title: CBE_VEGFA2_24h_HEK293T_500k_PEI_T7_rep2

description: Library name: CBE_VEGFA2_24h_HEK293T_500k_PEI_T7_rep2


title: Cauda sperm, Low-protein diet, rep1

status: Public on Jun 16 2026

type: SRA

city: Santa Cruz

first: Andrew

middle: David

last: Holmes

state: California

address: 1156 High Street

department: Molecular, Cell, and Developmental Biology

country: USA

institute: UC Santa Cruz

description: Library name: LP_CASP_1

library_source: transcriptomic

data_processing:
Sequences were trimmed with  "cutadapt --no-indels -O 15 -m 2 -a GATCGGAAGAGCACACGTCTGAACTCCAGTCAC" ,"cutadapt -u 7" , and then "cutadapt -u -1" to remove the adapter, the UMI, and the TPRT base (the UMI was not used for removing duplicates)  Only reads >65 bases were used for most analyses
Data was mapped and counted using TRAX, which uses an all-best mapping approach and uses Deseq2 for normalization and detection of differential expression
Assembly: mm10
Supplementary files format and content: tab-delimited raw counts for calculated by tRAX, with mitochondrial tRNA counts appended

molecule: total RNA

organism: Mus musculus

source_name: Sperm

growth_protocol: Mice were group-housed (maximum of 5 per cage) with a 12-hour light-dark cycle (lights off at 6 pm) and free access to food and water ad libitum.

extract_protocol:
Samples were vortexed for 5 minutes to ensure complete breakdown of the sperm, followed by centrifugation at 12,000 RCF for 4 minutes. The aqueous phase was then removed and transferred to a low-binding RNase/DNase-free microcentrifuge tube, followed by the addition of 20 µg of glycoblue (Invitrogen) and 1 volume of Isopropanol. The RNA was then precipitated for 30 minutes or greater at -20°C, followed by centrifugation at 18,000 RCF for 30 minutes at 4°C, and one wash with 70% cold ethanol followed by centrifugation at 12,000 RCF for 10 minutes at 4°C. Finally, the RNA was reconstituted in nuclease-free water.
Library was constructed using Ottr-seq protocol.  Input RNA was PNK treated and labelled at the 3’ end by incubation in buffer containing ddATP for 90 minutes in 30˚C, followed by an addition of ddGTP and another incubation at 30˚C for 30 minutes. The reaction was stopped by incubating at 65°C for 5 minutes, followed by the addition of 5 mM MgCl2 and 0.5 units of shrimp alkaline phosphatase (NEB, cat# M0371S) at 37°C for 15 minutes, then stopped by the addition of 5 mM EGTA, and incubated at 65°C for 5 minutes. Samples were then incubated in templated cDNA synthesis buffer, adaptors, and dNTPs at 37˚C for 20 minutes, followed by heat inactivation at 65˚C for 5 minutes and RNase A/H treatment. cDNA was size selected on a 10% PAGE urea gel to minimize adaptor dimers. Size selected cDNA was PCR amplified for 12 cycles with Q5 high fidelity polymerase (NEB, cat# M0491S). The final PCR product was cleaned up with AMPure XP beads (Beckman, cat # A63881) and finally separated by 6% TBE gel to remove adaptor dimers. The desired product was excised from the gel and eluted in 400ul elution buffer (300 mM NaCl, 10 mM Tris pH 8, 1 mM EDTA) overnight at -20, followed by isopropanol precipitation and resuspension in 9µl nuclease-free H2O.

treatment_protocol: Animals were raised on one of four diets – a low protein diet (LP; 10% of protein rather than 18%, remaining mass made up with sucrose, BioServ, cat# S3156), control for low protein diet (C; BioServ AIN-93g, cat# F3156), a high fat diet (HF; 60% of fat calories rather than 16%, BioServ, cat# S3282) , or control for high-fat diet  (C_HF; 7.2% fat calories, BioServ, cat# S4031)

tag: tissue

value: Sperm

tag: treatment

value: Low-protein diet


title: s11_POMS_Hardship-0

city: Leuven

first: Bernard

middle: Klaas

last: van der Veer

state: Vlaams-Brabant

address: Herestraat 49 - box 651

department: Deparment of Human Genetics

country: Belgium

institute: KU Leuven

description: Library name: 11

library_source: genomic

data_processing:
TrimGalore (v0.6.4_dev)
Bismark (v0.22.3)
methyldackel (v0.5.0)
Assembly: hg38
Supplementary files format and content: bedGraph file - file containing methylation calls generated with methyldackel

molecule: genomic DNA

organism: Homo sapiens

source_name: PBMC

extract_protocol: Zymo-Seq RRBS Library Kit

value: PBMC

tag: disease onset

value: Pediatric

tag: hardship


title: Cauda sperm, Control diet, rep4

description: Library name: CASP_C_4

value: Control diet


title: CBE_VEGFA2_24h_HEK293T_500k_PEI_T7_rep1

city: Shanghai

first: Zhu

last: Ming

address: No. 500, Dongchuan Road

country: China

institute: East China Normal University

description: Library name: CBE_VEGFA2_24h_HEK293T_500k_PEI_T7_rep1

data_processing:
Data were mapped to hg38 (human) using chromap.
Reads overlaped the ENCODE blacklist are removed
Bedtools was used to generate bedGraph files, which were then normalized and converted to BigWig files by bedGraphToBigWig
Assembly: hg38
Supplementary files format and content: BigWig of genome-editing signals

extract_protocol:
Cells were fixed with Concanavalin A bead, washed, and resuspended with buffer containing RPA2/MRE11/IgG antibodies. pA-MNase was added to cleavage the DNA. Cleavaged fragments were collected and then digested with DNase. For Tracking-seq, DNA was purified with DNA Clean Beads and then HL-dsDNase was added to remove dsDNA.
The strand-specific ssDNA libraries were constructed using VAHTS ssDNA Library Prep Kit. CUT&RUN-MRE11 library was constructed using NEBNext® Ultra™ II DNA Library Prep Kit.

tag: cell line


title: Cauda sperm, Control diet, rep5

description: Library name: CASP_C_5


title: s6_POMS_Hardship-1

description: Library name: 6


description: Library name: Cas9_VEGFA2_48h_293_500k_PEI_KU-60648_rep3

data_processing:
Tracking-seq/2: Data were analyzed using Offtracker (https://github.com/Lan-lab/offtracker)
GUIDE-seq-2: Data were analyzed using guideseq (https://github.com/tsailabSJ/guideseq)
Assembly: hg38
Supplementary files format and content: BigWig of genome-editing signals

extract_protocol:
Tracking-seq/2: Cells were fixed with Concanavalin A bead, washed, and resuspended with buffer containing RPA2 antibodies. pA-MNase was added to cleavage the DNA. Cleavaged fragments were collected and then digested with DNase. DNA was purified with DNA Clean Beads and then HL-dsDNase was added to remove dsDNA. GUIDE-seq-2 were performed according to doi: 10.1101/2025.02.10.637517
Tracking-seq/2: The strand-specific ssDNA libraries were constructed using VAHTS ssDNA Library Prep Kit.GUIDE-seq-2 libraries were constructed according to doi: 10.1101/2025.02.10.637517


title: Cauda sperm, Control diet, rep3

description: Library name: CASP_C_3


title: Cauda sperm, Control diet, rep2

description: Library name: CASP_C_2


title: CBE_VEGFA2_24h_HEK293T_500k_PEI_T5_rep2

description: Library name: CBE_VEGFA2_24h_HEK293T_500k_PEI_T5_rep2


title: LC_230201_15_TCR

city: Beijing

first: Yanhua

last: Li

address: No.1 Beichen West Road, Chaoyang District

institute: Institute of Microbiology, Chinese Academy of Sciences

description:
Library name: Sample 28
1-3 weeks post BA.5.2 or BF.7 infection

library_source: transcriptomic single cell

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes
map reads to the genome and transcriptome using the STAR aligner
down-sample reads as required to generate normalized aggregate data across samples
producing a matrix of gene counts versus cells
The Seurat R package (v4.3.0) was used to integrate and analyze single-cell data clusters across different samples. Strict quality control criteria were implemented, including the removal of cells with mitochondrial gene proportions exceeding 20%, as well as those with UMI counts below 600 or above 10,000, and gene counts below 300 or above 3,000. Cells with ribosomal gene proportions exceeding 50% were also excluded. These criteria aimed to eliminate dead cells, RNA-degraded cells, and potential doublets. Furthermore, the DoubletFinder R package (v2.0.3) was applied to identify and remove doublets. Post-quality control, 217,724 cells were collected, with 178,841 single cells retained for subsequent analysis. Normalization and standardization were performed using Seurat, and the top 2,000 genes with the highest variance were selected for principal component analysis (PCA) and downstream clustering. The Harmony algorithm (v0.1.1) was applied to mitigate batch effects during cell clustering. Following evaluation of principal components (PCs) and the inflection point, the top 30 PCs were selected for clustering, with varying resolutions used to identify distinct cell clusters. Dimensionality reduction and visualization were performed using uniform manifold approximation and projection (UMAP). A detailed workflow can be referenced in the tutorial at the following website (https://satijalab.org/seurat/v4.0/pbmc3k_tutorial.html).
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell, features table and barcode for every cell
Supplementary files format and content: filtered_contig_annotations of TCR and BCR for every T or B cell

molecule: polyA RNA

extract_protocol:
Frozen peripheral blood mononuclear cells (PBMCs) were resuscitated and converted into single-cell suspensions when cell viability exceeded 85%. We utilized Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) (Cat. CG000331, 10x Genomics, USA) for single-cell library preparation. The prepared cell suspension, 10X barcode gel beads, and reaction reagents were distributed to different channels of the Chromium Next GEM Chip G, forming water-in-oil GEMs (gel bead in emulsion) through microfluidics. These GEMs facilitated gel bead dissolution, cell lysis to release mRNA, reverse transcription for cDNA generation, and barcode incorporation for sequencing. Following the disruption of the liquid oil layer, a cDNA amplification reaction ensued, culminating in quality inspection after purification.
The single-cell suspension was prepared in water for cDNA library amplification using the 10× Genomics Chromium Next GEM Single Cell 5ʹ Reagent Kits (version 2.0; Cat. No. 1000165). The Chromium™ Single Cell 5ʹ Library Construction Kit (Cat. No. 1000020) was used to construct the DNA library. The constructed library was then sequenced using PE150 sequencing on an Illumina Nova 6000 platform. T cell V(D)J and B cell V(D)J enrichment analyses were performed using the 10× Genomics Chromium™ Single Cell V(D)J Enrichment Kit, Human T Cell (Cat. No. 1000005) and Human B Cell (Cat. No. 1000016) according to the manufacturer’s instructions. The libraries were amplified using a Chromium TCR amplification kit (Cat. No. 1000252) and BCR amplification kit (Cat. No. 1000253), and the experiment was performed according to the manufacturer’s instructions.

value: No

tag: cell type


title: Cauda sperm, Control diet, rep1

description: Library name: CASP_C_1


title: CBE_VEGFA2_24h_HEK293T_500k_PEI_T5_rep1

description: Library name: CBE_VEGFA2_24h_HEK293T_500k_PEI_T5_rep1


title: LC_230201_14_TCR

description:
Library name: Sample 27
1-3 weeks post BA.5.2 or BF.7 infection


title: 3Pseq_EXOSC3_dTAG_EPAP_rep3

city: Aarhus

first: Jerome

middle: O

last: Rouviere

address: Universitetsbyen 81

country: Denmark

institute: Aarhus University

description: Library name: 3Pseq_EXOSC3_dTAG_EPAP_rep3

data_processing:
The raw sequence reads received from service providers were first quality checked using FastQC (Babraham Bioinformatics group). For RNAseq libraires, reads were then trimmed for adaptors and filtered using Trim Galore (Babraham Bioinformatics group). Trimmed reads were mapped to hg38, using Hisat2 in paired-end mode. Mapped files were sorted and checked for pairing using SAMtools. Reads were then deduplicated using MarkDuplicates (Picard – Broad Institute) and further filtered to keep only unique mappers by using SAMtools. Relative samples size was then estimated by generating coverage counts using htseq-count (HTSeq-counts) over the Genecode annotation and analyzing then with DEseq2 to define size factors. In the case of fractionated pA+ RNAseq, size factors were measured separately for the nuclear and cytoplasmic fractions to avoid any compensation of compartment specific phenotypes. Finally, reads were converted to bigwig (bw) files normalized to size factors, with a binning of 5, using bamCoverage (Deeptools). For iCLIP libraires,using only "R1" reads, adaptors were trimmed using Trim Galore, UMI deduplication was performed using seqkit. The first 15nt were trimmed with Trim Galore, and reads were filtered to be bellow 100bp length using seqkit. Reads were mapped to hg38 using STAR allowing only unique mappers. To get single positions, using a combination of Bedtools and bash script, mapped bam files were converted to bed, shifted one base, filtered to contain only primary assemby chromosomes (except chrM) and separated by strand. The resulting bedgraph files where then converted to bw (without binning) using bedGraphToBigWig.  For 3'end sequencing, adapters and A18 stretches were trimmed using Trim Galore. Mapping to hg38 was performed using STAR. A combinations of samtools and bash code was used to keep only unique mappers, reduce the reads to their 5'end (due to Quant-seq REV sequencing) and filter them to only correspond to the primary assembly chromosomes (except chrM). Htseq-count, was used on the resulting mapped files, over the last exon of protein coding genes and the output was used to define size factor with DEseq2 which was used in bamCoverage to convert the files to bw (without binning)
Assembly: hg38
Supplementary files format and content: bigwig (bw) - normalized coverage with a binning of 5 for RNAseq and no binning for iCLIP and 3'end seq

source_name: cervix

growth_protocol: HeLa and HCT116 cells were cultured in standard DMEM medium supplemented with 10% FBS and penicillin-streptomycin mix.

extract_protocol:
Total RNA was extracted using TRIZOL reagent according to manufacturer’s instructions
For iCLIP libraries were constructed in-house and seqenced by Lexogen. For all other libraries construction and sequencing were paid services from Lexogen

treatment_protocol: When specified, cells were treated with dTAGV-1 at a concentration of 500nM for 4H

value: cervix

value: HeLa Kyoto

tag: genotype

value: 4H dTAGV-1 500nM - EPAP


description: Library name: CBE_VEGFA2_24h_HEK293T_500k_PEI_mock_rep2


title: Cauda, High-fat diet, rep4

description: Library name: HF_CA_4

source_name: Cauda

value: Cauda

value: High-fat diet


title: Bovine endometrium sample F_3, P4 arm, day 7 treatment cycle

city: Towada

first: Masaki

last: Watanabe

department: School of Veterinary Medicine

country: Japan

institute: Kitasato University

description:
Library name: F_3
Animal F; study arm: P4 arm; condition: day 7 treatment cycle; cycle: treatment cycle; sampling time: day 7 after estrus; treatment administered on day 4; count matrix column: F_3.

data_processing:
Raw paired-end FASTQ files were reprocessed in-house for transcriptome analysis.
Reads were quality- and adaptor-trimmed using Cutadapt and read quality was assessed using FastQC.
Clean reads were aligned to the bovine reference genome ARS-UCD2.0 (NCBI RefSeq GCF_002263795.3) using STAR with the corresponding annotation as the splice-junction database.
Aligned reads were assigned to gene features using featureCounts based on the same annotation to generate a raw gene-level count matrix.
Downstream differential expression analyses were performed in R using DESeq2.
Assembly: ARS-UCD2.0 (NCBI RefSeq GCF_002263795.3)
Supplementary files format and content: bovine_endometrium_gene_raw_counts.tsv: tab-delimited text file containing raw gene-level read counts for all 18 RNA-seq libraries. The first two columns contain gene symbol and gene identifier, followed by columns A_1 through F_3 corresponding to the GEO library names.

organism: Bos taurus

source_name: endometrium

growth_protocol: Holstein cattle were maintained at a commercial dairy farm in Miyazaki Prefecture, Japan. Animals underwent Ovsynch treatment for ovarian synchronization, and the day of estrus corresponding to the timing of artificial insemination was defined as day 0.

extract_protocol:
Endometrial samples were collected using a sterile cytobrush introduced into the uterine horn ipsilateral to the corpus luteum and rotated once through 360 degrees. Collected material was immediately immersed in RNAlater and stored at -20 °C until RNA extraction and library preparation. Total RNA was extracted from each sample.
mRNA library construction and RNA-seq were performed by Azenta Japan. One microgram of total RNA was used for library preparation. Poly(A)+ mRNA was isolated using oligo(dT) beads and fragmented. First-strand cDNA synthesis was performed using random primers, followed by second-strand cDNA synthesis, end repair, dA-tailing, adaptor ligation, size selection, PCR amplification, library validation, multiplexing, and 2 x 150 bp paired-end sequencing on a DNBSEQ-G400 platform.

treatment_protocol: During the first synchronized cycle, endometrial samples were collected on days 4 and 7 without exogenous progestogen administration and were treated as untreated control-cycle samples. After a second Ovsynch-synchronized cycle, animals received either a depot formulation containing 100 mg 17α-hydroxyprogesterone caproate and 10 mg progesterone or 100 mg progesterone on day 4, and endometrial samples were collected on day 7.

value: endometrium

tag: time

value: day 7 treatment cycle


title: LC_230201_13_TCR

description:
Library name: Sample 26
1-3 weeks post BA.5.2 or BF.7 infection


title: Cauda, High-fat diet, rep3

description: Library name: HF_CA_3


title: Bovine endometrium sample F_2, P4 arm, day 7 untreated control cycle

description:
Library name: F_2
Animal F; study arm: P4 arm; condition: day 7 untreated control cycle; cycle: untreated control cycle; sampling time: day 7 after estrus; count matrix column: F_2.

value: none (untreated control cycle)

value: day 7 untreated control cycle


description: Library name: CBE_VEGFA2_24h_HEK293T_500k_PEI_mock_rep1


title: LC_230201_12_TCR

description:
Library name: Sample 25
1-3 weeks post BA.5.2 or BF.7 infection


title: Cauda, High-fat diet, rep2

description: Library name: HF_CA_2


title: CBE_HEK4_24h_HEK293T_500k_PEI_T7_rep1

description: Library name: CBE_HEK4_24h_HEK293T_500k_PEI_T7_rep1


title: Bovine endometrium sample E_3, P4 arm, day 7 treatment cycle

description:
Library name: E_3
Animal E; study arm: P4 arm; condition: day 7 treatment cycle; cycle: treatment cycle; sampling time: day 7 after estrus; treatment administered on day 4; count matrix column: E_3.


title: Bovine endometrium sample F_1, P4 arm, day 4 untreated control cycle

description:
Library name: F_1
Animal F; study arm: P4 arm; condition: day 4 untreated control cycle; cycle: untreated control cycle; sampling time: day 4 after estrus; count matrix column: F_1.

value: day 4 untreated control cycle


title: LC_230201_11_TCR

description:
Library name: Sample 24
1-3 weeks post BA.5.2 or BF.7 infection


title: Cauda, High-fat diet, rep1

description: Library name: HF_CA_1


title: CBE_HEK4_24h_HEK293T_500k_PEI_T5_rep1

description: Library name: CBE_HEK4_24h_HEK293T_500k_PEI_T5_rep1


title: Bovine endometrium sample E_2, P4 arm, day 7 untreated control cycle

description:
Library name: E_2
Animal E; study arm: P4 arm; condition: day 7 untreated control cycle; cycle: untreated control cycle; sampling time: day 7 after estrus; count matrix column: E_2.


title: LC_230201_10_TCR

description:
Library name: Sample 23
1-3 weeks post BA.5.2 or BF.7 infection


title: Cauda, High-fat control diet, rep5

description: Library name: C_HF_CA_5

value: High-fat control diet


title: CBE_HEK4_24h_HEK293T_500k_PEI_mock_rep1

description: Library name: CBE_HEK4_24h_HEK293T_500k_PEI_mock_rep1


title: LC_230201_9_TCR

description:
Library name: Sample 22
1-3 weeks post BA.5.2 or BF.7 infection


title: Bovine endometrium sample E_1, P4 arm, day 4 untreated control cycle

description:
Library name: E_1
Animal E; study arm: P4 arm; condition: day 4 untreated control cycle; cycle: untreated control cycle; sampling time: day 4 after estrus; count matrix column: E_1.


title: Bovine endometrium sample D_3, P4 arm, day 7 treatment cycle

description:
Library name: D_3
Animal D; study arm: P4 arm; condition: day 7 treatment cycle; cycle: treatment cycle; sampling time: day 7 after estrus; treatment administered on day 4; count matrix column: D_3.


title: Cas9_WT_48h_HEK293T_500k_PEI_T5_rep1

description: Library name: Cas9_WT_48h_HEK293T_500k_PEI_T5_rep1


title: Cauda, High-fat control diet, rep4

description: Library name: C_HF_CA_4


title: LC_230201_8_TCR

description:
Library name: Sample 21
1-3 weeks post BA.5.2 or BF.7 infection


title: Cauda, High-fat control diet, rep3

description: Library name: C_HF_CA_3


title: Bovine endometrium sample D_2, P4 arm, day 7 untreated control cycle

description:
Library name: D_2
Animal D; study arm: P4 arm; condition: day 7 untreated control cycle; cycle: untreated control cycle; sampling time: day 7 after estrus; count matrix column: D_2.


description: Library name: Cas9_WT_48h_HEK293T_500k_PEI_KU-60648_rep1


title: LC_230201_7_TCR

description:
Library name: Sample 20
1-3 weeks post BA.5.2 or BF.7 infection


title: Cauda, High-fat control diet, rep2

description: Library name: C_HF_CA_2


description: Library name: Cas9_VEGFA2_48h_HEK293T_500k_PEI_T7_rep2


title: LC_230201_6_TCR

description:
Library name: Sample 19
1-3 weeks post BA.5.2 or BF.7 infection


title: Frac_HCT116_LENG8_4HdTAG_Cyto_rep2b

description: Library name: Frac_HCT116_LENG8_4HdTAG_Cyto_rep2b

source_name: colon

value: colon

value: 4H dTAGV-1 500nM


title: Cauda, High-fat control diet, rep1

description: Library name: C_HF_CA_1


title: Bovine endometrium sample D_1, P4 arm, day 4 untreated control cycle

description:
Library name: D_1
Animal D; study arm: P4 arm; condition: day 4 untreated control cycle; cycle: untreated control cycle; sampling time: day 4 after estrus; count matrix column: D_1.


description: Library name: Cas9_VEGFA2_48h_HEK293T_500k_PEI_T7_rep1


title: Bovine endometrium sample C_3, 17-OHPC/P4 formulation arm, day 7 treatment cycle

description:
Library name: C_3
Animal C; study arm: 17-OHPC/P4 formulation arm; condition: day 7 treatment cycle; cycle: treatment cycle; sampling time: day 7 after estrus; treatment administered on day 4; count matrix column: C_3.

value: 100 mg 17-OHPC plus 10 mg P4 depot formulation


title: LC_230201_4_TCR

description:
Library name: Sample 17
1-3 weeks post BA.5.2 or BF.7 infection

value: PBMC


title: Cauda, Low-protein diet, rep4

description: Library name: LP_CA_5

value: Low-protein diet


description: Library name: Cas9_VEGFA2_48h_HEK293T_500k_PEI_T5_rep2


title: LC_230201_5_TCR

description:
Library name: Sample 18
1-3 weeks post BA.5.2 or BF.7 infection

value: No


title: Cauda, Low-protein diet, rep3

description: Library name: LP_CA_4


description: Library name: Cas9_VEGFA2_48h_HEK293T_500k_PEI_T5_rep1


title: Bovine endometrium sample C_1, 17-OHPC/P4 formulation arm, day 4 untreated control cycle

description:
Library name: C_1
Animal C; study arm: 17-OHPC/P4 formulation arm; condition: day 4 untreated control cycle; cycle: untreated control cycle; sampling time: day 4 after estrus; count matrix column: C_1.


title: LC_230201_2_TCR

description:
Library name: Sample 16
1-3 weeks post BA.5.2 or BF.7 infection


title: Cauda, Low-protein diet, rep2

description: Library name: LP_CA_3


title: Bovine endometrium sample B_3, 17-OHPC/P4 formulation arm, day 7 treatment cycle

description:
Library name: B_3
Animal B; study arm: 17-OHPC/P4 formulation arm; condition: day 7 treatment cycle; cycle: treatment cycle; sampling time: day 7 after estrus; treatment administered on day 4; count matrix column: B_3.


description: Library name: Cas9_VEGFA2_48h_HEK293T_500k_PEI_T5-KU-60648_rep2


title: LC_230201_1_TCR

description:
Library name: Sample 15
1-3 weeks post BA.5.2 or BF.7 infection


title: Cauda, Low-protein diet, rep1

description: Library name: LP_CA_2


description: Library name: Cas9_VEGFA2_48h_HEK293T_500k_PEI_T5-KU-60648_rep1


title: Bovine endometrium sample B_2, 17-OHPC/P4 formulation arm, day 7 untreated control cycle

description:
Library name: B_2
Animal B; study arm: 17-OHPC/P4 formulation arm; condition: day 7 untreated control cycle; cycle: untreated control cycle; sampling time: day 7 after estrus; count matrix column: B_2.


title: LC_230201_15_BCR

description:
Library name: Sample 14
1-3 weeks post BA.5.2 or BF.7 infection


title: Cauda, Control diet, rep5

description: Library name: CA_C_5

value: Control diet


title: Bovine endometrium sample B_1, 17-OHPC/P4 formulation arm, day 4 untreated control cycle

description:
Library name: B_1
Animal B; study arm: 17-OHPC/P4 formulation arm; condition: day 4 untreated control cycle; cycle: untreated control cycle; sampling time: day 4 after estrus; count matrix column: B_1.


title: Cauda, Control diet, rep4

description: Library name: CA_C_4


description: Library name: Cas9_VEGFA2_48h_HEK293T_500k_PEI_RI-1_rep2


title: Bovine endometrium sample A_3, 17-OHPC/P4 formulation arm, day 7 treatment cycle

description:
Library name: A_3
Animal A; study arm: 17-OHPC/P4 formulation arm; condition: day 7 treatment cycle; cycle: treatment cycle; sampling time: day 7 after estrus; treatment administered on day 4; count matrix column: A_3.


title: Cauda, Control diet, rep3

description: Library name: CA_C_3


description: Library name: Cas9_VEGFA2_48h_HEK293T_500k_PEI_RI-1_rep1


title: LC_230201_12_BCR

description:
Library name: Sample 11
1-3 weeks post BA.5.2 or BF.7 infection


title: Bovine endometrium sample A_2, 17-OHPC/P4 formulation arm, day 7 untreated control cycle

description:
Library name: A_2
Animal A; study arm: 17-OHPC/P4 formulation arm; condition: day 7 untreated control cycle; cycle: untreated control cycle; sampling time: day 7 after estrus; count matrix column: A_2.


title: Cauda, Control diet, rep2

description: Library name: CA_C_2


description: Library name: Cas9_VEGFA2_48h_HEK293T_500k_PEI_RE1B_rep1


title: Bovine endometrium sample A_1, 17-OHPC/P4 formulation arm, day 4 untreated control cycle

description:
Library name: A_1
Animal A; study arm: 17-OHPC/P4 formulation arm; condition: day 4 untreated control cycle; cycle: untreated control cycle; sampling time: day 4 after estrus; count matrix column: A_1.


title: LC_230201_11_BCR

description:
Library name: Sample 10
1-3 weeks post BA.5.2 or BF.7 infection


title: Cauda, Control diet, rep1

description: Library name: CA_C_1


description: Library name: Cas9_VEGFA2_48h_HEK293T_500k_PEI_Olaparib_rep2


title: LC_230201_10_BCR

description:
Library name: Sample 9
1-3 weeks post BA.5.2 or BF.7 infection


description: Library name: Cas9_VEGFA2_48h_HEK293T_500k_PEI_Olaparib_rep1


title: LC_230201_9_BCR

description:
Library name: Sample 8
1-3 weeks post BA.5.2 or BF.7 infection


title: Patient12 12weeks treatment

type: protein

city: Shimamoto-cho, Mishima-gun

first: Keiichi

last: Minami

state: OSAKA

address: 3-1-1 Sakurai

department: Minase Research Institute

institute: Ono Pharmaceutical

hyb_protocol: In this study, SOMAscan was used, and the measurements were outsourced. (SomaLogic Operating Co., Inc.)

label: SOMAmer

molecule: protein

source_name: non-CIPN

growth_protocol: Patient-derived samples were used in this study.

value: Plasma


title: Patient12 8weeks treatment

scan_protocol: In this study, SOMAscan was used, and the measurements were outsourced. (SomaLogic Operating Co., Inc.)


title: Caput, High-fat diet,rep3

description: Library name: CP_HF_3

source_name: Caput

value: Caput


description: Library name: Cas9_VEGFA2_48h_HEK293T_500k_PEI_NU7441_rep2


title: LC_230201_8_BCR

description:
Library name: Sample 7
1-3 weeks post BA.5.2 or BF.7 infection


description: Library name: Cas9_VEGFA2_48h_HEK293T_500k_PEI_NU7441_rep1


title: LC_230201_7_BCR

description:
Library name: Sample 6
1-3 weeks post BA.5.2 or BF.7 infection


title: Patient12 4weeks treatment

data_processing: In this study, SOMAscan was used, and the measurements were outsourced. (SomaLogic Operating Co., Inc.)


description: Library name: Cas9_VEGFA2_48h_HEK293T_500k_PEI_mock_rep2


title: Patient11 12weeks treatment

source_name: CIPN

label_protocol: In this study, SOMAscan was used, and the measurements were outsourced. (SomaLogic Operating Co., Inc.)


title: Caput, High-fat control diet, rep5

description: Library name: CP_C_HF_5


description: Library name: Cas9_VEGFA2_48h_HEK293T_500k_PEI_mock_rep1


title: LC_230201_5_BCR

description:
Library name: Sample 4
1-3 weeks post BA.5.2 or BF.7 infection


description: Library name: Cas9_VEGFA2_48h_HEK293T_500k_PEI_KU-60648_rep2


title: LC_230201_4_BCR

description:
Library name: Sample 3
1-3 weeks post BA.5.2 or BF.7 infection


title: Patient11 4weeks treatment

extract_protocol: In this study, SOMAscan was used, and the measurements were outsourced. (SomaLogic Operating Co., Inc.)


title: Caput, High-fat control diet, rep3

description: Library name: CP_C_HF_3


description: Library name: Cas9_VEGFA2_48h_HEK293T_500k_PEI_KU-60648_rep1


title: LC_230201_2_BCR

description:
Library name: Sample 2
1-3 weeks post BA.5.2 or BF.7 infection


title: Patient11 pre treatment


title: Caput, High-fat control diet, rep2

description: Library name: CP_C_HF_2


title: Bovine endometrium sample C_2, 17-OHPC/P4 formulation arm, day 7 untreated control cycle

description:
Library name: C_2
Animal C; study arm: 17-OHPC/P4 formulation arm; condition: day 7 untreated control cycle; cycle: untreated control cycle; sampling time: day 7 after estrus; count matrix column: C_2.


description: Library name: Cas9_VEGFA2_48h_HEK293T_500k_PEI_KP32_rep1


title: Caput, High-fat control diet, rep1

description: Library name: CP_C_HF_1


title: LC_230201_1_BCR

description:
Library name: Sample 1
1-3 weeks post BA.5.2 or BF.7 infection


title: Patient10 8weeks treatment


description: Library name: Cas9_VEGFA2_48h_HEK293T_500k_PEI_IBR2_rep1


title: HO199

city: Rochester

first: Martin

last: Fernandez-Zapico

state: MN

address: 200 1st St SW

institute: Mayo Clinic

description: Library name: Sample 8

data_processing:
Libraries were combined across flow cells and trimmed using Cutadapt 1.16.5 to remove the Nextera adapters. Trimmed reads were aligned to Hg38 using Bowtie2 2.5.0 with the preset --very sensitive end-to-end. Reads were filtered for mapQuality (phred scale) ≥ 30, properly paired reads, and removal of mitochondrial reads. Duplicates were removed using Picard 2.26.10 MarkDuplicates.
BAM files were converted to bigwig using Deeptools 3.3.2 bamCoverage with a bin size of 50 bases and RPKM normalization.
Assembly: GRCh38
Supplementary files format and content: BAM files were converted to bigwig using Deeptools 3.3.2 bamCoverage with a bin size of 50 bases and RPKM normalization.
Supplementary files format and content: Narrow Peaks were called using MACS2 2.2.9 Callpeak with a set extension size of 200 and a set shift size of -100. Peak detection was based on a minimum FDR cutoff of ≤0.01.

source_name: Tumor

growth_protocol: PDOs were grown in PaTOM media

extract_protocol:
100,000 cells were collected in a 1.5 mL low-binding microcentrifuge tube and brought to a total volume of 1 mL in ice-cold PBS and mixed gently. Cells were pelleted and resuspended in 100 µL of ice-cold anti-freezing buffer (10% DMSO, 10% FBS in DMEM) and mixed gently. Approximately 50 – 100K cells were subjected to ATAC following the Omni-ATAC protocol.
Libraries were purified by AMPure XP magnetic beads (Beckman Coulter, A63881) and the size distribution of library DNA was determined by Fragment Analyzer (Advanced Analytical Technologies) using a High Sensitivity NGS Fragment Analysis Kit (Advanced Analytical Technologies, DNF-486). Real-time PCR analysis was performed using SYBR Green universal PCR mixes (Bio-Rad) to measure enrichment of accessible regions in the library DNAs. The following primers were used: for accessible regions, Fam86fp-F: 5’-GGCATTAGGGCGGGGATAAA-3’, Fam86fp-R: 5’-TAAGACCTGTCTCCTGGGCT-3’; Ccdc146-F: 5’-GCTCCGCCTCTTAGAAACCA-3’, Ccdc146-R: 5’-GCGATTCTAACACCTGCCCT-3’; for inaccessible region, hATAC-C19 inter-F: 5’-GCTTGTCTTTCCCAAGTTTACTC-3’, hATAC-C19 inter-R: 5’-TAGCTGTCGCACTTCAGAGGA-3’. The libraries were sequenced to 51 base pairs from both ends on an Illumina NovaSeq 6000 SP platform. The concentration and fragmentation profile of submitted ATAC libraries were determined using Qubit fluorometry (Invitrogen) and the Agilent Bioanalyzer. The libraries were sequenced using Illumina's standard protocol for the NovaSeq 6000. The flow cells were sequenced as 50 X 2 paired end reads using the NovaSeq SP sequencing kit and NovaSeq Control Software v1.8.0. Base-calling was performed using Illumina’s RTA version 3.4.4.

treatment_protocol: No treatment

value: Tumor

value: peritoneal metastsis

value: Colorectal cancer


title: Patient10 4weeks treatment


title: Caput,  Low-protein diet, rep4

description: Library name: CP_LP_4


description: Library name: Cas9_VEGFA2_48h_HEK293T_500k_PEI_HY-122727_rep2


title: Patient10 pre treatment


title: HO198

description: Library name: Sample 7


title: Caput,  Low-protein diet, rep3

description: Library name: CP_LP_3


description: Library name: Cas9_VEGFA2_48h_HEK293T_500k_PEI_HY-122727_rep1


title: HO197

description: Library name: Sample 6


title: Patient09 12weeks treatment


title: Caput,  Low-protein diet, rep2

description: Library name: CP_LP_2


description: Library name: Cas9_VEGFA2_48h_HEK293T_500k_PEI_EXO_rep1


title: Patient09 8weeks treatment


title: Caput,  Low-protein diet, rep1

description: Library name: CP_LP_1


title: HO196

description: Library name: Sample 5


description: Library name: Cas9_VEGFA2_48h_HEK293T_500k_PEI_EXO1_rep1


title: Caput, Control diet, rep5

description: Library name: CP_C_5


title: HO195

description: Library name: Sample 4


description: Library name: Cas9_VEGFA2_48h_HEK293T_500k_PEI_DIDS_rep2


title: HO179

description: Library name: Sample 3


title: Patient09 pre treatment


title: Caput, Control diet, rep4

description: Library name: CP_C_4


description: Library name: Cas9_VEGFA2_48h_HEK293T_500k_PEI_DIDS_rep1


title: HO178

description: Library name: Sample 2


title: Patient08 4weeks treatment


title: Caput, Control diet, rep3

description: Library name: CP_C_3


title: Cas9_HEK4_48h_HEK293T_500k_PEI_T7_rep2

description: Library name: Cas9_HEK4_48h_HEK293T_500k_PEI_T7_rep2


title: Patient08 pre treatment


title: HO176

description: Library name: Sample 1


title: Caput, Control diet, rep2

description: Library name: CP_C_2


title: Cas9_HEK4_48h_HEK293T_500k_PEI_T7_rep1

description: Library name: Cas9_HEK4_48h_HEK293T_500k_PEI_T7_rep1


title: LC_230201_14_BCR

description:
Library name: Sample 13
1-3 weeks post BA.5.2 or BF.7 infection


description: Library name: Cas9_VEGFA2_48h_HEK293T_500k_PEI_RocE_rep1


title: Patient09 4weeks treatment


title: LC_230201_13_BCR

description:
Library name: Sample 12
1-3 weeks post BA.5.2 or BF.7 infection


title: Patient07 12weeks treatment


title: OSC Treated Retinal Sample (ATAC)

city: Berkeley

first: Dario

last: Tommasini

address: 242 Stanley Hall

institute: UC Berkeley

description:
Library name: OSC_ATAC
Single-nucleus ATAC-seq library from multiome assay

data_processing:
Joint alignment, quantification, and cell calling were performed using CellRanger-ARC (10X Genomics).
Assembly: Species-specific reference genomes for Ambystoma mexicanum and Pleurodeles waltl
Supplementary files format and content: For each sample, paired single-nucleus RNA-seq and single-nucleus ATAC-seq feature-barcode matrices are provided containing synchronized transcriptomic profiles and open-chromatin fragments per individual nucleus.

organism: Ambystoma mexicanum

source_name: Retina

growth_protocol: N/A (Wild-type adult animals: 5 axolotls aged 4–8 months, 5 Iberian ribbed newts aged 6 months)

extract_protocol:
Salamander retinas were dissected in cold amphibian PBS (PBS + 25% volume water) and snap-frozen by submerging in an isopentane bath cooled on liquid nitrogen. Nuclei were isolated according to the described protocol (PMID: 39240519) using 30 seconds of lysis incubation. Isolated nuclei were resuspended in 1X Diluted Nuclei Buffer (10X Genomics; PN-2000207).
8000–16000 nuclei were loaded per reaction. Single-nucleus transcriptomes and chromatin accessibility profiles were generated using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Kit (10X Genomics cat. PN-1000285) following 10X Genomics protocol CG000338 Rev F. Libraries were sequenced at the Novogene Sequencing Core (Sacramento, CA & Beaverton, OR) on the NovaSeq X Plus instrument (Illumina).

value: Retina

value: Nuclei

value: Wild-type

value: OSC

tag: batch


title: Caput, Control diet, rep1

description: Library name: CP_C_1


title: Cas9_HEK4_48h_HEK293T_500k_PEI_T5_rep2

description: Library name: Cas9_HEK4_48h_HEK293T_500k_PEI_T5_rep2


title: Caput, High-fat diet,rep4

description: Library name: CP_HF_4

value: High-fat diet


title: Testis, High-fat diet, rep4

description: Library name: HF_TESTIS_4

source_name: Testis

value: Testis


title: OSC Treated Retinal Sample (RNA)

description:
Library name: OSC_RNA
Single-nucleus RNA-seq library from multiome assay


title: Patient07 8weeks treatment


title: Cas9_HEK4_48h_HEK293T_500k_PEI_T5_rep1

description: Library name: Cas9_HEK4_48h_HEK293T_500k_PEI_T5_rep1


title: Intact Retinal Sample 2 (ATAC)

description:
Library name: Intact_2_ATAC
Single-nucleus ATAC-seq library from multiome assay


title: Caput, High-fat diet,rep2

description: Library name: CP_HF_2


title: Patient07 4weeks treatment


title: Testis, High-fat diet, rep3

description: Library name: HF_TESTIS_3


description: Library name: Cas9_HEK4_48h_HEK293T_500k_PEI_T5-KU-60648_rep2


title: Caput, High-fat diet,rep1

description: Library name: CP_HF_1


title: Intact Retinal Sample 2 (RNA)

description:
Library name: Intact_2_RNA
Single-nucleus RNA-seq library from multiome assay


title: Patient12 pre treatment


title: LC_230201_6_BCR

description:
Library name: Sample 5
1-3 weeks post BA.5.2 or BF.7 infection


title: Testis, High-fat diet, rep2

description: Library name: HF_TESTIS_2


title: Patient07 pre treatment


description: Library name: Cas9_HEK4_48h_HEK293T_500k_PEI_T5-KU-60648_rep1


title: Intact Retinal Sample 1 (ATAC)

description:
Library name: Intact_1_ATAC
Single-nucleus ATAC-seq library from multiome assay


title: Testis, High-fat diet, rep1

description: Library name: HF_TESTIS_1


title: Patient11 8weeks treatment


title: Patient06 4weeks treatment


description: Library name: Cas9_HEK4_48h_HEK293T_500k_PEI_RocE_rep2


title: Caput, High-fat control diet, rep4

description: Library name: CP_C_HF_4

value: High-fat control diet


title: Intact Retinal Sample 1 (RNA)

description:
Library name: Intact_1_RNA
Single-nucleus RNA-seq library from multiome assay


title: Testis, High-fat control diet, rep5

description: Library name: C_HF_TESTIS_5


description: Library name: Cas9_HEK4_48h_HEK293T_500k_PEI_RocE_rep1


title: Patient06 pre treatment


title: Testis, High-fat control diet, rep4

description: Library name: C_HF_TESTIS_4


description: Library name: Cas9_HEK4_48h_HEK293T_500k_PEI_RI-1_rep2


title: 526, 530, 498 Patient-Derived High Grade Serous Ovarian Cancer Spheroid Tissue Microarray

city: London

first: Fred

last: Dick

state: Ontario

address: 790 Commissioners Road East

department: Pathology & Laboratory Medicine

country: Canada

institute: Western University

description:
Library name: TMA_2-B
Visium CytAssist Spatial Gene Expression For Formalin-Fixed Paraffin Embedded For Human Tissue, Spatial Transcriptome Sequencing

data_processing:
FASTQ files obtained from sequencing facility were aligned to the GRCh38 genome to gene expression count using 10X Genomics Space Ranger's default settings
Gene expression level of Refseq coding genes were quantified using Space Ranger's default settings with manually identifed fiducials in Visium images and selected spots under tissue
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz: filtered (tissue assocciated barcodes) list of spatial barcodes
Supplementary files format and content: features.tsv.gz: filtered (tissue associated barcodes) list of gene IDs
Supplementary files format and content: matrix.mtx.gz: filtered (tissue associated barcodes) gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors_json.json.gz: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv.gz: list of spatial barcodes and the coordinates of specifying spots
Library strategy: Spatial Transcriptomics

source_name: Ascites Derived Patient High Grade Serous Ovarian Cancer (ID's 526, 530, 498) microarray

growth_protocol: 3 High Grade Serous Ovarian Cancer Cell Lines (HeyA8, OVCAR8 and iOvCa147) were used to generate cell-line derived spheroid samples. Patient-derived high grade serous ovarian cancer spheroids were isolated from ascites fluid obtained from debulking surgery of 3 patients (526, 530, 498). Patient spheroids were prepared by filtering the ascites fluid through a 100 um mesh filter.

extract_protocol:
Both cell line- and patient-derived spheroid samples were washed with PBS, fixed in 10% formalin, embedded into paraffin blocks and sectioned to generate tissue microarrays (TMA_1-A = cell lines, TMA_2-B = patient samples).
Spatial transcriptomic sequencing libraries were prepared with the 10X Genomics Visium Gene Expression Slides and Reagents for FFPE Human Tissue kit according to manufacturer's construction

treatment_protocol: Cell lines growing on adherent cell culture plates were transferred on to ultra low attachment plates and incubated for 7 days to allow spheroid formation. Patient spheroids were prepared by filtering the ascites fluid through a 100 um mesh filter.

value: High Grade Serous Ovarian Cancer Spheroids


title: Patient05 12weeks treatment


title: Testis, High-fat control diet, rep3

description: Library name: C_HF_TESTIS_3


description: Library name: Cas9_HEK4_48h_HEK293T_500k_PEI_RI-1_rep1


title: HeyA8, OVCAR8, iOvCa147 Cell Line-Derived High Grade Serous Ovarian Cancer Spheroid Tissue Microarray

description:
Library name: TMA_1-A
Visium CytAssist Spatial Gene Expression For Formalin-Fixed Paraffin Embedded For Human Tissue, Spatial Transcriptome Sequencing

source_name: HeyA8, OVCAR8, iOvCa147 microarray

value: HeyA8, OVCAR8, iOvCa147 microarray


title: Patient05 8weeks treatment


title: Engineered Heart Tissue, day 30, biol rep 2

city: Chicago

first: Zachary

middle: Thomas

last: Weber

state: Illinois

department: Human Genetics

institute: University of Chicago

description: Library name: EHT-2

data_processing:
We used 10X Cell Ranger v7.1.0 for demultiplexing, barcode processing, gene counting, cell filtering, and agreggation. Intronic reads were counted in gene counts.
Doublets were predicted and filtered using Scrublet in python and removed prior to downstream analyses.
Quality control, dimensionality reduction, clustering, marker discovery, and differential expression analysis was done in R using Seurat in R
Assembly: Human GRCh38
Supplementary files format and content: tab separated value files and matrix files

source_name: derived cells

growth_protocol: EHTs were cultured in media containing DMEM low glucose, 10% horse serum, 1% Penicillin/Streptomycin, and 0.1% human insulin. For 72 hours following EHT generation, the cells were supplemented with 5 μg/mL recombinant human TGF-β1. On day 3 after tissue casting, TGF-β1 was removed from culture medium and media was exchanged with 500 μL fresh media per well. EHT media was exchanged every 2 days throughout the course of tissue maturation. EHTs were harvested for downstream applications at day 20 post tissue casting

extract_protocol:
Engineered heart tissues were pooled from 2x 48 well plates and incubated at 37° C for 1.5-2 hours in a dissociation solution containing 1mg/ml Collagenase II,10 mM HEPES pH 7.4, 2 mM Thiazovivin, and 30 mM N-Benzyl-p-Toluenesulfonamide to obtain a single cell suspension. cells were filtered through 70 um cell strainer.
Libraries were constructed according to manufacturers specifications using the 10X Chromium platform and 3' V3 chemistry targeting 10,000 cells per library.

value: derived cells

value: stem cells, cardiac fibroblasts


title: Testis, High-fat control diet, rep2

description: Library name: C_HF_TESTIS_2


title: Patient05 4weeks treatment


title: Engineered Heart Tissue, day 30, biol rep 1

description: Library name: EHT-1


description: Library name: Cas9_HEK4_48h_HEK293T_500k_PEI_RE1B_rep1


description:
Library name: EXOSC3_4h_rep3
EXOSC3 4h rep3 (same as GSM9295329) RNAseq

source_name: Cervix

value: Cervix

value: HeLa Kyoto

value: 4h dTAGV-1 100nM


title: Patient05 pre treatment

value: Plasma


title: Patient04 8weeks treatment


description: Library name: Cas9_HEK4_48h_HEK293T_500k_PEI_Olaparib_rep2


title: Patient04 4weeks treatment


title: Testis,  Low-protein diet, rep4

description: Library name: LP_TESTIS_4

value: Low-protein diet


description: Library name: Cas9_HEK4_48h_HEK293T_500k_PEI_Olaparib_rep1


description:
Library name: EXOSC3_4h_rep1
EXOSC3 4h rep1 (same as GSM9295327) RNAseq


title: Testis,  Low-protein diet, rep3

description: Library name: LP_TESTIS_3


title: Patient04 pre treatment


description: Library name: Cas9_HEK4_48h_HEK293T_500k_PEI_NU7441_rep2


description:
Library name: EXOSC3_0h_rep3
EXOSC3 0h rep3 (same as GSM9295326) RNAseq

value: no treatment


title: Testis,  Low-protein diet, rep2

description: Library name: LP_TESTIS_2


title: Patient03 12weeks treatment


description: Library name: Cas9_HEK4_48h_HEK293T_500k_PEI_NU7441_rep1


description:
Library name: EXOSC3_0h_rep2
EXOSC3 0h rep2 (same as GSM9295325) RNAseq


title: Testis,  Low-protein diet, rep1

description: Library name: LP_TESTIS_1


description: Library name: Cas9_HEK4_48h_HEK293T_500k_PEI_mock_rep2


description:
Library name: EXOSC3_0h_rep1
EXOSC3 0h rep1 (same as GSM9295324) RNAseq


title: Testis, Control diet, rep5

description: Library name: TESTIS_C_5

value: Control diet


title: Patient03 4weeks treatment


description: Library name: Cas9_HEK4_48h_HEK293T_500k_PEI_mock_rep1


title: Total_ZFC3H1_4HdTAG_rep3

description: Library name: Total_ZFC3H1_4HdTAG_rep3

data_processing:
The raw sequence reads received from service providers were first quality checked using FastQC (Babraham Bioinformatics group). Reads were then trimmed for adaptors and filtered using Trim Galore (Babraham Bioinformatics group). Trimmed reads were mapped to hg38, using Hisat2 in paired-end mode. Mapped files were sorted and checked for pairing using SAMtools. Reads were then deduplicated using MarkDuplicates (Picard – Broad Institute) and further filtered to keep only unique mappers by using SAMtools. Relative samples size was then estimated by generating coverage counts using htseq-count (HTSeq-counts) over the Genecode annotation and analyzing then with DEseq2 to define size factors. In the case of fractionated pA+ RNAseq, size factors were measured separately for the nuclear and cytoplasmic fractions to avoid any compensation of compartment specific phenotypes. Finally, reads were converted to bigwig (bw) files normalized to size factors, with a binning of 5, using bamCoverage (Deeptools).
Assembly: hg38
Supplementary files format and content: bigwig (bw) - normalized coverage with a binning of 5

growth_protocol: HeLa cells were cultured in standard DMEM medium supplemented with 10% FBS and penicillin-streptomycin mix.

extract_protocol:
Total RNA was extracted using TRIZOL reagent according to manufacturer’s instructions
Library construction and sequencing were paid services from the Beijing Genome Institute (BGI) in case of total pA+ RNAseq and from Lexogen for the fractionated and exogenously expressing ZFC3H1 pA+ RNAseq.

treatment_protocol: When specified, cels were treated with dTAGV-1 at a concentration of 500nM for 4H

value: cervix

value: 4H dTAGV-1 500nM


title: Patient03 pre treatment


title: Testis, Control diet, rep4

description: Library name: TESTIS_C_4


description: Library name: Cas9_HEK4_48h_HEK293T_500k_PEI_KU-60648_rep2


title: Total_ZFC3H1_4HdTAG_rep2

description: Library name: Total_ZFC3H1_4HdTAG_rep2


title: Patient02 12weeks treatment


description: Library name: Cas9_HEK4_48h_HEK293T_500k_PEI_KU-60648_rep1


title: Total_ZFC3H1_4HdTAG_rep1

description: Library name: Total_ZFC3H1_4HdTAG_rep1


title: Patient02 8weeks treatment


title: Testis, Control diet, rep2

description: Library name: TESTIS_C_2


title: Total_ZFC3H1_0HdTAG_rep3

description: Library name: Total_ZFC3H1_0HdTAG_rep3


description: Library name: Cas9_HEK4_48h_HEK293T_500k_PEI_KP32_rep1


title: Testis, Control diet, rep1

description: Library name: TESTIS_C_1


title: Heart, High-fat diet, rep4

description: Library name: HEART_HF_4

source_name: Heart

value: Heart


description: Library name: Cas9_HEK4_48h_HEK293T_500k_PEI_IBR2_rep2


title: Total_ZFC3H1_0HdTAG_rep1

description: Library name: Total_ZFC3H1_0HdTAG_rep1


title: Heart, High-fat diet, rep3

description: Library name: HEART_HF_3

value: High-fat diet


description: Library name: Cas9_HEK4_48h_HEK293T_500k_PEI_IBR2_rep1


title: Total_LENG8_4HdTAG_rep3

description: Library name: Total_LENG8_4HdTAG_rep3


title: Patient01 8weeks treatment


title: Heart, High-fat diet, rep2

description: Library name: HEART_HF_2


description: Library name: Cas9_HEK4_48h_HEK293T_500k_PEI_HY-122727_rep2


title: Patient01 4weeks treatment


title: Total_LENG8_4HdTAG_rep2

description: Library name: Total_LENG8_4HdTAG_rep2


title: Heart, High-fat diet, rep1

description: Library name: HEART_HF_1


description: Library name: Cas9_HEK4_48h_HEK293T_500k_PEI_HY-122727_rep1


title: Patient01 pre treatment


title: Patient02 pre treatment


title: Heart, High-fat control diet, rep5

description: Library name: HEART_C_HF_5


title: Cas9_HEK4_48h_HEK293T_500k_PEI_EXO_rep2

description: Library name: Cas9_HEK4_48h_HEK293T_500k_PEI_EXO_rep2


title: LNAC12

city: Philadelphia

first: Stephanie

last: Daws

state: PA

address: 3500 N Broad St

institute: Temple University

description: 10 days of saline self-administration

data_processing:
Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts. In this step, clean data (clean reads) were obtained by removing reads containing poly-N, with 5’ adapter contaminants, without 3’ adapter or the insert tag, containing poly A or T or G or C and low quality reads from raw data.
The small RNA tags were mapped to reference sequence by Bowtie
Mapped small RNA tags were used to look for known miRNA. miRBase22.0 was used as reference, and mirdeep2  and srna-tools-cli were used to obtain the potential miRNA. Custom scripts were used to obtain the miRNA counts
To remove tags originating from protein-coding genes, repeat sequences, rRNA, tRNA, snRNA, and snoRNA, small RNA tags were mapped to RepeatMasker, Rfam database or those types of datas from the specified species itself
miRNA expression levels were estimated by TPM (transcript per million) through the following criteria: Normalization formula: Normalized expression = mapped readcount/Total reads*1000000
Assembly: rn6
Supplementary files format and content: TPM in .xls format

organism: Rattus norvegicus

source_name: nucleus accumbens

extract_protocol:
Total RNA was extracted from prefrontal cortex and nucleus accumbens tissue samples with Trizol, according to manufacter's protocols. Exosomal RNA was extracted from blood serum using the SeraMir kit, using manufacturer's protocols.
Small RNA sequencing was performed on six biological replicate samples per treatment group, per region of interest (prefrontal cortex, nucleus accumbens, or serum). 3’ and 5’ adaptors were ligated to 3’ and 5’ end of small RNA, respectively. Then the first strand cDNA was synthesized after hybridization with reverse transcription primer. The double-stranded cDNA library was generated through PCR enrichment. After purification and size selection, libraries with insertions between 18~40 bp were ready for sequencing

treatment_protocol: Adult male Sprague Dawley rats were aged 8 weeks on arrival. Forheroin exposure, animals were acclimited to the animal facility for 1 week then underwent jugular vein catheterization. Following 1 week of recovery, animals self-administered  heroin at a dose of 0.075mg/kg/infusion for 6 hours per day in 10 daily sessions. Saline animals underwent the same surgical procedures but self-administered saline for 10 days. Following the last self-administration session, animals were euthanized with 60 minutes and their brains were frozen in ice cold isopentane. Trunk blood was collected during decapitation. Blood was collected into sterile tubes, allowed to clot, and then spun at 2g for 10 min to collect serum. Prefrontal cortex and nucleus accumbens tissue was dissected from each animal on dry ice then RNA extraction proceeded.

value: nucleus accumbens

tag: strain

value: Sprague-Dawley

tag: Sex

value: male

tag: age

value: adult

value: saline self-administration for 10 days


title: Total_LENG8_0HdTAG_rep3

description: Library name: Total_LENG8_0HdTAG_rep3


title: Heart, High-fat control diet, rep4

description: Library name: HEART_C_HF_4

value: High-fat control diet


title: Cas9_HEK4_48h_HEK293T_500k_PEI_EXO_rep1

description: Library name: Cas9_HEK4_48h_HEK293T_500k_PEI_EXO_rep1


title: LNAC11

description: 10 days of saline self-administration


title: Total_LENG8_0HdTAG_rep2

description: Library name: Total_LENG8_0HdTAG_rep2


title: Heart, High-fat control diet, rep3

description: Library name: HEART_C_HF_3


description: Library name: Cas9_HEK4_48h_HEK293T_500k_PEI_EXO1_rep2


title: LNAC10

description: 10 days of saline self-administration


title: Total_LENG8_0HdTAG_rep1

description: Library name: Total_LENG8_0HdTAG_rep1


title: Heart, High-fat control diet, rep2

description: Library name: HEART_C_HF_2


description: Library name: Cas9_HEK4_48h_HEK293T_500k_PEI_EXO1_rep1


title: LNAC9

description: 10 days of saline self-administration


title: Total_LENG8_4HdTAG_rep1

description: Library name: Total_LENG8_4HdTAG_rep1


title: Testis, High-fat control diet, rep1

description: Library name: C_HF_TESTIS_1

value: Testis


description: Library name: Cas9_HEK4_48h_HEK293T_500k_PEI_RE1B_rep2


title: Total_Hela_4HdTAG_rep3

description: Library name: Total_Hela_4HdTAG_rep3

value: HeLa Kyoto

value: WT


title: Testis,  Low-protein diet, rep5

description: Library name: LP_TESTIS_5


description:
Library name: EXOSC3_4h_rep2
EXOSC3 4h rep2 (same as GSM9295328) RNAseq

value: Cervix

value: 4h dTAGV-1 100nM


title: Heart, High-fat control diet, rep1

description: Library name: HEART_C_HF_1


description: Library name: Cas9_HEK4_48h_HEK293T_500k_PEI_DIDS_rep2


title: LNAC8

description: 10 days of saline self-administration


title: Muscle, ID ELMIH012, After_exercise, Group 2

city: Amsterdam

first: Georges

last: Janssens

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC

description: Library name: Sample_14

data_processing:
Analysis for read mapping was performed in R v4.1.0 and Bioconductor v3.13. Reads were subjected to quality control FastQC v0.11.15 and trimmed using Trimmomatic v0.36 and aligned using HISAT2 v2.1.0 to the GRCh38 (v94) human genome reference assembly. Counts were obtained using HTSeq (v0.11.0, default parameters) using the corresponding GTF taking into account the directions of the reads. Statistical analyses were performed using the edgeR v3.34.1 and limma/voom v 3.48.344 R packages. All genes with more than 2 counts in at least 4 of the samples were kept. Count data were transformed to log2-counts per million (logCPM), normalized by applying the trimmed mean of M-values method and precision weighted using voom. Genes were reannotated using the Ensembl genome database (v104) and the biomaRt package.
Assembly: GRCh38 (v94)
Supplementary files format and content: Count data, 93 human muscle samples with annotation of 58735 Ensembl Gene IDs

source_name: Muscle

extract_protocol:
Human muscle tissues were homogenized with a 5 mm steel bead using a TissueLyser II (QIAGEN) for 5 min at frequency of 30 times/second. RNA was extracted according to the instructions of the RNaesy Mini Kit (QIAGEN). Contaminating genomic DNA was removed using RNase-Free DNase (QIAGEN). RNA was quantified with a NanoDrop 2000 spectrophotometer (Thermo Scientific; Breda, The Netherlands) and stored at -80°C until use.
RNA libraries were prepared and sequenced with the Illumina platform by Genome Scan (Leiden, The Netherlands). The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina was used to process the sample(s). The sample preparation was performed according to the protocol "NEBNext Ultra II Directional RNA Library Prep Kit for Illumina" (NEB #E7760S/L). Briefly, mRNA was isolated from total RNA using the oligo-dT magnetic beads. After fragmentation of the mRNA, cDNA synthesis was performed. This was used for ligation with the sequencing adapters and PCR amplification of the resulting product. The quality and yield after sample preparation was measured with the Fragment Analyzer. The size of the resulting products was consistent with the expected size distribution (a broad peak between 300-500 bp). Clustering and DNA sequencing using the NovaSeq6000 was performed according to manufacturer's protocols. A concentration of 1.1 nM of DNA was used. NovaSeq control software NCS v1.6 was used.

value: Muscle


title: Muscle, ID ELMIH116, After_exercise, Group 1

description: Library name: Sample_12


title: Skin_WT_UV3hrs_rep2

city: LEBANON

first: SLADJANA

last: SKOPELJA-GARDNER

address: ONE MEDICAL CENTER DR

institute: DARTMOUTH COLLEGE

description:
Library name: SSG_027_S16
Column name in featurecounts.readcounts.ann.tsv: SSG_027
featurecounts.readcounts.ann.tsv

data_processing:
Reads were trimmed using Cutadapt v4.6  (Bulk RNA)
Reads were aligned GRCm38 using hisat2 version 2.1.0 (Bulk RNA)
Reads were quantified using featurecounts (subread) version 2.0.1 (Bulk RNA)
Assembly: GRCm38.97 (Bulk RNA)
Supplementary files format and content: TSV file containing counts matrix (raw counts for bulk RNA)

source_name: Skin

growth_protocol: 12-week old female mice were used.

extract_protocol:
Total RNA from skin was isolated using the RNeasy Fibrous Tissue kit (Qiagen). cDNA was reverse transcribed using the iScript cDNA synthesis kit (Bio-rad) and quantitative PCR performed with iTaq Universal SYBR Green Supermix (Bio-rad). For single cell RNA: Formalin fixed paraffin embedded (FFPE) skin tissues blocks were prepared for the 10x Genomics Flex assay following demonstrated manufacturer’s protocol CG000606. For each block, 4 x 25um sections were placed into C tubes, deparaffinized with xylene, rehydrated with progressive dilutions of ethanol and dissociated in Liberase TM solution on a gentleMACS instrument (Miltenyi). The resulting cell/nuclei suspension was filtered through a 70um strainer and quantified using AO/PI staining on a Luna FX7 automated fluorescent cell counter.
RNA quantity and integrity were assessed using a Qubit fluorometer (Thermo Fisher Scientific) and an Agilent Bioanalyzer 2100 (Agilent Technologies), respectively. Only samples with RNA integrity number (RIN) ≥ 8 were used for library preparation. rRNA depletion was performed using the Ribo-Zero Gold rRNA Removal Kit (Illumina) to enrich for coding and noncoding RNAs. cDNA libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit (Illumina) according to the manufacturer’s instructions. Sequencing was performed on an Illumina HiSeq 2000 platform to generate 100 bp paired-end reads, aiming for a depth of approximately [e.g., 30–50 million reads] per sample.

treatment_protocol: Mice were shaved and naired 5 days prior to acute UVB exposure (500mj/cm2) or no exposure. Mice were euthanized 1 day after UV exposure and skin was isolated and placed in RNAlater.

value: Skin


title: Early flowering, drought-stressed

city: Nugegoda

first: Dona Vihara

middle: Sugandhika

last: Kaluthanthri

state: Western province

address: Gangodawila

department: Botany

country: Sri Lanka

institute: University of Sri Jayewardenepura

data_processing:
Total RNA was sequenced using a HiSeq 2500 sequencer following HCS 2.2.70 sequencing control software.
Filtering Criteria - To exclude gene with at least one zero Counts.
Normalization : TMM Normalization - In order to reduce systematic bias, size factors were estimated from the read count data (calcNormFactors method). Using them, the read count data was normalized with Trimmed mean of M-values (TMM) method in edgeR library. Then, statistical test was performed with the normalized data.
Signal+1 and Logarithm for Visualization - log2(Counts per Million reads (CPM)+1) and log2(TMM normalized count+1) values were used for data visualization. Raw read counts are scattered around wide range and most of them lean to the low level. Therefore, logarithm transformation facilitates to reduce the range of the read counts and flatten a data distribution. To prevent a negative value resulting from logarithm transformation, 1 was added to PM(Counts per Million reads) or normalized read count. These logarithm figures were used only for visualization. To proceed a statistical test, TMM normalized count was adopted for exact test (exactTest) in edgeR.
Assembly: GCF_000003195.3
Supplementary files format and content: Microsoft excel worksheet, include gene counts for each sample
Supplementary files format and content: Microsoft excel worksheet, include transcript count for each sample

organism: Sorghum bicolor

source_name: Flag leaf

growth_protocol: A total of fifty biological replicates of each germplasm accession was maintained in a net house under controlled environment at the Department of Botany, Faculty of Applied Seeds of each germplasm accession were sown in small plastic pots filled with normal soil at a depth of 1/2 inch keeping uniform space between the seeds. Pots were irrigated soon after sowing. Approximately 25-day old seedlings were later transplanted separately in large plastic pots filled with approximately 5 kg mixture of soil and compost (1:1). The pots were arranged in five blocks with 10 replicates from each accession following the Completely Randomized Design (CRD).

extract_protocol:
All leaves were frozen in liquid nitrogen immediately after collecting and were then stored at minus 80 °C. Total RNA was separately isolated from frozen flag leaves samples (those collected from three different plants of each group when pollen shed began) using NucleoSpin® RNA Plant kit (MACHEREY-NAGEL). RNA quality and integrity were assessed using Quantus™ Fluorometer (Promega) prior to RNA-sequencing (at Macrogen Inc., Seoul, South Korea).
The cDNA library preparation was done using a TrueSeq Stranded mRNA LT Sample prep kit.

treatment_protocol: The plants from each germplasm accession were divided into two groups: the well-watered (WW) and drought-stressed (DS) groups. Drought stress was administered to 25 days old seedlings from the DS group by withdrawing water whilst the remaining (control) plants were well-watered. The WW pots were maintained at potentials >−0.2 MPa (15–20 % soil water content) with irrigation, while DS pots were maintained at <−1.5 MPa (5–8 % soil water content). When pollen shed began, flag leaf tissues were harvested from three different plants in each replicate group and condition.

value: Flag leaf

value: Early flowering

value: Drought-Stressed


title: Puck_240108_11

status: Public on Jun 17 2026

city: New Haven

first: Hattie

last: Chung

state: CT

address: 300 George St

institute: Yale University

description: Library name: 2024-02-12_Puck_240108_11

data_processing:
Raw sequencing data were processed using the Slide-seq pipeline following Stickels et al. Nat Biotech 2021.
Assembly: mm10
Supplementary files format and content: [puck_name].h5ad: processed raw counts of beads (rows) and genes (columns)
Library strategy: Spatial Transcriptomics

source_name: Ovary

growth_protocol: Female C57BL/6 mice were maintained under SPF conditions on a 12-hour light-dark cycle with standard chow and water provided ad libitum.

extract_protocol:
10µm frozen sections were cut on the cryostat
Spatial transcriptome libraries were prepared using the Slide-seq V2 protocol

treatment_protocol: Mice were staged near-daily for their estrous cycle and harvested at the estrus or metestrus stage via intracardial perfusion with PBS. Ovaries were fresh frozen embedded in OCT.

value: Ovary

tag: Stage

value: Estrus

tag: group

value: Young


title: Heart, Low-protein diet, rep5

description: Library name: HEART_LP_5

data_processing:
Sequences were trimmed with  "cutadapt --no-indels -O 15 -m 2 -a GATCGGAAGAGCACACGTCTGAACTCCAGTCAC" ,"cutadapt -u 7" , and then "cutadapt -u -1" to remove the adapter, the UMI, and the TPRT base (the UMI was not used for removing duplicates)  Only reads >65 bases were used for most analyses
Data was mapped and counted using TRAX, which uses an all-best mapping approach and uses Deseq2 for normalization and detection of differential expression
Assembly: mm10
Supplementary files format and content: tab-delimited raw counts for calculated by tRAX, with mitochondrial tRNA counts appended

extract_protocol:
Samples were vortexed for 5 minutes to ensure complete breakdown of the sperm, followed by centrifugation at 12,000 RCF for 4 minutes. The aqueous phase was then removed and transferred to a low-binding RNase/DNase-free microcentrifuge tube, followed by the addition of 20 µg of glycoblue (Invitrogen) and 1 volume of Isopropanol. The RNA was then precipitated for 30 minutes or greater at -20°C, followed by centrifugation at 18,000 RCF for 30 minutes at 4°C, and one wash with 70% cold ethanol followed by centrifugation at 12,000 RCF for 10 minutes at 4°C. Finally, the RNA was reconstituted in nuclease-free water.
Library was constructed using Ottr-seq protocol.  Input RNA was PNK treated and labelled at the 3’ end by incubation in buffer containing ddATP for 90 minutes in 30˚C, followed by an addition of ddGTP and another incubation at 30˚C for 30 minutes. The reaction was stopped by incubating at 65°C for 5 minutes, followed by the addition of 5 mM MgCl2 and 0.5 units of shrimp alkaline phosphatase (NEB, cat# M0371S) at 37°C for 15 minutes, then stopped by the addition of 5 mM EGTA, and incubated at 65°C for 5 minutes. Samples were then incubated in templated cDNA synthesis buffer, adaptors, and dNTPs at 37˚C for 20 minutes, followed by heat inactivation at 65˚C for 5 minutes and RNase A/H treatment. cDNA was size selected on a 10% PAGE urea gel to minimize adaptor dimers. Size selected cDNA was PCR amplified for 12 cycles with Q5 high fidelity polymerase (NEB, cat# M0491S). The final PCR product was cleaned up with AMPure XP beads (Beckman, cat # A63881) and finally separated by 6% TBE gel to remove adaptor dimers. The desired product was excised from the gel and eluted in 400ul elution buffer (300 mM NaCl, 10 mM Tris pH 8, 1 mM EDTA) overnight at -20, followed by isopropanol precipitation and resuspension in 9µl nuclease-free H2O.

value: Heart

value: Low-protein diet


title: Muscle, ID ELMIH071, After_exercise, Group 4

description: Library name: Sample_09


description: Library name: Cas9_HEK4_48h_HEK293T_500k_PEI_DIDS_rep1

data_processing:
Data were mapped to hg38 (human) using chromap.
Reads overlaped the ENCODE blacklist are removed
Bedtools was used to generate bedGraph files, which were then normalized and converted to BigWig files by bedGraphToBigWig
Assembly: hg38
Supplementary files format and content: BigWig of genome-editing signals

extract_protocol:
Cells were fixed with Concanavalin A bead, washed, and resuspended with buffer containing RPA2/MRE11/IgG antibodies. pA-MNase was added to cleavage the DNA. Cleavaged fragments were collected and then digested with DNase. For Tracking-seq, DNA was purified with DNA Clean Beads and then HL-dsDNase was added to remove dsDNA.
The strand-specific ssDNA libraries were constructed using VAHTS ssDNA Library Prep Kit. CUT&RUN-MRE11 library was constructed using NEBNext® Ultra™ II DNA Library Prep Kit.


title: Total_Hela_4HdTAG_rep2

description: Library name: Total_Hela_4HdTAG_rep2

source_name: cervix

value: cervix

value: 4H dTAGV-1 500nM


title: Total_Hela_4HdTAG_rep1

description: Library name: Total_Hela_4HdTAG_rep1


title: LNAC7

description: 10 days of saline self-administration

value: nucleus accumbens

value: Sprague-Dawley

value: male

value: adult

value: saline self-administration for 10 days


title: Heart, Low-protein diet, rep4

description: Library name: HEART_LP_4


description: Library name: Cas12a_DNMT1-3_48h_HEK293T_500k_PEI_T5_rep1


title: LNAC6

description: 10 days of heroin self-administration (0.075mg/kg)

value: heroin self-administration for 10 days


title: Patient03 8weeks treatment

value: Plasma


title: Heart, Low-protein diet, rep3

description: Library name: HEART_LP_3


title: Total_Hela_0HdTAG_rep3

description: Library name: Total_Hela_0HdTAG_rep3

value: HeLa Kyoto

value: WT


title: LNAC5


description: Library name: Cas12a_DNMT1-3_48h_HEK293T_500k_PEI_T5-KU-60648_rep1


title: Total_Hela_0HdTAG_rep2

description: Library name: Total_Hela_0HdTAG_rep2


description: Library name: Cas12a_DNMT1-3_48h_HEK293T_500k_PEI_mock_rep1


title: LNAC4


title: Heart, Low-protein diet, rep2

description: Library name: HEART_LP_2


title: Total_Hela_0HdTAG_rep1

description: Library name: Total_Hela_0HdTAG_rep1


title: Heart, Low-protein diet, rep1

description: Library name: HEART_LP_1


description: Library name: Cas12a_DNMT1-3_48h_HEK293T_500k_PEI_KU-60648_rep1


title: LNAC3


title: Total_GANP_4HdTAG_rep3

description: Library name: Total_GANP_4HdTAG_rep3


title: Heart, Control diet, rep5

description: Library name: HEART_C_5

value: Control diet


description: Library name: Cas12a_CCR5-1_48h_HEK293T_500k_PEI_T5-KU-60648_rep1


title: LNAC2


title: Heart, Control diet, rep4

description: Library name: HEART_C_4


title: LNAC1


title: Total_GANP_4HdTAG_rep2

description: Library name: Total_GANP_4HdTAG_rep2


description: Library name: Cas12a_CCR5-1_48h_HEK293T_500k_PEI_mock_rep1


title: Heart, Control diet, rep3

description: Library name: HEART_C_3


title: Testis, Control diet, rep3

description: Library name: TESTIS_C_3

value: Testis


title: ABE_VEGFA2_24h_HEK293T_500k_PEI_T7_rep2

description: Library name: ABE_VEGFA2_24h_HEK293T_500k_PEI_T7_rep2


title: Total_GANP_4HdTAG_rep1

description: Library name: Total_GANP_4HdTAG_rep1


title: Total_GANP_0HdTAG_rep3

description: Library name: Total_GANP_0HdTAG_rep3


title: LPFC12

description: 10 days of saline self-administration

source_name: prefrontal cortex

value: prefrontal cortex


title: Heart, Control diet, rep2

description: Library name: HEART_C_2


description: Library name: Cas9_HEK4_48h_HEK293T_500k_PEI_KP32_rep2


title: ABE_VEGFA2_24h_HEK293T_500k_PEI_T7_rep1

description: Library name: ABE_VEGFA2_24h_HEK293T_500k_PEI_T7_rep1


title: Cas9_VEGFA2_48h_293_500k_PEI_IBR2_rep3

description: Library name: Cas9_VEGFA2_48h_293_500k_PEI_IBR2_rep3

data_processing:
Tracking-seq/2: Data were analyzed using Offtracker (https://github.com/Lan-lab/offtracker)
GUIDE-seq-2: Data were analyzed using guideseq (https://github.com/tsailabSJ/guideseq)
Assembly: hg38
Supplementary files format and content: BigWig of genome-editing signals

extract_protocol:
Tracking-seq/2: Cells were fixed with Concanavalin A bead, washed, and resuspended with buffer containing RPA2 antibodies. pA-MNase was added to cleavage the DNA. Cleavaged fragments were collected and then digested with DNase. DNA was purified with DNA Clean Beads and then HL-dsDNase was added to remove dsDNA. GUIDE-seq-2 were performed according to doi: 10.1101/2025.02.10.637517
Tracking-seq/2: The strand-specific ssDNA libraries were constructed using VAHTS ssDNA Library Prep Kit.GUIDE-seq-2 libraries were constructed according to doi: 10.1101/2025.02.10.637517


title: LPFC11

description: 10 days of saline self-administration


description: Library name: Cas9_VEGFA2_48h_293_10k_PEI_T5-KU-60648_rep1


title: Total_GANP_0HdTAG_rep2

description: Library name: Total_GANP_0HdTAG_rep2


title: Heart, Control diet, rep1

description: Library name: HEART_C_1


title: Total_GANP_0HdTAG_rep1

description: Library name: Total_GANP_0HdTAG_rep1


title: ABE_VEGFA2_24h_HEK293T_500k_PEI_T5_rep2

description: Library name: ABE_VEGFA2_24h_HEK293T_500k_PEI_T5_rep2


title: LPFC10

description: 10 days of saline self-administration


title: LPFC9

description: 10 days of saline self-administration


title: ABE_VEGFA2_24h_HEK293T_500k_PEI_T5_rep1

description: Library name: ABE_VEGFA2_24h_HEK293T_500k_PEI_T5_rep1


title: Liver, High-fat diet, rep3

description: Library name: LIVER_HF_3

source_name: Liver

value: Liver

value: High-fat diet


description: Library name: ABE_VEGFA2_24h_HEK293T_500k_PEI_mock_rep2


title: Patient02 4weeks treatment

source_name: non-CIPN


title: SARS-CoV2_NSP14-WT passage 11  in VERO-AT cells

city: San Antonio

first: Yan

last: Xiang

state: TX

address: 7703 FLOYD CURL DR

department: Microbiology, Immunology and Molecular Genetics

institute: UT Health San Antonio

description: Library name: P11_NSP14-WT-VERO-AT

data_processing:
Sequencing reads were mapped to the reference genome using minimap2
Per-position read depth was calculated using samtools
Variants were called from samtools mpileup by quantifying reference and alternate base counts at each position, followed by filtering based on sequencing quality, minimum coverage thresholds, and a minimum alternate allele frequency of 1.5%.
Assembly: recombinant SARS-CoV-2 genome included in the supplemental file
Supplementary files format and content: reference gemone in fasta format
Supplementary files format and content: reference GTF file
Supplementary files format and content: excel file containg read depth of every samples
Supplementary files format and content: excel file containg error rate per position of every samples
Supplementary files format and content: excel file containg SNP frequency of every samples

organism: Severe acute respiratory syndrome coronavirus 2

source_name: Vero cells expressing ACE2 and Tmprss2

growth_protocol: Five micrograms of SARS-CoV-2 BAC DNA was transfected into Vero-NP cells in 6-well plates using Lipofectamine 3000 transfection reagent (Invitrogen). After 4 hours, the transfection medium was replaced with DMEM containing 5% FBS. Cells were incubated at 37 °C with 5% CO₂ for 3–21 days, after which the tissue culture supernatant was collected and designated passage 0 (P0). Subsequent passages were generated by infecting fresh Vero-NP or Vero-AT cells with 500 µL of virus from the previous passage.

extract_protocol:
Culture supernatants from serial passages of recombinant SARS-CoV-2 in Vero-NP or Vero-AT cells were processed for RNA extraction using TRIzol LS reagent (Invitrogen) according to the manufacturer’s instructions.
The extracted RNA was converted into sequencing libraries and subjected to paired-end deep sequencing (100 or 150 bp reads) with NovaSeq 6000 system

value: Vero cells expressing ACE2 and Tmprss2

tag: timepoint

value: passage 11


title: LPFC7

description: 10 days of saline self-administration


description: Library name: ABE_VEGFA2_24h_HEK293T_500k_PEI_mock_rep1


title: SARS-CoV2_NSP14-WT passage 9 in VERO-AT cells

description: Library name: P9_NSP14-WT-VERO-AT

value: passage 9


title: Liver, High-fat diet, rep1

city: Santa Cruz

first: Andrew

last: Holmes

institute: UC Santa Cruz

description: Library name: LIVER_HF_1


title: ABE_HEK4_24h_HEK293T_500k_PEI_T7_rep1

description: Library name: ABE_HEK4_24h_HEK293T_500k_PEI_T7_rep1


title: LPFC6


title: SARS-CoV2_NSP14-WT passage 7 in VERO-AT cells

description: Library name: P7_NSP14-WT-VERO-AT

value: passage 7


title: Liver, High-fat control diet, rep4

description: Library name: LIVER_C_HF_5

value: High-fat control diet


title: ABE_HEK4_24h_HEK293T_500k_PEI_T5_rep1

description: Library name: ABE_HEK4_24h_HEK293T_500k_PEI_T5_rep1


title: LPFC5

description: 10 days of heroin self-administration (0.075mg/kg)

value: Sprague-Dawley

value: male


title: SARS-CoV2_NSP14-WT passage 5 in VERO-AT cells

description: Library name: P5_NSP14-WT-VERO-AT

value: passage 5


title: Liver, High-fat control diet, rep3

description: Library name: LIVER_C_HF_4


title: LPFC4

value: adult

value: heroin self-administration for 10 days


title: ABE_HEK4_24h_HEK293T_500k_PEI_mock_rep1

description: Library name: ABE_HEK4_24h_HEK293T_500k_PEI_mock_rep1


title: SARS-CoV2_NSP14-WT passage 3 in VERO-AT cells

description: Library name: P3_NSP14-WT-VERO-AT

value: passage 3


title: Liver, High-fat control diet, rep2

description: Library name: LIVER_C_HF_3


title: LPFC3


title: Liver, High-fat control diet, rep1

description: Library name: LIVER_C_HF_1


title: SARS-CoV2_NSP14-WT passage 1 in VERO-AT cells

description: Library name: P1_NSP14-WT-VERO-AT

value: passage 1


title: Pw Retina Sample (RNA)

description:
Library name: Pw_Retina_RNA
Single-nucleus RNA-seq library from multiome assay

organism: Pleurodeles waltl

source_name: Retina

value: Retina

value: Nuclei

value: Wild-type


title: LPFC2

value: prefrontal cortex


title: SARS-CoV2_NSP14-WT passage 0 in VERO-AT cells

description: Library name: P0_NSP14-WT-VERO-AT

value: passage 0


title: Cas9_IDS_48h_293_500k_PEI_mock_rep1

description: Library name: Cas9_IDS_48h_293_500k_PEI_mock_rep1


title: SARS-CoV2_NSP14-mut passage 13 in VERO-AT cells

description: Library name: P13_NSP14-mut-VERO-AT

value: Vero cells expressing ACE2 and Tmprss2

value: passage 13


title: LS12

description: 10 days of saline self-administration

source_name: blood serum

value: blood serum

value: saline self-administration for 10 days


title: Liver, Low-protein diet, rep3

description: Library name: LIVER_LP_3

value: Liver

value: Low-protein diet


title: C57BL/6J mouse liver,resmetirom-treated MASH,12 weeks,replicate 1

city: nanjing

first: xin

last: Qian

address: No. 24 Tongjia Lane, Gulou District, Nanjing, Jiangsu Province, P.R.China

institute: China Pharmaceutical University

description: Library name: RE1

data_processing:
Raw paired-end reads were trimmed and quality controlled by fastp with default parameters to remove adapter sequences, low-quality reads, reads with high N content, and reads shorter than 20 bp after trimming, generating clean reads.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text file includes gene expression matrix for all samples.

source_name: liver tissue

growth_protocol: C57BL/6J mice were housed under standard laboratory conditions with free access to food and water. Mice were maintained under a 12 h light/12 h dark cycle before and during the experiment.

extract_protocol:
Total RNA was extracted from mouse liver tissues using TRIzol Reagent according to the manufacturer's instructions. RNA quality was assessed using an Agilent 5300 Bioanalyzer, and RNA concentration was quantified using a NanoDrop ND-2000 spectrophotometer. Only high-quality RNA samples were used for library construction.
RNA-seq libraries were prepared using the Illumina Stranded mRNA Prep, Ligation kit according to the manufacturer's instructions. Briefly, mRNA was enriched from total RNA using oligo(dT) beads, fragmented, reverse-transcribed into cDNA, end-repaired, adapter-ligated, size-selected, PCR-amplified, and purified. The qualified libraries were sequenced on the Illumina NovaSeq X Plus platform using paired-end 150 bp sequencing.

treatment_protocol: C57BL/6J mice were divided into four groups: normal control group, high-fat diet-induced MASH model group, Eleutheroside E-treated MASH group, and resmetirom-treated MASH group. After 8 weeks of model establishment, mice in the Eleutheroside E-treated group were orally administered Eleutheroside E at 100 mg/kg for 4 weeks, and mice in the resmetirom-treated group were orally administered resmetirom at 3 mg/kg for 4 weeks. Mice in the normal control group and MASH model group were orally administered 0.5% CMC-Na as vehicle control for 4 weeks. At the end of treatment, liver tissues were collected for RNA extraction, library construction, and high-throughput RNA sequencing.

value: liver tissue

value: high-fat diet-induced MASH + resmetirom


title: C57BL/6J mouse liver,Eleutheroside E-treated MASH,12 weeks,replicate 3

description: Library name: H9

value: high-fat diet-induced MASH + Eleutheroside E


title: LS10

description: 10 days of saline self-administration

value: Sprague-Dawley

value: male

value: adult


title: Liver, Low-protein diet, rep1

description: Library name: LIVER_LP_1


title: C57BL/6J mouse liver,Eleutheroside E-treated MASH,12 weeks,replicate 2

description: Library name: H6


title: LS9

description: 10 days of saline self-administration


title: Liver, Control diet, rep4

description: Library name: LIVER_C_5

value: Control diet


title: C57BL/6J mouse liver,Eleutheroside E-treated MASH,12 weeks,replicate 1

description: Library name: H5


title: Liver, Control diet, rep3

description: Library name: LIVER_C_4


title: Subject 1 - human cells transfected with negative control miRNA mimic

city: Stockholm

first: Nicolas

last: Pillon

address: Solnavägen 9

country: Sweden

institute: Karolinska Institutet

description: Library name: P29458_1001

data_processing:
Quality and adapter trimming of reads was performed using Cutadapt (v3.5). Sample quality was assessed using FastQC (v0.11.8) and MultiQC (v1.14). Reads were aligned to the Ensembl GRCh38/GRCm38 reference genome using STAR (v2.7.9d). Counts for each gene were obtained using featureCounts (v1.5.1).
Assembly: GRCh38/GRCm38
Supplementary files format and content: CSV file, raw counts following featureCounts
Supplementary files format and content: CSV file, raw counts following featureCounts

source_name: skeletal muscle

growth_protocol: Mouse C2C12 muscle cells were obtained from the American Type Culture Collection (ATCC® CRL-1772™). Primary cells were isolated from vastus lateralis skeletal muscle biopsies derived from six healthy individuals (two females, four males, 35±17 years old, BMI 22.6±1.9 kg/m2). The ethical committee at Karolinska Institutet approved the protocols. Mouse and human cells were cultured and differentiated as described (Abdelmoez et al, 2020). Differentiation was monitored under the microscope and the absence of mycoplasma contamination was routinely confirmed by PCR.

extract_protocol:
On the fifth day of differentiation, cells were harvested for gene expression analysis using QIAzol Lysis Reagent.
Libraries were generated using TruSeq Stranded Total RNA (Illumina) following manufacturer's instructions.

treatment_protocol: Muscle cells were transfected on the first and third day of differentiation, with either miR-339-5p mirVana® miRNA mimic (Thermo Fisher Scientific, MC12347) or negative Control #1 mirVana™ miRNA mimic (Thermo Fisher Scientific, 4464059). Transfections were performed using Lipofectamine RNAiMAX as transfection reagent. In primary human skeletal muscle cells, transfection was performed with 25 nM miRNA mimics for 5 hours. For C2C12, miRNA mimics were used at a final concentration of 200 nM for 24h.

value: skeletal muscle

value: primary

value: skeletal myotube

value: control


title: Cas9_HEK4_48h_293_500k_PEI_T5_rep3

city: Shanghai

first: Zhu

last: Ming

institute: East China Normal University

description: Library name: Cas9_HEK4_48h_293_500k_PEI_T5_rep3


title: Frac_HCT116_GANP_4HdTAG_Nuc_rep1

city: Aarhus

first: Jerome

last: Rouviere

institute: Aarhus University

description: Library name: Frac_HCT116_GANP_4HdTAG_Nuc_rep1

data_processing:
The raw sequence reads received from service providers were first quality checked using FastQC (Babraham Bioinformatics group). For RNAseq libraires, reads were then trimmed for adaptors and filtered using Trim Galore (Babraham Bioinformatics group). Trimmed reads were mapped to hg38, using Hisat2 in paired-end mode. Mapped files were sorted and checked for pairing using SAMtools. Reads were then deduplicated using MarkDuplicates (Picard – Broad Institute) and further filtered to keep only unique mappers by using SAMtools. Relative samples size was then estimated by generating coverage counts using htseq-count (HTSeq-counts) over the Genecode annotation and analyzing then with DEseq2 to define size factors. In the case of fractionated pA+ RNAseq, size factors were measured separately for the nuclear and cytoplasmic fractions to avoid any compensation of compartment specific phenotypes. Finally, reads were converted to bigwig (bw) files normalized to size factors, with a binning of 5, using bamCoverage (Deeptools). For iCLIP libraires,using only "R1" reads, adaptors were trimmed using Trim Galore, UMI deduplication was performed using seqkit. The first 15nt were trimmed with Trim Galore, and reads were filtered to be bellow 100bp length using seqkit. Reads were mapped to hg38 using STAR allowing only unique mappers. To get single positions, using a combination of Bedtools and bash script, mapped bam files were converted to bed, shifted one base, filtered to contain only primary assemby chromosomes (except chrM) and separated by strand. The resulting bedgraph files where then converted to bw (without binning) using bedGraphToBigWig.  For 3'end sequencing, adapters and A18 stretches were trimmed using Trim Galore. Mapping to hg38 was performed using STAR. A combinations of samtools and bash code was used to keep only unique mappers, reduce the reads to their 5'end (due to Quant-seq REV sequencing) and filter them to only correspond to the primary assembly chromosomes (except chrM). Htseq-count, was used on the resulting mapped files, over the last exon of protein coding genes and the output was used to define size factor with DEseq2 which was used in bamCoverage to convert the files to bw (without binning)
Assembly: hg38
Supplementary files format and content: bigwig (bw) - normalized coverage with a binning of 5 for RNAseq and no binning for iCLIP and 3'end seq

source_name: colon

extract_protocol:
Total RNA was extracted using TRIZOL reagent according to manufacturer’s instructions
For iCLIP libraries were constructed in-house and seqenced by Lexogen. For all other libraries construction and sequencing were paid services from Lexogen

value: colon

value: 4H dTAGV-1 500nM


title: C57BL/6J mouse liver,MASH model,12 weeks, replicate 3

description: Library name: M7

value: high-fat diet-induced MASH


title: SARS-CoV2_NSP14-mut passage 1 in VERO-AT cells

description: Library name: P1_NSP14-mut-VERO-AT

value: Vero cells expressing ACE2 and Tmprss2

value: passage 1


title: Liver, Control diet, rep2

address: 1156 High Street

description: Library name: LIVER_C_3

value: Liver


title: C57BL/6J mouse liver,MASH model,12 weeks, replicate 2

description: Library name: M6

value: liver tissue


title: LS6

value: blood serum

value: heroin self-administration for 10 days


title: SARS-CoV2_NSP14-mut passage 0 in VERO-AT cells

description: Library name: P0_NSP14-mut-VERO-AT

value: passage 0


title: C57BL/6J mouse liver,MASH model,12 weeks, replicate 1

description: Library name: M2


title: LS5

value: Sprague-Dawley

value: male


title: SARS-CoV2_NSP14-WT passage 14 in VERO-NP cells

description: Library name: P14_NSP14-WT-VERO-NP

source_name: Vero cells expressing Sars-CoV-2 NP

value: Vero cells expressing Sars-CoV-2 NP

value: passage 14


title: HPAC Daraxonrasib

city: Redwood City

first: Ximo

last: Pechuan-Jorge

state: CA

address: 700 Saginaw Drive

institute: Revolution Medicines

description: Library name: Sample 2

data_processing:
Somatic variants were identified from HPAC whole-exome sequencing data using Sentieon TNscope in tumor-only mode.
VCF files were converted to Mutation Annotation Format files using vcf2maf with Ensembl VEP-based annotation.
Assembly: hg38
Supplementary files format and content: MAF

source_name: Pancreas

growth_protocol: HPAC tumor cells (ATCC CRL-2119) were maintained as a monolayer culture in RPMI 1640 medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C in a humidified atmosphere containing 5% CO₂. The culture medium was refreshed every 2–3 days, and cells were routinely subcultured at 80–90% confluence using trypsin-EDTA, with passages limited to a maximum of 4–5.

extract_protocol:
DNA was extracted from approximately 2 million cells using the DNeasy Blood & Tissue Kit.
Whole-exome sequencing libraries were prepared from genomic DNA using the Agilent SureSelect Human All Exon target-enrichment workflow according to the manufacturer’s protocol.

value: Pancreas

value: HPAC

value: epithelial

value: KRAS G12D/WT

value: Daraxonrasib


title: C57BL/6J mouse liver,resmetirom-treated MASH,12 weeks,replicate 3

description: Library name: RE9

value: high-fat diet-induced MASH + resmetirom


title: Liver, Low-protein diet, rep5

description: Library name: LIVER_LP_5

value: Low-protein diet


title: SARS-CoV2_NSP14-mut passage 11  in VERO-AT cells

description: Library name: P11_NSP14-mut-VERO-AT

value: Vero cells expressing ACE2 and Tmprss2

value: passage 11


title: SARS-CoV2_NSP14-WT passage 11 in VERO-NP cells

description: Library name: P11_NSP14-WT-VERO-NP


title: LS4

value: adult


title: SARS-CoV2_NSP14-mut passage 9 in VERO-AT cells

description: Library name: P9_NSP14-mut-VERO-AT

value: passage 9


title: LS11

description: 10 days of saline self-administration

value: blood serum

value: saline self-administration for 10 days


title: HPAC DMSO

description: Library name: Sample 1

value: DMSO


title: SARS-CoV2_NSP14-mut passage 7 in VERO-AT cells

description: Library name: P7_NSP14-mut-VERO-AT

value: passage 7


title: C57BL/6J mouse liver,control,12 weeks, replicate 2

description: Library name: C9

value: liver tissue

value: normal chow diet


title: LS3

value: Sprague-Dawley

value: male

value: heroin self-administration for 10 days


title: SARS-CoV2_NSP14-WT passage 9 in VERO-NP cells

description: Library name: P9_NSP14-WT-VERO-NP

value: Vero cells expressing Sars-CoV-2 NP


title: C57BL/6J mouse liver,control,12 weeks,replicate 1

description: Library name: C7


title: LS2


title: SARS-CoV2_NSP14-WT passage 7 in VERO-NP cells

description: Library name: P7_NSP14-WT-VERO-NP


title: 526MEL treated with supernatant and RSL3 replicate 1

city: Nagasaki

first: Daisuke

last: Ehara

address: 1-12-4 Sakamoto

department: Dermatology

institute: Nagasaki University Graduate School of Biomedical Sciences

description: Library name: supRSL3_1

data_processing:
Raw reads were generated on an Illumina sequencing platform by Novogene. Adapter-containing reads, reads containing >10% ambiguous bases (N), and low-quality reads containing >50% bases with Qscore ≤5 were removed to generate clean reads.
Gene expression matrices were generated from the sequencing data and exported in CSV format for downstream analyses. Ensembl-like gene identifiers were converted to gene symbols when applicable, and duplicate symbols were collapsed by mean expression values.
Group-wise Z-scores were calculated across experimental conditions. Statistical analyses were performed using two-sided Student’s t-tests with Benjamini–Hochberg correction.
Assembly: GRCh38/hg38
Supplementary files format and content: Processed data files consist of gene-level expression matrices in CSV format. Rows represent genes and columns represent individual samples. The files contain normalized expression values used for downstream analyses.

source_name: tumor

extract_protocol:
Total RNA from two biological samples was individually isolated using the RNeasy Mini kit and treated with DNase I (Life Technologies, Gaithersburg, MD, USA), according to the manufacturer’s protocol. In addition, 0.5 μL of RNase inhibitor (Nippon Gene, Toyama, Japan) was added to each tube before the RNA purification.
RNA sequencing was performed by Novogene, where directional mRNA libraries were prepared using poly(A) enrichment and dUTP-based strand-specific library construction.

value: tumor

value: melanoma cells


title: LS1


title: SARS-CoV2_NSP14-WT passage 5 in VERO-NP cells

description: Library name: P5_NSP14-WT-VERO-NP

value: passage 5


title: LS8

description: 10 days of saline self-administration


title: 526MEL treated with supernatant replicate 2

description: Library name: sup2


title: ELF3 knockout primary mouse tubular epithelial cells under TNFα + IFNγ stimulation (replicate 3)

city: PHILADELPHIA

first: Yanjuan

last: Hou

address: 3400 civic center blvd

department: Perelman School of Medicine, Department of Medicine

institute: university of pennsylvania

description:
Library name: KO_3
Bulk RNA-seq of primary mouse tubular epithelial cells under TNFα + IFNγ stimulation

data_processing:
Raw sequencing reads were subjected to quality control and adaptor trimming.
Clean reads were aligned to the Mus musculus reference genome (mm10).
Gene-level counts were generated using featureCounts / Salmon quantification.
Expression values were normalized to TPM.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files containing raw gene counts and TPM-normalized expression values for all samples.

source_name: primary culture

growth_protocol: Primary mouse renal tubular epithelial cells were isolated and cultured under standard conditions in appropriate growth medium at 37°C in a humidified atmosphere containing 5% CO₂.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. RNA quality and concentration were assessed before library preparation.
RNA-seq libraries were prepared using an Illumina-compatible library preparation kit following the manufacturer’s protocol, including mRNA enrichment, cDNA synthesis, adaptor ligation, and PCR amplification.

treatment_protocol: Cells were infected with adenovirus expressing Cre recombinase (AdvCre) to induce ELF3 deletion or with control adenovirus. Following viral transduction, cells were stimulated with TNFα and IFNγ prior to RNA extraction.

value: kidney

value: renal tubular epithelial cells

value: ELF3 knockout

value: TNFα + IFNγ

value: batch 1


title: MI+ART3

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

description: Library name: Sample 9

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data(raw reads) of fastq format were firstly processed through in-houseperl scripts.In this step,clean data(clean reads) were obtained by removing reads containing adapter,reads containing ploy-N and low quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly.Index of the reference genome was built using Hisat 2v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat 2v2.0.5.
Feature Counts v1.5.0-p3 was used to count the reads numbers mapped to each gene.And then FPKM of each gene was calculated based on the length of the gene and readscount mapped to this gene.
Differential expression analysis of two conditions/groups was performed using the DESeq R package (1.8.3).
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: tab_delimited text files include Counts for each Sample
Supplementary files format and content: txt files include Counts for each Sample

organism: Mus

source_name: atria

growth_protocol: Rats were randomly assigned to four experimental groups: Sham + Vehicle, MI + Vehicle, and MI+ART.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA w as used for the construction of sequencing libraries.
RNA libraries for RNA-seq w ere prepared using SMARTER mRNA-Seq Library Prep Kitfollow ing manufacturer's protocols.

treatment_protocol: Male wild-type (WT) C57BL/6J mice (8–10 weeks old, 20–23 g) were purchased from SPF Biotechnology Co., Ltd. (Beijing, China). Myocardial infarction (MI) was induced by permanent ligation of the left anterior descending (LAD) coronary artery, as previously described. Sham-operated mice underwent identical surgical procedures except for LAD ligation. Artesunate (ART; MCE, Monmouth Junction, NJ, USA) was dissolved in dimethyl sulfoxide (DMSO) and administered intraperitoneally at a dose of 25 mg/kg body weight daily, beginning immediately after surgery and continuing for 7 consecutive days.

value: atria

value: WT

value: MI + ART


title: SARS-CoV2_NSP14-WT passage 3 in VERO-NP cells

description: Library name: P3_NSP14-WT-VERO-NP

value: passage 3


title: 526MEL treated with supernatant replicate 1

description: Library name: sup1


title: MI+ART2

description: Library name: Sample 8


title: SARS-CoV2_NSP14-WT passage 1 in VERO-NP cells

description: Library name: P1_NSP14-WT-VERO-NP

value: passage 1


title: 526MEL treated with IFN-γ and RSL3 replicate 2

description: Library name: IFNgRSL3_2


title: ELF3 knockout primary mouse tubular epithelial cells under TNFα + IFNγ stimulation (replicate 1)

description:
Library name: KO_1
Bulk RNA-seq of primary mouse tubular epithelial cells under TNFα + IFNγ stimulation


title: MI+ART1

description: Library name: Sample 7


title: SARS-CoV2_NSP14-mut passage 15 in VERO-NP cells

description: Library name: P15_NSP14-mut-VERO-NP

value: passage 15


title: 526MEL treated with IFN-γ and RSL3 replicate 1

description: Library name: IFNgRSL3_1


title: MI4

description: Library name: Sample 6

value: MI + Vehicle


title: SARS-CoV2_NSP14-mut passage 14 in VERO-NP cells

description: Library name: P14_NSP14-mut-VERO-NP

value: passage 14


title: 526MEL treated with IFN-γ replicate 2

description: Library name: IFNg2


title: Control primary mouse tubular epithelial cells under TNFα + IFNγ stimulation (replicate 2)

description:
Library name: CTR_2
Bulk RNA-seq of primary mouse tubular epithelial cells under TNFα + IFNγ stimulation

value: wild type


title: MI3

description: Library name: Sample 5

value: MI+ Vehicle