title: Control, NestinCre-Ai14, Cut&tag, H3K9ac

description: Library name: Control-H3K9ac


title: P. promelas larvae, UP, biological replicate UP_FIELD02, lane 2, time step = NA, analyzed on 20161005

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: 20161005_ UP_FIELD_02_GTTTCG_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: NCKO, NestinCre-Ai14-MEN1-KO, Cut&tag, H3K27me3

city: Xiamen

first: shuzhong

last: wang

state: Fujian

address: Xiangan South Road

department: School of Medicine

country: China

institute: Xiamen University

description: Library name: NCKO-H3K27me3

library_source: genomic

data_processing:
Neurons were performed using Bcl2Fastq for Novaseq output
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Mus musculus

source_name: cortex

extract_protocol:
The dorsal pallium was isolated from embryonic brains by micro-dissecting, and the tissue was transferred into ice-cold HBSS (no Ca2+, Mg2+) (Gibco) supplemented with B27 (Gibco) on a 24-well plate. After identification of Nestin-Cre; Ai14 (Control) and Nestin-Cre; Men1flox/flox; Ai14 (NCKO) genotypes, the cortices were digested in the solution containing 2 mg/mL Papain (Sigma) and 200 units/mL DNase (Sigma), followed by incubation for 20 minutes at 37°C. Subsequently, gently manual trituration of the tissue in the plate. The cell suspension was dropped across a 70 μm filter and then washed twice. The cells were incubated with 2-(4-Amidinophenyl)-6-indolecarbamidine dihydrochloride (DAPI) before sorting, Flash-tag+ Ai14+ cells were isolated using Beckman MoFlo Astrios EQS. Singlet cells were first sorted by forward and Side scattering properties (FSC and SSC), then the thresholds for FITC and PE sorting gates were set labeling cells. The negativity for DAPI to collect approximately 5×104 living cells in every biological replicate. The solution collected sorted cells kept at room temperature without Ca2+ and Mg2+
Cut&tag-seq was performed as previously described, using Hyperactive Universal CUT&Tag Assay Kit for Illumina. The positive cell enrichment was performed essentially using the ATAC-seq protocol. The cells were bound to Concanavalin A beads in wash buffer added complete protease inhibitors (Roche), then the cells were incubated with primary antibody in antibody buffer at 4°C overnight, followed by incubation with secondary antibodies goat anti-rabbit IgG H&L or goat anti-mouse IgG H&L for 1h at room temperature. Subsequently, the cells were incubated with pA/G-Tn5 adapter complex in Dig-300 buffer for 1h at room temperature after washing with Dig-Wash buffer. The cells were washed with Dig-300 buffer for three times and performed tagmentation in Dig-300 Wash buffer with Mg2+ for 1h at 37°C, then stop tagmentation with 0.1% SDS and digested with Proteinase K for 10 min at 55°C. The tagmented DNA was purified by DNA Extract Beads and amplified by PCR connecting sequencing adapters. The libraries were purified, using VAHTS DNA Clean Beads (N411, Vazyme Biotech). After library quality, the sequencing was performed, using PE150 reads on Illumina NovaSeq3000 (Novogene, Beijing, China).

value: cortex

tag: cell line

value: neurons

tag: cell type

tag: genotype

value: Men1-NCKO (Ai14)


title: Library_01

city: Québec

first: Aldcejam

last: Martins da Fonseca Junior

state: QC

address: Services Pavilion, 2440 Bd Hochelaga Suite 1710

department: Animal Sciences

country: Canada

institute: Laval University

description: Library name: Library_01

data_processing:
Adapter trimming and quality filtering were performed using fastp (version 0.23.1) (Chen et al., 2018).  Reads with Phred scores < 30 were discarded, and only sequences ≥ 50 bp were retained. Read conversion, alignment to the Bos taurus reference genome (ARS-UCD1.2.104), and methylation calling were performed using Bismark (Krueger and Andrews, 2011). These steps were implemented within the DRAGEN Methylation Pipeline, which was executed on an Illumina DRAGEN server using default parameters. Lambda DNA spike-in was used to calculate conversion efficiency, and only samples with conversion rates >98% were included in downstream analyses
Adapter sequences and low-quality bases were trimmed using fastp (v0.23.1), applying default quality thresholds. Reads were aligned to the ARS-UCD1.2 (bosTau9) reference genome using Bismark (v0.23.0), with Bowtie2 as the underlying aligner.
Quality control metrics were compiled for each sample, including alignment rates, duplication levels, and conversion efficiency.
Only samples meeting stringent QC thresholds were retained for downstream analyses.
Methylation Extraction: PCR duplicates were removed, and single-nucleotide methylation extraction was strictly executed within the CpG context using Bismark's methylation extractor to generate the final context reports.
Assembly: Alignment to the Bos taurus reference genome (ARS-UCD1.2.104)
Supplementary files format and content: The submitted *.CX_report.txt processed files represent the base-resolution single-nucleotide methylation status generated by Bismark. These tab-delimited files contain the following structured columns for user interpretation:
Supplementary files format and content: 1. Chromosome (Bovine ARS-UCD1.2 scaffolds)
Supplementary files format and content: 2. Position (1-based genomic coordinate)
Supplementary files format and content: 3. Strand (+ or -)
Supplementary files format and content: 4. Count of methylated cytosines (coverage count supporting methylation)
Supplementary files format and content: 5. Count of unmethylated cytosines (coverage count supporting unmethylated status)
Supplementary files format and content: 6. Cytosine context (explicitly categorized into CG, CHG, or CHH contexts)
Supplementary files format and content: 7. Trinucleotide context
Library strategy: EM-seq

organism: Bos taurus

source_name: blood

extract_protocol:
Genomic DNA was extracted from whole-blood samples, and libraries were prepared with the NEBNext Enzymatic Methyl-seq Kit (New England Biolabs, Ipswich, MA) according to the manufacturer’s instructions. This protocol utilizes TET2 oxidation and APOBEC deamination to achieve base-resolution methylation calls while minimizing DNA degradation
Libraries were sequenced on the Illumina NovaSeq 6000 platform with 150 bp paired-end reads at the Génome Québec Innovation Centre (Montreal, QC, Canada). Each sample generated hundreds of millions of reads, providing deep coverage for CpG-resolution analysis.

treatment_protocol: forty-eight female Holstein calves were selected in the Canadian province of Quebec as part of a longitudinal health surveillance program. All animals were sampled at approximately 40 days of age, representing the preweaning window of susceptibility. Calves were stratified into three phenotypically defined groups based on clinical veterinary records: low body mass index (BMI), respiratory disease (RESP), and diarrhea (DIAR), using established indicators for morbidity and growth in dairy calves [30]. A fourth group of resilient calves, showing no signs of these conditions, was used as a control.

value: blood

value: Holstein

tag: treatment

value: Low BMI and Diarrhea vs Resilient Control Contrast


title: P. promelas larvae, UP, biological replicate UP_FIELD02, lane 1, time step = NA, analyzed on 20161005

description: Library name: 20161005_ UP_FIELD_02_GTTTCG_L001_R1_001


title: Control, NestinCre-Ai14, Cut&tag, H3K27me3

description: Library name: Control-H3K27me3

value: Men1-WT (Ai14)


title: HepG2_B2_minus_AhR_gRNA_Day12_RNA_rep3

city: Palo Alto

first: Yohei

last: Abe

state: California

address: 3181 Porter Dr

institute: Arc Institute

description: Library name: Sample 174

data_processing:
FASTQ files were processed to assess quality by determining general sequencing bias, clonality and adapter sequence contamination.
RNA sequencing reads were aligned to the hg38 human or mm10 mouse reference genome using STAR using default parameters.  Gene expression levels were calculated using HOMER by counting all strand specific reads within exons.  Only the most abundant transcripts, including multiple alternative variants, were selected for each gene, and the genes with a length smaller than 250 bp were removed.  Transcripts per million (TPM) were used to evaluate the correlation among replicates.
FASTQ files were mapped to the hg38 human or mm10 mouse reference genome with Bowtie2 using default parameters.
Assembly: hg38 or mm10
Supplementary files format and content: TPM expression matrices

organism: Homo sapiens

extract_protocol:
For RNA-seq, total RNA was isolated from culture cells and purified using a Direct-zol RNA MicroPrep Kit (Zymo Research) as described by the manufacturer.
RNA-seq library preparation was performed according to the manufacturer’s instructions of the QuantSeq 3’ mRNA-Seq V2 Library Prep Kit (Lexogen Inc). In detail, RNA-seq libraries were prepared from 500 ng of total RNA using a reverse transcription–based workflow incorporating Illumina-compatible adapter sequences. First-strand cDNA synthesis was performed using an oligo(dT) primer containing an Illumina-compatible sequence at its 5′ end. The primer was annealed to polyadenylated RNA, and reverse transcription was carried out according to the manufacturer’s instructions to generate first-strand cDNA. Following first-strand synthesis, the RNA template was enzymatically degraded to enable efficient second-strand synthesis. Reaction plates were briefly centrifuged prior to removal of the sealing film to ensure complete recovery of reaction volume. Second-strand synthesis was initiated using a random primer harboring an Illumina-compatible linker sequence at its 5′ end, resulting in double-stranded cDNA (dsDNA) libraries. Double-stranded cDNA libraries were purified using magnetic beads to remove residual enzymes, primers, nucleotides, and buffer components. Beads were equilibrated to room temperature for 30 min prior to use and thoroughly resuspended before addition to samples. Libraries were washed and eluted in an elution buffer according to the manufacturer’s protocol. Purified dsDNA libraries were PCR-amplified (14–16 cycles) to introduce full-length Illumina adapter sequences required for cluster generation, as well as unique dual indices for multiplexed sequencing. Amplified libraries were purified using magnetic beads to remove residual PCR components that may interfere with downstream applications. Final libraries were quantified using a QubitTM 1× dsDNA HS Assay Kit (Thermo Fisher Scientific) and subjected to quality control prior to sequencing.

treatment_protocol: Control vs. Vitamin B2 deficiency


title: 150L013-1

city: Beijing

first: Xiao

last: Yu

address: No. 17, Panjiayuan Nanli, Chaoyang District, Beijing

institute: Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College

description: Library name: 4#

data_processing:
Utilize magnetic beads with oligo-dT to isolate mRNA from total RNA, and fragment the captured mRNA. Then, utilize reverse transcriptase to synthesize the first and second strands of cDNA, perform end repair on the reverse transcription products, and add A bases at the 3' end.
Subsequently, connect the fragment with sequencing adapters. After purifying the connection product, remove the products with incomplete connections and empty adapter self-ligation products, and then perform PCR amplification using primers complementary to the adapter sequence.
Finally, purify with magnetic beads to obtain the sequencing library
Assembly: h19
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: Cells were cltured with RPMI-1640 supplemented with 10% FBS and 1% P/S in humidified atmosphere with 5%CO2 at 37℃

extract_protocol:
RNA was harvested using TRIzol Regant
The libiary were prepared using SAMRTER mRNA-seq library Prep Kit following manufacturer's protocols

value: WT


title: 150DMSO-3

description: Library name: 3#

value: DMSO


title: P. promelas larvae, EFP, biological replicate EFP_FIELD48, lane 2, time step = NA, analyzed on 20161005

description: Library name: 20161005_ EFP_FIELD_48_ACAGTG_L002_R1_001

value: EFP


title: NCKO, NestinCre-Ai14-MEN1-KO, Cut&tag, H3K4me3

description: Library name: NCKO-H3K4me3


title: HepG2_B2_minus_AhR_gRNA_Day12_RNA_rep2

description: Library name: Sample 173


title: 150DMSO-2

description: Library name: 2#


title: Control, NestinCre-Ai14, Cut&tag, H3K4me3

description: Library name: Control-H3K4me3


title: P. promelas larvae, EFP, biological replicate EFP_FIELD48, lane 1, time step = NA, analyzed on 20161005

description: Library name: 20161005_ EFP_FIELD_48_ACAGTG_L001_R1_001


title: 150DMSO-1

description: Library name: 1#


title: HepG2_Cont_AhR_gRNA_Day12_RNA_rep3

description: Library name: Sample 171

value: Control


title: NCKO, NestinCre-Ai14-MEN1-KO, Cut&tag, Menin

description: Library name: NCKO-Menin


title: SJMBSHH-13-5634 vehicle.8

city: Toronto

first: Alexandria

last: DeCarlo

state: Ontario

address: 686 Bay Street

department: Developmental and Stem Cell Biology

institute: Hospital for Sick Children

description: Library name: F8

data_processing:
HISAT2v2.0.5
featureCounts v1.5.0-p3 was used to count read numbers mapped to each gene
DESeq2 was used for expression analysis
Assembly: hg38
Supplementary files format and content: includes FPKM values for each sample

molecule: polyA RNA

source_name: brain

growth_protocol: All tumors were propograted in vivo in the hindbrain within the cerebellum

extract_protocol:
RNA was extracted by trizol
cDNA was synthesized using random hexamer primers after fragmentation, followed by second strand cDNA synthesis using either dTTP for non-directional library
or dUTP for directional library. Generated libraries were checked with Qubit and real-time PCR for quantification and the bioanalyzer for size distribution detection.

treatment_protocol:
IACS 010759 10mg/kg four times per week via oral gavage until endpoint
Vehicle is 0.5% methylcellulose 10ul/g body weight four times per week via oral gavage until endpoint

value: brain

value: SHH medulloblastoma

value: TP53 mut


title: Control, NestinCre-Ai14, Cut&tag, Menin

description: Library name: Control-Menin


title: P. promelas larvae, EFP, biological replicate EFP_B26, lane 1, time step = 4, analyzed on 20161005

description: Library name: 20161005_ EFP_4_B26_GCCAAT_L001_R1_001

value: whole larvae


title: P. promelas larvae, DWIP, biological replicate DWIP_B27, lane 2, time step = NA, analyzed on 20161005

description: Library name: 20161005_ DWIP_B27_GTGAAA_L002_R1_001

value: 2 dpf

value: DWIP


title: HepG2_Cont_AhR_gRNA_Day12_RNA_rep1

description: Library name: Sample 169


title: SJMBSHH-13-5634 vehicle.7

description: Library name: F7


title: SJMBSHH-13-5634 vehicle.6

description: Library name: F6


title: Control, NestinCre-Ai14, Cut&tag, IgG

description: Library name: Control-IgG

value: cortex


title: HepG2_B2_minus_Cont_gRNA_Day12_RNA_rep3

description: Library name: Sample 168


title: MEN1-NCKO

description:
Library name: MEN1-NCKO
10x Genomics

library_source: transcriptomic single cell

data_processing:
The sequence data were performed quality control (QC) by a cellranger to apply the cell filtration. The clean reads were aligned to the reference genome mm10 by using cellranger. The unfiltered feature-barcode matrix was corrected, and rank-plot visualization was generated. After gene expression quantification, the expression matrix was loaded into Seurat for further analysis. The identification of GEMs of multiple cells using DoubletFinder. Subsequently, the filtering criteria for data followed by Gene count per Single Cell (200 - 5300), UMI count per single cell (<18,000), and proportion of mitochondrial gene expression (<10%). After removing low-quality cells, the data integration and batch effect correction using Harmony. The UMAP visualization of cell subtypes shows a pronounced clustering effect, and the clusterswere annotated by singleR tentatively. Different expression analysis (P<0.01,log2FC≥0.36) of subtypes visualized by volcano plot. Gene Ontology and KEGG Pathway analysis of target cluster. The pseudotime analysis simulated the developmental trajectory by Monocle2, Monocle3, and Slingshot.
Assembly: Mus musculus Ensembl_release110
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: Cortex

extract_protocol:
Timed male mice were sacrificed for this experiment. The neocortices were isolated from embryonic brains by micro-dissecting under a stereo microscope, then collected in DNase/RNase-Free tubes and immersed in liquid nitrogen quickly.
Nucleus isolation and RNA Integrity Number (RIN) detection after tissue dissociation. 10× Genomics Chromium Single Cell 30 v3 Reagents Kits and sequencing on Illumina NovaSeq 6000 were used in labeled nucleus.

value: Cortex

value: cortical cells


title: MEN1-FF

description:
Library name: MEN1-FF
10x Genomics


title: HepG2_B2_minus_Cont_gRNA_Day12_RNA_rep2

description: Library name: Sample 167


title: P. promelas larvae, DSP, biological replicate DSP_B26, lane 1, time step = NA, analyzed on 20161005

description: Library name: 20161005_ DSP_B26_CTTGTA_L001_R1_001

value: DSP


title: SJMBSHH-13-5634 vehicle.4

description: Library name: F4


title: NCKO-2, NestinCre-Ai14-MEN1-KO, ATAC

description: Library name: NCKO-2

data_processing:
Neurons were performed using Bcl2Fastq for Novaseq output
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
The dorsal pallium was isolated from embryonic brains by micro-dissecting, and the tissue was transferred into ice-cold HBSS (no Ca2+, Mg2+) (Gibco) supplemented with B27 (Gibco) on a 24-well plate. After identification of Nestin-Cre; Ai14 (Control) and Nestin-Cre; Men1flox/flox; Ai14 (NCKO) genotypes, the cortices were digested in the solution containing 2 mg/mL Papain (Sigma) and 200 units/mL DNase (Sigma), followed by incubation for 20 minutes at 37°C. Subsequently, gently manual trituration of the tissue in the plate. The cell suspension was dropped across a 70 μm filter and then washed twice. The cells were incubated with 2-(4-Amidinophenyl)-6-indolecarbamidine dihydrochloride (DAPI) before sorting, Flash-tag+ Ai14+ cells were isolated using Beckman MoFlo Astrios EQS. Singlet cells were first sorted by forward and Side scattering properties (FSC and SSC), then the thresholds for FITC and PE sorting gates were set labeling cells. The negativity for DAPI to collect approximately 5×104 living cells in every biological replicate. The solution collected sorted cells kept at room temperature without Ca2+ and Mg2+
ATAC-seq libraries were carried out as previously described using the Hyperactive ATAC-Seq Library Prep Kit for Illumina. Briefly, the positive cells were enriched by FACS and DAPI staining and collected in a cold buffer (PBS without Ca2+ and Mg2+) within the appropriate number. The cell permeabilization was performed in a mild permeabilizing agent (0.05% Digitonin) incubated at 4°C for 5 min. After that, the permeabilized cells were mixed with the transposase and incubated at 37°C for 30 min, then stop buffer was added. The reaction products were purified by DNA extraction beads to remove proteins and other impurities. The library construction follows the purified DNA fragments end-repairing, adding Poly-A tails, and connecting sequencing adapters. The constructed libraries were purified, and the sequencing was performed using PE150 reads on Illumina NovaSeq3000 (Novogene, Beijing, China).

value: neurons

value: Men1-NCKO (Ai14)


title: SJMBSHH-13-5634 vehicle.3

description: Library name: F3


title: P. promelas larvae, MHW, biological replicate MHW_B17, lane 2, time step = NA, analyzed on 20161005

description: Library name: 20161005_ 15-08_B17_AGTCAA_L002_R1_001

value: MHW


title: NCKO-1, NestinCre-Ai14-MEN1-KO, ATAC

description: Library name: NCKO-1


title: HepG2_Cont_Cont_gRNA_Day12_RNA_rep3

description: Library name: Sample 165


title: SJMBSHH-13-5634 vehicle.2

description: Library name: F2


title: Control-2, NestinCre-Ai14, ATAC

description: Library name: Control-2

value: Men1-WT (Ai14)


title: P. promelas larvae, MHW, biological replicate MHW_B17, lane 1, time step = NA, analyzed on 20161005

description: Library name: 20161005_ 15-08_B17_AGTCAA_L001_R1_001


title: SJMBSHH-13-5634 IACS Treated.8

description: Library name: E8


title: P. promelas larvae, UP, biological replicate UP_B07, lane 1, time step = 4, analyzed on 20161005

description: Library name: 20161005_ UP_4_B07_GGCTAC_L001_R1_001

value: UP


title: HepG2_Cont_Cont_gRNA_Day12_RNA_rep2

description: Library name: Sample 164


title: SJMBSHH-13-5634 IACS Treated.7

description: Library name: E7


title: HepG2_B2_minus_IDO_TDOinh_Day12_RNA_EX3_rep3

description: Library name: Sample 92


title: S24K0967_rep1_1_miRNA

first: Boxin

last: Zhang

address: 良渚实验室1369号

institute: 良渚实验室

description: Library name: Sample12

data_processing:
The adapter sequences of raw reads were initially removed using cutadapt  v4.0
The processed reads were aligned to the mouse genome mm10 using Hisat2 v2.2.1  with default parameters
Peak calling was done using macs2 v 2.2.7.1  with these key parameters: -f BED –nolambda --nomodel --extsize 50. Peak distribution across genomic regions was calculated using HOMER  v4.11 annotatePeaks
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: 3_za_pladB input

extract_protocol:
The immunoprecipitated RNA was extracted with the TRIzol method and used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEB Next Ultra RNA Library Prep Kit (New England Biolabs) following manufacturer's protocols.

value: MEF

tag: ip reagent

value: FLAG beads

tag: group

value: input


title: S24K0966_rep1_1_miRNA

description: Library name: Sample11

source_name: 2_za_pladB input


title: P. promelas larvae, UP, biological replicate UP_B21, lane 2, time step = 3, analyzed on 20161005

description: Library name: 20161005_ UP_3_B21_ACTGAT_L002_R1_001


title: HepG2_B2_minus_IDO_TDOinh_Day12_RNA_EX3_rep2

description: Library name: Sample 91


title: SJMBSHH-13-5634 IACS Treated.6

description: Library name: E6

value: brain

value: SHH medulloblastoma


title: P. promelas larvae, UP, biological replicate UP_B21, lane 1, time step = 3, analyzed on 20161005

description: Library name: 20161005_ UP_3_B21_ACTGAT_L001_R1_001

value: whole larvae


title: S24K1401_rep1_1_miRNA

description: Library name: Sample10

source_name: 1_za_pladB input


title: HepG2_Cont_Cont_gRNA_Day12_RNA_rep1

description: Library name: Sample 163

value: Control


title: HepG2_B2_minus_AhR_gRNA_Day12_RNA_rep1

description: Library name: Sample 172


title: P. promelas larvae, EFP, biological replicate EFP_B26, lane 2, time step = 4, analyzed on 20161005

description: Library name: 20161005_ EFP_4_B26_GCCAAT_L002_R1_001

value: 2 dpf

value: EFP


title: HepG2_B2_minus_IDO_TDOinh_Day12_RNA_EX3_rep1

description: Library name: Sample 90


title: SJMBSHH-13-5634 IACS Treated.5

description: Library name: E5

value: TP53 mut


title: P. promelas larvae, UP, biological replicate UP_B12, lane 2, time step = 2, analyzed on 20161005

description: Library name: 20161005_ UP_2_B12_ACTTGA_L002_R1_001


title: S24K1397_rep1_1_miRNA

description: Library name: Sample9

source_name: 3_za_pladB IP

value: IP


title: HepG2_Cont_IDO_TDOinh_Day12_RNA_EX3_rep3

description: Library name: Sample 89


title: HepG2_Cont_AhR_gRNA_Day12_RNA_rep2

description: Library name: Sample 170


title: SJMBSHH-13-5634 IACS Treated.4

description: Library name: E4


title: P. promelas larvae, DWIP, biological replicate DWIP_B27, lane 1, time step = NA, analyzed on 20161005

description: Library name: 20161005_ DWIP_B27_GTGAAA_L001_R1_001

value: DWIP


title: SJMBSHH-13-5634 vehicle.5

description: Library name: F5


title: P. promelas larvae, UP, biological replicate UP_B12, lane 1, time step = 2, analyzed on 20161005

description: Library name: 20161005_ UP_2_B12_ACTTGA_L001_R1_001


title: HepG2_Cont_IDO_TDOinh_Day12_RNA_EX3_rep2

description: Library name: Sample 88


title: S24K1396_rep1_1_miRNA

description: Library name: Sample8

source_name: 2_za_pladB IP


title: SJMBSHH-13-5634 IACS Treated.3

description: Library name: E3


title: P. promelas larvae, UP, biological replicate UP_B19, lane 2, time step = 1, analyzed on 20161005

description: Library name: 20161005_ UP_1_B19_GTGGCC_L002_R1_001


title: P. promelas larvae, DSP, biological replicate DSP_B26, lane 2, time step = NA, analyzed on 20161005

description: Library name: 20161005_ DSP_B26_CTTGTA_L002_R1_001

value: DSP


title: S24K0959_rep1_1_miRNA

description: Library name: Sample7

source_name: 1_za_pladB IP


title: HepG2_Cont_IDO_TDOinh_Day12_RNA_EX3_rep1

description: Library name: Sample 87


title: SJMBSHH-13-5634 IACS Treated.2

description: Library name: E2


title: P. promelas larvae, UP, biological replicate UP_B19, lane 1, time step = 1, analyzed on 20161005

description: Library name: 20161005_ UP_1_B19_GTGGCC_L001_R1_001


title: S24K1385_rep1_1_miRNA

description: Library name: Sample6

source_name: 3_zbp1_pladB IP


title: HepG2_B2_minus_Cont_gRNA_Day12_RNA_rep1

description: Library name: Sample 166


title: P. promelas larvae, EFP, biological replicate EFP_B22, lane 2, time step = 2, analyzed on 20161005

description: Library name: 20161005_ EFP_2_B22_GAGTGG_L002_R1_001


title: SJMBSHH-13-5634 IACS Treated.1

description: Library name: E1


title: HepG2_B2_minus_Day12_RNA_EX3_rep3

description: Library name: Sample 86


title: 2112FH vehicle.5

description: Library name: D5

value: Group 3 medulloblastoma

value: MYC amplified


title: HepG2_B2_minus_Day12_RNA_EX3_rep2

description: Library name: Sample 85


title: S24K1384_rep1_1_miRNA

description: Library name: Sample5

source_name: 2_zbp1_pladB IP


title: P. promelas larvae, EFP, biological replicate EFP_B22, lane 1, time step = 2, analyzed on 20161005

description: Library name: 20161005_ EFP_2_B22_GAGTGG_L001_R1_001


title: HepG2_B2_minus_Day12_RNA_EX3_rep1

description: Library name: Sample 84


title: S24K1383_rep1_1_miRNA

description: Library name: Sample4

source_name: 1_zbp1_pladB IP


title: 2112FH vehicle.4

description: Library name: D4


title: P. promelas larvae, EFP, biological replicate EFP_B13, lane 2, time step = 1, analyzed on 20161005

description: Library name: 20161005_ EFP_1_B13_GTCCGC_L002_R1_001


title: S24K0979_rep1_1_miRNA

description: Library name: Sample3

source_name: 3_zbp1_pladB input


title: P. promelas larvae, UP, biological replicate UP_B07, lane 2, time step = 4, analyzed on 20161005

description: Library name: 20161005_ UP_4_B07_GGCTAC_L002_R1_001


title: Control-1, NestinCre-Ai14, ATAC

description: Library name: Control-1

value: cortex

value: neurons

value: Men1-WT (Ai14)


title: SJMBSHH-13-5634 vehicle.1

description: Library name: F1


title: P. promelas larvae, EFP, biological replicate EFP_B13, lane 1, time step = 1, analyzed on 20161005

description: Library name: 20161005_ EFP_1_B13_GTCCGC_L001_R1_001


title: HepG2_Cont_Day12_RNA_EX3_rep3

description: Library name: Sample 83


title: 2112FH vehicle.3

description: Library name: D3


title: P. promelas larvae, DSP, biological replicate DSP_B02, lane 2, time step = NA, analyzed on 20161005

description: Library name: 20161005_ DSP_B02_ATCACG_L002_R1_001


title: HepG2_Cont_Day12_RNA_EX3_rep2

description: Library name: Sample 82


title: HepG2_Cont_Day12_RNA_EX3_rep1

description: Library name: Sample 81


title: S24K0978_rep1_1_miRNA

description: Library name: Sample2

source_name: 2_zbp1_pladB input

value: MEF

value: FLAG beads


title: S24K0977_rep1_1_miRNA

description: Library name: Sample1

source_name: 1_zbp1_pladB input

value: input


title: 2112FH vehicle.1

description: Library name: D1

value: brain


title: P. promelas larvae, DSP, biological replicate DSP_B02, lane 1, time step = NA, analyzed on 20161005

description: Library name: 20161005_ DSP_B02_ATCACG_L001_R1_001

source_name: whole larvae

value: whole larvae


title: WT Cis1,scRNAseq

city: Shanghai

first: Bo

last: Deng

address: 639 Zhizaoju Road

department: Division of Nephrology

institute: Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiaotong University

description: 10x Genomics

data_processing:
The demultiplexing,barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1
Assembly: GRCm38.p6
Supplementary files format and content: Tap-separated values files and matrix files

source_name: kidneys

extract_protocol:
The collected kidneys were decapsulated, minced, and digested with 1 mg/ml type IV collagenase and DNase I for 40 minutes at 37°C with agitation. After digestion, samples were filtered through 70-µm cell strainers to remove cell aggregate. Then pelleted cells were suspended in red blood cell lysis buffer to lyse erythrocytes. Then cell pellets were suspended and filtered to obtain single cell suspensions for single-cell sequencing.The single-cell suspension was enriched using Dead Cell Removal Micro Beads.
Library was performed according to the manufacturer's protocols(single cell 3' v2 protocol,10x Genomics).Briefy, kidney cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion.The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA.The pooled barcoded cDNA was amplified by PCR and the apropiated sized fragments were selected with SPRI select reagent for subsequent library construction. protocol,10x Genomics).

treatment_protocol: Cisplatin-induced AKI was established by cisplatin administration,injected i.p.

value: kidneys

value: WT

value: Cisplatin treat


title: HepG2_B2_minus_AhRinh_Day12_RNA_EX2_rep3

description: Library name: Sample 80


title: 2112FH IACS Treated.3

description: Library name: C3


title: HepG2_B2_minus_AhRinh_Day12_RNA_EX2_rep2

description: Library name: Sample 79


title: S24G1395_rep1_1_miRNA

data_processing:
The adapter sequences of raw reads were initially removed using cutadapt v4.0
The processed reads were aligned to the mouse genome mm10 using Hisat2 v2.2.1 with default parameters
Peak calling was done using macs2 v 2.2.7.1 with these key parameters: -f BED –nolambda --nomodel --extsize 50. Peak distribution across genomic regions was calculated using HOMER v4.11 annotatePeaks
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: MEF

tag: antibody

value: 3 I+P input


title: P. promelas larvae, MHW, biological replicate MHW_B12, lane 2, time step = NA, analyzed on 20161005

description: Library name: 20161005_ 15-07_B12_TAGCTT_L002_R1_001

value: 2 dpf

value: MHW


title: 2112FH vehicle.2

description: Library name: D2

source_name: brain


title: P. promelas larvae, MHW, biological replicate MHW_B12, lane 1, time step = NA, analyzed on 20161005

description: Library name: 20161005_ 15-07_B12_TAGCTT_L001_R1_001


title: 2112FH IACS Treated.2

description: Library name: C2


title: S24G1394_rep1_1_miRNA

value: 3 I input


title: P. promelas larvae, UP, biological replicate UP_FIELD32, lane 2, time step = NA, analyzed on 20161004

description: Library name: 20161004_ UP_FIELD_32_GTTTCG_L002_R1_001

value: UP


title: S24G1393_rep1_1_miRNA

value: 2 I input


title: HepG2_Cont_AhRinh_Day12_RNA_EX2_rep3

description: Library name: Sample 77


title: HepG2_B2_minus_AhRinh_Day12_RNA_EX2_rep1

description: Library name: Sample 78


title: 2112FH IACS Treated.1

description: Library name: C1

value: Group 3 medulloblastoma

value: MYC amplified


title: SJMBSHH-14-4106 vehicle.5

description: Library name: B5

value: SHH medulloblastoma

value: TP53 mut


title: P. promelas larvae, UP, biological replicate UP_FIELD32, lane 1, time step = NA, analyzed on 20161004

description: Library name: 20161004_ UP_FIELD_32_GTTTCG_L001_R1_001


title: S24G1392_rep1_1_miRNA

value: MEF

value: 1 I input


title: HepG2_Cont_AhRinh_Day12_RNA_EX2_rep2

description: Library name: Sample 76


title: SJMBSHH-14-4106 vehicle.4

description: Library name: B4

value: brain


title: P. promelas larvae, UP, biological replicate UP_FIELD19, lane 2, time step = NA, analyzed on 20161004

description: Library name: 20161004_ UP_FIELD_19_CTTGTA_L002_R1_001

value: whole larvae


title: HepG2_Cont_AhRinh_Day12_RNA_EX2_rep1

description: Library name: Sample 75


title: SJMBSHH-14-4106 vehicle.3

description: Library name: B3


title: S24G1390_rep1_1_miRNA

value: 1 I+P input


title: P. promelas larvae, UP, biological replicate UP_FIELD19, lane 1, time step = NA, analyzed on 20161004

description: Library name: 20161004_ UP_FIELD_19_CTTGTA_L001_R1_001


title: HepG2_Day12_B2_minus_RNA_rep3

description: Library name: Sample 24


title: SJMBSHH-14-4106 vehicle.2

description: Library name: B2


title: P. promelas larvae, EMZ, biological replicate EMZ_B30, lane 2, time step = NA, analyzed on 20161004

description: Library name: 20161004_ EMZ_B30_ACAGTG_L002_R1_001

value: EMZ


title: HepG2_Day12_B2_minus_RNA_rep2

description: Library name: Sample 23


title: SJMBSHH-14-4106 vehicle.1

description: Library name: B1


title: P. promelas larvae, EMZ, biological replicate EMZ_B30, lane 1, time step = NA, analyzed on 20161004

description: Library name: 20161004_ EMZ_B30_ACAGTG_L001_R1_001


title: S24H0659_rep1_1_miRNA

value: 2 I+P zbp1


title: S24H0660_rep1_1_miRNA

value: 3 I+P zbp1


title: S24G1391_rep1_1_miRNA

value: 2 I+P input


title: SJMBSHH-14-4106 IACS Treated.4

description: Library name: A4


title: HepG2_Day12_B2_minus_RNA_rep1

description: Library name: Sample 22


title: P. promelas larvae, EFP, biological replicate EFP_FIELD35, lane 2, time step = NA, analyzed on 20161004

description: Library name: 20161004_ EFP_FIELD_35_GTGAAA_L002_R1_001

value: 2 dpf

value: EFP


title: HepG2_Day12_Cont_RNA_rep3

description: Library name: Sample 21

value: Control


title: P. promelas larvae, EFP, biological replicate EFP_FIELD35, lane 1, time step = NA, analyzed on 20161004

description: Library name: 20161004_ EFP_FIELD_35_GTGAAA_L001_R1_001


title: HepG2_Day12_Cont_RNA_rep2

description: Library name: Sample 20


title: SJMBSHH-14-4106 IACS Treated.3

description: Library name: A3


title: S24H0657_rep1_1_miRNA

value: 3 I zbp1


title: S24H0658_rep1_1_miRNA

value: 1 I+P zbp1


title: SJMBSHH-14-4106 IACS Treated.2

description: Library name: A2


title: P. promelas larvae, EFP, biological replicate EFP_FIELD29, lane 2, time step = NA, analyzed on 20161004

description: Library name: 20161004_ EFP_FIELD_29_AGTTCC_L002_R1_001


title: HepG2_Day12_Cont_RNA_rep1

description: Library name: Sample 19


title: S24H0656_rep1_1_miRNA

value: 2 I zbp1


title: P. promelas larvae, EFP, biological replicate EFP_FIELD29, lane 1, time step = NA, analyzed on 20161004

description: Library name: 20161004_ EFP_FIELD_29_AGTTCC_L001_R1_001


title: SJMBSHH-14-4106 IACS Treated.1

description: Library name: A1

value: SHH medulloblastoma


title: HepG2_Day9_B2_minus_RNA_rep3

description: Library name: Sample 18


title: RPMI-8226-R (2)

city: İzmir

first: Yagmur

last: Kiraz

address: Sakarya st. No:156

department: Genetics and Bioengineering

country: Turkey

institute: İzmir University of Economics

description: Library name: sample-6

data_processing:
Sequencing was performed on the Illumina NovaSeq 6000 platform, targeting an average of 30 million paired-end (150 bp) reads per sample. Library quantification, dilution, and loading were executed per the manufacturer's guidelines.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: csv files include FPKM values for each sample

extract_protocol:
Total RNA was harvested with PureLink™ RNA Mini Kit, Invitrogen™
The library preparation was carried out using the Illumina Total RNA Prep kit (Illumina, USA, #20040529). The process involved removing ribosomal RNA from the total RNA, fragmenting the remaining RNA, and synthesizing primary and secondary cDNA strands. Steps such as ribosomal RNA removal, fragmentation, RNA purification, cDNA synthesis, addition of index and barcode sequences, and final purification were performed following the manufacturer's instructions.

value: B-lymphocytes

value: no treatment


title: S24H0655_rep1_1_miRNA

value: MEF

value: 1 I zbp1


title: P. promelas larvae, EFP, biological replicate EFP_B17, lane 2, time step = 4, analyzed on 20161004

description: Library name: 20161004_ EFP_4_B17_AGTCAA_L002_R1_001

value: whole larvae


title: FIgG

city: beijing

first: xinjie

last: zhong

address: No. 95 Yong 'an Road

institute: Beijing Friendship Hospital

data_processing:
Basecalls were performed using Novaseq 6000 platform PE150.
After the library construction, Qubit 2.0 was used for preliminary quantification, and then Agilent 2100 was used to detect the insert size of the library. After the insert size met the expectation, qPCR was used to accurately quantify the effective concentration of the library to ensure the quality of the library.
When the number of N in single-ended paired reads was greater than 3, or the base ratio with quality value＜5 was >=20%, the paired reads were removed. And when removing the adapter sequence, the adapter sequence must >= 8bp.
bigWig files were generated using Vaztme cloud CUT_Tag_tool.
Assembly: mm9
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: spleen and lymph node

extract_protocol:
Gata2 antibody (2B5A1, proteintech) and Hyperactive Universal CUT & Tag Assay Kit (TD903-01, Vazyme) were used to extract binding site of Gata2 according to the manufacturer’s instructions.
TruePrep Index Kit V2 (TD202, Vazyme) was used to amplify the cDNA libraries according to the manufacturer’s instructions.

value: spleen and lymph node

tag: chip antibody

value: Rabbit IgG

value: T cell

value: F


title: HepG2_Day9_B2_minus_RNA_rep2

description: Library name: Sample 17


title: P. promelas larvae, EFP, biological replicate EFP_B17, lane 1, time step = 4, analyzed on 20161004

description: Library name: 20161004_ EFP_4_B17_AGTCAA_L001_R1_001


title: CIgG

value: C


title: HepG2_Day9_B2_minus_RNA_rep1

description: Library name: Sample 16


title: RPMI-8226-R (1)

description: Library name: sample-5


title: RPMI-8226 (2)

description: Library name: sample-4


title: Fgata2

value: 2B5A1, proteintech


title: HepG2_Day9_Cont_RNA_rep3

description: Library name: Sample 15


title: P. promelas larvae, EFP, biological replicate EFP_B16, lane 2, time step = 3, analyzed on 20161004

description: Library name: 20161004_ EFP_3_B16_GCCAAT_L002_R1_001

value: 2 dpf

value: EFP


title: RPMI-8226 (1)

description: Library name: sample-3


title: P. promelas larvae, EFP, biological replicate EFP_B16, lane 1, time step = 3, analyzed on 20161004

description: Library name: 20161004_ EFP_3_B16_GCCAAT_L001_R1_001


title: Cgata2


title: HepG2_Day9_Cont_RNA_rep2

description: Library name: Sample 14

value: Control


title: NCI-BL2171 (2)

description: Library name: sample-2


title: P. promelas larvae, MHW, biological replicate MHW_B11, lane 2, time step = NA, analyzed on 20161004

description: Library name: 20161004_ 15-08_B11_ATGTCA_L002_R1_001

value: MHW


title: Heart, M3 (bio rep3), lncRNA and mRNA-seq

city: Guiyang

first: kaiyuan

last: chen

state: Guizhou Province

address: Beijing Road,Yunyan District

department: Cardiovascular

institute: the Affiliated Hospital of Guizhou Medical University

description:
M3
All.transcript.fpkm.with_anno.txt

data_processing:
bcl2fastq (v2.19.1.403) -R /BCLdir --sample-sheet SampleSheet.csv -o /Rawfq -r 14 -p 14 -w 14 --tiles s_[1-8] --barcode-mismatches=0 --use-bases-mask y150n,I*,I*,y150n
fastp-v0.23.0 -i sample_R1_001.fastq.gz -l 50 -n 5 -q 20 -W 4 -M 20 -f 0 -t 0 -h sample.html -j sample.json -o sample.filtered.1.fq.gz -I sample_R2_001.fastq.gz -F 0 -T 0 --detect_adapter_for_pe -O sample.filtered.2.fq.gz -w 4
hisat2(v2.1.0) -p 5 -5 0 -3 0 --min-intronlen 20 --max-intronlen 500000 -k 3 --phred33 --rna-strandness RF --novel-splicesite-outfile T_1_novel_splicesite.txt -x Mus_musculus.GRCm39.dna.toplevel -1 sample.filtered.1.fq.gz -2 sample.filtered.2.fq.gz > sample.hisat2.bam
htseq-count(v0.10.0) -f bam -s reverse -a 10 -m union -i transcript_id --nonunique none sample.hisat2.bam Mus_Musculus.GRCm38.102/mm10.gtf > sample.htseq.result
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: heart

growth_protocol: Using the Langendorff system for isolated mouse heart perfusion

extract_protocol:
0.1-1 μg of total RNA per sample was prepared for library preparation. The NEBNext®Poly(A) mRNA Magnetic Isolation Module and NEBNext® Ultra™ II mRNA Library Prep Kit for Illumina® were used for mRNA isolation and library construction following the manufacturers’ protocols.
RNA libraries for RNA-seq were prepared using mRNA-Seq library prep kit following manufacturer's protocols

treatment_protocol: The sham surgery group did not stop jumping, in the model group, Tomas cardioplegia was employed to induce a temporary suspension of cardiac contractions for a duration of 30 minutes, followed by a subsequent reperfusion period of 1 hour.

value: heart

tag: Sex

value: male

value: Ischemia for 30min- reperfusion for 1h


title: HepG2_Day9_Cont_RNA_rep1

description: Library name: Sample 13


title: NCI-BL2171 (1)

description: Library name: sample-1

value: B-lymphocytes

value: no treatment


title: P. promelas larvae, MHW, biological replicate MHW_B11, lane 1, time step = NA, analyzed on 20161004

description: Library name: 20161004_ 15-08_B11_ATGTCA_L001_R1_001


title: Heart, M2 (bio rep2), lncRNA and mRNA-seq

description:
M2
All.transcript.fpkm.with_anno.txt


title: P. promelas larvae, UP, biological replicate UP_FIELD05, lane 2, time step = NA, analyzed on 20161004

description: Library name: 20161004_ UP_FIELD_05_ATCACG_L002_R1_001

value: UP


title: Human macrophages, Donor H5, IFNy stimulated and Mtb infected

city: Greifswald - Insel Riems

first: Björn

last: Corleis

state: Mecklenburg-Western Pomerania

address: Südufer 10

department: Institute of immunology

country: Germany

institute: Friedrich-Loeffler-Institut

description: Library name: H5_IFNyMtb

data_processing:
STAR (version 2.7.9a) read alignment
Subread featureCounts (version 2.0.3) read counting
Assembly: GRCh38.p14, GRCm39
Supplementary files format and content: tab delimeted .txt file containing raw read counts for each gene

source_name: monocyte derived macrophages

growth_protocol: For transcriptomic analysis, macrophages were differentiated in 48-well plates at a density of 1 × 10⁶ cells per well in RPMI 1640 supplemented with 10% FCS, 2 mM L-glutamine, and 1 mM sodium pyruvate.

extract_protocol:
RNA was extracted from 1 ml Trizol™ using PhaseMaker tubes and chloroform. After phase separation by centrifugation (12,000 × g, 15 min, 4°C), the aqueous phase was precipitated with glycogen and isopropanol (–20°C, 60 min), pelleted, washed with 75% ethanol, and air-dried. RNA was resuspended in 20 µl nuclease-free water and incubated at 60°C for 15 min.
TotTotal RNA was purified with RNA-SPRI beads and ethanol washes. Whole-transcriptome amplification was performed using Smart-seq2. cDNA was synthesized, amplified, and purified with DNA-SPRI beads. Quality was assessed via Qubit and Bioanalyzer. Libraries were prepared using Nextera XT for tagmentation and adapter ligation, PCR-amplified, bead-purified, and stored at –20 °C

treatment_protocol: Cells were pre-treated with 500 ng/ml recombinant IFNγ for 24 hours, followed by infection with M. tuberculosis (Mtb) at a multiplicity of infection (MOI) of 1 for an additional 24 hours

value: monocyte derived macrophages

value: IFNy stimulated and Mtb infected


title: HepG2_Day6_B2_minus_RNA_rep3

description: Library name: Sample 12


title: HepG2_Day6_B2_minus_RNA_rep2

description: Library name: Sample 11


title: Human macrophages, Donor H5, Mtb infected

description: Library name: H5_Mtb

value: Mtb infected


title: Heart, C3 (bio rep3), lncRNA and mRNA-seq

description:
C3
All.transcript.fpkm.with_anno.txt

value: Sham


title: Heart, M1 (bio rep1), lncRNA and mRNA-seq

description:
M1
All.transcript.fpkm.with_anno.txt


title: P. promelas larvae, UP, biological replicate UP_FIELD05, lane 1, time step = NA, analyzed on 20161004

description: Library name: 20161004_ UP_FIELD_05_ATCACG_L001_R1_001

value: whole larvae


title: HepG2_Day6_B2_minus_RNA_rep1

description: Library name: Sample 10


title: Heart, C2 (bio rep2), lncRNA and mRNA-seq

description:
C2
All.transcript.fpkm.with_anno.txt


title: HepG2_Day6_Cont_RNA_rep3

description: Library name: Sample 9


title: Human macrophages, Donor H5, untreated control

description: Library name: H5_CTR

value: untreated control


title: Human macrophages, Donor H5, IFNy stimulated

description: Library name: H5_IFNy

value: IFNy stimulated


title: P. promelas larvae, UP, biological replicate UP_FIELD02, lane 1, time step = NA, analyzed on 20161004

description: Library name: 20161004_ UP_FIELD_02_TAGCTT_L001_R1_001

value: 2 dpf


title: Heart, C1 (bio rep1), lncRNA and mRNA-seq

description:
C1
All.transcript.fpkm.with_anno.txt


title: Heart, M3 (bio rep3), miRNA-seq

data_processing:
bcl2fastq (v2.19.1.403) -R /BCLdir --sample-sheet SampleSheet.csv -o /Rawfq -r 14 -p 14 -w 14 --tiles s_[1-8] --barcode-mismatches=0 --use-bases-mask y150n,I*,I*,y150n
fastp-v0.23.0 -i sample_R1_001.fastq.gz -l 0 -n 0 -q 20 -W 4 -M 20 -f 0 -t 0 -h sample.html -j sample.json -o sample.filtered.1.fq.gz --adapter_sequence AACTGTAGGCACCATCAAT -w 4
perl decompressionFile.pl -i sample.filtered.1.fq.gz -o sample.fq
perl mergeGZFile.pl -i sample.LengthFilter.fq.gz -o sample.fq.gz
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample


title: P. promelas larvae, UP, biological replicate UP_B02, lane 2, time step = 4, analyzed on 20161004

description: Library name: 20161004_ UP_4_B02_GTCCGC_L002_R1_001


title: Human macrophages, Donor H4, IFNy stimulated and Mtb infected

description: Library name: H4_IFNyMtb


title: P. promelas larvae, UP, biological replicate UP_B02, lane 1, time step = 4, analyzed on 20161004

description: Library name: 20161004_ UP_4_B02_GTCCGC_L001_R1_001


title: Heart, M2 (bio rep2), miRNA-seq


title: HepG2_Day6_Cont_RNA_rep2

description: Library name: Sample 8


title: Human macrophages, Donor H4, IFNy stimulated

description: Library name: H4_IFNy


title: Heart, M1 (bio rep1), miRNA-seq


title: Human macrophages, Donor H4, untreated control

description: Library name: H4_CTR


title: HepG2_Day3_B2_minus_RNA_rep2

description: Library name: Sample 5


title: P. promelas larvae, UP, biological replicate UP_B02, lane 1, time step = 3, analyzed on 20161004

description: Library name: 20161004_ UP_3_B02_GGCTAC_L001_R1_001


title: P. promelas larvae, UP, biological replicate UP_B02, lane 2, time step = 3, analyzed on 20161004

description: Library name: 20161004_ UP_3_B02_GGCTAC_L002_R1_001


title: Heart, C3 (bio rep3), miRNA-seq


title: Human macrophages, Donor H3, IFNy stimulated and Mtb infected

description: Library name: H3_IFNyMtb


title: HepG2_Day3_B2_minus_RNA_rep1

description: Library name: Sample 4


title: Heart, C2 (bio rep2), miRNA-seq


title: Human macrophages, Donor H3, Mtb infected

description: Library name: H3_Mtb


title: HepG2_Day3_Cont_RNA_rep3

description: Library name: Sample 3


title: P. promelas larvae, UP, biological replicate UP_B03, lane 1, time step = 2, analyzed on 20161004

description: Library name: 20161004_ UP_2_B03_ACTGAT_L001_R1_001


title: Heart, C1 (bio rep1), miRNA-seq


title: HepG2_Day3_Cont_RNA_rep2

description: Library name: Sample 2


title: HepG2_Day3_Cont_RNA_rep1

description: Library name: Sample 1


title: P. promelas larvae, UP, biological replicate UP_B07, lane 1, time step = 1, analyzed on 20161004

description: Library name: 20161004_ UP_1_B07_ACTTGA_L001_R1_001


title: Patient 10, Primary prostate cancer, PSMA low tumor area

city: Vienna

first: Gerda

last: Egger

address: Waehringer Guertel 18-20

department: Pathology

country: Austria

institute: Medical University of Vienna

description: Library name: p10_low

data_processing:
RRBS pools were sequenced on a HiSeq 3000 instrument (Illumina, San Diego, CA, USA) following a 50-base-pair, single-end recipe. Raw data acquisition (HiSeq Control Software, HCS, HD 3.4.0.38) and base calling (Real-Time Analysis Software, RTA, 2.7.7) was performed on-instrument, while the subsequent raw data processing off the instruments involved two custom programs based on Picard tools (2.19.2). In a first step, base calls were converted into lane-specific, multiplexed, unaligned BAM files suitable for long-term archival (IlluminaBasecallsToMultiplexSam, 2.19.2-CeMM), thereby annotating an eventual start of NGS adapter sequences in XT tags. In a second step, archive BAM files were demultiplexed into sample-specific, unaligned BAM files (IlluminaSamDemux, 2.19.2-CeMM).
Custom scripts were used to calculate the digestion metrics for the TaqI and MspI restriction enzymes. Unaligned BAM files were converted into FASTQ files and pre-processed with Trimmomatic using options ILLUMINACLIP:RRBS_adapters.fa:2:40:7 SLIDINGWINDOW:4:15 MAXINFO:20:0.50 MINLEN:18. Trimmed NGS reads were aligned to the reference genome with the methylation-aware BSMAP aligner in RRBS mode for MspI (-D C-CGG) and TaqI (-D T-CGA) restriction sites, a filter of 5 Ns (-f 5), a quality threshold of 0 (-q 0), a seed size of 12 (-s 12), a mismatch rate of 0.08 (-v 0.08, or 4 mismatches in 50), a minimal inset size of 20 (-m 20), a maximal insert size of 500 (-x 500) mapping to forward strands only (-n 0). (Options: -D C-CGG -D T-CGA -f 5 -m 20 -n 0 -p 4 -q 0 -r 1 -s 12 -S 0 -u -v 0.08 -V 2 -w 100 -x 500). Methylated bases were called with the biseqMethCalling script and the resulting UCSC Genome Browser BED files were converted into BigBed files for integration into a UCSC Genome Browser Track Hub for visual inspection. Internal standards comprised of fully methylated and unmethylated double stranded synthetic oligo sequences were added to each sample to determine the rates of conversion and over-conversion, respectively. The internal standards were aligned with Bismark and methylation calls were evaluated with a custom script.
Assembly: hg38
Supplementary files format and content: bigwig

source_name: Primary Prostate Cancer

extract_protocol:
DNA was extracted automated with the Qiagen EZ1 using the Qiagen EZ1 DNA FFPE Kit following manufacturers instruction for sample preparation.
Reduced Representation Bisulphite Sequencing (RRBS) libraries were generated as described previously. Briefly, up to 100 ng of genomic DNA were digested for 12 hours at 37 °C with 20 U of MspI (R0106L, New England Biolabs, Inc., Ipswich, MA, USA) in 30 μl of 1 x NEB buffer 2. To retain even the smallest fragments and to minimize the loss of material, end preparation and adaptor ligation were performed in a single-tube setup. End fill-in and A-tailing were performed by addition of Klenow Fragment 3’ > 5’ exo-mix (P7010-LC-L, Enzymatics) and dNTP mix (10 mM dATP, 1 mM dCTP, 1 mM dGTP, N0446S, New England Biolabs). After ligation to methylated Illumina TruSeq LT v2 adaptors using T4 DNA Ligase rapid (L6030-HC-L, Enzymatics), the libraries were size selected via a 0.75 x clean-up with AMPure XP beads (A63881, Beckman Coulter). The libraries were pooled based on qPCR data and subjected to bisulfite conversion using the EZ DNA Methylation Direct Kit (D5020, Zymo Research) with changes to the manufacturer’s protocol: conversion reagent was used at 0.9 x concentration, incubation performed for 20 cycles of 1 min at 95 °C, 10 min at 60 °C and the desulfonation time was extended to 30 min. These changes increase the number of CpG dinucleotides covered, by reducing double strand break formation in larger library fragments. Bisulfite-converted libraries were enriched via KAPA HiFi HS Uracil+ RM (07959079001, Roche Molecular Systems, Inc.). The minimum number of enrichment cycles was estimated based on a qPCR experiment. After a 1 x AMPure XP clean-up, library concentrations were quantified with the Qubit Fluorometric Quantitation system (Q32854, Thermo Fisher Scientific, Waltham, MA, USA) and the size distribution was assessed using the High Sensitivity DNA Kit (5067-4626, Agilent, Santa Clara, CA, USA) on a 2100 Bioanalyzer (Agilent) instrument. Sample-specific RRBS libraries were diluted and pooled in equimolar amounts.

value: Primary Prostate Cancer

value: bulk


title: HepG2_Day12_B2_minus_CEBPa_ChIP_rep1

description: Library name: Sample 67

data_processing:
FASTQ files were processed to assess quality by determining general sequencing bias, clonality and adapter sequence contamination.
FASTQ files were mapped to the hg38 human or mm10 mouse reference genome with Bowtie2 using default parameters. Alignment files were processed using HOMER. Peaks were called by combining replicate conditions and using HOMER (findPeaks) using parameters “-style factor -size 200”.
Assembly: hg38 or mm10
Supplementary files format and content: Peak files (BED format)

extract_protocol:
For ChIP-seq, crosslinked cells were resuspended in ice-cold hypotonic buffer (10 mM HEPES-KOH (pH 7.9), 85 mM KCl, 1 mM EDTA, 1% NP-40, 1× protease inhibitor cocktail), and centrifuged at 1,000 × g for 5 min at 4°C to obtain a nuclear fraction.
Chromatin immunoprecipitation (ChIP) was performed in biological replicates as previously described58 with modifications as follows. For H3K27ac ChIP assays, cells were cross-linked with 1% (vol/vol) formaldehyde in PBS for 10 min at room temperature. For AhR and C/EBPα ChIP assays, cells were cross-linked with 2 mM disuccinimidyl glutarate (DSG) (ProteoChem) in PBS for 30 min at room temperature, and then directly a second crosslinking was performed by the addition of 1% (vol/vol) formaldehyde in PBS for 10 min. The crosslinking reaction was quenched by 0.125 M glycine (Sigma-Aldrich). Cells were washed once with ice-cold PBS and pelleted at 1,000 × g for 5 min at 4°C. Crosslinked cells were resuspended in ice-cold hypotonic buffer (10 mM HEPES-KOH (pH 7.9), 85 mM KCl, 1 mM EDTA, 1% NP-40, 1× protease inhibitor cocktail), and centrifuged at 1,000 × g for 5 min at 4°C to obtain a nuclear fraction. Nuclear pellets were resuspended in 100 µl of either LB3 buffer (10 mM Tris-HCl (pH 7.5), 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate, 0.5% N-laurosylsarcosine, 1× protease inhibitor cocktail, for H3K27ac ChIP) or PIPA-NR buffer (20 mM Tris-HCl (pH 7.5), 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.4% sodium deoxycholate, 0.1% SDS, 1% NP-40, 0.5 mM DTT, 1× protease inhibitor cocktail, for AhR and C/EBPα ChIPs). Chromatin DNA was sonicated in a 0.2 ml microtube (Diagenode) using a Bioruptor® Pico sonication device (30 sec ON / 30 sec OFF cycles) for 10 min at 4°C. Samples were centrifuged at 15,000 rpm for 10 min at 4C, and the supernatant was used for immunoprecipitation. LB3 lysate was diluted 1.1-fold with 10% Triton X-100. 1% of the lysate was kept as ChIP input. The lysates were rotated with each antibody pre-bound to 20 µl of beads (10 µl of Dynabeads protein A (Thermo Fisher Scientific) + 10 µl of Dynabeads protein G (Thermo Fisher Scientific)) overnight at 4°C. After the immunoprecipitation, beads were collected on a magnet and washed three times each with wash buffer I (20 mM Tris-HCl (pH 7.5), 150 mM NaCl, 1% Triton X-100, 0.1% SDS, 2 mM EDTA, 1× protease inhibitor cocktail), wash buffer III (10 mM Tris-HCl (pH 7.5), 250 mM LiCl, 1% Triton X-100, 0.7% sodium deoxycholate, 1 mM EDTA, 1× protease inhibitor cocktail) and twice with TET (10 mM Tris-HCl (pH 7.5), 1 mM EDTA, 0.2% Tween-20, 1× protease inhibitor cocktail), and then resuspended in 25 µl of TT (10mM Tris-HCl (pH 7.5), 0.05% Tween-20). The immunoprecipitated chromatin samples were used for library preparation with NEBNext Ultra II Library kit (NEB) according to the manufacturer’s instructions. DNA in 46.5 µl of NEB reactions was revers crosslinked by adding 4 µl of 10% SDS, 4.5 µl of 5 M NaCl, 3 µl of 500 mM EDTA, 1 µl of 20 mg/ml proteinase K and 20 µl of water by incubation for 1 hr at 55°C, and then 30 min at 65°C. DNA was purified with 2 µl of SpeedBeads in 20% PEG 8000/1.5 M NaCl (Final 12% PEG 8000), and eluted with 25 µl of TT. The eluted DNA was amplified for 14 cycles in 50 µl of PCR reactions using NEBNext High-Fidelity 2× PCR Master Mix (NEB) and 0.5 mM each of primers Solexa 1GA and Solexa 1GB. The amplified libraries were purified with 2 µl of SpeedBeads in 20% PEG 8000/2.5 M NaCl (Final 13% PEG 8000), eluted with 20 µl of TT, size selected using PAGE/TBE gel for 225-325 bp fragments by gel extraction, and single-end sequenced on NextSeq 2000 or NovaSeq X Plus (Illumina). ChIP input material (1% of sheared DNA) in 46.5 µl of TE was revers crosslinked by adding 4 µl of 10% SDS, 4.5 µl of 5 M NaCl, 3 µl of 500 mM EDTA, 1 µl of 20 mg/ml proteinase K and 20 µl of water by incubation for 1 hr at 55°C, and then 30 min at 65°C. The input DNA was purified with SpeedBeads as described above, and eluted with 25 µl of TT. The eluted input DNA was prepared for libraries and amplified as described for ChIP samples.

value: CEBPa


title: Human macrophages, Donor H2, Mtb infected

description: Library name: H2_Mtb


title: Patient 09, Primary prostate cancer, PSMA low tumor area

description: Library name: p09_low


title: HepG2_Cont_Day12_CEBPa_ChIP_Input_rep2

description: Library name: Sample 66

value: Control


title: P. promelas larvae, MHW, biological replicate MHW_B03, lane 2, time step = NA, analyzed on 20161004

description: Library name: 20161004_ 15-07_B03_GTGGCC_L002_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.

value: MHW


title: OE_CTL, rep1

city: Boston

first: Xiang-Yu

last: Liu

state: MA

address: 3 Blackfan St

institute: Harvard University

description:
Library name: Sample 7
OE_CTL, rep1, AML12_hepatocytes, (G13)

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: Patient 09, Primary prostate cancer, PSMA high tumor area

description: Library name: p09_high


title: HepG2_Cont_Day12_CEBPa_ChIP_Input_rep1

description: Library name: Sample 65


title: Human macrophages, Donor H2, untreated control

description: Library name: H2_CTR


title: P. promelas larvae, MHW, biological replicate MHW_B03, lane 1, time step = NA, analyzed on 20161004

description: Library name: 20161004_ 15-07_B03_GTGGCC_L001_R1_001

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.


title: Patient 08, Primary prostate cancer, PSMA low tumor area

description: Library name: p08_low


title: HepG2_Cont_Day12_CEBPa_ChIP_rep2

description: Library name: Sample 64


title: Human macrophages, Donor H1, IFNy stimulated and Mtb infected

description: Library name: H1_IFNyMtb


title: Control Female Biological Rep 1, Technical Replicate

city: New York

first: Gordana

last: Vunjak-Novakovic

state: NY

institute: Columbia University

description: Library name: GR010

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: Untreated


title: P. promelas larvae, UP, biological replicate UP_FIELD04, lane 2, time step = NA, analyzed on 20161003

description: Library name: 20161003_ UP_FIELD_04_GTTTCG_L002_R1_001

value: UP


title: HepG2_Cont_Day12_CEBPa_ChIP_rep1

description: Library name: Sample 63


title: Human macrophages, Donor H1, Mtb infected

description: Library name: H1_Mtb

value: monocyte derived macrophages


title: P. promelas larvae, UP, biological replicate UP_FIELD04, lane 1, time step = NA, analyzed on 20161003

description: Library name: 20161003_ UP_FIELD_04_GTTTCG_L001_R1_001


title: Patient 07, Primary prostate cancer, PSMA low tumor area

description: Library name: p07_low


title: HepG2_Day12_B2_minus_AhR_CEBPa_ChIP_Input_rep2

description: Library name: Sample 62


title: P. promelas larvae, EFP, biological replicate EFP_B18, lane 2, time step = 1, analyzed on 20161011

description: Library name: 20161011_ EFP_1_B18_ATCACG_L002_R1_001

value: EFP


title: Patient 07, Primary prostate cancer, PSMA high tumor area

description: Library name: p07_high


title: HepG2_Day12_B2_minus_AhR_CEBPa_ChIP_Input_rep1

description: Library name: Sample 61


title: Isogenic control day 25 untreated

city: Paris

first: Damelys

last: Calderon

address: 24 boulevard du Montparnasse

country: France

institute: Institut Imagine

description:
Library name: SAMPLES 6
10x Genomics

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using the Cell Ranger software v7.2 (https://www.10xgenomics.com/support/software/cell-ranger/latest). Assembly: GRCh38 (hg38)
Assembly: hg38
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: Kidney organoid

growth_protocol: Control and Mutant (NPHP1-/-) iPSC were differentiated into kidney organoids using the Morizane protocol. Organoids were harvest on day 25 or 38 of the differentiation.

extract_protocol:
Total mRNA was isolated using an Extraction Mini Kit (Qiagen) following the recommendations of the manufacturer
Libraries were generated using Chromium Next GEM Single Cell 3’ and Next GEM Chip G Single Cell Kits (10x Genomics) at the genomics platform at the Institute du Cerveau. The quality of the libraries was assessed using the High Sensitivity D5000 ScreenTape Assay for TapeStation Systems (Agilent), and the libraries were sequenced on NovaSeq 6000. The minimum requested coverage was 50,000 reads per cell.

treatment_protocol: On day 36, IL1B (10ng/ml) was added or not to kidney organoids for 48 hours.

value: Kidney organoid

value: iPSC line

value: Control crispr (del c.-15_-10;  c.-9_-8insT)


title: P. promelas larvae, EMZ, biological replicate EMZ_B02, lane 1, time step = NA, analyzed on 20161003

description: Library name: 20161003_ EMZ_B02_AGTTCC_L001_R1_001

value: whole larvae

value: EMZ


title: P. promelas larvae, DWIP, biological replicate DWIP_B11, lane 1, time step = NA, analyzed on 20161011

description: Library name: 20161011_ DWIP_B11_GAGTGG_L001_R1_001

value: 2 dpf

value: DWIP


title: d20_OKS_ctrl_R9

city: Quebec City

first: Samer

last: Hussein

state: Quebec

address: 9 rue Mcmahon

department: Departement of medecine

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: Reprogramming timeline to induced pluripotent stem cells

value: OKS-Luciferase-AS

value: FBS-LIF + dox


title: HFD/DMSO_preventive_n1

city: Leipzig

first: Jes-Niels

last: Boeckel

address: Johannisalle 30

department: Klinik und Poliklinik für Kardiologie

institute: Universitätsklinikum Leipzig

description:
Library name: KK_01
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: Patient 06, Primary prostate cancer, PSMA low tumor area

description: Library name: p06_low

value: Primary Prostate Cancer

value: bulk


title: HepG2_Day12_Cont_AhR_ChIP_Input_rep2

description: Library name: Sample 60

value: Control


title: Patient 08, Primary prostate cancer, PSMA high tumor area

description: Library name: p08_high


title: Isogenic control day 38 IL1B treated

description:
Library name: SAMPLES 5
10x Genomics

value: On day 36, IL1B (10ng/ml) was added to kidney organoids for 48 hours.


title: P. promelas larvae, EFP, biological replicate EFP_FIELD22, lane 2, time step = NA, analyzed on 20161003

city: Durham

first: Steven

last: Purucker

address: 109 TW Alexander Dr

institute: US EPA

description: Library name: 20161003_ EFP_FIELD_22_GTGAAA_L002_R1_001


title: Patient 04, Primary prostate cancer, PSMA low tumor area

description: Library name: p04_low


title: HepG2_Day12_Cont_AhR_ChIP_Input_rep1

description: Library name: Sample 59


title: P. promelas larvae, EFP, biological replicate EFP_FIELD22, lane 1, time step = NA, analyzed on 20161003

description: Library name: 20161003_ EFP_FIELD_22_GTGAAA_L001_R1_001


title: Isogenic control day 38 untreated

description:
Library name: SAMPLES 4
10x Genomics

value: Untreated


title: Patient 04, Primary prostate cancer, PSMA high tumor area

description: Library name: p04_high


title: HepG2_Day12_B2_minus_AhR_ChIP_rep2

description: Library name: Sample 58

value: AhR


title: Mutant day 25 untreated

description:
Library name: SAMPLES 3
10x Genomics

value: Kidney organoid


title: P. promelas larvae, EFP, biological replicate EFP_FIELD05, lane 2, time step = NA, analyzed on 20161003

description: Library name: 20161003_ EFP_FIELD_05_ACAGTG_L002_R1_001

value: EFP


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

description: Library name: 20161011_ UP_2_B22_ATGTCA_L002_R1_001

value: UP


title: SAMPLE 72

city: Little Rock

first: Roopa

last: Siddaiah

state: AR

address: 1 Children's way

department: Pediatrics

institute: Arkansas Children's Hospital

description:
Library name: G923-39
Small RNA library prepared using QIAseq miRNA kit with UMI

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. 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: F


title: Control_rep3

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: Control3

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: Human macrophages, Donor H1, IFNy stimulated

description: Library name: H1_IFNy

value: monocyte derived macrophages

value: IFNy stimulated


title: P. promelas larvae, UP, biological replicate UP_FIELD02, lane 2, time step = NA, analyzed on 20161004

description: Library name: 20161004_ UP_FIELD_02_TAGCTT_L002_R1_001

value: whole larvae

value: 2 dpf


title: Patient 03, Primary prostate cancer, PSMA low tumor area

description: Library name: p03_low

value: Primary Prostate Cancer


title: P. promelas larvae, EMZ, biological replicate EMZ_B02, lane 2, time step = NA, analyzed on 20161003

description: Library name: 20161003_ EMZ_B02_AGTTCC_L002_R1_001

value: EMZ


title: HepG2_Day12_B2_minus_AhR_ChIP_rep1

first: Yohei

last: Abe

address: 3181 Porter Dr

institute: Arc Institute

description: Library name: Sample 57


title: P. promelas larvae, EFP, biological replicate EFP_FIELD05, lane 1, time step = NA, analyzed on 20161003

description: Library name: 20161003_ EFP_FIELD_05_ACAGTG_L001_R1_001


title: Human macrophages, Donor H4, Mtb infected

description: Library name: H4_Mtb

value: Mtb infected


title: HepG2_Day6_Cont_RNA_rep1

description: Library name: Sample 7

data_processing:
FASTQ files were processed to assess quality by determining general sequencing bias, clonality and adapter sequence contamination.
RNA sequencing reads were aligned to the hg38 human or mm10 mouse reference genome using STAR using default parameters.  Gene expression levels were calculated using HOMER by counting all strand specific reads within exons.  Only the most abundant transcripts, including multiple alternative variants, were selected for each gene, and the genes with a length smaller than 250 bp were removed.  Transcripts per million (TPM) were used to evaluate the correlation among replicates.
FASTQ files were mapped to the hg38 human or mm10 mouse reference genome with Bowtie2 using default parameters.
Assembly: hg38 or mm10
Supplementary files format and content: TPM expression matrices

extract_protocol:
For RNA-seq, total RNA was isolated from culture cells and purified using a Direct-zol RNA MicroPrep Kit (Zymo Research) as described by the manufacturer.
RNA-seq library preparation was performed according to the manufacturer’s instructions of the QuantSeq 3’ mRNA-Seq V2 Library Prep Kit (Lexogen Inc). In detail, RNA-seq libraries were prepared from 500 ng of total RNA using a reverse transcription–based workflow incorporating Illumina-compatible adapter sequences. First-strand cDNA synthesis was performed using an oligo(dT) primer containing an Illumina-compatible sequence at its 5′ end. The primer was annealed to polyadenylated RNA, and reverse transcription was carried out according to the manufacturer’s instructions to generate first-strand cDNA. Following first-strand synthesis, the RNA template was enzymatically degraded to enable efficient second-strand synthesis. Reaction plates were briefly centrifuged prior to removal of the sealing film to ensure complete recovery of reaction volume. Second-strand synthesis was initiated using a random primer harboring an Illumina-compatible linker sequence at its 5′ end, resulting in double-stranded cDNA (dsDNA) libraries. Double-stranded cDNA libraries were purified using magnetic beads to remove residual enzymes, primers, nucleotides, and buffer components. Beads were equilibrated to room temperature for 30 min prior to use and thoroughly resuspended before addition to samples. Libraries were washed and eluted in an elution buffer according to the manufacturer’s protocol. Purified dsDNA libraries were PCR-amplified (14–16 cycles) to introduce full-length Illumina adapter sequences required for cluster generation, as well as unique dual indices for multiplexed sequencing. Amplified libraries were purified using magnetic beads to remove residual PCR components that may interfere with downstream applications. Final libraries were quantified using a QubitTM 1× dsDNA HS Assay Kit (Thermo Fisher Scientific) and subjected to quality control prior to sequencing.

value: Control


title: Mutant day 38 IL1B treated

description:
Library name: SAMPLES 2
10x Genomics

value: iPSC line

value: On day 36, IL1B (10ng/ml) was added to kidney organoids for 48 hours.


title: Patient 03, Primary prostate cancer, PSMA high tumor area

description: Library name: p03_high

value: bulk


title: HepG2_Day3_B2_minus_RNA_rep3

description: Library name: Sample 6


title: HepG2_Day12_Cont_AhR_ChIP_rep2

description: Library name: Sample 56

value: AhR


title: P. promelas larvae, EFP, biological replicate EFP_B06, lane 2, time step = 4, analyzed on 20161003

description: Library name: 20161003_ EFP_4_B06_CTTGTA_L002_R1_001

value: EFP


title: Human macrophages, Donor H2, IFNy stimulated and Mtb infected

description: Library name: H2_IFNyMtb

value: IFNy stimulated and Mtb infected


title: Mutant day 38 untreated

description:
Library name: SAMPLES 1
10x Genomics

value: Kidney organoid

value: Untreated


title: HepG2_Day12_Cont_AhR_ChIP_rep1

description: Library name: Sample 55