title: Immunotherapy colitis 003

city: Nijmegen

first: Harm

last: Westdorp

address: Geert Grooteplein Zuid

department: Medical Oncology

institute: Radboudumc

description: Library name: S9

data_processing:
QUOTED from publication Wester et al iScience 2021 ( doi: 10.1016/j.isci.2021.103444):  RNA-seq data was processed using seq2science using default options (Van der Sande et al., 2020). In short, reads were first trimmed using Fastp. Sequencing reads were aligned to the mm10 (mouse) or hg38 (human) transcript assembly from UCSC using STAR, after which a count table was generated using HTSeq. For experiments without replicates (mouse experiments), counts per million reads were calculated for each sample and any transcript not detected in all samples was filtered, log2 values were calculated and genes were ranked. For experiments with replicates (human), differential gene expression analysis was performed with the DESeq2 package (Love et al., 2014). The ‘rlogTransformation’ function in DESeq2 was used to normalize, log2 transform and noise-stabilize the expression data for visualization purposes. Heatmaps for expression data were created with the ComplexHeatmap package (Gu et al., 2016). All pairwise comparisons have been made using control samples from the same organoid batch.
Assembly: Sequencing reads were aligned to the or hg38 transcript assembly from UCSC using STAR.
Supplementary files format and content: Processed data is submitted in one matrix file with column headers matching the library sample name.

source_name: Colon (FFPE)

extract_protocol:
For bulk RNA sequencing, archival FFPE pinch biopsies were sectioned at 5 or 10 μm. RNA isolation was performed with RNeasy FFPE Kit according to manufacturer’s instruction. RNA quality assessment was performed using Qubit (concentration) and TapeStation (RIN values) and 120 ng per sample was collected for cDNA conversion
QUOTED from publication Wester et al iScience 2021 ( doi: 10.1016/j.isci.2021.103444):  A total amount of 1 μg RNA per mouse small intestinal sample or 100ng RNA per CRC organoid sample was used for the preparation of RNA sequencing libraries using the KAPA RNA HyperPrep Kit with RiboErase (HMR) (KAPA Biosystems). In short, oligo hybridization and rRNA depletion, rRNA depletion cleanup, Dnase digestion, Dnase digestion cleanup, and RNA elution were performed according to protocol. Fragmentation and priming were performed at 94 C for 6:30 min. First strand synthesis, second strand synthesis, and A- tailing was performed according to protocol. For the adapter ligation, a 7 μM stock was used (NextFlex DNA barcodes, Bioo Scientific). First, and second post-ligation cleanup was performed according protocol. For the library amplification, 6 cycli were used. The library amplification cleanup was performed using a 0.8x bead-based cleanup. Library size was determined using the High Sensitivity DNA bioanalyzer (Agilent Technologies), library concentration was measured using the DeNovix dsDNA High Sensitivity Assay (DeNovix).

value: Colon (FFPE)


title: P. promelas larvae, UP, biological replicate UP_B03, lane 2, time step = 1, analyzed on 20161013

status: Public on Aug 01 2026

type: SRA

city: Durham

first: Steven

middle: Thomas

last: Purucker

state: NC

address: 109 TW Alexander Dr

country: USA

institute: US EPA

description: Library name: 20161013_ UP_1_B03_CTTGTA_L002_R1_001

library_source: transcriptomic

data_processing:
Raw read quality assessment with FastQC 0.11.9 & MultiQC 1.12
Reads were processed with fastp 0.23.2 trimming with quality, length, and adapter trimming all enabled by default, and polyX trimming (flag: -x) enabled manually
Alignment with STAR 2.7.10a (--outSAMattributes NH HI AS NM MD --outSAMtype BAM SortedByCoordinate --outSAMheaderHD @HD VN 1.4 SO:sorted --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --outSAMunmapped Within --outFilterType BySJout)
Quantification with STAR 2.7.10a (--quantMode GeneCounts TranscriptomeSAM)
Assembly: P. promelas, GCF_016745375.1_EPA_FHM_2.0
Supplementary files format and content: Tab delimited text file with gene counts: all_counts_20220629.txt uploaded separately.

molecule: total RNA

organism: Pimephales promelas

source_name: whole larvae

growth_protocol: Lab-reared individual fathead minnow larvae (Pimephales promelas) 2 days post-fertilization.

extract_protocol:
Total RNA was isolated from individual FHM using the MagMAX-96 Total RNA Isolation Kit (ThermoFisher Scientific) following manufacturer's protocols. RNA was quantified by spectrophotometric analysis with a Synergy HTX multi-mode plate reader (BioTek).
Neoprep Library Prep System (Illumina) and the TruSeq Stranded mRNA Library Prep for NeoPrep (Illumina). Library concentrations were determined using either the KAPA Library Quantification Kit (Kapa Biosystems) or Qubit dsDNA HS Assay (ThermoFisher Scientific), normalized to equimolar amounts, and then combined into pools of eight samples each. Sequencing was performed at Michigan State University’s RTSF Genomics Core on the Illumina HiSeq 2500 Rapid Run flow cell (v2) for 1x50 bp single-end reads with Rapid SBS reagents.

treatment_protocol: 48 hour lab exposures to moderately hard reconstituted water or river water grab samples collected in August 15 for 6 locations in the vicinity of a wastewater treatment plant (WWTP): upstream of WWTP, WWTP effluent discharging point, proximal location downstream WWTP outfall, distal location downstream of WWTP outfall, a downstream drinking water intake, and treated drinking water collected prior to discharge to the distribution system. Other exposures included 48 hour field fish deployments in exposure vessels secured to a minnow trap at 2 locations (upstream of a WWTP, WWTP effluent discharging point).

tag: tissue

value: whole larvae

tag: age

value: 2 dpf

tag: treatment-replicate id

tag: treatment-time

tag: treatment-location

value: UP

tag: batch


title: Sinorhizobium meliloti MB1129, biological rep3

type: RNA

city: Stanford

first: Melanie

middle: J

last: Barnett

state: CA

address: 371 Jane Stanford Way

department: Biology

institute: Stanford University

description: gene expression data log phase cultures

hyb_protocol: Four micrograms of biotinylated cDNA was hybridized to each chip at 48 degrees celsius for 16 hours as described by Barnett et al. 2004. GeneChips were washed and stained in the Affymetrix Fluidics Station 400

scan_protocol: Chips were scanned at the Stanford PAN facility using an Affymetrix Scanner 3000 7G

data_processing: The data were analyzed using Partek Genomics Suite 6.6 software, with the following settings: RMA for background correction; quantile normalization; log base 2 transformation; median polish summarization

label: biotin

organism: Sinorhizobium meliloti

source_name: exoX deletion strain MB1129 (deletion marked with hygromycin resistance)

label_protocol: cDNA was fragmented and biotinylated as described by Barnett et al. 2004.

growth_protocol: Each culture was grown from a single colony inoculated into TY medium supplemented with 500 ug ml-1 Sm, in 250 ml baffled flasks, and allowed to grow with shaking (250 rpm) at 30°C. Cells were harvested at an OD-600 ranging from 0.67 to 0.72.

extract_protocol: Total RNA was extracted using a Qiagen RNeasy kit with modifications as described by Barnett et al. 2004 Proc Natl Acad Sci USA volume 101 pages 16636 to 16641.

treatment_protocol: Stop solution (5% buffer equilibrated phenol in ethanol) was added to bacterial cultures, at one tenth the culture volume, before centrifugation at 4 degrees celsius. Bacterial cell pellets were frozen in liquid nitrogen and stored at -80 degrees celsius until RNA extraction.

tag: strain


title: Immunotherapy colitis 002

country: Netherlands

description: Library name: S8

organism: Homo sapiens


title: HONE-1 RNA-seq si-FBXO8 si1_3

city: guangzhou

first: ran

last: ding

state: guangdong

address: School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou 511442, China.

country: China

institute: South china university of technology

description:
Library name: si1_3
RNA-seq from HONE-1 cells transfected with FBXO8-targeting siRNA, replicate 3.

data_processing:
Raw sequencing reads were quality-checked, and adaptor sequences and low-quality reads were removed to generate clean reads.
Clean paired-end reads were aligned to the Homo sapiens reference genome GRCh38/hg38.
Gene-level read counts were quantified from aligned reads.
Gene expression levels were normalized and reported as FPKM.
Differential expression analysis was performed between FBXO8 knockdown and negative control groups using R-based statistical methods.
Assembly: Homo sapiens GRCh38/hg38
Supplementary files format and content: processed_HONE1_FBXO8_RNAseq_FPKM_matrix.txt

source_name: nasopharynx

growth_protocol: HONE-1 nasopharyngeal carcinoma cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum at 37 °C in a humidified incubator containing 5% CO2.

extract_protocol:
Total RNA was extracted from HONE-1 cells using TRIzol reagent following the manufacturer’s instructions. RNA quality and integrity were assessed before library construction.
RNA-seq libraries were constructed using standard protocols and sequenced on an Illumina NovaSeq 6000 platform using paired-end 150 bp sequencing.

treatment_protocol: HONE-1 cells were transfected with negative control siRNA or FBXO8-targeting siRNA. Cells were harvested after transfection for RNA extraction and downstream RNA-seq analysis.

value: nasopharynx

tag: cell line

tag: cell type

value: nasopharyngeal carcinoma cell

tag: genotype

value: not modified

tag: treatment

value: FBXO8 siRNA-mediated knockdown

value: batch 1


title: HONE-1 RNA-seq si-FBXO8 si1_2

description:
Library name: si1_2
RNA-seq from HONE-1 cells transfected with FBXO8-targeting siRNA, replicate 2.


title: P. promelas larvae, UP, biological replicate UP_B03, lane 1, time step = 1, analyzed on 20161013

description: Library name: 20161013_ UP_1_B03_CTTGTA_L001_R1_001


title: Immunotherapy colitis 001

description: Library name: S7


title: Sinorhizobium meliloti MB1129, biological rep2

description: gene expression data log phase cultures


title: P. promelas larvae, EFP, biological replicate EFP_B13, lane 2, time step = 2, analyzed on 20161013

description: Library name: 20161013_ EFP_2_B13_GTTTCG_L002_R1_001

value: EFP


title: Sinorhizobium meliloti MB1129, biological rep1

description: gene expression data log phase cultures


title: HONE-1 RNA-seq si-FBXO8 si1_1

description:
Library name: si1_1
RNA-seq from HONE-1 cells transfected with FBXO8-targeting siRNA, replicate 1.


title: Single-cell RNA-seq of orthotopic RM-1 prostate tumor, IRE-treated, biological replicate 2

city: wuhan

first: Qi-Dong

last: Xia

address: No. 1095 Jiefang Avenue

department: Urology

institute: Tongji Hospital

description:
Library name: OT_IRE_02_LIB1
Whole-cell suspension from a orthotopic RM-1 prostate tumor collected 7 days after irreversible electroporation; biological replicate 02.

library_source: transcriptomic single cell

data_processing:
Raw FASTQ files for all libraries were previously submitted to SRA under BioProject PRJNA1497318 and are linked here through the corresponding SRA run accessions.
Filtered feature-barcode matrices were generated from the mouse FASTQ files using SeekSoul Tools v1.3.0 with STAR v2.7.10a, Subread/featureCounts v2.0.3, and samtools v1.16.1.
Reads were aligned against the mouse mm10 reference genome, specified as GRCm38.p6 with paired GENCODE M25 annotation.
The processed files deposited to GEO are compressed Matrix Exchange (MEX) files for each sample: barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz.
These processed matrices were used for downstream Seurat-based quality control, integration, clustering, and annotation.
Assembly: mm10 (GRCm38.p6; GENCODE M25)
Supplementary files format and content: Each sample is represented by three gzip-compressed Matrix Exchange (MEX) files: barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz.
Supplementary files format and content: barcodes.tsv.gz lists filtered cell barcodes; features.tsv.gz lists gene features; matrix.mtx.gz stores the sparse gene-by-cell UMI count matrix used for downstream analysis.

organism: Mus musculus

source_name: orthotopic RM-1 prostate tumor

growth_protocol: Male C57BL/6 mice bearing RM-1 prostate tumors were maintained under standard specific-pathogen-free conditions. RM-1 cells (1 x 10^6 cells per mouse) were implanted either subcutaneously or orthotopically into the prostate. Each resected tumor corresponds to one biological replicate.

extract_protocol:
Fresh tumors were transferred to ice-cold medium, trimmed to remove skin, fat, fibrous capsule, large clots, and visibly liquefied necrotic tissue, and cut into approximately 1-2 mm pieces. Tissue was dissociated with SeekMate Tissue Dissociation Reagent Kit A Pro (SeekGene, K01801301) at 37 C for 20-30 min with gentle agitation. Suspensions were quenched with ice-cold RPMI 1640 containing 10% FBS, filtered through a 70-um strainer, washed, and evaluated for viability before single-cell library construction.
Whole-cell suspensions were processed with the SeekOne Digital Droplet Single Cell 3' Library Preparation Kit (SeekGene, K00202). Cell suspensions were combined with reverse-transcription reagents and loaded into a SeekOne Chip S3 with barcoded hydrogel beads and partitioning oil. After droplet generation and reverse transcription, cDNA was recovered, amplified, fragmented, end repaired, A-tailed, adaptor ligated, and enriched by indexed PCR. Libraries were purified with VAHTS DNA Clean Beads, quantified by Qubit, assessed with a fragment analyzer, and sequenced on an Illumina NovaSeq 6000.

treatment_protocol: At a tumor volume of approximately 300 mm3, mice were assigned to sham or irreversible electroporation (IRE). Under anesthesia, two monopolar electrodes connected to a BTX ECM830 electroporator were inserted into each tumor. IRE-treated tumors received 80 pulses at 2,000 V/cm, 100 microseconds per pulse, with 50-ms intervals. Sham-treated mice underwent anesthesia and electrode insertion without pulse delivery. Tumors were harvested 7 days later.

value: orthotopic RM-1 prostate tumor

value: whole tumor cell suspension

value: wild type C57BL/6 tumor-bearing mouse

value: IRE-treated tumor, biological replicate 02

value: not recorded


title: Ulcerative colitis 003

description: Library name: S6


title: HONE-1 RNA-seq negative control NC3

description:
Library name: NC3
RNA-seq from HONE-1 cells transfected with negative control siRNA, replicate 3.

value: negative control siRNA


title: P. promelas larvae, EFP, biological replicate EFP_B13, lane 1, time step = 2, analyzed on 20161013

description: Library name: 20161013_ EFP_2_B13_GTTTCG_L001_R1_001


title: Diarrhea only 003

description: Library name: S5


title: HONE-1 RNA-seq negative control NC2

description:
Library name: NC2
RNA-seq from HONE-1 cells transfected with negative control siRNA, replicate 2.


title: Single-cell RNA-seq of orthotopic RM-1 prostate tumor, IRE-treated, biological replicate 1

description:
Library name: OT_IRE_01_LIB1
Whole-cell suspension from a orthotopic RM-1 prostate tumor collected 7 days after irreversible electroporation; biological replicate 01.

value: IRE-treated tumor, biological replicate 01


title: P. promelas larvae, EFP, biological replicate EFP_B11, lane 2, time step = 1, analyzed on 20161013

description: Library name: 20161013_ EFP_1_B11_GTGAAA_L002_R1_001


title: Single-cell RNA-seq of orthotopic RM-1 prostate tumor, sham-treated, biological replicate 2

description:
Library name: OT_SHAM_02_LIB1
Whole-cell suspension from a orthotopic RM-1 prostate tumor collected 7 days after sham intervention; biological replicate 02.

value: sham-treated tumor, biological replicate 02


title: Diarrhea only 002

description: Library name: S4

value: Colon (FFPE)


title: HONE-1 RNA-seq negative control NC1

description:
Library name: NC1
RNA-seq from HONE-1 cells transfected with negative control siRNA, replicate 1.


title: P. promelas larvae, EFP, biological replicate EFP_B11, lane 1, time step = 1, analyzed on 20161013

description: Library name: 20161013_ EFP_1_B11_GTGAAA_L001_R1_001

value: whole larvae

value: 2 dpf


title: Single-cell RNA-seq of orthotopic RM-1 prostate tumor, sham-treated, biological replicate 1

description:
Library name: OT_SHAM_01_LIB1
Whole-cell suspension from a orthotopic RM-1 prostate tumor collected 7 days after sham intervention; biological replicate 01.

value: sham-treated tumor, biological replicate 01


title: Ulcerative colitis 002

description: Library name: S3


title: P. promelas larvae, MHW, biological replicate MHW_B12, lane 2, time step = NA, analyzed on 20161013

description: Library name: 20161013_ 15-08_B12_GCCAAT_L002_R1_001

value: MHW


title: Single-cell RNA-seq of subcutaneous RM-1 tumor, IRE-treated, biological replicate 3

description:
Library name: SC_IRE_03_LIB1
Whole-cell suspension from a subcutaneous RM-1 tumor collected 7 days after irreversible electroporation; biological replicate 03.

source_name: subcutaneous RM-1 tumor

value: subcutaneous RM-1 tumor

value: IRE-treated tumor, biological replicate 03


title: EndMT_KL2

city: Leipzig

first: Jes-Niels

last: Boeckel

address: Johannisalle 30

department: Klinik und Poliklinik für Kardiologie

country: Germany

institute: Universitätsklinikum Leipzig

description:
Library name: SID15657
CHIP-seq

library_source: genomic

data_processing:
Raw Fastq reads were mapped against the human reference genome (hg19) using bowtie2. Duplicates were extracted using Picard tool v3.0.0. ChIP peaks were called with MACS2 v2.2.7.1 peak caller software using broad peak enrichment analysis. BigWig files were generated using deeptools v3.5.4
Assembly: Reference transcriptome consisting of: human hg19
Supplementary files format and content: bigwig files

molecule: genomic DNA

source_name: HUVEC

growth_protocol: Primary ECs isolated from pooled donors (CC-2519, Lonza, CH) and from single donors (C-12221, Promocell, DE) were cultivated in either EGM (CC-3124, Lonza, CH), EGM+ medium (CC-5035, Lonza, CH) or EGM-2 (CC-3162, Lonza, CH) containing all supplements. Culture Medium was supplemented with 10% heat-inactivated FBS (10082147, ThermoFisher Scientific, US). Cells were cultured at 37°C, 20% O2 and 5% CO2 and split at approximately 70% confluency using 0.25% Trypsin/EDTA (25200056, ThermoFisher Scientific, US) with subsequent inactivation through culture medium.

extract_protocol:
ChIP was performed using the SimpleChIP Plus Enzymatic Chromatin IP Kit (9005S, Cell signaling, US). Approximately 2 * 107 EC were used as input per condition. Chromatin shearing was performed at 30% with 10 seconds of pulses using a sonicator followed by 30 s of pausing on wet ice 3 consecutive times. Successful chromatin shearing was validated using agarose gel electrophoresis. 2% input was taken prior to the IP. 4 µg of antibody were used for each IP experiment. The following antibodies were used: RNA pol II mAb (Clone 1F4B6, 61667, Active Motif, US) and IgG (MIgG, Dianova, US).
ChIP-seq libraries were prepared using the Simple ChIP ChIP-seq DNA Library Prep Kit for Illumina (56795S) and Multiplex Oligos for Illumina (Dual index primers, 47538S, both Cell signaling, US). Sequencing was performed on a NovaSeq 6000 (Illumina, US) and Fastq-reads were generated using CASAVA v.1.82 (Illumina, US).

treatment_protocol: EC were treated with SEC inhibitors KL-1 or KL-2 at 20 µM or solvent control (DMSO) for 4 h in culture medium. EC were subsequently treated with either culture medium (Control) or EndMT conditions (see above) as well as SEC inhibitors for 2 more hours.

value: HUVEC

value: Endothelial cell

value: EndMT+KL-2 (20µM)


title: P. promelas larvae, MHW, biological replicate MHW_B12, lane 1, time step = NA, analyzed on 20161013

description: Library name: 20161013_ 15-08_B12_GCCAAT_L001_R1_001


title: EndMT_KL1

description:
Library name: SID15650
CHIP-seq

value: EndMT+KL-1 (20µM)


title: Diarrhea only 001

description: Library name: S2


title: Single-cell RNA-seq of subcutaneous RM-1 tumor, IRE-treated, biological replicate 2

description:
Library name: SC_IRE_02_LIB1
Whole-cell suspension from a subcutaneous RM-1 tumor collected 7 days after irreversible electroporation; biological replicate 02.

value: whole tumor cell suspension

value: wild type C57BL/6 tumor-bearing mouse


title: Ulcerative colitis 001

description: Library name: S1


title: EndMT_DMSO

description:
Library name: SID15643
CHIP-seq

value: EndMT+DMSO


title: P. promelas larvae, MHW, biological replicate MHW_B09, lane 2, time step = NA, analyzed on 20161013

description: Library name: 20161013_ 15-07_B09_AGTCAA_L002_R1_001


title: Single-cell RNA-seq of subcutaneous RM-1 tumor, IRE-treated, biological replicate 1

description:
Library name: SC_IRE_01_LIB1
Whole-cell suspension from a subcutaneous RM-1 tumor collected 7 days after irreversible electroporation; biological replicate 01.

value: not recorded


title: Control_DMSO

description:
Library name: SID15622
CHIP-seq

value: solvent control DMSO


title: P. promelas larvae, MHW, biological replicate MHW_B09, lane 1, time step = NA, analyzed on 20161013

description: Library name: 20161013_ 15-07_B09_AGTCAA_L001_R1_001


title: Week5_CIS_scMulti_GEX_2024_03_26

city: Seattle

first: Kevin

middle: Z.

last: Lin

state: Washington

address: 3980 15th Avenue NE

department: Biostatistics

institute: University of Washington

description:
Library name: Sample28
10X Multiome

data_processing:
Cell Ranger ARC (version 2.0.1) was used for demultiplexing cell barcodes and aligning reads.
SAVER was used to recover gene expression signal
FastTopics was used to perform dimensionality reduction on RNA data
Seurat was used to normalize data, perform dimensionality reduction and UMAP visalization
MAC2 was used to identify peaks
PeakVI was used to generate a bin-by-cell matrix, perform dimensionality reduction and UMAP visualization on ATAC data
Assembly: hg38
Supplementary files format and content: metadata.csv: contains information on treatment, time point, cell barcode metadata, lineage barcode assignment
Supplementary files format and content: cells_rna.tsv: cell barcodes used in analysis
Supplementary files format and content: features_rna.csv: genes used in analysis
Supplementary files format and content: counts_rna.mtx: transcript count per gene per cell used in analysis
Supplementary files format and content: features_atac.csv: genomic peaks called in analysis
Supplementary files format and content: counts_atac.mtx: Tn5 insertion count per peak per cell used in analysis
Supplementary files format and content: features_lineage.csv: lineage barcodes present in study
Supplementary files format and content: counts_lineage.mtx: : lineage barcode read count per cell
Supplementary files format and content: umap_rna.csv: UMAP coordinates based on RNA modality
Supplementary files format and content: umap_atac.csv: UMAP coordinates based on ATAC modality
Supplementary files format and content: umap_wnn.csv: UMAP coordinates based on both RNA and ATAC modality
Supplementary files format and content: dimred_fasttopic.csv: FastTopics dimensionality reduction embedding based on RNA data
Supplementary files format and content: dimred_peakvi.csv: PeakVI dimensionality redicution embedding based on ATAC data

molecule: nuclear RNA

source_name: WM989 A6-G3 cells

extract_protocol:
Single nuclei were pooled and loaded onto a 10X Genomics Chromium controller for generation of 10X scMultiome libraries.
Single cell library preparation was performed following the 10X Multiome kit

value: WM989 A6-G3 cells

value: Cisplatin 5 weeks post treatment


title: Week5_CIS_scMulti_GEX_2022_04_28

description:
Library name: Sample27
10X Multiome


title: EndMT_KL2_10min

description:
Library name: SID14766
4sU-seq

data_processing:
Raw Fastq reads were trimmed with TrimGalore and mapped to the human reference genome (hg19) using bowtie2. Read density over the gene body was plotted using deeptools. BigWig files were generated using deeptools
Assembly: Reference transcriptome consisting of: human hg19
Supplementary files format and content: bigwig files

growth_protocol: Primary ECs isolated from pooled donors (CC-2519, Lonza, CH) and from single donors (C-12221, Promocell, DE) were cultivated in EGM+ medium (CC-5035, Lonza, CH) containing all supplements. Culture Medium was supplemented with 10% heat-inactivated FBS (10082147, ThermoFisher Scientific, US). Two million EC were seeded in 150 mm tissue culture plates and cultured at 37°C, 20% O2 and 5% CO2.

extract_protocol:
Total RNA was extracted from cells using the miRNeasy mini Kit and DRB treatment was validated using qPCR. Biotin-IP of nascent RNA was performed as previously described. Briefly, RNA labelled with 4sU was biotinylated using EZ-Link™ HPDP-Biotin (21341, ThermoFisher Scientific, US) for 1.5 h under rotation in the dark. Biotin-labelled RNA was separated from unlabeled RNA with streptavidin-coated magnetic beads (µMACS Streptavidin Kit, 130-074-101, Miltenyi Biotech, DE), eluted with 100 mM DTT (10197777001, Merck, DE) from the beads and precipitated overnight at -20°C with ethanol and 10 µg glycogen (R0551, ThermoFisher Scientific, US) as a precipitate enhancer. RNA pellet was purified.
Library was prepared for RNA sequencing using the Truseq stranded total RNA library kit (20020597, Illumina, US). Sequencing was performed on a NovaSeq 6000 (Illumina, US) and Fastq-reads were generated using CASAVA v.1.82 (Illumina, US).

treatment_protocol: After 48 h, cells were treated with either 20 µM of SEC inhibitor KL-1 or KL-2 in culture medium for 4 h at 37°C. Cells were then treated with differential medium including TGF-ß2 (10 ng/mL) or culture medium and SEC inhibitors for 1 h, before the transcription inhibitor 5,6-Dichlor-benzimidazol-1-β-D-ribofuranosid (DRB, D1916, Merck, DE) was added to a final concentration of 100 µM for 1 h. DRB was washed out with PBS, subsequently, EC were treated with differential medium including TGF-ß2 (10 ng/mL) or culture medium and SEC inhibitors. In this step, 4-thiouridine (4sU, T4509, Merck, DE) was added to the media and cells were harvested after 10 min.

value: EndMT+KL-2 (20 µM)


title: Single-cell RNA-seq of subcutaneous RM-1 tumor, sham-treated, biological replicate 3

description:
Library name: SC_SHAM_03_LIB1
Whole-cell suspension from a subcutaneous RM-1 tumor collected 7 days after sham intervention; biological replicate 03.

value: sham-treated tumor, biological replicate 03


title: Single-cell RNA-seq of subcutaneous RM-1 tumor, sham-treated, biological replicate 2

description:
Library name: SC_SHAM_02_LIB1
Whole-cell suspension from a subcutaneous RM-1 tumor collected 7 days after sham intervention; biological replicate 02.

value: sham-treated tumor, biological replicate 02


title: Week5_CIS_scMulti_GEX_2022_04_04

description:
Library name: Sample26
10X Multiome


title: EndMT_KL2_0min

description:
Library name: SID14765
4sU-seq


title: P. promelas larvae, UP, biological replicate UP_FIELD55, lane 1, time step = NA, analyzed on 20161012

description: Library name: 20161012_ UP_FIELD_55_GAGTGG_L001_R1_001

value: whole larvae

value: 2 dpf

value: UP


title: P. promelas larvae, UP, biological replicate UP_FIELD55, lane 2, time step = NA, analyzed on 20161012

description: Library name: 20161012_ UP_FIELD_55_GAGTGG_L002_R1_001


title: Single-cell RNA-seq of subcutaneous RM-1 tumor, sham-treated, biological replicate 1

description:
Library name: SC_SHAM_01_LIB1
Whole-cell suspension from a subcutaneous RM-1 tumor collected 7 days after sham intervention; biological replicate 01.

value: subcutaneous RM-1 tumor

value: sham-treated tumor, biological replicate 01


title: Week5_CIS_scMulti_GEX_2022_04_03

description:
Library name: Sample25
10X Multiome


title: EndMT_KL2

description:
Library name: SID14764
4sU-seq

value: HUVEC

value: Endothelial cell


title: P. promelas larvae, UP, biological replicate UP_FIELD54, lane 2, time step = NA, analyzed on 20161012

description: Library name: 20161012_ UP_FIELD_54_GGCTAC_L002_R1_001


title: MLE-12 cells, dexmedetomidine + hypoxia/reoxygenation, biological replicate 3

city: Wuxi

first: Youyi

last: Liu

state: Jiangsu

address: No. 1800, Lihu Avenue

department: Wuxi School of Medicine

institute: Jiangnan University

description:
Library name: IR_Dex_3
Original sample ID: C-3; experimental group: I/R + Dex; biological replicate 3; poly(A)-enriched RNA-seq; paired-end 150-bp reads.

data_processing:
Raw paired-end reads were filtered to remove adaptor sequences and non-AGCT bases at the 5' end, trim low-quality bases (quality score <Q20), remove reads containing ≥10% undetermined bases (N), and discard reads shorter than 25 bp after trimming.
Clean reads were aligned to the Mus musculus reference genome (GRCm39, Ensembl release 109) using HISAT2 v2.1.0.
Transcript assembly and gene/transcript abundance estimation were performed using StringTie v2.2.4. Expression values were reported as raw read counts and fragments per kilobase of transcript per million mapped reads (FPKM), as applicable.
Differential expression analysis between the I/R + Dex group and the I/R group was performed using DESeq2 v1.30. Genes or transcripts with an FDR <0.05 and |log2 fold change| ≥1 were considered differentially expressed.
Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed using the differentially expressed genes/transcripts to identify enriched biological functions and pathways.
Assembly: Mus musculus GRCm39; Ensembl release 109
Supplementary files format and content: Tab-delimited text file containing gene-level raw read counts for all six samples. Rows represent genes and columns represent individual biological replicates from the I/R and I/R + Dex groups.
Supplementary files format and content: Tab-delimited text files containing transcript-level FPKM values, DESeq2 differential-expression statistics (including log2 fold change, P value and FDR), and GO/KEGG enrichment results for I/R + Dex versus I/R.

growth_protocol: MLE-12 cells were cultured in DMEM supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C in a humidified incubator containing 5% CO2.

extract_protocol:
Total RNA was extracted using the HiPure Universal RNA Mini Kit (Magen, China) according to the manufacturer's instructions. RNA integrity and potential DNA contamination were evaluated by agarose gel electrophoresis. RNA purity was assessed using a NanoPhotometer spectrophotometer, and RNA integrity was further evaluated using an Agilent 2100 Bioanalyzer.
Poly(A)+ mRNA was isolated from total RNA using the Hieff NGS® mRNA Isolation Master Kit (Yeasen, China). Enriched mRNA was fragmented, reverse-transcribed into first-strand cDNA, and converted to double-stranded cDNA. Following end repair, A-tailing and adaptor ligation, libraries were size-selected and PCR-amplified. Library concentration and insert size were evaluated using a Qubit 2.0 Fluorometer, Agilent 2100 Bioanalyzer and qRT-PCR. Qualified libraries were pooled and sequenced on an Illumina NovaSeq 6000 platform using a paired-end 150-bp configuration.

treatment_protocol: For the hypoxia/reoxygenation group, cells were incubated under hypoxic conditions (1% O2, 94% N2 and 5% CO2) for 12 h and then returned to normoxic conditions (21% O2 and 5% CO2) for 4 h. For the I/R + Dex group, cells were pretreated with 10 µM dexmedetomidine for 12 h before hypoxia and then subjected to the same hypoxia/reoxygenation procedure.

value: mouse lung epithelial cells

value: wild type

value: Cells were pretreated with 10 µM dexmedetomidine for 12 h before hypoxia, exposed to hypoxia (1% O2, 94% N2 and 5% CO2) for 12 h, and then reoxygenated under normoxic conditions (21% O2 and 5% CO2) for 4 h.

value: batch 1


title: Week5_COCL2_scMulti_GEX_2024_03_26

description:
Library name: Sample24
10X Multiome

value: CoCl2 for 5 weeks


title: EndMT_KL1_10min

description:
Library name: SID14763
4sU-seq

value: EndMT+KL-1 (20 µM)


title: P. promelas larvae, UP, biological replicate UP_FIELD54, lane 1, time step = NA, analyzed on 20161012

description: Library name: 20161012_ UP_FIELD_54_GGCTAC_L001_R1_001


title: HAP1 WT cells, Bu-DIF-3, 24 h, biological replicate 3

city: Tokorozawa-shi

first: Taichi

last: Hara

state: Saitama

address: 2-579-15 Mikajima

department: Faculty of Human Science

country: Japan

institute: Waseda university

description: Library name: Bu3

data_processing:
Raw sequencing reads were filtered by removing reads containing adapter contamination, reads containing more than 10% undetermined nucleotides (N), and reads for which more than 50% of bases had a Phred quality score of 5 or lower.
Paired-end clean reads were aligned to the Homo sapiens hg38 reference genome using HISAT2 v2.0.5 with default parameters.
Gene-level read counts were generated using featureCounts v1.5.0-p3 based on a Homo sapiens GRCh38/hg38 gene annotation file. FPKM values were calculated based on gene length and the number of mapped reads.
Differential expression analysis was performed for Bu-DIF-3 versus control, CP-DIF-3 versus control, and Bu-DIF-3 versus CP-DIF-3 using DESeq2 v1.20.0 with a negative binomial model and Benjamini-Hochberg multiple-testing correction.
Differentially expressed genes used for downstream enrichment analyses were selected using an adjusted P value (padj) < 0.05 and |log2FC| > 1 for Bu-DIF-3 versus control. For CP-DIF-3 versus control, padj < 0.05 and |log2FC| > 0.585 were used.
Assembly: GRCh38/hg38
Supplementary files format and content: gene_count.xls is a tab-delimited plain-text matrix containing unfiltered gene-level raw read counts for 58,735 annotated genes across all nine samples. The file also includes Ensembl gene identifiers, gene symbols, genomic coordinates, gene length, gene biotype, and gene descriptions.

molecule: polyA RNA

growth_protocol: HAP1 WT cells were cultured in Iscove's Modified Dulbecco's Medium (IMDM; Gibco) supplemented with 10% fetal bovine serum (FBS; Gibco), 100 U/mL penicillin, and 100 µg/mL streptomycin (Gibco) at 37°C in a humidified incubator containing 5% CO2.

extract_protocol:
Total RNA was extracted from HAP1 WT cells using the ReliaPrep RNA Cell Miniprep System (Promega, Madison, WI, USA) according to the manufacturer's instructions.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads and fragmented. First-strand cDNA was synthesized using random hexamer primers, followed by second-strand cDNA synthesis. Libraries were prepared by end repair, A-tailing, adapter ligation, size selection, PCR amplification, and purification. Libraries were quantified using Qubit and real-time PCR, and size distributions were assessed using a bioanalyzer before pooling and paired-end sequencing as 2 × 150 bp reads on an Illumina NovaSeq 6000.

treatment_protocol: HAP1 WT cells were seeded at 2 × 10^5 cells/well in 6-well plates and treated with 0.1% DMSO (vehicle control), 5 µM Bu-DIF-3, or 5 µM CP-DIF-3 for 24 h. Three independent biological replicates were prepared for each condition.

value: WT

value: Bu-DIF-3; 5 µM; 24 h

value: biological replicate 3


title: MLE-12 cells, dexmedetomidine + hypoxia/reoxygenation, biological replicate 2

description:
Library name: IR_Dex_2
Original sample ID: C-2; experimental group: I/R + Dex; biological replicate 2; poly(A)-enriched RNA-seq; paired-end 150-bp reads.


title: P. promelas larvae, EFP, biological replicate EFP_FIELD55, lane 2, time step = NA, analyzed on 20161012

description: Library name: 20161012_ EFP_FIELD_55_ACTGAT_L002_R1_001

value: EFP


title: MLE-12 cells, dexmedetomidine + hypoxia/reoxygenation, biological replicate 1

description:
Library name: IR_Dex_1
Original sample ID: C-1; experimental group: I/R + Dex; biological replicate 1; poly(A)-enriched RNA-seq; paired-end 150-bp reads.


title: EndMT_KL1_0min

description:
Library name: SID14762
4sU-seq


title: Week5_COCL2_scMulti_GEX_2022_04_04

description:
Library name: Sample22
10X Multiome

value: WM989 A6-G3 cells


title: EndMT_KL1

description:
Library name: SID14761
4sU-seq


title: P. promelas larvae, EFP, biological replicate EFP_FIELD55, lane 1, time step = NA, analyzed on 20161012

description: Library name: 20161012_ EFP_FIELD_55_ACTGAT_L001_R1_001

value: whole larvae

value: 2 dpf


title: Week5_COCL2_scMulti_GEX_2022_04_28

description:
Library name: Sample23
10X Multiome


title: Week5_COCL2_scMulti_GEX_2022_04_03

description:
Library name: Sample21
10X Multiome


title: MLE-12 cells, hypoxia/reoxygenation, biological replicate 3

description:
Library name: IR_3
Original sample ID: B-3; experimental group: I/R; biological replicate 3; poly(A)-enriched RNA-seq; paired-end 150-bp reads.

value: Cells were exposed to hypoxia (1% O2, 94% N2 and 5% CO2) for 12 h, followed by reoxygenation under normoxic conditions (21% O2 and 5% CO2) for 4 h.


title: EndMT_DMSO_10min

description:
Library name: SID14760
4sU-seq

value: EndMT+DMSO


title: P. promelas larvae, EFP, biological replicate EFP_B23, lane 2, time step = 4, analyzed on 20161012

description: Library name: 20161012_ EFP_4_B23_GTGGCC_L002_R1_001


title: THP-1, H3K4me3,CN1

city: Shanghai

first: Lifei

last: Liang

address: 180 Fenglin Road

institute: Zhongshan Hospital, Fudan University

description:
Library name: Sample1
Cut&Tag

data_processing:
The raw sequence data were firstly quality trimmed by fatsp software to obtain the clean reads. Then the clean reads were aligned to the (input your reference genome and version, eg, the human genome GRCh38.p12) using Bowtie2 and subsequently analyzed by the SEACR software based the ‘stringent’parameter to detect genomic regions enriched for multiple overlapping DNA fragments (peaks) that we considered to be putative binding sites. Visualization of peak distribution along genomic regions of interested genes was performed with IGV.Peaks were then annotated using chipseeker software to obtain the genes and gene annotations about peaks. Significant Motif of peaks were analyzed by MEME and DREME software and aligned to the motif database.
Assembly: hg38
Supplementary files format and content: BigWig signal tracks generated from CUT&Tag sequencing analysis.
Library strategy: CUT&Tag

extract_protocol:
CUT&Tag assay was performed using HyperactiveTM In-Situ ChIP Library Prep Kit for Illumina (cat.no.TD901-TD902, Vazyme Biotech, China) according to manufacturer's instruction. Briefly, prepared concanavalin A-coated magnetic beads (ConA beads) were added to resuspended cells and incubated at room temperature to bound cells.
Non-ionic detergent Digitonin was used to permeate cell membrane. Then, primary VISTA antibody, secondary antibody and the Hyperactive pA-Tn5 Transposase were incubated with the cells that were bounded by ConA beads in order. Therefore, the Hyperactive pA-Tn5 Transposase can exactly cut off the DNA fragments that were bound with target protein. In addition, the cut DNA fragments can be ligated with P5 and P7 adaptors by Tn5 transposase and the libraries were amplified by PCR with the P5 and P7 primers. The purified PCR products were evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Finally, these libraries were sequenced on the Illumina NovaSeq6000 platform and 150bp paired-end reads were generated for the following analysis.

value: Lenti-Con


title: Sinorhizobium meliloti MB1157, biological rep1

description: gene expression data log phase cultures

source_name: control strain MB1157 (carries hygromycin resistance in the SMc01380-SMc01267 intergenic region


title: MLE-12 cells, hypoxia/reoxygenation, biological replicate 2

description:
Library name: IR_2
Original sample ID: B-2; experimental group: I/R; biological replicate 2; poly(A)-enriched RNA-seq; paired-end 150-bp reads.


title: Week5_DABTRAM_scMulti_GEX_2024_03_26

description:
Library name: Sample20
10X Multiome

value: Dabrafenib and Trametinib for 5 weeks


title: EndMT_DMSO_0min

description:
Library name: SID14759
4sU-seq

value: HUVEC

value: Endothelial cell


title: MLE-12 cells, hypoxia/reoxygenation, biological replicate 1

description:
Library name: IR_1
Original sample ID: B-1; experimental group: I/R; biological replicate 1; poly(A)-enriched RNA-seq; paired-end 150-bp reads.

value: mouse lung epithelial cells

value: wild type


title: P. promelas larvae, EFP, biological replicate EFP_B23, lane 1, time step = 4, analyzed on 20161012

description: Library name: 20161012_ EFP_4_B23_GTGGCC_L001_R1_001


title: P. promelas larvae, EFP, biological replicate EFP_B23, lane 2, time step = 3, analyzed on 20161012

description: Library name: 20161012_ EFP_3_B23_TAGCTT_L002_R1_001


title: Week5_DABTRAM_scMulti_GEX_2022_04_28

description:
Library name: Sample19
10X Multiome


title: EndMT_DMSO

description:
Library name: SID14758
4sU-seq


title: Heart, Day5,ISO2

description:
Library name: Sample4
10X Genomics

data_processing:
The Single Cell 3’ Protocol produced Illumina-ready sequencing libraries. A Single Cell 3’ Library comprised standard Illumina paired-end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI were encoded in Read 1, while Read 2 was used to sequence the cDNA fragment. Sample index sequences were incorporated as the i7 index read. Read 1 and Read 2 were standard Illumina® sequencing primer sites used in paired-end sequencing.10X Genomics Cell Ranger software (version 3.1.0) was used to convert raw BCL files to FASTQ files, alignment and counts quantification.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: Tranplanted heart

extract_protocol:
Cellular suspensions were loaded on a 10X Genomics GemCode Single-cell instrument that generates single-cell Gel Bead-In-EMlusion (GEMs). Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3’ Reagent Kits v3.1. Upon dissolution of the Gel Bead in a GEM, primers containing (i) an Illumina® R1 sequence (read 1 sequencing primer), (ii) a 16 nt 10x Barcode, (iii) a 10 nt Unique Molecular Identifier (UMI), and (iv) a poly-dT primer sequence were released and mixed with cell lysate and Master Mix. Barcoded, full-length cDNAs were then reverse-transcribed from poly-adenylated mRNA.Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full-length, barcoded cDNAs were then amplified by PCR to generate sufficient mass for library construction.
R1 (read 1 primer sequence) were added to the molecules during GEM incubation. P5, P7, a sample index, and R2 (read 2 primer sequence) were added during library construction via End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contained the P5 and P7 primers used in Illumina bridge amplification.

value: Tranplanted heart

value: Isogeneic


title: Week5_DABTRAM_scMulti_GEX_2022_04_04

description:
Library name: Sample18
10X Multiome


title: Control_10min

description:
Library name: SID14751
4sU-seq

value: culture medium


title: P. promelas larvae, EFP, biological replicate EFP_B23, lane 1, time step = 3, analyzed on 20161012

description: Library name: 20161012_ EFP_3_B23_TAGCTT_L001_R1_001


title: Heart, Day5,AR3

description:
Library name: Sample3
10X Genomics

value: Allogeneic


title: Heart, Day5,AR2

description:
Library name: Sample2
10X Genomics


title: Control

description:
Library name: SID14749
4sU-seq


title: Control_0min

description:
Library name: SID14750
4sU-seq


title: Day10_CIS_scMulti_GEX_2024_03_26

description:
Library name: Sample16
10X Multiome

value: Cisplatin 10 days post treatment


title: P. promelas larvae, EFP, biological replicate EFP_B16, lane 1, time step = 2, analyzed on 20161012

description: Library name: 20161012_ EFP_2_B16_ATCACG_L001_R1_001

value: EFP


title: Day10_CIS_scMulti_GEX_2022_04_28

description:
Library name: Sample15
10X Multiome

value: WM989 A6-G3 cells


title: Heart, Day5,AR1

description:
Library name: Sample1
10X Genomics


title: P. promelas larvae, DWIP, biological replicate DWIP_B17, lane 2, time step = NA, analyzed on 20161012

description: Library name: 20161012_ DWIP_B17_GTCCGC_L002_R1_001

value: whole larvae

value: DWIP


title: SAMPLE 90

city: Little Rock

first: Roopa

last: Siddaiah

state: AR

address: 1 Children's way

department: Pediatrics

institute: Arkansas Children's Hospital

description:
Library name: G778-17
Small RNA library prepared using QIAseq miRNA kit with UMI
combined miRNA data 20_SAMPLE88-90.xlsx
G778.17.miRNAcounts

data_processing:
The libraries were pooled and diluted to 3 nM using 10 mM Tris-HCl, pH 8.5 and denatured. The denatured libraries were then loaded onto an SP flow cell on an Illumina® NovaSeq 6000 instrument and run for 68 cycles according to the manufacturer’s instructions.
Assembly: Fitlered reads were aligned to the human reference genome (GRCh38 using HISAT2 (version 2.1.0) and the resulting ded-duplicated reads were summarized to each gene using HTSeq.
Supplementary files format and content: XLS

source_name: Tracheal Aspirate

extract_protocol:
Frozen tracheal aspirate (TA) samples were thawed on ice, and mixed by pipetting. For each sample, 300 uL of the aspirate was transferred to a 1.5 ml tube and 75 ul of ExoQuick Exosome Precipitation Solution (System biosciences, cat # EXOQ5A-1) was added. Sample and solution were mixed well by inverting, incubated upright and undisturbed at 4 C overnight. Sample mixture was then centrifuged at 1550 x g for 30 min at 4 C. After centrifugation, supernatant was discarded without disturbing the pellet. Pellet was then resuspended in 100 uL 1x PBS. All 100 uL of the sample was used for RNA extraction. RNA was extracted using Zymo Research Quick-RNA Micro Prep Kit following manufacturer's protocol. The typical size distribution for the small RNA ranged between 13.14 and 283.50 ng.
Small RNA libraries were prepared from 5–250 ng total RNA using the QIAseq miRNA Library Kit (QIAGEN) as per the manufacturer’s instructions.

value: Tracheal Aspirate

value: PH

tag: Sex

value: F


title: SAMPLE 89

description:
Library name: G778-16
Small RNA library prepared using QIAseq miRNA kit with UMI
combined miRNA data 20_SAMPLE88-90.xlsx
G778.16.miRNAcounts

value: M


title: Day10_CIS_scMulti_GEX_2022_04_04

description:
Library name: Sample14
10X Multiome


title: P. promelas larvae, DWIP, biological replicate DWIP_B17, lane 1, time step = NA, analyzed on 20161012

description: Library name: 20161012_ DWIP_B17_GTCCGC_L001_R1_001

value: 2 dpf


title: Day10_CIS_scMulti_GEX_2022_04_03

description:
Library name: Sample13
10X Multiome


title: P. promelas larvae, DSP, biological replicate DSP_B27, lane 2, time step = NA, analyzed on 20161012

description: Library name: 20161012_ DSP_B27_ACTTGA_L002_R1_001

value: DSP


title: SAMPLE 88

description:
Library name: G778-15
Small RNA library prepared using QIAseq miRNA kit with UMI
combined miRNA data 20_SAMPLE88-90.xlsx
G778.15.miRNAcounts


title: OE_Gm15663, rep2

city: Boston

first: Xiang-Yu

state: MA

address: 3 Blackfan St

institute: Harvard University

description:
Library name: Sample 12
OE_Gm15663, rep2, AML12_hepatocytes, (G20)

data_processing:
The quality of pair-end sequence .fastq files was assessed using FastQC (Version 0.11.3). The alignment of reads was evaluated using STAR (Version 2.7.0) and Qualimap (Version 2.2.1). Reads were subsequently mapped to mm10 cDNA references using Salmon. Systematic quality assessment was performed using MultiQC (Version 1.5). The relative expression levels of genes were defined using DEseq2.
Assembly: mm10
Supplementary files format and content: DESeq2-normalized counts were exported in .xlsx files

extract_protocol:
RNA was isolated using TRIzol or RNeasy Mini Kit (Qiagen).
Libraries were constructed according to the KAPA mRNA HyperPrep Kit protocol.

value: hepatocytes

value: WT


title: P. promelas larvae, DSP, biological replicate DSP_B27, lane 1, time step = NA, analyzed on 20161012

description: Library name: 20161012_ DSP_B27_ACTTGA_L001_R1_001


title: OE_Gm15663, rep1

description:
Library name: Sample 11
OE_Gm15663, rep1, AML12_hepatocytes, (G19)


title: LPS Female Biological Rep 3, Technical Replicate

city: New York

first: Gordana

last: Vunjak-Novakovic

state: NY

institute: Columbia University

description: Library name: GR044

data_processing:
RTA (Illumina) was used for base calling and bcl2fastq2 (version 2.19) was used for converting BCL to fastq format, coupled with adaptor trimming.
Pseudoalignment to a kallisto index created from transcriptomes (Ensembl v96, Human: GRCh38.12) was performed using kallisto (0.44.0).
Estimated counts and tpm values for each gene were computed from tximport R package.
Assembly: GRCh38.p12
Supplementary files format and content: tpm_values_transcripts_kallisto.txt: tab delimited file includes transcripts per million (tpm) values for each transcript for all samples
Supplementary files format and content: est_counts_transcripts_kallisto.txt: tab delimited file includes estimated counts for each transcript for all samples
Supplementary files format and content: tpm_values_genes_kallisto.txt: tab delimited file includes tpm values for each gene for all samples
Supplementary files format and content: est_counts_genes_kallisto.txt: tab delimited file includes estimated counts for each gene for all samples

growth_protocol: All iPSC lines were expanded and cultured in mTeSR Plus medium on tissue culture treated plates coated with 1:100 Matrigel in RPMI 1640. Cells were passaged every 3-4 days, and passaged upon reaching 70% confluency using 0.5 mM EDTA in PBS. iPSCs were replated on tissue culture plates coated with 1:175 Matrigel with low agitation to enable cell clusters to attach at approximately 8-16 clusters/cm2. Cells were first differentiated into hematopoietic stem and progenitors using a STEMdiff Hematopoietic Kit, according to the manufacturer’s instructions. At day 12, cells in suspension were removed and the adherent hemogenic endothelial cell fraction was cultured in X-VIVO 15 Serum-free Hematopoietic Cell Medium supplemented with 1:100 GlutaMAX, 1:100 2-mercaptoethanol, 100 ng/mL recombinant human macrophage colony stimulating factor (M-CSF), and 25 ng/mL recombinant human interleukin 3 (IL-3). Hemogenic endothelial cells were maintained for over 8 weeks with weekly media exchange, with cells in the suspension fraction discarded during week 1. Myeloid- and monocytic-specific lineage cells subsequently collected in the suspension fraction were replated onto 6-well ultra-low attachment plasticin X-VIVO 15 media containing 100 ng/mL M-CSF for at least 5 days to achieve macrophage differentiation. CD14+ macrophages were positively selected prior to use via CD14 microbeads, according to the manufacturer’s protocol.

extract_protocol:
Following treatment, iMacs were lysed in Buffer RLT and stored at –20°C. Samples were thawed on ice and total RNA was isolated using a Qiagen RNeasy Micro Kit, according to the manufacturer's instructions. The quality and quantity of total RNA was assessed using an Agilent 2100 Bioanalyzer with an RNA Pico Chip at Columbia's Molecular Pathology core. All samples had an RNA integrity number (RIN) ≥ 9.6 and were considered acceptable for further analysis. Total RNA samples were submitted to the JP Sulzberger Columbia Genome Center for sequencing.
A poly-A pulldown was used to enrich mRNAs from total RNA samples, then a library was constructed using TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer’s protocol.

treatment_protocol: Human iPSC-derived macrophages were cultured in X-VIVO 15 media supplemented with 100 ng/mL M-CSF in the absence (control) or presence of 100 ng/mL LPS for 48 h.

value: iPSC-derived macrophage

value: LPS


title: LPS Female Biological Rep 3

description: Library name: GR043


title: Day10_COCL2_scMulti_GEX_2024_03_26

description:
Library name: Sample12
10X Multiome

value: CoCl2 for 10 days


title: Day10_COCL2_scMulti_GEX_2022_04_28

description:
Library name: Sample11
10X Multiome


title: P. promelas larvae, TRUP, technical replicate TR_FIELD2-TR, lane 2, time step = NA, analyzed on 20161012

description: Library name: 20161012_ UP_FIELD_2-TR_AGTCAA_L002_R1_001

value: TR


title: OE_CTL, rep4

description:
Library name: Sample 10
OE_CTL, rep4, AML12_hepatocytes, (G17)


title: Day10_COCL2_scMulti_GEX_2022_04_04

description:
Library name: Sample10
10X Multiome


title: Control Female Biological Rep 3, Technical Replicate

description: Library name: GR040

value: Untreated


title: P. promelas larvae, TRUP, technical replicate TR_FIELD2-TR, lane 1, time step = NA, analyzed on 20161012

description: Library name: 20161012_ UP_FIELD_2-TR_AGTCAA_L001_R1_001


title: OE_CTL, rep3

description:
Library name: Sample 9
OE_CTL, rep3, AML12_hepatocytes, (G16)


title: Control Female Biological Rep 3

description: Library name: GR041


title: Day10_COCL2_scMulti_GEX_2022_04_03

description:
Library name: Sample9
10X Multiome


title: OE_CTL, rep2

description:
Library name: Sample 8
OE_CTL, rep2, AML12_hepatocytes, (G15)


title: P. promelas larvae, UP, biological replicate UP_B27, lane 2, time step = 4, analyzed on 20161012

description: Library name: 20161012_ UP_4_B27_GTGAAA_L002_R1_001

value: UP


title: Day10_DABTRAM_scMulti_GEX_2024_03_26

description:
Library name: Sample8
10X Multiome

value: WM989 A6-G3 cells

value: Dabrafenib and Trametinib for 10 days


title: P. promelas larvae, UP, biological replicate UP_B27, lane 1, time step = 4, analyzed on 20161012

description: Library name: 20161012_ UP_4_B27_GTGAAA_L001_R1_001

value: whole larvae


title: Day10_DABTRAM_scMulti_GEX_2022_04_28

description:
Library name: Sample7
10X Multiome


title: LPS Male Biological Rep 3

description: Library name: GR035


title: P. promelas larvae, UP, biological replicate UP_B28, lane 2, time step = 3, analyzed on 20161012

description: Library name: 20161012_ UP_3_B28_ATGTCA_L002_R1_001


title: P. promelas larvae, UP, biological replicate UP_B28, lane 1, time step = 3, analyzed on 20161012

description: Library name: 20161012_ UP_3_B28_ATGTCA_L001_R1_001


title: Control Male Biological Rep 3, Technical Replicate

description: Library name: GR034


title: siRNA_Tmtc2, rep2

description:
Library name: Sample 5
siRNA_Tmtc2, rep2, primary hepatocytes, (T10)

source_name: primary hepatocytes

value: primary hepatocytes


title: Day10_DABTRAM_scMulti_GEX_2022_04_03

description:
Library name: Sample5
10X Multiome


title: Control Male Biological Rep 3

description: Library name: GR033


title: P. promelas larvae, UP, biological replicate UP_B28, lane 2, time step = 2, analyzed on 20161012

description: Library name: 20161012_ UP_2_B28_ACAGTG_L002_R1_001


title: siRNA_Tmtc2, rep1

description:
Library name: Sample 4
siRNA_Tmtc2, rep1, primary hepatocytes, (T9)


title: Day0_scMulti_GEX_2024_03_26

description:
Library name: Sample4
10X Multiome

value: No Treatment


title: C0176

city: Chengdu

first: Heng

last: Xu

state: Sichuan

address: 17#, section 3, South Renmin Road

institute: Sichuan University

data_processing:
Processed and selected high-quality reads using FastQC (v0.11.8), excluding any reads with low base quality
Aligned to the GRCh37 human reference genome provided by GENCODE, employing STAR v2.74a
Gene and transcript expression levels were then quantified using RSEM v1.3.3
Assembly: hg19
Supplementary files format and content: comma-delimited csv file include raw counts for each sample

source_name: stomach

extract_protocol:
Total RNA was extracted from 108 paired tumor and normal tissue samples using the Qiagen AllPrep DNA/RNA Mini Kit (Cat. No. 80204, Qiagen, Germany) following the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: stomach

value: Male

value: Tumor

tag: diagnosis

value: Advanced Gastric Cancer (AGC)


title: C0173

value: Female


title: STIC_1__FOXJ1pos_Epithelium_sample91

city: Chicago

first: CRI

last: Bioinformatics

state: IL

address: 5801 S. Ellis Ave.

institute: University of Chicago

description: Library name: DSP-1001660009342-B-A06

data_processing:
Sequencing files were processed into DCC format using the GeoMx NGS Pipeline software v1.0. GeoMx counts were log2 transformed in preparation for statistic data analysis.
Assembly: GRCh38.p13
Supplementary files format and content: DCC files include raw read counts along with RTS_IDs for each ROI
Supplementary files format and content: PKC file includes probe metadata describing the targets and is needed to interpret RTS_IDs in the DCC files

source_name: Fallopian tube, dysplastic lesion or invasive cancer

extract_protocol:
Tissue processing began with sectioning FFPE samples to a 5 μm thickness following the Nanostring GeoMx user manual (MAN-10132-04). After deparaffinization and rehydration, protein target retrieval was performed using Tris-EDTA antigen retrieval buffer for 20 minutes in a pressure cooker. RNA targets were retrieved through proteinase K digestion for 15 minutes at 37 °C. Tissues were then post-fixed in 10% NBF and hybridized overnight at 37 °C with RNA probes (Human Whole Transcriptome Atlas, containing 18,000 protein-coding genes coupled to UV-cleavable oligonucleotide barcodes). Following hybridization, excess probes were removed by stringent washing at 37 °C and incubated in blocking buffer W (Nanostring LOT#:2-23020032). The tissue sections were subsequently stained with conjugated primary antibodies targeting pan-cytokeratin (mouse monoclonal antibody, Novus NBP2-33200AF488) and p53 (Dako primary and secondary antibodies), along with CAPS (primary and secondary antibodies) and SYTO13 nuclear stain (ThermoFisher Scientific, S7575) for one hour at room temperature. For transcriptomic data acquisition, slides were analyzed on the GeoMx Digital Spatial Profiler (DSP) at 20× magnification. Regions of interest (ROIs) were identified based on immunofluorescence images with a pathologist's (AB) supervision and matched to regions selected in DVP. Following ROI selection, RNA probes were photocleaved using UV illumination within each ROI, and oligonucleotide barcodes were collected into a 96-well plate, allowing precise separation of tissue compartments.
Sequencing libraries were prepared using Illumina TruSeq technology for adaptor ligation and amplification. The amplified libraries underwent two rounds of Ampure XP magnetic bead cleanup (1.2:1 beads ratio) (HighPrep PCR from MAGBIO, Cat#: AC-60500). Purified libraries were sequenced on an Illumina NovaSeq flowcell PE50 at a depth of 100× per μm².

value: Epithelium

tag: cohort


title: P. promelas larvae, UP, biological replicate UP_FIELD07, lane 2, time step = NA, analyzed on 20161109

description: Library name: 20161109_ UP_FIELD_07_AGTCAA_L002_R1_001

value: 2 dpf


title: STIC_1__STIC_Epithelium_sample89

description: Library name: DSP-1001660009342-B-A04

value: Fallopian tube, dysplastic lesion or invasive cancer

value: STIC


title: P. promelas larvae, UP, biological replicate UP_B28, lane 1, time step = 2, analyzed on 20161012

description: Library name: 20161012_ UP_2_B28_ACAGTG_L001_R1_001


title: siRNA_CTL, rep3

description:
Library name: Sample 3
siRNA_CTL, rep3, primary hepatocytes, (T4)

value: WT


title: Day0_scMulti_GEX_2022_04_28

description:
Library name: Sample3
10X Multiome


title: LPS Female Biological Rep 2

description: Library name: GR027

value: iPSC-derived macrophage

value: LPS


title: P. promelas larvae, UP, biological replicate UP_B28, lane 2, time step = 1, analyzed on 20161012

description: Library name: 20161012_ UP_1_B28_AGTTCC_L002_R1_001

value: UP


title: siRNA_CTL, rep2

description:
Library name: Sample 2
siRNA_CTL, rep2, primary hepatocytes, (T3)


title: Day0_scMulti_GEX_2022_04_04

description:
Library name: Sample2
10X Multiome

value: WM989 A6-G3 cells


title: Control Female Biological Rep 2, Technical Replicate

description: Library name: GR026

value: Untreated


title: P. promelas larvae, EFP, biological replicate EFP_B16, lane 2, time step = 2, analyzed on 20161012

description: Library name: 20161012_ EFP_2_B16_ATCACG_L002_R1_001

value: whole larvae

value: EFP


title: Day0_scMulti_GEX_2022_04_03

description:
Library name: Sample1
10X Multiome

value: No Treatment


title: P. promelas larvae, UP, biological replicate UP_B28, lane 1, time step = 1, analyzed on 20161012

description: Library name: 20161012_ UP_1_B28_AGTTCC_L001_R1_001


title: siRNA_CTL, rep1

description:
Library name: Sample 1
siRNA_CTL, rep1, primary hepatocytes, (T1)

value: primary hepatocytes


title: Control Female Biological Rep 2

description: Library name: GR025


title: Week5_DABTRAM_scMulti_GEX_2022_04_03

description:
Library name: Sample17
10X Multiome

value: Dabrafenib and Trametinib for 5 weeks


title: P. promelas larvae, EMZ, biological replicate EMZ_B22, lane 2, time step = NA, analyzed on 20161012

description: Library name: 20161012_ EMZ_B22_GCCAAT_L002_R1_001

value: EMZ


title: HFD/KL-2_therapeutic_n5

description:
Library name: 284 L
bulk-seq

data_processing:
After demultiplexing with the bcl2fastq software (Illumina, version 2.20), the fastq files underwent trimming and adapter removal using Trim Galore. On average, 18.2 million reads (therapeutic mouse model liver bulk RNA-seq) and 27.9 million reads (preventive mouse model liver bulk RNA-seq) per sample passed quality control and were retained for downstream analysis. Read mapping was performed against the respective reference genome (mouse mm39) using Hisat2. Gene expression quantification was achieved by read counting using FeatureCounts (R package). The resulting counts were then converted to transcripts per million (TPM) for normalization in R. Differential expression analysis was performed using the R package edgeR. Differences in mean expression between conditions were assessed using a negative binomial exact test.
Assembly: Reference transcriptome consisting of: mouse mm39
Supplementary files format and content: Tab-separated values files

source_name: liver

growth_protocol: C57BL/6NTac (Charles River) male mice were maintained in a room under pathogen-free conditions with controlled 21 ± 1°C on a 12:12 h light/dark cycle (6 a.m./6 p.m.). Two different treatment models were analyzed: preventive and therapeutical treatment with KL-2. In both models, mice were randomly divided into two groups: hypercholesterolemia-induced atherosclerosis and control group. At 8 weeks, the first group received a vector containing a Pcsk9-D377Y gain-of-function variant with liver-specific promoter packed in an AAV8 virus was injected in the tail vein of mice, which were subsequently fed ad libitum with a modified, cholesterol (Chol)-enriched semisynthetic Clinton/Cybulsky diet (Sniff, Soest, Germany) starting at the age of 9 weeks.

extract_protocol:
RNA from mouse liver tissue was homogenized with BD Microlances (22G and 18G, 304100, BD). RNA from homogenized mouse tissue was extracted using the miRNeasy mini Kit.
Quality control and quantification of the isolated RNA were performed using Fragment Analyzer 5200 (Agilent) using the High Sensitivity RNA quantification kit and Fragment Analyzer Controller Software (Agilent v3.1.0.12). Random primed library preparation was started with 150 ng of total RNA using the Watchmaker RNA library prep kit with Polaris depletion (Watchmaker Genomics) according to the instructions of the manufacturer. The barcoded libraries were purified and quantified using Qubit Fluorometric Quantification (ThermoFisher Scientific). Size distribution of the library DNA was analyzed using the Fragment Analyzer 5200 (Agilent). Sequencing of 2x150 bp was performed with an Illumina NovaSeq 6000 sequencer (Illumina, San Diego, CA, USA).

treatment_protocol: Preventive treatment: PCSK9-AAV8 was injected into the tail vein of C57BL/6NTac mice, after 1-week mice were subjected to a high fat diet (HFD). After four weeks, the levels of cholesterol in the serum were analysed and the mice were randomly and blindly selected for injection with either KL-2 (10 mg/kg BW) or the corresponding volume of DMSO, at fortnightly intervals until the end of the 20-week experiment. Therapeutic treatment: PCSK9-AAV8 was injected into the tail vein of C57BL/6NTac mice, after 1-week mice were subjected to a high fat diet (HFD). After four weeks, the levels of cholesterol in the serum were analysed and the mice were randomly and blindly selected for injection with either KL-2 (10 mg/kg BW) or the corresponding volume of DMSO, at weekly intervals until the end of the 24-week experiment.

value: liver


title: control and IR treatment-3

first: LAN

last: FANG

address: 1239 Siping Road

institute: Tongji University

description: Library name: NC_IR3

data_processing:
Data were aligned to mouse reference genome mm10 using Bowtie2. HTSeq was used to map aligned reads to genes and to generate a gene count matrix. Normalized counts and differential expression analysis was performed using the DESeq2 R package.
Assembly: GRCm39
Supplementary files format and content: tab-delimilated file

source_name: cell line

extract_protocol:
Rnf19a deficient or control B16F10 cells were stimulated with IR treatment for 24 h. RNA was extracted from cell pellets using the Qiagen RNeasy Mini kit according to the manufacturer’s instructions.
First-strand Illumina-barcoded libraries were generated using the NEB RNA Ultra Directional kit according to the manufacturer’s instructions, using ribosomal RNA depletion and including a 12-cycle PCR enrichment. Libraries were sequenced on an Illumina NextSeq 500 instrument using paired-end 37-bp reads.

value: cell line

value: tumor cells


title: LPS Male Biological Rep 2, Technical Replicate

description: Library name: GR020


title: HFD/KL-2_therapeutic_n4

description:
Library name: 281 L
bulk-seq


title: P. promelas larvae, EMZ, biological replicate EMZ_B22, lane 1, time step = NA, analyzed on 20161012

description: Library name: 20161012_ EMZ_B22_GCCAAT_L001_R1_001

data_processing:
Raw read quality assessment with FastQC 0.11.9 & MultiQC 1.12
Reads were processed with fastp 0.23.2 trimming with quality, length, and adapter trimming all enabled by default, and polyX trimming (flag: -x) enabled manually
Alignment with STAR 2.7.10a (--outSAMattributes NH HI AS NM MD --outSAMtype BAM SortedByCoordinate --outSAMheaderHD @HD VN 1.4 SO:sorted --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --outSAMunmapped Within --outFilterType BySJout)
Quantification with STAR 2.7.10a (--quantMode GeneCounts TranscriptomeSAM)
Assembly: P. promelas, GCF_016745375.1_EPA_FHM_2.0
Supplementary files format and content: Tab delimited text file with gene counts: all_counts_20220629.txt uploaded separately.

extract_protocol:
Total RNA was isolated from individual FHM using the MagMAX-96 Total RNA Isolation Kit (ThermoFisher Scientific) following manufacturer's protocols. RNA was quantified by spectrophotometric analysis with a Synergy HTX multi-mode plate reader (BioTek).
Neoprep Library Prep System (Illumina) and the TruSeq Stranded mRNA Library Prep for NeoPrep (Illumina). Library concentrations were determined using either the KAPA Library Quantification Kit (Kapa Biosystems) or Qubit dsDNA HS Assay (ThermoFisher Scientific), normalized to equimolar amounts, and then combined into pools of eight samples each. Sequencing was performed at Michigan State University’s RTSF Genomics Core on the Illumina HiSeq 2500 Rapid Run flow cell (v2) for 1x50 bp single-end reads with Rapid SBS reagents.

value: 2 dpf


title: LPS Male Biological Rep 2

description: Library name: GR019


title: control and IR treatment-2

description: Library name: NC_IR2


title: OE_Gm15663, rep4

description:
Library name: Sample 14
OE_Gm15663, rep4, AML12_hepatocytes, (G22)

value: hepatocytes


title: OE_Gm15663, rep3

description:
Library name: Sample 13
OE_Gm15663, rep3, AML12_hepatocytes, (G21)

value: WT


title: LPS Female Biological Rep 2, Technical Replicate

description: Library name: GR028

value: iPSC-derived macrophage


title: P. promelas larvae, EFP, biological replicate EFP_B23, lane 2, time step = 1, analyzed on 20161012

description: Library name: 20161012_ EFP_1_B23_GTTTCG_L002_R1_001


title: HFD/KL-2_therapeutic_n3

description:
Library name: 279 L
bulk-seq


title: Control Male Biological Rep 2, Technical Replicate

description: Library name: GR018


title: HFD/KL-2_therapeutic_n2

description:
Library name: 277 L
bulk-seq


title: control and IR treatment-1

description: Library name: NC_IR1


title: P. promelas larvae, EFP, biological replicate EFP_B23, lane 1, time step = 1, analyzed on 20161012

description: Library name: 20161012_ EFP_1_B23_GTTTCG_L001_R1_001


title: control-3

description: Library name: NC_ctr3


title: Control Male Biological Rep 2

description: Library name: GR017


title: P. promelas larvae, MHW, biological replicate MHW_B23, lane 2, time step = NA, analyzed on 20161012

description: Library name: 20161012_ 15-07_B23_CTTGTA_L002_R1_001

value: MHW


title: control-2

description: Library name: NC_ctr2


title: HFD/KL-2_therapeutic_n1

description:
Library name: 268 L
bulk-seq


title: LPS Female Biological Rep 1, Technical Replicate

description: Library name: GR012

value: LPS


title: P. promelas larvae, MHW, biological replicate MHW_B23, lane 1, time step = NA, analyzed on 20161012

description: Library name: 20161012_ 15-07_B23_CTTGTA_L001_R1_001


title: HFD/DMSO_therapeutic_n4

description:
Library name: 291 L
bulk-seq


title: LPS Female Biological Rep 1

description: Library name: GR011


title: control-1

description: Library name: NC_ctr1


title: P. promelas larvae, EMZ, biological replicate EMZ_B11, lane 2, time step = NA, analyzed on 20161011

description: Library name: 20161011_ EMZ_B11_ACTGAT_L002_R1_001


title: HFD/DMSO_therapeutic_n3

description:
Library name: 290 L
bulk-seq


title: P. promelas larvae, EMZ, biological replicate EMZ_B11, lane 1, time step = NA, analyzed on 20161011

description: Library name: 20161011_ EMZ_B11_ACTGAT_L001_R1_001


title: sgRnf19a and IR treatment-2

description: Library name: A2_IR2


title: sgRnf19a and IR treatment-3

description: Library name: A2_IR3


title: HFD/DMSO_therapeutic_n2

description:
Library name: 289 L
bulk-seq


title: Control Female Biological Rep 1

description: Library name: GR009


title: P. promelas larvae, EFP, biological replicate EFP_FIELD38, lane 2, time step = NA, analyzed on 20161011

description: Library name: 20161011_ EFP_FIELD_38_GGCTAC_L002_R1_001


title: HFD/DMSO_therapeutic_n1

description:
Library name: 288 L
bulk-seq


title: LPS Male Biological Rep 1, Technical Replicate

description: Library name: GR004


title: sgRnf19a and IR treatment-1

description: Library name: A2_IR1


title: P. promelas larvae, EFP, biological replicate EFP_FIELD38, lane 1, time step = NA, analyzed on 20161011

description: Library name: 20161011_ EFP_FIELD_38_GGCTAC_L001_R1_001


title: sgRnf19a-3

description: Library name: A2_Ctr3


title: LPS Male Biological Rep 1

description: Library name: GR003


title: NormalChow_therapeutic_n4

description:
Library name: 138 L
bulk-seq


title: P. promelas larvae, EFP, biological replicate EFP_B13, lane 2, time step = 4, analyzed on 20161011

description: Library name: 20161011_ EFP_4_B13_ACTTGA_L002_R1_001


title: NormalChow_therapeutic_n3

description:
Library name: 294 L
bulk-seq


title: sgRnf19a-2

description: Library name: A2_Ctr2


title: P. promelas larvae, EFP, biological replicate EFP_B13, lane 1, time step = 4, analyzed on 20161011

description: Library name: 20161011_ EFP_4_B13_ACTTGA_L001_R1_001


title: Day10_DABTRAM_scMulti_GEX_2022_04_04

description:
Library name: Sample6
10X Multiome

value: WM989 A6-G3 cells

value: Dabrafenib and Trametinib for 10 days


title: Control Male Biological Rep 1, Technical Replicate

description: Library name: GR002

value: Untreated


title: siRNA_Tmtc2, rep3

description:
Library name: Sample 6
siRNA_Tmtc2, rep3, primary hepatocytes, (T11)


title: NormalChow_therapeutic_n2

description:
Library name: 293 L
bulk-seq


title: P. promelas larvae, EFP, biological replicate EFP_B17, lane 2, time step = 3, analyzed on 20161011

description: Library name: 20161011_ EFP_3_B17_GTGGCC_L002_R1_001

value: whole larvae

value: EFP


title: NPCs_OKS_ctrl_R9

city: Quebec City

first: Samer

last: Hussein

state: Quebec

address: 9 rue Mcmahon

department: Departement of medecine

country: Canada

institute: CHU de Québec - Université Laval

data_processing:
Raw fast5 files from R9 sequencing were converted to the more recent pod5 format using the pod5-file-format software from nanoporetech's github. pod5 files from R9 and R10 libraries files were then basecalled using Guppy v.6.5.7 using the super accurate basecalling settings.
Samples were demultiplexed according to barcodes with the guppy_barcoder software.
The resulting FASTQ reads were aligned to the mm10 mouse reference genome with Minimap2 version 2.24-r1122. Reads with MAPQ<13 were filtered out.
Aligned reads were quality-controlled with the NanoPlot software.
Strand for spliced transcripts were detemined using Minimap2's ts tag ("transcript strand"). As this tag is empty for mono-exonic transcripts, these were oriented with the pychopper software from nanoporetech's github. Stranded BAM files are provided as raw files (..._sup.XS_tag.bam files)
Transcriptome assembly was performed using the Tama software, with the tama_collapse.py script.
Isoform classification was performed on the transcriptome assembly using the SQANTI3 software. SQANTI3 QC was used to classify isoforms. Artifactual isoforms were then filtered using SQANTI3 filter with the "Rules filter" using default rules. Filtered-out isoforms were then rescued using SQANTI3 rescue. A final filter was performed to remove isoforms without a detected polyA as well as isoforms derived from RT-switching events.
Read counts were performed using the Isoquant software, using the previously generated and filtered transcriptome assembly.
Assembly: mm10
Supplementary files format and content: GSE282319_Isoquant.gene_name_id.cpm.txt.gz: Normalized gene-level read counts (in Counts per million, CPM) obtained with the Isoquant software. Annotation file used for this analysis was the "Repro_filter_tst.gtf" file included as a processed data file.
Supplementary files format and content: GSE282319_Isoquant.transcript_name_id.tpm.txt.gz: Normalized transcript-level read counts (in Transcripts per million, TPM) obtained with the Isoquant software. Annotation file used for this analysis was the "Repro_filter_tst.gtf" file included as a processed data file.
Supplementary files format and content: GSE282319_Repro_filter_tst.gtf.gz: Filtered transcriptome annotation file generated with the Tama software from the long-read RNA sequencing data presented here and filtered with the SQANTI3 pipeline.
Supplementary files format and content: GSE282319_Repro_unfiltered_tst.gtf.gz: Transcriptome annotation file generated with the Tama software from the long-read RNA sequencing data presented here (before isoform QC and filtering).
Supplementary files format and content: GSE282319_Repro_unfiltered_tst_classification.txt.gz: SQANTI3 classification file for GSE282319_Repro_unfiltered_tst.gtf.gz transcriptome annotation.

growth_protocol: Stably transfected Oct4-GFP ESC-derived NPC cell lines were grown in NPC medium on Geltrex™-coated plates (hESC-qualified, growth factor-reduced, ThermoFisher Scientific, #A1413302). NPC medium consists of N2B27 medium with added supplements. N2B27 medium consists of a 1:1 mixture of DMEM/F-12 media mix (ThermoFisher Scientific #11330057) supplemented with 1X N-2 supplement (ThermoFisher Scientific #17502048) and 20μg/mL human recombinant Insulin (ThermoFisher Scientific #12585014), and Neurobasal™ media (ThermoFisher Scientific #21103049) supplemented with 1X B-27™ supplement (ThermoFisher Scientific #17504044), 1mM sodium pyruvate (ThermoFisher Scientific #11360070), 2mM L-glutamine (ThermoFisher Scientific #35050061), 1X MEM Non-Essential Amino Acid solution (ThermoFisher Scientific #11140050) and 10-4M 2-Mercaptoethanol (ThermoFisher Scientific #21985023). Supplements to add for NPC media : 20ng/mL human recombinant EGF, 20ng/mL human recombinant FGF-2 and 500ng/mL heparin sodium salt. Medium was refreshed every other day and NPCs were passaged every 2-3 days. For passaging, cells were washed with DPBS (ThermoFisher Scientific #14190250) and treated with StemPro™ Accutase™ Cell Dissociation Reagent (ThermoFisher Scientific #A1110501) for 5 minutes. Then, StemPro™ Accutase™ Cell Dissociation Reagent was neutralized using DMEM (high glucose, ThermoFisher Scientific #11965118) with 5% KSR (ThermoFisher Scientific #10828-028) and cells were passaged as single-cells (usually 1/6-1/8 ratio). All cell lines were maintained in a humidified incubator at 37°C under 5% CO2 and were negative for mycoplasma.

extract_protocol:
Cell lysates were homogenized with QIAshredder columns (Qiagen #79656) and total RNA was extracted using RNeasy Kit (Qiagen #74106) according to the manufacturer’s instructions. RNA was quantified using a NanoDropTM 2000 Spectrophotometer (ThermoFisher #ND-2000C) and then DNase-treated using TURBOTM DNase (ThermoFisher Scientific #AM2238) according to the manufacturer’s instructions. 300ng of DNase-treated and non-treated RNA were loaded onto a 1% Agarose A (Bio Basic #D0012) gel to verify the RNA integrity and purity. RNA was also quantified using the Qubit™ RNA Broad Range Kit (ThermoFisher Scientific #Q10210) on Qubit™ 4 Fluorometer (ThermoFisher Scientific #Q33238) according to the manufacturer’s instructions. RNA quality was further verified using an RNA 6000 Nano Kit (Agilent Technologies #5067-1511) on a 2100 Bioanalyzer instrument (Agilent Technologies #G2939B) according to the manufacturer’s instructions. Samples all had RNA integrity numbers of 7.8 or more. For samples sequenced on R9 Flow Cells, polyadenylated RNA was enriched from 7.5-20μg of total RNA using NEB®Next Poly(A) mRNA Magnetic Isolation Module (NEB #E7490) and a DynaMag™-2 Magnet (ThermoFisher Scientific #12-321-D). PolyA+-enriched RNA was quantified using the Qubit™ RNA High Sensitivity Kit (ThermoFisher Scientific #Q32852) on Qubit™ 4 Fluorometer according to the manufacturer’s instructions and RNA quality was verified using an RNA 6000 Pico Kit (Agilent Technologies #5067-1513) on a 2100 Bioanalyzer instrument according to the manufacturer’s instructions. For samples sequenced on R10 Flow Cells, total RNA was used for RT (Poly(A) enrichment step was omitted).
R9 samples were processed with Oxford Nanopore Technologies' (ONT) SQK-DCS109 kit according to the manufacturer's protocol: "Direct cDNA Native Barcoding (SQK-DCS109 with EXP-NBD104 and EXP-NBD114)" version DCB_9091_v109_revF_04Feb2019. 55-100ng of poly(A)+ RNA were used for each sample's RT reaction. Samples were barcoded with the ONT EXP-NBD104 native barcoding expansion. Barcoded samples were pooled, loaded on a MinION sequencer (ONT) using eight R9.4.1 Flow Cells (ONT #FLO-MIN106D), and sequenced using the MinKNOW (v19) software. Purification of DNA between each step was performed with KAPA Hyperpure Beads (Roche). Flow cells were washed and reloaded with the Flow Cell Wash Kit (ONT #EXP-WSH003) to increase sequencing depth obtained per flow cell. R10 samples were processed with ONT's SQK-NBD114.24 kit using 50ng of total RNA, with each sample assigned to a specific barcode. Briefly, an oligo-dT primer (VNP, sequence: 5'-5phos/ACTTGCCTGTCGCTCTATCTTCTTTTTTTTTTTTTTTTTTTTVN-3' , where V=A, C, or G, and N=A, C, G, or T) was used to reverse-transcribe poly(A) RNA into cDNA with the Maxima H Minus RT (ThermoFisher Scientific). A Strand Switching Primer (SSP 5'-TTTCTGTTGGTGCTGATATTGCTmGmGmG-3' , where mG = 2' O-Methyl RNA bases) was used for strand switching during the RT reaction. Libraries were PCR amplified for 14 cycles with LongAmp Taq polymerase (NEB #M0287). cDNA was quantified using the Qubit™ 1X dsDNA High Sensitivity Kit (ThermoFisher Scientific #Q33230) on Qubit™ 4 Fluorometer according to the manufacturer’s instructions and cDNA smear quality was verified using a DNA 12000 Kit (Agilent Technologies #5067-1508) on a 2100 Bioanalyzer instrument (Agilent Technologies #G2939B) according to the manufacturer’s instructions. The blunt DNA ends were prepared using the NEBNext Ultra II End Repair/dA-Tailing module (NEB), adding a 3' dA tail and phosphorylating the 5' end. Barcodes were ligated to the DNA fragments with a Blunt/TA ligase (NEB), barcoded samples were pooled and motor protein adapters were finally ligated with the NEBNext Quick Ligation Module (NEB). Purification of DNA between each step was performed with KAPA Hyperpure Beads (Roche). Library was loaded on a PromethION 2 Solo (ONT) sequencer using two R10.4.1 Flow Cells (ONT #FLO-PRO114M), and sequenced using the MinKNOW (v23.07.15) software.

treatment_protocol: Stably transfected Oct4-GFP ESC-derived NPC cell lines were seeded at 3 x 103 cells/cm2 on a 0.1% porcine gelatin (Sigma-Aldrich #G1890) coating in NPC medium supplemented with 2%  Fetal Bovine Serum (FBS) to promote adhesion. The following day, medium was replaced with FBS-LIF supplemented with 1µg/mL doxycycline hyclate (Sigma-Aldrich #D9891) to induce overexpression of the reprogramming factors. FBS-LIF medium consists of DMEM (high glucose, ThermoFisher Scientific #11965118) supplemented with 15% FBS, ThermoFisher Scientific #12483020), 1mM sodium pyruvate (ThermoFisher Scientific #11360070), 2mM L-glutamine (ThermoFisher Scientific #35050061), 1X MEM Non-Essential Amino Acid solution (ThermoFisher Scientific #11140050) and 10-4M 2-mercaptoethanol (ThermoFisher Scientific #21985023). Medium was refreshed every other day until D6. From D6, samples noted as "2i-LIF at D6" (D14 and D20) were maintained in 2i-LIF medium and passaged every 2-4 days depending on colonies density. 2i-LIF medium consists of Leukemia Inhibitory Factor (LIF, home-made from pGEX-2T-MLIF, Mereau et al., J. Cell. Biol. 1993) at 20ng/mL, 3μM CHIR-99021 (Selleck Chemicals #S2924) and 1μM PD0325901 (Selleck Chemicals #S1036) in N2B27 media. D10, D14 and D20 samples noted as "FBS-LIF + dox" were instead maintained in FBS-LIF medium supplemented with 1µg/mL doxycycline hyclate. For passaging or collection of time points, cells were washed with DPBS (ThermoFisher Scientific #14190250) and treated with TrypLE Express Enzyme (ThermoFisher Scientific #12604021) for 5 minutes. Then, TrypLE Express Enzyme was neutralized using DMEM (high glucose, ThermoFisher Scientific #11965118) with 5% KSR (ThermoFisher Scientific #10828-028) and cells were passaged as single-cells (1/3-1/30 ratio depending on density). Long-read RNAseq time points were pelletted and flash frozen in liquid nitrogen, then kept in a -80°C Bio-freezer until RNA extraction. Evolution of the proportion of mCherry+ and GFP+ cells was monitored using fluorescence microscopy and flow cytometry with a BD Accuri™ C6 Plus flow cytometer (BD Biosciences). iPSCs could readily be maintained in 2i-LIF medium after 20 days. All cell lines were negative for mycoplasma. Mouse ESC control lines are maintained in 2i-LIF medium. NPC control lines were maintained in NPC medium.

value: Neural progenitor cells

value: OKS-Luciferase-AS

value: NPC medium


title: NormalChow_therapeutic_n1

description:
Library name: 292 L
bulk-seq

value: liver


title: sgRnf19a-1

description: Library name: A2_Ctr1

value: cell line


title: SAMPLE 87

description:
Library name: G778-27
Small RNA library prepared using QIAseq miRNA kit with UMI

extract_protocol:
Frozen tracheal aspirate (TA) samples were thawed on ice, and mixed by pipetting. For each sample, 300 uL of the aspirate was transferred to a 1.5 ml tube and 75 ul of ExoQuick Exosome Precipitation Solution (System biosciences, cat # EXOQ5A-1) was added. Sample and solution were mixed well by inverting, incubated upright and undisturbed at 4 C overnight. Sample mixture was then centrifuged at 1550 x g for 30 min at 4 C. After centrifugation, supernatant was discarded without disturbing the pellet. Pellet was then resuspended in 100 uL 1x PBS. All 100 uL of the sample was used for RNA extraction. RNA was extracted using Zymo Research Quick-RNA Micro Prep Kit following manufacturer's protocol. The typical size distribution for the small RNA ranged between 13.14 and 283.50 ng. Frozen saliva (SA) samples were thawed on ice. RNA was extracted using Quick-RNA Microprep purification kits (Zymo Research). RNA Pico BioAnalyzer (Agilent technologies) was used to determine the RNA quality and quantity. The typical size distribution for the small RNA and quantities for saliva ranged between 33.90 and 922.50 ng
Small RNA libraries were prepared from 5–250 ng total RNA using the QIAseq miRNA Library Kit (QIAGEN) as per the manufacturer’s instructions.

value: Tracheal Aspirate

value: PH

value: M


title: HFD/KL-2_preventive_n3

description:
Library name: KK_29
bulk-seq


title: SAMPLE 86

description:
Library name: G778-25
Small RNA library prepared using QIAseq miRNA kit with UMI

value: BPD

value: F


title: NPCs_OKMS_ctrl_R9

value: OKMS-Luciferase-AS


title: P. promelas larvae, EFP, biological replicate EFP_B08, lane 2, time step = 2, analyzed on 20161011

description: Library name: 20161011_ EFP_2_B08_TAGCTT_L002_R1_001

value: 2 dpf


title: NPCs_ctrl_2_R9

value: WT


title: SAMPLE 85

description:
Library name: G778-24
Small RNA library prepared using QIAseq miRNA kit with UMI


title: P. promelas larvae, EFP, biological replicate EFP_B08, lane 1, time step = 2, analyzed on 20161011

description: Library name: 20161011_ EFP_2_B08_TAGCTT_L001_R1_001


title: HFD/KL-2_preventive_n1

description:
Library name: KK_23
bulk-seq


title: NPCs_crtl_1_R9


title: SAMPLE 84

description:
Library name: G778-22
Small RNA library prepared using QIAseq miRNA kit with UMI


title: NormalChow_preventive_n4

description:
Library name: KK_12
bulk-seq


title: mESCs_R1_R9

value: Embryonic stem cells


title: SAMPLE 83

description:
Library name: G778-21
Small RNA library prepared using QIAseq miRNA kit with UMI


title: P. promelas larvae, EFP, biological replicate EFP_B18, lane 1, time step = 1, analyzed on 20161011

description: Library name: 20161011_ EFP_1_B18_ATCACG_L001_R1_001


title: NormalChow_preventive_n3

description:
Library name: KK_11
bulk-seq


title: mESCs_O4G_R9


title: SAMPLE 82

description:
Library name: G778-19
Small RNA library prepared using QIAseq miRNA kit with UMI


title: P. promelas larvae, DWIP, biological replicate DWIP_B11, lane 2, time step = NA, analyzed on 20161011

description: Library name: 20161011_ DWIP_B11_GAGTGG_L002_R1_001

value: DWIP


title: NormalChow_preventive_n2

description:
Library name: KK_10
bulk-seq


title: d6_OKS_ctrl_R9

value: Reprogramming timeline to induced pluripotent stem cells

value: FBS-LIF + dox


title: SAMPLE 81

description:
Library name: G778-28
Small RNA library prepared using QIAseq miRNA kit with UMI


title: NormalChow_preventive_n1

description:
Library name: KK_09
bulk-seq


title: SAMPLE 80

description:
Library name: G778-26
Small RNA library prepared using QIAseq miRNA kit with UMI


title: d6_OKMS_ctrl_R9


title: HFD/DMSO_preventive_n4

description:
Library name: KK_04
bulk-seq


title: P. promelas larvae, MHW, biological replicate MHW_B27, lane 2, time step = NA, analyzed on 20161011

description: Library name: 20161011_ 15-08_B27_GTCCGC_L002_R1_001

value: whole larvae

value: MHW


title: d4_OKS_ctrl_R9

value: OKS-Luciferase-AS


title: HFD/DMSO_preventive_n3

description:
Library name: KK_03
bulk-seq

value: liver


title: d4_OKMS_ctrl_R9


title: P. promelas larvae, MHW, biological replicate MHW_B27, lane 1, time step = NA, analyzed on 20161011

description: Library name: 20161011_ 15-08_B27_GTCCGC_L001_R1_001


title: SAMPLE 78

description:
Library name: G778-20
Small RNA library prepared using QIAseq miRNA kit with UMI


title: HFD/DMSO_preventive_n2

description:
Library name: KK_02
bulk-seq


title: P. promelas larvae, UP, biological replicate UP_FIELD35, lane 2, time step = NA, analyzed on 20161011

description: Library name: 20161011_ UP_FIELD_35_CTTGTA_L002_R1_001

value: UP


title: d2_OKS_ctrl_R9


title: SAMPLE 77

description:
Library name: G923-46
Small RNA library prepared using QIAseq miRNA kit with UMI

value: Tracheal Aspirate


title: P. promelas larvae, UP, biological replicate UP_FIELD35, lane 1, time step = NA, analyzed on 20161011

description: Library name: 20161011_ UP_FIELD_35_CTTGTA_L001_R1_001


title: SAMPLE 76

description:
Library name: G923-43
Small RNA library prepared using QIAseq miRNA kit with UMI


title: d2_OKMS_ctrl_R9


title: P. promelas larvae, UP, biological replicate UP_FIELD22, lane 2, time step = NA, analyzed on 20161011

description: Library name: 20161011_ UP_FIELD_22_GCCAAT_L002_R1_001


title: d2_FBSL_ctrl_2_R9

value: Control non-reprogramming cells


title: SAMPLE 75

description:
Library name: G923-42
Small RNA library prepared using QIAseq miRNA kit with UMI

value: M


title: HSBD_rep4

city: Beijing

first: jun

last: Huang

address: No.16, Nanxiao Street, Dongzhimen, Dongcheng District, Beijing, China.

institute: Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing

description: Library name: HBG4

data_processing:
Step 1: Quality Control and Preprocessing Raw sequencing reads in FASTQ format were first processed through FastQC (v0.11.9) to assess read quality. Low-quality reads, adapter sequences, and poly-N sequences were trimmed using Trimmomatic (v0.39) (or Cutadapt/fastp) to obtain clean reads.  Step 2: Read Alignment The cleaned reads were mapped to the mouse reference genome (Mus musculus, e.g., GRCm39/mm10) using STAR (v2.7.9a) (or HISAT2) with default parameters. The alignment files (BAM format) were generated for downstream quantification.  Step 3: Quantification of Gene Expression The number of reads mapped to each gene was counted using featureCounts (v2.0.1) (or HTSeq-count) based on the corresponding GTF annotation file.  Step 4: Normalization and Differential Expression Analysis Differential expression analysis between groups (Control, Model, and HBG doses L/M/G) was performed using the DESeq2 (v1.34.0) R package. Read counts were normalized using the median-of-ratios method. Genes with an adjusted p-value < 0.05 and |log2FoldChange| > 1 were identified as differentially expressed genes (DEGs).  Step 5: Functional Enrichment Analysis Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted using the clusterProfiler R package to explore the biological functions and signaling pathways (e.g., TGF-β/Smad, PI3K-Akt) associated with the therapeutic effects of HBG.
Assembly: mm10
Supplementary files format and content: The processed data file (e.g., all_counts_matrix.txt) is a tab-delimited text file containing raw read counts and FPKM/TPM values for each sample. Each row represents a gene and each column represents a sample.
Supplementary files format and content: The processed data file (expression_matrix.xls) contains normalized expression values for all samples. Rows represent Ensembl gene IDs and columns represent biological replicates.

source_name: Lung tissue

growth_protocol: Male C57BL/6 mice (6-8 weeks old) were housed under standard pathogen-free conditions with a 12h light/dark cycle and free access to food and water. Pulmonary fibrosis was induced by a single intratracheal instillation of bleomycin

extract_protocol:
Total RNA was extracted from fresh lung tissues using TRIzol reagent (Invitrogen) following the manufacturer’s instructions. RNA integrity and concentration were assessed using the Agilent 2100 Bioanalyzer.
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Libraries were constructed using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit. Sequencing was performed on the Illumina NovaSeq 6000 platform with 150 bp paired-end reads.

treatment_protocol: Starting from day 7 post-modeling, mice in the HBG groups were orally administered HBG daily at doses of L, M, or G (specify doses, e.g., 7g/kg for G) for 14 consecutive days. The control and model groups received an equal volume of distilled water.

value: Lung tissue


title: P. promelas larvae, UP, biological replicate UP_FIELD22, lane 1, time step = NA, analyzed on 20161011

first: Steven

institute: US EPA

description: Library name: 20161011_ UP_FIELD_22_GCCAAT_L001_R1_001


title: HSBD_rep3

description: Library name: HBG3


title: P. promelas larvae, UP, biological replicate UP_B13, lane 2, time step = 4, analyzed on 20161011

description: Library name: 20161011_ UP_4_B13_GTTTCG_L002_R1_001


title: SAMPLE 74

description:
Library name: G923-41
Small RNA library prepared using QIAseq miRNA kit with UMI

value: PH

value: F


title: HSBD_rep2

description: Library name: HBG2


title: d20_OKMS_ctrl_R9

value: OKMS-Luciferase-AS


title: SAMPLE 73

description:
Library name: G923-40
Small RNA library prepared using QIAseq miRNA kit with UMI

value: BPD


title: P. promelas larvae, UP, biological replicate UP_B13, lane 1, time step = 4, analyzed on 20161011

description: Library name: 20161011_ UP_4_B13_GTTTCG_L001_R1_001

value: 2 dpf


title: HSBD_rep1

description: Library name: HBG1


title: d20_2iL_OKS_ctrl_R9

value: Induced pluripotent stem cells

value: 2i-LIF at D6


title: P. promelas larvae, UP, biological replicate UP_B13, lane 2, time step = 3, analyzed on 20161011

description: Library name: 20161011_ UP_3_B13_GTGAAA_L002_R1_001


title: Model_rep4

description: Library name: Model4


title: SAMPLE 71

description:
Library name: G923-36
Small RNA library prepared using QIAseq miRNA kit with UMI


title: P. promelas larvae, UP, biological replicate UP_B13, lane 1, time step = 3, analyzed on 20161011

description: Library name: 20161011_ UP_3_B13_GTGAAA_L001_R1_001


title: d20_2iL_OKMS_ctrl_R9


title: Control Male Biological Rep 1

description: Library name: GR001

value: iPSC-derived macrophage

value: Untreated


title: Model_rep3

description: Library name: Model3


title: d14_OKS_ctrl_R9

value: Reprogramming timeline to induced pluripotent stem cells

value: FBS-LIF + dox


title: SAMPLE 70

description:
Library name: G923-35
Small RNA library prepared using QIAseq miRNA kit with UMI


title: P. promelas larvae, EFP, biological replicate EFP_B17, lane 1, time step = 3, analyzed on 20161011

description: Library name: 20161011_ EFP_3_B17_GTGGCC_L001_R1_001

value: whole larvae

value: EFP


title: Model_rep2

description: Library name: Model2


title: d14_OKMS_ctrl_R9


title: SAMPLE 69

description:
Library name: G984-12
Small RNA library prepared using QIAseq miRNA kit with UMI

value: Tracheal Aspirate


title: P. promelas larvae, UP, biological replicate UP_B22, lane 1, time step = 2, analyzed on 20161011

description: Library name: 20161011_ UP_2_B22_ATGTCA_L001_R1_001

value: UP


title: Model_rep1

description: Library name: Model1


title: P. promelas larvae, UP, biological replicate UP_B18, lane 2, time step = 1, analyzed on 20161011

description: Library name: 20161011_ UP_1_B18_ACAGTG_L002_R1_001


title: SAMPLE 68

description:
Library name: G984-11
Small RNA library prepared using QIAseq miRNA kit with UMI


title: d14_2iL_OKMS_ctrl_R9


title: Control_rep4

description: Library name: Control4


title: d10_OKS_ctrl_R9

value: OKS-Luciferase-AS


title: SAMPLE 67

description:
Library name: G984-10
Small RNA library prepared using QIAseq miRNA kit with UMI

value: M


title: P. promelas larvae, UP, biological replicate UP_B18, lane 1, time step = 1, analyzed on 20161011

description: Library name: 20161011_ UP_1_B18_ACAGTG_L001_R1_001


title: d10_OKMS_ctrl_R9


title: SAMPLE 66

description:
Library name: G984-8
Small RNA library prepared using QIAseq miRNA kit with UMI


title: P. promelas larvae, EFP, biological replicate EFP_FIELD37, lane 2, time step = NA, analyzed on 20161011

description: Library name: 20161011_ EFP_FIELD_37_AGTCAA_L002_R1_001


title: SAMPLE 65

description:
Library name: G984-7
Small RNA library prepared using QIAseq miRNA kit with UMI

value: PH