 1T), a 16 bp 10x GEM barcode, a 12 bp unique molecular identifier (UMI), and Capture Sequence 1. After GEMs were broken, Silane DynaBeads were used for cleanup, followed by pre-amplification and SPRIselect size selection. During library construction, P5 and P7 sequences, Illumina sample indices (i5, i7), and Read 2 (Read 2S) adapters were added to generate sequencing-ready libraries. Libraries were sequenced on a NovaSeq X Plus (10B flow cell) with the following read configuration: R1: 28 cycles, i7: 10 cycles, i5: 10 cycles, R2: 90 cycles.

treatment_protocol: IL-5tg received subcutaneous immunizations on days 0 and 7 of 100 μg myosin heavy chain α (MyHCα) 614 peptide (Ac-SLKL MATL FSTY ASAD), or 790 peptide (Ac-IQAQ ARGQ LMRI EFKK) emulsified in complete Freund’s adjuvant (CFA) supplemented to 5 mg/ml heat-killed Mycobacterium tuberculosis strain H37Ra. On day 0, mice also received 500 ng pertussis toxin intraperitoneally.

value: heart

value: heart single cell suspension

value: CD2.IL5 transgenic

value: none, control peptide or myocarditic peptide


title: G-G_Case26_4W

description: Library name: G-G_Case26_4W


title: mouse hepatocyte,G14.5,Il6stHMKO,CUT&RUN,rep1

description: Library name: G14.5_Il6stKO_Stat3_rep1


title: G-G_Case26_0W

description: Library name: G-G_Case26_0W


title: mouse hepatocyte,G14.5,WT,CUT&RUN,rep3

description: Library name: G14.5_Il6stWT_Stat3_rep3


title: G-G_Case25_12W

description: Library name: G-G_Case25_12W


title: mouse hepatocyte,P4L,WT,CUT&RUN,rep2

description: Library name: P4L_Acss2WT_H3K27ac_rep2


title: G-G_Case25_4W

description: Library name: G-G_Case25_4W


title: mouse hepatocyte,G14.5,WT,CUT&RUN,rep1

description: Library name: G14.5_Il6stWT_Stat3_rep1


title: G-G_Case24_0W

description: Library name: G-G_Case24_0W


title: G-G_Case25_0W

description: Library name: G-G_Case25_0W


title: TSK, skin, scRNAseq

city: los angeles

first: Sandra

last: Orsulic

state: california

address: 10833 Le conte ave

department: OBGYN

institute: UCLA

description:
Library name: Sample 2
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v9.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
scRNA-seq
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Skin

extract_protocol:
Skin collected from the flanks fof WT and TSK mice were pooled and minced into 1mm pieces. Tissue was further dissociated by enzymatic digestion by rotating at 37°C for 60 minutes with 10 mg/ml Collagenase I, 5 mg/ml collaganase IV, 10 mg/ml Collagenase D,and 5mg/ml DNAse I in DPBS. After dissociation, the suspension was strained (70 micron strainer) followed by centrifugation (8 minutes at 300g). Red blood lysis buffer (Thermo Fisher) was used followed by dead cell removal (STEMCELL) to deplete the samples of erythrocytes and dead cells, respectively according to the manufacturer’s instructions. Finally, cells were resuspended in 0.04% BSA-PBS solution at a concentration of 700-1000 cells/microliter without selection for specific cell types.
Library construction was performed according to the manufacturer’s instructions (Next GEM 3’ Gene Expression v3, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI), and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR, and the appropriate-sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, single-end constructs were added

value: Skin

value: epithelial

value: TSK

value: Male

value: 6-8 weeks old


title: G-G_Case24_4W

description: Library name: G-G_Case24_4W


title: root nodule, cpop1_21dpi_rep3

city: Beijing

first: Yufang

last: Tian

address: No. 1 West Beichen Road, Chaoyang District

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

data_processing:
Sequence raw reads were filtered by OAPnuke. Align clean reads to genome sequences HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts) using Bowtie2 v2.2.5.
Assembly: Lotusjaponicus_Gifu_v1.3
Supplementary files format and content: tab-delimited text file include FPKM values for each samples

organism: Lotus japonicus

source_name: root nodule

growth_protocol: The L. japonicus seedlings were inoculated with rhizobia M. loti MAFF 303099 strain three days after transferring to vermiculite.

extract_protocol:
RNA samples was extracted from L. japonicus or soybean tissues using the RNeasy® Plant Mini Kit (QIAGEN, 74904)
DNBSEQ Transcriptome

value: root nodule

tag: time

value: 21 dpi


title: G-G_Case22_12W

description: Library name: G-G_Case22_12W

value: periheral blood


title: root nodule, cpop1_21dpi_rep2


title: WT, breast tumor, scRNAseq

description:
Library name: Sample 1
10x Genomics

source_name: subcutaneous tumor

extract_protocol:
Subcutaneous Tumors collected from the flanks fof WT and TSK mice were pooled and minced into 1mm pieces. Tissue was further dissociated by enzymatic digestion by rotating at 37°C for 30 minutes with 1 mg/ml Collagenase/Hyaluronidase (STEMCELL), DNAse and trypsin (0.01%). After dissociation, the suspension was strained (70 micron strainer) followed by centrifugation (8 minutes at 300g). Red blood lysis buffer (Thermo Fisher) was used followed by dead cell removal (STEMCELL) to deplete the samples of erythrocytes and dead cells, respectively according to the manufacturer’s instructions. Finally, cells were resuspended in 0.04% BSA-PBS solution at a concentration of 700-1000 cells/microliter without selection for specific cell types.
Library construction was performed according to the manufacturer’s instructions (Next GEM 3’ Gene Expression v3, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI), and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR, and the appropriate-sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, single-end constructs were added

value: subcutaneous tumor

value: WT

value: Female


title: G-G_Case23_12W

description: Library name: G-G_Case23_12W

value: Lymphocyte

value: Guselkumab


title: G-G_Case23_0W

description: Library name: G-G_Case23_0W


title: WT, melanoma, scRNAseq

description:
Library name: Sample 1
10x Genomics

value: B16-M10 melanoma cell line


title: G-G_Case23_4W

description: Library name: G-G_Case23_4W


title: TSK, breast tumor, scRNAseq

description:
Library name: Sample 2
10x Genomics


title: mouse hepatocyte,G14.5,Il6stHMKO,CUT&RUN,rep3

last: Xu

description: Library name: G14.5_Il6stKO_Stat3_rep3

value: liver

value: hepatocyte

value: female


title: root nodule, cpop1_21dpi_rep1


title: TSK, melanoma, scRNAseq

description:
Library name: Sample 2
10x Genomics


title: G-G_Case24_12W

description: Library name: G-G_Case24_12W


title: mouse hepatocyte,G14.5,WT,CUT&RUN,rep2

description: Library name: G14.5_Il6stWT_Stat3_rep2


title: G-G_Case21_4W

description: Library name: G-G_Case21_4W


title: root nodule, cpop1_10dpi_rep3

value: 10 dpi


title: root nodule, cpop1_10dpi_rep2


title: G-G_Case21_12W

description: Library name: G-G_Case21_12W


title: root nodule, cpop1_10dpi_rep1


title: G-G_Case21_0W

description: Library name: G-G_Case21_0W


title: root nodule, WT_21dpi_rep3


title: WT, skin, scRNAseq

description:
Library name: Sample 1
10x Genomics

value: Skin

value: epithelial


title: G-G_Case19_4W

description: Library name: G-G_Case19_4W


title: root nodule, WT_21dpi_rep2


title: G-G_Case22_4W

description: Library name: G-G_Case22_4W


title: G-G_Case19_0W

description: Library name: G-G_Case19_0W


title: root nodule, WT_10dpi_rep2


title: G-G_Case18_12W

description: Library name: G-G_Case18_12W


title: G-G_Case22_0W

description: Library name: G-G_Case22_0W


title: G-G_Case18_0W

description: Library name: G-G_Case18_0W


title: G-G_Case16_12W

description: Library name: G-G_Case16_12W


title: Germinal center B cells (CD19+IgD-CD95+CD38-) isolated from mice immunised with NP-KLH (D7) (H3K4me3 ChIP)

city: Clayton

first: Kim

middle: L

last: Good-Jacobson

state: Vitoria

address: 19 Innovation Walk

department: Biochemistry & Molecular Biology

country: Australia

institute: Monash University

description: Library name: ChIP_H3K4me3_GC

data_processing:
FASTQ files were
Pair-end files were coupled, aligned to the mm10 genome using the Bowtie package and then filtered for quality (>20).
PCR duplicates were the removed using the Samstools package.
Peaks were called using the resulting files from the Input and ChIP processed samples via the MACS2 package in order to generate Bigwig files for visualisation using the IGV genome browser and BED files for further downstream analysis.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak (BED)

source_name: Spleen

extract_protocol:
Cells were fixed in 0.6% formaldehyde for 8 minutes, while rotating, before quenching with 1.25M glycine and washed thrice with Dulbecco's phosphate buffered saline. Cell were lysed via a BioRuptor sonicator. Histone modification-specific antibodies were used to pull down DNA fragments via chromatin immunoprecipitation and input sampels representing the fragmented DNA prior to pulldown were generated for each sample.
ChIP-processed and input control samples were processed using the MGI Easy DNA FS Library preparation kit V1 (MGI Tech) and sequenced using a MGISEQ-2000RS High-Throughput Sequencing Set (PE100).

treatment_protocol: Mature naïve B cell and early developing B cells were derived from the spleens and bone marrow of naïve wildtype mice. Germinal center B cells were isolated from the spleens of wildtype mice immunized 7-days prior with NP-KLH precipitated in 10% alum. Cells were extracted via fluorescence-assisted cell sorting and resuspended in 10mL RPMI containing 10% foetal calf serum and 2mM glutamine.

value: Spleen

value: Germinal center B cells

value: Wildtype

value: NP-KLH immunisation (+10% alum) 7 days prior

tag: chip antibody

value: H3K4me3 (Abcam, #ab1342)


title: G-G_Case16_0W

description: Library name: G-G_Case16_0W

value: periheral blood


title: Germinal center B cells (CD19+IgD-CD95+CD38-) isolated from mice immunised with NP-KLH (D7) (ATAC-seq)

description: Library name: ATAC-seq GC


title: regeneration_5 time-point

city: Shanghai

first: yue

last: chen

address: 320 Yue-Yang Road

institute: Shanghai Institute of Biochemistry and Cell Biology

data_processing:
library strategy: Spatial transcriptome
Spatial transcriptome data of regenerated fragments was generated by 10X Visium (10X Genomics), aligned to S. mediterranea transcriptome smed_20140614 as the SAW pipeline.
Assembly: Schmidtea mediterranea transcriptome is available from GSE72389

organism: Schmidtea mediterranea

source_name: neck

growth_protocol: Asexual S. mediterranea (strain CIW4) anamials were maintained at 20 °C as previously described (Newmark and Sanchez Alvarado, 2000). For all experiments, animals were starved for at least 7 days.

extract_protocol: Regenerating planarian fragments of different time points were killed by 5% NAC in PBS for 1 minute, embedded using pre-cooled OCT, and placed in a -80 °C refrigerator for storage. The tissues were placed into -20 °C freezing microtome for acclimation 30min before sectioning. Agilent 2100 bioanalyzer was used to assess the RNA quality of cryosections. Continuous cryosectioned 10 µm to the largest section cutting plane and collected for spatial transcriptomics sequencing (10x Genomics, Pleasanton, CA, USA). Libraries were constructed according to the Visium Spatial Gene Expression User Guide (10X Genomics, CG000239).

value: neck

value: asexual strain CIW4

value: wild type

value: amputation


title: root nodule, WT_10dpi_rep1

value: root nodule

value: WT


title: Germinal center B cells (CD19+IgD-CD95+CD38-) isolated from mice immunised with NP-KLH (D7) (H3K27me3 ChIP)

description: Library name: ChIP_H3K27me3_GC


title: Germinal center B cells (CD19+IgD-CD95+CD38-CD138-) isolated from mice immunised with NP-KLH (D7) (DNA Input), Rep2

description: Library name: Input_H3K79me2_GC_Replicate2


title: G-G_Case19_12W

description: Library name: G-G_Case19_12W

value: Lymphocyte

value: Guselkumab


title: Germinal center B cells (CD19+IgD-CD95+CD38-CD138-) isolated from mice immunised with NP-KLH (D7) (H3K79me2 ChIP), Rep2

description: Library name: ChIP_H3K79me2_GC_Replicate2


title: Germinal center B cells (CD19+IgD-CD95+CD38-CD138-) isolated from mice immunised with NP-KLH (D7) (DNA Input), Rep1

description: Library name: Input_H3K79me2_GC_Replicate1


title: G-G_Case15_0W

description: Library name: G-G_Case15_0W


title: G-G_Case14_12W

description: Library name: G-G_Case14_12W


title: G-G_Case14_4W

description: Library name: G-G_Case14_4W


title: Germinal center B cells (CD19+IgD-CD95+CD38-CD138-) isolated from mice immunised with NP-KLH (D7) (H3K79me2 ChIP), Rep1

description: Library name: ChIP_H3K79me2_GC_Replicate1


title: G-G_Case18_4W

description: Library name: G-G_Case18_4W


title: root nodule, WT_21dpi_rep1

value: 21 dpi


title: G-G_Case15_4W

description: Library name: G-G_Case15_4W


title: Naïve B cells (CD19+IgD+) isolated from naïve WT mice (DNA Input), Biological replicate 2

description: Library name: Input_H3K79me2_Naive_Replicate2

value: Naive B cells


title: Naïve B cells (CD19+IgD+) isolated from naïve WT mice (DNA Input), Biological replicate 1

description: Library name: Input_H3K79me2_Naive_Replicate1


title: G-G_Case14_0W

description: Library name: G-G_Case14_0W


title: Naïve B cells (CD19+IgD+) isolated from naïve WT mice (H3K79me2 ChIP), Biological replicate 2

description: Library name: ChIP_H3K79me2_Naive_Replicate2


title: G-G_Case16_4W

description: Library name: G-G_Case16_4W


title: G-G_Case13_4W

description: Library name: G-G_Case13_4W


title: mouse liver tissue isolated hepatocyte,P7-L,snRNA-seq

description:
Library name: M_P7L_liver_tissue_hepatocyte_Nuclei_001-308
Smart-seq3xpress

data_processing:
We used Trimmomatic (v0.39) to remove index, primer, and adapter sequences from the paired-end reads. The trimmed reads were then aligned to the Mus musculus reference genome (GRCm38/mm10) using Hisat2 (v2.1.0) with default parameters. For snRNA-seq, transcript quantification for both sets of nuclei was performed using featureCounts (v1.5.3) with the parameter -t transcript to comprehensively include intronic reads, ensuring robust detection of nuclear transcripts. Gene expression values were calculated as transcripts per 0.1 million (TP0.1M) and log-transformed. To prevent transcriptome perturbations by extremely highly expressed genes, the genes Apoa2, Alb, and Fabp1 were excluded from the total transcript calculations.
Please note that each processed data column header corresponds to the fastq file from which the data was generated from. The fastq files associated with each sample records and their computed md5 checksums are listed in the 'sample_to_processed_data_readme.txt'.
Assembly: mm10
Supplementary files format and content: Smart-seq3xpress output files: Comma-separated expression value matrix files

extract_protocol:
Mouse hepatocytes isolation was performed as previously reported. Mice were anesthetized by intraperitoneal injection of 2,2,2-tribromoethanol and then perfused through the inferior vena cava with 10 mL of pre-warmed (37°C) phosphate-buffered saline (PBS) containing 1 mM EGTA. The portal vein was cut at the start of perfusion to allow blood clearance. The liver was then perfused and digested with 10 mL of pre-warmed 1 mg/mL collagenase IV (Sigma-Aldrich, C5138) in RPMI 1640 medium (Gibco, 21870076). The digested liver tissue was collected into PBS and filtered through a 70 μm cell strainer. The cell suspension was centrifuged at 50 × g for 2 minutes at 4°C, and the cell pellets were resuspended in RPMI 1640 medium supplemented with 1% fetal bovine serum (FBS). To enrich for viable hepatocytes, Percoll (GE, 17-0891-09) diluted in PBS was added to the cell suspension, followed by centrifugation at 50 × g for 2 minutes. The cell pellets were then collected, washed once, and resuspended in RPMI 1640 medium supplemented with 1% FBS. Smart-seq3xpress scRNA-seq experiments was performed according to the published procedure(Hagemann-Jensen et al., 2022). Briefly, purified single hepatocytes were manually picked with a microcapillary pipette under a microscope and transferred into the 384-well PCR plates containing 0.3 μL of lysis buffer and 3 μL of silicone oil (Merck, 317667). The mRNA was reverse transcribed into cDNA using 0.2 μL of dispensed RT mix. The cDNA was then amplified using 0.6 μL PCR mix. The library of each cell was constructed separately using the TruePrep DNA Library Prep Kit (Vazyme, TD501)
Smart-seq3xpress scRNA-seq experiments was performed according to the published procedure(Hagemann-Jensen et al., 2022). Briefly, purified single hepatocytes were manually picked with a microcapillary pipette under a microscope and transferred into the 384-well PCR plates containing 0.3 μL of lysis buffer and 3 μL of silicone oil (Merck, 317667). The mRNA was reverse transcribed into cDNA using 0.2 μL of dispensed RT mix. The cDNA was then amplified using 0.6 μL PCR mix. The library of each cell was constructed separately using the TruePrep DNA Library Prep Kit (Vazyme, TD501)

value: liver

value: hepatocyte

value: female


title: G-G_Case15_12W

description: Library name: G-G_Case15_12W


title: mouse perfusion isolated hepatocyte,G14.5,snRNA-seq

description:
Library name: M_G14.5_perfusion_hepatocyte_Nuclei_001-301
Smart-seq3xpress


title: G-G_Case12_4W

description: Library name: G-G_Case12_4W


title: Naïve B cells (CD19+IgD+) isolated from naïve WT mice (H3K79me2 ChIP), Biological replicate 1

description: Library name: ChIP_H3K79me2_Naive_Replicate1

value: Spleen

value: Wildtype


title: G-G_Case13_12W

description: Library name: G-G_Case13_12W