title: C15, control

city: Toulouse

first: Rüçhan

last: Ekren

address: CHU Purpan – BP 3028 –  Toulouse Cedex, 3

department: INFINITY

country: France

institute: Inserm UMR 1291

description:
Control healthy skin
D30

data_processing:
Fastq files processed using nf-core/rnaseq(v3.14.0) of the nf-core collection of workflows, utilizing reproducible software environments from the Bioconda  and Biocontainers  projects. The alignment and quantification of the reads were executed via Nextflow v24.10.0  with the following command:
nf-core/rnseq pipeline (v 3.18.0) was initiated for alignment and quantification of the RNA reads
nextflow run nf-core/rnaseq -r 3.18.0 -profile genotoul --input samplesheet.csv --outdir alignNquant/ --fasta /refs/Homo_sapiens.GRCh38.111.dna_rm.toplevel.fa.gz --gtf /refs/Homo_sapiens.GRCh38.111.gtf.gz --remove_ribo_rna --aligner star_salmon --star_index /refs/genome/index/star/ --salmon_index /refs/genome/index/salmon/ --extra_star_align_args '--alignIntronMax 1000000 --alignIntronMin 20 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --outFilterMismatchNmax 10 --outFilterType BySJout --outFilterMismatchNoverLmax 0.05' --multiqc_title DupEczeMain Alignment and QC assessment
STAR and then Salmon was preferred for alignment and quantification respectively
Assembly: GRCh38.111
Supplementary files format and content: $sampleName”_quant.sf” files contain quantified transcript abundances per sample
Supplementary files format and content: $sampleName”_quant.genes.sf” files contain quantified gene abundances per sample

source_name: Skin

extract_protocol:
Samples were collected into RNAlaterTM (Qiagen) and stored at 4°C for 48 hours after collection and transferred to -80 °C until RNA extraction. For RNA extraction, each skin sample was transferred in a gentleMACS M Tube (Miltenyi) filled with 700 μl of TRIzol (Invitrogen) and put on ice. Sample was then dissociated using the GentleMAXTM Octo Dissociator (Miltenyi, Program: RNA_1) and centrifuged shortly. The content of the M tube was then transferred to a 1.5mL tube and 140μl of chloroform was added. Tube was vortexed for 15 seconds twice and then centrifuged for 15 minutes at 8000 rpm at 4°C. The upper phase of the tube was collected and transferred to a new 1.5mL tube filled with 300μL of 70% ethanol, homogenized and put on ice. The homogenized lysate was transferred on RNeasy spin column placed in a 2 ml collection tube and processed using the RNAeasy Plus Mini KIT (Qiagen #74104) according to the manufacturer instructions. The RNA collected were stored at -80°C until sequencing.
Samples quality controls and libraries preparation were performed at the GeT-Santé facility (Inserm, Toulouse, France, get.genotoul.fr). RNA concentration and purity were determined using a ND-2000 Spectrophotometer (Thermo Fisher Scientific, Waltham, USA). Integrity of RNA was checked with a Fragment Analyzer (Agilent Technologies, Santa Clara, USA), using the RNA Standard Sensitivity Kit. RNA-seq paired-end libraries were prepared according to Illumina’s protocol with some adjustments, using the TruSeq Stranded mRNA library prep Kit (Illumina, San Diego, USA). Briefly, mRNAs were first selected from 1000ng total RNA using poly-T beads. Then, RNA were fragmented during 2' and retrotranscribed to generate double stranded cDNA. Compatible adaptors were ligated, allowing the barcoding of the samples with unique dual indices. 12 cycles of PCR were applied to amplify libraries, and a final purification step allowed to obtain 280-1000 pb fragments. Libraries quality was assessed using the HS NGS kit on the Fragment Analyzer (Agilent Technologies, Santa Clara, USA). Libraries quantification and sequencing were performed at the GeT-PlaGe core facility (INRAE, Toulouse, France). Libraries were quantified by qPCR using the KAPA Library Quantification Kit (Roche, Basel, Switzerland) to obtain an accurate quantification.Libraries were equimolarly pooled and RNA sequencing was then performed on one S4 lane of the Illumina NovaSeq 6000 instrument (Illumina, San Diego, USA), using the NovaSeq 6000 S4 v1.5 Reagent Kit (300 cycles), and a paired-end 2 x 150 pb strategy.

treatment_protocol:
A baseline 4-mm biopsy was taken on lesional skin from the back of the hand whenever possible. When the back of the hand was unaffected at baseline, biopsy was taken on lesional skin from the interface of the back and palm of the hand. When the interface zone was unaffected too, biopsy was taken in the lesional palm. Biopsies were repeated at week 16, 1 to 2 cm far from the baseline sampling site. Control skin samples from healthy donors were obtained via GENOSKIN® from surgical residues of skin plastic surgeries (mainly abdomen and arms). Controls and patients were age- and sex-matched.                                                                                All samples were transferred directly into clean 1.5 mL Eppendorf tubes. Each sample was heated in lysis buffer (2% SDS; 100 mM HEPES pH8.5; 10 mM TCEP; 30 mM Chloroacetamide; 1 mM EDTA and Antiprotease cOmplete) and then successively ground with UFO beads and sonicated by micro cavitation (Bioruptor Pico, Diagenode) with glass beads (Diagenode protein extraction beads). The beads were rinsed with 100 μL HEPES buffer before a centrifugation step. The protein concentration of the supernatant was determined by a BCA method compatible with reducing agents. 100 μg of proteins were precipitated with SP3 beads (PreOmics, Gmbh) and digested with a mix of Trypsin and LysC, following the PreOmics instructions for the use of iST-BCT kit (PreOmics, Gmbh). Peptides were purified using mixed mode reverse phase cation exchanger SPE column (PreOmics Gmbh), eluted, dried and solubilized in 100 μL of 3% acetonitrile 0.1% formic acid aqueous solution. Then, peptide concentration in each sample was determined using the BCA method.
A baseline 4-mm biopsy was taken on lesional skin from the back of the hand whenever possible. When the back of the hand was unaffected at baseline, biopsy was taken on lesional skin from the interface of the back and palm of the hand. When the interface zone was unaffected too, biopsy was taken in the lesional palm. Biopsies were repeated at week 16, 1 to 2 cm far from the baseline sampling site. Control skin samples from healthy donors were obtained via GENOSKIN® from surgical residues of skin plastic surgeries (mainly abdomen and arms). Controls and patients were age- and sex-matched.                                                                                All samples were transferred directly into clean 1.5 mL Eppendorf tubes. Each sample was heated in lysis buffer (2% SDS; 100 mM HEPES pH8.5; 10 mM TCEP; 30 mM Chloroacetamide; 1 mM EDTA and Antiprotease cOmplete) and then successively ground with UFO beads and sonicated by micro cavitation (Bioruptor Pico, Diagenode) with glass beads (Diagenode protein extraction beads). The beads were rinsed with 100 μL HEPES buffer before a centrifugation step. The protein concentration of the supernatant was determined by a BCA method compatible with reducing agents. 100 μg of proteins were precipitated with SP3 beads (PreOmics, Gmbh) and digested with a mix of Trypsin and LysC, following the PreOmics instructions for the use of iST-BCT kit (PreOmics, Gmbh). Peptides were purified using mixed mode reverse phase cation exchanger SPE column (PreOmics Gmbh), eluted, dried and solubilized in 100 μL of 3% acetonitrile 0.1% formic acid aqueous solution. Then, peptide concentration in each sample was determined using the BCA method.

value: Skin

value: Week 0


title: Placental DNA from Gestational Diabetes Mellitus pregnant women 67

status: Public on Jan 24 2026

type: genomic

city: Gandhinagar

first: Surya

last: Ramachandran

state: Gujarat

address: near the Gujarat International Finance Tec (GIFT)-City

country: India

institute: Gujarat Biotechnology University

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to human Infinium methylation EPIC bead chip (Ilumina) using standard illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan system

data_processing:
Quality control was provided by using a R package (minfi). Complete analysis was performed using the GenomeStudio Methylation module. Illumina Custom Model is the error model used in the comparison.
GenomeStudio Methylation module software computed differential methylation between condition group (GDM) to a reference group (NG). Illumina Custom Model is the error model used in the comparison. This model operates under the assumption that the methylation value ß is normally distributed among replicates corresponding to a set of biological conditions.

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Placental DNA

label_protocol: Standard illumina protocol

extract_protocol: Placental DNA was extracted from DNAeasy blood and tissue kit(Qiagen) according to standard instructions

tag: Sex

value: Female

tag: disease state

value: Gestational Diabetes Mellitus

tag: tissue

value: Placental DNA


title: C14, control

type: SRA

description:
Control healthy skin
D27

library_source: transcriptomic

molecule: polyA RNA

tag: treatment


title: DIPGIV

city: Rochester

first: Alexandra

last: Krivonos

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

country: USA

institute: Mayo Clinic

description: Library name: DIPGIV

data_processing:
trimmed reads to hg19 (patch 13) (genome.ucsc.edu/ENCODE/releaseLog.html) using RNA STAR v2.5 and counted using HTSeq.
Assembly: Hg19
Supplementary files format and content: raw counts for each sample
Supplementary files format and content: fpkm normalized counts for each sample

molecule: total RNA

source_name: Brain-derived

extract_protocol:
RNeasy Plus micro kit (QIAGEN)
NEBNext UltraTM RNA Library Prep Kit for Illumina (New
AMPure XP magnetic beads (Beckman Coulter)

value: Brain-derived

tag: cell line

value: Patient-derived

tag: cell type

value: Primary cell line


title: DIPG24

description: Library name: DIPG24


title: DIPGVI

description: Library name: DIPGVI


title: Placental DNA from Gestational Diabetes Mellitus pregnant women 63


title: C11, control

description:
Control healthy skin
D22


title: C12, control

description:
Control healthy skin
D24


title: C13, control

description:
Control healthy skin
D25


title: Placental DNA from Gestational Diabetes Mellitus pregnant women 59


title: Placental DNA from normoglycemic pregnant women 39

value: Normoglycemic


title: C7, control

description:
Control healthy skin
D13


title: C8, control

description:
Control healthy skin
D14


title: Placental DNA from Gestational Diabetes Mellitus pregnant women 54


title: C10, control

description:
Control healthy skin
D17


title: Placental DNA from normoglycemic pregnant women 23


title: C6, control

description:
Control healthy skin
D10


title: Placental DNA from normoglycemic pregnant women 9


title: C9, control

description:
Control healthy skin
D15


title: Placental DNA from normoglycemic pregnant women 17


title: Placental DNA from Gestational Diabetes Mellitus pregnant women 22


title: C3, control

description:
Control healthy skin
D7


title: Placental DNA from normoglycemic pregnant women 26


title: C4, control

description:
Control healthy skin
D8


title: pGF-DSS-0

city: Tianjin

first: Zichan

last: He

address: 94 Weijin Road, Nankai District

country: China

institute: Nankai university

description:
Library name: Sample4
10×Genomics

library_source: transcriptomic single cell

data_processing:
CellRanger (v6.1.2) was used to process raw data, demultiplex cellular barcodes, map reads to the mouse genome (mm10) and generated digital gene expression matrices. R (v4.1.3) and Seurat (v4.1.1) were used for downstream analysis.
Assembly: Mouse genome (mm10)
Supplementary files format and content: Tab-separated values files and matrix files

organism: Mus musculus

source_name: colon

extract_protocol:
The intestines of mice were dissected and washed with pre-cooled PBS to remove feces and mucus until the cleaning solution became clear. Subsequently, the intestines were sectioned into 0.5 cm segments, transferred into preheated epithelial cell removal solution (PBS with 10 mM EDTA), and incubated at 37 °C, 30 rpm for 15 min on a rotating shaker. The tissues were then incubated on ice for 15 min, and then washed twice with PBS containing 2 % fetal bovine serum (FBS). The remaining tissues were placed in a preheated digestive solution [RPMI-1640, 100 μg/ml Liberase TL (5401020001, Roche, Switzerland), and 50 μg/ml DNase I (11284932001, Roche, Switzerland)] at 37 °C, 40 rpm for 30 min on a rotating shaker. The supernatant was collected, and pre-cooled MACS buffer (PBS, 2 % FBS, and 2 mM EDTA) was added to terminate digestion.After washing with MACS buffer, cells were resuspended in MACS buffer containing 0.125 μg/100 μl fluorescein-coupled CD45 monoclonal antibody (12-0451-82, Thermo Fisher, USA) at a concentration of 2×106 cells/100 μl. After incubation at room temperature for 30 min, the unlabeled antibody was washed away. The cells were re-suspended in MACS buffer for flow sorting. CD45-positive cells were collected in a collection tube containing RPMI-1640 and 5 % FBS.
ScRNA-seq was performed using Chromium Single Cell 5’ Gel Bead and Library Construction Kit (10×Genomics, USA) and Single Cell V(D)J Amplification Kit (10×Genomics, USA). Reverse transcription, cDNA recovery, cDNA amplification, and library construction were performed according to the manufacturer’s protocol.

value: colon

tag: genotype

value: wild type

value: Antibiotic treatment for 4 weeks


title: C1, control

description:
Control healthy skin
D3


title: Placental DNA from normoglycemic pregnant women 3


title: pGF-DSS-2

description:
Library name: Sample5
10×Genomics

value: After 4 weeks of antibiotic treatment, the animals were then subjected to antibiotic treatment combined with DSS for another 2 days.


title: pGF-DSS-7

description:
Library name: Sample6
10×Genomics

value: After 4 weeks of antibiotic treatment, the animals were then subjected to antibiotic treatment combined with DSS for another 7 days.


title: SPF-DSS-7

description:
Library name: Sample3
10×Genomics

value: DSS treatment for 7 days


title: SPF-DSS-0

description:
Library name: Sample1
10×Genomics

value: control


title: C5, control

description:
Control healthy skin
D9


title: SPF-DSS-2

description:
Library name: Sample2
10×Genomics

value: Dextran sodium sulfate (DSS) treatment for 2 days


title: C2, control

description:
Control healthy skin
D6

value: Skin


title: D12, week 0, Dupilumab

description:
Dupilumab arm
01023V1

value: Week 0


title: D12, week 16, Dupilumab

description:
Dupilumab arm
01023V9

value: Week 16


title: P9, week 0, Placebo

description:
Placebo arm
01022V1


title: P6, week 16, Placebo

description:
Placebo arm
01018V9


title: P6, week 0, Placebo

description:
Placebo arm
01018V1


title: 8CLC-HNRNPU-KD-RNA-seq-1

city: HangZhou

first: Zhengyi

last: Li

state: ZheJiang

address: 866 Yuhangtang Rd, Hangzhou

department: Institute of Genetics

institute: Zhejiang University School of Medicine

description: Library name: 8CLC-HNRNPU KD-1

data_processing:
Quality control for raw reads was performed by FastQC v0.11.9
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cutadapt v4.1
The trimmed-reads were mapped to human reference genome GRCh38.99 using STAR (2.7.10a). Reads with no more than 2000 mapped loci were retained, and only the best hit was kept (--outSAMprimaryFlag AllBestScore --outSAMmultNmax 1 --outFilterMultimapNmax 2000 --winAnchorMultimapNmax 2000 --genomeLoad LoadAndKeep --limitBAMsortRAM 10000000000).
Quantification was calculated by FeatureCounts (v2.0.1) (-M, -O)
Differentially expressed genes (DEGs) and transposable elements (DE-TEs) were generated by the R package edgeR (v3.30.3)
Assembly: GRCh38 (hg38)
Supplementary files format and content: bigwig
Supplementary files format and content: txt

growth_protocol: cells were cultured in mTeSR medium.

extract_protocol:
RNA was purified using 2.2× RNA Clean Beads (Beckman Coulter) and eluted in 18 μL of 0.1 M DTT.
Libraries were constructed using the SMARTer Stranded Total RNA-Seq Kit v2 (Takara Bio) with ribosomal cDNA depletion and subjected to sequencing.

treatment_protocol: To label de novo transcribed nascent RNA, 4-Thiouridine (4-sU) was added into the cell culture medium and incubated for 4h. Later, RNA was extracted and 4sU-to-cytidine conversion was performed as previously described (77) with minor modifications. Briefly, ice-cold conversion buffer was added to RNA. The reaction was initiated by adding 1.3 μL of 192 mM NaIO4, followed by incubation at 45°C for 1h. To quench the reaction, 2 μL of 10x reducing master mix was added and incubated at 37°C for 30 min.

value: human embryonic stem cell

value: transfection with HNRNPU KD


title: 8CLC-MLT2A1-KD-RNA-seq-1

description: Library name: 8CLC-MLT2A1 KD-1

value: transfection with MLT2A1 KD


title: 8CLC-HNRNPU-KD-RNA-seq-2

description: Library name: 8CLC-HNRNPU KD-2


title: 8CLC-NC-RNA-seq-2

description: Library name: 8CLC-Control KD-2

value: transfection with control KD


title: hESC-NC-RNA-seq-1

description: Library name: hESC-Control KD-1

value: hESC


title: 8CLC-MLT2A1-KD-RNA-seq-2

description: Library name: 8CLC-MLT2A1 KD-2


title: P4, week 16, Placebo

description:
Placebo arm
01014V9


title: hESC-FL-1

description: Library name: hESC-FL-1

source_name: human embryonic stem cell

extract_protocol:
TRIZOL was used for RNA extraction following manufacturer's instructions
Vazyme TD503 and TD202 were used for library construction following manufacturer's instructions

treatment_protocol: GFP, 5' MLT2A1, 3' fusion and FL RNAs were respectively transfected into hESC. After 48h, samples were colltected for RNA-seq.

value: transfection with FL


title: 8CLC-NC-RNA-seq-1

description: Library name: 8CLC-Control KD-1


title: D10, week 16, Dupilumab

description:
Dupilumab arm
01016V9


title: hESC-FL-2

description: Library name: hESC-FL-2


title: hESC-NC-RNA-seq-2

description: Library name: hESC-Control KD-2


title: P2, week 16, Placebo

description:
Placebo arm
01009V9


title: P2, week 0, Placebo

description:
Dupilumab arm
01009V1


title: D10, week 0, Dupilumab

description:
Dupilumab arm
01016V1


title: D8, week 0, Dupilumab

description:
Dupilumab arm
01011V1


title: D6, week 0, Dupilumab

description:
Dupilumab arm
01008V1


title: hESC-3'-Fusion-2

description: Library name: hESC-3_-Fusion-2

value: transfection with 3' fusion


title: hESC-GFP-1

description: Library name: hESC-GFP-1

value: transfection with GFP


title: D6, week 16, Dupilumab

description:
Dupilumab arm
01008V9


title: D5, week 0, Dupilumab

description:
Dupilumab arm
01007V1


title: D8, week 16, Dupilumab

description:
Dupilumab arm
01011V9


title: D4, week 16, Dupilumab

description:
Dupilumab arm
01006V9


title: 4C-2477 KD-1

description: Library name: 4C-2477 KD-1

data_processing:
Quality control for raw reads was performed by FastQC v0.11.9
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cutadapt v4.1
The trimmed-reads were mapped to human reference genome GRCh38.99 using STAR (2.7.10a). Reads with no more than 2000 mapped loci were retained, and only the best hit was kept (--outSAMprimaryFlag AllBestScore --outSAMmultNmax 1 --outFilterMultimapNmax 2000 --winAnchorMultimapNmax 2000 --genomeLoad LoadAndKeep --limitBAMsortRAM 10000000000).
Quantification was calculated by FeatureCounts (v2.0.1) (-M, -O)
Differentially expressed genes (DEGs) and transposable elements (DE-TEs) were generated by the R package edgeR (v3.30.3)
Assembly: GRCh38 (hg38)
Supplementary files format and content: bigwig, tpm.csv, counts.csv

source_name: human 4C embryo

growth_protocol: embryos from zygote to 4C stages were cultured in G-1 plus medium.

extract_protocol:
RNA was extracted and reverse-transcribed using SMART-SEQ2
Vazyme TD503 and TD202 were used for library construction following manufacturer's instructions

treatment_protocol: Human 3PN zygotes were respectively micor-injected with Ctrl ASO (Ctrl KD), dup_161 ASO (161 KD) and dup_2477 ASO (2477 KD) at day 1 and in vitro cultured.

value: human 4C embryo

value: micro-injection with 2477 ASO


title: hESC-5'-MLT2A1-2

description: Library name: hESC-5_-MLT2A1-2

value: transfection with 5' MLT2A1


title: hESC-GFP-2

description: Library name: hESC-GFP-2


title: P3, week 16, Placebo

description:
Placebo arm
01012V9


title: D2, week 16, Dupilumab

description:
Dupilumab arm
01004V9


title: D4, week 0, Dupilumab

description:
Dupilumab arm
01006V1


title: hESC-5'-MLT2A1-1

description: Library name: hESC-5_-MLT2A1-1


title: 4C-2477 KD-2

description: Library name: 4C-2477 KD-2


title: 4C-161 KD-3

description: Library name: 4C-161 KD-3

value: micro-injection with 161 ASO


title: 4C-161 KD-1

description: Library name: 4C-161 KD-1


title: hESC-3'-Fusion-1

description: Library name: hESC-3_-Fusion-1


title: D5, week 16, Dupilumab

description:
Dupilumab arm
01007V9


title: 4C-Control KD-3

description: Library name: 4C-Control KD-3

value: micro-injection with Ctrl ASO


title: 4C-161 KD-2

description: Library name: 4C-161 KD-2


title: 4C-Control KD-2

description: Library name: 4C-Control KD-2


title: P4, week 0, Placebo

description:
Placebo arm
01014V1


title: P1, week 0, Placebo

description:
Placebo arm
01001V1


title: arrest 8C embryo:3PN_4

data_processing:
Quality control for raw reads was performed by FastQC v0.11.9
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cutadapt v4.1
The trimmed-reads were mapped to human reference genome GRCh38.99 using STAR (2.7.10a). Reads with no more than 2000 mapped loci were retained, and only the best hit was kept (--outSAMprimaryFlag AllBestScore --outSAMmultNmax 1 --outFilterMultimapNmax 2000 --winAnchorMultimapNmax 2000 --genomeLoad LoadAndKeep --limitBAMsortRAM 10000000000).
Quantification was calculated by FeatureCounts (v2.0.1) (-M, -O)
Differentially expressed genes (DEGs) and transposable elements (DE-TEs) were generated by the R package edgeR (v3.30.3)
Assembly: GRCh38 (hg38)
Supplementary files format and content: bigwig

source_name: human development-arrest 8C stage embryo

growth_protocol: Embryos from day 1 to day 3 were cultured in G-1 plus medium (Vitrolife, 10128) in 6% CO2, 37°C incubator. From the end of day 3 to day 4, G-2 plus medium (Vitrolife, 10132) was used instead.

extract_protocol:
To collect embryos arrested at 8-Cell stage, when embryos reached 8-Cell at day 3, they were cultured for another 24h and embryos that ceased development were considered as 8-Cell arrested embryos and were collected for transcriptome profiling.
RNA libraries for single embryos were constructed using Smart-seq2 following the instructions.

treatment_protocol: no treatment

value: human 3PN embryo

value: micro-injection


title: P3, week 0, Placebo

description:
Placebo arm
01012V1

value: Skin

value: Week 0


title: arrest 8C embryo:3PN_2

value: human development-arrest 8C stage embryo


title: arrest 8C embryo:2PN_9

value: human 2PN embryo


title: 8CLC-truncation-rescue-2

description: Library name: 8CLC-truncation rescue-2

treatment_protocol: ASO for dup_161/2477 double KD and non-targetable RNAs were mixed and transfected into human 8CLC.

value: human embryonic stem cell

value: trasnfection with DKD ASO and truncated RNA


title: 8CLC-truncation-rescue-1

description: Library name: 8CLC-truncation rescue-1


title: D2, week 0, Dupilumab

description:
Dupilumab arm
01004V1


title: arrest 8C embryo:2PN_5


title: arrest 8C embryo:2PN_7


title: 8CLC-Input

description: Library name: 8CLC-Input

library_source: genomic

data_processing:
Quality control for raw reads was performed by FastQC v0.11.8
TrimGalore (v0.5.0) was used for trimming adapters
The remaining high-quality reads were mapped to human reference genome downloaded from Ensembl (GRCh38.99) by BWA (v0.7.17).
PCR duplicates were marked by PICARD (v2.19.0)
MACS2 (v2.1.2) was used for calling peaks
Assembly: GRCh38 (hg38)
Supplementary files format and content: bigwig
Supplementary files format and content: txt

extract_protocol:
genomic DNA was extracted using ChIRP protocol.
Vazyme ND607 were used for library construction following manufacturer's instructions

treatment_protocol: cells were cross-linked by 2mM DSP at room temperature for 30min with rotation and then 4% formaldehyde at room temperature for 15min with rotation. 0.25M glycine was used to stop the cross-linking.

value: cross-linking


title: arrest 8C embryo:2PN_6


title: 4C-2477 KD-3

description: Library name: 4C-2477 KD-3


title: 8CLC-L1-KD-2

description: Library name: 8CLC-LINE1 KD-2

treatment_protocol: LINE-1 ASO and control ASO were respectively transfected into 8CLC by endofectin.

value: transfection with LINE-1 ASO


title: P47, week 0, Placebo

description:
Placebo arm
01003V1


title: 4C-Control KD-1

description: Library name: 4C-Control KD-1


title: D1, week 0, Dupilumab

description:
Dupilumab arm
01002V1


title: arrest 8C embryo:2PN_10


title: 8CLC-NC-control KD-2

description: Library name: 8CLC-Control KD-2

value: transfection with control ASO


title: arrest 8C embryo:3PN_3


title: D1, week 16, Dupilumab

description:
Dupilumab arm
01002V9

value: Week 16


title: arrest 8C embryo:2PN_2


title: arrest 8C embryo:2PN_1


title: P1, week 16, Placebo

description:
Placebo arm
01001V9


title: 8CLC-mutation-rescue-1

description: Library name: 8CLC-mutation rescue-1

value: trasnfection with DKD ASO and mutated RNA


title: 8C-HNRNPU-KD-5

description: Library name: 8C-HNRNPU KD-5

source_name: human 8C embryo

growth_protocol: embryos from zygote to 8C stages were cultured in G-1 plus medium.

treatment_protocol: Human 3PN zygotes were micor-injected with Ctrl siRNA (Ctrl KD) and HNRNPU siRNA (HNRNPU KD) at day 1 and in vitro cultured.

value: human 8C embryo

value: micro-injection with HNRNPU siRNA


title: 8CLC-NC-1

description: Library name: 8CLC-Control KD-1


title: 8C-HNRNPU-KD-3

description: Library name: 8C-HNRNPU KD-3


title: 8C-HNRNPU-KD-2

description: Library name: 8C-HNRNPU KD-2


title: 8C-NC-3_1

source_name: human 8C stage embryo

growth_protocol: Human 4-Cell and 8-Cell embryos were cultured in commercially available G-1 plus medium

extract_protocol:
When embryos reached 4-Cell stage at day 2 and 8-Cell stage at day 3, they were harvested for RNA-seq
RNA libraries for single embryos were constructed using Smart-seq2 following the instructions.

treatment_protocol: Human 3PN zygotes were micor-injected with Ctrl ASO (Ctrl KD) and MLT2A1 ASO (MLT2A1 KD) at day 1 and in vitro cultured.

value: human 8C stage embryo


title: 8CLC-DKD-1

description: Library name: 8CLC-double KD-1

value: transfection with DKD ASO mix


title: 8C-NC-1_1


title: 8C-NC-3

description: Library name: 8C-Control KD-3

value: micro-injection with Ctrl siRNA


title: 8CLC-DKD-2

description: Library name: 8CLC-double KD-2


title: arrest 8C embryo:2PN_8

value: micro-injection


title: 8CLC-mutation-rescue-2

description: Library name: 8CLC-mutation rescue-2


title: 8C-NC-1

description: Library name: 8C-Control KD-1


title: 8C-NC-2

description: Library name: 8C-Control KD-2


title: arrest 8C embryo:2PN_3


title: arrest 8C embryo:2PN_4


title: 8CLC-L1-KD-1

description: Library name: 8CLC-LINE1 KD-1


title: 8CLC-NC-2

description: Library name: 8CLC-Control KD-2


title: arrest 8C embryo:3PN_1

value: human 3PN embryo


title: 4C-truncation-rescue-3

description: Library name: 4C-truncation rescue-3

treatment_protocol: Human 3PN zygotes were micor-injected with Ctrl ASO (Ctrl KD), double KD ASO (DKD), truncation rescue and mutation rescue RNAs at day 1 and in vitro cultured.

value: human 4C embryo

value: micro-injection with DKD ASO and truncation RNA


title: 4C-truncation-rescue-2

description: Library name: 4C-truncation rescue-2


title: 8CLC-NC-control KD-1

description: Library name: 8CLC-Control KD-1


title: 4C-mutation-rescue-3

description: Library name: 4C-mutation rescue-3

value: micro-injection with DKD ASO and mutation RNA


title: 8CLC-LINE1-ChIRP

description: Library name: 8CLC-LINE1-ChIRP

value: human embryonic stem cell


title: 8C-KD-1_1


title: 8C-KD-3_1


title: 8C-HNRNPU-KD-4

description: Library name: 8C-HNRNPU KD-4


title: 4C-mutation-rescue-2

description: Library name: 4C-mutation rescue-2


title: 4C-DKD-3

description: Library name: 4C-double KD-3

value: micro-injection with DKD ASO


title: 4C-NC-3_1

source_name: human 4C stage embryo

value: human 4C stage embryo


title: 4C-KD-1_1


title: 8C-NC-2_1


title: 4C-NC-3

description: Library name: 4C-Control KD-3

value: micro-injection with Ctrl ASO


title: DUX4OE_MLT2A1_KD_rep2

source_name: ICM

growth_protocol: H1 cells were cultured in commercially available mTeSR medium on Matrix gel pre-coated plates

extract_protocol:
24H after dox induction, total RNA was extracted by Trizol
RNA libraries for RNA-seq were prepared using NEB Next R UltraTM RNA Library Prep Kit (strand-unspecific, ployA-specific) following manufacturer's protocols.

treatment_protocol: Firstly, ASO mix for MLT2A1 sub-family KD and ASO for Ctrl KD were respectivly transfected into the cells and cultured for 24H. Later, dox (final concentration 1ug/ml) was added into the medium to induce DUX4 expression

value: ICM

value: dox induction


title: DUX4OE_Ctrl_KD_rep2


title: 8C-HNRNPU-KD-1

description: Library name: 8C-HNRNPU KD-1


title: ChIRP_input

data_processing:
Quality control for raw reads was performed by FastQC v0.11.8
TrimGalore (v0.5.0) was used for trimming adapters
The remaining high-quality reads were mapped to human reference genome downloaded from Ensembl (GRCh38.99) by BWA (v0.7.17).
PCR duplicates were marked by PICARD (v2.19.0)
MACS2 (v2.1.2) was used for calling peaks
Assembly: GRCh38 (hg38)
Supplementary files format and content: bigwig
Library strategy: ChIRP-seq

growth_protocol: H1 cells were cultured in commercially available mTeSR medium on Matrix gel pre-coated plates.

extract_protocol:
Cells were sequentially crosslinked by 2mM DSP at room temperature for 30min with rotation and 4% formaldehyde at room temperature for 15min with rotation. 0.25M glycine was used to stop the crosslinking. Genomic DNA was fragmentated by DNase I for 10min at 37°C with rotation and sonicated by 25% amplitude for 30s. Streptavidin beads and biotin-labeled probes were added into the supernatant to precipitate RNA-gDNA complex. To elute DNA, RNase H (NEB, M0297S) was used to digest RNA and release genomic DNA.
DNA library was constructed with NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S)

treatment_protocol: Dox (final concentration 1ug/ml) was added into mTeSR medium to induce DUX4 expression.


title: 8C-KD-2_1


title: DUX4OE_Ctrl_KD_rep1


title: 4C-NC-2_1


title: DUX4OE_MLT2A1_KD_rep1


title: 4C-truncation-rescue-1

description: Library name: 4C-truncation rescue-1


title: 4C-KD-3_1


title: 4C-NC-1_1


title: 4C-KD-2_1


title: 4C-NC-2

description: Library name: 4C-Control KD-2


title: 4C-NC-1

description: Library name: 4C-Control KD-1


title: ChIRP_IP


title: 4C-DKD-1

description: Library name: 4C-double KD-1


title: 4C-FL-2

description: Library name: 4C-FL-2

treatment_protocol: Human 3PN zygotes were micor-injected with GFP RNA and MLT2A1 RNA at day 1 and in vitro cultured.

value: micro-injection with FL RNA


title: DUX4OE_dup_2477_KD_rep2

treatment_protocol: Firstly, ASO for Ctrl KD, dup_161 KD and dup_2477 KD were respectively transfected into the cells and cultured for 24H. Later, dox (final concentration 1ug/ml) was added into the medium to induce DUX4 expression


title: 4C-FL-3

description: Library name: 4C-FL-3


title: 4C-mutation-rescue-1

description: Library name: 4C-mutation rescue-1


title: DUX4OE_dup_2477_KD_rep1


title: 4C-FL-1

description: Library name: 4C-FL-1


title: hESC_Ctrl_KD_rep2

value: no treatment


title: hESC_Ctrl_KD_rep1


title: 4C-DKD-2

description: Library name: 4C-double KD-2


title: 4C-GFP-2

description: Library name: 4C-GFP-2

value: micro-injection with GFP RNA


title: G/GM/P-S@H group

city: Shanghai

first: Lingsen

last: You

state: Shanghai

address: 180 Fenglin Road, Xuhui District

institute: Zhongshan Hospital Fudan University

description: Library name: G/GM/P-S@H

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline for alignment to the rabbit reference genome (rabbit reference genome (OryCun2.0).
The resulting feature-spot matrices were analyzed using the Seurat package in R (v4.3.1).
Data were normalized, and cell types were deconvoluted using SingleR.
Assembly: OryCun2.0
Supplementary files format and content: BRS - processed.gz, pocessed data for the bare-metal stent implant group
Supplementary files format and content: G-GM-P-S@H.tar - processed.gz, processed data for the hydrogel-covered stent implant group
Library strategy: Spatial Transcriptomics

organism: Oryctolagus cuniculus

source_name: iliac artery

extract_protocol:
Freshly harvested arterial segments were embedded in OCT, snap-frozen, and cryosectioned (10 µm)
Spatial transcriptnomics libraries were prepared with the Stereo-seq (SpaTial Enhanced REsolution Omics-sequencing) technology, following the manufacturer’s protocol.

value: iliac artery


title: DUX4OE_dup_161_KD_rep1


title: DUX4OE_dup_161_KD_rep2


title: WT monkey  spinal cord_line4

city: Guangzhou

first: BoFeng

last: Han

state: Guangdong

address: No. 601, West Huangpu Avenue, Tianhe District, Guangzhou, Guangdong Province, China

institute: Jinan University

description: Library name: WT_SP_line4

data_processing:
Upstream alignment processing uses cellranger, while downstream processing uses scanpy.
Assembly: Ensembl Macaca fascicularis_5.0
Supplementary files format and content: The h5ad file generated after being processed by Scanpy includes the "group" and "sample" grouping information in the "obs" column.

molecule: nuclear RNA

organism: Macaca fascicularis

source_name: spinal cord

extract_protocol:
Approximately 500 mg of fresh-frozen tissue was dissected from the striatum, hippocampus, and spinal cord of transgenic monkey (Tau P301L) and wild-type control using sterile disposable surgical blades on dry ice. Tissues were weighed and transferred to cold Dounce homogenizers containing ice-cold homogenization buffer (0.25 M sucrose, 5 mM CaCl₂, 3 mM MgAc₂, 10 mM Tris-HCl pH 8.0, 0.1 mM EDTA, 1× protease inhibitors, 1 U/μL Ribolock RNase inhibitor). Homogenization was performed with 10 strokes using the loose (A) pestle followed by 10 strokes with the tight (B) pestle. The homogenate was filtered through a 70-μm cell strainer to remove debris.
The Illumina NovaSeq PE150 sequencing strategy was utilised to generate one lane of sequencing data, yielding approximately 120 gigabytes of raw data. The raw image files from high-throughput sequencing were processed using CASAVA for base calling, resulting in sequenced reads stored in FASTQ format. FASTQ is a prevalent text format for the storage of biological sequences alongside their corresponding quality scores. In data generated by the Illumina NovaSeq PE150 platform, both paired-end reads are 150 base pairs (bp) in length. For 10X Genomics libraries, the first 26 base pairs of read 1 contain cell barcode and UMI (unique molecular identifier) information, which is crucial for distinguishing the origin of read 2. It is considered that the bases following the initial 26 base pairs in read 1 are non-informative. In read 292 bp are regarded as informative data.

value: spinal cord


title: polysome_KO_rep3

city: Daejeon

first: Haemyeong

last: Jung

address: 125 Gwahak-ro, Yuseong-gu

department: Plant Systems Engineering Research Center

country: South Korea

institute: KRIBB

description: polysomal RNA was extracted

data_processing:
Raw sequencing data were filtered using standard RNA-seq parameters (Illumina pipeline).
The transcriptome short reads (< 25 bp) were filtered out using DynamicTrim and LengthSort of solexaQA package
The read counts were calculated by mapping the filtered reads that passed the pre-processing using HTSeq
The filtered reads were normalised using the DESeq library
The IR ratio was calculated by dividing the read depth of introns by the average read depth of two adjacent exons
Assembly: The intron retention (IR) ratio was calculated by dividing the read depth of introns by the average read depth of two adjacent exons. AS occurred outside of IRs requiring junction reads, junction information was extracted using regtools
Supplementary files format and content: IRGSP-1.0 (Oryza sativa Japonica Group (Japanese rice) genome assembly)
Supplementary files format and content: Xlsx was processed data

organism: Oryza sativa Japonica Group

source_name: Shoot

growth_protocol: Rice seeds were sown on 1/2 MS gel for 3 days germination and transfer and growth the 50 mL conical ture 4 days in rice chamber (26℃, light/dart 14 h/10 h, and 65% humidity)

extract_protocol:
Monosomal or polysomal RNA was prepared from leaf using WizPrepTM Plant RNA Mini Kit (WIZBIOsolutions, Seongnam, South Korea)
Extracted RNA was extracted from the leaves, and cDNA was synthesized using PrimeScript™ RT reagent Kit (TaKara, Japan). The resultant cDNA fragments were purifed, end-reparided, and ligated to index adapters following the Illumina protocol using Ribo-zero kit.

treatment_protocol: 1-week-old rices were treated 20% PEG-6000 for 6 hours, ribosome profiling by sucrose gradient was analyzed using rice shoots, monosomal or polysomal RNA was precipitated from each fractionation, and extracted.

value: Shoot


title: DUX4OE_Ctrl_KD (161 and 2477)_rep2


title: 4C-GFP-1

description: Library name: 4C-GFP-1


title: polysome_KO_rep2

description: polysomal RNA was extracted


title: 8C_nanopore

data_processing:
Fastq files of different samples were obtained using demultiplex (v 1.2.2) based on sample unqiue barcode. Barcode of each sample was removed using porechop (v 0.2.4).
Full-length non-concatemer (FLNC) reads were mapped to the GRCh38 genome assembly using minimap2 (v 2.26-r1175), with the following parameters: minimap2 -ax splice -uf --secondary=no -C5 -MD
And then sam files containing aligned FLNC reads were processed using TranscriptClean (v 2.0.2) in order to correct mis-matches, indels
Sam files filter by TranscriptClean were then converted to bam files using Samtools, bam files were sorted and indexed with Samtools
TranscriptClean-filtered and Samtools-sorted bam file was used to obtain transcript assembly files using StringTie2 (v 2.2.1) for each sample
Assembly: GRCh38 (hg38)
Supplementary files format and content: bigwig

growth_protocol: H1 cells were cultured in commercially available mTeSR medium on Matrix gel pre-coated plates. Human 8-Cell embryos were cultured in commercially available G-1 plus medium.

extract_protocol:
For toti-like cells, RNA was extracted by trizol. For human 8C embryos, RNA was extracted using Smart-seq2 protocols.
OligodT was used to generate full-length cDNA, and template switching was performed for final full-length DNA libraries.

value: human 8C embryo


title: DUX4OE_Ctrl_KD (161 and 2477)_rep1


title: DUX4OE_siHNRNPU_rep2

treatment_protocol: Firstly, siRNA for NC KD and HNRNPU KD were respectively transfected into the cells and cultured for 24H. Later, dox (final concentration 1ug/ml) was added into the medium to induce DUX4 expression


title: DUX4OE_nanopore


title: 4C-L1-KD-3

description: Library name: 4C-LINE1 KD-3

treatment_protocol: Human 3PN zygotes were micor-injected with Ctrl ASO (Ctrl KD) and LINE-1 ASO (LINE-1 KD) at day 1 and in vitro cultured.

value: micro-injection with LINE-1 ASO


title: 4C-L1-KD-1

description: Library name: 4C-LINE1 KD-1

value: human 4C embryo


title: polysome_WT_rep2

description: polysomal RNA was extracted


title: DUX4OE_siHNRNPU_rep1


title: WT monkey striatum_line2

description: Library name: WT_STR_line2

source_name: striatum

value: striatum


title: BRS group

description: Library name: BRS


title: WT monkey  spinal cord_line1

description: Library name: WT_SP_line1


title: WT monkey  spinal cord_line3

description: Library name: WT_SP_line3


title: DUX4OE_siNC_rep1


title: DUX4OE_siNC_rep2


title: 4C-GFP-3

description: Library name: 4C-GFP-3


title: polysome_KO_rep1

description: polysomal RNA was extracted


title: polysome_WT_rep3

description: polysomal RNA was extracted


title: WT monkey striatum_line4

description: Library name: WT_STR_line4


title: WT monkey  spinal cord_line2

description: Library name: WT_SP_line2


title: 4C-NC-Control KD-2

description: Library name: 4C-Control KD-2


title: 4C-L1-KD-2

description: Library name: 4C-LINE1 KD-2


title: 4C-NC-Control KD-3

description: Library name: 4C-Control KD-3


title: polysome_WT_rep1

description: polysomal RNA was extracted


title: WT monkey striatum_line3

description: Library name: WT_STR_line3


title: 8C-3PN-control-3

description: Library name: 8C-3PN Control-3


title: HSC cells, MC38 2

city: guangzhou

first: Songqi

last: Zhu

state: guangdong

address: No. 74, Zhongshan 2nd Road, Yuexiu District

institute: Sun Yat-sen University

description:
Library name: Sample5
B2

data_processing:
RNA-seq reads were aligned to mouse genome mm10 and gene annotation from the Ensembl database.
Low quality reads were removed and the adaptor sequences were trimmed by Trim Galore (v0.5.0).
The remaining pair-end reads were mapped to the reference genome by STAR (v2.6.1) with ENCODE options.
The uniquely mapped reads were counted by HTSeq (v0.10.0), and normalized by trimmed mean of M values.
Assembly: mm10
Supplementary files format and content: count.txt.gz

source_name: Bone Marrow

extract_protocol:
In brief, intact bone marrows from mice at the age of 6-8weeks were flushed from mouse femora and tibiae. Bone marrow cells by pipetting with 1 mL syringe, and then underwent red blood cell lysis using 0.16 M ammonium chloride solution.
Low input RNA seq was performed according to published scRNA seq protocols with modifications (Picelli et al., 2014). Briefly, FACS-sorted 1500 HSCs in 3-5 μl PBS were transferred into 40 μl cell lysis buffer prepared by adding 2 μl of RNase inhibitor to 38 μl of a 0.25% (vol/vol) Triton X-100 solution. Quickly vortex the tube to mix, and then purify RNA using 80 μl VAHTS RNA Clean Beads (N412, Vayzme), following reverse transcription with 5 μl purified RNA and 15 μl RT mix. cDNAs were purified by VAHTS DNA Clean Beads (N411, Vazyme) for PCR enrichment with 12 cycles. Enriched cDNA was quantified using Qubit dsDNA HS Assay Kit after purification. TruePrepTM DNA library Prep Kit V2 (TD503, Vazyme) was used to prepare RNA seq library following the manufacturer's protocol. Individual libraries were sequenced as Illumina HiSeq 3000 platform. At least three replicates were included.

value: Bone Marrow

value: Hematopoietic Stem Cell

tag: sample group

value: MC38 colon cancer C57BL/6J


title: monosome_KO_rep1

description: monosomal RNA was extracted


title: HSC cells, MC38 3

description:
Library name: Sample6
B3


title: monosome_WT_rep3

description: monosomal RNA was extracted


title: WT monkey hippocampus_line3

description: Library name: WT_HIP_line3

source_name: hippocampus

value: hippocampus


title: HSC cells, MC38 4

description:
Library name: Sample7
B4


title: monosome_WT_rep2

description: monosomal RNA was extracted


title: monosome_KO_rep3

description: monosomal RNA was extracted


title: HSC cells, MC38 1

description:
Library name: Sample4
B1


title: HSC cells, Ctrl 2

description:
Library name: Sample2
w2

value: control


title: 4C-NC-Control KD-1

description: Library name: 4C-Control KD-1

value: micro-injection with Ctrl ASO


title: 8C-0PN-arrest-5

description: Library name: 8C-0PN Arrest-5


title: 8C-3PN-control-2

description: Library name: 8C-3PN Control-2


title: WT monkey hippocampus_line1

description: Library name: WT_HIP_line1


title: 8C-3PN-control-1

description: Library name: 8C-3PN Control-1


title: monosome_KO_rep2

description: monosomal RNA was extracted


title: 8C-0PN-arrest-4

description: Library name: 8C-0PN Arrest-4


title: WT monkey striatum_line1

description: Library name: WT_STR_line1


title: HSC cells, Ctrl 1

description:
Library name: Sample1
w1


title: Tau monkey  spinal cord_line2

description: Library name: Tau_SP_line2


title: 8C-0PN-arrest-2

description: Library name: 8C-0PN Arrest-2


title: monosome_WT_rep1

description: monosomal RNA was extracted


title: WT monkey hippocampus_line2

description: Library name: WT_HIP_line2


title: HSC cells, Ctrl 3

description:
Library name: Sample3
w3


title: WT monkey hippocampus_line4

description: Library name: WT_HIP_line4


title: 8C-0PN-arrest-3

description: Library name: 8C-0PN Arrest-3


title: Shoot, PEG_osfkbp20-1b_rep2

description:
KO_P-5
IR4.KO_P_vs_WT_P.xlsx

data_processing:
Raw sequencing data were filtered using standard RNA-seq parameters (Illumina pipeline).
The transcriptome short reads (< 25 bp) were filtered out using DynamicTrim and LengthSort of solexaQA package
The read counts were calculated by mapping the filtered reads that passed the pre-processing using HTSeq
The filtered reads were normalised using the DESeq library
The IR ratio was calculated by dividing the read depth of introns by the average read depth of two adjacent exons
Assembly: The intron retention (IR) ratio was calculated by dividing the read depth of introns by the average read depth of two adjacent exons. AS occurred outside of IRs requiring junction reads, junction information was extracted using regtools
Supplementary files format and content: IRGSP-1.0 (Oryza sativa Japonica Group (Japanese rice) genome assembly)
Supplementary files format and content: Xlsx contains Normalized count

extract_protocol:
Total RNA was prepared from leaf using WizPrepTM Plant RNA Mini Kit (WIZBIOsolutions, Seongnam, South Korea)
Total RNA was extracted from the leaves, and cDNA was synthesized using PrimeScript™ RT reagent Kit (TaKara, Japan). The resultant cDNA fragments were purifed, end-reparided, polyA-tailed, and ligated to index adapters following the Illumina protocol.

treatment_protocol: 1-week-old rices were treated mock or 20% PEG-6000 for 6 hours

tag: cultivar

value: PEG


title: pTh17_cells, BTP2 Treatment, Day4, biorep1 [Control-3_BTP2_pTh17_S12]

city: Los Angeles

first: Yousang

last: Gwack

state: CA

address: 10833 Le Conte Ave, 53-159 CHS

department: Physiology

institute: Uuniversity of California Los Angeles

description:
Library name: Sample12
Library name: Column names in raw_count file: Control-1_BTP2_pTh17_Raw_Read_Counts, Control-2_BTP2_pTh17_Raw_Read_Counts, Control-3_BTP2_pTh17_Raw_Read_Counts (technical replicates)

data_processing:
Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq v2.19.1.403 software
The reads were mapped by STAR 2.7.9a and read counts per gene were quantified using the mouse Ensembl GRCm39.105 GTF file.
In Partek Flow, read counts were normalized by CPM +1.0E-4.
Assembly: mm10
Supplementary files format and content: tab-delimited files include RAW and CPM normalized counts for each sample

source_name: Lymph nodes, Spleen

growth_protocol: Naive CD4+ T-cells were isolated and purified from wild-type mice. Naïve CD4+ T cells were enriched by magnetic sorting from single-cell suspensions generated by mechanical disruption of spleens and lymph nodes of adult mice using MagniSort naïve CD4+ T cell enrichment kit (catalog # 8804-6824-74,ThermoFisher Scientific). For effector T cell differentiation, cells were stimulated with anti-CD3 antibody (1452C11, Bio X Cell) and anti-CD28 antibody (Clone 37.51, Bio X Cell) for 48 hours on a plate coated with rabbit anti-hamster antibody (MP Biomedicals). CD4 + CD25 - T cells were cultured with anti-IL-4 antibody (Peprotech) and 10 μg/ml anti-IFN-γ antibody, 30 ng/ml IL-6 (Peprotech), 10 ng/ml IL-23 (R&D Systems) and 10 ng/ml IL-1β (R&D Systems) for pathogenic Th17 differentiation and cultured in T cell medium. For Th1 cell differentiation, CD4 + CD25 - T cells were cultured with anti-IL-4 antibody (Peprotech) and IL-12 for Th1 differentiation. In the BTP2 treatment groups, BTP2 was applied transiently between 24-48 hrs during differentiation. After 48 h, cells were taken off the plate and cultured in medium containing 10 U/ml recombinant human IL-2 (NCI Preclinical repository, for Th1 cells) for two days. At day 4 post isolation, ~3 million control and BTP2 Treated Th1 and pathogenic Th17 cells were stimulated with anti-CD3 and anti-CD28 antibodies for 5 h and harvested in TriZol reagent (Invitrogen) for RNA preparation.

extract_protocol:
~3 million control and BTP2 Treated Th1 and Pathogenic  Th17 cells were harvested in TriZol reagent (Invitrogen) for RNA preparation.  3 Biological replicates per genotype were pooled after harvesting and divided into 3 technical replicates per condition. RNA was isolated using RNA purification kit (ThermoFisher Scientific), quantified and used for purification of mRNA, cDNA synthesis and library preparation using  KAPA stranded RNA seq-kit Sample following manufacturer’s instructions.
Libraries for RNA-Seq were prepared with KAPA Stranded RNA-Seq Kit. The workflow consists of depletion of rRNA by hybridization of complementary DNA oligonucleotides, followed by treatment with RNase H and DNase and RNA fragmentaion. First strand cDNA synthesis using random priming followed by second strand synthesis converting cDNA:RNA hybrid to double-stranded cDNA (dscDNA), and incorporates dUTP into the second cDNA strand. cDNA generation is followed by A-tailing, adaptor ligation and PCR amplification. Different adapters were used for multiplexing samples in one lane. Sequencing was performed on Illumina HiSeq3000 for a SE 1x50 run. Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq v2.19.1.403 software.

treatment_protocol: Wild-type vs BTP2 Treated Th1 and Pathogenic Th17cells _96h differentiation

value: Lymph nodes, Spleen

tag: age

value: Female

value: Wild-type

tag: batch


title: Shoot, PEG_osfkbp20-1b_rep1

description:
KO_P-1
IR4.KO_P_vs_WT_P.xlsx


title: pTh17_cells, Control, Day4, biorep1 [Control-3_pTh17_S9]

description:
Library name: Sample10
Library name: Column names in raw_count file: Control-1_pTh17_Raw_Read_Counts, Control-2_pTh17_Raw_Read_Counts, Control-3_pTh17_Raw_Read_Counts  (technical replicates)


title: 8C-0PN-arrest-1

description: Library name: 8C-0PN Arrest-1

value: no treatment


title: 8C-0PN-control-2

description: Library name: 8C-0PN Control-2


title: Th1_cells, BTP2 Treatment, Day4, biorep1 [Control-3_BTP2_Th1_S6]

description:
Library name: Sample11
Library name: Column names in raw_count file: Control-1_BTP2_Th1_Raw_Read_Counts, Control-2_BTP2_Th1_Raw_Read_Counts, Control-3_BTP2_Th1_Raw_Read_Counts (technical replicates)


title: Tau monkey  spinal cord_line3

description: Library name: Tau_SP_line3

value: spinal cord


title: Shoot, PEG_WT_rep1

description:
WT_P-6
IR4.KO_P_vs_WT_P.xlsx

value: Shoot

value: WT


title: Shoot, PEG_osfkbp20-1b_rep3

description:
KO_P-8
IR4.KO_P_vs_WT_P.xlsx


title: Shoot, PEG_WT_rep2

description:
WT_P-7
IR4.KO_P_vs_WT_P.xlsx


title: 8C-0PN-control-3

description: Library name: 8C-0PN Control-3

value: human 8C embryo


title: Tau monkey  spinal cord_line4

description: Library name: Tau_SP_line4


title: 8C-0PN-control-1

description: Library name: 8C-0PN Control-1


title: Shoot, PEG_WT_rep3

description:
WT_P-8
IR4.KO_P_vs_WT_P.xlsx


title: pTh17_cells, BTP2 Treatment, Day4, biorep1 [Control-2_BTP2_pTh17_S11]

description:
Library name: Sample8
Library name: Column names in raw_count file: Control-1_BTP2_pTh17_Raw_Read_Counts, Control-2_BTP2_pTh17_Raw_Read_Counts, Control-3_BTP2_pTh17_Raw_Read_Counts (technical replicates)


title: Bone marrow-derived macrophages were co-cultured with LLC cells and treated with PBS for 24 hours02

city: Chongqing

first: Jianmin

last: Wang

address: No.6, Panxi Seventh Branch Road, Jiangbei District

institute: Chongqing Traditional Chinese Medicine Hospital

description:
Library name: Sample_M2_2
Column name in counts_anno.txt: Sample_M2_2

data_processing:
Raw data (raw reads) were processed usingTrimmomatic (version 0.36). The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.Then the clean reads were mapped to reference  genome using  hisat2 (version 2.2.1.0).
Assembly: GRCm38.p6 (mm10)
Supplementary files format and content: counts_anno.txt.gz

source_name: bone marrow

growth_protocol: Bone marrow was harvested by flushing the femurs and tibias of C57BL/6 mice, and cultured in high-glucose DMEM containing 10% FBS, 1% Penicillin/ Streptomycin, and 50 ng/ml macrophage colony-stimulating factor at 37 °C with 5% CO2.

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. Then these libraries were sequenced on the Illumina sequencing platform ( Illumina HiSeq X Ten) and 125bp/150bp paired-end reads were generated.

treatment_protocol: BMDM were co-cultured with LLC cells using a 0.4 µm pore size transwell system for 48 hours. The medium was then replaced, and the BMDM were treated with either 100 µg/mL β-elemene or an equal volume of PBS for 24 hours.

value: bone marrow

value: macrophages

value: PBS for 24 hours


title: Tau monkey  spinal cord_line1

description: Library name: Tau_SP_line1


title: Th1_cells, BTP2 Treatment, Day4, biorep1 [Control-2_BTP2_Th1_S5]

description:
Library name: Sample7
Library name: Column names in raw_count file: Control-1_BTP2_Th1_Raw_Read_Counts, Control-2_BTP2_Th1_Raw_Read_Counts, Control-3_BTP2_Th1_Raw_Read_Counts (technical replicates)


title: Shoot, Mock_osfkbp20-1b_rep2

description:
KO_M-2
IR3.KO_M_vs_WT_M.xlsx

value: Mock


title: Th1_cells, Control, Day4, biorep1  [Control-3_Th1_S3]

description:
Library name: Sample9
Library name: Column names in raw_count file: Control-1_Th1_Raw_Read_Counts,  Control-2_Th1_Raw_Read_Counts,  Control-3_Th1_Raw_Read_Counts(technical replicates)


title: Bone marrow-derived macrophages were co-cultured with LLC cells and treated with PBS for 24 hours01

description:
Library name: Sample_M2_1
Column name in counts_anno.txt: Sample_M2_1


title: Shoot, Mock_WT_rep3

description:
WT_M-3
IR3.KO_M_vs_WT_M.xlsx


title: Tau monkey striatum_line3

description: Library name: Tau_STR_line3

value: striatum


title: Bone marrow-derived macrophages were co-cultured with LLC cells and treated with 100 µg/mL β-elemene for 24 hours03

description:
Library name: Sample_M1_3
Column name in counts_anno.txt: Sample_M1_3

value: 100 µg/mL β-elemene for 24 hours


title: pTh17_cells, BTP2 Treatment, Day4, biorep1 [Control-1_BTP2_pTh17_S10]

description:
Library name: Sample4
Library name: Column names in raw_count file: Control-1_BTP2_pTh17_Raw_Read_Counts, Control-2_BTP2_pTh17_Raw_Read_Counts, Control-3_BTP2_pTh17_Raw_Read_Counts (technical replicates)


title: Bone marrow-derived macrophages were co-cultured with LLC cells and treated with 100 µg/mL β-elemene for 24 hours02

description:
Library name: Sample_M1_2
Column name in counts_anno.txt: Sample_M1_2


title: pTh17_cells, Control, Day4, biorep1 [Control-2_pTh17_S8]

description:
Library name: Sample6
Library name: Column names in raw_count file: Control-1_pTh17_Raw_Read_Counts, Control-2_pTh17_Raw_Read_Counts, Control-3_pTh17_Raw_Read_Counts  (technical replicates)


title: Bone marrow-derived macrophages were co-cultured with LLC cells and treated with PBS for 24 hours03

description:
Library name: Sample_M2_3
Column name in counts_anno.txt: Sample_M2_3


title: Tau monkey striatum_line4

description: Library name: Tau_STR_line4


title: pTh17_cells, Control, Day4, biorep1 [Control-1_pTh17_S7]

description:
Library name: Sample2
Library name: Column names in raw_count file: Control-1_pTh17_Raw_Read_Counts, Control-2_pTh17_Raw_Read_Counts, Control-3_pTh17_Raw_Read_Counts  (technical replicates)


title: Th1_cells, Control, Day4, biorep1  [Control-1_Th1_S1]

description:
Library name: Sample1
Library name: Column names in raw_count file: Control-1_Th1_Raw_Read_Counts,  Control-2_Th1_Raw_Read_Counts,  Control-3_Th1_Raw_Read_Counts(technical replicates)


title: Tau monkey striatum_line1

description: Library name: Tau_STR_line1


title: Tau monkey striatum_line2

description: Library name: Tau_STR_line2


title: Shoot, Mock_osfkbp20-1b_rep1

description:
KO_M-1
IR3.KO_M_vs_WT_M.xlsx


title: Tau monkey hippocampus_line3

description: Library name: Tau_HIP_line3

value: hippocampus


title: Th1_cells, BTP2 Treatment, Day4, biorep1 [Control-1_BTP2_Th1_S4]

description:
Library name: Sample3
Library name: Column names in raw_count file: Control-1_BTP2_Th1_Raw_Read_Counts, Control-2_BTP2_Th1_Raw_Read_Counts, Control-3_BTP2_Th1_Raw_Read_Counts (technical replicates)


title: Shoot, Mock_osfkbp20-1b_rep3

description:
KO_M-3
IR3.KO_M_vs_WT_M.xlsx


title: Ctrl-3

status: Public on Jan 23 2026

city: Urumqi

first: xinyi

last: deng

address: No. 393 Xinyi Road

department: College of Pharmacy

institute: Xinjiang Medical University

description:
Library name: Ctrl-3
DMSO group, replicate biosample 3

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to DM 1-3 516 R44 (v6.1)  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes fpkm for each sample

source_name: Hela

extract_protocol:
RNA was extracted from tissue using TRIzol reagent. Briefly, cells were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA (1 µg, RIN >7) was enriched for mRNA using poly(A) selection (for eukaryotes) or rRNA depletion (for prokaryotes). The RNA was fragmented (∼200–300 nt) and reverse-transcribed into cDNA using random hexamers and SuperScript IV. Second-strand synthesis was performed with dUTP incorporation (strand-specific libraries). The cDNA was end-repaired, A-tailed, and ligated to Illumina-compatible adapters. Post-ligation cleanup (AMPure XP beads) was followed by size selection (200–500 bp) and uracil digestion (for strand specificity). Library amplification (8–12 cycles) used indexed primers, and final quantification (Qubit) and quality control (Bioanalyzer/TapeStation) ensured optimal fragment size (∼300 bp) and concentration (>10 nM). Libraries were pooled and sequenced (Illumina platforms, 150 bp paired-end).

value: Hela


title: Th1_cells, Control, Day4, biorep1  [Control-2_Th1_S2]

description:
Library name: Sample5
Library name: Column names in raw_count file: Control-1_Th1_Raw_Read_Counts,  Control-2_Th1_Raw_Read_Counts,  Control-3_Th1_Raw_Read_Counts(technical replicates)


title: 119LV17 IL-17 deleter; RRDD fibrosis adventitial biol rep 9

city: Tübingen

first: Jun-Hoe

last: Lee

address: Otfried-Müller-Str. 37

department: Quantitative Biology Centre (QBiC)

country: Germany

institute: University of Tuebingen

description:
Library name: QLRIU133AI
FFPE spatial transcriptome sequencing

data_processing:
Libraries were sequenced on an Illumina NovaSeq 6000 (paired-end 2 × 151 bp, 100 reads/µm²).
FASTQ files were converted to DCC files using the GeoMx NGS Pipeline (v2.0.0.16).
The converted GeoMx data (DCC files) were imported into R studio (v1.1.456, R v4.3.2) for bioinformatics  analysis  primarily  using  the  R  packages  GeomxTools (v3.5.0) and NanoStringNCTools (v1.10.0).
Differential expression analysis was performed using a linear mixed-effect model across the different condition, and models were adjusted for sex and test slide as a random intercept.
Assembly: mm10
Supplementary files format and content: Digital Count Conversion (DCC) files converted from raw fastq files using GeoMX NGS Pipeline (v2.0.0.16).
Supplementary files format and content: Statistic (stats) files as part of the output from GeoMX NGS Pipeline (v2.0.0.16).
Library strategy: Spatial Transcriptomics

source_name: liver

extract_protocol:
5 µm sections were cut from the FFPE blocks of two liver tissue samples from each of the four mouse groups
PCR amplification, indexing, library purification, and quality control were performed according to the manufacturer’s instructions (NanoString GeoMx).

value: liver

value: IL-5;IL-17A double deleter


title: 119LV17 IL-17 deleter; RRDD fibrosis adventitial biol rep 7

description:
Library name: QLRIU131A2
FFPE spatial transcriptome sequencing


title: wild type IGP2 and ∆GID1/2/7/8/9 gametocytes at day 3,6,9 and 12 of development.

city: Melbourne

first: Danushka

middle: Sujeeva

last: Marapana

state: VIC

address: 1G Royal Parade

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

description: Library name: Mini-bulk samples on plate Danu_MB_1 indexed with RPI-43

data_processing:
gene count matrix generated using scPipe v2.2.0
reads were aligned using Rsubread v2.16.0
All code used to perform data processing and analysis of the RNA-seq data are available from https://github.com/WEHISCORE/G000396_Danu
Assembly: PlasmoDB-66_Pfalciparum3D7
Supplementary files format and content: CSV, gene count matrix, rows represent genes and each column is a well, values corresponding to read counts
Supplementary files format and content: CSV, sample sheet, rows represent a sample and columns contain metadata on the sample in the well

organism: Plasmodium falciparum

source_name: Parasite grown in human red blood cells

growth_protocol: Blood stage cultures of P. falciparum were grown in O+ erythrocytes (Lifeblood Australia) and maintained in Roswell Park Memorial Institute (RPMI) RPMI 1640 medium, Glutamax, HEPES (ThermoFisher) supplemented with, 50 μg/ml hypoxanthine, 20 μg/ml gentamicin, 0.25% (w/v) Albumax IITM (ThermoFisher), and 5% (v/v) heat-inactivated human serum (Lifeblood, Australia. Agreement number 21-06VIC-01). The parasite cultures were maintained in microisolator boxes gassed with malaria gas mix (94% N2, 1% O2 and 5% CO2) and grown at 37 °C. In this study, the inducible gametocyte producing (iGP2) parasite line was used as the parental line. To stop commitment to gametocyte production, the parasites were cultured in the presence of 2.5 mM D-(+)-glucosamine hydrochloride.

extract_protocol:
Parasite cultures were harvested at the desired lifecycle stage, centrifuged at 500 x g and the supernatant discarded. Infected RBC pellets were then lysed with 5 pellet volumes of 0.03% saponin and incubated on ice for 15 minutes. The samples were centrifuged at 16,000 x g, the supernatants discarded, and the pellets washed 3 time with 1xPBS. From these pellets RNA was isolated from the PfGID1, 2, 7, 8 and 9 knockouts and parental iGP2 parasites at day 3, 6, 9 and 12 of gametocyte (five biological replicates for each cell line and timepoint were performed) development using the Isolate II RNA mini kit (Bioline).
The RNA concentration of each sample was calculated using the QuantiFluor RNA system (Promega), and RNA quality was determined using high-sensitivity RNA screen tape analysis (Agilent). The RNA concentrations were then normalized to 1 ng/µL by dilution with the FlexDrop automated dispenser (Revvity), and then re-quantified. 1.1 ng of total RNA was reverse transcribed using SuperScript II (Invitrogen) and processed using an adapted CelSeq2 protocol. Briefly, barcoded samples with unique molecular identifiers (UMIs) were pooled after first strand cDNA synthesis and second strand synthesis performed using the MEGAscript T7 transcription kit (ThermoFisher). Amplified RNA was reverse transcribed using a tagged random hexamer without fragmentation, followed by sequencing on a NextSeq 2000 P3 flow cell (Illumina). Technical replicates were performed for each RNA sample.

treatment_protocol: Wild type and ∆GID1/2/7/8/9 parasites grown to day 3,6,9 and 12 of gametocyte development.

value: Parasite grown in human red blood cells

value: P. falciparum

value: Wild type or knockout of PfGID1/2/7/8/9


title: 119LV17 IL-17 deleter; RRDD fibrosis fibrotic tract biol rep 2

description:
Library name: QLRIU126A1
FFPE spatial transcriptome sequencing


title: 119LV16 IL-17 deleter; RRDD fibrosis adventitial biol rep 9

description:
Library name: QLRIU124AJ
FFPE spatial transcriptome sequencing


title: 119LV17 IL-17 deleter; RRDD fibrosis parenchymal biol rep 5

description:
Library name: QLRIU129AP
FFPE spatial transcriptome sequencing


title: 119LV17 IL-17 deleter; RRDD fibrosis fibrotic tract biol rep 3

description:
Library name: QLRIU127A9
FFPE spatial transcriptome sequencing


title: Shoot, Mock_WT_rep2

description:
WT_M-2
IR3.KO_M_vs_WT_M.xlsx


title: Tau monkey hippocampus_line4

description: Library name: Tau_HIP_line4


title: 119LV17 IL-17 deleter; RRDD fibrosis adventitial biol rep 8

description:
Library name: QLRIU132AA
FFPE spatial transcriptome sequencing


title: Bone marrow-derived macrophages were co-cultured with LLC cells and treated with 100 µg/mL β-elemene for 24 hours01

description:
Library name: Sample_M1_1
Column name in counts_anno.txt: Sample_M1_1


title: 119LV16 IL-17 deleter; RRDD fibrosis fibrotic tract biol rep 1

description:
Library name: QLRIU116AS
FFPE spatial transcriptome sequencing


title: 119LV16 IL-17 deleter; RRDD fibrosis fibrotic tract biol rep 3

description:
Library name: QLRIU118AA
FFPE spatial transcriptome sequencing


title: 119LV16 IL-17 deleter; RRDD fibrosis fibrotic tract biol rep 2

description:
Library name: QLRIU117A2
FFPE spatial transcriptome sequencing


title: Tau monkey hippocampus_line1

description: Library name: Tau_HIP_line1


title: Shoot, Mock_WT_rep1

description:
WT_M-1
IR3.KO_M_vs_WT_M.xlsx


title: 15 RRDD fibrosis parenchymal biol rep 6

description:
Library name: QLRIU112AU
FFPE spatial transcriptome sequencing

value: IL-5 deleter


title: iPSC Small Intestine Organoid, PEGstiff, Mesenchymal, Rep j

city: Lausanne

first: Eileen

last: Gentleman

address: Quartier Centre

country: Switzerland

institute: University of Lausanne

description:
Library name: PEGstiff---mes---j
Organoids generated in PEG, then encapsulated for 6 days in a PEG with higher polymer concentration

data_processing:
Reads were quality-controlled and trimmed. Alignment was performed using STAR (version 2.5.2b) to the human reference genome (GRCh38) using a splice-aware aligner. Gene-level counts were generated based on the corresponding GRCh38 annotation, filtered for lowly expressed genes, and normalized.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file containing raw gene counts.

source_name: Human iPSC (Control 1, clone 1.5; female, 42 years, 46,XX)  form Maastricht University

growth_protocol: hIOs were formed from hiPSC. iPSCs were seeded on plates pre-coated with Matrigel or Vitronectin XF in E8 basal media. Differentiation was induced (Day 0) by adding Activin A to generate definitive endoderm, followed by induction of midgut identity on Day 4 using media supplemented with FGF4 and CHiR99021. On Day 7, spheroids were collected for encapsulation.

extract_protocol:
Sorted EPCAM+ and CD90+ populations were lysed in RLT buffer (Qiagen) supplemented with β-mercaptoethanol. Samples were sent to Azenta for RNA extraction using their standard pipeline.
Libraries were prepared using a standard RNA-seq workflow (Azenta). Sequencing was performed on an Illumina NovaSeq 6000 instrument to a depth of ~30 million paired-end reads per sample (2x150 bp configuration).

treatment_protocol: For Matrigel samples: Spheroids were encapsulated in Matrigel and cultured in maturation media (ENR) supplemented with EGF, Rspondin, Noggin, and IL-2. For PEG samples: Spheroids were encapsulated in 2.5% PEG-ACRL hydrogels, then passaged to 2.5% PEG-VS hydrogels. For PEG Stiff samples: At day 28, hIOs were passaged from 2.5% PEG-VS to 3.0% PEG-VS hydrogels and cultured for 6 days. Sorting: Prior to sequencing, organoids were dissociated and sorted via FACS to isolate Epithelial (EPCAM+) and Mesenchymal (CD90+) populations.

value: small intestine organoid

value: mesenchymal cell

value: Control 1, clone 1.5

value: PEGstiff enviroment


title: iPSC Small Intestine Organoid, MG, Mesenchymal, Rep g

description:
Library name: MG--mes---g
Organoids generated in Matrigel (Control conditions).

value: Matrigel enviroment


title: Ctrl-1

description:
Library name: Ctrl-1
DMSO group, replicate biosample 1


title: DXY-2

description:
Library name: DXY-2
The lead compound, B1, treatment group, replicate biosample 2


title: 15 RRDD fibrosis parenchymal biol rep 5

description:
Library name: QLRIU111AM
FFPE spatial transcriptome sequencing


title: iPSC Small Intestine Organoid, MG, Mesenchymal, Rep e

description:
Library name: MG--mes---e
Organoids generated in Matrigel (Control conditions).


title: Tau monkey hippocampus_line2

description: Library name: Tau_HIP_line2


title: DXY-1

description:
Library name: DXY-1
The lead compound, B1, treatment group, replicate biosample 1


title: 15 RRDD fibrosis parenchymal biol rep 4

description:
Library name: QLRIU110AE
FFPE spatial transcriptome sequencing


title: DXY-3

description:
Library name: DXY-3
The lead compound, B1, treatment group, replicate biosample 3


title: Ctrl-2

description:
Library name: Ctrl-2
DMSO group, replicate biosample 2


title: 119LV17 IL-17 deleter; RRDD fibrosis parenchymal biol rep 6

description:
Library name: QLRIU130AS
FFPE spatial transcriptome sequencing


title: 119LV17 IL-17 deleter; RRDD fibrosis parenchymal biol rep 4

description:
Library name: QLRIU128AH
FFPE spatial transcriptome sequencing


title: 119LV16 IL-17 deleter; RRDD fibrosis parenchymal biol rep 6

description:
Library name: QLRIU121AT
FFPE spatial transcriptome sequencing


title: 119LV16 IL-17 deleter; RRDD fibrosis adventitial biol rep 7

description:
Library name: QLRIU122A3
FFPE spatial transcriptome sequencing


title: 119LV17 IL-17 deleter; RRDD fibrosis fibrotic tract biol rep 1

description:
Library name: QLRIU125AR
FFPE spatial transcriptome sequencing


title: iPSC Small Intestine Organoid, PEG, Mesenchymal, Rep d

description:
Library name: PEG---mes---d
Organoids generated in standard PEG culture conditions

value: PEG enviroment


title: 119LV16 IL-17 deleter; RRDD fibrosis adventitial biol rep 8

description:
Library name: QLRIU123AB
FFPE spatial transcriptome sequencing


title: 15 RRDD fibrosis fibrotic tract biol rep 2

description:
Library name: QLRIU108A3
FFPE spatial transcriptome sequencing


title: 119LV16 IL-17 deleter; RRDD fibrosis parenchymal biol rep 4

description:
Library name: QLRIU119AI
FFPE spatial transcriptome sequencing


title: 119LV16 IL-17 deleter; RRDD fibrosis parenchymal biol rep 5

description:
Library name: QLRIU120AL
FFPE spatial transcriptome sequencing


title: iPSC Small Intestine Organoid, PEGstiff, Epithelial, Rep k

description:
Library name: PEGstiff---epi---k
Organoids generated in PEG, then encapsulated for 6 days in a PEG with higher polymer concentration

value: epithelial cell


title: 14 RRDD fibrosis adventitial biol rep 7

description:
Library name: QLRIU104A5
FFPE spatial transcriptome sequencing


title: 15 RRDD fibrosis adventitial biol rep 7

description:
Library name: QLRIU113A4
FFPE spatial transcriptome sequencing


title: 15 RRDD fibrosis adventitial biol rep 9

description:
Library name: QLRIU115AK
FFPE spatial transcriptome sequencing


title: 14 RRDD fibrosis parenchymal biol rep 6

description:
Library name: QLRIU103AV
FFPE spatial transcriptome sequencing


title: iPSC Small Intestine Organoid, MG, Epithelial, Rep 1

description:
Library name: MG--epi---1
Organoids generated in Matrigel (Control conditions).


title: iPSC Small Intestine Organoid, MG, Epithelial, Rep g

description:
Library name: MG--epi---g
Organoids generated in Matrigel (Control conditions).


title: iPSC Small Intestine Organoid, MG, Epithelial, Rep e

description:
Library name: MG--epi---e
Organoids generated in Matrigel (Control conditions).


title: 15 RRDD fibrosis adventitial biol rep 8

description:
Library name: QLRIU114AC
FFPE spatial transcriptome sequencing


title: iPSC Small Intestine Organoid, PEGstiff, Mesenchymal, Rep i

description:
Library name: PEGstiff---mes---i
Organoids generated in PEG, then encapsulated for 6 days in a PEG with higher polymer concentration


title: 14 RRDD fibrosis fibrotic tract biol rep 2

description:
Library name: QLRIU099A0
FFPE spatial transcriptome sequencing


title: iPSC Small Intestine Organoid, MG, Mesenchymal, Rep f

description:
Library name: MG--mes---f
Organoids generated in Matrigel (Control conditions).


title: iPSC Small Intestine Organoid, PEG, Epithelial, Rep d

description:
Library name: PEG---epi---d
Organoids generated in standard PEG culture conditions


title: iPSC Small Intestine Organoid, MG, Mesenchymal, Rep h

description:
Library name: MG--mes---h
Organoids generated in Matrigel (Control conditions).


title: iPSC Small Intestine Organoid, PEG, Epithelial, Rep c

description:
Library name: PEG---epi---c
Organoids generated in standard PEG culture conditions


title: iPSC Small Intestine Organoid, MG, Epithelial, Rep f

description:
Library name: MG--epi---f
Organoids generated in Matrigel (Control conditions).


title: iPSC Small Intestine Organoid, PEG, Mesenchymal, Rep b

description:
Library name: PEG---mes---b
Organoids generated in standard PEG culture conditions


title: 15 RRDD fibrosis fibrotic tract biol rep 3

description:
Library name: QLRIU109AB
FFPE spatial transcriptome sequencing


title: 14 RRDD fibrosis adventitial biol rep 8

description:
Library name: QLRIU105AD
FFPE spatial transcriptome sequencing


title: 13 RR control adventitial biol rep 4

description:
Library name: QLRIU077A4
FFPE spatial transcriptome sequencing

value: vector


title: iPSC Small Intestine Organoid, PEGstiff, Mesenchymal, Rep k

description:
Library name: PEGstiff---mes---k
Organoids generated in PEG, then encapsulated for 6 days in a PEG with higher polymer concentration


title: iPSC Small Intestine Organoid, PEG, Epithelial, Rep b

description:
Library name: PEG---epi---b
Organoids generated in standard PEG culture conditions


title: 15 RRDD fibrosis fibrotic tract biol rep 1

description:
Library name: QLRIU107AT
FFPE spatial transcriptome sequencing


title: iPSC Small Intestine Organoid, PEG, Epithelial, Rep a

description:
Library name: PEG---epi---a
Organoids generated in standard PEG culture conditions


title: 14 RRDD fibrosis fibrotic tract biol rep 3

description:
Library name: QLRIU100A7
FFPE spatial transcriptome sequencing


title: 786-O_H4K12la_DEX_rep2

city: Beijing

first: Lin

address: Xueyuan Road 38

institute: Peking University

description:
Library name: H4K12la_DEX_rep2
CUT&Tag profiling of H4K12 lactylation in dexamethasone-treated 786-O cells

data_processing:
Raw data were preprocessed by using fastp version0.19.6.
Filtered reads were aligned to the genome (GRCh38, hg38) assembly using Bowtie2.
Peaks were called using MACS version2.
Assembly: GRCh38, hg38
Supplementary files format and content: bigwig files were generated using deepTools.
Library strategy: CUT&Tag

growth_protocol: 786-O cells were maintained according to the ATCC’s recommendation.

extract_protocol:
CUT&Tag was performed using the NovoNGS CUT&Tag 4.0 High-Sensitivity Kit (for Illumina) (Novoprotein) according to the manufacturer’s instructions. Briefly, 786-O cells were harvested and immobilized on Concanavalin A–coated magnetic beads. Cells were incubated sequentially with specific antibodies against H4K12 lactylation or GR and a secondary antibody. Subsequently, pA-Tn5 transposase was added to bind antibody-labeled chromatin. After transposase activation and tagmentation, genomic DNA fragments were released, amplified, and purified for library preparation.
The library for sequencing was constructed and NovoNGS DNA Clean beads were used for purification steps. The library was quantified with NovoNGS CUT&Tag 4.0 High-Sensitivity Kit (for Illumina) and sequenced on an Illumina novaseq 150PE.

treatment_protocol: 786-O cells were either left untreated as the control group or treated with dexamethasone at a final concentration of 10 μM for 48 hours prior to CUT&Tag profiling.

value: Human renal carcinoma cells

value: genomic DNA

value: Dexamethasone


title: 14 RRDD fibrosis adventitial biol rep 9

description:
Library name: QLRIU106AL
FFPE spatial transcriptome sequencing

value: liver


title: 14 RRDD fibrosis parenchymal biol rep 5

description:
Library name: QLRIU102AN
FFPE spatial transcriptome sequencing


title: 786-O_H4K12la_CTRL_rep2

description:
Library name: H4K12la_CTRL_rep2
CUT&Tag profiling of H4K12 lactylation in untreated 786-O cells

value: Control


title: 12 RR control adventitial biol rep 6

description:
Library name: QLRIU073A6
FFPE spatial transcriptome sequencing


title: 786-O_H4K12la_CTRL_rep1

description:
Library name: H4K12la_CTRL_rep1
CUT&Tag profiling of H4K12 lactylation in untreated 786-O cells


title: 786-O_H4K12la_DEX_rep1

description:
Library name: H4K12la_DEX_rep1
CUT&Tag profiling of H4K12 lactylation in dexamethasone-treated 786-O cells


title: 13 RR control parenchymal biol rep 1

description:
Library name: QLRIU074AE
FFPE spatial transcriptome sequencing


title: Caki-1-H4K12la_Rep2

description: Library name: Caki-1-H4K12la_Rep2

growth_protocol: 786-O and Caki-1 cells were maintained according to the ATCC’s recommendation.

extract_protocol:
CUT&Tag was performed using NovoNGS CUT&Tag 4.0 High-Sensitivity Kit (for Illumina) (Novoprotein) according to manufacturer’s instructions. In brief, 786-O or Caki-1 cells were collected and bounded to Concanavalin A–coated beads. Subsequently, cells were resuspended in antibody buffer and incubated with primary antibody against H4K12 lactylation and secondary antibodies in order. The samples were incubated with pA-Tn5 transposase. After transposon activation and tagmentation, DNA was isolated, amplified, and purified to construct library.
The library for sequencing was constructed and NovoNGS DNA Clean beads were used for purification steps. The library was quantified with NovoNGS CUT&Tag 4.0 High-Sensitivity Kit (for Illumina) and sequenced on an Illumina novaseq 150PE.

treatment_protocol: Untreated

value: Human renal cancer cells


title: iPSC Small Intestine Organoid, PEG, Mesenchymal, Rep a

description:
Library name: PEG---mes---a
Organoids generated in standard PEG culture conditions


title: 14 RRDD fibrosis fibrotic tract biol rep 1

description:
Library name: QLRIU098AQ
FFPE spatial transcriptome sequencing


title: iPSC Small Intestine Organoid, PEGstiff, Epithelial, Rep i

description:
Library name: PEGstiff---epi---i
Organoids generated in PEG, then encapsulated for 6 days in a PEG with higher polymer concentration


title: iPSC Small Intestine Organoid, PEGstiff, Epithelial, Rep j

description:
Library name: PEGstiff---epi---j
Organoids generated in PEG, then encapsulated for 6 days in a PEG with higher polymer concentration


title: 12 RR control parenchymal biol rep 2

description:
Library name: QLRIU069AD
FFPE spatial transcriptome sequencing


title: 13 RR control adventitial biol rep 5

description:
Library name: QLRIU078AC
FFPE spatial transcriptome sequencing


title: 12 RR control parenchymal biol rep 1

description:
Library name: QLRIU068A5
FFPE spatial transcriptome sequencing


title: 14 RRDD fibrosis parenchymal biol rep 4

description:
Library name: QLRIU101AF
FFPE spatial transcriptome sequencing


title: 13 RR control parenchymal biol rep 3

description:
Library name: QLRIU076AU
FFPE spatial transcriptome sequencing


title: GR

description:
Library name: 786-O_GR
CUT&Tag profiling of GR in dexamethasone-treated 786-O cells


title: 13 RR control parenchymal biol rep 2

description:
Library name: QLRIU075AM
FFPE spatial transcriptome sequencing


title: 5 RR fibrosis parenchymal biol rep 6

description:
Library name: QLRIU094AS
FFPE spatial transcriptome sequencing


title: 738_hTCR

first: Geoffrey

last: Owens

address: 300 Stein Plaza Ste 562

department: Neurosurgery

institute: UCLA

description:
Library name: 738_hTCR_S1
10x Genomics

data_processing:
Reads were demultiplexed and aligned to the Genome Reference Consortium Human Reference 38 (GRCh Build 38) and VDJ reference data (based on Ensembl 94 release) using Cell Ranger count and Cell Ranger VDJ pipelines.
Assembly: Human GRCh Build 38
Supplementary files format and content: mtx, tsv
Library strategy: TCR-seq

source_name: brain

extract_protocol:
Fresh brain tissue collected from the operating room in ice cold Hibernate® containing penicillin/streptomycin (120U/ml and 100ug/ml respectively) was transferred to magnesium calcium free Hanks Balanced Salt Solution containing HEPES (20mM), glucose (5mM) and penicillin/streptomycin, and finely minced on ice with spring scissors. Tissue fragments were transferred to RPM1 containing 10% human and HEPES (20mM) and digested overnight at room temperature with Type IV collagenase (~800U/ml) followed by fractionation on a 70%:30% Percoll® (Millipore Sigma, St. Louis MO) step gradient.
Two 10x Genomics Chromium single cell gene expression libraries (5’ gene expression and TCR V(D)J) were made from each sample and sequenced on a NovaSeq 6000 instrument in a SP flow cell (2x50 bp).

value: brain

tag: tissue source

value: Rasmussen encephalitis (RE) surgery case

value: immune cells

tag: library type

value: TCR V(D)J


title: 12 RR control adventitial biol rep 5

description:
Library name: QLRIU072AW
FFPE spatial transcriptome sequencing


title: 13 RR control adventitial biol rep 6

description:
Library name: QLRIU079AK
FFPE spatial transcriptome sequencing


title: 5 RR fibrosis parenchymal biol rep 5

description:
Library name: QLRIU093AK
FFPE spatial transcriptome sequencing


title: 738_5GEX

description:
Library name: 738_5GEX_S2
10x Genomics

data_processing:
Reads were demultiplexed and aligned to the Genome Reference Consortium Human Reference 38 (GRCh Build 38) and VDJ reference data (based on Ensembl 94 release) using Cell Ranger count and Cell Ranger VDJ pipelines.
Assembly: Human GRCh Build 38
Supplementary files format and content: mtx, tsv

value: 5’ gene expression


title: 5 RR fibrosis fibrotic tract biol rep 3

description:
Library name: QLRIU091A4
FFPE spatial transcriptome sequencing


title: Caki-1-H4K12la_Rep1

description: Library name: Caki-1-H4K12la_Rep1


title: 12 RR control adventitial biol rep 4

description:
Library name: QLRIU071AO
FFPE spatial transcriptome sequencing


title: 12 RR control parenchymal biol rep 3

description:
Library name: QLRIU070AG
FFPE spatial transcriptome sequencing


title: MCF-7 cell, HiFi FaDe Cas9 editing treatment, 48 hours, replicate 2

city: Mölndal

first: Benjamin

last: Keith

address: Pepparedsleden 1

country: Sweden

institute: AstraZeneca

description: Library name: MCF7_KI_48h_rep2

data_processing:
Libraries were assessed using FastQC (v0.12.1), Qualimap (v2.2.2c) and SAMtools stats (v1.18). Alignment was performed using STAR (version 2.7.2b) with alignment against the human genome (GRCh38, Ensembl v105). Sequencing Quality control metrics were obtained using Qualimap (v2.2.2c) and summarized using MultiQC (v1.17). Trimming of adapters was performed using NGmerge (v0.3). A human transcriptome index consisting of cDNA and ncRNA entries from Ensembl v105) was generated and gene abundances were obtained using Salmon (v1.1.0). The bioinformatics workflow was organized using Nextflow workflow management system (v20.10) and Bioconda software management tool.
Differential gene expression analysis was performed using Dream (variancePartition v1.32.2). Gene set enrichment analysis was performed with FGSEA (v1.28.0) using Kyoto Encyclopedia of Genes and Genomes (KEGG; C2_CP:KEGG of the MSigDB collection v7.5.123). For plotting and data wrangling, Tidyverse (v2.0.0), PCAtools (v2.14.0) EnhancedVolcano (v1.18.0), and ComplexHeatmap (v2.18.024) were used. R 4.3.2 was used for downstream analyses.
Assembly: GRCh38, Ensembl 105
Supplementary files format and content: Raw counts from tximport, tab seprated
Supplementary files format and content: Transcripts per Million  counts from tximport abundances, tab separated

source_name: breast

growth_protocol: MCF7 cells (ATCC HTB-22) were maintained in RPMI 1640 Medium, GlutaMAX, HEPES (Gibco #72400-047) with 10% FBS (Gibco #10270-106). HepG2 (ATCC HB-8065) were cultured in MEM, GlutaMAX (Gibco #41090-036) with 1x MEM non-essential amino acids solution (Gibco #11140-050), 1% (v/v) sodium pyruvate (Gibco #11360-070), and 10% FBS (Gibco #10270-106). Cell lines were regularly tested for mycoplasma contaminations, and cell identity was confirmed through STR profiling.

extract_protocol:
Total RNA was isolated from 5 × 10⁶ cells using a lysis buffer mix containing Proteinase K from the RNAdvance Tissue kit (Beckman Coulter). Cells were vortexed thoroughly and incubated at 37°C for 25 minutes. RNA isolation, including a 15-minute DNase I treatment, was carried out according to the manufacturer’s protocol on a Biomek i7 Hybrid robotic workstation (Beckman Coulter). RNA quantity and quality were assessed using a Fragment Analyzer 5300 system (Agilent), and RNA integrity number (RIN) values were recorded.
Total RNA-seq libraries were prepared using the KAPA RNA HyperPrep with RiboErase kit (Roche) on a Tecan Fluent® liquid handler, following the manufacturer’s instructions. Library integrity and quality were evaluated with the SS NGS Fragment Kit (1–6000 bp; Agilent) on a fragment analyzer. Sequencing was performed as paired-end 2 × 100 bp on an Illumina NovaSeq 6000 platform using a v1.5 SP Reagent kit (Illumina).

treatment_protocol: CRISPR reagents: For cell engineering purposes to specifically address precise KI efficiency, we used synthetic sgRNAs targeting SERPINA1 locus in combination with a single-strand DNA (HDR template) consisting of 39 nt to be integrated, flanked by 30 nt homology arms. Synthetic sgRNAs and HDR template were synthesized by Sigma-Aldrich, MERCK. Spacers and donor sequences are summarized in Table S1. The following small molecules were used in this study. PolQi1 (WO2021/028643, Example 158), PolQi2 (WO2020/243459, Example 99) were provided by AstraZeneca (Gothenburg, Sweden), and AZD7648 (HY-111783, MedChemExpress) is commercially available. All compounds were dissolved in DMSO (Sigma-Aldrich, MERCK #D2650) at a concentration of 10 mM. Transfections – RNP preparation and delivery: To prepare RNP complexes, spCas9-GFP (Sigma, MERCK #CAS9GFPPRO), sgRNAs, and ssDNA HDR template were incubated in a [1:1:1 molar ratio] for 10-15 min at room temperature. RNPs were kept on ice until electroporation. During RNP incubation, cells were washed with PBS (Gibco #10010023), detached with TrypLE Express Enzyme (Gibco #12604013), resuspended in cell culture medium, and cell number and viability were assessed using Nucleocounter NC-3000 cell counter (ChemoMetec). Prior to electroporation, cells were transferred into 15 ml tubes, washed with PBS and resuspended in Buffer R (Neon Transfection System, Invitrogen, #MPK1025) to a final density of 1 x 107 cells/ml. For electroporation, 5 x 105 cells (MCF7 or HepG2) were combined with 60 pmol spCas9 nuclease, 60pmol sgRNA (30pmol per guide), and 60pmol ssDNA. Electroporation was performed using Neon system (Invitrogen) applying the following settings: 1600V, 10ms pulse, 3 pulses. Afterwards, cells were transferred into 24-well plate format containing cell culture media with DMSO or small molecules at different concentrations (PolQi1 and PolQi2 at 1.5 µM, AZD7648 at 1µM). Transient transfections – plasmid delivery:  MCF7 cells were seeded into T75 flasks (60,000 cells/cm2) 24 hours before transfections. pMAZ-CMV-PCNA plasmid was transfected using Lipofectamine 3000 transfection reagent (Invitrogen, #L3000001) following manufacturer’s instructions. Briefly, a total of 8µg of plasmid DNA was used to transfect cells in T75 format. As positive control, the same number of cells were transfected in T75 flasks using pMAZ-CMV-EGFP, to address transfection efficiency and CMV promoter activity. Cells were cultured for 48h before the editing experiments.

value: breast

value: MCF-7 cell

value: epithelia

value: HiFi FaDe Cas9 editing

tag: treatment duration

value: 48 hours


title: 786-O-H4K12la_Rep2

description: Library name: 786-O-H4K12la_Rep2


title: 5 RR fibrosis fibrotic tract biol rep 1

description:
Library name: QLRIU089AR
FFPE spatial transcriptome sequencing


title: 769_TCR

description:
Library name: 769_TCR_S2
10x Genomics


title: 754_hTCR

description:
Library name: 754_hTCR_S4
10x Genomics


title: 4 RR fibrosis adventitial biol rep 9

description:
Library name: QLRIU088AJ
FFPE spatial transcriptome sequencing


title: MCF-7 cell, HiFi FaDe Cas9 editing treatment, 48 hours, replicate 4

description: Library name: MCF7_KI_48h_rep4


title: 5 RR fibrosis adventitial biol rep 8

description:
Library name: QLRIU096AA
FFPE spatial transcriptome sequencing


title: 4 RR fibrosis adventitial biol rep 8

description:
Library name: QLRIU087AB
FFPE spatial transcriptome sequencing


title: MCF-7 cell, HiFi FaDe Cas9 editing treatment, 24 hours, replicate 3

description: Library name: MCF7_KI_24h_rep3

value: 24 hours


title: 769_5GEX

description:
Library name: 769_5GEX_S1
10x Genomics


title: 5 RR fibrosis adventitial biol rep 9

description:
Library name: QLRIU097AI
FFPE spatial transcriptome sequencing


title: 5 RR fibrosis parenchymal biol rep 4

description:
Library name: QLRIU092AC
FFPE spatial transcriptome sequencing


title: 754_5GEX

description:
Library name: 754_5GEX_S3
10x Genomics


title: MCF-7 cell, HiFi FaDe Cas9 editing treatment, 48 hours, replicate 1

description: Library name: MCF7_KI_48h_rep1


title: 5 RR fibrosis adventitial biol rep 7

description:
Library name: QLRIU095A2
FFPE spatial transcriptome sequencing


title: MCF-7 cell, HiFi FaDe Cas9 editing treatment, 24 hours, replicate 1

description: Library name: MCF7_KI_24h_rep1


title: 4 RR fibrosis parenchymal biol rep 4

description:
Library name: QLRIU083AD
FFPE spatial transcriptome sequencing


title: MCF-7 cell, HiFi FaDe Cas9 editing treatment, 48 hours, replicate 3

description: Library name: MCF7_KI_48h_rep3


title: MCF-7 cell, Electroporation control treatment, 48 hours, replicate 3

description: Library name: MCF7_ctrl_48h_rep3

value: Electroporation control


title: 5 RR fibrosis fibrotic tract biol rep 2

description:
Library name: QLRIU090AU
FFPE spatial transcriptome sequencing


title: MCF-7 cell, Electroporation control treatment, 24 hours, replicate 4

description: Library name: MCF7_ctrl_24h_rep4


title: 4 RR fibrosis fibrotic tract biol rep 2

description:
Library name: QLRIU081AV
FFPE spatial transcriptome sequencing


title: MCF-7 cell, HiFi FaDe Cas9 editing treatment, 24 hours, replicate 4

description: Library name: MCF7_KI_24h_rep4


title: MCF-7 cell, Electroporation control treatment, 24 hours, replicate 3

description: Library name: MCF7_ctrl_24h_rep3


title: MCF-7 cell, Electroporation control treatment, 48 hours, replicate 2

description: Library name: MCF7_ctrl_48h_rep2


title: MCF-7 cell, HiFi FaDe Cas9 editing treatment, 24 hours, replicate 2

description: Library name: MCF7_KI_24h_rep2


title: Negative control

description:
Library name: QLRIU134AQ
FFPE spatial transcriptome sequencing


title: BBp53n_OPCs

city: New York

first: Patrizia

last: Casaccia

state: NY

address: 85 St Nicholas Terrace

department: Neuroscience

institute: ASRC-CUNY

description:
Library name: BBp53n_OPCs
10X Genomics

data_processing:
demultiplexing, barcoded processing, gene counting were done using 10X cellranger tools v8.0.1
Assembly: mouse mm39
Supplementary files format and content: tab delimited barcode, features, and matrix files

source_name: primary cells

extract_protocol:
steps to extract nuclei followed a slightly modified version of the 10X nuclei isolation kit (cat# 1000493) protocol for gene expression libraries. The frozen tissue was dissociated in lysis buffer and filtered. At the debris removal step, we replaced the 10X kit solution with Miltenyi’s debris removal solution (cat# 130-109-398) and followed Miltenyi’s protocol. After debris removal, the nuclei were resuspended in 0.1% BSA in PBS and continued following the 10X nuclei isolation kit protocol. OPC sample derived from cultured cells and followed nuclei isolation protocol withouth debris removal or filtering. Nuclei yield ranged from 5,000-20,000/mg.
After nuclei extraction, the purified nuclei were transported to the CUNY ASRC’s epigenetics core at a concentration of 10e6/mL for 10X 3’ Gene Expression library preparation (Chromium Next GEM Single Cell 3ʹ Kit v3.1, 16 rxns PN-1000268). Samples were sequenced with a target of 10,000 nuclei per sample and 40,000 reads per nuclei a Novaseq 6000 sequencer

value: primary cells


title: Hep-G2 cell, HiFi FaDe Cas9 editing treatment, 48 hours, replicate 4

description: Library name: HepG2_KI_48h_rep4

value: Hep-G2 cell


title: Hep-G2 cell, HiFi FaDe Cas9 editing treatment, 48 hours, replicate 2

description: Library name: HepG2_KI_48h_rep2

value: liver


title: 4 RR fibrosis parenchymal biol rep 5

description:
Library name: QLRIU084AL
FFPE spatial transcriptome sequencing


title: 4 RR fibrosis adventitial biol rep 7

description:
Library name: QLRIU086A3
FFPE spatial transcriptome sequencing


title: Hep-G2 cell, HiFi FaDe Cas9 editing treatment, 48 hours, replicate 1

description: Library name: HepG2_KI_48h_rep1


title: MCF-7 cell, Electroporation control treatment, 24 hours, replicate 1

description: Library name: MCF7_ctrl_24h_rep1


title: 4 RR fibrosis parenchymal biol rep 6

description:
Library name: QLRIU085AT
FFPE spatial transcriptome sequencing


title: Hep-G2 cell, HiFi FaDe Cas9 editing treatment, 24 hours, replicate 3

description: Library name: HepG2_KI_24h_rep3


title: Hep-G2 cell, HiFi FaDe Cas9 editing treatment, 24 hours, replicate 4

description: Library name: HepG2_KI_24h_rep4


title: 9_Inosine combined with hypoxanthine

city: Jinan

first: Fabao

last: Liu

state: Shandong

address: #44 wenhua xi road

institute: Shandong university

description: Library name: C_3

data_processing:
Sequencing reads were aligned to the Mus musculus genome (mm10) using HISAT2.
Duplicated reads and reads with low mapping quality were eliminated using Sambamba tools (v0.7.1). Feature Counts (subread package, v2.0.1) was used to count reads as a measure of gene expression. Differentially expressed genes were identified by DESeq2 (v1.38.3) in R.
Assembly: mm10
Supplementary files format and content: Differential_allgene.annot.results.txt

source_name: Primary cells

growth_protocol: All media were supplemented with 10% dialyzed fetal bovine serum (FBS).

extract_protocol:
The samples were sent to Bioyi Biotechnology Co., Ltd. (Wuhan, China) for RNA-seq.
Each library was sequenced in paired-end mode using the Illumina NovaSeq 6000 platforms.

treatment_protocol: 2mM glucose; 2mM inosine; 2mM inosine combined with 100 M hypoxanthine for 24h. Live cells (about 80%) were sorted by CytoFLEX SRT Cell Sorter (V5-B2-Y5-R0, Beckman)

value: CD8+ T cells

value: wild type

value: Inosine combined with hypoxanthine

value: Day 0


title: 4 RR fibrosis fibrotic tract biol rep 1

description:
Library name: QLRIU080AN
FFPE spatial transcriptome sequencing


title: MCF-7 cell, Electroporation control treatment, 48 hours, replicate 1

description: Library name: MCF7_ctrl_48h_rep1


title: MCF-7 cell, Electroporation control treatment, 48 hours, replicate 4

description: Library name: MCF7_ctrl_48h_rep4


title: Hep-G2 cell, HiFi FaDe Cas9 editing treatment, 24 hours, replicate 1

description: Library name: HepG2_KI_24h_rep1


title: M0-Exo-3

city: Lanzhou

first: Zhenchang

last: Zhang

state: Gansu

address: No. 222, Tianshui South Road

department: The Second Hospital & Clinical Medical School

institute: Lanzhou University

description:
Library name: Sample3
M0-Exo-3.norm

data_processing:
Analysis workflow established on a local server v 1.1
Assembly: mm39
Supplementary files format and content: tab-delimited textfile includes CPMs for each Sample

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent (Plant RNA Purification Reagent for plant tissue) according the manufacturer’s instructions (Invitrogen)
Small RNA libraries were constructed using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs, Inc.) according to the manufacturer's instructions.

value: macrophage


title: Hep-G2 cell, Electroporation control treatment, 48 hours, replicate 4

description: Library name: HepG2_ctrl_48h_rep4


title: M2-Exo-3

description:
Library name: Sample6
M2-Exo-3.norm

value: IL-4 and IL-13


title: Hep-G2 cell, Electroporation control treatment, 48 hours, replicate 3

description: Library name: HepG2_ctrl_48h_rep3


title: 3_Glucose

description: Library name: A_3

value: Glucose


title: 6_Inosine

description: Library name: B_3

value: Inosine


title: Hep-G2 cell, Electroporation control treatment, 48 hours, replicate 1

description: Library name: HepG2_ctrl_48h_rep1


title: 4 RR fibrosis fibrotic tract biol rep 3

description:
Library name: QLRIU082A5
FFPE spatial transcriptome sequencing


title: M2-Exo-2

description:
Library name: Sample5
M2-Exo-2.norm


title: M0-Exo-2

description:
Library name: Sample2
M0-Exo-2.norm


title: M2-Exo-1

description:
Library name: Sample4
M2-Exo-1.norm


title: Hep-G2 cell, Electroporation control treatment, 24 hours, replicate 3

description: Library name: HepG2_ctrl_24h_rep3